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Mahto FK, Bhattacharya A, Bhattacharya S. Molecular dynamics simulations shows real-time lid opening in Hsp70 chaperone. J Mol Graph Model 2024; 129:108726. [PMID: 38377794 DOI: 10.1016/j.jmgm.2024.108726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 12/12/2023] [Accepted: 02/08/2024] [Indexed: 02/22/2024]
Abstract
The stress-inducible mammalian heat shock protein Hsp70 and its bacterial orthologue DnaK are highly conserved molecular chaperones and a crucial part of the machinery responsible for protein folding and homeostasis. Hsp70 is a three-domain, 70 kDa protein that cycles between an ATP-bound state in which all three domains are securely coupled into one unit and an ADP-bound state in which they are loosely attached via a flexible interdomain linker. The Hsp70 presents an alluring novel therapeutic target since it is crucial for maintaining cellular proteostasis and is particularly crucial to cancer cells. We have performed molecular dynamics simulations of the SBD (substrate binding domain) along with the Lid domain in response to experimental efforts to identify small molecule inhibitors that impair the functioning of Hsp70. Our intent has been to characterize the motion of the SBD/Lid allosteric machinery and in, addition, to identify the effect of the PET16 molecule on this motion. Interestingly, we noticed the opening of the entire Lid domain in the apo-form of the dimer. The configuration of the open structure was very different from previously published structures (PDB 4JN4) of the open and docked conformation of the ATP bound form. MD simulations revealed the Lid to be capable of far greater dynamical excursions than has been anticipated by experimental structural biology. This is of value in future drug discovery efforts targeted to modulating Hsp70 activity. The PET16 molecule appears to be weakly bound and its effect on the dynamics of the complex is yet to be elucidated.
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Affiliation(s)
- Farindra Kumar Mahto
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
| | | | - Swati Bhattacharya
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, 400076, India.
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2
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Schönauer R, Sierks D, Boerrigter M, Jawaid T, Caroff L, Audrezet MP, Friedrich A, Shaw M, Degenhardt J, Forberger M, de Fallois J, Bläker H, Bergmann C, Gödiker J, Schindler P, Schlevogt B, Müller RU, Berg T, Patterson I, Griffiths WJ, Sayer JA, Popp B, Torres VE, Hogan MC, Somlo S, Watnick TJ, Nevens F, Besse W, Cornec-Le Gall E, Harris PC, Drenth JPH, Halbritter J. Sex, Genotype, and Liver Volume Progression as Risk of Hospitalization Determinants in Autosomal Dominant Polycystic Liver Disease. Gastroenterology 2024; 166:902-914. [PMID: 38101549 DOI: 10.1053/j.gastro.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND & AIMS Autosomal dominant polycystic liver disease is a rare condition with a female preponderance, based mainly on pathogenic variants in 2 genes, PRKCSH and SEC63. Clinically, autosomal dominant polycystic liver disease is characterized by vast heterogeneity, ranging from asymptomatic to highly symptomatic hepatomegaly. To date, little is known about the prediction of disease progression at early stages, hindering clinical management, genetic counseling, and the design of randomized controlled trials. To improve disease prognostication, we built a consortium of European and US centers to recruit the largest cohort of patients with PRKCSH and SEC63 liver disease. METHODS We analyzed an international multicenter cohort of 265 patients with autosomal dominant polycystic liver disease harboring pathogenic variants in PRKCSH or SEC63 for genotype-phenotype correlations, including normalized age-adjusted total liver volumes and polycystic liver disease-related hospitalization (liver event) as primary clinical end points. RESULTS Classifying individual total liver volumes into predefined progression groups yielded predictive risk discrimination for future liver events independent of sex and underlying genetic defects. In addition, disease severity, defined by age at first liver event, was considerably more pronounced in female patients and patients with PRKCSH variants than in those with SEC63 variants. A newly developed sex-gene score was effective in distinguishing mild, moderate, and severe disease, in addition to imaging-based prognostication. CONCLUSIONS Both imaging and clinical genetic scoring have the potential to inform patients about the risk of developing symptomatic disease throughout their lives. The combination of female sex, germline PRKCSH alteration, and rapid total liver volume progression is associated with the greatest odds of polycystic liver disease-related hospitalization.
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Affiliation(s)
- Ria Schönauer
- Department of Nephrology and Internal Intensive Care Medicine, Charité Universitätsmedizin Berlin (corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany; Division of Nephrology, Department of Internal Medicine, University of Leipzig Medical Center, Leipzig, Germany
| | - Dana Sierks
- Division of Nephrology, Department of Internal Medicine, University of Leipzig Medical Center, Leipzig, Germany; Department of Pediatric Surgery, Universitätsklinikum Leipzig, Leipzig, Germany
| | - Melissa Boerrigter
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tabinda Jawaid
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Lea Caroff
- University of Brest, Institut National de la Santé et de la Recherche Médicale, UMR 1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Brest, France; Centre Hospitalier Universitaire Brest, Service de Néphrologie, Centre de Référence Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Brest, France
| | - Marie-Pierre Audrezet
- Centre Hospitalier Universitaire Brest, Service de Génétique Moléculaire, Brest, France
| | - Anja Friedrich
- Medizinische Genetik Mainz, Limbach Genetics, Mainz, Germany
| | - Melissa Shaw
- Departments of Internal Medicine and Nephrology, Yale University School of Medicine, New Haven, Connecticut
| | - Jan Degenhardt
- Department 2 of Internal Medicine, University of Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Mirjam Forberger
- Department of Pathology, University of Leipzig Medical Center, Leipzig, Germany
| | - Jonathan de Fallois
- Division of Nephrology, Department of Internal Medicine, University of Leipzig Medical Center, Leipzig, Germany
| | - Hendrik Bläker
- Department of Pathology, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Juliana Gödiker
- Department of Internal Medicine B, University Hospital Münster, Münster, Germany
| | | | - Bernhard Schlevogt
- Department of Internal Medicine B, University Hospital Münster, Münster, Germany; Department of Gastroenterology, Medical Center Osnabrück, Osnabrück, Germany
| | - Roman-U Müller
- Department 2 of Internal Medicine, University of Cologne, Faculty of Medicine, University Hospital Cologne, Cologne, Germany; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD) University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Thomas Berg
- Division of Hepatology, Department of Medicine II, University of Leipzig Medical Center, Leipzig, Germany
| | - Ilse Patterson
- Department of Radiology, Cambridge University Hospitals, Cambridge, United Kingdom
| | - William J Griffiths
- Department of Hepatology, Cambridge Liver Unit, Cambridge University Hospitals, Cambridge, United Kingdom
| | - John A Sayer
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom; Renal Services, Newcastle upon Tyne National Health Service Foundation Trust, Newcastle upon Tyne, United Kingdom; National Institute for Health Research Newcastle Biomedical Research Centre, Newcastle upon Tyne, United Kingdom
| | - Bernt Popp
- Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Center of Functional Genomics, Berlin, Germany
| | - Vicente E Torres
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Marie C Hogan
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Stefan Somlo
- Departments of Internal Medicine and Nephrology, Yale University School of Medicine, New Haven, Connecticut
| | - Terry J Watnick
- Department of Medicine, University of Maryland School of Medicine, Baltimore, Maryland
| | - Frederik Nevens
- Department of Hepatology and Liver Transplantation Unit, University Hospitals Katholieke Universiteit Leuven, Leuven, Belgium
| | - Whitney Besse
- Departments of Internal Medicine and Nephrology, Yale University School of Medicine, New Haven, Connecticut
| | - Emilie Cornec-Le Gall
- University of Brest, Institut National de la Santé et de la Recherche Médicale, UMR 1078, Génétique, Génomique Fonctionnelle et Biotechnologies, Brest, France; Centre Hospitalier Universitaire Brest, Service de Néphrologie, Centre de Référence Maladies Rénales Héréditaires de l'Enfant et de l'Adulte, Brest, France
| | - Peter C Harris
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, Minnesota
| | - Joost P H Drenth
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Jan Halbritter
- Department of Nephrology and Internal Intensive Care Medicine, Charité Universitätsmedizin Berlin (corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin), Berlin, Germany; Division of Nephrology, Department of Internal Medicine, University of Leipzig Medical Center, Leipzig, Germany.
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Litberg TJ, Horowitz S. Roles of Nucleic Acids in Protein Folding, Aggregation, and Disease. ACS Chem Biol 2024; 19:809-823. [PMID: 38477936 DOI: 10.1021/acschembio.3c00695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
The role of nucleic acids in protein folding and aggregation is an area of continued research, with relevance to understanding both basic biological processes and disease. In this review, we provide an overview of the trajectory of research on both nucleic acids as chaperones and their roles in several protein misfolding diseases. We highlight key questions that remain on the biophysical and biochemical specifics of how nucleic acids have large effects on multiple proteins' folding and aggregation behavior and how this pertains to multiple protein misfolding diseases.
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Affiliation(s)
- Theodore J Litberg
- Department of Chemistry & Biochemistry and The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80208, United States
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Center for Synthetic Biology, Northwestern University, Evanston, Illinois 60208, United States
| | - Scott Horowitz
- Department of Chemistry & Biochemistry and The Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado 80208, United States
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4
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Sarva H, Rodriguez-Porcel F, Rivera F, Gonzalez CD, Barkan S, Tripathi S, Gatto E, Ruiz PG. The role of genetics in the treatment of dystonia with deep brain stimulation: Systematic review and Meta-analysis. J Neurol Sci 2024; 459:122970. [PMID: 38520940 DOI: 10.1016/j.jns.2024.122970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/15/2024] [Accepted: 03/17/2024] [Indexed: 03/25/2024]
Abstract
BACKGROUND Dystonia is a movement disorder characterized by sustained or intermittent muscle contractions that lead to involuntary postures or repetitive movements. Genetic mutations are being increasingly recognized as a cause of dystonia. Deep brain stimulation (DBS) is one of the limited treatment options available. However, there are varying reports on its efficacy in genetic dystonias. This systematic review of the characteristics of genetic dystonias treated with DBS and their outcomes aims to aid in the evaluation of eligibility for such treatment. METHODS We performed a PUBMED search of all papers related to genetic dystonias and DBS up until April 2022. In addition to performing a systematic review, we also performed a meta-analysis to assess the role of the mutation on DBS response. We included cases that had a confirmed genetic mutation and DBS along with pre-and post-operative BFMDRS. RESULTS Ninety-one reports met our inclusion criteria and from them, 235 cases were analyzed. Based on our analysis DYT-TOR1A dystonia had the best evidence for DBS response and Rapid-Onset Dystonia Parkinsonism was among the least responsive to DBS. CONCLUSION While our report supports the role of genetics in DBS selection and response, it is limited by the rarity of the individual genetic conditions, the reliance on case reports and case series, and the limited ability to obtain genetic testing on a large scale in real-time as opposed to retrospectively as in many cases.
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Affiliation(s)
- Harini Sarva
- Parkinson's Disease and Movement Disorders Institute, Weill Cornell Medicine, 428 E72nd Street, Suite 400, NY, NY 10021, USA.
| | | | - Francisco Rivera
- CEMIC University Institute, School of Medicine, Department of Pharmacology, Buenos Aires, Argentina
| | - Claudio Daniel Gonzalez
- CEMIC University Institute, School of Medicine, Department of Pharmacology, Buenos Aires, Argentina
| | - Samantha Barkan
- Parkinson's Disease and Movement Disorders Institute, Weill Cornell Medicine, 428 E72nd Street, Suite 400, NY, NY 10021, USA
| | - Susmit Tripathi
- Parkinson's Disease and Movement Disorders Institute, Weill Cornell Medicine, 428 E72nd Street, Suite 400, NY, NY 10021, USA
| | - Emilia Gatto
- Instituto de Neurociencias Buenos Aires, INEBA, Facultad de Medicina, Universidad de Buenos Aires, Argentina
| | - Pedro Garcia Ruiz
- Movement Disorders Unit, Department of Neurology, Fundacion Jimenez Diaz, Universidad Autónoma de Madrid, Madrid, Spain
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5
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Wang L, Kumar R, Winblad B, Pavlov PF. Structure-based discovery of small molecule inhibitors of FKBP51-Hsp90 protein-protein interaction. Eur J Med Chem 2024; 270:116356. [PMID: 38579621 DOI: 10.1016/j.ejmech.2024.116356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/07/2024]
Abstract
The heat shock protein 90 kDa (Hsp90) molecular chaperone machinery is responsible for the folding and activation of hundreds of important clients such as kinases, steroid hormone receptors, transcription factors, etc. This process is dynamically regulated in an ATP-dependent manner by Hsp90 co-chaperones including a group of tetratricopeptide (TPR) motif proteins that bind to the C-terminus of Hsp90. Among these TPR containing co-chaperones, FK506-binding protein 51 kDa (FKBP51) is reported to play an important role in stress-related pathologies, psychiatric disorders, Alzheimer's disease, and cancer, making FKBP51-Hsp90 interaction a potential therapeutic target. In this study, we report identification of potent and selective inhibitors of FKBP51-Hsp90 protein-protein interaction using a structure-based virtual screening approach. Upon in vitro evaluation, the identified hits show a considerable degree of selectivity towards FKBP51 over other TPR proteins, particularly for highly homologous FKBP52. Tyr355 of FKBP51 emerged as an important contributor to inhibitor's specificity. Additionally, we demonstrate the impact of these inhibitors on cellular energy metabolism, and neurite outgrowth, which are subjects of FKBP51 regulation. Overall, the results from this study highlight a novel pharmacological approach towards regulation of FKBP51 function and more generally, Hsp90 function via its interaction with TPR co-chaperones.
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Affiliation(s)
- Lisha Wang
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden.
| | - Rajnish Kumar
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden; Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (BHU), 221005, Varanasi, India.
| | - Bengt Winblad
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden; Theme Inflammation and Aging, Karolinska University Hospital, 14186, Huddinge, Sweden
| | - Pavel F Pavlov
- Department of Neurobiology, Care Sciences and Society, Division of Neurogeriatrics, Karolinska Institutet, 17164, Solna, Sweden
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Cao M, Cui B. Clinically relevant plasma proteome for adiposity depots: evidence from systematic mendelian randomization and colocalization analyses. Cardiovasc Diabetol 2024; 23:126. [PMID: 38614964 PMCID: PMC11016216 DOI: 10.1186/s12933-024-02222-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/31/2024] [Indexed: 04/15/2024] Open
Abstract
BACKGROUND The accumulation of visceral and ectopic fat comprise a major cause of cardiometabolic diseases. However, novel drug targets for reducing unnecessary visceral and ectopic fat are still limited. Our study aims to provide a comprehensive investigation of the causal effects of the plasma proteome on visceral and ectopic fat using Mendelian randomization (MR) approach. METHODS We performed two-sample MR analyses based on five large genome-wide association study (GWAS) summary statistics of 2656 plasma proteins, to screen for causal associations of these proteins with traits of visceral and ectopic fat in over 30,000 participants of European ancestry, as well as to assess mediation effects by risk factors of outcomes. The colocalization analysis was conducted to examine whether the identified proteins and outcomes shared casual variants. RESULTS Genetically predicted levels of 14 circulating proteins were associated with visceral and ectopic fat (P < 4.99 × 10- 5, at a Bonferroni-corrected threshold). Colocalization analysis prioritized ten protein targets that showed effect on outcomes, including FST, SIRT2, DNAJB9, IL6R, CTSA, RGMB, PNLIPRP1, FLT4, PPY and IL6ST. MR analyses revealed seven risk factors for visceral and ectopic fat (P < 0.0024). Furthermore, the associations of CTSA, DNAJB9 and IGFBP1 with primary outcomes were mediated by HDL-C and SHBG. Sensitivity analyses showed little evidence of pleiotropy. CONCLUSIONS Our study identified candidate proteins showing putative causal effects as potential therapeutic targets for visceral and ectopic fat accumulation and outlined causal pathways for further prevention of downstream cardiometabolic diseases.
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Affiliation(s)
- Min Cao
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Bin Cui
- Department of Endocrine and Metabolic Diseases, Shanghai Institute of Endocrine and Metabolic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai National Clinical Research Center for Metabolic Diseases, Key Laboratory for Endocrine and Metabolic Diseases of the National Health Commission of the PR China, Shanghai Key Laboratory for Endocrine Tumor, State Key Laboratory of Medical Genomics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Higashi K, Sonoda Y, Kaku N, Fujii F, Yamashita F, Lee S, Tocan V, Ebihara G, Matsuoka W, Tetsuhara K, Sonoda M, Chong PF, Mushimoto Y, Kojima‐Ishii K, Ishimura M, Koga Y, Fukuta A, Tsuchihashi NA, Kikuchi Y, Karashima T, Sawada T, Hotta T, Yoshimitsu M, Terazono H, Tajiri T, Nakagawa T, Sakai Y, Nakamura K, Ohga S. Rapid and long-lasting efficacy of high-dose ambroxol therapy for neuronopathic Gaucher disease: A case report and literature review. Mol Genet Genomic Med 2024; 12:e2427. [PMID: 38553911 PMCID: PMC10980885 DOI: 10.1002/mgg3.2427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 03/06/2024] [Accepted: 03/19/2024] [Indexed: 04/02/2024] Open
Abstract
Gaucher disease (GD) is a lysosomal storage disorder caused by a deficiency in the GBA1-encoded enzyme, β-glucocerebrosidase. Enzyme replacement therapy is ineffective for neuronopathic Gaucher disease (nGD). High-dose ambroxol has been administered as an alternative treatment for a group of patients with nGD. However, little is known about the clinical indication and the long-term outcome of patients after ambroxol therapy. We herein report a case of a female patient who presented with a progressive disease of GD type 2 from 11 months of age and had the pathogenic variants of p.L483P (formerly defined as p.L444P) and p.R502H (p.R463H) in GBA1. A combined treatment of imiglucerase with ambroxol started improving the patient's motor activity in 1 week, while it kept the long-lasting effect of preventing the deteriorating phenotype for 30 months. A literature review identified 40 patients with nGD, who had received high-dose ambroxol therapy. More than 65% of these patients favorably responded to the molecular chaperone therapy, irrespective of p.L483P homozygous, heterozygous or the other genotypes. These results highlight the long-lasting effect of ambroxol-based chaperone therapy for patients with an expanding spectrum of mutations in GBA1.
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Affiliation(s)
- Kanako Higashi
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Emergency and Critical Care CenterKyushu University HospitalFukuokaJapan
| | - Yuri Sonoda
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Noriyuki Kaku
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Emergency and Critical Care CenterKyushu University HospitalFukuokaJapan
| | - Fumihiko Fujii
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Fumiya Yamashita
- Department of PediatricsNational Hospital Organization Fukuoka Higashi Medical CenterKogaJapan
| | - Sooyoung Lee
- Department of PediatricsNational Hospital Organization Fukuoka Higashi Medical CenterKogaJapan
| | - Vlad Tocan
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Go Ebihara
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Wakato Matsuoka
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Emergency and Critical Care CenterKyushu University HospitalFukuokaJapan
| | - Kenichi Tetsuhara
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
- Emergency and Critical Care CenterKyushu University HospitalFukuokaJapan
| | - Motoshi Sonoda
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Pin Fee Chong
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yuichi Mushimoto
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kanako Kojima‐Ishii
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Masataka Ishimura
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yuhki Koga
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Atsuhisa Fukuta
- Department of Pediatric Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Nana Akagi Tsuchihashi
- Department of Otorhinolaryngology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yoshikazu Kikuchi
- Department of Otorhinolaryngology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takahito Karashima
- Department of Clinical Chemistry and Laboratory of MedicineKyushu University HospitalFukuokaJapan
| | - Takaaki Sawada
- Department of Pediatrics, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Taeko Hotta
- Department of Clinical Chemistry and Laboratory of MedicineKyushu University HospitalFukuokaJapan
| | - Makoto Yoshimitsu
- Department of Hematology and Rheumatology, Graduate School of Medical and Dental SciencesKagoshima UniversityKagoshimaJapan
| | - Hideyuki Terazono
- Department of Clinical Pharmacy and PharmacologyKagoshima University Graduate School of Medical and Dental SciencesKagoshimaJapan
| | - Tatsuro Tajiri
- Department of Pediatric Surgery, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Takashi Nakagawa
- Department of Otorhinolaryngology, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
| | - Kimitoshi Nakamura
- Department of Pediatrics, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical SciencesKyushu UniversityFukuokaJapan
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Moosavi-Movahedi F, Saboury AA, Ghasemi A, Pirhaghi M, Mamashli F, Mohammad-Zaheri M, Arghavani P, Yousefi R, Moosavi-Movahedi AA. Exploring the significance of potassium homeostasis in copper ion binding to human αB-Crystallin. Int J Biol Macromol 2024; 263:130261. [PMID: 38368978 DOI: 10.1016/j.ijbiomac.2024.130261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 02/20/2024]
Abstract
αB-Crystallin (αB-Cry) is a small heat shock protein known for its protective role, with an adaptable structure that responds to environmental changes through oligomeric dynamics. Cu(II) ions are crucial for cellular processes but excessive amounts are linked to diseases like cataracts and neurodegeneration. This study investigated how optimal and detrimental Cu(II) concentrations affect αB-Cry oligomers and their chaperone activity, within the potassium-regulated ionic-strength environment. Techniques including isothermal titration calorimetry, differential scanning calorimetry, fluorescence spectroscopy, inductively coupled plasma atomic emission spectroscopy, cyclic voltammetry, dynamic light scattering, circular dichroism, and MTT assay were employed and complemented by computational methods. Results showed that potassium ions affected αB-Cry's structure, promoting Cu(II) binding at multiple sites and scavenging ability, and inhibiting ion redox reactions. Low concentrations of Cu(II), through modifications of oligomeric interfaces, induce regulation of surface charge and hydrophobicity, resulting in an increase in chaperone activity. Subunit dynamics were regulated, maintaining stable interfaces, thereby inhibiting further aggregation and allowing the functional reversion to oligomers after stress. High Cu(II) disrupted charge/hydrophobicity balance, sewing sizable oligomers together through subunit-subunit interactions, suppressing oligomer dissociation, and reducing chaperone efficiency. This study offers insights into how Cu(II) and potassium ions influence αB-Cry, advancing our understanding of Cu(II)-related diseases.
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Affiliation(s)
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mitra Pirhaghi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Fatemeh Mamashli
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Payam Arghavani
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Reza Yousefi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Arai H, Yang Y, Baca Y, Millstein J, Denda T, Ou FS, Innocenti F, Takeda H, Kubota Y, Doi A, Horie Y, Umemoto K, Izawa N, Wang J, Battaglin F, Jayachandran P, Algaze S, Soni S, Zhang W, Goldberg RM, Hall MJ, Scott AJ, Hwang JJ, Lou E, Weinberg BA, Marshall J, Goel S, Xiu J, Michael Korn W, Venook AP, Sunakawa Y, Lenz HJ. Predictive value of CDC37 gene expression for targeted therapy in metastatic colorectal cancer. Eur J Cancer 2024; 201:113914. [PMID: 38359495 DOI: 10.1016/j.ejca.2024.113914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 01/25/2024] [Accepted: 02/04/2024] [Indexed: 02/17/2024]
Abstract
BACKGROUND CDC37 is a key determinant of client kinase recruitment to the HSP90 chaperoning system. We hypothesized that kinase-specific dependency on CDC37 alters the efficacy of targeted therapies for metastatic colorectal cancer (mCRC). MATERIAL AND METHODS Two independent mCRC cohorts were analyzed to compare the survival outcomes between CDC37-high and CDC37-low patients (stratified by the median cutoff values): the CALGB/SWOG 80405 trial (226 and 207 patients receiving first-line bevacizumab- and cetuximab-containing chemotherapies, respectively) and Japanese retrospective (50 refractory patients receiving regorafenib) cohorts. A dataset of specimens submitted to a commercial CLIA-certified laboratory was utilized to characterize molecular profiles of CDC37-high (top quartile, N = 5055) and CDC37-low (bottom quartile, N = 5055) CRCs. RESULTS In the bevacizumab-treated group, CDC37-high patients showed significantly better progression-free survival (PFS) (median 13.3 vs 9.6 months, hazard ratio [HR] 0.59, 95% confidence interval [CI] 0.44-0.79, p < 0.01) than CDC37-low patients. In the cetuximab-treated group, CDC37-high and CDC37-low patients had similar outcomes. In the regorafenib-treated group, CDC37-high patients showed significantly better overall survival (median 11.3 vs 6.0 months, HR 0.24, 95% CI 0.11-0.54, p < 0.01) and PFS (median 3.5 vs 1.9 months, HR 0.51, 95% CI 0.28-0.94, p = 0.03). Comprehensive molecular profiling revealed that CDC37-high CRCs were associated with higher VEGFA, FLT1, and KDR expressions and activated hypoxia signature. CONCLUSIONS CDC37-high mCRC patients derived more benefit from anti-VEGF therapies, including bevacizumab and regorafenib, but not from cetuximab. Molecular profiles suggested that such tumors were dependent on angiogenesis-relating pathways.
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Affiliation(s)
- Hiroyuki Arai
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yan Yang
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yasmine Baca
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Joshua Millstein
- Department of Population and Public Health Sciences, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Tadamichi Denda
- Department of Gastroenterology, Chiba Cancer Center, Chiba, Japan
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN, USA
| | - Federico Innocenti
- UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Hiroyuki Takeda
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yohei Kubota
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ayako Doi
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshiki Horie
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Kumiko Umemoto
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoki Izawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Jingyuan Wang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Francesca Battaglin
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Priya Jayachandran
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra Algaze
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Wu Zhang
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Michael J Hall
- Department of Clinical Genetics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Aaron James Scott
- Department of Medicine, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Jimmy J Hwang
- Department of Solid Tumor Oncology, GI Medical Oncology, Levine Cancer Institute, Charlotte, NC, USA
| | - Emil Lou
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin A Weinberg
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - John Marshall
- Ruesch Center for the Cure of Gastrointestinal Cancers, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Sanjay Goel
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Joanne Xiu
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - W Michael Korn
- Clinical & Translational Research, Medical Affairs, Caris Life Sciences, Phoenix, AZ, USA
| | - Alan P Venook
- University of California, San Francisco, San Francisco, CA, USA
| | - Yu Sunakawa
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Heinz-Josef Lenz
- Division of Medical Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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10
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Nierengarten I. Nanoscale scythe cuts molecular tethers using mechanical forces. Nature 2024; 628:269-270. [PMID: 38600266 DOI: 10.1038/d41586-024-00909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
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11
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Zhang Q, Zhang J, Lan T, He J, Lei B, Wang H, Mei Z, Lv C. Integrative analysis revealed a correlation of PIAS family genes expression with prognosis, immunomodulation and chemotherapy. Eur J Med Res 2024; 29:195. [PMID: 38528630 DOI: 10.1186/s40001-024-01795-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/13/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Protein inhibitor of activated STATs (PIAS) has pleiotropic biological effects, such as protein post-translational modification, transcriptional coregulation and gene editing. It is reported that PIAS family genes are also correlated with immune cells infiltration in cancers that highlights their unnoticed biological role in tumor progression. However, the relationship of their expression with prognosis, immune cell infiltration, tumor microenvironment, and immunotherapy in pan-cancer has been rarely reported. METHODS The multi-omics data were used to investigate the expression level of PIAS family members in pan-cancer, and the prognostic value of their expression in different tumors was analyzed by univariate Cox regression and Kaplan-Meier. Correlation analysis was used to investigate the relationship of PIAS gene expression with tumor microenvironment, immune infiltrating subtypes, stemness score and drug sensitivity. In addition, we also used wound healing and transwell assays to verify the biological effects of PIAS family gene expression on invasion and metastasis of HCC cells. RESULTS We found that PIAS family genes expression is significantly heterogeneous in tumors by multi-genomic analysis, and associated with poor prognosis in patients with multiple types of cancer. Furthermore, we also found that genetic alterations of PIAS family genes were not only common in different types of human tumors, but were also significantly associated with disease-free survival (DFS) across pan-cancer. Single-cell analysis revealed that PIAS family genes were mainly distributed in monocytes/macrophages. Additionally, we also found that their expression was associated with tumor microenvironment (including stromal cells and immune cells) and stemness score (DNAss and RNAss). Drug sensitivity analysis showed that PIAS family genes were able to predict the response to chemotherapy and immunotherapy. PIAS family genes expression is closely related to tumor metastasis, especially PIAS3. High PIAS3 expression significantly promotes the migration and invasion of liver cancer cell lines (HCC-LM3 and MHCC97-H). CONCLUSIONS Taking together, these findings contribute to determine whether the PIAS family genes are a potential oncogenic target gene, which have important contribution for the development of cancer immunotherapy.
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Affiliation(s)
- Qiqi Zhang
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Junkui Zhang
- Pharmaceutical Institute, Henan University, Kaifeng, 475004, China
| | - Tianyi Lan
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Jiayue He
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Bin Lei
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Hongnan Wang
- College of Integrative Chinese and Western Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China
| | - Zhiqiang Mei
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
| | - Chaoxiang Lv
- The Research Center for Preclinical Medicine, Southwest Medical University, Luzhou, 646000, Sichuan, China.
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12
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Žoldák G, Knappe TA, Geitner AJ, Scholz C, Dobbek H, Schmid FX, Jakob RP. Bacterial Chaperone Domain Insertions Convert Human FKBP12 into an Excellent Protein-Folding Catalyst-A Structural and Functional Analysis. Molecules 2024; 29:1440. [PMID: 38611720 PMCID: PMC11013033 DOI: 10.3390/molecules29071440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/14/2024] Open
Abstract
Many folding enzymes use separate domains for the binding of substrate proteins and for the catalysis of slow folding reactions such as prolyl isomerization. FKBP12 is a small prolyl isomerase without a chaperone domain. Its folding activity is low, but it could be increased by inserting the chaperone domain from the homolog SlyD of E. coli near the prolyl isomerase active site. We inserted two other chaperone domains into human FKBP12: the chaperone domain of SlpA from E. coli, and the chaperone domain of SlyD from Thermococcus sp. Both stabilized FKBP12 and greatly increased its folding activity. The insertion of these chaperone domains had no influence on the FKBP12 and the chaperone domain structure, as revealed by two crystal structures of the chimeric proteins. The relative domain orientations differ in the two crystal structures, presumably representing snapshots of a more open and a more closed conformation. Together with crystal structures from SlyD-like proteins, they suggest a path for how substrate proteins might be transferred from the chaperone domain to the prolyl isomerase domain.
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Affiliation(s)
- Gabriel Žoldák
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, Pavol Jozef Šafárik University in Košice, 040 11 Kosice, Slovakia
| | - Thomas A. Knappe
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Anne-Juliane Geitner
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | | | - Holger Dobbek
- Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany;
| | - Franz X. Schmid
- Laboratorium für Biochemie und Bayreuther Zentrum für Molekulare Biowissenschaften, Universität Bayreuth, 95447 Bayreuth, Germany
| | - Roman P. Jakob
- Departement Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland
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13
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Jaros SW, Florek M, Bażanów B, Panek J, Krogul-Sobczak A, Oliveira MC, Król J, Śliwińska-Hill U, Nesterov DS, Kirillov AM, Smoleński P. Silver Coordination Polymers Driven by Adamantoid Blocks for Advanced Antiviral and Antibacterial Biomaterials. ACS Appl Mater Interfaces 2024; 16:13411-13421. [PMID: 38456838 PMCID: PMC10958451 DOI: 10.1021/acsami.3c15606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/31/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]
Abstract
The development of sustainable biomaterials and surfaces to prevent the accumulation and proliferation of viruses and bacteria is highly demanded in healthcare areas. This study describes the assembly and full characterization of two new bioactive silver(I) coordination polymers (CPs) formulated as [Ag(aca)(μ-PTA)]n·5nH2O (1) and [Ag2(μ-ada)(μ3-PTA)2]n·4nH2O (2). These products were generated by exploiting a heteroleptic approach based on the use of two different adamantoid building blocks, namely 1,3,5-triaza-7-phosphaadamantane (PTA) and 1-adamantanecarboxylic (Haca) or 1,3-adamantanedicarboxylic (H2ada) acids, resulting in the assembly of 1D (1) and 3D (2). Antiviral, antibacterial, and antifungal properties of the obtained compounds were investigated in detail, followed by their incorporation as bioactive dopants (1 wt %) into hybrid biopolymers based on acid-hydrolyzed starch polymer (AHSP). The resulting materials, formulated as 1@AHSP and 2@AHSP, also featured (i) an exceptional antiviral activity against herpes simplex virus type 1 and human adenovirus (HAd-5) and (ii) a remarkable antibacterial activity against Gram-negative bacteria. Docking experiments, interaction with human serum albumin, mass spectrometry, and antioxidation studies provided insights into the mechanism of antimicrobial action. By reporting these new silver CPs driven by adamantoid building blocks and the derived starch-based materials, this study endows a facile approach to access biopolymers and interfaces capable of preventing and reducing the proliferation of a broad spectrum of different microorganisms, including bacteria, fungi, and viruses.
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Affiliation(s)
- Sabina W. Jaros
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Magdalena Florek
- Department
of Veterinary Microbiology, Wrocław
University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland
| | - Barbara Bażanów
- Department
of Veterinary Microbiology, Wrocław
University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland
| | - Jarosław Panek
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | | | - M. Conceição Oliveira
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Jarosław Król
- Department
of Veterinary Microbiology, Wrocław
University of Environmental and Life Sciences, Norwida 31, 50-375 Wrocław, Poland
| | - Urszula Śliwińska-Hill
- Faculty
of Pharmacy, Department of Basic Chemical Sciences, Wrocław Medical University, Borowska 211, 50-566 Wrocław, Poland
| | - Dmytro S. Nesterov
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Alexander M. Kirillov
- Centro
de Química Estrutural, Institute of Molecular Sciences, Departamento
de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisbon, Portugal
| | - Piotr Smoleński
- Faculty
of Chemistry, University of Wrocław, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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14
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Singh R, Kaur N, Choubey V, Dhingra N, Kaur T. Endoplasmic reticulum stress and its role in various neurodegenerative diseases. Brain Res 2024; 1826:148742. [PMID: 38159591 DOI: 10.1016/j.brainres.2023.148742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 12/07/2023] [Accepted: 12/24/2023] [Indexed: 01/03/2024]
Abstract
The Endoplasmic reticulum (ER), a critical cellular organelle, maintains cellular homeostasis by regulating calcium levels and orchestrating essential functions such as protein synthesis, folding, and lipid production. A pivotal aspect of ER function is its role in protein quality control. When misfolded proteins accumulate within the ER due to factors like protein folding chaperone dysfunction, toxicity, oxidative stress, or inflammation, it triggers the Unfolded protein response (UPR). The UPR involves the activation of chaperones like calnexin, calreticulin, glucose-regulating protein 78 (GRP78), and Glucose-regulating protein 94 (GRP94), along with oxidoreductases like protein disulphide isomerases (PDIs). Cells employ the Endoplasmic reticulum-associated degradation (ERAD) mechanism to counteract protein misfolding. ERAD disruption causes the detachment of GRP78 from transmembrane proteins, initiating a cascade involving Inositol-requiring kinase/endoribonuclease 1 (IRE1), Activating transcription factor 6 (ATF6), and Protein kinase RNA-like endoplasmic reticulum kinase (PERK) pathways. The accumulation and deposition of misfolded proteins within the cell are hallmarks of numerous neurodegenerative diseases. These aberrant proteins disrupt normal neuronal signalling and contribute to impaired cellular homeostasis, including oxidative stress and compromised protein degradation pathways. In essence, ER stress is defined as the cellular response to the accumulation of misfolded proteins in the endoplasmic reticulum, encompassing a series of signalling pathways and molecular events that aim to restore cellular homeostasis. This comprehensive review explores ER stress and its profound implications for the pathogenesis and progression of neurodegenerative diseases.
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Affiliation(s)
- Rimaljot Singh
- Department of Biophysics, Panjab University Chandigarh, India
| | - Navpreet Kaur
- Department of Biophysics, Panjab University Chandigarh, India
| | - Vinay Choubey
- Department of Pharmacology, University of Tartu, Ravila 19, 51014 Tartu, Estonia
| | - Neelima Dhingra
- University Institute of Pharmaceutical Sciences, Panjab University Chandigarh, India
| | - Tanzeer Kaur
- Department of Biophysics, Panjab University Chandigarh, India.
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15
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Cuevas-Bermúdez A, Martínez-Fernández V, Garrido-Godino AI, Jordán-Pla A, Peñate X, Martín-Expósito M, Gutiérrez G, Govind CK, Chávez S, Pelechano V, Navarro F. The association of the RSC remodeler complex with chromatin is influenced by the prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae. Biochim Biophys Acta Gene Regul Mech 2024; 1867:194995. [PMID: 37967810 DOI: 10.1016/j.bbagrm.2023.194995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/01/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023]
Abstract
The tripartite interaction between the chromatin remodeler complex RSC, RNA polymerase subunit Rpb5 and prefoldin-like Bud27 is necessary for proper RNA pol II elongation. Indeed lack of Bud27 alters this association and affects transcription elongation. This work investigates the consequences of lack of Bud27 on the chromatin association of RSC and RNA pol II, and on nucleosome positioning. Our results demonstrate that RSC binds chromatin in gene bodies and lack of Bud27 alters this association, mainly around polyA sites. This alteration impacts chromatin organization and leads to the accumulation of RNA pol II molecules around polyA sites, likely due to pausing or arrest. Our data suggest that RSC is necessary to maintain chromatin organization around those sites, and any alteration of this organization results in the widespread use of alternative polyA sites. Finally, we also find a similar molecular phenotype that occurs upon TOR inhibition with rapamycin, which suggests that alternative polyadenylation observed upon TOR inhibition is likely Bud27-dependent.
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Affiliation(s)
- Abel Cuevas-Bermúdez
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Verónica Martínez-Fernández
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Ana I Garrido-Godino
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | - Antonio Jordán-Pla
- Instituto Biotecmed, Facultad de Biológicas, Universitat de València, E-46100 Burjassot, Valencia, Spain
| | - Xenia Peñate
- Departamento de Genética, Universidad de Sevilla, Seville, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Manuel Martín-Expósito
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain
| | | | - Chhabi K Govind
- Department of Biological Sciences, Oakland University, Rochester, MI 48309, USA
| | - Sebastián Chávez
- Departamento de Genética, Universidad de Sevilla, Seville, Spain; Instituto de Biomedicina de Sevilla, Universidad de Sevilla-CSIC-Hospital Universitario V. del Rocío, Seville, Spain
| | - Vicent Pelechano
- SciLifeLab, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 65 Solna, Sweden
| | - Francisco Navarro
- Departamento de Biología Experimental-Genética, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain; Instituto Universitario de Investigación en Olivar y Aceites de Oliva, Universidad de Jaén, Paraje de las Lagunillas, s/n, E-23071, Jaén, Spain.
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16
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Dawar S, Benitez MC, Lim Y, Dite TA, Yousef JM, Thio N, Garciaz S, Jackson TD, Milne JV, Dagley LF, Phillips WA, Kumar S, Clemons NJ. Caspase-2 protects against ferroptotic cell death. Cell Death Dis 2024; 15:182. [PMID: 38429264 PMCID: PMC10907636 DOI: 10.1038/s41419-024-06560-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/05/2024] [Accepted: 02/13/2024] [Indexed: 03/03/2024]
Abstract
Caspase-2, one of the most evolutionarily conserved members of the caspase family, is an important regulator of the cellular response to oxidative stress. Given that ferroptosis is suppressed by antioxidant defense pathways, such as that involving selenoenzyme glutathione peroxidase 4 (GPX4), we hypothesized that caspase-2 may play a role in regulating ferroptosis. This study provides the first demonstration of an important and unprecedented function of caspase-2 in protecting cancer cells from undergoing ferroptotic cell death. Specifically, we show that depletion of caspase-2 leads to the downregulation of stress response genes including SESN2, HMOX1, SLC7A11, and sensitizes mutant-p53 cancer cells to cell death induced by various ferroptosis-inducing compounds. Importantly, the canonical catalytic activity of caspase-2 is not required for its role and suggests that caspase-2 regulates ferroptosis via non-proteolytic interaction with other proteins. Using an unbiased BioID proteomics screen, we identified novel caspase-2 interacting proteins (including heat shock proteins and co-chaperones) that regulate cellular responses to stress. Finally, we demonstrate that caspase-2 limits chaperone-mediated autophagic degradation of GPX4 to promote the survival of mutant-p53 cancer cells. In conclusion, we document a novel role for caspase-2 as a negative regulator of ferroptosis in cells with mutant p53. Our results provide evidence for a novel function of caspase-2 in cell death regulation and open potential new avenues to exploit ferroptosis in cancer therapy.
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Affiliation(s)
- Swati Dawar
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Mariana C Benitez
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yoon Lim
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5001, Australia
| | - Toby A Dite
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Jumana M Yousef
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Niko Thio
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Sylvain Garciaz
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
| | - Thomas D Jackson
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Julia V Milne
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Laura F Dagley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Wayne A Phillips
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Surgery (St Vincent's Hospital), The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sharad Kumar
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, 5001, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Nicholas J Clemons
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, 3010, Australia.
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17
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Bican R, Goddard V, Abreu N, Peifer D, Basinger A, Sveda M, Tanner K, de Los Reyes EC. Developmental Skills and Neurorehabilitation for Children With Batten Disease: A Retrospective Chart Review of a Comprehensive Batten Clinic. Pediatr Neurol 2024; 152:107-114. [PMID: 38242022 DOI: 10.1016/j.pediatrneurol.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND Batten disease is a rare, progressive neurogenetic disorder composed of 13 genotypes that often presents in childhood. Children present with seizures, vision loss, and developmental regression. Neurorehabilitation services (i.e., physical therapy, occupational therapy, and speech-language therapy) can help improve the quality of life for children and their families. Owing to the rarity of Batten disease, there are no standardized clinical recommendations or outcome assessments. To describe developmental profiles, current dose of neurorehabilitation, and outcome assessments used clinically for children diagnosed with Batten disease. METHODS Electronic medical records of 70 children with Batten disease (subtypes n = 5 CLN1; n = 25 CLN2; n = 23 CLN3; n = 17 CLN6) were reviewed (7.0 ± 3.4 years). Descriptive statistics were used to describe clinical features, developmental skills, dose of neurorehabilitation, and outcome assessment use. RESULTS Across CLN subtypes, most children experienced vision impairments (61%) and seizures (68%). Most children demonstrated delays in fine motor (65%), gross motor (80%), cognitive (63%), and language skills (83%). The most common frequency of neurorehabilitation was weekly (42% to 43%). Two standardized outcome assessments were used to track developmental outcomes: Peabody Developmental Motor Scales, second edition (30% of children completed this assessment) and Preschool Language Scales, fifth edition (27.4% of children completed this assessment). CONCLUSIONS Neurorehabilitation professionals should understand the clinical features and prognosis for children with Batten disease. The child's clinical features and family preferences should guide the rehabilitation plan of care. Future work needs to be completed to define dosing parameters and validate outcome assessments for neurorehabilitation services.
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Affiliation(s)
- Rachel Bican
- Division of Physical Therapy, Ohio University, Athens, Ohio.
| | - Virginia Goddard
- Division of Clinical Therapies, Nationwide Children's Hospital, Columbus, Ohio
| | - Nicolas Abreu
- Division of Neurology, Nationwide Children's Hospital, Columbus, Ohio
| | - Danielle Peifer
- Division of Clinical Therapies, Nationwide Children's Hospital, Columbus, Ohio
| | - Andrea Basinger
- Division of Clinical Therapies, Nationwide Children's Hospital, Columbus, Ohio
| | - Michelle Sveda
- Division of Clinical Therapies, Nationwide Children's Hospital, Columbus, Ohio
| | - Kelly Tanner
- Division of Clinical Therapies, Nationwide Children's Hospital, Columbus, Ohio
| | - Emily C de Los Reyes
- Division of Neurology, Nationwide Children's Hospital, Nationwide Children's Hospital Batten Disease Center for Excellence, The Ohio State University, Columbus, Ohio
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18
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Koushki M, Amiri-Dashatan N, Rezaei-Tavirani M, Robati RM, Fateminasab F, Rahimi S, Razzaghi Z, Farahani M. Screening the critical protein subnetwork to delineate potential mechanisms and protective agents associated with arsenic-induced cutaneous squamous cell carcinoma: A toxicogenomic study. Food Chem Toxicol 2024; 185:114451. [PMID: 38219847 DOI: 10.1016/j.fct.2024.114451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/01/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
Recent studies show that complex mechanisms are involved in arsenic-induced malignant transformation of cells. This study aimed to decipher molecular mechanisms associated with arsenic-induced cutaneous squamous cell carcinoma (cSCC) and suggest potential protective factors. RNA-seq-based differentially expressed genes between arsenic-exposed human keratinocytes (HaCaT) and controls were used to construct a protein-protein interaction (PPI) network and discover critical subnetwork-based mechanisms. Protective compounds against arsenic toxicity were determined and their target interactions in the core sub-network were identified by the comparative toxicogenomic database (CTD). The binding affinity between the effective factor and target was calculated by molecular docking. A total of 15 key proteins were screened out as critical arsenic-responsive subnetwork (FN1, IL-1A, CCN2, PECAM1, FGF5, EDN1, FGF1, PXDN, DNAJB9, XBP1, ERN1, PDIA4, DNAJB11, FOS, PDIA6) and 7 effective protective agents were identified (folic acid, quercetin, zinc, acetylcysteine, methionine, catechin, selenium). The GeneMANIA predicted detailed interactions of the subnetwork and revealed terms related to unfolded protein response as the main processes. FN1, IL1A and CCN2, as top significant genes, had good docking affinity with folic acid and quercetin, as selected key compounds. Integration of gene expression and protein-protein interaction related to arsenic exposure in cSCC explored the potential mechanisms and protective agents.
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Affiliation(s)
- Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Nasrin Amiri-Dashatan
- Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mostafa Rezaei-Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Reza M Robati
- Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Department of Dermatology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Fateminasab
- Department of Physical Chemistry, Faculty of Chemistry, University of Mazandaran, Babolsar, 47416-95447, Iran
| | - Shadi Rahimi
- Division of Systems and Synthetic Biology, Department of Life Sciences, Chalmers University of Technology, SE-41296, Gothenburg, Sweden
| | - Zahra Razzaghi
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Farahani
- Skin Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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19
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Beyeler R, Jordan M, Dorner L, He B, Cyrklaff M, Roques M, Stanway R, Frischknecht F, Heussler V. Putative prefoldin complex subunit 5 of Plasmodium berghei is crucial for microtubule formation and parasite development in the mosquito. Mol Microbiol 2024; 121:481-496. [PMID: 38009402 DOI: 10.1111/mmi.15196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/11/2023] [Accepted: 11/01/2023] [Indexed: 11/28/2023]
Abstract
Plasmodium sporozoite development in and egress from oocysts in the Anopheles mosquito remains largely enigmatic. In a previously performed high-throughput knockout screen, the putative subunit 5 of the prefoldin complex (PbPCS5, PBANKA_0920100) was identified as essential for parasite development during mosquito and liver stage development. Here we generated and analyzed a PbPCS5 knockout parasite line during its development in the mosquito. Interestingly, PbPCS5 deletion does not significantly affect oocyst formation but leads to a growth defect resulting in aberrantly shaped sporozoites. Sporozoites produced in the absence of PbPCS5 were thinner, markedly elongated, and did, in most cases, not contain a nucleus. Sporozoites contained fewer subpellicular microtubules, which reached deep into the sporoblast during sporogony where they contacted and indented nuclei. These aberrantly shaped sporozoites did not reach the salivary glands, and we, therefore, conclude that PbPCS5 is essential for sporogony and the life cycle progression of the parasite during its mosquito stage.
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Affiliation(s)
- Raphael Beyeler
- Institute of Cell Biology, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Melanie Jordan
- Integrative Parasitology, Center for Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Lilian Dorner
- Integrative Parasitology, Center for Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Buyuan He
- Integrative Parasitology, Center for Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Marek Cyrklaff
- Integrative Parasitology, Center for Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
| | - Magali Roques
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Rebecca Stanway
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, University of Heidelberg Medical School, Heidelberg, Germany
- German Center for Infection Research, DZIF Partner Site Heidelberg, Heidelberg, Germany
| | - Volker Heussler
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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20
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Christou E, Kotsia A, Tziouvas K, Filias P, Patsoura A. A Rare Case of COVID-19 Related Acute Necrotizing Encephalopathy With the RANBP2 Mutation in a Pediatric Patient. Pediatr Infect Dis J 2024; 43:e84-e86. [PMID: 38091492 DOI: 10.1097/inf.0000000000004215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Acute necrotizing encephalopathy (ANE) is a rare childhood neurological disorder. The familiar type of ANE (ANE1) is associated with a mutation in the RANBP2 gene. Both SARS-CoV-2 and RANBP2 mutations are responsible for the manifestation of a hyper-inflammatory response that invades the central nervous system and plays a key role in the rapid progression of encephalopathy.
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Affiliation(s)
| | | | | | - Panagiotis Filias
- Department of Neurosurgery, General Children's Hospital "Panagiotis and Aglaia Kyriakou", Athens, Greece
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21
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Heins-Marroquin U, Singh RR, Perathoner S, Gavotto F, Merino Ruiz C, Patraskaki M, Gomez-Giro G, Kleine Borgmann F, Meyer M, Carpentier A, Warmoes MO, Jäger C, Mittelbronn M, Schwamborn JC, Cordero-Maldonado ML, Crawford AD, Schymanski EL, Linster CL. CLN3 deficiency leads to neurological and metabolic perturbations during early development. Life Sci Alliance 2024; 7:e202302057. [PMID: 38195117 PMCID: PMC10776888 DOI: 10.26508/lsa.202302057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024] Open
Abstract
Juvenile neuronal ceroid lipofuscinosis (or Batten disease) is an autosomal recessive, rare neurodegenerative disorder that affects mainly children above the age of 5 yr and is most commonly caused by mutations in the highly conserved CLN3 gene. Here, we generated cln3 morphants and stable mutant lines in zebrafish. Although neither morphant nor mutant cln3 larvae showed any obvious developmental or morphological defects, behavioral phenotyping of the mutant larvae revealed hyposensitivity to abrupt light changes and hypersensitivity to pro-convulsive drugs. Importantly, in-depth metabolomics and lipidomics analyses revealed significant accumulation of several glycerophosphodiesters (GPDs) and cholesteryl esters, and a global decrease in bis(monoacylglycero)phosphate species, two of which (GPDs and bis(monoacylglycero)phosphates) were previously proposed as potential biomarkers for CLN3 disease based on independent studies in other organisms. We could also demonstrate GPD accumulation in human-induced pluripotent stem cell-derived cerebral organoids carrying a pathogenic variant for CLN3 Our models revealed that GPDs accumulate at very early stages of life in the absence of functional CLN3 and highlight glycerophosphoinositol and BMP as promising biomarker candidates for pre-symptomatic CLN3 disease.
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Affiliation(s)
- Ursula Heins-Marroquin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Randolph R Singh
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- https://ror.org/00hj8s172 Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Simon Perathoner
- Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Floriane Gavotto
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carla Merino Ruiz
- Institut d'Investigació Sanitària Pere Virgili, Tarragona, Spain
- Biosfer Teslab SL, Reus, Spain
| | - Myrto Patraskaki
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Gemma Gomez-Giro
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Felix Kleine Borgmann
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Melanie Meyer
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Anaïs Carpentier
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
| | - Marc O Warmoes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Christian Jäger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Michel Mittelbronn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- National Center of Pathology (NCP), Laboratoire national de santé (LNS), Dudelange, Luxembourg
- Department of Oncology (DONC), Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Dudelange, Luxembourg
- Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Life Science and Medicine (DLSM), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Jens C Schwamborn
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Alexander D Crawford
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
- Department of Preclinical Sciences and Pathology, Norwegian University of Life Sciences (NMBU), Ås, Norway
- Institute for Orphan Drug Discovery, Bremerhaven, Germany
| | - Emma L Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | - Carole L Linster
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
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22
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Lauer SM, Omar MH, Golkowski MG, Kenerson HL, Lee KS, Pascual BC, Lim HC, Forbush K, Smith FD, Gordan JD, Ong SE, Yeung RS, Scott JD. Recruitment of BAG2 to DNAJ-PKAc scaffolds promotes cell survival and resistance to drug-induced apoptosis in fibrolamellar carcinoma. Cell Rep 2024; 43:113678. [PMID: 38236773 PMCID: PMC10964278 DOI: 10.1016/j.celrep.2024.113678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/23/2023] [Accepted: 01/02/2024] [Indexed: 01/30/2024] Open
Abstract
The DNAJ-PKAc fusion kinase is a defining feature of fibrolamellar carcinoma (FLC). FLC tumors are notoriously resistant to standard chemotherapies, with aberrant kinase activity assumed to be a contributing factor. By combining proximity proteomics, biochemical analyses, and live-cell photoactivation microscopy, we demonstrate that DNAJ-PKAc is not constrained by A-kinase anchoring proteins. Consequently, the fusion kinase phosphorylates a unique array of substrates, including proteins involved in translation and the anti-apoptotic factor Bcl-2-associated athanogene 2 (BAG2), a co-chaperone recruited to the fusion kinase through association with Hsp70. Tissue samples from patients with FLC exhibit increased levels of BAG2 in primary and metastatic tumors. Furthermore, drug studies implicate the DNAJ-PKAc/Hsp70/BAG2 axis in potentiating chemotherapeutic resistance. We find that the Bcl-2 inhibitor navitoclax enhances sensitivity to etoposide-induced apoptosis in cells expressing DNAJ-PKAc. Thus, our work indicates BAG2 as a marker for advanced FLC and a chemotherapeutic resistance factor in DNAJ-PKAc signaling scaffolds.
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Affiliation(s)
- Sophia M Lauer
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Mitchell H Omar
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Martin G Golkowski
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Heidi L Kenerson
- Department of Surgery, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Kyung-Soon Lee
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Bryan C Pascual
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Huat C Lim
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Katherine Forbush
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - F Donelson Smith
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - John D Gordan
- Division of Hematology and Oncology, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Shao-En Ong
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA
| | - Raymond S Yeung
- Department of Surgery, University of Washington Medical Center, Seattle, WA 98195, USA
| | - John D Scott
- Department of Pharmacology, University of Washington Medical Center, Seattle, WA 98195, USA.
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23
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Nothnick WB, Cui W, Falcone T, Graham A. Prefoldin-5 Expression Is Elevated in Eutopic and Ectopic Endometriotic Epithelium and Modulates Endometriotic Epithelial Cell Proliferation and Migration In Vitro. Int J Mol Sci 2024; 25:2390. [PMID: 38397067 PMCID: PMC10888559 DOI: 10.3390/ijms25042390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
Endometriosis is a common disease among women of reproductive age in which endometrial tissue grows in ectopic localizations, primarily within the pelvic cavity. These ectopic "lesions" grow as well as migrate and invade underlying tissues. Despite the prevalence of the disease, an understanding of factors that contribute to these cellular attributes remains poorly understood. Prefoldin-5 (PFDN5) has been associated with both aberrant cell proliferation and migration, but a potential role in endometriosis is unknown. As such, the purpose of this study was to examine PFDN5 expression in endometriotic tissue. PFDN5 mRNA and protein were examined in ectopic (lesion) and eutopic endometrial tissue from women with endometriosis and in eutopic endometrium from those without endometriosis using qRT-PCR and immunohistochemistry, respectively, while function of PFDN5 in vitro was evaluated using cell count and migration assays. PFDN5 mRNA and protein were expressed in eutopic and ectopic endometrial tissue, predominantly in the glandular epithelium, but not in endometrium from control subjects. Expression of both mRNA and protein was variable among endometriotic eutopic and ectopic endometrial tissue but showed an overall net increase. Knockdown of PFDN5 by siRNA transfection of endometriotic epithelial 12Z cells was associated with reduced cell proliferation/survival and migration. PFDN5 is expressed in eutopic and ectopic glandular epithelium and may play a role in proliferation and migration of these cells contributing to disease pathophysiology.
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Affiliation(s)
- Warren B. Nothnick
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA;
- Department of Obstetrics and Gynecology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
- Institute for Reproductive and Developmental Sciences, Center for Reproductive Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA;
| | - Wei Cui
- Institute for Reproductive and Developmental Sciences, Center for Reproductive Sciences, University of Kansas Medical Center, Kansas City, KS 66160, USA;
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Tommaso Falcone
- Section of Reproductive Endocrinology and Infertility—Obstetrics and Gynecology Institute, Cleveland Clinic Lerner College of Medicine, Cleveland, OH 44195, USA;
| | - Amanda Graham
- Department of Cell Biology and Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA;
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24
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Tan Y, Zhu J, Hashimoto K. Autophagy-related gene model as a novel risk factor for schizophrenia. Transl Psychiatry 2024; 14:94. [PMID: 38351068 PMCID: PMC10864401 DOI: 10.1038/s41398-024-02767-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/03/2024] [Accepted: 01/10/2024] [Indexed: 02/16/2024] Open
Abstract
Autophagy, a cellular process where cells degrade and recycle their own components, has garnered attention for its potential role in psychiatric disorders, including schizophrenia (SCZ). This study aimed to construct and validate a new autophagy-related gene (ARG) risk model for SCZ. First, we analyzed differential expressions in the GSE38484 training set, identifying 4,754 differentially expressed genes (DEGs) between SCZ and control groups. Using the Human Autophagy Database (HADb) database, we cataloged 232 ARGs and pinpointed 80 autophagy-related DEGs (AR-DEGs) after intersecting them with DEGs. Subsequent analyses, including metascape gene annotation, pathway and process enrichment, and protein-protein interaction enrichment, were performed on the 80 AR-DEGs to delve deeper into their biological roles and associated molecular pathways. From this, we identified 34 candidate risk AR-DEGs (RAR-DEGs) and honed this list to final RAR-DEGs via a constructed and optimized logistic regression model. These genes include VAMP7, PTEN, WIPI2, PARP1, DNAJB9, SH3GLB1, ATF4, EIF4G1, EGFR, CDKN1A, CFLAR, FAS, BCL2L1 and BNIP3. Using these findings, we crafted a nomogram to predict SCZ risk for individual samples. In summary, our study offers deeper insights into SCZ's molecular pathogenesis and paves the way for innovative approaches in risk prediction, gene-targeted diagnosis, and community-based SCZ treatments.
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Affiliation(s)
- Yunfei Tan
- Center for Rehabilitation Medicine, Department of Psychiatry, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, 310014, Hangzhou, Zhejiang, China.
| | - Junpeng Zhu
- Center for Rehabilitation Medicine, Department of Psychiatry, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, 310014, Hangzhou, Zhejiang, China
| | - Kenji Hashimoto
- Division of Clinical Neuroscience, Chiba University Center for Forensic Mental Health, Chiba, 260-8670, Japan.
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25
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Huang MB, Brena D, Wu JY, Shelton M, Bond VC. SMR peptide antagonizes Staphylococcus aureus biofilm formation. Microbiol Spectr 2024; 12:e0258323. [PMID: 38170991 PMCID: PMC10846015 DOI: 10.1128/spectrum.02583-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024] Open
Abstract
The emergence and international dissemination of multi-drug resistant Staphylococcus aureus (S. aureus) strains challenge current antibiotic-based therapies, representing an urgent threat to public health worldwide. In the U.S. alone, S. aureus infections are responsible for 11,000 deaths and 500,000 hospitalizations annually. Biofilm formation is a major contributor to antibiotic tolerance and resistance-induced delays in empirical therapy with increased infection severity, frequency, treatment failure, and mortality. Developing novel treatment strategies to prevent and disrupt biofilm formation is imperative. In this article, we test the Secretion Modification Region (SMR) peptides for inhibitory effects on resistant S. aureus biofilm-forming capacity by targeting the molecular chaperone DnaK. The dose effect of SMR peptides on biofilm formation was assessed using microtiter plate methods and confocal microscopy. Interaction between the antagonist and DnaK was determined by immune precipitation with anti-Flag M2 Affinity and Western blot analysis. Increasing SMR peptide concentrations exhibited increasing blockade of S. aureus biofilm formation with significant inhibition found at 18 µM, 36 µM, and 72 µM. This work supports the potential therapeutic benefit of SMR peptides in reducing biofilm viability and could improve the susceptibility to antimicrobial agents.IMPORTANCEThe development of anti-biofilm agents is critical to restoring bacterial sensitivity, directly combating the evolution of resistance, and overall reducing the clinical burden related to pervasive biofilm-mediated infections. Thus, in this study, the SMR peptide, a novel small molecule derived from the HIV Nef protein, was preliminarily explored for anti-biofilm properties. The SMR peptide was shown to effectively target the molecular chaperone DnaK and inhibit biofilm formation in a dose-dependent manner. These results support further investigation into the mechanism of SMR peptide-mediated biofilm formation and inhibition to benefit rational drug design and the identification of therapeutic targets.
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Affiliation(s)
- Ming-Bo Huang
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Dara Brena
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
| | - Jennifer Y. Wu
- Columbia University School of International and Public Affairs, Columbia University, New York, New York, USA
| | - Martin Shelton
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
- NanoString Technologies, Inc, Seattle, Washington, USA
| | - Vincent C. Bond
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Atlanta, Georgia, USA
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26
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Straka B, Koblížek M, Splítková B, Valkovičová R, Krsková L, Kalinová M, Vlčková M, Zámečník J, Laššuthová P, Sedláčková L, Staněk D, Maulisová A, Tichý M, Kynčl M, Kršek P. A 5-year-old boy with super-refractory status epilepticus and RANBP2 variant warranting life-saving hemispherotomy. Epilepsia Open 2024; 9:424-431. [PMID: 37943122 PMCID: PMC10839359 DOI: 10.1002/epi4.12863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 11/05/2023] [Indexed: 11/10/2023] Open
Abstract
Focal cortical dysplasia (FCD) represents the most common cause of drug-resistant epilepsy in adult and pediatric surgical series. However, genetic factors contributing to severe phenotypes of FCD remain unknown. We present a patient with an exceptionally rapid development of drug-resistant epilepsy evolving in super-refractory status epilepticus. We performed multiple clinical (serial EEG, MRI), biochemical (metabolic and immunological screening), genetic (WES from blood- and brain-derived DNA), and histopathological investigations. The patient presented 1 month after an uncomplicated varicella infection. MRI was negative, as well as other biochemical and immunological examinations. Whole-exome sequencing of blood-derived DNA detected a heterozygous paternally inherited variant NM_006267.4(RANBP2):c.5233A>G p.(Ile1745Val) (Chr2[GRCh37]:g.109382228A>G), a gene associated with a susceptibility to infection-induced acute necrotizing encephalopathy. No combination of anti-seizure medication led to a sustained seizure freedom and the patient warranted induction of propofol anesthesia with high-dose intravenous midazolam and continuous respiratory support that however failed to abort seizure activity. Brain biopsy revealed FCD type IIa; this finding led to the indication of an emergency right-sided hemispherotomy that rendered the patient temporarily seizure-free. Postsurgically, he remains on antiseizure medication and experiences rare nondisabling seizures. This report highlights a uniquely severe clinical course of FCD putatively modified by the RANBP2 variant. PLAIN LANGUAGE SUMMARY: We report a case summary of a patient who came to our attention for epilepsy that could not be controlled with medication. His clinical course progressed rapidly to life-threatening status epilepticus with other unusual neurological findings. Therefore, we decided to surgically remove a piece of brain tissue in order to clarify the diagnosis that showed features of a structural brain abnormality associated with severe epilepsy, the focal cortical dysplasia. Later, a genetic variant in a gene associated with another condition, was found, and we hypothesize that this genetic variant could have contributed to this severe clinical course of our patient.
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Affiliation(s)
- Barbora Straka
- Department of Paediatric NeurologyMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Miroslav Koblížek
- Department of Pathology and Molecular MedicineMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Barbora Splítková
- Department of Paediatric NeurologyMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Radka Valkovičová
- Department of Paediatric NeurologyMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Lenka Krsková
- Department of Pathology and Molecular MedicineMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Markéta Kalinová
- Department of Pathology and Molecular MedicineMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
- Present address:
University Hospital Královské VinohradyŠrobárova 1150/50Prague 10100 34Czech Republic
| | - Markéta Vlčková
- Department of Biology and Medical GeneticsMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Josef Zámečník
- Department of Pathology and Molecular MedicineMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Petra Laššuthová
- Department of Paediatric NeurologyMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Lucie Sedláčková
- Department of Paediatric NeurologyMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - David Staněk
- Second Faculty of Medicine, Charles UniversityPragueCzech Republic
- Present address:
DNAnexus Czech RepublicPernerova 697/35, KarlínPrague186 00Czech Republic
| | - Alice Maulisová
- Department of Clinical PsychologyMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Michal Tichý
- Department of NeurosurgeryMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Martin Kynčl
- Department of RadiologyMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
| | - Pavel Kršek
- Department of Paediatric NeurologyMotol University Hospital and Second Faculty of Medicine, Charles UniversityPragueCzech Republic
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Yin P, Chen M, Rao M, Lin Y, Zhang M, Xu R, Hu X, Chen R, Chai W, Huang X, Yu H, Yao Y, Zhao Y, Li Y, Zhang L, Tang P. Deciphering Immune Landscape Remodeling Unravels the Underlying Mechanism for Synchronized Muscle and Bone Aging. Adv Sci (Weinh) 2024; 11:e2304084. [PMID: 38088531 PMCID: PMC10837389 DOI: 10.1002/advs.202304084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/30/2023] [Indexed: 02/04/2024]
Abstract
Evidence from numerous studies has revealed the synchronous progression of aging in bone and muscle; however, little is known about the underlying mechanisms. To this end, human muscles and bones are harvested and the aging-associated transcriptional dynamics of two tissues in parallel using single-cell RNA sequencing are surveyed. A subset of lipid-associated macrophages (triggering receptor expressed on myeloid cells 2, TREM2+ Macs) is identified in both aged muscle and bone. Genes responsible for muscle dystrophy and bone loss, such as secreted phosphoprotein 1 (SPP1), are also highly expressed in TREM2+ Macs, suggesting its conserved role in aging-related features. A common transition toward pro-inflammatory phenotypes in aged CD4+ T cells across tissues is also observed, activated by the nuclear factor kappa B subunit 1 (NFKB1). CD4+ T cells in aged muscle experience Th1-like differentiation, whereas, in bone, a skewing toward Th17 cells is observed. Furthermore, these results highlight that degenerated myocytes produce BAG6-containing exosomes that can communicate with Th17 cells in the bone through its receptor natural cytotoxicity triggering receptor 3 (NCR3). This communication upregulates CD6 expression in Th17 cells, which then interact with TREM2+ Macs through CD6-ALCAM signaling, ultimately stimulating the transcription of SPP1 in TREM2+ Macs. The negative correlation between serum exosomal BCL2-associated athanogene 6 (BAG6) levels and bone mineral density further supports its role in mediating muscle and bone synchronization with aging.
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Affiliation(s)
- Pengbin Yin
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Ming Chen
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Man Rao
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
- Analytical Biosciences LimitedBeijing100191China
| | - Yuan Lin
- The Department of Orthopedic SurgerySecond Affiliated Hospital of Harbin Medical UniversityHarbin150086China
| | - Mingming Zhang
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Ren Xu
- State Key Laboratory of Cellular Stress BiologySchool of MedicineFaculty of Medicine and Life SciencesXiamen UniversityXiamen361102China
| | - Xueda Hu
- Analytical Biosciences LimitedBeijing100191China
| | - Ruijing Chen
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Wei Chai
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Xiang Huang
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Haikuan Yu
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Yao Yao
- Center for Healthy Aging and Development StudiesNational School of DevelopmentPeking UniversityBeijing100871China
| | - Yali Zhao
- Central LaboratoryHainan Hospital of Chinese People's Liberation Army General HospitalSanya572013China
| | - Yi Li
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Licheng Zhang
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
| | - Peifu Tang
- Senior Department of OrthopedicsThe Fourth Medical Center of PLA General HospitalBeijing100048China
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationBeijing100048China
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Pandey AK, Trivedi V. Hemin competitively inhibits HSPA8 ATPase activity mitigating its foldase function. Arch Biochem Biophys 2024; 752:109889. [PMID: 38215959 DOI: 10.1016/j.abb.2024.109889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/19/2023] [Accepted: 01/09/2024] [Indexed: 01/14/2024]
Abstract
Hemolysis in red blood cells followed by hemoglobin degradation results in high hemin levels in the systemic circulation. Such a level of hemin is disastrous for cells and tissues and is considerably responsible for the pathologies of diseases like severe malaria. Hemin's hydrophobic chemical nature and structure allow it to bind several proteins leading to their functional modification. Such modifications in physiologically relevant proteins can have a high impact on various cellular processes. HSPA8 is a chaperone that has a protective role in oxidative stress by aiding protein refolding. Through ATPase activity assays we found that hemin can competitively inhibit ATP hydrolysis by the chaperone HSPA8. Hemin as such does not affect the structural integrity of the protein which is inferred from CD spectroscopy and Gel filtration but it hinders the ATP-dependent foldase function of the chaperone. HSPA8 was not able to cause the refolding of the model protein lysozyme in the presence of hemin. The loss in HSPA8 function was due to competition between hemin and ATP as the chaperone was able to regain the foldase function when the concentration of ATP was gradually increased with hemin present at the inhibitory concentration. In-silico studies to establish the competition for the specific binding site revealed that ATP was unable to replace hemin from the ATP binding pocket of HSPA8 and was forced to form a non-specific and unstable complex. In-vitro isothermal calorimetry revealed that the affinity of ATP for binding to HSPA8 was reduced 22 folds in the presence of hemin. The prevention of HSPA8's cytoprotective function by hemin can be a major factor contributing to the overall cellular damage during hemin accumulation in the case of severe malaria and other hemolytic diseases.
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Affiliation(s)
- Alok Kumar Pandey
- Malaria Research Group, Department of Bioscience and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, 781039, Assam, India
| | - Vishal Trivedi
- Malaria Research Group, Department of Bioscience and Bioengineering, Indian Institute of Technology-Guwahati, Guwahati, 781039, Assam, India.
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Hernández-Preciado MR, Torres-Mendoza BM, Mireles-Ramírez MA, Kobayashi-Gutiérrez A, Sánchez-Rosales NA, Vázquez-Valls E, Marquez-Pedroza J. Gene expression in multiple sclerosis during pregnancy based on integrated bioinformatics analysis. Mult Scler Relat Disord 2024; 82:105373. [PMID: 38154347 DOI: 10.1016/j.msard.2023.105373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 11/17/2023] [Accepted: 12/10/2023] [Indexed: 12/30/2023]
Abstract
BACKGROUND The modulation of the activity disease in patients with Multiple Sclerosis (MS) that occurs during pregnancy is a helpful model which could provide insight into central disease mechanisms and facilitate treatment. Therefore, the aim of the study was to identify differentially expressed genes in-silico to perform biological function pathway enrichment analysis and protein-protein interaction from pregnant women with MS. METHODS Transcriptome data were obtained from the Gene Expression Omnibus (GEO) database. We selected the microarray dataset GSE17449. The gene expression dataset contains the data of mononuclear cells from four different groups sought, including seven healthy women (H), four healthy pregnant women (HP), eight women with multiple sclerosis (WMS), and nine women nine months pregnant with multiple sclerosis (PMS). The GSEA software was employed for enrichment analysis, and the REACTOME database was used for biological pathways. The protein-protein interaction (PPI) network was plotted with STRING. The databases used to identify the connection of DEGs with different signaling pathways were KEGG and WIKIPATHWAYS. RESULTS We identified 42 differentially expressed genes in pregnant women with MS. The significant pathways included IL-10 signaling pathway, ErbB2 activates, the hemoglobin complex (HBD, HBB, HBA1, AHSP, and HBA2), IL-17 signaling pathway (LCN2 and MMP9), antigen processing and presentation, and Th17 cell differentiation (HLA-DQA1), Rap1 signaling pathway (ID1), NOD-Like receptor signaling pathway (CAMP and DEFA4), PD-L1 Signaling, Interferon gamma signaling (MMP9 and ARG1), Neutrophil degranulation (CAMP, DEFA4, ELANE, CEACAM8, S100P, CHI3L1, AZU1, OLFM4, CRISP3, LTF, ARG1, PGLYRP1, and TCN1). In the WIKIPATHWAYS set, significance was found Vitamin B12 metabolism (TCN1, HBB, and HBA2), and IL-18 signaling pathway (S100P). CONCLUSION This study can be used to understand several essential target genes and pathways identified in the present study, which may serve as feasible targets for MS therapies.
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Affiliation(s)
- Martha Rocio Hernández-Preciado
- High Specialty Medical Unit, Pediatric Hospital, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44340, Mexico; Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Blanca Miriam Torres-Mendoza
- Department of Philosophical and Methodological Disciplines, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico; Neurosciences Division, Western Biomedical Research Center (IMSS), Guadalajara 44340, Mexico
| | - Mario Alberto Mireles-Ramírez
- High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44340, Mexico
| | - Antonio Kobayashi-Gutiérrez
- High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44340, Mexico; PhD in Psychology of Health, University Health Sciences Center, University of Guadalajara, Guadalajara 44340, Mexico
| | - Nayeli Alejandra Sánchez-Rosales
- High Specialty Medical Unit, Western National Medical Center of the Mexican Institute of Social Security, Guadalajara 44340, Mexico
| | - Eduardo Vázquez-Valls
- Directorate of Generation of Professional Resources, Research, and Development, Secretary of Health, Guadalajara 44100, Mexico
| | - Jazmin Marquez-Pedroza
- Neurosciences Division, Western Biomedical Research Center (IMSS), Guadalajara 44340, Mexico.
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Li Y, Yu J, Li R, Zhou H, Chang X. New insights into the role of mitochondrial metabolic dysregulation and immune infiltration in septic cardiomyopathy by integrated bioinformatics analysis and experimental validation. Cell Mol Biol Lett 2024; 29:21. [PMID: 38291374 PMCID: PMC10826082 DOI: 10.1186/s11658-024-00536-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 01/10/2024] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND Septic cardiomyopathy (SCM), a common cardiovascular comorbidity of sepsis, has emerged among the leading causes of death in patients with sepsis. SCM's pathogenesis is strongly affected by mitochondrial metabolic dysregulation and immune infiltration disorder. However, the specific mechanisms and their intricate interactions in SCM remain unclear. This study employed bioinformatics analysis and drug discovery approaches to identify the regulatory molecules, distinct functions, and underlying interactions of mitochondrial metabolism and immune microenvironment, along with potential interventional strategies in SCM. METHODS GSE79962, GSE171546, and GSE167363 datasets were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) and module genes were identified using Limma and Weighted Correlation Network Analysis (WGCNA), followed by functional enrichment analysis. Machine learning algorithms, including support vector machine-recursive feature elimination (SVM-RFE), least absolute shrinkage and selection operator (LASSO) regression, and random forest, were used to screen mitochondria-related hub genes for early diagnosis of SCM. Subsequently, a nomogram was developed based on six hub genes. The immunological landscape was evaluated by single-sample gene set enrichment analysis (ssGSEA). We also explored the expression pattern of hub genes and distribution of mitochondria/inflammation-related pathways in UMAP plots of single-cell dataset. Potential drugs were explored using the Drug Signatures Database (DSigDB). In vivo and in vitro experiments were performed to validate the pathogenetic mechanism of SCM and the therapeutic efficacy of candidate drugs. RESULTS Six hub mitochondria-related DEGs [MitoDEGs; translocase of inner mitochondrial membrane domain-containing 1 (TIMMDC1), mitochondrial ribosomal protein S31 (MRPS31), F-box only protein 7 (FBXO7), phosphatidylglycerophosphate synthase 1 (PGS1), LYR motif containing 7 (LYRM7), and mitochondrial chaperone BCS1 (BCS1L)] were identified. The diagnostic nomogram model based on the six hub genes demonstrated high reliability and validity in both the training and validation sets. The immunological microenvironment differed between SCM and control groups. The Spearman correlation analysis revealed that hub MitoDEGs were significantly associated with the infiltration of immune cells. Upregulated hub genes showed remarkably high expression in the naive/memory B cell, CD14+ monocyte, and plasma cell subgroup, evidenced by the feature plot. The distribution of mitochondria/inflammation-related pathways varied across subgroups among control and SCM individuals. Metformin was predicted to be the most promising drug with the highest combined score. Its efficacy in restoring mitochondrial function and suppressing inflammatory responses has also been validated. CONCLUSIONS This study presents a comprehensive mitochondrial metabolism and immune infiltration landscape in SCM, providing a potential novel direction for the pathogenesis and medical intervention of SCM.
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Affiliation(s)
- Yukun Li
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China
- National Clinical Research Center for Cardiovascular Diseases, Beijing, China
| | - Jiachi Yu
- Department of Cardiology, The Sixth Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Ruibing Li
- Department of Cardiology, The Sixth Medical Center of People's Liberation Army General Hospital, Beijing, China
| | - Hao Zhou
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
- Department of Cardiology, The Sixth Medical Center of People's Liberation Army General Hospital, Beijing, China.
| | - Xing Chang
- Department of Cardiology, Beijing Anzhen Hospital, Capital Medical University, Beijing, China.
- Guanganmen Hospital, China Academy of Chinese Medical Sciences, Beijing, China.
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31
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Vogelsang TLR, Schmoeckel E, Topalov NE, Ganster F, Mahner S, Jeschke U, Vattai A. Prognostic Impact of Heat Shock Protein 90 Expression in Women Diagnosed with Cervical Cancer. Int J Mol Sci 2024; 25:1571. [PMID: 38338850 PMCID: PMC10855426 DOI: 10.3390/ijms25031571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
Heat Shock Protein 90 (HSP90), a major molecular chaperone, plays a crucial role in cell function by folding and stabilizing proteins and maintaining proteostasis. This study aimed to elucidate the prognostic impact of HSP90 in cervical cancer. We analyzed HSP90 expression using immunohistochemistry in cervical cancer tissue microarrays from 250 patients. This study investigated correlations between HSP90 expression levels and key clinical outcomes, including overall survival (OS), progression-free survival (PFS), and FIGO classification. The statistical analyses employed included the Kruskal-Wallis-H test, log-rank (Mantel-Cox), and Cox regression. Our findings indicate that high nuclear HSP90 expression is associated with improved OS, while high cytoplasmic HSP90 expression correlates with better PFS and a lower FIGO classification in cervical squamous cell carcinoma patients. These results suggest that HSP90 could serve as a positive prognostic factor in patients diagnosed with cervical squamous cell carcinoma, underlining its potential as a biomarker for patient prognosis and as a target for therapeutic strategies.
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Affiliation(s)
- Tilman L. R. Vogelsang
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 80337 Munich, Germany
- Department of Obstetrics and Gynecology, Medical University of Graz, 8010 Graz, Austria
| | - Elisa Schmoeckel
- Institute of Pathology, Faculty of Medicine, LMU Munich, 80337 Munich, Germany;
| | | | - Franziska Ganster
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Sven Mahner
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 80337 Munich, Germany
| | - Udo Jeschke
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 80337 Munich, Germany
- Department of Obstetrics and Gynecology, University Hospital Augsburg, 86156 Augsburg, Germany
| | - Aurelia Vattai
- Department of Obstetrics and Gynecology, University Hospital, LMU Munich, 80337 Munich, Germany
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Thomsen M, Lange LM, Zech M, Lohmann K. Genetics and Pathogenesis of Dystonia. Annu Rev Pathol 2024; 19:99-131. [PMID: 37738511 DOI: 10.1146/annurev-pathmechdis-051122-110756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Dystonia is a clinically and genetically highly heterogeneous neurological disorder characterized by abnormal movements and postures caused by involuntary sustained or intermittent muscle contractions. A number of groundbreaking genetic and molecular insights have recently been gained. While they enable genetic testing and counseling, their translation into new therapies is still limited. However, we are beginning to understand shared pathophysiological pathways and molecular mechanisms. It has become clear that dystonia results from a dysfunctional network involving the basal ganglia, cerebellum, thalamus, and cortex. On the molecular level, more than a handful of, often intertwined, pathways have been linked to pathogenic variants in dystonia genes, including gene transcription during neurodevelopment (e.g., KMT2B, THAP1), calcium homeostasis (e.g., ANO3, HPCA), striatal dopamine signaling (e.g., GNAL), endoplasmic reticulum stress response (e.g., EIF2AK2, PRKRA, TOR1A), autophagy (e.g., VPS16), and others. Thus, different forms of dystonia can be molecularly grouped, which may facilitate treatment development in the future.
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Affiliation(s)
- Mirja Thomsen
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Lara M Lange
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Katja Lohmann
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany;
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Yu F, Li L, Gu Y, Wang S, Zhou L, Cheng X, Jiang H, Huang Y, Zhang Y, Qian W, Li X, Liu Z. Lysine demethylase 5C inhibits transcription of prefoldin subunit 5 to activate c-Myc signal transduction and colorectal cancer progression. Mol Med 2024; 30:9. [PMID: 38216914 PMCID: PMC10785505 DOI: 10.1186/s10020-023-00775-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/22/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Lysine demethylase 5C (KDM5C) has been implicated in the development of several human cancers. This study aims to investigate the role of KDM5C in the progression of colorectal cancer (CRC) and explore the associated molecular mechanism. METHODS Bioinformatics tools were employed to predict the target genes of KDM5C in CRC. The expression levels of KDM5C and prefoldin subunit 5 (PFDN5) in CRC cells were determined by RT-qPCR and western blot assays. The interaction between KDM5C, H3K4me3, and PFDN5 was validated by chromatin immunoprecipitation. Expression and prognostic values of KDM5C and PFDN5 in CRC were analyzed in a cohort of 72 patients. The function of KDM5C/PFDN5 in c-Myc signal transduction was analyzed by luciferase assay. Silencing of KDM5C and PFDN5 was induced in CRC cell lines to analyze the cell malignant phenotype in vitro and tumorigenic activity in nude mice. RESULTS KDM5C exhibited high expression, while PFDN5 displayed low expression in CRC cells and clinical CRC samples. High KDM5C levels correlated with poor survival and unfavorable clinical presentation, whereas elevated PFDN5 correlated with improved patient outcomes. KDM5C mediated demethylation of H3K4me3 on the PFDN5 promoter, suppressing its transcription and thereby enhancing the transcriptional activity of c-Myc. KDM5C knockdown in CRC cells suppressed cell proliferation, migration and invasion, epithelial-mesenchymal transition, and tumorigenic activity while increasing autophagy and apoptosis rates. However, the malignant behavior of cells was restored by the further silencing of PFDN5. CONCLUSION This study demonstrates that KDM5C inhibits PFDN5 transcription, thereby activating c-Myc signal transduction and promoting CRC progression.
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Affiliation(s)
- Fulong Yu
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Liang Li
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, People's Republic of China
| | - Yimei Gu
- Emergency ICU, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000, Anhui, People's Republic of China
| | - Song Wang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Lianbang Zhou
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Xiaohu Cheng
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Heng Jiang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Yang Huang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Yingfeng Zhang
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China
| | - Wenbao Qian
- Department of Molecular Pathology, Hefei Da'an Medical Laboratory Co., Ltd., Hefei, 230012, Anhui, People's Republic of China
| | - Xianghua Li
- Department of Molecular Pathology, Hefei Da'an Medical Laboratory Co., Ltd., Hefei, 230012, Anhui, People's Republic of China.
| | - Zhining Liu
- Department of General Surgery, The Second Affiliated Hospital of Anhui Medical University, No. 678 Furong Road, Hefei, 230601, Anhui, People's Republic of China.
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Lu H, Yang X, Wang H. Tuning Phase Transition of Molecular Self-Assembly by Artificial Chaperones through Aromatic-Aromatic Interactions. Biomacromolecules 2024; 25:466-473. [PMID: 38147794 DOI: 10.1021/acs.biomac.3c01082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
The molecular chaperones are essential and play significant roles in controlling the protein phase transition and maintaining physiological homeostasis. However, manipulating phase transformation in biomimetic peptide self-assembly is still challenging. This work shows that an artificial chaperone modulates the energy landscape of supramolecular polymerization, thus controlling the phase transition of amyloid-like assemblies from crystals to hydrogels to solution. The absence of a chaperone allows the NapP to form crystals, while the presence of the chaperone biases the pathway to form nanofibrous hydrogels to soluble oligomers by adjusting the chaperone ratios. Mechanistic studies reveal that the aromatic-aromatic interaction is the key to trapping the molecules in a higher energy fold. Adding the chaperone relieves this restriction, lowers the energy barrier, and transforms the crystal into a hydrogel. This phase transformation can also be achieved in the macromolecular crowding environment, thus providing new insights into understanding molecular self-assembly in multiple component systems.
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Affiliation(s)
- Honglei Lu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang Province 310027, China
- Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou, Zhejiang Province 310024, China
| | - Xuejiao Yang
- Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou, Zhejiang Province 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China
| | - Huaimin Wang
- Department of Chemistry, School of Science, Institute of Natural Sciences, Westlake Institute for Advanced Study, Westlake University, No. 600 Dunyu Road, Hangzhou, Zhejiang Province 310024, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou, Zhejiang Province 310024, China
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Brima T, Freedman EG, Prinsloo KD, Augustine EF, Adams HR, Wang KH, Mink JW, Shaw LH, Mantel EP, Foxe JJ. Assessing the integrity of auditory sensory memory processing in CLN3 disease (Juvenile Neuronal Ceroid Lipofuscinosis (Batten disease)): an auditory evoked potential study of the duration-evoked mismatch negativity (MMN). J Neurodev Disord 2024; 16:3. [PMID: 38183037 PMCID: PMC10770910 DOI: 10.1186/s11689-023-09515-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
BACKGROUND We interrogated auditory sensory memory capabilities in individuals with CLN3 disease (juvenile neuronal ceroid lipofuscinosis), specifically for the feature of "duration" processing. Given decrements in auditory processing abilities associated with later-stage CLN3 disease, we hypothesized that the duration-evoked mismatch negativity (MMN) of the event related potential (ERP) would be a marker of progressively atypical cortical processing in this population, with potential applicability as a brain-based biomarker in clinical trials. METHODS We employed three stimulation rates (fast: 450 ms, medium: 900 ms, slow: 1800 ms), allowing for assessment of the sustainability of the auditory sensory memory trace. The robustness of MMN directly relates to the rate at which the regularly occurring stimulus stream is presented. As presentation rate slows, robustness of the sensory memory trace diminishes. By manipulating presentation rate, the strength of the sensory memory trace is parametrically varied, providing greater sensitivity to detect auditory cortical dysfunction. A secondary hypothesis was that duration-evoked MMN abnormalities in CLN3 disease would be more severe at slower presentation rates, resulting from greater demand on the sensory memory system. RESULTS Data from individuals with CLN3 disease (N = 21; range 6-28 years of age) showed robust MMN responses (i.e., intact auditory sensory memory processes) at the medium stimulation rate. However, at the fastest rate, MMN was significantly reduced, and at the slowest rate, MMN was not detectable in CLN3 disease relative to neurotypical controls (N = 41; ages 6-26 years). CONCLUSIONS Results reveal emerging insufficiencies in this critical auditory perceptual system in individuals with CLN3 disease.
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Affiliation(s)
- Tufikameni Brima
- The Frederick J. and Marion A. Schindler Cognitive Neurophysiology Laboratory, Department of Neuroscience and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
| | - Edward G Freedman
- The Frederick J. and Marion A. Schindler Cognitive Neurophysiology Laboratory, Department of Neuroscience and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Kevin D Prinsloo
- The Frederick J. and Marion A. Schindler Cognitive Neurophysiology Laboratory, Department of Neuroscience and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Erika F Augustine
- University of Rochester Batten Center (URBC), Department of Neurology and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
- Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Heather R Adams
- University of Rochester Batten Center (URBC), Department of Neurology and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Kuan Hong Wang
- The Frederick J. and Marion A. Schindler Cognitive Neurophysiology Laboratory, Department of Neuroscience and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Jonathan W Mink
- University of Rochester Batten Center (URBC), Department of Neurology and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Luke H Shaw
- The Frederick J. and Marion A. Schindler Cognitive Neurophysiology Laboratory, Department of Neuroscience and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Emma P Mantel
- The Frederick J. and Marion A. Schindler Cognitive Neurophysiology Laboratory, Department of Neuroscience and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - John J Foxe
- The Frederick J. and Marion A. Schindler Cognitive Neurophysiology Laboratory, Department of Neuroscience and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
- University of Rochester Batten Center (URBC), Department of Neurology and The Ernest J. Del Monte Institute for Neuroscience, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
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Katsuyama M. [Toward the complete understanding of the pathogenic mechanism of clioquinol-induced subacute myelo-optic neuropathy (SMON)]. Nihon Yakurigaku Zasshi 2024; 159:78-82. [PMID: 38432923 DOI: 10.1254/fpj.23085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2024]
Abstract
Clioquinol was extensively used as an amebicide to treat indigestion and diarrhea in the mid-1900s. However, it was withdrawn from the market in Japan because its use was epidemiologically linked to an increase in the incidence of subacute myelo-optic neuropathy (SMON). SMON is characterized by the subacute onset of sensory and motor disturbances in the lower extremities with occasional visual impairments, which are preceded by abdominal symptoms. Although pathological studies demonstrated axonopathy of the spinal cord and optic nerves, the underlying mechanisms of clioquinol toxicity have not been elucidated in detail. We previously performed a global analysis of human neuroblastoma cells using DNA chips and demonstrated that clioquinol induced 1) DNA double-strand breaks and subsequent activation of ATM/p53 signaling; 2) the expression of VGF, the precursor of neuropeptides involved in pain reactions, by inducing c-Fos; 3) the expression of interleukin-8, which is reported to be involved in intestinal inflammation, optic neuropathy, and neuropathic pain, by down-regulating GATA-2 and GATA-3. We also demonstrated that clioquinol induced zinc influx and oxidation of the copper chaperone ATOX1, leading to the impairment of the functional maturation of a copper-dependent enzyme dopamine-β-hydroxylase and the inhibition of noradrenaline biosynthesis. Thus, clioquinol-induced neurotoxicity in SMON seems to be mediated by multiple pathways.
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Tsutsuki H, Zhang T, Sawa T. [Redox Biology Involved in the Toxicity of Enterohemorrhagic Escherichia coli Toxin SubAB]. YAKUGAKU ZASSHI 2024; 144:57-60. [PMID: 38171796 DOI: 10.1248/yakushi.23-00162-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
AB5 toxins of pathogenic bacteria enter host cells and utilize the retrograde trafficking pathway to translocate to the cytoplasm and exert its pathogenesis. Cholera toxin and Shiga toxin reach the endoplasmic reticulum (ER), and the A subunit undergoes redox regulation by ER proteins to become active fragments, which pass through the ER membrane and translocate to the cytoplasm. By acting on molecular targets in the cytoplasm, the normal function of host cells are disrupted, causing diseases. ER chaperone proteins such as protein disulfide isomerase (PDI) and binding immunoglobulin protein (BiP) induce conformational changes triggered by the reduction of disulfide bonds in the A subunit. This is thought to be dependent on cysteine thiol-mediated redox regulation, but the detailed mechanism remains unclear. On the other hand, subtilase cytotoxin (SubAB), produced by enterohemorrhagic Escherichia coli (EHEC), localizes to the ER without translocating to the cytoplasm and cleaves BiP as a substrate. Therefore, it is thought that ER stress-based cytotoxicity and intestinal bleeding occur without translocating to the cytoplasm. We reported that PDI is involved in BiP cleavage through SubAB localization to the ER. Like other AB5 toxins, this indicates the involvement of redox regulation via chaperone proteins in the ER, but also suggests that SubAB does not translocate to the cytoplasm because it cleaves BiP. Although there are few reports on the redox state of ER protein thiols, it is suggested that polysulfidation, which is discussed in this symposium, may be involved.
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Affiliation(s)
- Hiroyasu Tsutsuki
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University
| | - Tianli Zhang
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University
| | - Tomohiro Sawa
- Department of Microbiology, Graduate School of Medical Sciences, Kumamoto University
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Werelusz P, Galiniak S, Mołoń M. Molecular functions of moonlighting proteins in cell metabolic processes. Biochim Biophys Acta Mol Cell Res 2024; 1871:119598. [PMID: 37774631 DOI: 10.1016/j.bbamcr.2023.119598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 09/10/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
Abstract
Moonlighting proteins have more than one physiologically significant role within one polypeptide chain. The multifunctionality of proteins was first described in 1987 by Joram Piatigorsky and Graeme Wistow. Cells can benefit from involvement of these proteins in biological processes in several ways, e.g. at the energy level. Furthermore, cells have developed a number of mechanisms to change these proteins' functions. Moonlighting proteins are found in all types of organisms, including prokaryotes, eukaryotes, and even viruses. These proteins include a variety of enzymes that serve as receptors, secreted cytokines, transcription factors, or proteasome components. Additionally, there are many combinations of functions, e.g. among receptors and transcription factors, chaperones and cytokines, as well as transcription factors within the ribosome. This work describes enzymes involved in several important metabolic processes in cells, namely cellular respiration, gluconeogenesis, the urea cycle, and pentose phosphate metabolism.
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Affiliation(s)
| | - Sabina Galiniak
- Institute of Medical Sciences, Rzeszów University, Rzeszów, Poland
| | - Mateusz Mołoń
- Institute of Biology, Rzeszów University, Rzeszów, Poland.
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Wang J, Zhang J, Guo Z, Hua H, Zhang H, Liu Y, Jiang Y. Targeting HSP70 chaperones by rhein sensitizes liver cancer to artemisinin derivatives. Phytomedicine 2024; 122:155156. [PMID: 37897861 DOI: 10.1016/j.phymed.2023.155156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/15/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023]
Abstract
BACKGROUND Liver cancer is one of common types of cancer with poor prognosis and limited therapies. Heat shock proteins (HSP) are molecular chaperones that have important roles in tumorigenesis, and emerging as therapeutic targets. Artemisinin and rhein are natural agents from Artemisia annua L. and Rheum undulatum L., respectively. Both rhein and artemisinin have anticancer effects; however, the molecular targets of rhein remain to be identified. It is also unclear whether rhein can synergize with artemisinin derivatives to inhibit liver cancer. PURPOSE We aim to identify the targets of rhein in the treatment of hepatocarcinoma and determine the effects of combining rhein and artemisinin derivatives on liver cancer cells. METHODS The targets of rhein were detected by mass spectrometry and validated by rhein-proteins interaction assays. The effects of rhein on the chaperone activity of HSP72/HSC70/GRP78 were determined by luciferase refolding assays. Cell viability and apoptosis were determined by CCK8 and flow cytometry assays. For in vivo study, xenograft tumor models were established and treated with rhein and artesunate. Tumor growth was monitored regularly. RESULTS Mass spectrometry analysis of rhein-binding proteins in HepG2 cells revealed that HSP72, HSC70 and GRP78 were more profoundly pulled down by rhein-crosslinked sepharose 4B beads compared to the control beads. Further experiments demonstrated that rhein directly interacted with HSP72/HSC70/GRP78 proteins, and inhibit their activity of refolding denatured luciferase. Meanwhile, rhein induced proteasomal degradation of HIF1α and β-catenin. Artesunate or dihydroartemisinin in combination with knockdown of both HSP72 and HSC70 significantly inhibited cell viability. The HSP70/HSC70/GRP78 inhibitors VER-155,008 and rhein phenocopied HSP72/HSC70 knockdown, synergizing with artesunate or dihydroartemisinin to inhibit hepatocarcinoma cell viability. Combinatorial treatment with rhein and artemisinin derivatives significantly induced hepatocarcinoma cell apoptosis, and inhibited tumor growth in vivo. CONCLUSIONS The current study demonstrates that rhein is a novel HSP72/HSC70/GRP78 inhibitor that suppresses the chaperone activity of HSP70s. Dual inhibition of HSP72 and HSC70 can enhance the sensitivity of hepatocarcinoma cells to artemisinin derivatives. Combined treatment with artemisinin derivative and rhein significantly inhibits hepatocarcinoma. Artemisinin derivatives in combination with dual inhibition of HSP72 and HSC70 represents a new approach to improve cancer therapy.
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Affiliation(s)
- Jiao Wang
- Cancer center, Laboratory of Oncogene, West China Hospital, Sichuan University, China; School of Basic Medicine, Chengdu University of Traditional Chinese Medicine, China
| | - Jin Zhang
- Cancer center, Laboratory of Oncogene, West China Hospital, Sichuan University, China
| | - Zeyu Guo
- Cancer center, Laboratory of Oncogene, West China Hospital, Sichuan University, China
| | - Hui Hua
- Laboratory of Stem Cell Biology, West China Hospital, Sichuan University, China
| | - Hongying Zhang
- Cancer center, Laboratory of Oncogene, West China Hospital, Sichuan University, China
| | - Yongliang Liu
- Cancer center, Laboratory of Oncogene, West China Hospital, Sichuan University, China
| | - Yangfu Jiang
- Cancer center, Laboratory of Oncogene, West China Hospital, Sichuan University, China.
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Bielawski A, Zelek-Molik A, Rafa-Zabłocka K, Kowalska M, Gruca P, Papp M, Nalepa I. Elevated Expression of HSP72 in the Prefrontal Cortex and Hippocampus of Rats Subjected to Chronic Mild Stress and Treated with Imipramine. Int J Mol Sci 2023; 25:243. [PMID: 38203414 PMCID: PMC10779295 DOI: 10.3390/ijms25010243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
The HSP70 and HSP90 family members belong to molecular chaperones that exhibit protective functions during the cellular response to stressful agents. We investigated whether the exposure of rats to chronic mild stress (CMS), a validated model of depression, affects the expression of HSP70 and HSP90 in the prefrontal cortex (PFC), hippocampus (HIP) and thalamus (Thal). Male Wistar rats were exposed to CMS for 3 or 8 weeks. The antidepressant imipramine (IMI, 10 mg/kg, i.p., daily) was introduced in the last five weeks of the long-term CMS procedure. Depressive-like behavior was verified by the sucrose consumption test. The expression of mRNA and protein was quantified by real-time PCR and Western blot, respectively. In the 8-week CMS model, stress alone elevated HSP72 and HSP90B mRNA expression in the HIP. HSP72 mRNA was increased in the PFC and HIP of rats not responding to IMI treatment vs. IMI responders. The CMS exposure increased HSP72 protein expression in the cytosolic fraction of the PFC and HIP, and this effect was diminished by IMI treatment. Our results suggest that elevated levels of HSP72 may serve as an important indicator of neuronal stress reactions accompanying depression pathology and could be a potential target for antidepressant strategy.
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Affiliation(s)
- Adam Bielawski
- Department of Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland; (A.B.); (A.Z.-M.); (K.R.-Z.); (M.K.)
| | - Agnieszka Zelek-Molik
- Department of Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland; (A.B.); (A.Z.-M.); (K.R.-Z.); (M.K.)
| | - Katarzyna Rafa-Zabłocka
- Department of Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland; (A.B.); (A.Z.-M.); (K.R.-Z.); (M.K.)
| | - Marta Kowalska
- Department of Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland; (A.B.); (A.Z.-M.); (K.R.-Z.); (M.K.)
| | - Piotr Gruca
- Behavioral Pharmacology Laboratory, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland; (P.G.); (M.P.)
| | - Mariusz Papp
- Behavioral Pharmacology Laboratory, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland; (P.G.); (M.P.)
| | - Irena Nalepa
- Department of Brain Biochemistry, Maj Institute of Pharmacology, Polish Academy of Sciences, Smętna 12, 31-343 Kraków, Poland; (A.B.); (A.Z.-M.); (K.R.-Z.); (M.K.)
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Sasaki T, Kawamura M, Okuno C, Lau K, Riel J, Lee MJ, Miller C. Impact of Maternal Mediterranean-Type Diet Adherence on Microbiota Composition and Epigenetic Programming of Offspring. Nutrients 2023; 16:47. [PMID: 38201877 PMCID: PMC10780434 DOI: 10.3390/nu16010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Understanding how maternal diet affects in utero neonatal gut microbiota and epigenetic regulation may provide insight into disease origins and long-term health. The impact of Mediterranean diet pattern adherence (MDA) on fetal gut microbiome and epigenetic regulation was assessed in 33 pregnant women. Participants completed a validated food frequency questionnaire in each trimester of pregnancy; the alternate Mediterranean diet (aMED) score was applied. Umbilical cord blood, placental tissue, and neonatal meconium were collected from offspring. DNA methylation patterns were probed using the Illumnia EPICarray Methylation Chip in parturients with high versus low MDA. Meconium microbial abundance in the first 24 h after birth was identified using 16s rRNA sequencing and compared among neonates born to mothers with high and low aMED scores. Twenty-one mothers were classified as low MDA and 12 as high MDA. Pasteurellaceae and Bacteroidaceae trended towards greater abundance in the high-MDA group, as well as other short-chain fatty acid-producing species. Several differentially methylated regions varied between groups and overlapped gene regions including NCK2, SNED1, MTERF4, TNXB, HLA-DPB, BAG6, and LMO3. We identified a beneficial effect of adherence to a Mediterranean diet on fetal in utero development. This highlights the importance of dietary counseling for mothers and can be used as a guide for future studies of meconium and immuno-epigenetic modulation.
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Affiliation(s)
- Tamlyn Sasaki
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Megan Kawamura
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Chirstyn Okuno
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Kayleen Lau
- John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96813, USA
| | - Jonathan Riel
- Department of Obstetrics, Gynecology and Women’s Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96826, USA
| | - Men-Jean Lee
- Department of Obstetrics, Gynecology and Women’s Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96826, USA
| | - Corrie Miller
- Department of Obstetrics, Gynecology and Women’s Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI 96826, USA
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Iqbal M, Lewis SL, Padhye S, Jinwal UK. Updates on Aβ Processing by Hsp90, BRICHOS, and Newly Reported Distinctive Chaperones. Biomolecules 2023; 14:16. [PMID: 38254616 PMCID: PMC10812967 DOI: 10.3390/biom14010016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Alzheimer's disease (AD) is an extremely devastating neurodegenerative disease, and there is no cure for it. AD is specified as the misfolding and aggregation of amyloid-β protein (Aβ) and abnormalities in hyperphosphorylated tau protein. Current approaches to treat Alzheimer's disease have had some success in slowing down the disease's progression. However, attempts to find a cure have been largely unsuccessful, most likely due to the complexity associated with AD pathogenesis. Hence, a shift in focus to better understand the molecular mechanism of Aβ processing and to consider alternative options such as chaperone proteins seems promising. Chaperone proteins act as molecular caretakers to facilitate cellular homeostasis under standard conditions. Chaperone proteins like heat shock proteins (Hsps) serve a pivotal role in correctly folding amyloid peptides, inhibiting mitochondrial dysfunction, and peptide aggregation. For instance, Hsp90 plays a significant role in maintaining cellular homeostasis through its protein folding mechanisms. In this review, we analyze the most recent studies from 2020 to 2023 and provide updates on Aβ regulation by Hsp90, BRICHOS domain chaperone, and distinctive newly reported chaperones.
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Affiliation(s)
| | | | | | - Umesh Kumar Jinwal
- Department of Pharmaceutical Sciences, USF-Health Taneja College of Pharmacy, University of South Florida, Tampa, FL 33612, USA; (M.I.)
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Chen J, Gao G, He Y, Zhang Y, Wu H, Dai P, Zheng Q, Huang H, Weng J, Zheng Y, Huang Y. Construction and validation of a novel lysosomal signature for hepatocellular carcinoma prognosis, diagnosis, and therapeutic decision-making. Sci Rep 2023; 13:22624. [PMID: 38114725 PMCID: PMC10730614 DOI: 10.1038/s41598-023-49985-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/14/2023] [Indexed: 12/21/2023] Open
Abstract
Lysosomes is a well-recognized oncogenic driver and chemoresistance across variable cancer types, and has been associated with tumor invasiveness, metastasis, and poor prognosis. However, the significance of lysosomes in hepatocellular carcinoma (HCC) is not well understood. Lysosomes-related genes (LRGs) were downloaded from Genome Enrichment Analysis (GSEA) databases. Lysosome-related risk score (LRRS), including eight LRGs, was constructed via expression difference analysis (DEGs), univariate and LASSO-penalized Cox regression algorithm based on the TCGA cohort, while the ICGC cohort was obtained for signature validation. Based on GSE149614 Single-cell RNA sequencing data, model gene expression and liver tumor niche were further analyzed. Moreover, the functional enrichments, tumor microenvironment (TME), and genomic variation landscape between LRRSlow/LRRShigh subgroup were systematically investigated. A total of 15 Lysosomes-related differentially expressed genes (DELRGs) in HCC were detected, and then 10 prognosis DELRGs were screened out. Finally, the 8 optimal DELRGs (CLN3, GBA, CTSA, BSG, APLN, SORT1, ANXA2, and LAPTM4B) were selected to construct the LRRS prognosis signature of HCC. LRRS was considered as an independent prognostic factor and was associated with advanced clinicopathological features. LRRS also proved to be a potential marker for HCC diagnosis, especially for early-stage HCC. Then, a nomogram integrating the LRRS and clinical parameters was set up displaying great prognostic predictive performance. Moreover, patients with high LRRS showed higher tumor stemness, higher heterogeneity, and higher genomic alteration status than those in the low LRRS group and enriched in metabolism-related pathways, suggesting its underlying role in the progression and development of liver cancer. Meanwhile, the LRRS can affect the proportion of immunosuppressive cell infiltration, making it a vital immunosuppressive factor in the tumor microenvironment. Additionally, HCC patients with low LRRS were more sensitive to immunotherapy, while patients in the high LRRS group responded better to chemotherapy. Upon single-cell RNA sequencing, CLN3, GBA, and LAPTM4B were found to be specially expressed in hepatocytes, where they promoted cell progression. Finally, RT-qPCR and external datasets confirmed the mRNA expression levels of model genes. This study provided a direct links between LRRS signature and clinical characteristics, tumor microenvironment, and clinical drug-response, highlighting the critical role of lysosome in the development and treatment resistance of liver cancer, providing valuable insights into the prognosis prediction and treatment response of HCC, thereby providing valuable insights into prognostic prediction, early diagnosis, and therapeutic response of HCC.
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Affiliation(s)
- Jianlin Chen
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
- Central Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Gan Gao
- Department of Clinical Laboratory, Liuzhou Hospital, Guangzhou Women and Children's Medical Center, Liuzhou, 545616, Guangxi, China
- Guangxi Clinical Research Center for Obstetrics and Gynecology, Liuzhou, 545616, Guangxi, China
| | - Yufang He
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
| | - Yi Zhang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Haixia Wu
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
| | - Peng Dai
- Department of Anesthesiology, The First People's Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Qingzhu Zheng
- Department of Clinical Laboratory, Fujian Medical University Union Hospital, Fuzhou, 350001, China
| | - Hengbin Huang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Jiamiao Weng
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Yue Zheng
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China
| | - Yi Huang
- Shengli Clinical Medical College, Fujian Medical University, Fujian, 350001, Fuzhou, China.
- Department of Clinical Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
- Central Laboratory, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
- Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fujian, 350001, Fuzhou, China.
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He C, Gu J, Wang D, Wang K, Wang Y, You Q, Wang L. Small molecules targeting molecular chaperones for tau regulation: Achievements and challenges. Eur J Med Chem 2023; 261:115859. [PMID: 37839344 DOI: 10.1016/j.ejmech.2023.115859] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/26/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023]
Abstract
Abnormal post-translational modification of microtubule-associated protein Tau (MAPT) is a prominent pathological feature in Alzheimer's disease (AD). Previous research has focused on designing small molecules to target Tau modification, aiming to restore microtubule stability and regulate Tau levels in vivo. However, progress has been hindered, and no effective Tau-targeted drugs have been successfully marketed, which urgently requires more strategies. Heat shock proteins (HSPs), especially Hsp90 and Hsp70, have been found to play a crucial role in Tau maturation and degradation. This review explores innovative approaches using small molecules that interact with the chaperone system to regulate Tau levels. We provide a comprehensive overview of the mechanisms involving HSPs and their co-chaperones in the Tau regulation cycle. Additionally, we analyze small molecules targeting these chaperone systems to modulate Tau function. By understanding the characteristics of the molecular chaperone system and its specific impact on Tau, we aim to provide a perspective that seeks to regulate Tau levels through the manipulation of the molecular chaperone system and ultimately develop effective treatments for AD.
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Affiliation(s)
- Chenxi He
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Jinying Gu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Danni Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Keran Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Yuxuan Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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45
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Szepetowski P. New insights into the genetics of stuttering. Brain 2023; 146:4788-4790. [PMID: 37987612 DOI: 10.1093/brain/awad369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 11/22/2023] Open
Abstract
This scientific commentary refers to ‘Stuttering associated with a pathogenic variant in the chaperone protein cyclophilin 40’ by Morgan et al. (https://doi.org/10.1093/brain/awad314).
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Aschenbrenner I, Siebenmorgen T, Lopez A, Parr M, Ruckgaber P, Kerle A, Rührnößl F, Catici D, Haslbeck M, Frishman D, Sattler M, Zacharias M, Feige MJ. Assembly-dependent Structure Formation Shapes Human Interleukin-23 versus Interleukin-12 Secretion. J Mol Biol 2023; 435:168300. [PMID: 37805067 DOI: 10.1016/j.jmb.2023.168300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/09/2023]
Abstract
Interleukin 12 (IL-12) family cytokines connect the innate and adaptive branches of the immune system and regulate immune responses. A unique characteristic of this family is that each member is anα:βheterodimer. For human αsubunits it has been shown that they depend on theirβsubunit for structure formation and secretion from cells. Since subunits are shared within the family and IL-12 as well as IL-23 use the same βsubunit, subunit competition may influence cytokine secretion and thus downstream immunological functions. Here, we rationally design a folding-competent human IL-23α subunit that does not depend on itsβsubunit for structure formation. This engineered variant still forms a functional heterodimeric cytokine but shows less chaperone dependency and stronger affinity in assembly with its βsubunit. It forms IL-23 more efficiently than its natural counterpart, skewing the balance of IL-12 and IL-23 towards more IL-23 formation. Together, our study shows that folding-competent human IL-12 familyαsubunits are obtainable by only few mutations and compatible with assembly and function of the cytokine. These findings might suggest that human α subunits have evolved for assembly-dependent folding to maintain and regulate correct IL-12 family member ratios in the light of subunit competition.
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Affiliation(s)
- Isabel Aschenbrenner
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Till Siebenmorgen
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany; Helmholtz Munich, Molecular Targets & Therapeutics Center, Institute of Structural Biology, Neuherberg, Germany
| | - Abraham Lopez
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, Germany; Helmholtz Munich, Molecular Targets & Therapeutics Center, Institute of Structural Biology, Neuherberg, Germany
| | - Marina Parr
- Technical University of Munich, TUM School of Life Sciences, Department of Bioinformatics, Freising, Germany
| | - Philipp Ruckgaber
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Anna Kerle
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Florian Rührnößl
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Dragana Catici
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Martin Haslbeck
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Dmitrij Frishman
- Technical University of Munich, TUM School of Life Sciences, Department of Bioinformatics, Freising, Germany
| | - Michael Sattler
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Bavarian NMR Center, Garching, Germany; Helmholtz Munich, Molecular Targets & Therapeutics Center, Institute of Structural Biology, Neuherberg, Germany
| | - Martin Zacharias
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany
| | - Matthias J Feige
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience, Center for Functional Protein Assemblies (CPA), Garching, Germany.
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Nie D, Zhan Y, Xu K, Zou H, Li K, Chen L, Chen Q, Zheng W, Peng X, Yu M, Zhang S. Artificial intelligence differentiates abdominal Henoch-Schönlein purpura from acute appendicitis in children. Int J Rheum Dis 2023; 26:2534-2542. [PMID: 37905746 DOI: 10.1111/1756-185x.14956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 10/08/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
Abstract
OBJECTIVE This study aims to construct an artificial intelligence (AI) model capable of effectively discriminating between abdominal Henoch-Schönlein purpura (AHSP) and acute appendicitis (AA) in pediatric patients. METHODS A total of 6965 participants, comprising 2201 individuals with AHSP and 4764 patients with AA, were enrolled in the study. Additionally, 53 laboratory indicators were taken into consideration. Five distinct artificial intelligence (AI) models were developed employing machine learning algorithms, namely XGBoost, AdaBoost, Gaussian Naïve Bayes (GNB), MLPClassifier (MLP), and support vector machine (SVM). The performance of these prediction models was assessed through receiver operating characteristic (ROC) curve analysis, calibration curve assessment, and decision curve analysis (DCA). RESULTS We identified 32 discriminative indicators (p < .05) between AHSP and AA. Five indicators, namely the lymphocyte ratio (LYMPH ratio), eosinophil ratio (EO ratio), eosinophil count (EO count), neutrophil ratio (NEUT ratio), and C-reactive protein (CRP), exhibited strong performance in distinguishing AHSP from AA (AUC ≥ 0.80). Among the various prediction models, the XGBoost model displayed superior performance evidenced by the highest AUC (XGBoost = 0.895, other models < 0.89), accuracy (XGBoost = 0.824, other models < 0.81), and Kappa value (XGBoost = 0.621, other models < 0.60) in the validation set. After optimization, the XGBoost model demonstrated remarkable diagnostic performance for AHSP and AA (AUC > 0.95). Both the calibration curve and decision curve analysis suggested the promising clinical utility and net benefits of the XGBoost model. CONCLUSION The AI-based machine learning model exhibits high prediction accuracy and can differentiate AHSP and AA from a data-driven perspective.
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Affiliation(s)
- Dan Nie
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Yishan Zhan
- Department of Rheumatology and Immunology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Kun Xu
- Department of Rheumatology and Immunology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Haibo Zou
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Kehao Li
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Leifeng Chen
- Department of General Surgery, Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Qiang Chen
- Department of Rheumatology and Immunology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Weiming Zheng
- Department of Nephrology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Xiaojie Peng
- Department of Nephrology, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
| | - Mengjie Yu
- Key Laboratory of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, Nanjing, Jiangsu, China
| | - Shouhua Zhang
- Department of General Surgery, Jiangxi Provincial Children's Hospital, Nanchang, Jiangxi, China
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Zhang YJ, Yi DH. CDK1-SRC Interaction-Dependent Transcriptional Activation of HSP90AB1 Promotes Antitumor Immunity in Hepatocellular Carcinoma. J Proteome Res 2023; 22:3714-3729. [PMID: 37949475 DOI: 10.1021/acs.jproteome.3c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
This study aimed to analyze multiomics data and construct a regulatory network involving kinases, transcription factors, and immune genes in hepatocellular carcinoma (HCC) prognosis. The researchers used transcriptomic, proteomic, and clinical data from TCGA and GEO databases to identify immune genes associated with HCC. Statistical analysis, meta-analysis, and protein-protein interaction analyses were performed to identify key immune genes and their relationships. In vitro and in vivo experiments validated the CDK1-SRC-HSP90AB1 network's effects on HCC progression and antitumor immunity. A prognostic risk model was developed using clinicopathological features and immune infiltration. The immune genes LPA, BIRC5, HSP90AB1, ROBO1, and CCL20 were identified as the key prognostic factors. The CDK1-SRC-HSP90AB1 network promoted HCC cell proliferation and migration, with HSP90AB1 being transcriptionally activated by the CDK1-SRC interaction. Manipulating SRC or HSP90AB1 reversed the effects of CDK1 and SRC on HCC. The CDK1-SRC-HSP90AB1 network also influenced HCC tumor formation and antitumor immunity. Overall, this study highlights the importance of the CDK1-SRC-HSP90AB1 network as a crucial immune-regulatory network in the HCC prognosis.
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Affiliation(s)
- Yi-Jie Zhang
- Department of Hepatobiliary and Organ Transplantation, The First Affiliated Hospital of China Medical University, Shenyang 110001, P. R. China
- The Key Laboratory of Organ Transplantation of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, P. R. China
| | - De-Hui Yi
- Department of Hepatobiliary and Organ Transplantation, The First Affiliated Hospital of China Medical University, Shenyang 110001, P. R. China
- The Key Laboratory of Organ Transplantation of Liaoning Province, The First Affiliated Hospital of China Medical University, Shenyang 110001, P. R. China
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Takeda K, Watanabe T, Smith JR, Vesey D, Tiberghien N, Lewis S, Powney B, Schapira AHV, Hoshikawa T, Takle AK. Identification of novel glucocerebrosidase chaperones by unexpected skeletal rearrangement reaction. Bioorg Med Chem Lett 2023; 96:129531. [PMID: 37866711 DOI: 10.1016/j.bmcl.2023.129531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/12/2023] [Accepted: 10/17/2023] [Indexed: 10/24/2023]
Abstract
Compound 5 was identified from a high-throughput screening campaign as a small molecule pharmacological chaperone of glucocerebrocidase (GCase), a lysosomal hydrolase encoded by the GBA1 gene, variants of which are associated with Gaucher disease and Parkinson's disease. Further investigations revealed that compound 5 was slowly transformed into a regio-isomeric compound (6) in PBS buffer, plausibly via a ring-opening at hemiaminal moiety accompanied by subsequent intramolecular CC bond formation. Utilising this unexpected skeletal rearrangement reaction, a series of compound 6 analogues was synthesized which yielded multiple potent GCase pharmacological chaperones with sub-micromolar EC50 values as exemplified by compound 38 (EC50 = 0.14 μM).
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Affiliation(s)
- Kunitoshi Takeda
- Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Toru Watanabe
- Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - James R Smith
- Charles River Laboratories, 7-9 Spire Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - David Vesey
- Charles River Laboratories, 7-9 Spire Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Nathalie Tiberghien
- Charles River Laboratories, 7-9 Spire Green Centre, Flex Meadow, Harlow, Essex CM19 5TR, United Kingdom
| | - Sian Lewis
- Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Ben Powney
- Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Tamaki Hoshikawa
- Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom.
| | - Andrew K Takle
- Hatfield Research Laboratories, Eisai Ltd., Hatfield AL10 9SN, United Kingdom
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50
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Jing C, Fu R, Liu X, Zang G, Zhu X, Wang C, Zhang W. A comprehensive cuproptosis score and associated gene signatures reveal prognostic and immunological features of idiopathic pulmonary fibrosis. Front Immunol 2023; 14:1268141. [PMID: 38035073 PMCID: PMC10682708 DOI: 10.3389/fimmu.2023.1268141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/30/2023] [Indexed: 12/02/2023] Open
Abstract
Background Cuproptosis, the most recently identified and regulated cell death, depends on copper ions in vivo. Copper regulates the pathogenesis of Idiopathic pulmonary fibrosis (IPF), but the mechanism of action underlying cuproptosis in IPF remains unclear. Methods We identified three cuproptosis patterns based on ten cuproptosis-related genes using unsupervised consensus clustering. We quantified these patterns using a PCA algorithm to construct a cuproptosis score. ssGSEA and the Cibersort algorithm assessed the immune profile of IPF patients. GSEA and GSVA were used to analyze the functional differences in different molecular patterns. Drug susceptibility prediction based on cuproptosis scores and meaningful gene markers was eventually screened in combination with external public data sets,in vitro experiments and our cases. Results Of the three types of cuproptosis-related clusters identified in the study, patients in the clusterA, geneclusterB, and score-high groups showed improved prognoses. Moreover, each cluster exhibited differential immune characteristics, with the subtype showing a poorer prognosis associated with an immune overreaction. Cuproptosis score can be an independent risk factor for predicting the prognosis of IPF patients. GSEA showed a significant functional correlation between the score and cuproptosis. The genes AKAP9, ANK3, C6orf106, LYRM7, and MBNL1, were identified as prognostic-related signatures in IPF patients. The functional role of immune regulation in IPF was further explored by correlating essential genes with immune factors. Also, the nomogram constructed by cumulative information from gene markers and cuproptosis score showed reliable clinical application. Conclusions Cuproptosis patterns differ significantly in the prognosis and immune characteristics of IPF patients. The cuproptosis score and five gene signatures can provide a reliable reference in the prognosis and diagnosis of IPF.
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Affiliation(s)
- Chuanqing Jing
- Clinical Department of Integrated Traditional Chinese and Western Medicine, The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Rong Fu
- Clinical Department of Integrated Traditional Chinese and Western Medicine, The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xue Liu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, China
| | - Guodong Zang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, China
| | - Xue Zhu
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, China
| | - Can Wang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, China
| | - Wei Zhang
- Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, China
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