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Tavares MEA, Pinto AP, da Rocha AL, Sampaio LV, Correia RR, Batista VRG, Veras ASC, Chaves-Neto AH, da Silva ASR, Teixeira GR. Combined physical exercise re-synchronizes expression of Bmal1 and REV-ERBα and up-regulates apoptosis and metabolism in the prostate during aging. Life Sci 2024; 351:122800. [PMID: 38880169 DOI: 10.1016/j.lfs.2024.122800] [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: 02/29/2024] [Revised: 05/17/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024]
Abstract
BACKGROUND Aging increases the prevalence of prostate cancer. The circadian clock coordinates metabolism, cell cycle, and tumor suppressor p53. Although physical exercise has several effects on preventing prostate diseases, its effect on regulating genes and proteins of the circadian rhythm of the prostate needs to be better evaluated. The present study verified expression of REV-ERBα (Nr1d1), Bmal1, apoptosis, tumor suppressors, energetic metabolism markers, and androgen receptors in the prostatic microenvironment in 18-month-old mice submitted to combined physical training. METHODS C57BL/6 J mice were divided into 2 groups: 6 months-old (n = 10) and 18 months-old, (n = 20). The 18-month-old animals were divided into 2 subgroups: sedentary (n = 10, 18 m Sed) and submitted to combined physical training (n = 10, 18 m TR). Combined physical training protocol was performed by running on the treadmill (40-60 % of incremental load test) and climbing strength training (40-50 % of maximum repetition test), consisting of 5×/week (3 days aerobic and 2 days strength) for 3 weeks. The prostate was prepared for Western blot and RT-qPCR analysis, and the plasm was prepared for the biochemistry analysis. RESULTS Combined physical exercise during aging led to increased levels of Bmal1 and decreased levels of REV-ERBα in the prostate. These results were accompanied by a reduction in the AMPK/SIRT1/PGC-1α proteins and an increase in the PI3K/AKT and p53/PTEN/caspase 3 pathways, promoting apoptotic potential. CONCLUSION These findings suggest that strength and aerobic physical exercise may be preventive in the development of preneoplastic molecular alterations and age-related features by re-synchronizes Bmal1 and REV-ERBα in prostatic tissues.
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Affiliation(s)
- Maria Eduarda Almeida Tavares
- Multicenter Graduate Program in Physiological Sciences, SBFis, São Paulo State University (UNESP), Presidente Prudente, SP, Brazil
| | - Ana Paula Pinto
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil; Postgraduate Program in Rehabilitation and Functional Performance, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Alisson Luiz da Rocha
- School of Applied Sciences, University of Campinas (UNICAMP), Limeira, São Paulo, Brazil
| | - Larissa Victorino Sampaio
- Multicenter Graduate Program in Physiological Sciences, SBFis, São Paulo State University (UNESP), Presidente Prudente, SP, Brazil; Department of Basic Sciences, São Paulo State University (UNESP), School of Dentistry, Araçatuba, São Paulo, Brazil
| | - Rafael Ribeiro Correia
- Multicenter Graduate Program in Physiological Sciences, SBFis, São Paulo State University (UNESP), Presidente Prudente, SP, Brazil
| | - Victor Rogério Garcia Batista
- Multicenter Graduate Program in Physiological Sciences, SBFis, São Paulo State University (UNESP), Presidente Prudente, SP, Brazil
| | - Allice Santos Cruz Veras
- Multicenter Graduate Program in Physiological Sciences, SBFis, São Paulo State University (UNESP), Presidente Prudente, SP, Brazil
| | - Antonio Hernandes Chaves-Neto
- Multicenter Graduate Program in Physiological Sciences, SBFis, São Paulo State University (UNESP), Presidente Prudente, SP, Brazil; Department of Basic Sciences, São Paulo State University (UNESP), School of Dentistry, Araçatuba, São Paulo, Brazil
| | - Adelino Sanchez Ramos da Silva
- School of Physical Education and Sport of Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, SP, Brazil; Postgraduate Program in Rehabilitation and Functional Performance, Ribeirão Preto Medical School, University of São Paulo (USP), São Paulo, Brazil
| | - Giovana Rampazzo Teixeira
- Department of Physical Education, São Paulo State University (UNESP), School of Technology and Sciences, Presidente Prudente, SP, Brazil; Multicenter Graduate Program in Physiological Sciences, SBFis, São Paulo State University (UNESP), Presidente Prudente, SP, Brazil.
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Makhnovskii PA, Kukushkina IV, Kurochkina NS, Popov DV. Knockout of Hsp70 genes significantly affects locomotion speed and gene expression in leg skeletal muscles of Drosophila melanogaster. Physiol Genomics 2024; 56:567-575. [PMID: 38881428 DOI: 10.1152/physiolgenomics.00143.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 05/31/2024] [Accepted: 06/11/2024] [Indexed: 06/18/2024] Open
Abstract
The functions of the heat shock protein 70 (Hsp70) genes were studied using a line of Drosophila melanogaster with a knockout of 6 of these genes out of 13. Namely, the effect of knockout of Hsp70 genes on negative geotaxis climbing (locomotor) speed and the ability to adapt to climbing training (0.5-1.5 h/day, 7 days/wk, 19 days) were examined. Seven- and 23-day-old Hsp70- flies demonstrated a comparable reduction (twofold) in locomotor speed and widespread changes in leg skeletal muscle transcriptome (RNA sequencing) compared with w1118 flies. To identify the functions of genes related to decreased locomotor speed, the overlapped differentially expressed genes at both time points were analyzed: the upregulated genes encoded extracellular proteins, regulators of drug metabolism, and the antioxidant response, whereas downregulated genes encoded regulators of carbohydrate metabolism and transmembrane proteins. In addition, in Hsp70- flies, activation of transcription factors related to disruption of the fibril structure and heat shock response (Hsf) was predicted, using the position weight matrix approach. In control flies, adaptation to chronic exercise training was associated mainly with gene response to a single exercise bout, whereas the predicted transcription factors were related to stress/immune (Hsf, NF-κB, etc.) and early gene response. In contrast, Hsp70- flies demonstrated no adaptation to training as well as a significantly impaired gene response to a single exercise bout. In conclusion, the knockout of Hsp70 genes not only reduced physical performance but also disrupted adaptation to chronic physical training, which is associated with changes in the leg skeletal muscle transcriptome and impaired gene response to a single exercise bout.NEW & NOTEWORTHY Knockout of six heat shock protein 70 (Hsp70) genes in Drosophila melanogaster reduced locomotion (climbing) speed that is associated with genotype-specific differences in leg skeletal muscle gene expression. Disrupted adaptation of Hsp70- flies to chronic exercise training is associated with impaired gene response to a single exercise bout.
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Affiliation(s)
- Pavel A Makhnovskii
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Inna V Kukushkina
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
- Lomonosov Moscow State University, Moscow, Russia
| | - Nadia S Kurochkina
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Daniil V Popov
- Institute of Biomedical Problems of the Russian Academy of Sciences, Moscow, Russia
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Stelloo S, Alejo-Vinogradova MT, van Gelder CAGH, Zijlmans DW, van Oostrom MJ, Valverde JM, Lamers LA, Rus T, Sobrevals Alcaraz P, Schäfers T, Furlan C, Jansen PWTC, Baltissen MPA, Sonnen KF, Burgering B, Altelaar MAFM, Vos HR, Vermeulen M. Deciphering lineage specification during early embryogenesis in mouse gastruloids using multilayered proteomics. Cell Stem Cell 2024; 31:1072-1090.e8. [PMID: 38754429 DOI: 10.1016/j.stem.2024.04.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 01/10/2024] [Accepted: 04/19/2024] [Indexed: 05/18/2024]
Abstract
Gastrulation is a critical stage in embryonic development during which the germ layers are established. Advances in sequencing technologies led to the identification of gene regulatory programs that control the emergence of the germ layers and their derivatives. However, proteome-based studies of early mammalian development are scarce. To overcome this, we utilized gastruloids and a multilayered mass spectrometry-based proteomics approach to investigate the global dynamics of (phospho) protein expression during gastruloid differentiation. Our findings revealed many proteins with temporal expression and unique expression profiles for each germ layer, which we also validated using single-cell proteomics technology. Additionally, we profiled enhancer interaction landscapes using P300 proximity labeling, which revealed numerous gastruloid-specific transcription factors and chromatin remodelers. Subsequent degron-based perturbations combined with single-cell RNA sequencing (scRNA-seq) identified a critical role for ZEB2 in mouse and human somitogenesis. Overall, this study provides a rich resource for developmental and synthetic biology communities endeavoring to understand mammalian embryogenesis.
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Affiliation(s)
- Suzan Stelloo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Maria Teresa Alejo-Vinogradova
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Charlotte A G H van Gelder
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Dick W Zijlmans
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marek J van Oostrom
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Juan Manuel Valverde
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Lieke A Lamers
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Teja Rus
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Paula Sobrevals Alcaraz
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Tilman Schäfers
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Cristina Furlan
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, 6708 WE Wageningen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marijke P A Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Katharina F Sonnen
- Hubrecht Institute, KNAW (Royal Netherlands Academy of Arts and Sciences), University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Boudewijn Burgering
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Maarten A F M Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CA Utrecht, the Netherlands; Netherlands Proteomics Center, 3584 CH Utrecht, the Netherlands
| | - Harmjan R Vos
- Molecular Cancer Research, Center for Molecular Medicine, Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, the Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands; Division of Molecular Genetics, Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands.
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Zhao JB, Fan MZ, Shi YX, Zhu YT, Gao SX, Li GL, Guan JC, Zhou P. Staphylococcal enterotoxin B exposed to pregnant rats inhibits the hedgehog signaling pathway in thymic T lymphocytes of the offspring. Microb Pathog 2024; 192:106723. [PMID: 38823465 DOI: 10.1016/j.micpath.2024.106723] [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: 10/30/2023] [Revised: 05/17/2024] [Accepted: 05/29/2024] [Indexed: 06/03/2024]
Abstract
The Hedgehog (Hh) signaling pathway is involved in T cell differentiation and development and plays a major regulatory part in different stages of T cell development. A previous study by us suggested that prenatal exposure to staphylococcal enterotoxin B (SEB) changed the percentages of T cell subpopulation in the offspring thymus. However, it is unclear whether prenatal SEB exposure impacts the Hh signaling pathway in thymic T cells. In the present study, pregnant rats at gestational day 16 were intravenously injected once with 15 μg SEB, and the thymi of both neonatal and adult offspring rats were aseptically acquired to scrutinize the effects of SEB on the Hh signaling pathway. It firstly found that prenatal SEB exposure clearly caused the increased expression of Shh and Dhh ligands of the Hh signaling pathway in thymus tissue of both neonatal and adult offspring rats, but significantly decreased the expression levels of membrane receptors of Ptch1 and Smo, transcription factor Gli1, as well as target genes of CyclinD1, C-myc, and N-myc in Hh signaling pathway of thymic T cells. These data suggest that prenatal SEB exposure inhibits the Hh signaling pathway in thymic T lymphocytes of the neonatal offspring, and this effect can be maintained in adult offspring via the imprinting effect.
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Affiliation(s)
- Jia-Bao Zhao
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, PR China
| | - Meng-Zhu Fan
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, PR China
| | - Yin-Xing Shi
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, PR China
| | - Yu-Ting Zhu
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, PR China
| | - Shu-Xian Gao
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, PR China; Department of Microbiology, Bengbu Medical College, Bengbu, Anhui, 233030, PR China
| | - Guang-Lin Li
- Majored in Biological Science, Bengbu Medical College, Bengbu, Anhui, 233030, PR China
| | - Jun-Chang Guan
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, PR China; Department of Microbiology, Bengbu Medical College, Bengbu, Anhui, 233030, PR China.
| | - Ping Zhou
- Anhui Key Laboratory of Infection and Immunity, Bengbu Medical College, Bengbu, Anhui, 233030, PR China; Department of Microbiology, Bengbu Medical College, Bengbu, Anhui, 233030, PR China.
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Alaiya A, Alharbi BM, Shinwari Z, Rashid M, Albinhassan TH, Bouchama A, Alwesmi MB, Mohammad S, Malik SS. Proteomics Analysis of Proteotoxic Stress Response in In-Vitro Human Neuronal Models. Int J Mol Sci 2024; 25:6787. [PMID: 38928492 PMCID: PMC11204259 DOI: 10.3390/ijms25126787] [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: 04/29/2024] [Revised: 06/02/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Heat stroke, a hazardous hyperthermia-related illness, is characterized by CNS injury, particularly long-lasting brain damage. A root cause for hyperthermic neurological damage is heat-induced proteotoxic stress through protein aggregation, a known causative agent of neurological disorders. Stress magnitude and enduring persistence are highly correlated with hyperthermia-associated neurological damage. We used an untargeted proteomic approach using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify and characterize time-series proteome-wide changes in dose-responsive proteotoxic stress models in medulloblastoma [Daoy], neuroblastoma [SH-SY5Y], and differentiated SH-SY5Y neuron-like cells [SH(D)]. An integrated analysis of condition-time datasets identified global proteome-wide differentially expressed proteins (DEPs) as part of the heat-induced proteotoxic stress response. The condition-specific analysis detected higher DEPs and upregulated proteins in extreme heat stress with a relatively conservative and tight regulation in differentiated SH-SY5Y neuron-like cells. Functional network analysis using ingenuity pathway analysis (IPA) identified common intercellular pathways associated with the biological processes of protein, RNA, and amino acid metabolism and cellular response to stress and membrane trafficking. The condition-wise temporal pathway analysis in the differentiated neuron-like cells detects a significant pathway, functional, and disease association of DEPs with processes like protein folding and protein synthesis, Nervous System Development and Function, and Neurological Disease. An elaborate dose-dependent stress-specific and neuroprotective cellular signaling cascade is also significantly activated. Thus, our study provides a comprehensive map of the heat-induced proteotoxic stress response associating proteome-wide changes with altered biological processes. This helps to expand our understanding of the molecular basis of the heat-induced proteotoxic stress response with potential translational connotations.
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Affiliation(s)
- Ayodele Alaiya
- Cell Therapy & Immunobiology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Bothina Mohammed Alharbi
- Experimental Medicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Zakia Shinwari
- Cell Therapy & Immunobiology Department, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Mamoon Rashid
- Department of AI and Bioinformatics, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, MNGHA, Riyadh 11426, Saudi Arabia
| | - Tahani H. Albinhassan
- Experimental Medicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- Zoology Department, College of Science, King Saud University, Riyadh 12372, Saudi Arabia
| | - Abderrezak Bouchama
- Experimental Medicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Mai B. Alwesmi
- Medical-Surgical Nursing Department, College of Nursing, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Sameer Mohammad
- Experimental Medicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
| | - Shuja Shafi Malik
- Experimental Medicine Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh 11426, Saudi Arabia
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Kimsa-Dudek M, Kruszniewska-Rajs C, Adamska J, Strzałka-Mrozik B, Matwijczuk A, Karcz D, Gagoś M, Gola JM. Redox homeostasis in human renal cells that had been treated with amphotericin B in combination with selected 1,3,4-thiadiazole derivatives. Pharmacol Rep 2024; 76:557-571. [PMID: 38587587 DOI: 10.1007/s43440-024-00592-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 03/30/2024] [Accepted: 04/03/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND The use of amphotericin B (AmB) in the therapy of systemic mycosis is associated with strong side effects, including nephrotoxicity, and hepatotoxicity. Therefore, agents that can reduce the toxic effects of AmB while acting synergistically as antifungal agents are currently being sought. 1,3,4-thiadiazole derivatives are promising compounds that have an antifungal activity and act synergically with AmB. Such combinations might allow the dose of AmB, which is essential for preventing patients from having serious side effects, to be decreased. This might result from the antioxidant properties of 1,3,4-thiadiazoles. Thus, the aim of the study was to investigate redox homeostasis in human renal proximal tubule epithelial cells (RPTEC) after they had been treated with AmB in combination with 1,3,4-thiadiazole derivatives. METHODS Cellular redox homeostasis was assessed by investigating the total antioxidant capacity (TAC) of cells, the malondialdehyde (MDA) concentration, and the activity of antioxidant enzymes such as superoxide dismutase (SOD), glutathione peroxidase (GPX), and catalase (CAT). TAC was measured using an ABTS method. The MDA concentration, and the activity of SOD, GPX, and CAT were determined spectrophotometrically using commercially available assays. Additionally, the antioxidant defense system-related gene expression profile was determined using oligonucleotide microarrays (HG-U133A 2.0). Quantitative reverse transcription polymerase chain reaction (RT-qPCR) was used to confirm the microarray results. RESULTS Amphotericin B and selected 1,3,4-thiadiazole derivatives had a significant effect on the total antioxidant capacity of the RPTEC cells, and the activity of the antioxidant enzymes. We also revealed that the effect of thiadiazoles on the SOD and CAT activities is dependent on the treatment of RPTEC cells with AmB. At the transcriptional level, the expression of several genes was affected by the studied compounds and their combinations. CONCLUSIONS The results confirmed that thiadiazoles can stimulate the RPTEC cells to defend against the oxidative stress that is generated by AmB. In addition, together with the previously demonstrated synergistic antifungal activity, and low nephrotoxicity, these compounds have the potential to be used in new therapeutic strategies in the treatment of fungal infections.
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Affiliation(s)
- Magdalena Kimsa-Dudek
- Department of Nutrigenomics, and Bromatology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland.
| | - Celina Kruszniewska-Rajs
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland
| | - Jolanta Adamska
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland
| | - Barbara Strzałka-Mrozik
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland
| | - Arkadiusz Matwijczuk
- Department of Biophysics, University of Life Sciences, Akademicka 13, Lublin, 20-950, Poland
- ECOTECH-COMPLEX-Analytical, and Programme Centre for Advanced Environmentally- Friendly Technologies, Maria Curie-Sklodowska University, Głęboka 39, Lublin, 20-033, Poland
| | - Dariusz Karcz
- Department of Chemical Technology, and Environmental Analytics, Cracow University of Technology, Cracow, 31-155, Poland
- ECOTECH-COMPLEX-Analytical, and Programme Centre for Advanced Environmentally- Friendly Technologies, Maria Curie-Sklodowska University, Głęboka 39, Lublin, 20-033, Poland
| | - Mariusz Gagoś
- Department of Cell Biology, Maria Curie-Sklodowska University, Akademicka 19, Lublin, 20-033, Poland
- Department of Biochemistry, and Molecular Biology, Medical University of Lublin, Lublin, 20-093, Poland
| | - Joanna Magdalena Gola
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, Katowice, 40-055, Poland
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Vargas-López M, Quiroz-Vicente CA, Pérez-Hernández N, Gómez-Chávez F, Bañuelos-Hernández AE, Pérez-Hernández E. The ketone body β-Hydroxybutyrate as a fuel source of chondrosarcoma cells. Heliyon 2024; 10:e30212. [PMID: 38694129 PMCID: PMC11061739 DOI: 10.1016/j.heliyon.2024.e30212] [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: 02/03/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 05/04/2024] Open
Abstract
Chondrosarcoma (CS) is a malignant bone tumor arising from cartilage-producing cells. The conventional subtype of CS typically develops within a dense cartilaginous matrix, creating an environment deficient in oxygen and nutrients, necessitating metabolic adaptation to ensure proliferation under stress conditions. Although ketone bodies (KBs) are oxidized by extrahepatic tissue cells such as the heart and brain, specific cancer cells, including CS cells, can undergo ketolysis. In this study, we found that KBs catabolism is activated in CS cells under nutrition-deprivation conditions. Interestingly, cytosolic β-hydroxybutyrate dehydrogenase 2 (BDH2), rather than mitochondrial BDH1, is expressed in these cells, indicating a specific metabolic adaptation for ketolysis in this bone tumor. The addition of the KB, β-Hydroxybutyrate (β-HB) in serum-starved CS cells re-induced the expression of BDH2, along with the key ketolytic enzyme 3-oxoacid CoA-transferase 1 (OXCT1) and monocarboxylate transporter-1 (MCT1). Additionally, internal β-HB production was quantified in supplied and starved cells, suggesting that CS cells are also capable of ketogenesis alongside ketolysis. These findings unveil a novel metabolic adaptation wherein nutrition-deprived CS cells utilize KBs for energy supply and proliferation.
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Affiliation(s)
- Misael Vargas-López
- Laboratorio de Microbiología Molecular, Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Mexico City, 07320, Mexico
| | - Carlos A. Quiroz-Vicente
- Laboratorio de Microbiología Molecular, Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Mexico City, 07320, Mexico
| | - Nury Pérez-Hernández
- Laboratorio de Microbiología Molecular, Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Mexico City, 07320, Mexico
| | - Fernando Gómez-Chávez
- Laboratorio de Microbiología Molecular, Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Mexico City, 07320, Mexico
| | - Angel E. Bañuelos-Hernández
- Laboratorio de Microbiología Molecular, Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Mexico City, 07320, Mexico
| | - Elizabeth Pérez-Hernández
- Laboratorio de Microbiología Molecular, Sección de Estudios de Posgrado e Investigación, ENMyH, Instituto Politécnico Nacional, Mexico City, 07320, Mexico
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Atkins D, Rosas JM, Månsson LK, Shahverdi N, Dey SS, Pitenis AA. Survival-Associated Cellular Response Maintained in Pancreatic Ductal Adenocarcinoma (PDAC) Switched Between Soft and Stiff 3D Microgel Culture. ACS Biomater Sci Eng 2024; 10:2177-2187. [PMID: 38466617 PMCID: PMC11005012 DOI: 10.1021/acsbiomaterials.3c01079] [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: 08/03/2023] [Revised: 02/26/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) accounts for about 90% of all pancreatic cancer cases. Five-year survival rates have remained below 12% since the 1970s, in part due to the difficulty in detection prior to metastasis (migration and invasion into neighboring organs and glands). Mechanical memory is a concept that has emerged over the past decade that may provide a path toward understanding how invading PDAC cells "remember" the mechanical properties of their diseased ("stiff", elastic modulus, E ≈ 10 kPa) microenvironment even while invading a healthy ("soft", E ≈ 1 kPa) microenvironment. Here, we investigated the role of mechanical priming by culturing a dilute suspension of PDAC (FG) cells within a 3D, rheologically tunable microgel platform from hydrogels with tunable mechanical properties. We conducted a suite of acute (short-term) priming studies where we cultured PDAC cells in either a soft (E ≈ 1 kPa) or stiff (E ≈ 10 kPa) environment for 6 h, then removed and placed them into a new soft or stiff 3D environment for another 18 h. Following these steps, we conducted RNA-seq analyses to quantify gene expression. Initial priming in the 3D culture showed persistent gene expression for the duration of the study, regardless of the subsequent environments (stiff or soft). Stiff 3D culture was associated with the downregulation of tumor suppressors (LATS1, BCAR3, CDKN2C), as well as the upregulation of cancer-associated genes (RAC3). Immunofluorescence staining (BCAR3, RAC3) further supported the persistence of this cellular response, with BCAR3 upregulated in soft culture and RAC3 upregulated in stiff-primed culture. Stiff-primed genes were stratified against patient data found in The Cancer Genome Atlas (TCGA). Upregulated genes in stiff-primed 3D culture were associated with decreased survival in patient data, suggesting a link between patient survival and mechanical priming.
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Affiliation(s)
- Dixon
J. Atkins
- Department
of Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Jonah M. Rosas
- Department
of Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Lisa K. Månsson
- Materials
Department, University of California Santa
Barbara, Santa
Barbara, California 93106, United States
| | - Nima Shahverdi
- Molecular,
Cellular, and Developmental Biology Department, University of California Santa Barbara, Santa Barbara, California 93106, United States
| | - Siddharth S. Dey
- Department
of Chemical Engineering, University
of California Santa Barbara, Santa
Barbara, California 93106, United States
- Department
of Bioengineering, University of California
Santa Barbara, Santa Barbara, California 93106, United States
| | - Angela A. Pitenis
- Materials
Department, University of California Santa
Barbara, Santa
Barbara, California 93106, United States
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9
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Müller JA, Schäffler N, Kellerer T, Schwake G, Ligon TS, Rädler JO. Kinetics of RNA-LNP delivery and protein expression. Eur J Pharm Biopharm 2024; 197:114222. [PMID: 38387850 DOI: 10.1016/j.ejpb.2024.114222] [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: 11/29/2023] [Revised: 01/23/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
Abstract
Lipid nanoparticles (LNPs) employing ionizable lipids are the most advanced technology for delivery of RNA, most notably mRNA, to cells. LNPs represent well-defined core-shell particles with efficient nucleic acid encapsulation, low immunogenicity and enhanced efficacy. While much is known about the structure and activity of LNPs, less attention is given to the timing of LNP uptake, cytosolic transfer and protein expression. However, LNP kinetics is a key factor determining delivery efficiency. Hence quantitative insight into the multi-cascaded pathway of LNPs is of interest to elucidate the mechanism of delivery. Here, we review experiments as well as theoretical modeling of the timing of LNP uptake, mRNA-release and protein expression. We describe LNP delivery as a sequence of stochastic transfer processes and review a mathematical model of subsequent protein translation from mRNA. We compile probabilities and numbers obtained from time resolved microscopy. Specifically, live-cell imaging on single cell arrays (LISCA) allows for high-throughput acquisition of thousands of individual GFP reporter expression time courses. The traces yield the distribution of mRNA life-times, expression rates and expression onset. Correlation analysis reveals an inverse dependence of gene expression efficiency and transfection onset-times. Finally, we discuss why timing of mRNA release is critical in the context of codelivery of multiple nucleic acid species as in the case of mRNA co-expression or CRISPR/Cas gene editing.
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Affiliation(s)
- Judith A Müller
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich, Germany
| | - Nathalie Schäffler
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich, Germany
| | - Thomas Kellerer
- Multiphoton Imaging Lab, Munich University of Applied Sciences, Munich, Germany
| | - Gerlinde Schwake
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich, Germany
| | | | - Joachim O Rädler
- Faculty of Physics and Center for NanoScience, Ludwig Maximilians-University, Munich, Germany.
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10
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Pechmann S. Single-cell expression predicts neuron-specific protein homeostasis networks. Open Biol 2024; 14:230386. [PMID: 38262604 PMCID: PMC10805596 DOI: 10.1098/rsob.230386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 11/17/2023] [Indexed: 01/25/2024] Open
Abstract
The protein homeostasis network keeps proteins in their correct shapes and avoids unwanted aggregation. In turn, the accumulation of aberrantly misfolded proteins has been directly associated with the onset of ageing-associated neurodegenerative diseases such as Alzheimer's and Parkinson's. However, a detailed and rational understanding of how protein homeostasis is achieved in health, and how it can be targeted for therapeutic intervention in diseases remains missing. Here, large-scale single-cell expression data from the Allen Brain Map are analysed to investigate the transcription regulation of the core protein homeostasis network across the human brain. Remarkably, distinct expression profiles suggest specialized protein homeostasis networks with systematic adaptations in excitatory neurons, inhibitory neurons and non-neuronal cells. Moreover, several chaperones and Ubiquitin ligases are found transcriptionally coregulated with genes important for synapse formation and maintenance, thus linking protein homeostasis to the regulation of neuronal function. Finally, evolutionary analyses highlight the conservation of an elevated interaction density in the chaperone network, suggesting that one of the most exciting aspects of chaperone action may yet be discovered in their collective action at the systems level. More generally, our work highlights the power of computational analyses for breaking down complexity and gaining complementary insights into fundamental biological problems.
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11
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Feng R, Luo L, Han Z, Qi Y, Xiao H, Huang C, Peng W, Liu R, Huang Z. 3'-Daidzein Sulfonate Sodium Protects against Glutamate-induced Neuronal Injuries by Regulating NMDA Receptors. Curr Pharm Des 2024; 30:1762-1770. [PMID: 38778603 DOI: 10.2174/0113816128299123240505172222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 03/08/2024] [Accepted: 03/12/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND It was previously found that 3'-Daidzein Sulfonate Sodium (DSS) exhibits protective effects on cerebral ischemia/reperfusion injury (CI/RI). AIM This study aimed to explore the underlying molecular mechanisms involved in the neuroprotective effects of DSS against ischemic stroke. METHODS In this study, rats with transient middle cerebral artery occlusion (tMCAO) were used as an in vivo model, whereas PC12 cells treated with glutamate alone and rat primary cortical neurons treated with the combination of glutamate and glycine were used as in vitro models. Cell viability and lactate dehydrogenase (LDH) release were used to evaluate cell injury. Cell apoptosis was determined by flow cytometry. Quantitative polymerase chain reaction (qPCR), Western blotting, and immunofluorescent staining methods were used to determine the mRNA expressions and protein levels and location. RESULTS It was found that DSS significantly suppressed the impaired viability of PC12 cells induced by glutamate. DSS also increased cell viability while reducing the LDH release and apoptosis in primary cortical neurons injured by glutamate and glycine. In addition, DSS decreased GluN2B subunit expression while enhancing the expressions of GluN2A subunit and PSD95 in tMCAO rats' brains. CONCLUSION This study demonstrated that DSS protects against excitotoxic damage in neurons induced by CI/RI through regulating the expression of NMDA receptors and PSD95. Our findings provide experimental evidence for the potential clinical administration of DSS in ischemic stroke.
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Affiliation(s)
- Ruixue Feng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- The First Clinical College of Gannan Medical University, Ganzhou 341000, China
| | - Li Luo
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- The First Clinical College of Gannan Medical University, Ganzhou 341000, China
| | - Zun Han
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- The First Clinical College of Gannan Medical University, Ganzhou 341000, China
| | - Yue Qi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Graduate School of Gannan Medical University, Ganzhou 341000, China
| | - Hai Xiao
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- The First Clinical College of Gannan Medical University, Ganzhou 341000, China
- First Affiliated Hospital of Gannan Medical University, Ganzhou 341000, China
| | - Cheng Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Ganzhou Key Laboratory of Neuroinflammation Research, Gannan Medical University, Ganzhou 341000, China
- School of Basic Medical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Weijie Peng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Ruizhen Liu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Ganzhou Key Laboratory of Neuroinflammation Research, Gannan Medical University, Ganzhou 341000, China
- School of Basic Medical Sciences, Gannan Medical University, Ganzhou 341000, China
| | - Zhihua Huang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 341000, China
- Ganzhou Key Laboratory of Neuroinflammation Research, Gannan Medical University, Ganzhou 341000, China
- School of Basic Medical Sciences, Gannan Medical University, Ganzhou 341000, China
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12
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Kandori H, Aoki M, Miyamoto Y, Nakamura S, Kobayashi R, Matsumoto M, Yokoyama K. Lobular distribution of enhanced expression levels of heat shock proteins using in-situ hybridization in the mouse liver treated with a single administration of CCl4. J Toxicol Pathol 2024; 37:29-37. [PMID: 38283376 PMCID: PMC10811382 DOI: 10.1293/tox.2023-0053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 10/13/2023] [Indexed: 01/30/2024] Open
Abstract
This study was conducted to visualize the lobular distribution of enhanced mRNA expression levels of heat shock proteins (HSPs) in liver samples from carbon tetra chloride (CCl4)-treated mice using in-situ hybridization (ISH). Male BALB/c mice given a single oral administration of CCl4 were euthanized 6 hours or 1 day after the administration (6 h or 1 day). Paraffin-embedded liver samples were obtained, ISH for HSPs was conducted, as well as hematoxylin-eosin staining and immunohistochemistry (IHC). At 6 h, centrilobular hepatocellular vacuolization was observed, and increased signals for Hspa1a, Hspa1b, and Grp78, which are HSPs, were noted in the centrilobular area using ISH. At 1 day, zonal hepatocellular necrosis was observed in the centrilobular area, but mRNA signal increases for HSPs were no longer observed there. Some discrepancies between ISH and IHC for HSPs were observed, and they might be partly caused by post-transcriptional gene regulation, including the ribosome quality control mechanisms. It is known that CCl4 damages centrilobular hepatocytes through metabolization by cytochrome P450, mainly located in the centrilobular region, and HSPs are induced under cellular stress. Therefore, our ISH results visualized increased mRNA expression levels of HSPs in the centrilobular hepatocytes of mice 6 hours after a single administration of CCl4 as a response to cellular stress, and it disappeared 1 day after the treatment when remarkable necrosis was observed there.
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Affiliation(s)
- Hitoshi Kandori
- Integrated Pathology, Frontier Technology, Integrated &
Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1 Muraoka-Higashi
2-chome, Fujisawa-shi, Kanagawa 251-0012, Japan
| | - Masami Aoki
- Integrated Pathology, Frontier Technology, Integrated &
Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1 Muraoka-Higashi
2-chome, Fujisawa-shi, Kanagawa 251-0012, Japan
| | - Yumiko Miyamoto
- Integrated Pathology, Frontier Technology, Integrated &
Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1 Muraoka-Higashi
2-chome, Fujisawa-shi, Kanagawa 251-0012, Japan
| | - Sayuri Nakamura
- Integrated Pathology, Frontier Technology, Integrated &
Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1 Muraoka-Higashi
2-chome, Fujisawa-shi, Kanagawa 251-0012, Japan
| | - Ryosuke Kobayashi
- Integrated Pathology, Frontier Technology, Integrated &
Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1 Muraoka-Higashi
2-chome, Fujisawa-shi, Kanagawa 251-0012, Japan
| | - Mitsuharu Matsumoto
- Integrated Biology, Kidney/Liver Disease, Integrated &
Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1 Muraoka-Higashi
2-chome, Fujisawa-shi, Kanagawa 251-0012, Japan
| | - Kotaro Yokoyama
- Integrated Pathology, Frontier Technology, Integrated &
Translational Science, Axcelead Drug Discovery Partners, Inc., 26-1 Muraoka-Higashi
2-chome, Fujisawa-shi, Kanagawa 251-0012, Japan
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13
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Kubica S, Szota-Czyż J, Strzałka-Mrozik B, Adamska J, Bębenek E, Chrobak E, Gola JM. The Influence of Betulin Derivatives EB5 and ECH147 on the Expression of Selected TGFβ Superfamily Genes, TGFβ1, GDF15 and BMP2, in Renal Proximal Tubule Epithelial Cells. Curr Issues Mol Biol 2023; 45:9961-9975. [PMID: 38132468 PMCID: PMC10741875 DOI: 10.3390/cimb45120622] [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: 10/31/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Betulin derivatives are proposed to serve as an alternative to the drugs already established in oncologic treatment. Drug-induced nephrotoxicity leading to acute kidney injury frequently accompanies cancer treatment, and thus there is a need to research the effects of betulin derivatives on renal cells. The objective of our study was to assess the influence of the betulin derivatives 28-propynylobetulin (EB5) and 29-diethoxyphosphoryl-28-propynylobetulin (ECH147) on the expression of TGFβ1, BMP2 and GDF15 in renal proximal tubule epithelial cells (RPTECs) cultured in vitro. The changes in mRNA expression and copy numbers were assessed using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) and the standard curve method, respectively. An enzyme-linked immunosorbent assay (ELISA) was used to evaluate the effect of the betulin derivatives on the protein concentration in the culture media's supernatant. The assessment of the betulin derivatives' influence on gene expression demonstrated that the mRNA level and protein concentration did not always correlate with each other. Each of the tested compounds affected the mRNA expression. The RT-qPCR analyses showed that EB5 and ECH147 induced effects similar to those of betulin or cisplatin and resulted in a decrease in the mRNA copy number of all the analyzed genes. The ELISA demonstrated that EB5 and ECH147 elevated the protein concentration of TGFβ1 and GDF15, while the level of BMP2 decreased. The concentration of the derivatives used in the treatment was crucial, but the effects did not always exhibit a simple linear dose-dependent relationship. Betulin and its derivatives, EB5 and ECH147, influenced the gene expression of TGFβ1, BMP2 and GDF15 in the renal proximal tubule epithelial cells. The observed effects raise the question of whether treatment with these compounds could promote the development of renal fibrosis.
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Affiliation(s)
- Sebastian Kubica
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (S.K.); (J.S.-C.); (J.A.); (J.M.G.)
| | - Justyna Szota-Czyż
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (S.K.); (J.S.-C.); (J.A.); (J.M.G.)
| | - Barbara Strzałka-Mrozik
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (S.K.); (J.S.-C.); (J.A.); (J.M.G.)
| | - Jolanta Adamska
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (S.K.); (J.S.-C.); (J.A.); (J.M.G.)
| | - Ewa Bębenek
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (E.B.); (E.C.)
| | - Elwira Chrobak
- Department of Organic Chemistry, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (E.B.); (E.C.)
| | - Joanna Magdalena Gola
- Department of Molecular Biology, Faculty of Pharmaceutical Sciences in Sosnowiec, Medical University of Silesia, 40-055 Katowice, Poland; (S.K.); (J.S.-C.); (J.A.); (J.M.G.)
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14
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Ponomarenko EA, Krasnov GS, Kiseleva OI, Kryukova PA, Arzumanian VA, Dolgalev GV, Ilgisonis EV, Lisitsa AV, Poverennaya EV. Workability of mRNA Sequencing for Predicting Protein Abundance. Genes (Basel) 2023; 14:2065. [PMID: 38003008 PMCID: PMC10671741 DOI: 10.3390/genes14112065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/03/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Transcriptomics methods (RNA-Seq, PCR) today are more routine and reproducible than proteomics methods, i.e., both mass spectrometry and immunochemical analysis. For this reason, most scientific studies are limited to assessing the level of mRNA content. At the same time, protein content (and its post-translational status) largely determines the cell's state and behavior. Such a forced extrapolation of conclusions from the transcriptome to the proteome often seems unjustified. The ratios of "transcript-protein" pairs can vary by several orders of magnitude for different genes. As a rule, the correlation coefficient between transcriptome-proteome levels for different tissues does not exceed 0.3-0.5. Several characteristics determine the ratio between the content of mRNA and protein: among them, the rate of movement of the ribosome along the mRNA and the number of free ribosomes in the cell, the availability of tRNA, the secondary structure, and the localization of the transcript. The technical features of the experimental methods also significantly influence the levels of the transcript and protein of the corresponding gene on the outcome of the comparison. Given the above biological features and the performance of experimental and bioinformatic approaches, one may develop various models to predict proteomic profiles based on transcriptomic data. This review is devoted to the ability of RNA sequencing methods for protein abundance prediction.
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Affiliation(s)
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow 119991, Russia;
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15
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Olanrewaju GO, Kruse CPS, Wyatt SE. Functional Meta-Analysis of the Proteomic Responses of Arabidopsis Seedlings to the Spaceflight Environment Reveals Multi-Dimensional Sources of Variability across Spaceflight Experiments. Int J Mol Sci 2023; 24:14425. [PMID: 37833871 PMCID: PMC10573023 DOI: 10.3390/ijms241914425] [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: 08/17/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
The human quest for sustainable habitation of extraterrestrial environments necessitates a robust understanding of life's adaptability to the unique conditions of spaceflight. This study provides a comprehensive proteomic dissection of the Arabidopsis plant's responses to the spaceflight environment through a meta-analysis of proteomics data from four separate spaceflight experiments conducted on the International Space Station (ISS) in different hardware configurations. Raw proteomics LC/MS spectra were analyzed for differential expression in MaxQuant and Perseus software. The analysis of dissimilarities among the datasets reveals the multidimensional nature of plant proteomic responses to spaceflight, impacted by variables such as spaceflight hardware, seedling age, lighting conditions, and proteomic quantification techniques. By contrasting datasets that varied in light exposure, we elucidated proteins involved in photomorphogenesis and skotomorphogenesis in plant spaceflight responses. Additionally, with data from an onboard 1 g control experiment, we isolated proteins that specifically respond to the microgravity environment and those that respond to other spaceflight conditions. This study identified proteins and associated metabolic pathways that are consistently impacted across the datasets. Notably, these shared proteins were associated with critical metabolic functions, including carbon metabolism, glycolysis, gluconeogenesis, and amino acid biosynthesis, underscoring their potential significance in Arabidopsis' spaceflight adaptation mechanisms and informing strategies for successful space farming.
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Affiliation(s)
- Gbolaga O. Olanrewaju
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
| | - Colin P. S. Kruse
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, NM 87545, USA;
| | - Sarah E. Wyatt
- Molecular and Cellular Biology Program, Ohio University, Athens, OH 45701, USA;
- Department of Environmental and Plant Biology, Ohio University, Athens, OH 45701, USA
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16
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Arad G, Geiger T. Functional impact of protein-RNA variation in clinical cancer analyses. Mol Cell Proteomics 2023:100587. [PMID: 37290530 PMCID: PMC10388586 DOI: 10.1016/j.mcpro.2023.100587] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 04/08/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023] Open
Abstract
Comprehensive molecular characterization of tumors aims to uncover cancer vulnerabilities, drug resistance mechanisms and biomarkers. Identification of cancer drivers was suggested as the basis for patient-tailored therapy, and transcriptomic analyses were proposed to reveal the phenotypic outcome of cancer mutations. With the maturation of the proteomic field, studies of protein-RNA discrepancies suggested that RNA analyses are insufficient to predict cellular functions. In this manuscript we discuss the importance of direct mRNA-protein comparisons in clinical cancer studies. We make use of the large amount of data generated by the Clinical Proteomic Tumor Analysis Consortium (CPTAC), which includes protein and mRNA expression analyses from the exact same samples. Analysis of protein-RNA correlations showed marked differences among cancer types, and highlighted the protein-RNA similarities and discrepancies among functional pathways and drug targets. Additionally, unsupervised clustering of the data based on protein or RNA showed substantial differences in tumor classification and the cellular processes that differentiate between clusters. These analyses show the difficulty to predict protein levels from mRNAs, and the critical role of protein analyses for phenotypic tumor characterization.
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Affiliation(s)
| | - Tamar Geiger
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
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17
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Klett KC, Martin-Villa BC, Villarreal VS, Melemenidis S, Viswanathan V, Manjappa R, Ashraf MR, Soto L, Lau B, Dutt S, Rankin EB, Loo BW, Heilshorn SC. Human enteroids as a tool to study conventional and ultra-high dose rate radiation. Integr Biol (Camb) 2023; 15:zyad013. [PMID: 37874173 PMCID: PMC10594601 DOI: 10.1093/intbio/zyad013] [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: 07/16/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/25/2023]
Abstract
Radiation therapy, one of the most effective therapies to treat cancer, is highly toxic to healthy tissue. The delivery of radiation at ultra-high dose rates, FLASH radiation therapy (FLASH), has been shown to maintain therapeutic anti-tumor efficacy while sparing normal tissues compared to conventional dose rate irradiation (CONV). Though promising, these studies have been limited mainly to murine models. Here, we leveraged enteroids, three-dimensional cell clusters that mimic the intestine, to study human-specific tissue response to radiation. We observed enteroids have a greater colony growth potential following FLASH compared with CONV. In addition, the enteroids that reformed following FLASH more frequently exhibited proper intestinal polarity. While we did not observe differences in enteroid damage across groups, we did see distinct transcriptomic changes. Specifically, the FLASH enteroids upregulated the expression of genes associated with the WNT-family, cell-cell adhesion, and hypoxia response. These studies validate human enteroids as a model to investigate FLASH and provide further evidence supporting clinical study of this therapy. Insight Box Promising work has been done to demonstrate the potential of ultra-high dose rate radiation (FLASH) to ablate cancerous tissue, while preserving healthy tissue. While encouraging, these findings have been primarily observed using pre-clinical murine and traditional two-dimensional cell culture. This study validates the use of human enteroids as a tool to investigate human-specific tissue response to FLASH. Specifically, the work described demonstrates the ability of enteroids to recapitulate previous in vivo findings, while also providing a lens through which to probe cellular and molecular-level responses to FLASH. The human enteroids described herein offer a powerful model that can be used to probe the underlying mechanisms of FLASH in future studies.
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Affiliation(s)
- Katarina C Klett
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | | | - Victoria S Villarreal
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
| | - Stavros Melemenidis
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Vignesh Viswanathan
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rakesh Manjappa
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ramish Ashraf
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Luis Soto
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brianna Lau
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Suparna Dutt
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
| | - Erinn B Rankin
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Department of Obstetrics and Gynecology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Billy W Loo
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Sarah C Heilshorn
- Department of Materials Science and Engineering, Stanford University, Stanford, CA, USA
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18
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Papež M, Jiménez Lancho V, Eisenhut P, Motheramgari K, Borth N. SLAM-seq reveals early transcriptomic response mechanisms upon glutamine deprivation in Chinese hamster ovary cells. Biotechnol Bioeng 2023; 120:970-986. [PMID: 36575109 DOI: 10.1002/bit.28320] [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: 09/14/2022] [Revised: 11/30/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Mammalian cells frequently encounter subtle perturbations during recombinant protein production. Identifying the genetic factors that govern the cellular stress response can facilitate targeted genetic engineering to obtain production cell lines that demonstrate a higher stress tolerance. To simulate nutrient stress, Chinese hamster ovary (CHO) cells were transferred into a glutamine(Q)-free medium and transcriptional dynamics using thiol(SH)-linked alkylation for the metabolic sequencing of RNA (SLAM-seq) along with standard RNA-seq of stressed and unstressed cells were investigated. The SLAM-seq method allows differentiation between actively transcribed, nascent mRNA, and total (previously present) mRNA in the sample, adding an additional, time-resolved layer to classic RNA-sequencing. The cells tackle amino acid (AA) limitation by inducing the integrated stress response (ISR) signaling pathway, reflected in Atf4 overexpression in the early hours post Q deprivation, leading to subsequent activation of its targets, Asns, Atf3, Ddit3, Eif4ebp1, Gpt2, Herpud1, Slc7a1, Slc7a11, Slc38a2, Trib3, and Vegfa. The GCN2-eIF2α-ATF4 pathway is confirmed by a significant halt in transcription of translation-related genes at 24 h post Q deprivation. The downregulation of lipid synthesis indicates the inhibition of the mTOR pathway, further confirmed by overexpression of Sesn2. Furthermore, SLAM-seq detects short-lived transcription factors, such as Egr1, that would have been missed in standard experimental designs with RNA-seq. Our results describe the successful establishment of SLAM-seq in CHO cells and therefore facilitate its future use in other scenarios where dynamic transcriptome profiling in CHO cells is essential.
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Affiliation(s)
- Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
| | | | - Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
| | | | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Graz, Austria
- University of Natural Resources and Life Sciences (BOKU), Vienna, Austria
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19
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Phenolic acids and a static magnetic field change the expression of transforming growth factor β isoforms in amelanotic melanoma cells. Mol Biol Rep 2023; 50:4207-4216. [PMID: 36899279 PMCID: PMC10147755 DOI: 10.1007/s11033-023-08336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/14/2023] [Indexed: 03/12/2023]
Abstract
BACKGROUND Melanoma is an aggressive type of cancer that can metastasize to numerous other organs. TGFβ is one of the key signaling pathways in melanoma progression. Previous studies on various types of cancer have shown that both: polyphenols and a static magnetic field (SMF) can be potential chemopreventive/therapeutic agents. Therefore, the aim of the study was to evaluate the effect of a SMF and selected polyphenols on the transcriptional activity of TGFβ genes in melanoma cells. METHODS AND RESULTS Experiments were performed on the C32 cell line treated with caffeic or chlorogenic acids, and with simultaneous exposure to a moderate-strength SMF. The RT-qPCR method was used to determine the mRNA level of genes encoding the TGFβ isoforms and their receptors. The concentration of the TGFβ1 and TGFβ2 proteins were also measured in the cell culture supernates. The first response of C32 melanoma cells to both factors is the reduction of TGFβ levels. Then, mRNA level of these molecules returned to values close to pre-treatment level by the end of experiment. CONCLUSION Our study results demonstrate the potential of polyphenols and a moderate-strength SMF to support cancer therapy by altering TGFβ expression, which is a very promising topic for the diagnosis and treatment of melanoma.
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20
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Decoupling of mRNA and Protein Expression in Aging Brains Reveals the Age-Dependent Adaptation of Specific Gene Subsets. Cells 2023; 12:cells12040615. [PMID: 36831282 PMCID: PMC9954025 DOI: 10.3390/cells12040615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/07/2023] [Accepted: 02/12/2023] [Indexed: 02/17/2023] Open
Abstract
During aging, changes in gene expression are associated with a decline in physical and cognitive abilities. Here, we investigate the connection between changes in mRNA and protein expression in the brain by comparing the transcriptome and proteome of the mouse cortex during aging. Our transcriptomic analysis revealed that aging mainly triggers gene activation in the cortex. We showed that an increase in mRNA expression correlates with protein expression, specifically in the anterior cingulate cortex, where we also observed an increase in cortical thickness during aging. Genes exhibiting an aging-dependent increase of mRNA and protein levels are involved in sensory perception and immune functions. Our proteomic analysis also identified changes in protein abundance in the aging cortex and highlighted a subset of proteins that were differentially enriched but exhibited stable mRNA levels during aging, implying the contribution of aging-related post- transcriptional and post-translational mechanisms. These specific genes were associated with general biological processes such as translation, ribosome assembly and protein degradation, and also important brain functions related to neuroplasticity. By decoupling mRNA and protein expression, we have thus characterized distinct subsets of genes that differentially adjust to cellular aging in the cerebral cortex.
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21
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Manuel JM, Guilloy N, Khatir I, Roucou X, Laurent B. Re-evaluating the impact of alternative RNA splicing on proteomic diversity. Front Genet 2023; 14:1089053. [PMID: 36845399 PMCID: PMC9947481 DOI: 10.3389/fgene.2023.1089053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative splicing (AS) constitutes a mechanism by which protein-coding genes and long non-coding RNA (lncRNA) genes produce more than a single mature transcript. From plants to humans, AS is a powerful process that increases transcriptome complexity. Importantly, splice variants produced from AS can potentially encode for distinct protein isoforms which can lose or gain specific domains and, hence, differ in their functional properties. Advances in proteomics have shown that the proteome is indeed diverse due to the presence of numerous protein isoforms. For the past decades, with the help of advanced high-throughput technologies, numerous alternatively spliced transcripts have been identified. However, the low detection rate of protein isoforms in proteomic studies raised debatable questions on whether AS contributes to proteomic diversity and on how many AS events are really functional. We propose here to assess and discuss the impact of AS on proteomic complexity in the light of the technological progress, updated genome annotation, and current scientific knowledge.
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Affiliation(s)
- Jeru Manoj Manuel
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Noé Guilloy
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Inès Khatir
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Xavier Roucou
- Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CRCHUS), Sherbrooke, QC, Canada,Quebec Network for Research on Protein Function Structure and Engineering, PROTEO, Québec, QC, Canada
| | - Benoit Laurent
- Research Center on Aging, Centre Intégré Universitaire de Santé et Services Sociaux de l’Estrie-Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC, Canada,Department of Biochemistry and Functional Genomics, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada,*Correspondence: Benoit Laurent,
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22
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Miyata H, Ishii M, Suehiro F, Komabashiri N, Ikeda N, Sakurai T, Nishimura M. Elucidation of adipogenic differentiation regulatory mechanism in human maxillary/mandibular bone marrow-derived stem cells. Arch Oral Biol 2023; 146:105608. [PMID: 36549198 DOI: 10.1016/j.archoralbio.2022.105608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/04/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
OBJECTIVE This study aims to investigate the underlying molecular mechanisms that regulate the adipogenic differentiation of maxillary/mandibular bone marrow-derived mesenchymal stem cells (MBMSCs). DESIGN MBMSCs and iliac bone marrow-derived MSCs (IBMSCs) were compared for osteogenic, chondrogenic, and adipogenic differentiation. Cell surface antigen expression was examined using flow cytometry, and stem cell marker expression was assessed using real-time polymerase chain reaction (PCR). Various adipogenic regulatory factors' expression was evaluated using real-time PCR and western blotting. RESULTS No significant differences in cell surface antigen profiles or stem cell marker expression in MBMSCs and IBMSCs were observed. MBMSCs and IBMSCs displayed similar osteogenic and chondrogenic potentials, whereas MBMSCs showed significantly lower adipogenic potentials than those shown by IBMSCs. Expression of CCAAT/enhancer binding protein β (C/EBPβ), C/EBPδ, early B-cell factor 1 (Ebf-1), and Krüppel-like factor 5 (KLF5), which are early adipogenic differentiation factors, was suppressed in MBMSCs compared to that in IBMSCs. Peroxisome proliferator-activated receptor-γ (PPARγ) and C/EBPα, which play important roles in the terminal differentiation of adipocytes, was lower in MBMSCs than that in IBMSCs. Furthermore, the level of zinc finger protein 423 (Zfp423), which is involved in the commitment of undifferentiated MSCs to the adipocyte lineage, was significantly lower in MBMSCs than that in IBMSCs. CONCLUSIONS MBMSCs are negatively regulated in the commitment of undifferentiated MSCs to the adipocyte lineage (preadipocytes) as well as in the terminal differentiation of preadipocytes into mature adipocytes. These results may elucidate the site-specific characteristics of MBMSCs.
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Affiliation(s)
- Haruka Miyata
- Department of Oral and Maxillofacial Prosthodontics, Kagoshima University Graduate school of Medical and Dental Science, Kagoshima 890-8544, Japan
| | - Masakazu Ishii
- Department of Oral and Maxillofacial Prosthodontics, Kagoshima University Graduate school of Medical and Dental Science, Kagoshima 890-8544, Japan.
| | - Fumio Suehiro
- Department of Oral and Maxillofacial Prosthodontics, Kagoshima University Graduate school of Medical and Dental Science, Kagoshima 890-8544, Japan
| | - Naohiro Komabashiri
- Department of Oral and Maxillofacial Prosthodontics, Kagoshima University Graduate school of Medical and Dental Science, Kagoshima 890-8544, Japan
| | - Nao Ikeda
- Department of Oral and Maxillofacial Prosthodontics, Kagoshima University Graduate school of Medical and Dental Science, Kagoshima 890-8544, Japan
| | - Tomoaki Sakurai
- Department of Oral and Maxillofacial Prosthodontics, Kagoshima University Graduate school of Medical and Dental Science, Kagoshima 890-8544, Japan
| | - Masahiro Nishimura
- Department of Oral and Maxillofacial Prosthodontics, Kagoshima University Graduate school of Medical and Dental Science, Kagoshima 890-8544, Japan
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23
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Liu Z, Zhang L, Qian C, Zhou Y, Yu Q, Yuan J, Lv Y, Zhang L, Chang X, Li Y, Liu Y. Recurrent hypoglycemia increases hepatic gluconeogenesis without affecting glycogen metabolism or systemic lipolysis in rat. Metabolism 2022; 136:155310. [PMID: 36063868 DOI: 10.1016/j.metabol.2022.155310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 08/29/2022] [Accepted: 08/31/2022] [Indexed: 11/26/2022]
Abstract
INTRODUCTION Recurrent hypoglycemia (RH) impairs secretion of counterregulatory hormones. Whether and how RH affects responses within metabolically important peripheral organs to counterregulatory hormones are poorly understood. OBJECTIVE To study the effects of RH on metabolic pathways associated with glucose counterregulation within liver, white adipose tissue and skeletal muscle. METHODS Using a widely adopted rodent model of 3-day recurrent hypoglycemia, we first checked expression of counterregulatory hormone G-protein coupled receptors (GPCRs), their inhibitory regulators and downstream enzymes catalyzing glycogen metabolism, gluconeogenesis and lipolysis by qPCR and western blot. Then, we examined epinephrine-induced phosphorylation of PKA substrates to validate adrenergic sensitivity in each organ. Next, we measured hepatic and skeletal glycogen content, degree of breakdown by epinephrine and abundance of phosphorylated glycogen phosphorylase under hypoglycemia and that of phosphorylated glycogen synthase during recovery to evaluate glycogen turnover. Further, we performed pyruvate and lactate tolerance tests to assess gluconeogenesis. Additionally, we measured circulating FFA and glycerol to check lipolysis. The abovementioned studies were repeated in streptozotocin-induced diabetic rat model. Finally, we conducted epinephrine tolerance test to investigate systemic glycemic excursions to counterregulatory hormones. Saline-injected rats served as controls. RESULTS RH increased counterregulatory hormone GPCR signaling in liver and epidydimal white adipose tissue (eWAT), but not in skeletal muscle. For glycogen metabolism, RH did not affect total content or epinephrine-stimulated breakdown in liver and skeletal muscle. Although RH decreased expression of phosphorylated glycogen synthase 2, it did not affect hepatic glycogen biosynthesis during recovery from hypoglycemia or after fasting-refeeding. For gluconeogenesis, RH upregulated fructose 1,6-bisphosphatase 1 and monocarboxylic acid transporter 1 that imports lactate as precursor, resulting in a lower blood lactate profile during hypoglycemia. In agreement, RH elevated fasting blood glucose and caused higher glycemic excursions during pyruvate tolerance test. For lipolysis, RH did not affect circulating levels of FFA and glycerol after overnight fasting or upon epinephrine stimulation. Interestingly, RH upregulated the trophic fatty acid transporter FATP1 and glucose transporter GLUT4 to increase lipogenesis in eWAT. These aforementioned changes of gluconeogenesis, lipolysis and lipogenesis were validated in streptozotocin-diabetic rats. Finally, RH increased insulin sensitivity to accelerate glucose disposal, which was attributable to upregulated visceral adipose GLUT4. CONCLUSIONS RH caused metabolic adaptations related to counterregulation within peripheral organs. Specifically, adrenergic signaling was enhanced in liver and visceral fat, but not in skeletal muscle. Glycogen metabolism remained unchanged. Hepatic gluconeogenesis was augmented. Systemic lipolysis was unaffected, but visceral lipogenesis was enhanced. Insulin sensitivity was increased. These findings provided insights into mechanisms underlying clinical problems associated with intensive insulin therapy, such as high gluconeogenic flux and body weight gain.
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Affiliation(s)
- Zejian Liu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Lingyu Zhang
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Chen Qian
- Department of Endocrinology, Zhangjiagang Hospital Affiliated to Soochow University, Zhangjiagang, Suzhou, Jiangsu 215699, China
| | - Ying Zhou
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu 211100, China
| | - Qiuyu Yu
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Jiaqi Yuan
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yunfan Lv
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Leheng Zhang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Xiaoai Chang
- Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, Jiangsu 211166, China
| | - Yangyang Li
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu 211100, China.
| | - Yu Liu
- Department of Endocrinology, Sir Run Run Hospital, Nanjing Medical University, Nanjing, Jiangsu 211100, China.
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24
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Uszczynska-Ratajczak B, Sugunan S, Kwiatkowska M, Migdal M, Carbonell-Sala S, Sokol A, Winata CL, Chacinska A. Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish. Life Sci Alliance 2022; 6:6/1/e202201514. [PMID: 36283702 PMCID: PMC9595208 DOI: 10.26508/lsa.202201514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (Danio rerio), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by the chchd4a -/- mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.
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Affiliation(s)
- Barbara Uszczynska-Ratajczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland .,Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sreedevi Sugunan
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Monika Kwiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland,Centre of New Technologies, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdal
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Silvia Carbonell-Sala
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Sokol
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany,Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agnieszka Chacinska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
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25
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Heat-Induced Proteotoxic Stress Response in Placenta-Derived Stem Cells (PDSCs) Is Mediated through HSPA1A and HSPA1B with a Potential Higher Role for HSPA1B. Curr Issues Mol Biol 2022; 44:4748-4768. [PMID: 36286039 PMCID: PMC9600182 DOI: 10.3390/cimb44100324] [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: 08/17/2022] [Revised: 09/28/2022] [Accepted: 10/07/2022] [Indexed: 11/18/2022] Open
Abstract
Placenta-derived stem cells (PDSCs), due to unique traits such as mesenchymal and embryonic characteristics and the absence of ethical constraints, are in a clinically and therapeutically advantageous position. To aid in stemness maintenance, counter pathophysiological stresses, and withstand post-differentiation challenges, stem cells require elevated protein synthesis and consequently augmented proteostasis. Stem cells exhibit source-specific proteostasis traits, making it imperative to study them individually from different sources. These studies have implications for understanding stem cell biology and exploitation in the augmentation of therapeutic applications. Here, we aim to identify the primary determinants of proteotoxic stress response in PDSCs. We generated heat-induced dose-responsive proteotoxic stress models of three stem cell types: placental origin cells, the placenta-derived mesenchymal stem cells (pMSCs), maternal origin cells, the decidua parietalis mesenchymal stem cells (DPMSCs), and the maternal–fetal interface cells, decidua basalis mesenchymal stem cells (DBMSCs), and measured stress induction through biochemical and cell proliferation assays. RT-PCR array analysis of 84 genes involved in protein folding and protein quality control led to the identification of Hsp70 members HSPA1A and HSPA1B as the prominent ones among 17 significantly expressed genes and with further analysis at the protein level through Western blotting. A kinetic analysis of HSPA1A and HSPA1B gene and protein expression allowed a time series evaluation of stress response. As identified by protein expression, an active stress response is in play even at 24 h. More prominent differences in expression between the two homologs are detected at the translational level, alluding to a potential higher requirement for HSPA1B during proteotoxic stress response in PDSCs.
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26
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Zulkapli R, Yusof MYPM, Abd Muid S, Wang SM, Firus Khan AY, Nawawi H. A Systematic Review on Attenuation of PCSK9 in Relation to Atherogenesis Biomarkers Associated with Natural Products or Plant Bioactive Compounds in In Vitro Studies: A Critique on the Quality and Imprecision of Studies. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12878. [PMID: 36232177 PMCID: PMC9566180 DOI: 10.3390/ijerph191912878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/27/2022] [Indexed: 06/16/2023]
Abstract
A systematic review was performed to identify all the related publications describing PCSK9 and atherogenesis biomarkers attenuation associated with a natural product and plant bioactive compounds in in vitro studies. This review emphasized the imprecision and quality of the included research rather than the detailed reporting of the results. Literature searches were conducted in Scopus, PubMed, and Science Direct from 2003 until 2021, following the Cochrane handbook. The screening of titles, abstracts, and full papers was performed by two independent reviewers, followed by data extraction and validity. Study quality and validity were assessed using the Imprecision Tool, Model, and Marker Validity Assessment that has been developed for basic science studies. A total of 403 articles were identified and 31 of those that met the inclusion criteria were selected. 13 different atherogenesis biomarkers in relation to PCSK9 were found, and the most studied biomarkers are LDLR, SREBP, and HNF1α. In terms of quality, our review suggests that the basic science study in investigating atherogenesis biomarkers is deficient in terms of imprecision and validity.
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Affiliation(s)
- Rahayu Zulkapli
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
- Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
- Faculty of Dentistry, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
| | - Mohd Yusmiaidil Putera Mohd Yusof
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
- Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
- Faculty of Dentistry, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
| | - Suhaila Abd Muid
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
- Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
| | - Seok Mui Wang
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
- Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
| | - Al’Aina Yuhainis Firus Khan
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
| | - Hapizah Nawawi
- Institute of Pathology, Laboratory and Forensic Medicine (I-PPerForM), Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
- Faculty of Medicine, Universiti Teknologi MARA (UiTM), Sungai Buloh Campus, Jalan Hospital, Sungai Buloh 47000, Selangor, Malaysia
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27
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Trotsyuk AA, Chen K, Hyung S, Ma KC, Henn D, Mermin-Bunnell AM, Mittal S, Padmanabhan J, Larson MR, Steele SR, Sivaraj D, Bonham CA, Noishiki C, Rodrigues M, Jiang Y, Jing S, Niu S, Chattopadhyay A, Perrault DP, Leeolou MC, Fischer KS, Gurusankar G, Choi Kussie H, Wan DC, Januszyk M, Longaker MT, Gurtner GC. Inhibiting Fibroblast Mechanotransduction Modulates Severity of Idiopathic Pulmonary Fibrosis. Adv Wound Care (New Rochelle) 2022; 11:511-523. [PMID: 34544267 DOI: 10.1089/wound.2021.0077] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Objective: Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease that affects 63 in every 100,000 Americans. Its etiology remains unknown, although inflammatory pathways appear to be important. Given the dynamic environment of the lung, we examined the significance of mechanotransduction on both inflammatory and fibrotic signaling during IPF. Innovation: Mechanotransduction pathways have not been thoroughly examined in the context of lung disease, and pharmacologic approaches for IPF do not currently target these pathways. The interplay between mechanical strain and inflammation in pulmonary fibrosis remains incompletely understood. Approach: In this study, we used conditional KO mice to block mechanotransduction by knocking out Focal Adhesion Kinase (FAK) expression in fibroblasts, followed by induction of pulmonary fibrosis using bleomycin. We examined both normal human and human IPF fibroblasts and used immunohistochemistry, quantitative real-time polymerase chain reaction, and Western Blot to evaluate the effects of FAK inhibitor (FAK-I) on modulating fibrotic and inflammatory genes. Results: Our data indicate that the deletion of FAK in mice reduces expression of fibrotic and inflammatory genes in lungs. Similarly, mechanical straining in normal human lung fibroblasts activates inflammatory and fibrotic pathways. The FAK inhibition decreases these signals but has a less effect on IPF fibroblasts as compared with normal human fibroblasts. Conclusion: Administering FAK-I at early stages of fibrosis may attenuate the FAK-mediated fibrotic response pathway in IPF, potentially mediating disease progression.
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Affiliation(s)
- Artem A Trotsyuk
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Kellen Chen
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Sun Hyung
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Kun Cathy Ma
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Dominic Henn
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Alana M Mermin-Bunnell
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Smiti Mittal
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Jagannath Padmanabhan
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Madelyn R Larson
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Sydney R Steele
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Dharshan Sivaraj
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Clark A Bonham
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Chikage Noishiki
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Melanie Rodrigues
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Yuanwen Jiang
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - Serena Jing
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Simiao Niu
- Department of Chemical Engineering, Stanford University, Stanford, California, USA
| | - Arhana Chattopadhyay
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - David P Perrault
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Melissa C Leeolou
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Katharina S Fischer
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | | | - Hudson Choi Kussie
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Derrick C Wan
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Michael Januszyk
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
| | - Michael T Longaker
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Palo Alto, California, USA
| | - Geoffrey C Gurtner
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, California, USA
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Lee CH, Hunt D, Roth JG, Chiu CC, Suhar RA, LeSavage BL, Seymour AJ, Lindsay C, Krajina B, Chen YT, Chang KH, Hsieh IC, Chu PH, Wen MS, Heilshorn SC. Tuning pro-survival effects of human induced pluripotent stem cell-derived exosomes using elastin-like polypeptides. Biomaterials 2022; 291:121864. [DOI: 10.1016/j.biomaterials.2022.121864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/28/2022]
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Pro-Inflammatory and Pro-Apoptotic Effects of the Non-Protein Amino Acid L-Azetidine-2-Carboxylic Acid in BV2 Microglial Cells. Curr Issues Mol Biol 2022; 44:4500-4516. [PMID: 36286023 PMCID: PMC9600089 DOI: 10.3390/cimb44100308] [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: 08/12/2022] [Revised: 09/14/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022] Open
Abstract
L-Azetidine-2-carboxylic acid (AZE) is a toxic non-protein coding amino acid (npAA) that is highly abundant in sugar and table beets. Due to its structural similarity with the amino acid L-proline, AZE can evade the editing process during protein assembly in eukaryotic cells and be misincorporated into L-proline-rich proteins, potentially causing protein misfolding and other detrimental effects to cells. In this study, we sought to determine if AZE treatment triggered pro-inflammatory and pro-apoptotic responses in BV2 microglial cells. BV2 microglial cells exposed to AZE at increasing concentrations (0−2000 µM) at 0, 3, 6, 12 and 24 h were assayed for cell viability (MTT) and nitric oxide release (Griess assay). Annexin V-FITC/propidium iodide (PI) staining was used to assess apoptosis. Real-time qPCR, Western blot and immunocytochemistry were used to interrogate relevant pro- and anti-inflammatory and other molecular targets of cell survival response. AZE (at concentrations > 1000 µM) significantly reduced cell viability, increased BAX/Bcl2 ratio and caused cell death. Results were mirrored by a robust increase in nitric oxide release, percentage of activated/polarised cells and expression of pro-inflammatory markers (IL-1β, IL-6, NOS2, CD68 and MHC-2a). Additionally, we found that AZE induced the expression of the extracellular matrix degrading enzyme matrix metalloproteinase 9 (MMP-9) and brain derived neurotrophic factor (BDNF), two critical regulators of microglial motility and structural plasticity. Collectively, these data indicate that AZE-induced toxicity is associated with increased pro-inflammatory activity and reduced survival in BV2 microglia. This evidence may prompt for an increased monitoring of AZE consumption by humans.
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Urbantat RM, Jelgersma C, Vajkoczy P, Brandenburg S, Acker G. Combining TMZ and SB225002 induces changes of CXCR2 and VEGFR signalling in primary human endothelial cells in vitro. Oncol Rep 2022; 48:158. [PMID: 35856448 PMCID: PMC9350968 DOI: 10.3892/or.2022.8373] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/27/2022] [Indexed: 11/20/2022] Open
Abstract
Standard of care therapy for glioblastoma (GBM) consisting of surgical removal, temozolomide (TMZ) and radiotherapy fails to cure the disease and median survival is limited to 15 months. Therapeutic approaches targeting vascular endothelial growth factor (VEGF)-mediated angiogenesis, one of the major drivers of tumour growth, have not prolonged patient survival as reported in clinical studies. Apart from VEGFR signalling, proangiogenic C-X-C motif chemokine receptor 2 (CXCR2) is of special interest as its ligands C-X-C motif chemokine ligand 2 (CXCL2) and interleukin-8 (IL8) are upregulated and associated with reduced survival in GBM patients. As CXCR2 is also expressed by endothelial cells, the aim of the present study was to elucidate the effect of combination therapy on gene and protein expression of primary human endothelial cells (HUVECs). To mimic the GBM specific CXCL2/IL8 oversupply environment [referred to as stimulation (STIM)], HUVECs were treated with a cocktail of CXCL2/IL8 and/or TMZ and/or CXCR2-antagonist SB225002 (SB). In brief, six treatment conditions were utilized: i) Control, ii) STIM (CXCL2/IL8), iii) TMZ + SB, iv) STIM + TMZ, v) STIM + SB, vi) STIM + TMZ + SB followed by either RNA-isolation and RT-qPCR for BAX, BCL2, vascular endothelial growth receptor (VEGFR)1/2, VEGF, CXCR1/2, CXCL2 and IL8 or immunofluorescence staining for VEGFR2 and CXCR2. SB and TMZ led to morphological changes of HUVECs and downregulated antiapoptotic BCL2 in vitro. In addition, gene expression of the alternative proangiogenic CXCL2/IL8/CXCR2 signalling pathway was significantly altered by the combination therapy, while the VEGF/VEGFR1/2 axis was only mildly affected. Furthermore, VEGFR2 and CXCR2 gene and protein expression regulation differed. VEGFR2 was not altered at the gene expression level, while combination therapy with TMZ and SB led to a 74% upregulation of VEGFR2 at the protein level. By contrast, CXCR2 was upregulated 5-fold by the combination therapy at the gene expression level and downregulated by 72.5% at the protein expression level. The present study provided first insights into the molecular changes of two major proangiogenic pathways in primary endothelial cells during treatment with TMZ and SB. Different gene and protein expression levels of the proangiogenic receptors CXCR2 and VEGFR2 in vitro must be taken into consideration in future studies.
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Affiliation(s)
- Ruth M Urbantat
- Department of Neurosurgery, Charité‑Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‑Universität zu Berlin, D‑10117 Berlin, Germany
| | - Claudius Jelgersma
- Department of Neurosurgery, Charité‑Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‑Universität zu Berlin, D‑10117 Berlin, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité‑Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‑Universität zu Berlin, D‑10117 Berlin, Germany
| | - Susan Brandenburg
- Department of Neurosurgery, Charité‑Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‑Universität zu Berlin, D‑10117 Berlin, Germany
| | - Gueliz Acker
- Department of Neurosurgery, Charité‑Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt‑Universität zu Berlin, D‑10117 Berlin, Germany
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Chidananda AH, Khandelwal R, Jhamkhindikar A, Pawar AD, Sharma AK, Sharma Y. Secretagogin is a Ca 2+-dependent stress-responsive chaperone that may also play a role in aggregation-based proteinopathies. J Biol Chem 2022; 298:102285. [PMID: 35870554 PMCID: PMC9425029 DOI: 10.1016/j.jbc.2022.102285] [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: 12/09/2021] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 11/17/2022] Open
Abstract
Secretagogin (SCGN) is a three-domain hexa-EF-hand Ca2+-binding protein that plays a regulatory role in the release of several hormones. SCGN is expressed largely in pancreatic β-cells, certain parts of the brain, and also in neuroendocrine tissues. The expression of SCGN is altered in several diseases, such as diabetes, cancers, and neurodegenerative disorders; however, the precise associations that closely link SCGN expression to such pathophysiologies are not known. In this work, we report that SCGN is an early responder to cellular stress, and SCGN expression is temporally upregulated by oxidative stress and heat shock. We show the overexpression of SCGN efficiently prevents cells from heat shock and oxidative damage. We further demonstrate that in the presence of Ca2+, SCGN efficiently prevents the aggregation of a broad range of model proteins in vitro. Small-angle X-ray scattering (BioSAXS) studies further reveal that Ca2+ induces the conversion of a closed compact apo-SCGN conformation into an open extended holo-SCGN conformation via multistate intermediates, consistent with the augmentation of chaperone activity of SCGN. Furthermore, isothermal titration calorimetry establishes that Ca2+ enables SCGN to bind α-synuclein and insulin, two target proteins of SCGN. Altogether, our data not only demonstrate that SCGN is a Ca2+-dependent generic molecular chaperone involved in protein homeostasis with broad substrate specificity but also elucidate the origin of its altered expression in several cancers. We describe a plausible mechanism of how perturbations in Ca2+ homeostasis and/or deregulated SCGN expression would hasten the process of protein misfolding, which is a feature of many aggregation-based proteinopathies.
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Affiliation(s)
- Amrutha H Chidananda
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India
| | - Radhika Khandelwal
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Aditya Jhamkhindikar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India
| | - Asmita D Pawar
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India; Indian Institute of Scientific and Education Research (IISER), Berhampur-760010, India
| | - Anand K Sharma
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India.
| | - Yogendra Sharma
- CSIR-Centre for Cellular and Molecular Biology (CCMB), Uppal Road, Hyderabad-500 007, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India; Indian Institute of Scientific and Education Research (IISER), Berhampur-760010, India.
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32
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Steele LA, Spiller KL, Cohen S, Rom S, Polyak B. Temporal Control over Macrophage Phenotype and the Host Response via Magnetically Actuated Scaffolds. ACS Biomater Sci Eng 2022; 8:3526-3541. [PMID: 35838679 DOI: 10.1021/acsbiomaterials.2c00373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic strain generated at the cell-material interface is critical for the engraftment of biomaterials. Mechanosensitive immune cells, macrophages regulate the host-material interaction immediately after implantation by priming the environment and remodeling ongoing regenerative processes. This study investigated the ability of mechanically active scaffolds to modulate macrophage function in vitro and in vivo. Remotely actuated magnetic scaffolds enhance the phenotype of murine classically activated (M1) macrophages, as shown by the increased expression of the M1 cell-surface marker CD86 and increased secretion of multiple M1 cytokines. When scaffolds were implanted subcutaneously into mice and treated with magnetic stimulation for 3 days beginning at either day 0 or day 5 post-implantation, the cellular infiltrate was enriched for host macrophages. Macrophage expression of the M1 marker CD86 was increased, with downstream effects on vascularization and the foreign body response. Such effects were not observed when the magnetic treatment was applied at later time points after implantation (days 12-15). These results advance our understanding of how remotely controlled mechanical cues, namely, cyclic strain, impact macrophage function and demonstrate the feasibility of using mechanically active nanomaterials to modulate the host response in vivo.
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Affiliation(s)
- Lindsay A Steele
- Department of Surgery, College of Medicine, Drexel University, 245 N. 15th Street, Philadelphia 19102, Pennsylvania, United States
| | - Kara L Spiller
- School of Biomedical Engineering, Science and Health Systems, Drexel University, 3141 Chestnut Street, Bossone 712, Philadelphia 19104, Pennsylvania, United States
| | - Smadar Cohen
- The Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, Beer Sheva Blvd. 1, Bldg. 42, Room 328, Beer-Sheva 84105, Israel
| | - Slava Rom
- Department of Pathology and Laboratory Medicine, Temple University, Philadelphia 19140, Pennsylvania, United States.,Center for Substance Abuse Research, Temple University, 3500 N. Broad Street, Medical Education and Research Building, Room 842, Philadelphia 19140, Pennsylvania, United States
| | - Boris Polyak
- Department of Surgery, College of Medicine, Drexel University, 245 N. 15th Street, Philadelphia 19102, Pennsylvania, United States
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33
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Andeen NK, Kung VL, Robertson J, Gurley SB, Avasare RS, Sitaraman S. Fibrillary Glomerulonephritis, DNAJB9, and the Unfolded Protein Response. GLOMERULAR DISEASES 2022; 2:164-175. [PMID: 36817290 PMCID: PMC9936766 DOI: 10.1159/000525542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 05/30/2022] [Indexed: 11/19/2022]
Abstract
Background Fibrillary glomerulonephritis (FGN) is found in approximately 1% of native kidney biopsies and was traditionally defined by glomerular deposition of fibrils larger than amyloid (12-24 nm diameter) composed of polyclonal IgG. Recent identification of DNAJB9 as a sensitive and specific marker of FGN has revolutionized FGN diagnosis and opened new avenues to studying FGN pathogenesis. In this review, we synthesize recent literature to provide an updated appraisal of the clinical and pathologic features of FGN, discuss diagnostic challenges and pitfalls, and propose molecular models of disease in light of DNAJB9. Summary DNAJB9 tissue assays, paraffin immunofluorescence studies, and IgG subclass testing demonstrate that FGN is distinct from other glomerular diseases with organized deposits and highlight FGN morphologic variants. Additionally, these newer techniques show that FGN is only rarely monoclonal, and patients with monoclonal FGN usually do not have a monoclonal gammopathy. DNAJB9 mutation does not appear to affect the genetic architecture of FGN; however, the accumulation of DNAJB9 in FGN deposits suggests that disease is driven, at least in part, by proteins involved in the unfolded protein response. Treatments for FGN remain empiric, with some encouraging data suggesting that rituximab-based therapy is effective and that transplantation is a good option for patients progressing to ESKD. Key Messages DNAJB9 aids in distinguishing FGN from other glomerular diseases with organized deposits. Further investigations into the role of DNAJB9 in FGN pathogenesis are necessary to better understand disease initiation and progression and to ultimately develop targeted therapies.
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Affiliation(s)
- Nicole K. Andeen
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, Portland, Oregon, USA,*Nicole K. Andeen,
| | - Vanderlene L. Kung
- Department of Pathology and Laboratory Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Josh Robertson
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Susan B. Gurley
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Rupali S. Avasare
- Division of Nephrology and Hypertension, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
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34
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Chitiashvili T, Hsu FM, Dror I, Plath K, Clark A. FGFR3 is expressed by human primordial germ cells and is repressed after meiotic initiation to form primordial oocytes. Stem Cell Reports 2022; 17:1268-1278. [PMID: 35594860 PMCID: PMC9214056 DOI: 10.1016/j.stemcr.2022.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 04/15/2022] [Accepted: 04/19/2022] [Indexed: 01/19/2023] Open
Abstract
Human germ cell development is a highly regulated process beginning soon after embryo implantation with the specification of primordial germ cells (PGCs) and ending in adulthood with the differentiation of gametes. Here, we show that fibroblast growth factor receptor 3 (FGFR3) is expressed by human PGCs during the first and second trimester, becoming repressed as PGCs differentiate into primordial oocytes. Using fluorescence-activated cell sorting (FACS) with antibodies that recognize FGFR3 followed by single-cell RNA sequencing, we show that isolating FGFR3-positive cells enriches for human PGCs. Taken together, FGFR3 could be used in future studies as a strategy to identify maturing PGCs in vitro.
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Affiliation(s)
- Tsotne Chitiashvili
- Molecular Cell and Developmental Biology Department, University of California Los Angeles, Los Angeles, CA, USA,Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA,Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA
| | - Fei-man Hsu
- Molecular Cell and Developmental Biology Department, University of California Los Angeles, Los Angeles, CA, USA
| | - Iris Dror
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Kathrin Plath
- Department of Biological Chemistry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA,Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Amander Clark
- Molecular Cell and Developmental Biology Department, University of California Los Angeles, Los Angeles, CA, USA,Molecular Biology Institute, University of California Los Angeles, Los Angeles, CA, USA,Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles, Los Angeles, CA, USA,Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, CA, USA,Corresponding author
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35
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Consequences of Chromosome Loss: Why Do Cells Need Each Chromosome Twice? Cells 2022; 11:cells11091530. [PMID: 35563836 PMCID: PMC9101035 DOI: 10.3390/cells11091530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/25/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Aneuploidy is a cellular state with an unbalanced chromosome number that deviates from the usual euploid status. During evolution, elaborate cellular mechanisms have evolved to maintain the correct chromosome content over generations. The rare errors often lead to cell death, cell cycle arrest, or impaired proliferation. At the same time, aneuploidy can provide a growth advantage under selective conditions in a stressful, frequently changing environment. This is likely why aneuploidy is commonly found in cancer cells, where it correlates with malignancy, drug resistance, and poor prognosis. To understand this “aneuploidy paradox”, model systems have been established and analyzed to investigate the consequences of aneuploidy. Most of the evidence to date has been based on models with chromosomes gains, but chromosome losses and recurrent monosomies can also be found in cancer. We summarize the current models of chromosome loss and our understanding of its consequences, particularly in comparison to chromosome gains.
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36
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Allen M, Huang BS, Notaras MJ, Lodhi A, Barrio-Alonso E, Lituma PJ, Wolujewicz P, Witztum J, Longo F, Chen M, Greening DW, Klann E, Ross ME, Liston C, Colak D. Astrocytes derived from ASD individuals alter behavior and destabilize neuronal activity through aberrant Ca 2+ signaling. Mol Psychiatry 2022; 27:2470-2484. [PMID: 35365802 PMCID: PMC9135629 DOI: 10.1038/s41380-022-01486-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/01/2022] [Accepted: 02/11/2022] [Indexed: 01/08/2023]
Abstract
The cellular mechanisms of autism spectrum disorder (ASD) are poorly understood. Cumulative evidence suggests that abnormal synapse function underlies many features of this disease. Astrocytes regulate several key neuronal processes, including the formation of synapses and the modulation of synaptic plasticity. Astrocyte abnormalities have also been identified in the postmortem brain tissue of ASD individuals. However, it remains unclear whether astrocyte pathology plays a mechanistic role in ASD, as opposed to a compensatory response. To address this, we combined stem cell culturing with transplantation techniques to determine disease-specific properties inherent to ASD astrocytes. We demonstrate that ASD astrocytes induce repetitive behavior as well as impair memory and long-term potentiation when transplanted into the healthy mouse brain. These in vivo phenotypes were accompanied by reduced neuronal network activity and spine density caused by ASD astrocytes in hippocampal neurons in vitro. Transplanted ASD astrocytes also exhibit exaggerated Ca2+ fluctuations in chimeric brains. Genetic modulation of evoked Ca2+ responses in ASD astrocytes modulates behavior and neuronal activity deficits. Thus, this study determines that astrocytes derived from ASD iPSCs are sufficient to induce repetitive behavior as well as cognitive deficit, suggesting a previously unrecognized primary role for astrocytes in ASD.
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Affiliation(s)
- Megan Allen
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Ben S Huang
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA.,Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Michael J Notaras
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Aiman Lodhi
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Estibaliz Barrio-Alonso
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Pablo J Lituma
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Paul Wolujewicz
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Jonathan Witztum
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Francesco Longo
- Center for Neural Science, New York University, New York, NY, USA
| | - Maoshan Chen
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, VIC, Australia.,Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.,Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - David W Greening
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Baker Department of Cardiometabolic Health, The University of Melbourne, Melbourne, VIC, Australia.,Baker Department of Cardiovascular Research, Translation and Implementation, La Trobe University, Melbourne, VIC, Australia.,Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Eric Klann
- Center for Neural Science, New York University, New York, NY, USA
| | - M Elizabeth Ross
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Conor Liston
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA.,Department of Psychiatry, Weill Cornell Medicine, Cornell University, New York, NY, USA
| | - Dilek Colak
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, USA. .,Gale and Ira Drukier Institute for Children's Health, Weill Cornell Medicine, Cornell University, New York, NY, USA.
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37
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Borgonetti V, Benatti C, Governa P, Isoldi G, Pellati F, Alboni S, Tascedda F, Montopoli M, Galeotti N, Manetti F, Miraldi E, Biagi M, Rigillo G. Non-psychotropic Cannabis sativa L. phytocomplex modulates microglial inflammatory response through CB2 receptors-, endocannabinoids-, and NF-κB-mediated signaling. Phytother Res 2022; 36:2246-2263. [PMID: 35393641 PMCID: PMC9325551 DOI: 10.1002/ptr.7458] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 12/27/2021] [Accepted: 01/12/2022] [Indexed: 12/11/2022]
Abstract
Cannabis sativa L. is increasingly emerging for its protective role in modulating neuroinflammation, a complex process orchestrated among others by microglia, the resident immune cells of the central nervous system. Phytocannabinoids, especially cannabidiol (CBD), terpenes, and other constituents trigger several upstream and downstream microglial intracellular pathways. Here, we investigated the molecular mechanisms of a CBD- and terpenes-enriched C. sativa extract (CSE) in an in vitro model of neuroinflammation. We evaluated the effect of CSE on the inflammatory response induced by exposure to lipopolysaccharide (LPS) in BV-2 microglial cells, compared with CBD and β-caryophyllene (CAR), CB2 receptors (CB2r) inverse and full agonist, respectively. The LPS-induced upregulation of the pro-inflammatory cytokines IL-1β, IL-6, and TNF-α was significantly attenuated by CSE and only partially by CBD, whereas CAR was ineffective. In BV-2 cells, these anti-inflammatory effects exerted by CSE phytocomplex were only partially dependent on CB2r modulation and they were mediated by the regulation of enzymes responsible for the endocannabinoids metabolism, by the inhibition of reactive oxygen species release and the modulation of JNK/p38 cascade with consequent NF-κB p65 nuclear translocation suppression. Our data suggest that C. sativa phytocomplex and its multitarget mechanism could represent a novel therapeutic strategy for neuroinflammatory-related diseases.
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Affiliation(s)
- Vittoria Borgonetti
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmacology, University of Florence, Florence, Italy
| | - Cristina Benatti
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy.,Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paolo Governa
- Department of Biotechnology, Chemistry and Pharmacy (Department of Excellence 2018-2022), University of Siena, Siena, Italy
| | | | - Federica Pellati
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvia Alboni
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy.,Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabio Tascedda
- Center for Neuroscience and Neurotechnology, University of Modena and Reggio Emilia, Modena, Italy.,Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Consorzio Interuniversitario Biotecnologie, Trieste, Italy
| | - Monica Montopoli
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Nicoletta Galeotti
- Department of Neuroscience, Psychology, Drug Research and Child Health (NEUROFARBA), Section of Pharmacology, University of Florence, Florence, Italy
| | - Fabrizio Manetti
- Department of Biotechnology, Chemistry and Pharmacy (Department of Excellence 2018-2022), University of Siena, Siena, Italy
| | - Elisabetta Miraldi
- Department of Physical Sciences, Earth and Environment, University of Siena, Siena, Italy
| | - Marco Biagi
- Department of Physical Sciences, Earth and Environment, University of Siena, Siena, Italy
| | - Giovanna Rigillo
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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Privat-Maldonado A, Verloy R, Cardenas Delahoz E, Lin A, Vanlanduit S, Smits E, Bogaerts A. Cold Atmospheric Plasma Does Not Affect Stellate Cells Phenotype in Pancreatic Cancer Tissue in Ovo. Int J Mol Sci 2022; 23:ijms23041954. [PMID: 35216069 PMCID: PMC8878510 DOI: 10.3390/ijms23041954] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/04/2022] [Accepted: 02/08/2022] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a challenging neoplastic disease, mainly due to the development of resistance to radio- and chemotherapy. Cold atmospheric plasma (CAP) is an alternative technology that can eliminate cancer cells through oxidative damage, as shown in vitro, in ovo, and in vivo. However, how CAP affects the pancreatic stellate cells (PSCs), key players in the invasion and metastasis of PDAC, is poorly understood. This study aims to determine the effect of an anti-PDAC CAP treatment on PSCs tissue developed in ovo using mono- and co-cultures of RLT-PSC (PSCs) and Mia PaCa-2 cells (PDAC). We measured tissue reduction upon CAP treatment and mRNA expression of PSC activation markers and extracellular matrix (ECM) remodelling factors via qRT-PCR. Protein expression of selected markers was confirmed via immunohistochemistry. CAP inhibited growth in Mia PaCa-2 and co-cultured tissue, but its effectiveness was reduced in the latter, which correlates with reduced ki67 levels. CAP did not alter the mRNA expression of PSC activation and ECM remodelling markers. No changes in MMP2 and MMP9 expression were observed in RLT-PSCs, but small changes were observed in Mia PaCa-2 cells. Our findings support the ability of CAP to eliminate PDAC cells, without altering the PSCs.
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Affiliation(s)
- Angela Privat-Maldonado
- PLASMANT, Chemistry Department, Faculty of Sciences, University of Antwerp, 2610 Antwerp, Belgium; (R.V.); (A.L.); (A.B.)
- Solid Tumor Immunology Group, Center for Oncological Research, Integrated Personalized and Precision Oncology Network, Department of Molecular Imaging, Pathology, Radiotherapy and Oncology, University of Antwerp, 2610 Antwerp, Belgium;
- Correspondence: ; Tel.: +32-3265-25-76
| | - Ruben Verloy
- PLASMANT, Chemistry Department, Faculty of Sciences, University of Antwerp, 2610 Antwerp, Belgium; (R.V.); (A.L.); (A.B.)
- Solid Tumor Immunology Group, Center for Oncological Research, Integrated Personalized and Precision Oncology Network, Department of Molecular Imaging, Pathology, Radiotherapy and Oncology, University of Antwerp, 2610 Antwerp, Belgium;
| | - Edgar Cardenas Delahoz
- Industrial Vision Lab InViLab, Faculty of Applied Engineering, University of Antwerp, 2610 Antwerp, Belgium; (E.C.D.); (S.V.)
| | - Abraham Lin
- PLASMANT, Chemistry Department, Faculty of Sciences, University of Antwerp, 2610 Antwerp, Belgium; (R.V.); (A.L.); (A.B.)
- Solid Tumor Immunology Group, Center for Oncological Research, Integrated Personalized and Precision Oncology Network, Department of Molecular Imaging, Pathology, Radiotherapy and Oncology, University of Antwerp, 2610 Antwerp, Belgium;
| | - Steve Vanlanduit
- Industrial Vision Lab InViLab, Faculty of Applied Engineering, University of Antwerp, 2610 Antwerp, Belgium; (E.C.D.); (S.V.)
| | - Evelien Smits
- Solid Tumor Immunology Group, Center for Oncological Research, Integrated Personalized and Precision Oncology Network, Department of Molecular Imaging, Pathology, Radiotherapy and Oncology, University of Antwerp, 2610 Antwerp, Belgium;
| | - Annemie Bogaerts
- PLASMANT, Chemistry Department, Faculty of Sciences, University of Antwerp, 2610 Antwerp, Belgium; (R.V.); (A.L.); (A.B.)
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39
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Wong DCS, Seinkmane E, Zeng A, Stangherlin A, Rzechorzek NM, Beale AD, Day J, Reed M, Peak‐Chew SY, Styles CT, Edgar RS, Putker M, O’Neill JS. CRYPTOCHROMES promote daily protein homeostasis. EMBO J 2022; 41:e108883. [PMID: 34842284 PMCID: PMC8724739 DOI: 10.15252/embj.2021108883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 11/07/2021] [Accepted: 11/09/2021] [Indexed: 11/29/2022] Open
Abstract
The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild-type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild-type controls. Most strikingly, the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating large-scale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to maintain protein and osmotic homeostasis against daily perturbation.
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Affiliation(s)
| | | | - Aiwei Zeng
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | | | - Jason Day
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
| | - Martin Reed
- MRC Laboratory of Molecular BiologyCambridgeUK
| | | | | | - Rachel S Edgar
- Department of Infectious DiseasesImperial CollegeLondonUK
| | - Marrit Putker
- MRC Laboratory of Molecular BiologyCambridgeUK
- Present address:
Crown BioscienceUtrechtthe Netherlands
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40
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Abstract
Multiplexed enhanced protein dynamic mass spectrometry (mePROD MS) enables robust quantification of translation in cell culture. Tandem mass tags (TMT) are combined with pulsed stable isotope labeling in cell culture (pSILAC) to monitor newly synthesized proteins on a proteome wide scale. While approaches combining pSILAC and TMT typically require long labeling times to reach sufficient intensity of the newly synthesized peptides in the mass spectrometer, mePROD uses a carrier signal that boosts the survey scan intensity and strongly increases identification rates. Hence, this protocol provides an easy and cost-efficient method to profile proteome-wide translatome changes at a temporal resolution of minutes.
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Affiliation(s)
- Kevin Klann
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University, Frankfurt am Main, Germany.
- Frankfurt Cancer Institute, Frankfurt am Main, Germany.
- Cardio-Pulmonary Institute, Frankfurt am Main, Germany.
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41
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Schizophrenia is defined by cell-specific neuropathology and multiple neurodevelopmental mechanisms in patient-derived cerebral organoids. Mol Psychiatry 2022; 27:1416-1434. [PMID: 34789849 PMCID: PMC9095467 DOI: 10.1038/s41380-021-01316-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/03/2021] [Accepted: 09/22/2021] [Indexed: 01/02/2023]
Abstract
Due to an inability to ethically access developing human brain tissue as well as identify prospective cases, early-arising neurodevelopmental and cell-specific signatures of Schizophrenia (Scz) have remained unknown and thus undefined. To overcome these challenges, we utilized patient-derived induced pluripotent stem cells (iPSCs) to generate 3D cerebral organoids to model neuropathology of Scz during this critical period. We discovered that Scz organoids exhibited ventricular neuropathology resulting in altered progenitor survival and disrupted neurogenesis. This ultimately yielded fewer neurons within developing cortical fields of Scz organoids. Single-cell sequencing revealed that Scz progenitors were specifically depleted of neuronal programming factors leading to a remodeling of cell-lineages, altered differentiation trajectories, and distorted cortical cell-type diversity. While Scz organoids were similar in their macromolecular diversity to organoids generated from healthy controls (Ctrls), four GWAS factors (PTN, COMT, PLCL1, and PODXL) and peptide fragments belonging to the POU-domain transcription factor family (e.g., POU3F2/BRN2) were altered. This revealed that Scz organoids principally differed not in their proteomic diversity, but specifically in their total quantity of disease and neurodevelopmental factors at the molecular level. Single-cell sequencing subsequently identified cell-type specific alterations in neuronal programming factors as well as a developmental switch in neurotrophic growth factor expression, indicating that Scz neuropathology can be encoded on a cell-type-by-cell-type basis. Furthermore, single-cell sequencing also specifically replicated the depletion of BRN2 (POU3F2) and PTN in both Scz progenitors and neurons. Subsequently, in two mechanistic rescue experiments we identified that the transcription factor BRN2 and growth factor PTN operate as mechanistic substrates of neurogenesis and cellular survival, respectively, in Scz organoids. Collectively, our work suggests that multiple mechanisms of Scz exist in patient-derived organoids, and that these disparate mechanisms converge upon primordial brain developmental pathways such as neuronal differentiation, survival, and growth factor support, which may amalgamate to elevate intrinsic risk of Scz.
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42
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Ristau J, Watt K, Oertlin C, Larsson O. Polysome Fractionation for Transcriptome-Wide Studies of mRNA Translation. Methods Mol Biol 2022; 2418:223-241. [PMID: 35119669 DOI: 10.1007/978-1-0716-1920-9_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Protein synthesis and degradation determine the relationship between mRNA and corresponding protein amounts. This relationship can change in a dynamic and selective fashion when translational efficiencies of transcript subsets are altered downstream of, for example, translation factors and/or RNA binding proteins. Notably, even transcription factors such as estrogen receptor alpha (ERα) can modulate mRNA translation in a transcript-selective manner. Yet, despite ample evidence suggesting a key role for mRNA translation in shaping the proteome in health and disease, it remains largely unexplored. Here, we present a guide for the extraction of mRNA engaged in translation using polysome fractionation with linear and optimized sucrose gradients. The isolated polysome-associated RNA is then quantified, in parallel with total mRNA from the same conditions, using methods such as RNA sequencing; and the resulting data set is analyzed to derive transcriptome-wide insights into how mRNA translation is modulated. The methods we describe are applicable to cultured cells, small numbers of FACS-isolated primary cells, and small tissue samples from biobanks or animal studies. Accordingly, this approach can be applied to study in detail how ERα and other factors control gene expression by selectively modulating mRNA translation both in vitro and in vivo.
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Affiliation(s)
- Johannes Ristau
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Kathleen Watt
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Christian Oertlin
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institute, Stockholm, Sweden.
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43
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Duk MA, Gursky VV, Samsonova MG, Surkova SY. Application of Domain- and Genotype-Specific Models to Infer Post-Transcriptional Regulation of Segmentation Gene Expression in Drosophila. Life (Basel) 2021; 11:life11111232. [PMID: 34833107 PMCID: PMC8618293 DOI: 10.3390/life11111232] [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: 09/24/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
Unlike transcriptional regulation, the post-transcriptional mechanisms underlying zygotic segmentation gene expression in early Drosophila embryo have been insufficiently investigated. Condition-specific post-transcriptional regulation plays an important role in the development of many organisms. Our recent study revealed the domain- and genotype-specific differences between mRNA and the protein expression of Drosophila hb, gt, and eve genes in cleavage cycle 14A. Here, we use this dataset and the dynamic mathematical model to recapitulate protein expression from the corresponding mRNA patterns. The condition-specific nonuniformity in parameter values is further interpreted in terms of possible post-transcriptional modifications. For hb expression in wild-type embryos, our results predict the position-specific differences in protein production. The protein synthesis rate parameter is significantly higher in hb anterior domain compared to the posterior domain. The parameter sets describing Gt protein dynamics in wild-type embryos and Kr mutants are genotype-specific. The spatial discrepancy between gt mRNA and protein posterior expression in Kr mutants is well reproduced by the whole axis model, thus rejecting the involvement of post-transcriptional mechanisms. Our models fail to describe the full dynamics of eve expression, presumably due to its complex shape and the variable time delays between mRNA and protein patterns, which likely require a more complex model. Overall, our modeling approach enables the prediction of regulatory scenarios underlying the condition-specific differences between mRNA and protein expression in early embryo.
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Affiliation(s)
- Maria A. Duk
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (M.A.D.); (M.G.S.)
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia;
| | - Vitaly V. Gursky
- Theoretical Department, Ioffe Institute, 194021 St. Petersburg, Russia;
| | - Maria G. Samsonova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (M.A.D.); (M.G.S.)
| | - Svetlana Yu. Surkova
- Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, Russia; (M.A.D.); (M.G.S.)
- Correspondence:
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44
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Ho JJD, Cunningham TA, Manara P, Coughlin CA, Arumov A, Roberts ER, Osteen A, Kumar P, Bilbao D, Krieger JR, Lee S, Schatz JH. Proteomics reveal cap-dependent translation inhibitors remodel the translation machinery and translatome. Cell Rep 2021; 37:109806. [PMID: 34644561 PMCID: PMC8558842 DOI: 10.1016/j.celrep.2021.109806] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/28/2021] [Accepted: 09/16/2021] [Indexed: 12/15/2022] Open
Abstract
Tactical disruption of protein synthesis is an attractive therapeutic strategy, with the first-in-class eIF4A-targeting compound zotatifin in clinical evaluation for cancer and COVID-19. The full cellular impact and mechanisms of these potent molecules are undefined at a proteomic level. Here, we report mass spectrometry analysis of translational reprogramming by rocaglates, cap-dependent initiation disruptors that include zotatifin. We find effects to be far more complex than simple “translational inhibition” as currently defined. Translatome analysis by TMT-pSILAC (tandem mass tag-pulse stable isotope labeling with amino acids in cell culture mass spectrometry) reveals myriad upregulated proteins that drive hitherto unrecognized cytotoxic mechanisms, including GEF-H1-mediated anti-survival RHOA/JNK activation. Surprisingly, these responses are not replicated by eIF4A silencing, indicating a broader translational adaptation than currently understood. Translation machinery analysis by MATRIX (mass spectrometry analysis of active translation factors using ribosome density fractionation and isotopic labeling experiments) identifies rocaglate-specific dependence on specific translation factors including eEF1ε1 that drive translatome remodeling. Our proteome-level interrogation reveals that the complete cellular response to these historical “translation inhibitors” is mediated by comprehensive translational landscape remodeling. Tactical protein synthesis inhibition is actively pursued as a cancer therapy that bypasses signaling redundancies limiting current strategies. Ho et al. show that rocaglates, first identified as inhibitors of eIF4A activity, globally reprogram cellular translation at both protein synthesis machinery and translatome levels, inducing cytotoxicity through anti-survival GEF-H1/RHOA/JNK signaling.
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Affiliation(s)
- J J David Ho
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
| | - Tyler A Cunningham
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Molecular and Cellular Pharmacology Graduate Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Paola Manara
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Caroline A Coughlin
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Medical Scientist Training Program, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Artavazd Arumov
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sheila and David Fuente Graduate Program in Cancer Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Evan R Roberts
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Ashanti Osteen
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Preet Kumar
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Daniel Bilbao
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Cancer Modeling Shared Resource, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | | | - Stephen Lee
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Jonathan H Schatz
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
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45
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Tezel G. Multiplex protein analysis for the study of glaucoma. Expert Rev Proteomics 2021; 18:911-924. [PMID: 34672220 PMCID: PMC8712406 DOI: 10.1080/14789450.2021.1996232] [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: 08/18/2021] [Accepted: 10/15/2021] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Glaucoma, a leading cause of irreversible blindness in the world, is a chronic neurodegenerative disease of multifactorial origin. Extensive research is ongoing to better understand, prevent, and treat progressive degeneration of retinal ganglion cells in glaucoma. While experimental models of glaucoma and postmortem tissues of human donors are analyzed for pathophysiological comprehension and improved treatment of this blinding disease, clinical samples of intraocular biofluids and blood collected from glaucoma patients are analyzed to identify predictive, diagnostic, and prognostic biomarkers. Multiplexing techniques for protein analysis offer a valuable approach for translational glaucoma research. AREAS COVERED This review provides an overview of the increasing applications of multiplex protein analysis for glaucoma research and also highlights current research challenges in the field and expected solutions from emerging technological advances. EXPERT OPINION Analytical techniques for multiplex analysis of proteins can help uncover neurodegenerative processes for enhanced treatment of glaucoma and can help identify molecular biomarkers for improved clinical testing and monitoring of this complex disease. This evolving field and continuously growing availability of new technologies are expected to broaden the comprehension of this complex neurodegenerative disease and speed up the progress toward new therapeutics and personalized patient care to prevent blindness from glaucoma.
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Affiliation(s)
- Gülgün Tezel
- Department of Ophthalmology, Vagelos College of Physicians and Surgeons, Columbia University, Edward S. Harkness Eye Institute, New York, NY, USA
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46
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Wijerathna-Yapa A, Signorelli S, Fenske R, Ganguly DR, Stroeher E, Li L, Pogson BJ, Duncan O, Millar AH. Autophagy mutants show delayed chloroplast development during de-etiolation in carbon limiting conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:459-477. [PMID: 34365695 DOI: 10.1111/tpj.15452] [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: 06/27/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Autophagy is a conserved catabolic process that plays an essential role under nutrient starvation conditions and influences different developmental processes. We observed that seedlings of autophagy mutants (atg2, atg5, atg7, and atg9) germinated in the dark showed delayed chloroplast development following illumination. The delayed chloroplast development was characterized by a decrease in photosynthetic and chlorophyll biosynthetic proteins, lower chlorophyll content, reduced chloroplast size, and increased levels of proteins involved in lipid biosynthesis. Confirming the biological impact of these differences, photosynthetic performance was impaired in autophagy mutants 12 h post-illumination. We observed that while gene expression for photosynthetic machinery during de-etiolation was largely unaffected in atg mutants, several genes involved in photosystem assembly were transcriptionally downregulated. We also investigated if the delayed chloroplast development could be explained by lower lipid import to the chloroplast or lower triglyceride (TAG) turnover. We observed that the limitations in the chloroplast lipid import imposed by trigalactosyldiacylglycerol1 are unlikely to explain the delay in chloroplast development. However, we found that lower TAG mobility in the triacylglycerol lipase mutant sugardependent1 significantly affected de-etiolation. Moreover, we showed that lower levels of carbon resources exacerbated the slow greening phenotype whereas higher levels of carbon resources had an opposite effect. This work suggests a lack of autophagy machinery limits chloroplast development during de-etiolation, and this is exacerbated by limited lipid turnover (lipophagy) that physically or energetically restrains chloroplast development.
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Affiliation(s)
- Akila Wijerathna-Yapa
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Santiago Signorelli
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
- Laboratorio de Bioquímica, Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Uruguay
| | - Ricarda Fenske
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Diep R Ganguly
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Elke Stroeher
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - Lei Li
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
- Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, 300071, Tianjin, PR China
| | - Barry J Pogson
- ARC Centre of Excellence in Plant Energy Biology, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Owen Duncan
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Science, The University of Western Australia, 6009, Crawley, WA, Australia
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47
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Xing S, Pai A, Wu R, Lu Y. NHS-Ester Tandem Labeling in One Pot Enables 48-Plex Quantitative Proteomics. Anal Chem 2021; 93:12827-12832. [PMID: 34529408 DOI: 10.1021/acs.analchem.1c01314] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Stable-isotope labeling strategies are extensively used for multiplex quantitative proteomics. Hybrid-isotope labeling strategies that combine the use of isotopic mass difference labeling and isobaric tags can greatly increase sample multiplexity. In this work, we present a novel hybrid-isotope labeling approach that we termed NHS-ester tandem labeling in one pot (NETLOP). We first optimized 16-plex isobaric TMTpro labeling of lysine residues followed by 2-plex or 3-plex isotopic mTRAQ labeling of peptide N-termini, both of which with commercially available NHS-ester reactive reagents. We then demonstrated the utility of the NETLOP approach by labeling HeLa cell samples and performing proof-of-principle quantitative 32-plex and 48-plex proteomic analyses, each in a single LC-MS/MS experiment. Compared to current hybrid-isotope labeling methods, our NETLOP approach requires no sample cleanup between different labeling steps to minimize sample loss, induces no retention time shifts that compromise quantification accuracy, can be adapted to other NHS-ester isotopic labeling reagents to further increase multiplexity, and is compatible with samples from any origin in a wide array of biological and clinical proteomics applications.
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Affiliation(s)
- Sansi Xing
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Akshat Pai
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Ruilin Wu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
| | - Yu Lu
- Department of Biochemistry and Biomedical Sciences, McMaster University, Michael G. DeGroote Centre for Learning and Centre, Room 5033, 1280 Main Street West, Hamilton, ON L8S 4K1, Canada
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48
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Qu Q, Cui W, Xing X, Zou R, Huang X, Wang X, Wu T, Bello-Onaghise G, Yuan S, Li Y. Rutin, A Natural Inhibitor of IGPD Protein, Partially Inhibits Biofilm Formation in Staphylococcus xylosus ATCC700404 in vitro and in vivo. Front Pharmacol 2021; 12:728354. [PMID: 34456739 PMCID: PMC8385535 DOI: 10.3389/fphar.2021.728354] [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: 06/21/2021] [Accepted: 07/31/2021] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus xylosus (S. xylosus) has become an emerging opportunistic pathogen due to its strong biofilm formation ability. Simultaneously, the biofilm of bacteria plays an important role in antibiotic resistance and chronic infection. Here, we confirmed that rutin can effectively inhibit biofilm formation in S. xylosus, of which the inhibition mechanism involves its ability to interact with imidazole glycerol phosphate dehydratase (IGPD), a key enzyme in the process of biofilm formation. We designed experiments to target IGPD and inhibited its activities against S. xylosus. Our results indicated that the activity of IGPD and the amount of histidine decreased significantly under the condition of 0.8 mg/ml rutin. Moreover, the expression of IGPD mRNA (hisB) and IGPD protein was significantly down-regulated. Meanwhile, the results from molecular dynamic simulation and Bio-layer interferometry (BLI) technique showed that rutin could bind to IGPD strongly. Additionally, in vivo studies demonstrated that rutin treatment reduced inflammation and protect mice from acute mastitis caused by S. xylosus. In summary, our findings provide new insights into the treatment of biofilm mediated persistent infections and chronic bacterial infections. It could be helpful to design next generation antibiotics to against resistant bacteria.
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Affiliation(s)
- Qianwei Qu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Wenqiang Cui
- Shenzhen Institutes of Advanced Technology, University of Chinese Academy of Sciences, Beijing, China
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xiaoxu Xing
- College of Animal Science and Technology, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Rongfeng Zou
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xingyu Huang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Xiaozhen Wang
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - Tong Wu
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
| | - God’spower Bello-Onaghise
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
- Department of Animal Science, Faculty of Agriculture, University of Benin, Benin, Nigeria
| | - Shuguang Yuan
- Institute of Biomedicine and Biotechnology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yanhua Li
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China
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Overexpression of transcription factor BLIMP1/prdm1 leads to growth inhibition and enhanced secretory capacity in Chinese hamster ovary cells. Metab Eng 2021; 67:237-249. [PMID: 34265400 DOI: 10.1016/j.ymben.2021.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 06/06/2021] [Accepted: 07/07/2021] [Indexed: 01/11/2023]
Abstract
Chinese hamster ovary (CHO) cells present inherent limitations for processing and secretion of large amounts of recombinant proteins, especially for those requiring complex post-translational processing. To tackle these limitations, we engineered CHO host cells (CHOK1 and CHOS) to overexpress the transcription factor BLIMP1/prdm1 (a master regulator of the highly-secreting phenotype of antibody-producing plasma cells), generating novel CHO cell lines (referred to as CHOB). The CHOB cell lines exhibited decreased cell densities, prolonged stationary phase and arrested cell cycle in G1/G0 phase but simultaneously had significantly greater product titre for recombinant IgG1 (> 2-fold increase) coupled with a significantly greater cell-specific productivities (> 3-fold increase). We demonstrated that the improved productive phenotype of CHOB cells resulted from a series of changes to cell physiology and metabolism. CHOB cells showed a significantly greater ER size and increased protein synthesis and secretion capacity compared to control cells. In addition, CHOB cells presented a metabolic profile that favoured energy production to support increased recombinant protein production. This study indicated that a cell engineering approach based on BLIMP1 expression offers great potential for improving the secretory capacity of CHO cell hosts utilised for manufacture of recombinant biopharmaceuticals. Our findings also provides a greater understanding of the relationship between cell growth and productivity, valuable generic information for improving productive phenotypes for CHO cell lines during industrial cell line development.
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Almada M, Costa L, Fonseca B, Alves P, Braga J, Gonçalves D, Teixeira N, Correia-da-Silva G. The endocannabinoid 2-arachidonoylglycerol promotes endoplasmic reticulum stress in placental cells. Reproduction 2021; 160:171-180. [PMID: 32357311 PMCID: PMC7354702 DOI: 10.1530/rep-19-0539] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/01/2020] [Indexed: 12/19/2022]
Abstract
Proliferation, differentiation and apoptosis of trophoblast cells are required for normal placental development. Impairment of those processes may lead to pregnancy-related diseases. Disruption of endoplasmic reticulum (ER) homeostasis has been associated with several reproductive pathologies including recurrent pregnancy loss and preeclampsia. In the unfolded protein response (UPR), specific ER-stress signalling pathways are activated to restore ER homeostasis, but if the adaptive response fails, apoptosis is triggered. Protein kinase RNA-like endoplasmic reticulum kinase (PERK), inositol-requiring enzyme 1 (IRE1) and Activating transcription factor 6 (ATF6) are central players in UPR and in ER-stress-induced apoptosis, as well as downstream transcription factors, as C/EBP homologous protein (CHOP). Our previous studies have shown that the endocannabinoid 2-arachidonoylglycerol (2-AG) modulates trophoblast cell turnover. Nevertheless, the role of ER-stress on 2-AG induced apoptosis and cannabinoid signalling in trophoblast has never been addressed. In this work, we used BeWo cells and human primary cytotrophoblasts isolated from term-placenta. The expression of ER-stress markers was analysed by qRT-PCR and Western blotting. ROS generation was assessed by fluorometric methods, while apoptosis was detected by the evaluation of caspase -3/-7 activities and Poly (ADP-ribose) polymerase (PARP) cleavage. Our findings indicate that 2-AG is able to induce ER-stress and apoptosis. Moreover, the eukaryotic initiation factor 2 (eIF2α)/CHOP pathway involved in ER-stress-induced apoptosis is triggered through a mechanism dependent on cannabinoid receptor CB2 activation. The results bring novel insights on the importance of ER-stress and cannabinoid signalling on 2-AG mechanisms of action in placenta.
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Affiliation(s)
- Marta Almada
- UCIBIO, REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Lia Costa
- UCIBIO, REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal.,Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Bruno Fonseca
- UCIBIO, REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Patrícia Alves
- UCIBIO, REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Jorge Braga
- Departamento da Mulher e da Medicina Reprodutiva, Serviço de Obstetrícia, Centro Materno-Infantil do Norte Dr Albino Aroso, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Daniela Gonçalves
- Departamento da Mulher e da Medicina Reprodutiva, Serviço de Obstetrícia, Centro Materno-Infantil do Norte Dr Albino Aroso, Centro Hospitalar Universitário do Porto, Porto, Portugal
| | - Natércia Teixeira
- UCIBIO, REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Georgina Correia-da-Silva
- UCIBIO, REQUIMTE, Departamento de Ciências Biológicas, Laboratório de Bioquímica, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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