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Li J, Richards EM, Pepine CJ, Handberg EM, Smith SM, Alakrad E, Forsmark CE, Raizada MK. Reprograming of transcriptional profile of colonic organoids from patients with high blood pressure by minocycline. AMERICAN HEART JOURNAL PLUS : CARDIOLOGY RESEARCH AND PRACTICE 2023; 36:100343. [PMID: 38222308 PMCID: PMC10785309 DOI: 10.1016/j.ahjo.2023.100343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Minocycline, an anti-inflammatory antibiotic drug, rebalances impaired gut microbiota, attenuates neuroinflammation and lowers high blood pressure in animal models of hypertension and in hypertensive patients. Our objective in this study was to investigate if antihypertensive effects of minocycline involve the expression of gut epithelial genes relevant to blood pressure homeostasis using human colonic 3-dimensional organoid culture and high-throughput RNA sequencing. The data demonstrates that minocycline could restore impaired expression of functional genes linked to viral and bacterial immunity, inflammation, protein trafficking and autophagy in human hypertensive organoids.
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Affiliation(s)
- Jing Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, Hubei, China
- Hubei Jiangxia Laboratory, Wuhan 430299, Hubei, China
| | - Elaine M. Richards
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL, USA
| | - Carl J. Pepine
- Divisions of Cardiovascular Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Eileen M. Handberg
- Divisions of Cardiovascular Medicine, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Steven M. Smith
- Department of Pharmaceutical Outcomes & Policy, College of Pharmacy, University of Florida, Gainesville, FL, USA
| | - Eyad Alakrad
- Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Chris E. Forsmark
- Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mohan K. Raizada
- Department of Physiology and Aging, University of Florida College of Medicine, Gainesville, FL, USA
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Vacondio D, Nogueira Pinto H, Coenen L, Mulder IA, Fontijn R, van Het Hof B, Fung WK, Jongejan A, Kooij G, Zelcer N, Rozemuller AJ, de Vries HE, de Wit NM. Liver X receptor alpha ensures blood-brain barrier function by suppressing SNAI2. Cell Death Dis 2023; 14:781. [PMID: 38016947 PMCID: PMC10684660 DOI: 10.1038/s41419-023-06316-8] [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: 07/04/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023]
Abstract
In Alzheimer's disease (AD) more than 50% of the patients are affected by capillary cerebral amyloid-angiopathy (capCAA), which is characterized by localized hypoxia, neuro-inflammation and loss of blood-brain barrier (BBB) function. Moreover, AD patients with or without capCAA display increased vessel number, indicating a reactivation of the angiogenic program. The molecular mechanism(s) responsible for BBB dysfunction and angiogenesis in capCAA is still unclear, preventing a full understanding of disease pathophysiology. The Liver X receptor (LXR) family, consisting of LXRα and LXRβ, was reported to inhibit angiogenesis and particularly LXRα was shown to secure BBB stability, suggesting a major role in vascular function. In this study, we unravel the regulatory mechanism exerted by LXRα to preserve BBB integrity in human brain endothelial cells (BECs) and investigate its role during pathological conditions. We report that LXRα ensures BECs identity via constitutive inhibition of the transcription factor SNAI2. Accordingly, deletion of brain endothelial LXRα is associated with impaired DLL4-NOTCH signalling, a critical signalling pathway involved in vessel sprouting. A similar response was observed when BECs were exposed to hypoxia, with concomitant LXRα decrease and SNAI2 increase. In support of our cell-based observations, we report a general increase in vascular SNAI2 in the occipital cortex of AD patients with and without capCAA. Importantly, SNAI2 strongly associated with vascular amyloid-beta deposition and angiopoietin-like 4, a marker for hypoxia. In hypoxic capCAA vessels, the expression of LXRα may decrease leading to an increased expression of SNAI2, and consequently BECs de-differentiation and sprouting. Our findings indicate that LXRα is essential for BECs identity, thereby securing BBB stability and preventing aberrant angiogenesis. These results uncover a novel molecular pathway essential for BBB identity and vascular homeostasis providing new insights on the vascular pathology affecting AD patients.
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Affiliation(s)
- D Vacondio
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - H Nogueira Pinto
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - L Coenen
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
- Biomedical Primate Research Centre, Department of Neurobiology and Aging, Rijswijk, the Netherlands
| | - I A Mulder
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
- Amsterdam UMC location University of Amsterdam, Department of Biomedical Engineering and Physics, Meibergdreef 9, Amsterdam, the Netherlands
| | - R Fontijn
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - B van Het Hof
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - W K Fung
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - A Jongejan
- Amsterdam UMC location University of Amsterdam, Epidemiology and Data Science, Meibergdreef 9, Amsterdam, The Netherlands
- Amsterdam Public Health, Methodology, Amsterdam, The Netherlands
- Amsterdam Infection and Immunity, Inflammatory Diseases, Amsterdam, The Netherlands
| | - G Kooij
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - N Zelcer
- Amsterdam UMC location University of Amsterdam Department of Medical Biochemistry, Meibergdreef 9, Amsterdam, the Netherlands
- Amsterdam UMC location University of Amsterdam, Cardiovascular Sciences and Gastroenterology and Metabolism, Meibergdreef 9, Amsterdam, the Netherlands
| | - A J Rozemuller
- Amsterdam Neuroscience, Amsterdam, the Netherlands
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Pathology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - H E de Vries
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands
- Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - N M de Wit
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Molecular Cell Biology and Immunology, De Boelelaan 1108, Amsterdam, the Netherlands.
- Amsterdam Neuroscience, Amsterdam, the Netherlands.
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203
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Alencar RM, Sepulveda CCP, Martinez-Villegas L, Bahia AC, Santana RA, de Souza IB, D'Elia GMA, Duarte APM, de Lacerda MVG, Monteiro WM, Secundino NFC, Pimenta PFP, Koerich LB. Unravelling the genome of the brackish water malaria vector Anopheles aquasalis. Sci Rep 2023; 13:20472. [PMID: 37993652 PMCID: PMC10665375 DOI: 10.1038/s41598-023-47830-1] [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: 02/09/2023] [Accepted: 11/19/2023] [Indexed: 11/24/2023] Open
Abstract
Malaria is a severe public health problem in several developing tropical and subtropical countries. Anopheles aquasalis is the primary coastal malaria vector in Central and South America and the Caribbean Islands, and it has the peculiar feature of living in water with large changes in salinity. Recent research has recognised An. aquasalis as an important model for studying the interactions of murine and human Plasmodium parasites. This study presents the complete genome of An. aquasalis and offers insights into its evolution and physiology. The genome is similar in size and gene content to other Neotropical anophelines, with 162 Mb and 12,446 protein-coding genes. There are 1387 single-copy orthologs at the Diptera level (eg. An. gambiae, An. darlingi and Drosophila melanogaster). An. aquasalis diverged from An. darlingi, the primary malaria vector in inland South America, nearly 20 million years ago. Proteins related to ion transport and metabolism belong to the most abundant gene families with 660 genes. We identified gene families relevant to osmosis control (e.g., aquaporins, vacuolar-ATPases, Na+/K+-ATPases, and carbonic anhydrases). Evolutionary analysis suggests that all osmotic regulation genes are under strong purifying selection. We also observed low copy number variation in insecticide resistance and immunity-related genes for all known classical pathways. The data provided by this study offers candidate genes for further studies of parasite-vector interactions and for studies on how anophelines of brackish water deal with the high fluctuation in water salinity. We also established data and insights supporting An. aquasalis as an emerging Neotropical malaria vector model for genetic and molecular studies.
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Affiliation(s)
- Rodrigo Maciel Alencar
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Cesar Camilo Prado Sepulveda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Luis Martinez-Villegas
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
| | - Ana Cristina Bahia
- Laboratório de Bioquímica de Insetos e Parasitos, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, CEP 21.941-170, Brazil
| | - Rosa Amélia Santana
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisa Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas, CEP 69.027-070, Brazil
| | - Igor Belém de Souza
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Gigliola Mayara Ayres D'Elia
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Ana Paula Marques Duarte
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Marcus Vinicius Guimarães de Lacerda
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisa Leônidas & Maria Deane, Fundação Oswaldo Cruz, Manaus, Amazonas, CEP 69.027-070, Brazil
- University of Texas Medical Branch, Galveston, United States of America
| | - Wuelton Marcelo Monteiro
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
| | - Nágila Francinete Costa Secundino
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil
| | - Paulo Filemon Paolucci Pimenta
- Fundação de Medicina Tropical Dr. Heitor Vieira Dourado, Manaus, Amazonas, CEP 69.040-000, Brazil.
- Programa de Pós-Graduação em Medicina Tropical, Fundação de Medicina Tropical Heitor Vieira Dourado, Universidade do Estado do Amazonas, Manaus, Amazonas, CEP 69.040-000, Brazil.
- Instituto de Pesquisas René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil.
- Programa de Pós-Graduação em Ciências da Saúde, FIOCRUZ, Belo Horizonte, Minas Gerais, CEP 30.190-009, Brazil.
| | - Leonardo Barbosa Koerich
- Departamento de Parasitologia, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, CEP 31.270-901, Brazil.
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204
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Chu W, Zhu X, Jiang T, Wang S, Ni W. Genome-wide identification of peanut IGT family genes and their potential roles in the development of plant architecture. Sci Rep 2023; 13:20400. [PMID: 37990054 PMCID: PMC10663514 DOI: 10.1038/s41598-023-47722-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 11/17/2023] [Indexed: 11/23/2023] Open
Abstract
IGT family genes play essential roles in shaping plant architecture. However, limited amount of information is available about IGT family genes in peanuts (Arachis hypogaea). In the current study, 13 AhIGT genes were identified and classified into three groups based on their phylogenetic relationship. Gene structure, conserved domain analyses indicated all AhIGTs were observed to share a similar exon-intron distribution pattern. AhIGTs within the same subfamily maintained a consistent motif composition. Chromosomal localization and synteny analyses showed that AhIGTs were unevenly localized on 9 chromosomes and that segmental duplication and purifying selection may have played important roles in the evolution of AhIGT genes. The analysis of conserved motifs, GO annotation, and transcript profile suggested that AhLAZY1-3 may play roles in gravity sensing and shaping peanut plant architecture. Transcript profile analysis suggested that AhTAC1 could potentially be involved gynophore ('peg') penetration into the soil. The cis-element analysis revealed that the light-responsive elements accounted for most of all cis-acting elements. Furthermore, qRT-PCR analysis showed that the expression of several AhIGT genes, like AhTAC1-2/4, was light-dependent, indicating that these genes may regulate plant architecture in response to light signals. This study may facilitate functional studies of the IGT genes in peanut.
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Affiliation(s)
- Wen Chu
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Xiaofeng Zhu
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Tao Jiang
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Song Wang
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Wanli Ni
- Crops Research Institute, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
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205
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Zhang Q, Ma C, Chin LS, Pan S, Li L. Human brain glycoform co-regulation network and glycan modification alterations in Alzheimer's disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.13.566889. [PMID: 38014218 PMCID: PMC10680592 DOI: 10.1101/2023.11.13.566889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Despite the importance of protein glycosylation to brain health, current knowledge of glycosylated proteoforms or glycoforms in human brain and their alterations in Alzheimer's disease (AD) is limited. Here, we present a new paradigm of proteome-wide glycoform profiling study of human AD and control brains using intact glycopeptide-based quantitative glycoproteomics coupled with systems biology. Our study identified over 10,000 human brain N-glycoforms from nearly 1200 glycoproteins and uncovered disease signatures of altered glycoforms and glycan modifications, including reduced sialylation and N-glycan branching as well as elevated mannosylation and N-glycan truncation in AD. Network analyses revealed a higher-order organization of brain glycoproteome into networks of co-regulated glycoforms and glycans and discovered glycoform and glycan modules associated with AD clinical phenotype, amyloid-β accumulation, and tau pathology. Our findings provide novel insights and a rich resource of glycoform and glycan changes in AD and pave the way forward for developing glycosylation-based therapies and biomarkers for AD.
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206
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Jin Y, Zeng L, Xiao M, Feng Y, Gao Z, Wei J. Exploration of the B3 transcription factor superfamily in Aquilaria sinensis reveal their involvement in seed recalcitrance and agarwood formation. PLoS One 2023; 18:e0294358. [PMID: 37972007 PMCID: PMC10653465 DOI: 10.1371/journal.pone.0294358] [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: 07/05/2023] [Accepted: 10/31/2023] [Indexed: 11/19/2023] Open
Abstract
The endangered tree species of the Aquilaria genus produce agarwood, a high value material produced only after wounding; however, conservation of Aquilaria seeds is difficult. The B3 transcription factor family has diverse important functions in plant development, especially in seed development, although their functions in other areas, such as stress responses, remain to be revealed. Here germination tests proved that the seeds of A. sinensis were recalcitrant seeds. To provide insights into the B3 superfamily, the members were identified and characterized by bioinformatic approaches and classified by phylogenetic analysis and domain structure. In total, 71 members were identified and classified into four subfamilies. Each subfamily not only had similar domains, but also had conserved motifs in their B3 domains. For the seed-related LAV subfamily, the B3 domain of AsLAV3 was identical to that of AsVALs but lacked a typical zf-CW domain such as VALs. AsLAV5 lacks a typical PHD-L domain present in Arabidopsis VALs. qRT-PCR expression analysis showed that the LEC2 ortholog AsLAV4 was not expressed in seeds. RAVs and REMs induced after wound treatment were also identified. These findings provide insights into the functions of B3 genes and seed recalcitrance of A. sinensis and indicate the role of B3 genes in wound response and agarwood formation.This is the first work to investigate the B3 family in A. sinensis and to provide insights of the molecular mechanism of seed recalcitrance.This will be a valuable guidance for studies of B3 genes in stress responses, secondary metabolite biosynthesis, and seed development.
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Affiliation(s)
- Yue Jin
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lin Zeng
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
| | - Mengjun Xiao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yanan Feng
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihui Gao
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianhe Wei
- Key Laboratory of Bioactive Substances and Resources Utilization of Chinese Herbal Medicine, Ministry of Education & National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Hainan Provincial Key Laboratory of Resources Conservation and Development of Southern Medicine & Key Laboratory of State Administration of Traditional Chinese Medicine for Agarwood Sustainable Utilization, Hainan Branch of the Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Haikou, China
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207
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Machado H, Temudo A, Niz MD. The lymphatic system favours survival of a unique T. brucei population. Biol Open 2023; 12:bio059992. [PMID: 37870927 PMCID: PMC10651106 DOI: 10.1242/bio.059992] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Trypanosoma brucei colonise and multiply in the blood vasculature, as well as in various organs of the host's body. Lymph nodes have been previously shown to harbour large numbers of parasites, and the lymphatic system has been proposed as a key site that allows T. brucei distribution through, and colonization of the mammalian body. However, visualization of host-pathogen interactions in the lymphatic system has never captured dynamic events with high spatial and temporal resolution throughout infection. In our work, we used a mixture of tools including intravital microscopy and ex vivo imaging to study T. brucei distribution in 20 sets of lymph nodes. We demonstrate that lymph node colonization by T. brucei is different across lymph node sets, with the most heavily colonised being the draining lymph nodes of main tissue reservoirs: the gonadal white adipose tissue and pancreas. Moreover, we show that the lymphatic vasculature is a pivotal site for parasite dispersal, and altering this colonization by blocking LYVE-1 is detrimental for parasite survival. Additionally, parasites within the lymphatic vasculature have unique morphological and behavioural characteristics, different to those found in the blood, demonstrating that across both types of vasculature, these environments are physically separated. Finally, we demonstrate that the lymph nodes and the lymphatic vasculature undergo significant alterations during T. brucei infection, resulting in oedema throughout the host's body.
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Affiliation(s)
- Henrique Machado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - António Temudo
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
- Bioimaging Unit, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa 1649-028, Portugal
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208
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Kumar Chaudhary D, Bajagain R, Seo D, Hong Y, Han S. Depth-dependent microbial communities potentially mediating mercury methylation and various geochemical processes in anthropogenically affected sediments. ENVIRONMENTAL RESEARCH 2023; 237:116888. [PMID: 37586452 DOI: 10.1016/j.envres.2023.116888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 08/18/2023]
Abstract
Metal contamination and other geochemical alterations affect microbial composition and functional activities, disturbing natural biogeochemical cycles. Therefore, it is essential to understand the influences of multi-metal and geochemical interactions on microbial communities. This work investigated the distributions of total mercury (THg), methylmercury (MeHg), and trace metals in the anthropogenically affected sediment. The microbial communities and functional genes profiles were further determined to explore their association with Hg-methylation and geochemical features. The levels of THg and MeHg in sediment cores ranged between 10 and 40 mg/kg and 0.01-0.16 mg/kg, respectively, with an increasing trend toward bottom horizons. The major metals present at all depths were Al, Fe, Mn, and Zn. The enrichment and contamination indices confirmed that the trace metals were highly enriched in the anthropogenically affected sediment. Various functional genes were detected in all strata, indicating the presence of active microbial metabolic processes. The microbial community profiles revealed that the phyla Proteobacteria, Bacteroidetes, Bathyarchaeota, and Euryarchaeota, and the genera Thauera, Woeseia, Methanomethylovorans, and Methanosarcina were the dominant microbes. Correlating major taxa with geochemical variables inferred that sediment geochemistry substantially affects microbial community and biogeochemical cycles. Furthermore, archaeal methanogens and the bacterial phyla Chloroflexi and Firmicutes may play crucial roles in enhancing MeHg levels. Overall, these findings shed new light on the microbial communities potentially involved in Hg-methylation process and other biogeochemical cycles.
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Affiliation(s)
- Dhiraj Kumar Chaudhary
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Rishikesh Bajagain
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - DongGyun Seo
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea
| | - Yongseok Hong
- Department of Environmental Engineering, Korea University Sejong Campus, 2511 Sejong-ro, Sejong City, 30019, Republic of Korea.
| | - Seunghee Han
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju, 61005, Republic of Korea
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209
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Li D, Van De Werfhorst LC, Ervin J, Poresky A, Steets B, Rivers C, Sharp G, Smith J, Holden PA. Municipal separate storm sewer system (MS4) dry weather flows and potential flow sources as assessed by conventional and advanced bacterial analyses. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122521. [PMID: 37678735 DOI: 10.1016/j.envpol.2023.122521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
Municipal separate storm sewer systems (MS4s) function in urbanized areas to convey flows during both wet weather (i.e., stormwater) and dry weather (i.e., urban runoff as well as subsurface sources of flow) to receiving waters. While urban stormwater is known to contain microbial and chemical pollutants, MS4 dry weather flows, or non-stormwater discharges (NSWDs), are much less studied, although they are also known to contain pollutants, especially when these flows include raw sewage. In addition, some natural NSWDs (e.g., from groundwater infiltrating MS4 pipes) are critical for aquatic habitat protection. Thus, it is important to distinguish NSWD sources to prevent non-natural flows while retaining natural waters (i.e., groundwater). Here, MS4 dry weather flows were assessed by analyzing water samples from MS4 outfalls across multiple watersheds and water provider service areas in south Orange County, CA; potential NSWD sources including sewage, recycled water, potable water, and groundwater were sampled and analyzed for their likely contributions to overall NSWDs. Geochemical and microbiological water quality indicators, as well as bacterial communities, differed across NSWDs, yet water quality within most locations did not vary significantly diurnally or by sampling date. Meanwhile, NSWD source waters had distinctly different bacterial taxa abundances and specific bacterial genera. Shared geochemical and microbial characteristics of certain sources and outfall flows suggested the contributions of sources to outfall flows. The average proportions by sources contributing to MS4 outfalls were further estimated by SourceTracker and FEAST, respectively. The results of this study highlight the use of multiple tools when assessing chemical and microbiological water quality to predict sources of NSWDs contributing to urban MS4 flows during dry weather. This information can be used to support management actions to reduce unnatural and high risk sources of dry weather drainage while preserving natural sources important to environmental health in downstream receiving waters.
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Affiliation(s)
- Dong Li
- Bren School of Environmental Science & Management, University of California, Santa Barbara, USA
| | | | - Jared Ervin
- Geosyntec Consultants, Santa Barbara, CA, 93101, USA
| | - Aaron Poresky
- Geosyntec Consultants, Santa Barbara, CA, 93101, USA
| | | | - Cindy Rivers
- Orange County Public Works (OCPW), Orange County, CA, USA
| | - Grant Sharp
- Orange County Public Works (OCPW), Orange County, CA, USA
| | - Jen Smith
- California NanoSystems Institute, University of California, Santa Barbara, USA
| | - Patricia A Holden
- Bren School of Environmental Science & Management, University of California, Santa Barbara, USA.
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210
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Vucetic A, Lafleur A, Côté M, Kobasa D, Chan M, Alvarez F, Piccirillo C, Dong G, Olivier M. Extracellular vesicle storm during the course of Ebola virus infection in primates. Front Cell Infect Microbiol 2023; 13:1275277. [PMID: 38035334 PMCID: PMC10684970 DOI: 10.3389/fcimb.2023.1275277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Introduction Ebola virus (EBOV) is an RNA virus of the Filoviridae family that is responsible for outbreaks of hemorrhagic fevers in primates with a lethality rate as high as 90%. EBOV primarily targets host macrophages leading to cell activation and systemic cytokine storm, and fatal infection is associated with an inhibited interferon response, and lymphopenia. The EBOV surface glycoprotein (GP) has been shown to directly induce T cell depletion and can be secreted outside the virion via extracellular vesicles (EVs), though most studies are limited to epithelial cells and underlying mechanisms remain poorly elucidated. Methods To assess the role of GP on EBOV-induced dysregulation of host immunity, we first utilized EBOV virus-like particles (VLPs) expressing VP40 and NP either alone (Bald-VLP) or in conjunction with GP (VLP-GP) to investigate early inflammatory responses in THP-1 macrophages and in a murine model. We then sought to decipher the role of non-classical inflammatory mediators such as EVs over the course of EBOV infection in two EBOV-infected rhesus macaques by isolating and characterizing circulatory EVs throughout disease progression using size exclusion chromatography, nanoparticle tracking-analysis, and LC-MS/MS. Results While all VLPs could induce inflammatory mediators and recruit small peritoneal macrophages, pro-inflammatory cytokine and chemokine gene expression was exacerbated by the presence of GP. Further, quantification of EVs isolated from infected rhesus macaques revealed that the concentration of vesicles peaked in circulation at the terminal stage, at which time EBOV GP could be detected in host-derived exosomes. Moreover, comparative proteomics conducted across EV populations isolated from serum at various time points before and after infection revealed differences in host-derived protein content that were most significantly pronounced at the endpoint of infection, including significant expression of mediators of TLR4 signaling. Discussion These results suggest a dynamic role for EVs in the modification of disease states in the context of EBOV. Overall, our work highlights the importance of viral factors, such as the GP, and host derived EVs in the inflammatory cascade and pathogenesis of EBOV, which can be collectively further exploited for novel antiviral development.
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Affiliation(s)
- Andrea Vucetic
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Andrea Lafleur
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Marceline Côté
- Department of Biochemistry, Microbiology and Immunology and Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
| | - Darwyn Kobasa
- Special Pathogen Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Mable Chan
- Special Pathogen Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Fernando Alvarez
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Federation of Clinical Immunology (FOCiS) Centres of Excellence in Translational Immunology (CETI), Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Ciriaco Piccirillo
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Federation of Clinical Immunology (FOCiS) Centres of Excellence in Translational Immunology (CETI), Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - George Dong
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
| | - Martin Olivier
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, QC, Canada
- Federation of Clinical Immunology (FOCiS) Centres of Excellence in Translational Immunology (CETI), Research Institute of the McGill University Health Centre, Montréal, QC, Canada
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211
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Vemuri K, Kumar S, Chen L, Verzi MP. Dynamic RNA Polymerase II Recruitment Drives Differentiation of the Intestine under the direction of HNF4. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566322. [PMID: 37986803 PMCID: PMC10659318 DOI: 10.1101/2023.11.08.566322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Terminal differentiation requires a massive restructuring of the transcriptome. During intestinal differentiation, the expression patterns of nearly 4000 genes are altered as cells transition from progenitor cells in crypts to differentiated cells in villi. We identified dynamic recruitment of RNA Polymerase II (Pol II) to gene promoters as the primary driver of transcriptomic shifts during intestinal differentiation in vivo. Changes in enhancer-promoter looping interactions accompany dynamic Pol II recruitment and are dependent upon HNF4, a pro-differentiation transcription factor. Using genetic loss-of- function, ChIP-seq and IP mass spectrometry, we demonstrate that HNF4 collaborates with chromatin remodelers and loop-stabilizing proteins and facilitates Pol II recruitment at hundreds of genes pivotal to differentiation. We also explore alternate mechanisms which drive differentiation gene expression and find pause-release of Pol II and post- transcriptional mRNA stability regulate smaller subsets of differentially expressed genes. These studies provide insights into the mechanisms of differentiation in a renewing adult tissue.
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Affiliation(s)
- Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Sneha Kumar
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
| | - Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Michael P. Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 08854, USA
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition & Health, Rutgers University, New Brunswick, NJ 08901, USA
- NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI Piscataway, NJ 08854, USA
- Lead Contact
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212
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Tang D, Chen M, Huang X, Zhang G, Zeng L, Zhang G, Wu S, Wang Y. SRplot: A free online platform for data visualization and graphing. PLoS One 2023; 18:e0294236. [PMID: 37943830 PMCID: PMC10635526 DOI: 10.1371/journal.pone.0294236] [Citation(s) in RCA: 191] [Impact Index Per Article: 191.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 10/27/2023] [Indexed: 11/12/2023] Open
Abstract
Graphics are widely used to provide summarization of complex data in scientific publications. Although there are many tools available for drawing graphics, their use is limited by programming skills, costs, and platform specificities. Here, we presented a freely accessible easy-to-use web server named SRplot that integrated more than a hundred of commonly used data visualization and graphing functions together. It can be run easily using all Web browsers and there are no strong requirements on the computing power of users' machines. With a user-friendly graphical interface, users can simply paste the contents of the input file into the text box according to the defined file format. Modification operations can be easily performed, and graphs can be generated in real-time. The resulting graphs can be easily downloaded in bitmap (PNG or TIFF) or vector (PDF or SVG) format in publication quality. The website is updated promptly and continuously. Functions in SRplot have been improved, optimized and updated depend on feedback and suggestions from users. The graphs prepared with SRplot have been featured in more than five hundred peer-reviewed publications. The SRplot web server is now freely available at http://www.bioinformatics.com.cn/SRplot.
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Affiliation(s)
- Doudou Tang
- Department of Respiratory and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mingjie Chen
- Shanghai NewCore Biotechnology, Minhang District, Shanghai, China
| | - Xinhua Huang
- Shenzhen Ping’an Financial Technology Consulting Co. Ltd, Pudong New District, Shanghai, China
| | - Guicheng Zhang
- Shanghai NewCore Biotechnology, Minhang District, Shanghai, China
| | - Lin Zeng
- Shanghai NewCore Biotechnology, Minhang District, Shanghai, China
| | - Guangsen Zhang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shangjie Wu
- Department of Respiratory and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yewei Wang
- Department of Hematology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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213
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Bar S, Wilson KA, Hilsabeck TA, Alderfer S, Dammer EB, Burton JB, Shah S, Holtz A, Carrera EM, Beck JN, Chen JH, Kauwe G, Tracy TE, Seyfried NT, Schilling B, Ellerby LM, Kapahi P. Neuronal Glycogen Breakdown Mitigates Tauopathy via Pentose Phosphate Pathway-Mediated Oxidative Stress Reduction. RESEARCH SQUARE 2023:rs.3.rs-3526342. [PMID: 37986935 PMCID: PMC10659530 DOI: 10.21203/rs.3.rs-3526342/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Tauopathies encompass a range of neurodegenerative disorders, such as Alzheimer's disease (AD) and frontotemporal dementia (FTD). Unfortunately, current treatment approaches for tauopathies have yielded limited success, underscoring the pressing need for novel therapeutic strategies. We observed distinct signatures of impaired glycogen metabolism in the Drosophila brain of the tauopathy model and the brain of AD patients, indicating a link between tauopathies and glycogen metabolism. We demonstrate that the breakdown of neuronal glycogen by activating glycogen phosphorylase (GlyP) ameliorates the tauopathy phenotypes in flies and induced pluripotent stem cell (iPSC) derived neurons from FTD patients. We observed that glycogen breakdown redirects the glucose flux to the pentose phosphate pathway to alleviate oxidative stress. Our findings uncover a critical role for increased GlyP activity in mediating the neuroprotection benefit of dietary restriction (DR) through the cAMP-mediated protein kinase A (PKA) activation. Our studies identify impaired glycogen metabolism as a key hallmark for tauopathies and offer a promising therapeutic target in tauopathy treatment.
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Affiliation(s)
- Sudipta Bar
- Buck Institute for Research on Aging, Novato, CA 94947, USA
| | | | | | | | - Eric B. Dammer
- Emory Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory University, School of Medicine Core Labs, Atlanta, GA 30322, USA
| | | | - Samah Shah
- Buck Institute for Research on Aging, Novato, CA 94947, USA
| | - Anja Holtz
- Buck Institute for Research on Aging, Novato, CA 94947, USA
| | | | | | - Jackson H Chen
- Buck Institute for Research on Aging, Novato, CA 94947, USA
| | - Grant Kauwe
- Buck Institute for Research on Aging, Novato, CA 94947, USA
| | - Tara E. Tracy
- Buck Institute for Research on Aging, Novato, CA 94947, USA
| | - Nicholas T. Seyfried
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | - Pankaj Kapahi
- Buck Institute for Research on Aging, Novato, CA 94947, USA
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214
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Aamir M, Shanmugam V, Dubey MK, Husain FM, Adil M, Ansari WA, Rai A, Sah P. Transcriptomic characterization of Trichoderma harzianum T34 primed tomato plants: assessment of biocontrol agent induced host specific gene expression and plant growth promotion. BMC PLANT BIOLOGY 2023; 23:552. [PMID: 37940862 PMCID: PMC10631224 DOI: 10.1186/s12870-023-04502-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 09/30/2023] [Indexed: 11/10/2023]
Abstract
In this study, we investigated the intricate interplay between Trichoderma and the tomato genome, focusing on the transcriptional and metabolic changes triggered during the late colonization event. Microarray probe set (GSE76332) was utilized to analyze the gene expression profiles changes of the un-inoculated control (tomato) and Trichoderma-tomato interactions for identification of the differentially expressed significant genes. Based on principal component analysis and R-based correlation, we observed a positive correlation between the two cross-comaparable groups, corroborating the existence of transcriptional responses in the host triggered by Trichoderma priming. The statistically significant genes based on different p-value cut-off scores [(padj-values or q-value); padj-value < 0.05], [(pcal-values); pcal-value < 0.05; pcal < 0.01; pcal < 0.001)] were cross compared. Through cross-comparison, we identified 156 common genes that were consistently significant across all probability thresholds, and showing a strong positive corelation between p-value and q-value in the selected probe sets. We reported TD2, CPT1, pectin synthase, EXT-3 (extensin-3), Lox C, and pyruvate kinase (PK), which exhibited upregulated expression, and Glb1 and nitrate reductase (nii), which demonstrated downregulated expression during Trichoderma-tomato interaction. In addition, microbial priming with Trichoderma resulted into differential expression of transcription factors related to systemic defense and flowering including MYB13, MYB78, ERF2, ERF3, ERF5, ERF-1B, NAC, MADS box, ZF3, ZAT10, A20/AN1, polyol sugar transporter like zinc finger proteins, and a novel plant defensin protein. The potential bottleneck and hub genes involved in this dynamic response were also identified. The protein-protein interaction (PPI) network analysis based on 25 topmost DEGS (pcal-value < 0.05) and the Weighted Correlation Gene Network Analysis (WGCNA) of the 1786 significant DEGs (pcal-value < 0.05) we reported the hits associated with carbohydrate metabolism, secondary metabolite biosynthesis, and the nitrogen metabolism. We conclude that the Trichoderma-induced microbial priming re-programmed the host genome for transcriptional response during the late colonization event and were characterized by metabolic shifting and biochemical changes specific to plant growth and development. The work also highlights the relevance of statistical parameters in understanding the gene regulatory dynamics and complex regulatory networks based on differential expression, co-expression, and protein interaction networks orchestrating the host responses to beneficial microbial interactions.
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Affiliation(s)
- Mohd Aamir
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi-110012, Delhi, India.
| | - V Shanmugam
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi-110012, Delhi, India
| | - Manish Kumar Dubey
- Department of Biotechnology, University Centre for Research & Development (UCRD), Chandigarh University, Punjab, 140413, India
| | - Fohad Mabood Husain
- Department of Food Science and Nutrition, College of Food and Agriculture Sciences, King Saud University, Riyadh-11451, Saudi Arabia
| | - Mohd Adil
- Plant, Food and Environmental Sciences, Dalhousie University, Truro, NS, B2N2R9, Canada
| | - Waquar Akhter Ansari
- Department of Botany, Centre for Advanced Study, Institute of Science, Banaras Hindu University, Varanasi, 221002, India
| | - Ashutosh Rai
- Department of Basic and Social Sciences, College of Horticulture, Banda University of Agriculture and Technology, Uttar Pradesh, Banda, 210001, India
| | - Pankaj Sah
- Applied Sciences Department, College of Applied Sciences and Pharmacy, University of Technology and Applied Sciences-Muscat, Al Janubyyah Street, PO Box 74, Muscat, 133, Sultanate of Oman
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215
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Hubens WHG, Maié T, Schnitker M, Bocova L, Puri D, Wessiepe M, Kramer J, Rink L, Koschmieder S, Costa IG, Wagner W. Targeted DNA Methylation Analysis Facilitates Leukocyte Counts in Dried Blood Samples. Clin Chem 2023; 69:1283-1294. [PMID: 37708296 DOI: 10.1093/clinchem/hvad143] [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: 05/31/2023] [Accepted: 08/10/2023] [Indexed: 09/16/2023]
Abstract
BACKGROUND Cell-type specific DNA methylation (DNAm) can be employed to determine the numbers of leukocyte subsets in blood. In contrast to conventional methods for leukocyte counts, which are based on cellular morphology or surface marker protein expression, the cellular deconvolution based on DNAm levels is applicable for frozen or dried blood. Here, we further enhanced targeted DNAm assays for leukocyte counts in clinical application. METHODS DNAm profiles of 40 different studies were compiled to identify CG dinucleotides (CpGs) with cell-type specific DNAm using a computational framework, CimpleG. DNAm levels at these CpGs were then measured with digital droplet PCR in venous blood from 160 healthy donors and 150 patients with various hematological disorders. Deconvolution was further validated with venous blood (n = 75) and capillary blood (n = 31) that was dried on Whatman paper or on Mitra microsampling devices. RESULTS In venous blood, automated cell counting or flow cytometry correlated well with epigenetic estimates of relative leukocyte counts for granulocytes (r = 0.95), lymphocytes (r = 0.97), monocytes (r = 0.82), CD4 T cells (r = 0.84), CD8 T cells (r = 0.94), B cells (r = 0.96), and NK cells (r = 0.72). Similar correlations and precisions were achieved for dried blood samples. Spike-in with a reference plasmid enabled accurate epigenetic estimation of absolute leukocyte counts from dried blood samples, correlating with conventional venous (r = 0.86) and capillary (r = 0.80) blood measurements. CONCLUSIONS The advanced selection of cell-type specific CpGs and utilization of digital droplet PCR analysis provided accurate epigenetic blood counts. Analysis of dried blood facilitates self-sampling with a finger prick, thereby enabling easier accessibility to testing.
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Affiliation(s)
- Wouter H G Hubens
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Tiago Maié
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Matthis Schnitker
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Ledio Bocova
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Deepika Puri
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
| | - Martina Wessiepe
- Institute for Transfusion Medicine, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Jan Kramer
- Division of Nephrology and Transplantation Unit, Department of Internal Medicine I, University of Lübeck, Lübeck, Germany
- LADR Laboratory Group Dr. Kramer & Colleagues, Geesthacht, Germany
| | - Lothar Rink
- Institute of Immunology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Steffen Koschmieder
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - Wolfgang Wagner
- Institute for Stem Cell Biology, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
- Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Aachen, Germany
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216
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Chen L, Qiu X, Dupre A, Pellon-Cardenas O, Fan X, Xu X, Rout P, Walton KD, Burclaff J, Zhang R, Fang W, Ofer R, Logerfo A, Vemuri K, Bandyopadhyay S, Wang J, Barbet G, Wang Y, Gao N, Perekatt AO, Hu W, Magness ST, Spence JR, Verzi MP. TGFB1 induces fetal reprogramming and enhances intestinal regeneration. Cell Stem Cell 2023; 30:1520-1537.e8. [PMID: 37865088 PMCID: PMC10841757 DOI: 10.1016/j.stem.2023.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/03/2023] [Accepted: 09/28/2023] [Indexed: 10/23/2023]
Abstract
The gut epithelium has a remarkable ability to recover from damage. We employed a combination of high-throughput sequencing approaches, mouse genetics, and murine and human organoids and identified a role for TGFB signaling during intestinal regeneration following injury. At 2 days following irradiation (IR)-induced damage of intestinal crypts, a surge in TGFB1 expression is mediated by monocyte/macrophage cells at the location of damage. The depletion of macrophages or genetic disruption of TGFB signaling significantly impaired the regenerative response. Intestinal regeneration is characterized by the induction of a fetal-like transcriptional signature during repair. In organoid culture, TGFB1 treatment was necessary and sufficient to induce the fetal-like/regenerative state. Mesenchymal cells were also responsive to TGFB1 and enhanced the regenerative response. Mechanistically, pro-regenerative factors, YAP/TEAD and SOX9, are activated in the epithelium exposed to TGFB1. Finally, pre-treatment with TGFB1 enhanced the ability of primary epithelial cultures to engraft into damaged murine colon, suggesting promise for cellular therapy.
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Affiliation(s)
- Lei Chen
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China.
| | - Xia Qiu
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Abigail Dupre
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Oscar Pellon-Cardenas
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Xiaojiao Fan
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Xiaoting Xu
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Prateeksha Rout
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Katherine D Walton
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Joseph Burclaff
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27695, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Ruolan Zhang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Wenxin Fang
- School of Life Science and Technology, Key Laboratory of Developmental Genes and Human Disease, Southeast University, Nanjing 210096, China
| | - Rachel Ofer
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Alexandra Logerfo
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA
| | - Sheila Bandyopadhyay
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA
| | - Jianming Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA
| | - Gaetan Barbet
- Child Health Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08901, USA
| | - Yan Wang
- Center for Translation Medicine Research and Development, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Nan Gao
- Department of Biological Sciences, Rutgers University-Newark, Newark, NJ 07102, USA
| | - Ansu O Perekatt
- Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030, USA
| | - Wenwei Hu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA
| | - Scott T Magness
- Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, and North Carolina State University, Chapel Hill, NC 27695, USA; Center for Gastrointestinal Biology and Disease, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jason R Spence
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI 48109, USA
| | - Michael P Verzi
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers University, Piscataway, NJ 00854, USA; Rutgers Cancer Institute of New Jersey, Rutgers University-New Brunswick, New Brunswick, NJ 08903, USA; Rutgers Center for Lipid Research, New Jersey Institute for Food, Nutrition, and Health, Rutgers University-New Brunswick, New Brunswick, NJ 08901, USA; NIEHS Center for Environmental Exposures and Disease (CEED), Rutgers EOHSI, Piscataway, NJ 08854, USA.
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Yang J, Chen X, A L, Gao H, Zhao M, Ge L, Li M, Yang C, Gong Y, Gu Z, Xu H. Alleviation of Photoreceptor Degeneration Based on Fullerenols in rd1 Mice by Reversing Mitochondrial Dysfunction via Modulation of Mitochondrial DNA Transcription and Leakage. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2205998. [PMID: 37407519 DOI: 10.1002/smll.202205998] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 06/18/2023] [Indexed: 07/07/2023]
Abstract
Poor therapeutic outcomes of antioxidants in ophthalmologic clinical applications, including glutathione during photoreceptor degeneration in retinitis pigmentosa (RP), are caused by limited anti-oxidative capacity. In this study, fullerenols are synthesized and proven to be highly efficient in vitro radical scavengers. Fullerenol-based intravitreal injections significantly improve the flash electroretinogram and light/dark transition tests performed for 28 days on rd1 mice, reduce the thinning of retinal outer nuclear layers, and preserve the Rhodopsin, Gnat-1, and Arrestin expressions of photoreceptors. RNA-sequencing, RT-qPCR, and Western blotting validate that mitochondrial DNA (mt-DNA)-encoded genes of the electron transport chain (ETC), such as mt-Nd4l, mt-Co1, mt-Cytb, and mt-Atp6, are drastically downregulated in the retinas of rd1 mice, whereas nuclear DNA (n-DNA)-encoded genes, such as Ndufa1 and Atp5g3, are abnormally upregulated. Fullerenols thoroughly reverse the abnormal mt-DNA and n-DNA expression patterns of the ETC and restore mitochondrial function in degenerating photoreceptors. Additionally, fullerenols simultaneously repress Flap endonuclease 1 (FEN1)-mediated mt-DNA cleavage and mt-DNA leakage via voltage-dependent anion channel (VDAC) pores by downregulating the transcription of Fen1 and Vdac1, thereby inactivating the downstream pro-inflammatory cGAS-STING pathway. These findings demonstrate that fullerenols can effectively alleviate photoreceptor degeneration in rd1 mice and serve as a viable treatment for RP.
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Affiliation(s)
- Junling Yang
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Xia Chen
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Luodan A
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Hui Gao
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Maoru Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100049, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingling Ge
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Minghui Li
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Cao Yang
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
| | - Yu Gong
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
- Department of Ophthalmology, Medical Sciences Research Center, University-Town Hospital of Chongqing Medical University, Chongqing, 400038, China
| | - Zhanjun Gu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, Institute of High Energy Physics and National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100049, China
- College of Materials Science and Optoelectronic Technology, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiwei Xu
- Southwest Eye Hospital, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
- Key Lab of Visual Damage and Regeneration & Restoration of Chongqing, Southwest Eye Hospital, Southwest Hospital, Chongqing, 400038, China
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Bruschi M, Biancucci F, Masini S, Piacente F, Ligi D, Bartoccini F, Antonelli A, Mannello F, Bruzzone S, Menotta M, Fraternale A, Magnani M. The influence of redox modulation on hypoxic endothelial cell metabolic and proteomic profiles through a small thiol-based compound tuning glutathione and thioredoxin systems. Biofactors 2023; 49:1205-1222. [PMID: 37409789 DOI: 10.1002/biof.1988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/16/2023] [Indexed: 07/07/2023]
Abstract
Reduction in oxygen levels is a key feature in the physiology of the bone marrow (BM) niche where hematopoiesis occurs. The BM niche is a highly vascularized tissue and endothelial cells (ECs) support and regulate blood cell formation from hematopoietic stem cells (HSCs). While in vivo studies are limited, ECs when cultured in vitro at low O2 (<5%), fail to support functional HSC maintenance due to oxidative environment. Therefore, changes in EC redox status induced by antioxidant molecules may lead to alterations in the cellular response to hypoxia likely favoring HSC self-renewal. To evaluate the impact of redox regulation, HUVEC, exposed for 1, 6, and 24 h to 3% O2 were treated with N-(N-acetyl-l-cysteinyl)-S-acetylcysteamine (I-152). Metabolomic analyses revealed that I-152 increased glutathione levels and influenced the metabolic profiles interconnected with the glutathione system and the redox couples NAD(P)+/NAD(P)H. mRNA analysis showed a lowered gene expression of HIF-1α and VEGF following I-152 treatment whereas TRX1 and 2 were stimulated. Accordingly, the proteomic study revealed the redox-dependent upregulation of thioredoxin and peroxiredoxins that, together with the glutathione system, are the main regulators of intracellular ROS. Indeed, a time-dependent ROS production under hypoxia and a quenching effect of the molecule were evidenced. At the secretome level, the molecule downregulated IL-6, MCP-1, and PDGF-bb. These results suggest that redox modulation by I-152 reduces oxidative stress and ROS level in hypoxic ECs and may be a strategy to fine-tune the environment of an in vitro BM niche able to support functional HSC maintenance.
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Affiliation(s)
- Michela Bruschi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Federica Biancucci
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Sofia Masini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Francesco Piacente
- Department of Experimental Medicine, Section of Biochemistry, and CEBR, University of Genoa, Genoa, GE, Italy
| | - Daniela Ligi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Francesca Bartoccini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Antonella Antonelli
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Ferdinando Mannello
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, and CEBR, University of Genoa, Genoa, GE, Italy
- IRCCS, Ospedale Policlinico San Martino, Genoa, GE, Italy
| | - Michele Menotta
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Alessandra Fraternale
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, PU, Italy
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219
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Thakkar C, Alikunju S, Niranjan N, Rizvi W, Abbas A, Abdellatif M, Sayed D. Klf9 plays a critical role in GR -dependent metabolic adaptations in cardiomyocytes. Cell Signal 2023; 111:110886. [PMID: 37690661 PMCID: PMC10591860 DOI: 10.1016/j.cellsig.2023.110886] [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] [Revised: 08/29/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Glucocorticoids through activation of the Glucocorticoid receptor (GR) play an essential role in cellular homeostasis during physiological variations and in response to stress. Our genomic GR binding and transcriptome data from Dexamethasone (Dex) treated cardiomyocytes showed an early differential regulation of mostly transcription factors, followed by sequential change in genes involved in downstream functional pathways. We examined the role of Krüppel-like factor 9 (Klf9), an early direct target of GR in cardiomyocytes. Klf9-ChIPseq identified 2150 genes that showed an increase in Klf9 binding in response to Dex. Transcriptome analysis of Dex treated cardiomyocytes with or without knockdown of Klf9 revealed differential regulation of 1777 genes, of which a reversal in expression is seen in 1640 genes with knockdown of Klf9 compared to Dex. Conversely, only 137 (∼8%) genes show further dysregulation in expression with siKLf9, as seen with Dex treated cardiomyocytes. Functional annotation identified genes of metabolic pathways on the top of differentially expressed genes, including those involved in glycolysis and oxidative phosphorylation. Knockdown of Klf9 in cardiomyocytes inhibited Dex induced increase in glycolytic function and mitochondrial spare respiratory capacity, as measured by glycolysis and mito stress tests, respectively. Thus, we conclude that cyclic, diurnal GR activation, through Klf9 -dependent feedforward signaling plays a central role in maintaining cellular homeostasis through metabolic adaptations in cardiomyocytes.
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Affiliation(s)
- Chandni Thakkar
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Saleena Alikunju
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Nandita Niranjan
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Wajiha Rizvi
- High School Research Intern, Wayne Hills High School, Wayne, NJ 07470, United States of America
| | - Ali Abbas
- From the Department of Diagnostic Sciences, Rutgers School of Dental Medicine, Newark, NJ 07103, United States of America
| | - Maha Abdellatif
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America
| | - Danish Sayed
- From the Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, United States of America.
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220
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Romualdo GR, Valente LC, Dos Santos ACS, Grandini NA, Camacho CRC, Vinken M, Cogliati B, Hou DX, Barbisan LF. Effects of glyphosate exposure on western diet-induced non-alcoholic fatty liver disease in mice. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2023; 104:104286. [PMID: 37805155 DOI: 10.1016/j.etap.2023.104286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
We evaluated whether glyphosate promotes western diet (WD)-induced non-alcoholic fatty liver disease (NAFLD). Male C57BL/6J mice were fed WD and received intragastrical glyphosate (0.05, 5 or 50 mg/kg) for 6 months. Glyphosate did not promote WD-induced obesity, hypercholesterolemia, glucose intolerance, hepatic steatosis, and fibrosis. Nonetheless, the higher dose (50 mg) enhanced hepatic CD68+ macrophage density, p65, TNF-α, and IL-6 protein levels. Furthermore, this dose decreased hepatic Nrf2 levels, while enhancing lipid peroxidation in the liver and adipose tissue. Hepatic transcriptome revealed that glyphosate at 50 mg upregulated 212 genes and downregulated 731 genes. Genes associated with oxidative stress and inflammation were upregulated, while key cell cycle-related genes were downregulated. Our results indicate that glyphosate exposure - in a dose within the toxicological limits - impairs hepatic inflammation/redox dynamics in a NAFLD microenvironment.
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Affiliation(s)
- Guilherme R Romualdo
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform - Laboratory of Chemically induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Botucatu, SP, Brazil.
| | - Letícia Cardoso Valente
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform - Laboratory of Chemically induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Botucatu, SP, Brazil; Federal University of Grande Dourados (UFGD), Faculty of Health Sciences, Dourados, MS, Brazil
| | | | - Núbia Alves Grandini
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Botucatu, SP, Brazil
| | - Camila Renata Correa Camacho
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Botucatu, SP, Brazil
| | - Mathieu Vinken
- Vrije Universiteit Brussel. Brussels, Department of In Vitro Toxicology and Dermato-Cosmetology, Belgium
| | - Bruno Cogliati
- University of São Paulo (USP), School of Veterinary Medicine and Animal Science, Department of Pathology, São Paulo, SP, Brazil
| | - De-Xing Hou
- Kagoshima University, Faculty of Agriculture, Department of Food Science and Biotechnology, Japan
| | - Luís Fernando Barbisan
- São Paulo State University (UNESP), Botucatu Medical School, Experimental Research Unit (UNIPEX), Multimodel Drug Screening Platform - Laboratory of Chemically induced and Experimental Carcinogenesis (MDSP-LCQE), Botucatu, SP, Brazil; São Paulo State University (UNESP), Biosciences Institute, Department of Structural and Functional Biology, Botucatu, SP, Brazil.
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221
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Carroll JA, Striebel JF, Baune C, Chesebro B, Race B. CD11c is not required by microglia to convey neuroprotection after prion infection. PLoS One 2023; 18:e0293301. [PMID: 37910561 PMCID: PMC10619787 DOI: 10.1371/journal.pone.0293301] [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: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 11/03/2023] Open
Abstract
Prion diseases are caused by the misfolding of a normal host protein that leads to gliosis, neuroinflammation, neurodegeneration, and death. Microglia have been shown to be critical for neuroprotection during prion infection of the central nervous system (CNS), and their presence extends survival in mice. How microglia impart these benefits to the infected host are unknown. Previous transcriptomics and bioinformatics studies suggested that signaling through the heterodimeric integrin receptor CD11c/CD18, expressed by microglia in the brain, might be important to microglial function during prion disease. Herein, we intracerebrally challenged CD11c-/- mice with prion strain RML and compared them to similarly infected C57BL/6 mice as controls. We initially assessed changes in the brain that are associated with disease such as astrogliosis, microgliosis, prion accumulation, and survival. Targeted qRT-PCR arrays were used to determine alterations in transcription in mice in response to prion infection. We demonstrate that expression of Itgax (CD11c) and Itgb2 (CD18) increases in the CNS in correlation with advancing prion infection. Gliosis, neuropathology, prion deposition, and disease progression in prion infected CD11c deficient mice were comparable to infected C57BL/6 mice. Additionally, both CD11c deficient and C57BL/6 prion-infected mouse cohorts had a similar consortium of inflammatory- and phagocytosis-associated genes that increased as disease progressed to clinical stages. Ingenuity Pathway Analysis of upregulated genes in infected C57BL/6 mice suggested numerous cell-surface transmembrane receptors signal through Spleen Tyrosine Kinase, a potential key regulator of phagocytosis and innate immune activation in the prion infected brain. Ultimately, the deletion of CD11c did not influence prion pathogenesis in mice and CD11c signaling is not involved in the neuroprotection provided by microglia, but our analysis identified a conspicuous phagocytosis pathway in the CNS of infected mice that appeared to be activated during prion pathogenesis.
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Affiliation(s)
- James A. Carroll
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - James F. Striebel
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Chase Baune
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Bruce Chesebro
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
| | - Brent Race
- Laboratory of Neurological Infections and Immunity, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, United States of America
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222
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Alexander GD, Cavanah LR, Goldhirsh JL, Huey LY, Piper BJ. Medical Cannabis Legalization: No Contribution to Rising Stimulant Rates in the USA. PHARMACOPSYCHIATRY 2023; 56:214-218. [PMID: 37884027 DOI: 10.1055/a-2152-7757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
INTRODUCTION There has been a pronounced increase in the use of Schedule II stimulants to treat attention-deficit hyperactivity disorder (ADHD) in the United States over the last two decades. Interestingly, chronic medical cannabis (MC) use can present with cognitive impairments that resemble ADHD symptoms. This study aimed to determine if MC legalization increased prescription stimulant distribution. METHODS Information on the distribution of methylphenidate, amphetamine, and lisdexamfetamine for 2006 to 2021 was extracted from the Drug Enforcement Administration's comprehensive database and the three-year population-corrected slopes of stimulant distribution before and after MC program implementation were compared. RESULTS We found a significant main effect of time (p<0.001); however, contrary to the hypothesis, the sales status of states' MC, did not influence slopes of distribution (p=0.391). There was a significantly large interaction effect of time and MC sales status on slopes of distribution (p<0.001). Slopes of distribution rates of stimulants were significantly lower in states that proceeded to legalize MC prior to MC program implementation than those states that did not (p=0.022). After MC program implementation, however, the distribution rates of the Schedule II stimulants were not significantly different when comparing states with MC sales to those without (p=0.355). DISCUSSION These findings suggest that MC program legalization did not contribute to certain states having rapid increases in Schedule II stimulant distribution rates over time. Other factors, including the liberalization of the adult ADHD diagnostic criteria in the DSM-5 and the introduction of Binge Eating Disorder, also likely contributed to elevations in stimulant distribution.
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Affiliation(s)
| | - Luke R Cavanah
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
| | | | - Leighton Y Huey
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Behavioral Health Initiative, Scranton, PA, United States
| | - Brian J Piper
- Geisinger Commonwealth School of Medicine, Scranton, PA, United States
- Center for Pharmacy Innovation and Outcomes, Forty Fort, PA, United States
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223
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Howell MC, Green R, Cianne J, Dayhoff GW, Uversky VN, Mohapatra S, Mohapatra S. EGFR TKI resistance in lung cancer cells using RNA sequencing and analytical bioinformatics tools. J Biomol Struct Dyn 2023; 41:9808-9827. [PMID: 36524419 PMCID: PMC10272293 DOI: 10.1080/07391102.2022.2153269] [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: 08/05/2022] [Accepted: 11/07/2022] [Indexed: 12/23/2022]
Abstract
Epidermal Growth Factor Receptor (EGFR) signaling and EGFR mutations play key roles in cancer pathogenesis, particularly in the development of drug resistance. For the ∼20% of all non-small cell lung cancer (NSCLC) patients that harbor an activating mutation, EGFR tyrosine kinase inhibitors (TKIs) provide initial clinical responses. However, long-term efficacy is not possible due to acquired drug resistance. Despite a gradually increasing knowledge of the mechanisms underpinning the development of resistance in tumors, there has been very little success in overcoming it and it is probable that many additional mechanisms are still unknown. Herein, publicly available RNASeq (RNA sequencing) datasets comparing lung cancer cell lines treated with EGFR TKIs until resistance developed with their corresponding parental cells and protein array data from our own EGFR TKI treated xenograft tumors, were analyzed for differential gene expression, with the intent to investigate the potential mechanisms of drug resistance to EGFR TKIs. Pathway analysis, as well as structural disorder analysis of proteins in these pathways, revealed several key proteins, including DUSP1, DUSP6, GAB2, and FOS, that could be targeted using novel combination therapies to overcome EGFR TKI resistance in lung cancer.
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Affiliation(s)
- Mark C Howell
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
- Center for Research & Education in Nanobioengineering, Division of Translational Medicine, Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Ryan Green
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
- Center for Research & Education in Nanobioengineering, Division of Translational Medicine, Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Junior Cianne
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Guy W Dayhoff
- Department of Chemistry, College of Art and Sciences, University of South Florida, Tampa, FL, USA
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Shyam Mohapatra
- Center for Research & Education in Nanobioengineering, Division of Translational Medicine, Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- James A. Haley Veterans Hospital, Tampa, FL, USA
| | - Subhra Mohapatra
- Department of Molecular Medicine, University of South Florida, Tampa, FL, USA
- James A. Haley Veterans Hospital, Tampa, FL, USA
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Buzova D, Frohlich J, Zapletalova D, Raffaele M, Lo Re O, Tsoneva DK, Sterba J, Cerveny J, Vinciguerra M. Detection of cell-free histones in the cerebrospinal fluid of pediatric central nervous system malignancies by imaging flow cytometry. Front Mol Biosci 2023; 10:1254699. [PMID: 38028540 PMCID: PMC10646437 DOI: 10.3389/fmolb.2023.1254699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Pediatric brain tumours (PBT) are one of the most common malignancies during childhood, with variable severity according to the location and histological type. Certain types of gliomas, such a glioblastoma and diffuse intrinsic pontine glioma (DIPG), have a much higher mortality than ependymoma and medulloblastoma. Early detection of PBT is essential for diagnosis and therapeutic interventions. Liquid biopsies have been demonstrated using cerebrospinal fluid (CSF), mostly restricted to cell free DNA, which display limitations of quantity and integrity. In this pilot study, we sought to demonstrate the detectability and robustness of cell free histones in the CSF. Methods: We collected CSF samples from a pilot cohort of 8 children with brain tumours including DIPG, medulloblastoma, glioblastoma, ependymoma and others. As controls, we collected CSF samples from nine children with unrelated blood malignancies and without brain tumours. We applied a multichannel flow imaging approach on ImageStream(X) to image indiviual histone or histone complexes on different channels. Results: Single histones (H2A, macroH2A1.1, macroH2A1.2 H2B, H3, H4 and histone H3 bearing the H3K27M mutation), and histone complexes are specifically detectable in the CSF of PBT patients. H2A and its variants macroH2A1.1/macroH2A1/2 displayed the strongest signal and abundance, together with disease associated H3K27M. In contrast, mostly H4 is detectable in the CSF of pediatric patients with blood malignancies. Discussion: In conclusion, free histones and histone complexes are detectable with a strong signal in the CSF of children affected by brain tumours, using ImageStream(X) technology and may provide additive diagnostic and predictive information.
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Affiliation(s)
- Diana Buzova
- Department of Adaptive Biotechnologies, Global Change Research Institute CAS, Brno, Czechia
| | - Jan Frohlich
- International Clinical Research Center, St Anne’s University Hospital, Brno, Czechia
| | - Danica Zapletalova
- Department of Pediatric Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Marco Raffaele
- International Clinical Research Center, St Anne’s University Hospital, Brno, Czechia
| | - Oriana Lo Re
- International Clinical Research Center, St Anne’s University Hospital, Brno, Czechia
- Department of Stem Cell Biology and Transplantology, Research Institute of the Medical University of Varna, Varna, Bulgaria
| | - Desislava K. Tsoneva
- Department of Stem Cell Biology and Transplantology, Research Institute of the Medical University of Varna, Varna, Bulgaria
- Department of Medical Genetics, Medical University of Varna, Varna, Bulgaria
| | - Jaroslav Sterba
- International Clinical Research Center, St Anne’s University Hospital, Brno, Czechia
- Department of Pediatric Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Jan Cerveny
- Department of Adaptive Biotechnologies, Global Change Research Institute CAS, Brno, Czechia
| | - Manlio Vinciguerra
- International Clinical Research Center, St Anne’s University Hospital, Brno, Czechia
- Department of Stem Cell Biology and Transplantology, Research Institute of the Medical University of Varna, Varna, Bulgaria
- Faculty of Health, Liverpool John Moores University, Liverpool, United Kingdom
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Arshad U, Husnain A, Poindexter MB, Zimpel R, Nelson CD, Santos JEP. Rumen-protected choline reduces hepatic lipidosis by increasing hepatic triacylglycerol-rich lipoprotein secretion in dairy cows. J Dairy Sci 2023; 106:7630-7650. [PMID: 37641262 DOI: 10.3168/jds.2022-23182] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/25/2023] [Indexed: 08/31/2023]
Abstract
Objectives were to determine the effects of supplementing rumen-protected choline (RPC) on hepatic composition and secretion of triacylglycerol-rich lipoprotein when cows were subjected to feed restriction to develop fatty liver. It was hypothesized that RPC reduces hepatic triacylglycerol by enhancing secretion of hepatic lipoprotein. Pregnant, nonlactating parous Holstein cows (n = 33) at mean (± standard deviation) 234 ± 2.2 d of gestation were blocked by body condition (3.79 ± 0.49) and assigned to receive 0 g/d (CON), 25.8 g/d choline ion from a RPC product containing 28.8% choline chloride (CC; treatment L25.8), or 25.8 g/d of choline ion from a RPC product containing 60.0% CC (H25.8). Cows were fed for ad libitum intake for the first 5 d and restricted to 41% of the net energy for lactation required for maintenance and pregnancy from d 6 to 13. Intake of metabolizable methionine was maintained at 18 g/d during feed restriction by supplying rumen-protected methionine. Hepatic tissue was sampled on d 6 and 13 and analyzed for triacylglycerol and glycogen, and mRNA expression of hepatic tissue was investigated. On d 14, cows were not fed and received a 10% solution of tyloxapol intravenously at 120 mg/kg of body weight to block hydrolysis of triacylglycerols in very low density lipoprotein (VLDL). Blood was sampled sequentially for 720 min and analyzed for concentration of triacylglycerol and total cholesterol. Lymph was sampled 6 h after tyloxapol infusion, and analyzed for concentrations of fatty acids, β-hydroxybutyrate, glucose, triacylglycerol, and total cholesterol. A sample of serum collected at 720 min after tyloxapol was assayed for the metabolome composition. The area under the curve (AUC) of serum triacylglycerol, VLDL cholesterol, and total cholesterol were calculated. Orthogonal contrasts evaluated the effect of supplementing RPC (CON vs. [1/2 L25.8 + 1/2 H25.8]) and source of RPC (L25.8 vs. H25.8). Least squares means and standard errors of the means are presented in sequence as CON, L25.8, H25.8. During feed restriction, supplementation of RPC reduced hepatic triacylglycerol (9.0 vs. 4.1 vs. 4.5 ± 0.6%) and increased glycogen contents (1.9 vs. 3.5 vs. 4.1 ± 0.2%). Similarly, supplementation of RPC increased the expression of transcripts involved in the synthesis and assembly of lipoproteins (MTTP), cellular autophagy (ATG3), and inflammation (TNFA), and reduced the expression of transcripts associated with mitochondrial oxidation of fatty acids (HADHA, MLYCD) and stabilization of lipid droplets (PLIN2). After infusion of tyloxapol, RPC increased the AUC for serum triacylglycerol (21,741 vs. 32,323 vs. 28,699 ± 3,706 mg/dL × min) and VLDL cholesterol (4,348 vs. 6,465 vs. 5,740 ± 741 mg/dL × min) but tended to reduce the concentrations of triacylglycerol in lymph (16.7 vs. 13.8 vs. 11.9 ± 1.9 mg/dL). Feeding RPC tended to increase the concentrations of 89 metabolites in serum, after adjusting for false discovery, including 3 acylcarnitines, 1 AA-related metabolite, 11 bile acids, 1 ceramide, 6 diacylglycerols, 2 dihydroceramides, 1 glycerophospholipid, and 64 triacylglycerols compared with CON. Feeding 25.8 g/d of choline ion as RPC mediated increased hepatic triacylglycerol secretion to promote lipotropic effects that reduced hepatic lipidosis in dairy cows.
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Affiliation(s)
- U Arshad
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - A Husnain
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - M B Poindexter
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - R Zimpel
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - C D Nelson
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - J E P Santos
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611.
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Arai K, Saito F, Miyazaki M, Kushige H, Izu Y, Maeta N, Yamazoe K. Small Molecules Temporarily Induce Neuronal Features in Adult Canine Dermal Fibroblasts. Int J Mol Sci 2023; 24:15804. [PMID: 37958789 PMCID: PMC10648228 DOI: 10.3390/ijms242115804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
Several methods have been developed to generate neurons from other cell types for performing regeneration therapy and in vitro studies of central nerve disease. Small molecules (SMs) can efficiently induce neuronal features in human and rodent fibroblasts without transgenes. Although canines have been used as a spontaneous disease model of human central nerve, efficient neuronal reprogramming method of canine cells have not been well established. We aimed to induce neuronal features in adult canine dermal fibroblasts (ACDFs) by SMs and assess the permanency of these changes. ACDFs treated with eight SMs developed a round-shaped cell body with branching processes and expressed neuronal proteins, including βIII-tubulin, microtubule-associated protein 2 (MAP2), and neurofilament-medium. Transcriptome profiling revealed the upregulation of neuron-related genes, such as SNAP25 and GRIA4, and downregulation of fibroblast-related genes, such as COL12A1 and CCN5. Calcium fluorescent imaging demonstrated an increase in intracellular Ca2+ concentration upon stimulation with glutamate and KCl. Although neuronal features were induced similarly in basement membrane extract droplet culture, they diminished after culturing without SMs or in vivo transplantation into an injured spinal cord. In conclusion, SMs temporarily induce neuronal features in ACDFs. However, the analysis of bottlenecks in the neuronal induction is crucial for optimizing the process.
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Affiliation(s)
- Kiyotaka Arai
- Department of Veterinary Surgery, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoi-no-oka, Imabari 794-8555, Japan; (M.M.); (H.K.); (N.M.); (K.Y.)
| | - Fumiyo Saito
- Department of Toxicology, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoi-no-oka, Imabari 794-8555, Japan;
| | - Masashi Miyazaki
- Department of Veterinary Surgery, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoi-no-oka, Imabari 794-8555, Japan; (M.M.); (H.K.); (N.M.); (K.Y.)
| | - Haruto Kushige
- Department of Veterinary Surgery, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoi-no-oka, Imabari 794-8555, Japan; (M.M.); (H.K.); (N.M.); (K.Y.)
| | - Yayoi Izu
- Department of Laboratory Animal Science, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoi-no-oka, Imabari 794-8555, Japan;
| | - Noritaka Maeta
- Department of Veterinary Surgery, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoi-no-oka, Imabari 794-8555, Japan; (M.M.); (H.K.); (N.M.); (K.Y.)
| | - Kazuaki Yamazoe
- Department of Veterinary Surgery, Faculty of Veterinary Medicine, Okayama University of Science, 1-3 Ikoi-no-oka, Imabari 794-8555, Japan; (M.M.); (H.K.); (N.M.); (K.Y.)
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Acharya K, Borborah S, Chatterjee A, Ghosh M, Bhattacharya A. A comprehensive profiling of quorum quenching by bacterial pigments identifies quorum sensing inhibition and antibiofilm action of prodigiosin against Acinetobacter baumannii. Arch Microbiol 2023; 205:364. [PMID: 37906317 DOI: 10.1007/s00203-023-03710-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: 07/06/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023]
Abstract
Bacterial pigments represent a diverse group of secondary metabolites, which confer fitness advantages to the producers while residing in communities. The bioactive potential of such metabolites, including antimicrobial, anticancer, and immunomodulation, are being explored. Reckoning that a majority of such pigments are produced in response to quorum sensing (QS) mediated expression of biosynthetic gene clusters and, in turn, influence cell-cell communication, systemic profiling of the pigments for possible impact on QS appears crucial. A systemic screening of bacterial pigments for QS-inhibition combined with exploration of antibiofilm and antimicrobial action against Acinetobacter baumannii might offer viable alternatives to combat the priority pathogen. Major bacterial pigments are classified (clustered) based on their physicochemical properties, and representatives of the clusters are screened for QS inhibition. The screen highlighted prodigiosin as a potent quorum quencher, although its production from Serratia marcescens appeared to be QS-independent. In silico analysis indicated potential interactions between AbaI and AbaR, two major QS regulators in A. baumannii, and prodigiosin, which impaired biofilm formation, a major QS-dependent process in the bacteria. Prodigiosin augmented antibiotic action of ciprofloxacin against A. baumannii biofilms. Cell viability analysis revealed prodigiosin to be modestly cytotoxic against HEK293, a non-cancer human cell line. While developing dual-species biofilm, prodigiosin producer S. marcescens significantly impaired the fitness of A. baumannii. Enhanced susceptibility of A. baumannii toward colistin was also noted while growing in co-culture with S. marcescens. Antibiotic resistant isolates demonstrated varied responsiveness against prodigiosin, with two resistant strains demonstrating possible collateral sensitivity. Collectively, the results underpin the prospect of a prodigiosin-based therapeutic strategy in combating A. baumannii infection.
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Affiliation(s)
- Kusumita Acharya
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd., Kolkata, 700126, India
| | - Sonjukta Borborah
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd., Kolkata, 700126, India
| | - Abhishek Chatterjee
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd., Kolkata, 700126, India
| | - Mallika Ghosh
- Dr. Lal PathLabs-Kolkata Reference Lab, Newtown, Kolkata, 700156, India
| | - Arijit Bhattacharya
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd., Kolkata, 700126, India.
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228
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Ocaña MC, Bernal M, Yang C, Caro C, Domínguez A, Vu HS, Cárdenas C, García-Martín ML, DeBerardinis RJ, Quesada AR, Martínez-Poveda B, Medina MÁ. New insights in the targets of action of dimethyl fumarate in endothelial cells: effects on energetic metabolism and serine synthesis in vitro and in vivo. Commun Biol 2023; 6:1084. [PMID: 37880317 PMCID: PMC10600195 DOI: 10.1038/s42003-023-05443-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 10/11/2023] [Indexed: 10/27/2023] Open
Abstract
Dimethyl fumarate is an ester from the Krebs cycle intermediate fumarate. This drug is approved and currently used for the treatment of psoriasis and multiple sclerosis, and its anti-angiogenic activity was reported some years ago. Due to the current clinical relevance of this compound and the recently manifested importance of endothelial cell metabolism on the angiogenic switch, we wanted to elucidate whether dimethyl fumarate has an effect on energetic metabolism of endothelial cells. Different experimental approximations were performed in endothelial cells, including proteomics, isotope tracing and metabolomics experimental approaches, in this work we studied the possible role of dimethyl fumarate in endothelial cell energetic metabolism. We demonstrate for the first time that dimethyl fumarate promotes glycolysis and diminishes cell respiration in endothelial cells, which could be a consequence of a down-regulation of serine and glycine synthesis through inhibition of PHGDH activity in these cells. Dimethyl fumarate alters the energetic metabolism of endothelial cells in vitro and in vivo through an unknown mechanism, which could be the cause or the consequence of its pharmacological activity. This new discovery on the targets of this compound could open a new field of study regarding the mechanism of action of dimethyl fumarate.
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Affiliation(s)
- Mª Carmen Ocaña
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071, Málaga, Spain
- IBIMA Plataforma BIONAND (Biomedical Research Institute of Málaga and nano medicine Platform), E-29590, Málaga, Spain
| | - Manuel Bernal
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071, Málaga, Spain
- IBIMA Plataforma BIONAND (Biomedical Research Institute of Málaga and nano medicine Platform), E-29590, Málaga, Spain
| | - Chendong Yang
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Carlos Caro
- IBIMA Plataforma BIONAND (Biomedical Research Institute of Málaga and nano medicine Platform), E-29590, Málaga, Spain
- Biomedical Magnetic Resonance Laboratory-BMRL, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
| | - Alejandro Domínguez
- IBIMA Plataforma BIONAND (Biomedical Research Institute of Málaga and nano medicine Platform), E-29590, Málaga, Spain
| | - Hieu S Vu
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Casimiro Cárdenas
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071, Málaga, Spain
- Research Support Central Services (SCAI) of the University of Málaga, Málaga, Spain
| | - María Luisa García-Martín
- IBIMA Plataforma BIONAND (Biomedical Research Institute of Málaga and nano medicine Platform), E-29590, Málaga, Spain
- Biomedical Magnetic Resonance Laboratory-BMRL, Andalusian Public Foundation Progress and Health-FPS, Seville, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials & Nanomedicine (CIBER-BBN), 28029, Madrid, Spain
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Eugene McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Howard Hughes Medical Institute, The University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ana R Quesada
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071, Málaga, Spain
- IBIMA Plataforma BIONAND (Biomedical Research Institute of Málaga and nano medicine Platform), E-29590, Málaga, Spain
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Beatriz Martínez-Poveda
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071, Málaga, Spain.
- IBIMA Plataforma BIONAND (Biomedical Research Institute of Málaga and nano medicine Platform), E-29590, Málaga, Spain.
- CIBER de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain.
| | - Miguel Ángel Medina
- Universidad de Málaga, Andalucía Tech, Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, E-29071, Málaga, Spain.
- IBIMA Plataforma BIONAND (Biomedical Research Institute of Málaga and nano medicine Platform), E-29590, Málaga, Spain.
- CIBER de Enfermedades Raras (CIBERER), Madrid, Spain.
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229
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Hirani DV, Thielen F, Mansouri S, Danopoulos S, Vohlen C, Haznedar-Karakaya P, Mohr J, Wilke R, Selle J, Grosch T, Mizik I, Odenthal M, Alvira CM, Kuiper-Makris C, Pryhuber GS, Pallasch C, van Koningsbruggen-Rietschel S, Al-Alam D, Seeger W, Savai R, Dötsch J, Alejandre Alcazar MA. CXCL10 deficiency limits macrophage infiltration, preserves lung matrix, and enables lung growth in bronchopulmonary dysplasia. Inflamm Regen 2023; 43:52. [PMID: 37876024 PMCID: PMC10594718 DOI: 10.1186/s41232-023-00301-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023] Open
Abstract
Preterm infants with oxygen supplementation are at high risk for bronchopulmonary dysplasia (BPD), a neonatal chronic lung disease. Inflammation with macrophage activation is central to the pathogenesis of BPD. CXCL10, a chemotactic and pro-inflammatory chemokine, is elevated in the lungs of infants evolving BPD and in hyperoxia-based BPD in mice. Here, we tested if CXCL10 deficiency preserves lung growth after neonatal hyperoxia by preventing macrophage activation. To this end, we exposed Cxcl10 knockout (Cxcl10-/-) and wild-type mice to an experimental model of hyperoxia (85% O2)-induced neonatal lung injury and subsequent regeneration. In addition, cultured primary human macrophages and murine macrophages (J744A.1) were treated with CXCL10 and/or CXCR3 antagonist. Our transcriptomic analysis identified CXCL10 as a central hub in the inflammatory network of neonatal mouse lungs after hyperoxia. Quantitative histomorphometric analysis revealed that Cxcl10-/- mice are in part protected from reduced alveolar. These findings were related to the preserved spatial distribution of elastic fibers, reduced collagen deposition, and protection from macrophage recruitment/infiltration to the lungs in Cxcl10-/- mice during acute injury and regeneration. Complimentary, studies with cultured human and murine macrophages showed that hyperoxia induces Cxcl10 expression that in turn triggers M1-like activation and migration of macrophages through CXCR3. Finally, we demonstrated a temporal increase of macrophage-related CXCL10 in the lungs of infants with BPD. In conclusion, our data demonstrate macrophage-derived CXCL10 in experimental and clinical BPD that drives macrophage chemotaxis through CXCR3, causing pro-fibrotic lung remodeling and arrest of alveolarization. Thus, targeting the CXCL10-CXCR3 axis could offer a new therapeutic avenue for BPD.
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Affiliation(s)
- Dharmesh V Hirani
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Institute for Lung Health (ILH) and Cardio-Pulmonary Institute (CPI), Gießen, Germany
| | - Florian Thielen
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
| | - Siavash Mansouri
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Soula Danopoulos
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Christina Vohlen
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
- Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Institute for Lung Health (ILH) and Cardio-Pulmonary Institute (CPI), Gießen, Germany
- Department of Pediatric and Adolescent Medicine, Faculty of Medicine, University Hospital Cologne, and University of Cologne, Cologne, Germany
| | - Pinar Haznedar-Karakaya
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
| | - Jasmine Mohr
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
| | - Rebecca Wilke
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
| | - Jaco Selle
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
| | - Thomas Grosch
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
| | - Ivana Mizik
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
| | - Margarete Odenthal
- Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Faculty of Medicine, and University of Cologne, Cologne, Germany
- Institute for Pathology, University Hospital Cologne, Faculty of Medicine, and University of Cologne, Cologne, Germany
| | - Cristina M Alvira
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Celien Kuiper-Makris
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany
- Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Faculty of Medicine, and University of Cologne, Cologne, Germany
| | - Gloria S Pryhuber
- Department of Pediatrics, Division of Neonatology, University of Rochester Medical Center, Rochester, NY, USA
| | - Christian Pallasch
- Department I of Internal Medicine, Center for Integrated Oncology (CIO) Köln-Bonn, University of Cologne, Cologne, Germany
| | - S van Koningsbruggen-Rietschel
- Department of Pediatric and Adolescent Medicine, Faculty of Medicine, University Hospital Cologne, and University of Cologne, Cologne, Germany
| | - Denise Al-Alam
- Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Werner Seeger
- Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Institute for Lung Health (ILH) and Cardio-Pulmonary Institute (CPI), Gießen, Germany
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Rajkumar Savai
- Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Institute for Lung Health (ILH) and Cardio-Pulmonary Institute (CPI), Gießen, Germany
- Department of Lung Development and Remodeling, Max-Planck-Institute for Heart and Lung Research, Member of the German Center for Lung Research (DZL), Bad Nauheim, Germany
| | - Jörg Dötsch
- Department of Pediatric and Adolescent Medicine, Faculty of Medicine, University Hospital Cologne, and University of Cologne, Cologne, Germany
| | - Miguel A Alejandre Alcazar
- Department of Pediatric and Adolescent Medicine, Translational Experimental Pediatrics, Experimental Pulmonology, University Hospital Cologne, Faculty of Medicine, University of Cologne, Kerpener Strasse 62, Cologne, 50937, Germany.
- Universities of Giessen and Marburg Lung Center (UGMLC), member of the German Center for Lung Research (DZL), Institute for Lung Health (ILH) and Cardio-Pulmonary Institute (CPI), Gießen, Germany.
- Center for Molecular Medicine Cologne (CMMC), University Hospital Cologne, Faculty of Medicine, and University of Cologne, Cologne, Germany.
- Cologne Excellence Cluster On Stress Responses in Aging-Associated Diseases (CECAD), University Hospital of Cologne, University of Cologne, Cologne, Germany.
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230
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Page-McCaw PS, Pokidysheva EN, Darris CE, Chetyrkin S, Fidler AL, Murawala P, Gallup J, Hudson JK, Hudson BG. Collagen IV of basement membranes: I. Origin and diversification of COL4 genes enabling animal evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.18.563013. [PMID: 37905027 PMCID: PMC10614949 DOI: 10.1101/2023.10.18.563013] [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
Collagen IV is a primordial component of basement membranes, a specialized form of extracellular matrix that enabled multi-cellular epithelial tissues. In mammals, collagen IV assembles from a family of six α-chains (α1 to α6), encoded by six genes (COL4A1 to COL4A6), into three distinct scaffolds: the α121, the α345 and a mixed scaffold containing both α121 and α565. The six mammalian COL4A genes occur in pairs that occur in a head-to-head arrangement on three distinct chromosomes. In Alport syndrome, variants in the COL4A3, 4 or 5 genes cause either loss or defective assembly of the collagen IV α345 scaffold which results in a dysfunctional glomerular basement membrane, proteinuria and progression to renal failure in millions of people worldwide. Here, we determine the evolutionary emergence and diversification of the COL4A genes using comparative genomics and biochemical analyses. Using syntenic relationships to genes closely linked to the COL4A genes, we determine that the COL4A3 and COL4A4 gene pair appeared in cyclostomes (hagfish and lampreys) while the COL4A5 and COL4A6 gene pair emerged in gnathostomes, jawed vertebrates. The more basal chordate species, lancelets and tunicates, do not have discrete kidneys and have a single COL4A gene pair, though often with single isolated COL4 genes similar to those found in C elegans . Remarkably, while the six COL4A genes are conserved in vertebrates, amphibians have lost the COL4A3 and COL4A4 genes. Our findings of the evolutionary emergence of these genes, together with the amphibian double-knockout, opens an experimental window to gain insights into functionality of the Col IV α345 scaffold.
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231
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Clifton BD, Hariyani I, Kimura A, Luo F, Nguyen A, Ranz JM. Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages. Commun Biol 2023; 6:1069. [PMID: 37864070 PMCID: PMC10589255 DOI: 10.1038/s42003-023-05427-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 10/05/2023] [Indexed: 10/22/2023] Open
Abstract
How recently originated gene copies become stable genomic components remains uncertain as high sequence similarity of young duplicates precludes their functional characterization. The tandem multigene family Sdic is specific to Drosophila melanogaster and has been annotated across multiple reference-quality genome assemblies. Here we show the existence of a positive correlation between Sdic copy number and total expression, plus vast intrastrain differences in mRNA abundance among paralogs, using RNA-sequencing from testis of four strains with variable paralog composition. Single cell and nucleus RNA-sequencing data expose paralog expression differentiation in meiotic cell types within testis from third instar larva and adults. Additional RNA-sequencing across synthetic strains only differing in their Y chromosomes reveal a tissue-dependent trans-regulatory effect on Sdic: upregulation in testis and downregulation in male accessory gland. By leveraging paralog-specific expression information from tissue- and cell-specific data, our results elucidate the intraspecific functional diversification of a recently expanded tandem gene family.
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Affiliation(s)
- Bryan D Clifton
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
| | - Imtiyaz Hariyani
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Ashlyn Kimura
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Fangning Luo
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - Alvin Nguyen
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | - José M Ranz
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA.
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Shiota T, Li Z, Chen GY, McKnight KL, Shirasaki T, Yonish B, Kim H, Fritch EJ, Sheahan TP, Muramatsu M, Kapustina M, Cameron CE, Li Y, Zhang Q, Lemon SM. Hepatoviruses promote very-long-chain fatty acid and sphingolipid synthesis for viral RNA replication and quasi-enveloped virus release. SCIENCE ADVANCES 2023; 9:eadj4198. [PMID: 37862421 PMCID: PMC10588952 DOI: 10.1126/sciadv.adj4198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/15/2023] [Indexed: 10/22/2023]
Abstract
Virus-induced changes in host lipid metabolism are an important but poorly understood aspect of viral pathogenesis. By combining nontargeted lipidomics analyses of infected cells and purified extracellular quasi-enveloped virions with high-throughput RNA sequencing and genetic depletion studies, we show that hepatitis A virus, an hepatotropic picornavirus, broadly manipulates the host cell lipid environment, enhancing synthesis of ceramides and other sphingolipids and transcriptionally activating acyl-coenzyme A synthetases and fatty acid elongases to import and activate long-chain fatty acids for entry into the fatty acid elongation cycle. Phospholipids with very-long-chain acyl tails (>C22) are essential for genome replication, whereas increases in sphingolipids support assembly and release of quasi-enveloped virions wrapped in membranes highly enriched for sphingomyelin and very-long-chain ceramides. Our data provide insight into how a pathogenic virus alters lipid flux in infected hepatocytes and demonstrate a distinction between lipid species required for viral RNA synthesis versus nonlytic quasi-enveloped virus release.
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Affiliation(s)
- Tomoyuki Shiota
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhucui Li
- Center for Translational Biomedical Research, The University of North Carolina at Greensboro, Kannapolis, NC, USA
| | - Guan-Yuan Chen
- Center for Translational Biomedical Research, The University of North Carolina at Greensboro, Kannapolis, NC, USA
| | - Kevin L. McKnight
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Takayoshi Shirasaki
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Bryan Yonish
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Heyjeong Kim
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ethan J. Fritch
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Timothy P. Sheahan
- Department of Epidemiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Masamichi Muramatsu
- Department of Infectious Disease Research, Foundation for Biomedical Research and Innovation at Kobe, Kobe, Hyogo, Japan
| | - Maryna Kapustina
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Craig E. Cameron
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - You Li
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Qibin Zhang
- Center for Translational Biomedical Research, The University of North Carolina at Greensboro, Kannapolis, NC, USA
- Department of Chemistry and Biochemistry, The University of North Carolina at Greensboro, Greensboro, NC, USA
| | - Stanley M. Lemon
- Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Lokesh J, Delaygues M, Defaix R, Le Bechec M, Pigot T, Dupont-Nivet M, Kerneis T, Labbé L, Goardon L, Terrier F, Panserat S, Ricaud K. Interaction between genetics and inulin affects host metabolism in rainbow trout fed a sustainable all plant-based diet. Br J Nutr 2023; 130:1105-1120. [PMID: 36690577 DOI: 10.1017/s0007114523000120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Inulin affects nutrition and metabolism in many animals. Although inulin is widely used in the diet of teleosts, its mechanism of action is unknown. Here, we investigated the effect of inulin (2 %) on the intestinal microbiome and metabolism in rainbow trout (Oncorhynchus mykiss) selected for growth and survival when fed a 100 % plant-based diet (suave) and a control line (temoin). Metabolic responses to the two factors (line and inulin) in liver, intestine, muscle and adipose were tissue-specific, with line and interaction between the two factors influencing overall expression in liver. In the intestine, inulin and line and in muscle, line influenced the expression of metabolic genes. Microbiota between the mucus and digestive contents was significantly different, with genera from Proteobacteria being more abundant in the mucus, whereas genera from the Firmicutes and Planctomycetes being more abundant in contents. Effect of inulin and interaction between factors on the microbiome was evident in contents. The significant taxa of control and inulin-fed groups differed greatly with Streptococcus and Weissella being significantly abundant in the inulin-fed group. There was a general trend showing higher levels of all SCFA in temoin group with propionic acid levels being significantly higher. An operational taxonomic unit (OTU) belonging to the Ruminococcaceae was significantly abundant in suave. The tissue-specific correlations between OTU and gene expression may indicate the link between microbiome and metabolism. Together, these results suggest that line and inulin impact the gene expression in a tissue-specific manner, possibly driven by specific OTUs enriched in inulin-fed groups and suave.
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Affiliation(s)
- Jep Lokesh
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Marine Delaygues
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Raphaël Defaix
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Mickael Le Bechec
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IMT Mines Ales, IPREM, Pau, France; Institut des sciences analytiques et de Physicochimie pour l'environnement et les Matériaux, UMR5254, Hélioparc, 2 avenue Président Angot, 64 053 PAU cedex 9, France
| | - Thierry Pigot
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IMT Mines Ales, IPREM, Pau, France; Institut des sciences analytiques et de Physicochimie pour l'environnement et les Matériaux, UMR5254, Hélioparc, 2 avenue Président Angot, 64 053 PAU cedex 9, France
| | | | | | | | | | - Frédéric Terrier
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Stéphane Panserat
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
| | - Karine Ricaud
- Université de Pau et des Pays de l'Adour, E2S UPPA. INRAE, NUMEA, Saint-Pée-sur-Nivelle, France
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234
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Husnain A, Arshad U, Zimpel R, Schmitt E, Dickson MJ, Perdomo MC, Marinho MN, Ashrafi N, Graham SF, Bishop JV, Hansen TR, Jeong KC, Gonella-Diaza AM, Chebel RC, Sheldon IM, Bromfield JJ, Santos JEP. Induced endometrial inflammation compromises conceptus development in dairy cattle†. Biol Reprod 2023; 109:415-431. [PMID: 37540198 PMCID: PMC10577276 DOI: 10.1093/biolre/ioad088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/24/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
Endometrial inflammation is associated with reduced pregnancy per artificial insemination (AI) and increased pregnancy loss in cows. It was hypothesized that induced endometritis alters histotroph composition and induces inflammatory signatures on conceptus that compromise development. In Experiment 1, lactating cows were assigned to control (CON; n = 23) or to an intrauterine infusion of Escherichia coli and Trueperella pyogenes (ENDO; n = 34) to induce endometritis. Cows received AI 26 days after treatment, and the uterine fluid and conceptuses were collected on day 16 after AI. In Experiment 2, Holstein heifers were assigned to CON (n = 14) or ENDO (n = 14). An embryo was transferred on day 7 of the estrous cycle, and uterine fluid and conceptuses were recovered on day 16. Composition of histotroph and trophoblast and embryonic disc gene expression were assessed. Bacterial-induced endometritis in lactating cows altered histotroph composition and pathways linked to phospholipid synthesis, cellular energy production, and the Warburg effect. Also, ENDO reduced conceptus length in cows and altered expression of genes involved in pathogen recognition, nutrient uptake, cell growth, choline metabolism, and conceptus signaling needed for maternal recognition of pregnancy. The impact of ENDO was lesser on conceptuses from heifers receiving embryo transfer; however, the affected genes and associated pathways involved restricted growth and increased immune response similar to the observed responses to ENDO in conceptuses from lactating cows. Bacterial-induced endometrial inflammation altered histotroph composition, reduced conceptus growth, and caused embryonic cells to activate survival rather than anabolic pathways that could compromise development.
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Affiliation(s)
- Ali Husnain
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - Usman Arshad
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - Roney Zimpel
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - Eduardo Schmitt
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - Mackenzie J Dickson
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - Milerky C Perdomo
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - Mariana N Marinho
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - Nadia Ashrafi
- Metabolomics Department, Beaumont Health, Royal Oak, MI, USA
| | - Stewart F Graham
- Metabolomics Department, Beaumont Health, Royal Oak, MI, USA
- Oakland University-William Beaumont School of Medicine, Rochester, MI, USA
| | - Jeanette V Bishop
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Thomas R Hansen
- Animal Reproduction and Biotechnology Laboratory, Department of Biomedical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - Kwang C Jeong
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | | | - Ricardo C Chebel
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, FL, USA
| | - I Martin Sheldon
- Swansea University Medical School, Swansea University, Swansea, UK
| | - John J Bromfield
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
| | - José E P Santos
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, USA
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235
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Raman G, Choi KS, Lee EM, Morden CW, Shim H, Kang JS, Yang TJ, Park S. Extensive characterization of 28 complete chloroplast genomes of Hydrangea species: A perspective view of their organization and phylogenetic and evolutionary relationships. Comput Struct Biotechnol J 2023; 21:5073-5091. [PMID: 37867966 PMCID: PMC10589384 DOI: 10.1016/j.csbj.2023.10.010] [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: 09/05/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/24/2023] Open
Abstract
The tribe Hydrangeeae displays a unique, distinctive disjunct distribution encompassing East Asia, North America and Hawaii. Despite its complex trait variations and polyphyletic nature, comprehensive phylogenomic and biogeographical studies on this tribe have been lacking. To address this gap, we sequenced and characterized 28 plastomes of Hydrangeeae. Our study highlights the highly conserved nature of Hydrangeaceae chloroplast (cp) genomes in terms of gene content and arrangement. Notably, synapomorphic characteristics of tandem repeats in the conserved domain of accD were observed in the Macrophyllae, Chinenses, and Dichroa sections within the Hydrangeeae tribe. Additionally, we found lower expression of accD in these sections using structure prediction and quantitative real-time PCR analysis. Phylogenomic analyses revealed the subdivision of the Hydrangeeae tribe into two clades with robust support values. Consistent with polyphyletic relationships, sect. Broussaisia was identified as the basal group in the tribe Hydrangeeae. Our study also provides insights into the phylogenetic relationships of Hydrangea petiolaris in the Jeju and Ulleung Island populations, suggesting the need for further studies with more samples and molecular data. Divergence time estimation and biogeographical analyses suggested that the common ancestors of the tribe Hydrangeeae likely originated from North America and East Asia during the Paleocene period via the Bering Land Bridge, potentially facilitating migration within the tribe between these regions. In conclusion, this study enhances our understanding of the evolutionary history and biogeography of the tribe Hydrangeeae, shedding light on the dispersal patterns and origins of this intriguing plant group with its unique disjunct distribution.
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Affiliation(s)
- Gurusamy Raman
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Kyoung-Su Choi
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
- Plant Research Team, Animal and Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju, Republic of Korea
| | - Eun Mi Lee
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
| | - Clifford W. Morden
- School of Life Sciences, University of Hawai]i at Mānoa, Honolulu, HI, USA
| | - Hyeonah Shim
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Jong-Soo Kang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Tae-Jin Yang
- Department of Agriculture, Forestry and Bioresources, Plant Genomics and Breeding Institute, Research Institute of Agriculture and Life Science, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - SeonJoo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan, Gyeongsan-buk, Republic of Korea
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236
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Pramanik D, Becker A, Roessner C, Rupp O, Bogarín D, Pérez-Escobar OA, Dirks-Mulder A, Droppert K, Kocyan A, Smets E, Gravendeel B. Evolution and development of fruits of Erycina pusilla and other orchid species. PLoS One 2023; 18:e0286846. [PMID: 37815982 PMCID: PMC10564159 DOI: 10.1371/journal.pone.0286846] [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: 01/28/2023] [Accepted: 05/24/2023] [Indexed: 10/12/2023] Open
Abstract
Fruits play a crucial role in seed dispersal. They open along dehiscence zones. Fruit dehiscence zone formation has been intensively studied in Arabidopsis thaliana. However, little is known about the mechanisms and genes involved in the formation of fruit dehiscence zones in species outside the Brassicaceae. The dehiscence zone of A. thaliana contains a lignified layer, while dehiscence zone tissues of the emerging orchid model Erycina pusilla include a lipid layer. Here we present an analysis of evolution and development of fruit dehiscence zones in orchids. We performed ancestral state reconstructions across the five orchid subfamilies to study the evolution of selected fruit traits and explored dehiscence zone developmental genes using RNA-seq and qPCR. We found that erect dehiscent fruits with non-lignified dehiscence zones and a short ripening period are ancestral characters in orchids. Lignified dehiscence zones in orchid fruits evolved multiple times from non-lignified zones. Furthermore, we carried out gene expression analysis of tissues from different developmental stages of E. pusilla fruits. We found that fruit dehiscence genes from the MADS-box gene family and other important regulators in E. pusilla differed in their expression pattern from their homologs in A. thaliana. This suggests that the current A. thaliana fruit dehiscence model requires adjustment for orchids. Additionally, we discovered that homologs of A. thaliana genes involved in the development of carpel, gynoecium and ovules, and genes involved in lipid biosynthesis were expressed in the fruit valves of E. pusilla, implying that these genes may play a novel role in formation of dehiscence zone tissues in orchids. Future functional analysis of developmental regulators, lipid identification and quantification can shed more light on lipid-layer based dehiscence of orchid fruits.
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Affiliation(s)
- Dewi Pramanik
- Evolutionary Ecology Group, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- National Research and Innovation Agency Republic of Indonesia (BRIN), Central Jakarta, Indonesia
| | - Annette Becker
- Development Biology of Plants, Institute for Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Clemens Roessner
- Development Biology of Plants, Institute for Botany, Justus-Liebig-University Giessen, Giessen, Germany
| | - Oliver Rupp
- Department of Bioinformatics and Systems Biology, Justus Liebig University, Giessen, Germany
| | - Diego Bogarín
- Evolutionary Ecology Group, Naturalis Biodiversity Center, Leiden, The Netherlands
- Jardín Botánico Lankester, Universidad de Costa Rica, Cartago, Costa Rica
| | | | - Anita Dirks-Mulder
- Faculty of Science and Technology, University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Kevin Droppert
- Faculty of Science and Technology, University of Applied Sciences Leiden, Leiden, The Netherlands
| | - Alexander Kocyan
- Botanical Museum, Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Erik Smets
- Evolutionary Ecology Group, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Ecology, Evolution and Biodiversity Conservation, KU Leuven, Heverlee, Belgium
| | - Barbara Gravendeel
- Evolutionary Ecology Group, Naturalis Biodiversity Center, Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, The Netherlands
- Radboud Institute for Biological and Environmental Sciences, Radboud University, Nijmegen, The Netherlands
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237
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Zito P, Bekins BA, Martinović-Weigelt D, Harsha ML, Humpal KE, Trost J, Cozzarelli I, Mazzoleni LR, Schum SK, Podgorski DC. Photochemical mobilization of dissolved hydrocarbon oxidation products from petroleum contaminated soil into a shallow aquifer activate human nuclear receptors. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132312. [PMID: 37604033 DOI: 10.1016/j.jhazmat.2023.132312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/29/2023] [Accepted: 08/14/2023] [Indexed: 08/23/2023]
Abstract
Elevated non-volatile dissolved organic carbon (NVDOC) concentrations in groundwater (GW) monitoring wells under oil-contaminated hydrophobic soils originating from a pipeline rupture at the National Crude Oil Spill & Natural Attenuation Research Site near Bemidji, MN are documented. We hypothesized the elevated NVDOC is comprised of water-soluble photooxidation products transported from the surface to the aquifer. We use field and laboratory samples in combination with complementary analytical methods to test this hypothesis and determine the biological response to these products. Observations from optical spectroscopy and ultrahigh-resolution mass spectrometry reveal a significant correlation between the chemical composition of NVDOC leached from photochemically weathered soils and GW monitoring wells with high NVDOC concentrations measured in the aquifer beneath the contaminated soil. Conversely, the chemical composition from the uncontaminated soil photoleachate matches the NVDOC observed in the uncontaminated wells. Contaminated GW and photodissolution leachates from contaminated soil activated biological targets indicative of xenobiotic metabolism and exhibited potential for adverse effects. Newly formed hydrocarbon oxidation products (HOPs) from fresh oil could be distinguished from those downgradient. This study illustrates another pathway for dissolved HOPs to infiltrate GW and potentially affect human health and the environment.
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Affiliation(s)
- Phoebe Zito
- Department of Chemistry, Chemical Analysis Mass Spectrometry Facility, University of New Orleans, New Orleans, LA 70148, USA.
| | | | | | - Maxwell L Harsha
- Department of Chemistry, Chemical Analysis Mass Spectrometry Facility, University of New Orleans, New Orleans, LA 70148, USA
| | - Katherine E Humpal
- Department of Chemistry, Chemical Analysis Mass Spectrometry Facility, University of New Orleans, New Orleans, LA 70148, USA
| | - Jared Trost
- US Geological Survey, Mounds View, MN 55112, USA
| | - Isabelle Cozzarelli
- US Geological Survey, Geology, Energy & Minerals Science Center, Reston, VA 20191, USA
| | - Lynn R Mazzoleni
- Department of Chemistry, Chemical Advanced Resolution Methods Laboratory, Michigan Technological University, 1400, Townsend Dr., Houghton, MI 49931, USA
| | - Simeon K Schum
- Department of Chemistry, Chemical Advanced Resolution Methods Laboratory, Michigan Technological University, 1400, Townsend Dr., Houghton, MI 49931, USA
| | - David C Podgorski
- Department of Chemistry, Chemical Analysis Mass Spectrometry Facility, University of New Orleans, New Orleans, LA 70148, USA; Pontchartrain Institute for Environmental Sciences, Shea Penland Coastal Education Research Facility, University of New Orleans, New Orleans, LA 70148 USA
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238
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Arshad U, Zenobi MG, Tribulo P, Staples CR, Santos JEP. Dose-dependent effects of rumen-protected choline on hepatic metabolism during induction of fatty liver in dry pregnant dairy cows. PLoS One 2023; 18:e0290562. [PMID: 37796906 PMCID: PMC10553221 DOI: 10.1371/journal.pone.0290562] [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: 04/17/2023] [Accepted: 08/09/2023] [Indexed: 10/07/2023] Open
Abstract
Objectives were to determine the effects of supplementing increasing amounts of choline ion on hepatic composition and mRNA abundance in pregnant dry cows subjected to a fatty liver induction protocol. Holstein cows (35 primiparous and 41 multiparous) at mean (± standard deviation) of 211 ± 9.9 days of gestation were blocked by body condition (3.59 ± 0.33) and assigned to receive 0, 6.45, 12.90, 19.35, and 25.80 g/day of choline ion as rumen-protected choline (RPC) as a top-dress for 14 days. Cows were fed for ad libitum intake on days 1 to 5 and restricted to 30% of the required net energy for lactation from days 6 to 14 of the experiment. Hepatic tissue was sampled on days 5 and 14 and analyzed for concentrations of triacylglycerol and glycogen, and mRNA abundance was investigated. Orthogonal contrasts evaluated the effects of supplementing RPC (0 g/day vs. rest), and the linear, quadratic, and cubic effects of increasing intake of choline ion from 6.45 to 25.80 g/day. Results are depicted in sequence of treatments from 0 to 25.8. During feed restriction, RPC reduced the concentration of hepatic triacylglycerol by 28.5% and increased that of glycogen by 26.1%, and the effect of increasing RPC intake on triacylglycerol was linear (6.67 vs. 5.45 vs. 4.68 vs. 5.13 vs. 3.81 ± 0.92% wet-basis). Feeding RPC during feed restriction increased abundance of transcripts involved in choline metabolism (CHKA, PLD1), synthesis of apolipoprotein-B100 (APOB100), and antioxidant activity (GPX3), and decreased the abundance of transcripts involved in hepatic lipogenesis (DGAT2, SREBF1) and acute phase response (SAA3). Most effects were linear with amount of choline fed. Changes in hepatic mRNA abundance followed a pattern of reduced lipogenesis and enhanced lipids export, which help explain the reduced hepatic triacylglycerol content in cows fed RPC. Choline exerts lipotropic effects in dairy cows by altering transcript pathways linked to hepatic lipids metabolism.
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Affiliation(s)
- Usman Arshad
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States of America
| | - Marcos G. Zenobi
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States of America
| | - Paula Tribulo
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States of America
| | - Charles R. Staples
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States of America
| | - José E. P. Santos
- Department of Animal Sciences, University of Florida, Gainesville, FL, United States of America
- DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL, United States of America
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239
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Moreno IY, Parsaie A, Gesteira TF, Coulson-Thomas VJ. Characterization of the Limbal Epithelial Stem Cell Niche. Invest Ophthalmol Vis Sci 2023; 64:48. [PMID: 37906057 PMCID: PMC10619699 DOI: 10.1167/iovs.64.13.48] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Purpose Limbal epithelial stem cells (LESCs) reside within a LSC niche (LSCN). We recently identified that hyaluronan (HA) is a major constituent of the LSCN, and that HA is necessary for maintaining LESCs in the "stem cell" state, both in vitro and in vivo. Herein, we characterized the LSCN to identify key components of the HA-specific LSCN. Methods The cornea and limbal rim were dissected from mouse corneas, subjected to mRNA extraction, and sequenced using a NextSeq 500 (Illumina) and data processed using CLC Genomics Workbench 20 (Qiagen) and the STRING database to identify key components of the LSCN. Their expression was confirmed by real-time PCR, Western blotting, and immunohistochemistry. Furthermore, the differential expression of key compounds in different corneal cell types were determined with single-cell RNA sequencing. Results We identified that the hyaladherins inter-alpha-inhibitor (IαI), TSG-6 and versican are highly expressed in the limbus. Specifically, HA/HC complexes are present in the LSCN, in the stroma underlying the limbal epithelium, and surrounding the limbal vasculature. For IαI, heavy chains 5 and 2 (HC5 and HC2) were found to be the most highly expressed HCs in the mouse and human limbus and were associate with HA-forming HA/HC-specific matrices. Conclusions The LSCN contains HA/HC complexes, which have been previously correlated with stem cell niches. The identification of HA/HC complexes in the LSCN could serve as a new therapeutic avenue for treating corneal pathology. Additionally, HA/HC complexes could be used as a substrate for culturing LESCs before LESC transplantation.
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Affiliation(s)
- Isabel Y. Moreno
- College of Optometry, University of Houston, Houston, Texas, United States
| | - Arian Parsaie
- College of Optometry, University of Houston, Houston, Texas, United States
- College of Natural Science and Mathematics, University of Houston, Houston, Texas, United States
| | - Tarsis F. Gesteira
- College of Optometry, University of Houston, Houston, Texas, United States
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240
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Lopera SD, O'Kane VM, Goldhirsh JL, Piper BJ. Regional Disparities in Prescription Methamphetamine and Amphetamine Distribution Across the United States. J Atten Disord 2023; 27:1322-1331. [PMID: 37288726 DOI: 10.1177/10870547231177467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
OBJECTIVE The objectives of this report were to characterize the regional and state differences in prescription methamphetamine and amphetamine distribution in the US. METHODS Prescription methamphetamine and amphetamine distribution was obtained from the Drug Enforcement Administration for 2019. RESULTS Total per capita drug weight distribution of amphetamine was 4,000 times higher than methamphetamine. Regionally, total per capita drug weight for methamphetamine was highest in the West (32.2% of total distribution) and lowest in the Northeast (17.4%). The total per capita drug weight for amphetamine was highest in the South (37.0% of total distribution) and lowest in the Northeast (19.4%). Distribution of methamphetamine was 16.1% while amphetamine was 54.0% of its production quota. CONCLUSION Overall, prescription amphetamine distribution was common while prescription methamphetamine distribution was rare. The patterns observed in distribution are likely the result of stigmatization, differences in accessibility, and the efforts of initiatives such as the Montana Meth Project.
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Affiliation(s)
- Sarah D Lopera
- Geisinger Commonwealth School of Medicine, Scranton, PA, USA
| | | | | | - Brian J Piper
- Geisinger Commonwealth School of Medicine, Scranton, PA, USA
- Center for Pharmacy Innovation and Outcomes, Scranton, PA, USA
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241
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Li J, Abbas M, Desoky ESM, Zafar S, Soaud SA, Hussain SS, Abbas S, Hussain A, Ihtisham M, Ragauskas AJ, Wafa HA, El-Sappah AH. Analysis of metal tolerance protein (MTP) family in sunflower (Helianthus annus L.) and role of HaMTP10 as Cadmium antiporter under moringa seed extract. INDUSTRIAL CROPS AND PRODUCTS 2023; 202:117023. [DOI: 10.1016/j.indcrop.2023.117023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
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242
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Del Campo EM, Gasulla F, Hell AF, González-Hourcade M, Casano LM. Comparative Transcriptomic and Proteomic Analyses Provide New Insights into the Tolerance to Cyclic Dehydration in a Lichen Phycobiont. MICROBIAL ECOLOGY 2023; 86:1725-1739. [PMID: 37039841 PMCID: PMC10497648 DOI: 10.1007/s00248-023-02213-x] [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: 09/12/2022] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Desiccation tolerance (DT) is relatively frequent in non-vascular plants and green algae. However, it is poorly understood how successive dehydration/rehydration (D/R) cycles shape their transcriptomes and proteomes. Here, we report a comprehensive analysis of adjustments on both transcript and protein profiles in response to successive D/R cycles in Coccomyxa simplex (Csol), isolated from the lichen Solorina saccata. A total of 1833 transcripts and 2332 proteins were differentially abundant as a consequence of D/R; however, only 315 of these transcripts/proteins showed similar trends. Variations in both transcriptomes and proteomes along D/R cycles together with functional analyses revealed an extensive decrease in transcript and protein levels during dehydration, most of them involved in gene expression, metabolism, substance transport, signalling and folding catalysis, among other cellular functions. At the same time, a series of protective transcripts/proteins, such as those related to antioxidant defence, polyol metabolism and autophagy, was upregulated during dehydration. Overall, our results show a transient decrease in most cellular functions as a result of drying and a gradual reactivation of specific cell processes to accommodate the hydration status along successive D/R cycles. This study provides new insights into key mechanisms involved in the DT of Csol and probably other dehydration-tolerant microalgae. In addition, functionally characterising the high number of genes/proteins of unknown functions found in this study may lead to the discovery of new DT mechanisms.
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Affiliation(s)
- Eva M Del Campo
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain.
| | - Francisco Gasulla
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain
| | - Aline F Hell
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain
- Centre of Natural Sciences and Humanities, Federal University of ABC, 09606-070, São Bernardo Do Campo, SP, Brazil
| | - María González-Hourcade
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain
- Department of Forest Biomaterials and Technology, Swedish University of Agricultural Sciences, 90183, Umeå, Sweden
| | - Leonardo M Casano
- Department of Life Sciences, University of Alcalá, 28805, Alcalá de Henares (Madrid), Spain
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243
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Arshad U, Husnain A, Poindexter MB, Zimpel R, Perdomo MC, Santos JEP. Effect of source and amount of rumen-protected choline on hepatic metabolism during induction of fatty liver in dairy cows. J Dairy Sci 2023; 106:6860-6879. [PMID: 37210357 DOI: 10.3168/jds.2023-23270] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/05/2023] [Indexed: 05/22/2023]
Abstract
Objectives were to determine the effect of supplementing increased amounts of rumen-protected choline (RPC) from sources with low (L, 28.8%) or high (H, 60.0%) concentration of choline chloride on hepatic metabolism when cows were subjected to feed restriction to develop fatty liver. It was hypothesized that increased supplementation of RPC reduces hepatic triacylglycerol and enhances glycogen concentrations. Pregnant, nonlactating multiparous Holstein cows (n = 110) at mean (± standard deviation) 232 ± 3.9 d of gestation were blocked by body condition (4.01 ± 0.52) and assigned to receive 0 (CON), 12.9 (L12.9 or H12.9), or 25.8 (L25.8 or H25.8) g/d of choline ion. Cows were fed for ad libitum intake on d 1 to 5 and restricted to 50% of the NEL required for maintenance and pregnancy from d 6 to 13. Intake of metabolizable methionine was maintained at 19 g/d during the feed restriction period by supplying rumen-protected methionine. Hepatic tissue was sampled on d 6 and 13 and analyzed for triacylglycerol, glycogen, and mRNA expression of genes involved in choline, glucose, and fatty acids metabolism, cell signaling, inflammation, autophagy, lipid droplet dynamics, lipophagy, and endoplasmic reticulum stress response. Blood was sampled and analyzed for concentrations of fatty acids, β-hydroxybutyrate (BHB), glucose, triacylglycerol, total cholesterol, and haptoglobin. Orthogonal contrasts evaluated the effect of supplementing RPC [CON vs. (1/4·L12.9 + 1/4·L25.8 + 1/4·H12.9 + 1/4·H25.8)], source of RPC [(1/2·L12.9 + 1/2·L25.8) vs. (1/2·H12.9 + 1/2·H25.8)], amount of RPC [(1/2·L12.9 + 1/2·H12.9) vs. (1/2·L25.8 + 1/2·H25.8)], and interaction between source and amount [(1/2·L12.9 + 1/2·H25.8) vs. (1/2·H12.9 + 1/2·L25.8)]. Least squares means and standard error of the means are presented in sequence as CON, L12.9, L25.8, H12.9, H25.8. Supplementation of RPC reduced hepatic triacylglycerol (9.3 vs. 6.6 vs. 5.1 vs. 6.6 vs. 6.0 ± 0.6% as-is) and increased glycogen contents (1.8 vs. 2.6 vs. 3.6 vs. 3.1 vs. 4.1 ± 0.2% as-is) on d 13 of the experiment. Feeding RPC reduced serum haptoglobin (136.6 vs. 85.6 vs. 80.6 vs. 82.8 vs. 81.2 ± 4.6 µg/mL) during the feed restriction period; however, blood concentrations of fatty acids, BHB, glucose, triacylglycerol, and total cholesterol did not differ among treatments. During feed restriction, supplementation of RPC enhanced the mRNA expression of genes related to choline metabolism (BHMT), uptake of fatty acids (CD36), and autophagy (ATG3), and reduced the expression of a transcript associated with endoplasmic reticulum stress response (ERN1). An increase in the amount of choline ion from 12.9 to 25.8 g/d enhanced the mRNA expression of genes associated with synthesis and assembly of lipoproteins (APOB100), and inflammation (TNFA), whereas it reduced the expression of genes linked to gluconeogenesis (PC), oxidation of fatty acids (ACADM, MMUT), ketogenesis (ACAT1), and synthesis of antioxidants (SOD1) on d 13 of the experiment. Feeding RPC, independent of the product used, promoted lipotropic effects that reduced hepatic lipidosis in dairy cows.
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Affiliation(s)
- U Arshad
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - A Husnain
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - M B Poindexter
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - R Zimpel
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - M C Perdomo
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611
| | - J E P Santos
- Department of Animal Sciences, DH Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, FL 32611.
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244
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Sana I, Mantione ME, Meloni M, Riba M, Ranghetti P, Scarfò L, Ghia P, Muzio M. Dimethyl itaconate selectively targets inflammatory and metabolic pathways in chronic lymphocytic leukemia. Eur J Immunol 2023; 53:e2350418. [PMID: 37561992 DOI: 10.1002/eji.202350418] [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: 02/04/2023] [Revised: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 08/12/2023]
Abstract
Chronic lymphocytic leukemia (CLL) co-evolves with its own microenvironment where inflammatory stimuli including toll-like receptors (TLR) signaling can protect CLL cells from spontaneous and drug-induced apoptosis by upregulating IκBζ, an atypical co-transcription factor. To dissect IκBζ-centered signaling pathways, we performed a gene expression profile of primary leukemic cells expressing either high or low levels of IκBζ after stimulation, highlighting that IκBζ is not only an inflammatory gene but it may control metabolic rewiring of malignant cells thus pointing to a novel potential opportunity for therapy. We exploited the capacity of the dimethyl itaconate (DI), an anti-inflammatory electrophilic synthetic derivative of the metabolite Itaconate, to target IκBζ. CLL cells, murine leukemic splenocytes, and leukocytes from healthy donors were treated in vitro with DI that abolished metabolic activation and reduced cell viability of leukemic cells only, even in the presence of robust TLR prestimulation. RNA sequencing highlighted that in addition to the expected electrophilic stress signature observed after DI treatment, novel pathways emerged including the downregulation of distinct MHC class II complex genes. In conclusion, DI not only abrogated the proinflammatory effects of TLR stimulation but also targeted a specific metabolic vulnerability in CLL cells.
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Affiliation(s)
- Ilenia Sana
- Cell signaling Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Maria Elena Mantione
- Cell signaling Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Miriam Meloni
- Cell signaling Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Michela Riba
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Pamela Ranghetti
- B-cell neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Lydia Scarfò
- B-cell neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Vita-Salute San Raffaele University, Milano, Italy
| | - Paolo Ghia
- B-cell neoplasia Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
- Vita-Salute San Raffaele University, Milano, Italy
| | - Marta Muzio
- Cell signaling Unit, Division of Experimental Oncology, IRCCS San Raffaele Scientific Institute, Milano, Italy
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Carreón-Anguiano KG, Gómez-Tah R, Pech-Balan E, Ek-Hernández GE, De los Santos-Briones C, Islas-Flores I, Canto-Canché B. Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors. J Fungi (Basel) 2023; 9:970. [PMID: 37888226 PMCID: PMC10607838 DOI: 10.3390/jof9100970] [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: 08/11/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/28/2023] Open
Abstract
Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the development of conidia in fungal phytopathogens has been poorly investigated. To date, few reports have centered on the pathogenicity functions of fungal phytopathogen conidia. Pseudocercospora fijiensis is a hemibiotrophic fungus and the causal agent of the black Sigatoka disease in bananas and plantains. Here, a conidial transcriptome of P. fijiensis was characterized computationally. Carbohydrates, amino acids, and lipid metabolisms presented the highest number of annotations in Gene Ontology. Common conidial functions were found, but interestingly, pathogenicity factors and effectors were also identified. Upon analysis of the resulting proteins against the Pathogen-Host Interaction (PHI) database, 754 hits were identified. WideEffHunter and EffHunter effector predictors identified 618 effectors, 265 of them were shared with the PHI database. A total of 1107 conidial functions devoted to pathogenesis were found after our analysis. Regarding the conidial effectorome, it was found to comprise 40 canonical and 578 non-canonical effectors. Effectorome characterization revealed that RXLR, LysM, and Y/F/WxC are the largest effector families in the P. fijiensis conidial effectorome. Gene Ontology classification suggests that they are involved in many biological processes and metabolisms, expanding our current knowledge of fungal effectors.
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Affiliation(s)
- Karla Gisel Carreón-Anguiano
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Rufino Gómez-Tah
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Efren Pech-Balan
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Gemaly Elisama Ek-Hernández
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - César De los Santos-Briones
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico;
| | - Blondy Canto-Canché
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A.C., Calle 43 No. 130 x 32 y 34, Colonia Chuburná de Hidalgo, Mérida C.P. 97205, Yucatán, Mexico; (K.G.C.-A.); (R.G.-T.); (E.P.-B.); (G.E.E.-H.); (C.D.l.S.-B.)
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Ishioka M, Nihashi Y, Sunagawa Y, Umezawa K, Shimosato T, Kagami H, Morimoto T, Takaya T. Myogenetic Oligodeoxynucleotide Induces Myocardial Differentiation of Murine Pluripotent Stem Cells. Int J Mol Sci 2023; 24:14380. [PMID: 37762684 PMCID: PMC10532123 DOI: 10.3390/ijms241814380] [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: 08/05/2023] [Revised: 09/16/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023] Open
Abstract
An 18-base myogenetic oligodeoxynucleotide (myoDN), iSN04, acts as an anti-nucleolin aptamer and induces myogenic differentiation of skeletal muscle myoblasts. This study investigated the effect of iSN04 on murine embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). In the undifferentiated state, iSN04 inhibited the proliferation of ESCs and iPSCs but did not affect the expression of pluripotent markers. In the differentiating condition, iSN04 treatment of ESCs/iPSCs from day 5 onward dramatically induced differentiation into Nkx2-5+ beating cardiomyocytes with upregulation of Gata4, Isl1, and Nkx2-5, whereas iSN04 treatment from earlier stages completely inhibited cardiomyogenesis. RNA sequencing revealed that iSN04 treatment from day 5 onward contributes to the generation of cardiac progenitors by modulating the Wnt signaling pathway. Immunostaining showed that iSN04 suppressed the cytoplasmic translocation of nucleolin and restricted it to the nucleoli. These results demonstrate that nucleolin inhibition by iSN04 facilitates the terminal differentiation of cardiac mesoderm into cardiomyocytes but interferes with the differentiation of early mesoderm into the cardiac lineage. This is the first report on the generation of cardiomyocytes from pluripotent stem cells using a DNA aptamer. Since iSN04 did not induce hypertrophic responses in primary-cultured cardiomyocytes, iSN04 would be useful and safe for the regenerative therapy of heart failure using stem cell-derived cardiomyocytes.
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Affiliation(s)
- Mina Ishioka
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (M.I.); (T.S.)
| | - Yuma Nihashi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, Central 5-41, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan;
| | - Yoichi Sunagawa
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (Y.S.); (T.M.)
| | - Koji Umezawa
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (K.U.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Takeshi Shimosato
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (M.I.); (T.S.)
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (K.U.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
| | - Hiroshi Kagami
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (K.U.); (H.K.)
| | - Tatsuya Morimoto
- Division of Molecular Medicine, School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Suruga-ku, Shizuoka 422-8526, Japan; (Y.S.); (T.M.)
| | - Tomohide Takaya
- Department of Agriculture, Graduate School of Science and Technology, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (M.I.); (T.S.)
- Department of Agricultural and Life Sciences, Faculty of Agriculture, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan; (K.U.); (H.K.)
- Department of Biomolecular Innovation, Institute for Biomedical Sciences, Shinshu University, 8304 Minami-minowa, Kami-ina, Nagano 399-4598, Japan
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247
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Hooker JC, Smith M, Zapata G, Charette M, Luckert D, Mohr RM, Daba KA, Warkentin TD, Hadinezhad M, Barlow B, Hou A, Lefebvre F, Golshani A, Cober ER, Samanfar B. Differential gene expression provides leads to environmentally regulated soybean seed protein content. FRONTIERS IN PLANT SCIENCE 2023; 14:1260393. [PMID: 37790790 PMCID: PMC10544915 DOI: 10.3389/fpls.2023.1260393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/23/2023] [Indexed: 10/05/2023]
Abstract
Soybean is an important global source of plant-based protein. A persistent trend has been observed over the past two decades that soybeans grown in western Canada have lower seed protein content than soybeans grown in eastern Canada. In this study, 10 soybean genotypes ranging in average seed protein content were grown in an eastern location (control) and three western locations (experimental) in Canada. Seed protein and oil contents were measured for all lines in each location. RNA-sequencing and differential gene expression analysis were used to identify differentially expressed genes that may account for relatively low protein content in western-grown soybeans. Differentially expressed genes were enriched for ontologies and pathways that included amino acid biosynthesis, circadian rhythm, starch metabolism, and lipid biosynthesis. Gene ontology, pathway mapping, and quantitative trait locus (QTL) mapping collectively provide a close inspection of mechanisms influencing nitrogen assimilation and amino acid biosynthesis between soybeans grown in the East and West. It was found that western-grown soybeans had persistent upregulation of asparaginase (an asparagine hydrolase) and persistent downregulation of asparagine synthetase across 30 individual differential expression datasets. This specific difference in asparagine metabolism between growing environments is almost certainly related to the observed differences in seed protein content because of the positive correlation between seed protein content at maturity and free asparagine in the developing seed. These results provided pointed information on seed protein-related genes influenced by environment. This information is valuable for breeding programs and genetic engineering of geographically optimized soybeans.
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Affiliation(s)
- Julia C. Hooker
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Myron Smith
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Gerardo Zapata
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - Martin Charette
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Doris Luckert
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Ramona M. Mohr
- Brandon Research Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Ketema A. Daba
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | | | - Mehri Hadinezhad
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Brent Barlow
- Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Anfu Hou
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | | | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Elroy R. Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Bahram Samanfar
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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248
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Deshpande RA, Marin-Gonzalez A, Barnes HK, Woolley PR, Ha T, Paull TT. Genome-wide analysis of DNA-PK-bound MRN cleavage products supports a sequential model of DSB repair pathway choice. Nat Commun 2023; 14:5759. [PMID: 37717054 PMCID: PMC10505227 DOI: 10.1038/s41467-023-41544-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 09/07/2023] [Indexed: 09/18/2023] Open
Abstract
The Mre11-Rad50-Nbs1 (MRN) complex recognizes and processes DNA double-strand breaks for homologous recombination by performing short-range removal of 5' strands. Endonucleolytic processing by MRN requires a stably bound protein at the break site-a role we postulate is played by DNA-dependent protein kinase (DNA-PK) in mammals. Here we interrogate sites of MRN-dependent processing by identifying sites of CtIP association and by sequencing DNA-PK-bound DNA fragments that are products of MRN cleavage. These intermediates are generated most efficiently when DNA-PK is catalytically blocked, yielding products within 200 bp of the break site, whereas DNA-PK products in the absence of kinase inhibition show greater dispersal. Use of light-activated Cas9 to induce breaks facilitates temporal resolution of DNA-PK and Mre11 binding, showing that both complexes bind to DNA ends before release of DNA-PK-bound products. These results support a sequential model of double-strand break repair involving collaborative interactions between homologous and non-homologous repair complexes.
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Affiliation(s)
| | - Alberto Marin-Gonzalez
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Hannah K Barnes
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Phillip R Woolley
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21205, USA
| | - Tanya T Paull
- The Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA.
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Mauroux A, Joncour P, Brassard-Jollive N, Bacar H, Gillet B, Hughes S, Ardidie-Robouant C, Marchand L, Liabotis A, Mailly P, Monnot C, Germain S, Bordes S, Closs B, Ruggiero F, Muller L. Papillary and reticular fibroblasts generate distinct microenvironments that differentially impact angiogenesis. Acta Biomater 2023; 168:210-222. [PMID: 37406716 DOI: 10.1016/j.actbio.2023.06.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/07/2023]
Abstract
Papillary and reticular dermis show distinct extracellular matrix (ECM) and vascularization corresponding to their specific functions. These characteristics are associated with gene expression patterns of fibroblasts freshly isolated from their native microenvironment. In order to assess the relevance of these fibroblast subpopulations in a tissue engineering context, we investigated their contribution to matrix production and vascularization using cell sheet culture conditions. We first performed RNA-seq differential expression analysis to determine whether several rounds of cell amplification and high-density culture affected their gene expression profile. Bioinformatics analysis revealed that expression of angiogenesis-related and matrisome gene signatures were maintained, resulting in papillary and reticular ECMs that differ in composition and structure. The impact of secreted or ECM-associated factors was then assessed using two independent 3D angiogenesis assays: -1/ a fibrin hydrogel-based assay allowing investigation of diffusible secreted factors, -2/ a scaffold-free cell-sheet based assay for investigation of fibroblast-produced microenvironment. These analyses revealed that papillary fibroblasts secrete highly angiogenic factors and produce a microenvironment characterised by ECM remodelling capacity and dense and branched microvascular network, whereas reticular fibroblasts produced more structural core components of the ECM associated with less branched and larger vessels. These features mimick the characteristics of both the ECM and the vasculature of dermis subcompartments. In addition to showing that skin fibroblast populations differentially regulate angiogenesis via both secreted and ECM factors, our work emphasizes the importance of papillary and reticular fibroblasts for engineering and modelling dermis microenvironment and vascularization. STATEMENT OF SIGNIFICANCE: Recent advances have brought to the forefront the central role of microenvironment and vascularization in tissue engineering for regenerative medicine and microtissue modelling. We have investigated the role of papillary and reticular fibroblast subpopulations using scaffold-free cell sheet culture. This approach provides differentiated cells conditions allowing the production of their own microenvironment. Analysis of gene expression profiles and characterisation of the matrix produced revealed strong and specific angiogenic properties that we functionally characterized using 3D angiogenesis models targeting the respective role of either secreted or matrix-bound factors. This study demonstrates the importance of cell-generated extracellular matrix and questions the importance of cell source and the relevance of hydrogels for developing physio-pathologically relevant tissue engineered substitutes.
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Affiliation(s)
- Adèle Mauroux
- Center for Interdisciplinary Research in Biology (CIRB), College de France - CNRS, INSERM, Université PSL, 11 Place Marcelin Berthelot, Paris 75005, France; Institut de Génomique Fonctionnelle de Lyon (IGFL), ENS de Lyon, CNRS, Univ Lyon 1, 32-34 Avenue Tony Garnier, Lyon 69007, France; R&D Department, SILAB, ZI de la Nau, Saint Viance 19240, France; Sorbonne Université, Collège Doctoral, 15 rue de l'Ecole de Médecine, Paris 75006, France
| | - Pauline Joncour
- Institut de Génomique Fonctionnelle de Lyon (IGFL), ENS de Lyon, CNRS, Univ Lyon 1, 32-34 Avenue Tony Garnier, Lyon 69007, France
| | - Noémie Brassard-Jollive
- Center for Interdisciplinary Research in Biology (CIRB), College de France - CNRS, INSERM, Université PSL, 11 Place Marcelin Berthelot, Paris 75005, France; Sorbonne Université, Collège Doctoral, 15 rue de l'Ecole de Médecine, Paris 75006, France
| | - Hisoilat Bacar
- Institut de Génomique Fonctionnelle de Lyon (IGFL), ENS de Lyon, CNRS, Univ Lyon 1, 32-34 Avenue Tony Garnier, Lyon 69007, France
| | - Benjamin Gillet
- Institut de Génomique Fonctionnelle de Lyon (IGFL), ENS de Lyon, CNRS, Univ Lyon 1, 32-34 Avenue Tony Garnier, Lyon 69007, France
| | - Sandrine Hughes
- Institut de Génomique Fonctionnelle de Lyon (IGFL), ENS de Lyon, CNRS, Univ Lyon 1, 32-34 Avenue Tony Garnier, Lyon 69007, France
| | - Corinne Ardidie-Robouant
- Center for Interdisciplinary Research in Biology (CIRB), College de France - CNRS, INSERM, Université PSL, 11 Place Marcelin Berthelot, Paris 75005, France
| | | | - Athanasia Liabotis
- Center for Interdisciplinary Research in Biology (CIRB), College de France - CNRS, INSERM, Université PSL, 11 Place Marcelin Berthelot, Paris 75005, France; Sorbonne Université, Collège Doctoral, 15 rue de l'Ecole de Médecine, Paris 75006, France
| | - Philippe Mailly
- Center for Interdisciplinary Research in Biology (CIRB), College de France - CNRS, INSERM, Université PSL, 11 Place Marcelin Berthelot, Paris 75005, France
| | - Catherine Monnot
- Center for Interdisciplinary Research in Biology (CIRB), College de France - CNRS, INSERM, Université PSL, 11 Place Marcelin Berthelot, Paris 75005, France
| | - Stéphane Germain
- Center for Interdisciplinary Research in Biology (CIRB), College de France - CNRS, INSERM, Université PSL, 11 Place Marcelin Berthelot, Paris 75005, France
| | - Sylvie Bordes
- R&D Department, SILAB, ZI de la Nau, Saint Viance 19240, France
| | - Brigitte Closs
- R&D Department, SILAB, ZI de la Nau, Saint Viance 19240, France
| | - Florence Ruggiero
- Institut de Génomique Fonctionnelle de Lyon (IGFL), ENS de Lyon, CNRS, Univ Lyon 1, 32-34 Avenue Tony Garnier, Lyon 69007, France.
| | - Laurent Muller
- Center for Interdisciplinary Research in Biology (CIRB), College de France - CNRS, INSERM, Université PSL, 11 Place Marcelin Berthelot, Paris 75005, France.
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Lin JC, Liu TP, Chen YB, Yang PM. PF-429242 exhibits anticancer activity in hepatocellular carcinoma cells via FOXO1-dependent autophagic cell death and IGFBP1-dependent anti-survival signaling. Am J Cancer Res 2023; 13:4125-4144. [PMID: 37818050 PMCID: PMC10560959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 08/22/2023] [Indexed: 10/12/2023] Open
Abstract
Effective therapies for hepatocellular carcinoma (HCC) are urgently needed, as it is a type of cancer resistant to chemotherapy. Recent evidence showed that PF-429242, a membrane-bound transcription factor site-1 protease (MBTPS1) inhibitor, exhibited anticancer activities against glioblastomas, renal cell carcinoma, and pancreatic cancer. However, its anticancer activity against HCC has yet to be investigated. In this study, we found that PF-429242 induced autophagy-dependent cell death in HCC cells. RNA-sequencing analysis indicated that the primary effect of PF-429242 was inhibition of the sterol regulatory element-binding protein (SREBP) signaling pathway. However, overexpression of SREBP proteins did not efficiently rescue PF-429242-induced autophagy and cell death. Mechanistically, PF-429242 induced forkhead box protein O1 (FOXO1)-dependent autophagic cell death. Additionally, PF-429242 caused FOXO1-independent upregulation of insulin-like growth factor-binding protein 1 (IGFBP1), ultimately leading to autophagy-independent cell death. The in vivo anticancer activity of PF-429242 against HCC cells was demonstrated in a tumor xenograft mouse model. Therefore, PF-429242 is a potential anticancer agent to treat HCC by triggering FOXO1-dependent autophagic cell death and IGFBP1-mediated anti-survival signaling in parallel.
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Affiliation(s)
- Jiunn-Chang Lin
- Department of Surgery, MacKay Memorial HospitalTaipei 10449, Taiwan
- MacKay Junior College of Medicine, Nursing and ManagementNew Taipei 11260, Taiwan
- Department of Medicine, MacKay Medical CollegeNew Taipei 25245, Taiwan
- Liver Medical Center, MacKay Memorial HospitalTaipei 10449, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipei 11031, Taiwan
| | - Tsang-Pai Liu
- Department of Surgery, MacKay Memorial HospitalTaipei 10449, Taiwan
- MacKay Junior College of Medicine, Nursing and ManagementNew Taipei 11260, Taiwan
- Department of Medicine, MacKay Medical CollegeNew Taipei 25245, Taiwan
- Liver Medical Center, MacKay Memorial HospitalTaipei 10449, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipei 11031, Taiwan
| | - Yan-Bin Chen
- Department of Surgery, MacKay Memorial HospitalTaipei 10449, Taiwan
| | - Pei-Ming Yang
- Liver Medical Center, MacKay Memorial HospitalTaipei 10449, Taiwan
- Ph.D. Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia SinicaTaipei 11031, Taiwan
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical UniversityTaipei 11031, Taiwan
- TMU Research Center of Cancer Translational MedicineTaipei 11031, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical UniversityTaipei 11696, Taiwan
- TMU and Affiliated Hospitals Pancreatic Cancer Groups, Taipei Medical UniversityTaipei 11031, Taiwan
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