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Chen M, Dahl A. A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data. Nat Commun 2024; 15:5229. [PMID: 38898015 PMCID: PMC11186839 DOI: 10.1038/s41467-024-49242-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has been widely used to characterize cell types based on their average gene expression profiles. However, most studies do not consider cell type-specific variation across donors. Modelling this cell type-specific inter-individual variation could help elucidate cell type-specific biology and inform genes and cell types underlying complex traits. We therefore develop a new model to detect and quantify cell type-specific variation across individuals called CTMM (Cell Type-specific linear Mixed Model). We use extensive simulations to show that CTMM is powerful and unbiased in realistic settings. We also derive calibrated tests for cell type-specific interindividual variation, which is challenging given the modest sample sizes in scRNA-seq. We apply CTMM to scRNA-seq data from human induced pluripotent stem cells to characterize the transcriptomic variation across donors as cells differentiate into endoderm. We find that almost 100% of transcriptome-wide variability between donors is differentiation stage-specific. CTMM also identifies individual genes with statistically significant stage-specific variability across samples, including 85 genes that do not have significant stage-specific mean expression. Finally, we extend CTMM to partition interindividual covariance between stages, which recapitulates the overall differentiation trajectory. Overall, CTMM is a powerful tool to illuminate cell type-specific biology in scRNA-seq.
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Affiliation(s)
- Minhui Chen
- Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA.
| | - Andy Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL, 60637, USA.
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2
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Murali A, Brokesh AM, Cross LM, Kersey AL, Jaiswal MK, Singh I, Gaharwar A. Inorganic Biomaterials Shape the Transcriptome Profile to Induce Endochondral Differentiation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402468. [PMID: 38738803 DOI: 10.1002/advs.202402468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/27/2024] [Indexed: 05/14/2024]
Abstract
Minerals play a vital role, working synergistically with enzymes and other cofactors to regulate physiological functions including tissue healing and regeneration. The bioactive characteristics of mineral-based nanomaterials can be harnessed to facilitate in situ tissue regeneration by attracting endogenous progenitor and stem cells and subsequently directing tissue-specific differentiation. Here, cellular responses of human mesenchymal stem/stromal cells to traditional bioactive mineral-based nanomaterials, such as hydroxyapatite, whitlockite, silicon-dioxide, and the emerging synthetic 2D nanosilicates are investigated. Transcriptome sequencing is utilized to probe the cellular response and determine the significantly affected signaling pathways due to exposure to these inorganic nanomaterials. Transcriptome profiles of stem cells treated with nanosilicates reveals a stabilized skeletal progenitor state suggestive of endochondral differentiation. This observation is bolstered by enhanced deposition of matrix mineralization in nanosilicate treated stem cells compared to control or other treatments. Specifically, use of 2D nanosilicates directs osteogenic differentiation of stem cells via activation of bone morphogenetic proteins and hypoxia-inducible factor 1-alpha signaling pathway. This study provides insight into impact of nanomaterials on cellular gene expression profile and predicts downstream effects of nanomaterial induction of endochondral differentiation.
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Affiliation(s)
- Aparna Murali
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Anna M Brokesh
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Lauren M Cross
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Anna L Kersey
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Manish K Jaiswal
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA
| | - Irtisha Singh
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA
- Department of Cell Biology and Genetics, College of Medicine, Texas A&M University, Bryan, TX, 77807-3260, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, 77843, USA
| | - Akhilesh Gaharwar
- Department of Biomedical Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, 77843, USA
- Department of Material Science and Engineering, College of Engineering, Texas A&M University, College Station, TX, 77843, USA
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Yuan X, Sun X, Zhou B, Zhao S, Li Y, Ming H. HSPA4 regulated glioma progression via activation of AKT signaling pathway. Biochem Cell Biol 2024; 102:159-168. [PMID: 37339521 DOI: 10.1139/bcb-2022-0321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/22/2023] Open
Abstract
Glioma is still an incurable disease with high invasiveness. Heat shock 70 kDa protein 4 (HSPA4) is a member of the HSP110 family, and is associated with the development and progression of various cancers. In the current study, we assessed the expression of HSPA4 in clinical samples, and found that HSPA4 was up-regulated in glioma tissues and correlated with tumor recurrence and grade. Survival analyses demonstrated that glioma patients with high HSPA4 expression had lower overall survival and disease-free survival times. In vitro knockdown of HSPA4 inhibited glioma cell proliferation, mediated cell cycle arrest at G2 phase and apoptosis, and reduced the migration ability. In vivo, the growth of HSPA4-knockdown xenografts was markedly suppressed compared to the tumors formed by HSPA4-positive control cells. Additionally, Gene set enrichment analyses disclosed that HSPA4 was associated with the PI3K/Akt signaling pathway. The regulatory effect of the AKT activator SC79 on cell proliferation and apoptosis was suppressed by HSPA4 knockdown, indicating that HSPA4 is capable of promoting glioma development. In summary, these data showed that HSPA4 is likely to play a pivotal role in the progression of glioma, and consequently may be a promising therapeutic target for glioma therapy.
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Affiliation(s)
- Xi Yuan
- Department of Radiation Oncology, Jinling Hospital of Nanjing University, No.305, Zhongshan East Road, Nanjing, Jiangsu Province 210002, China
| | - Xiangdong Sun
- Department of Radiation Oncology, Jinling Hospital of Nanjing University, No.305, Zhongshan East Road, Nanjing, Jiangsu Province 210002, China
| | - Bin Zhou
- Department of Radiation Oncology, Jinling Hospital of Nanjing University, No.305, Zhongshan East Road, Nanjing, Jiangsu Province 210002, China
| | - Shuang Zhao
- Department of Radiation Oncology, Jinling Hospital of Nanjing University, No.305, Zhongshan East Road, Nanjing, Jiangsu Province 210002, China
| | - Yikun Li
- Department of Radiation Oncology, Jinling Hospital of Nanjing University, No.305, Zhongshan East Road, Nanjing, Jiangsu Province 210002, China
| | - Haolang Ming
- Department of Neurosurgery, Tianjin Medical University General Hospital, No.154 Anshan Road, Heping District, Tianjin 300052, China
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Yang J, Wu X, You J. Unveiling the potential of HSPA4: a comprehensive pan-cancer analysis of HSPA4 in diagnosis, prognosis, and immunotherapy. Aging (Albany NY) 2024; 16:2517-2541. [PMID: 38305786 PMCID: PMC10911360 DOI: 10.18632/aging.205496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/03/2024] [Indexed: 02/03/2024]
Abstract
With the global rise in cancer incidence and mortality rates, research on the topic has become increasingly urgent. Among the significant players in this field are heat shock proteins (HSPs), particularly HSPA4 from the HSP70 subfamily, which has recently garnered considerable interest for its role in cancer progression. However, despite numerous studies on HSPA4 in specific cancer types, a comprehensive analysis across all cancer types is lacking. This study employs various bioinformatics techniques to delve into the role of HSPA4 in pan-cancer. Our objective is to assess its potential in clinical diagnosis, prognosis, and as a future molecular target for therapy. The research findings reveal significant differences in HSPA4 expression across different cancer types, suggesting its diagnostic value and close association with cancer staging and patient survival rates. Furthermore, genetic variations and methylation status of HSPA4 play critical roles in tumorigenesis. Lastly, the interaction of HSPA4 with immune cells is linked to the tumor microenvironment (TME) and immunotherapy. In summary, HSPA4 emerges as a promising cancer biomarker and a vital member of the HSPs family, holding potential applications in diagnosis, prognosis, and immunotherapy.
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Affiliation(s)
- Junhao Yang
- Department of Surgical Oncology and General Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Xiaoxiao Wu
- Department of Rheumatology, Second Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310000, China
| | - Jianhong You
- Department of Ultrasound, Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361000, China
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Alhusaini AM, Alshehri SM, Sarawi WS, Alghibiwi HK, Alturaif SA, Al khbiah RA, Alali SM, Alsaif SM, Alsultan EN, Hasan IH. Implication of MAPK, Lipocalin-2, and Fas in the protective action of liposomal resveratrol against isoproterenol-induced kidney injury. Saudi Pharm J 2024; 32:101907. [PMID: 38178854 PMCID: PMC10764257 DOI: 10.1016/j.jsps.2023.101907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
Background and Objective Isoproterenol (ISO) is a non-selective β-adrenergic receptor agonist. It can be used to treat bradycardia and cardiogenic shock. Despite its usefulness, the overstimulation of β-receptors by ISO can cause "cardiorenal syndrome," a term used to describe heart and kidney damage. Resveratrol (RES), a natural polyphenol, has marked anti-inflammatory and antioxidant activities. The present work was designed to study the protective efficacy of liposomal resveratrol (L-RES) against ISO-induced kidney injury. Materials and Methods The kidney injury was induced in rats by administering ISO (50 mg/kg, s.c.) twice a week for 2 weeks. RES and L-RES were administered at a dose (20 mg/kg/ day, p.o.) along with ISO for 2 weeks. Inflammatory and apoptotic biomarkers were analyzed, which were validated using histochemical analysis. Results ISO caused renal dysfunction, which manifested as elevated urea, creatinine and uric acid, besides cystatin c and MAPK protein overexpression. In addition, ISO induced gene expression of Fas and lipocalin-2 and provoked genomic DNA fragmentation in renal tissues as compared with the control group. Histological examination confirmed morphological alterations of the kidney tissues obtained from the ISO group. Concurrent treatment of either RES or L-RES with ISO significantly ameliorated kidney damage as demonstrated by the improvement of all measured parameters with the best results for L-RES. The histopathological findings were correlated with the above biochemical parameters. Conclusion L-RES could be a promising approach for the prevention of kidney injury induced by ISO, most likely via the downregulation of MAPK, cystatin c, Fas, and lipocalin-2.
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Affiliation(s)
- Ahlam M. Alhusaini
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Samiyah M. Alshehri
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Wedad S. Sarawi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Hanan K. Alghibiwi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Sumayya A. Alturaif
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Reema A. Al khbiah
- Pharm D Program, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Shog M. Alali
- Pharm D Program, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Shaikha M. Alsaif
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Ebtesam N. Alsultan
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
| | - Iman H. Hasan
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, P.O Box 22452, Riyadh 11495, Saudi Arabia
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Schuhwerk H, Brabletz T. Mutual regulation of TGFβ-induced oncogenic EMT, cell cycle progression and the DDR. Semin Cancer Biol 2023; 97:86-103. [PMID: 38029866 DOI: 10.1016/j.semcancer.2023.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/06/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023]
Abstract
TGFβ signaling and the DNA damage response (DDR) are two cellular toolboxes with a strong impact on cancer biology. While TGFβ as a pleiotropic cytokine affects essentially all hallmarks of cancer, the multifunctional DDR mostly orchestrates cell cycle progression, DNA repair, chromatin remodeling and cell death. One oncogenic effect of TGFβ is the partial activation of epithelial-to-mesenchymal transition (EMT), conferring invasiveness, cellular plasticity and resistance to various noxae. Several reports show that both individual networks as well as their interface affect chemo-/radiotherapies. However, the underlying mechanisms remain poorly resolved. EMT often correlates with TGFβ-induced slowing of proliferation, yet numerous studies demonstrate that particularly the co-activated EMT transcription factors counteract anti-proliferative signaling in a partially non-redundant manner. Collectively, evidence piled up over decades underscore a multifaceted, reciprocal inter-connection of TGFβ signaling / EMT with the DDR / cell cycle progression, which we will discuss here. Altogether, we conclude that full cell cycle arrest is barely compatible with the propagation of oncogenic EMT traits and further propose that 'EMT-linked DDR plasticity' is a crucial, yet intricate facet of malignancy, decisively affecting metastasis formation and therapy resistance.
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Affiliation(s)
- Harald Schuhwerk
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany.
| | - Thomas Brabletz
- Department of Experimental Medicine 1, Nikolaus-Fiebiger Center for Molecular Medicine, Friedrich-Alexander University of Erlangen-Nürnberg, Erlangen, Germany; Comprehensive Cancer Center Erlangen-EMN, Erlangen University Hospital, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany.
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7
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Shahin RK, Elkady MA, Abulsoud AI, Abdelmaksoud NM, Abdel Mageed SS, El-Dakroury WA, Zewail MB, Elazazy M, Sobhy MH, Nomier Y, Elazazy O, Elballal MS, Mohammed OA, Midan HM, Elrebehy MA, Ziada BO, Doghish AS. miRNAs orchestration of gallbladder cancer - Particular emphasis on diagnosis, progression and drug resistance. Pathol Res Pract 2023; 248:154684. [PMID: 37454489 DOI: 10.1016/j.prp.2023.154684] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Gallbladder cancer (GBC) is characterized by a highly invasive nature and a poor prognosis, with adenocarcinoma being the main histological subtype. According to statistical data, patients diagnosed with advanced GBC have a survival rate of less than 5% for 5 years. Despite the novel therapeutic techniques, the unsatisfactory results could be related to the underlying biology of tumor cells and resistance to chemotherapy. Early diagnosis is more important than clinical therapy as it assists in determining the pathological stage of cancer and facilitates the selection of appropriate medication. Hence, it is very important to understand the precise pathogenesis of GBC and to discover potential novel biomarkers for early diagnosis of GBC. Non-coding RNAs, such as microRNAs, long non-coding RNAs, and circular RNAs, have been found to influence the transcriptional regulation of target genes associated with cancer, either directly or indirectly. microRNAs are a group of small, non-coding, single-stranded RNAs that are expressed endogenously. miRNAs play significant roles in various fundamental cellular processes. Therefore, miRNAs have the potential to serve as valuable biomarkers and therapeutic targets for GBC.
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Affiliation(s)
- Reem K Shahin
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mohamed A Elkady
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt
| | - Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | | | - Sherif S Abdel Mageed
- Department of Pharmacology & Toxicology, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Walaa A El-Dakroury
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Moataz B Zewail
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mahmoud Elazazy
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Mohamed H Sobhy
- Nanomedicine Research Labs, Center for Materials Science, Zewail City of Science and Technology, 6th of October City, Giza, Egypt
| | - Yousra Nomier
- Pharmacology Department, Pharmacy College, Jazan University, Saudi Arabia
| | - Ola Elazazy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mohammed S Elballal
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Osama A Mohammed
- Department of Clinical Pharmacology, Faculty of Medicine, Bisha University, Bisha 61922, Saudi Arabia; Department of Clinical Pharmacology, Faculty of Medicine, Ain Shams University, Cairo 11566, Egypt
| | - Heba M Midan
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Mahmoud A Elrebehy
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt.
| | - Bassant O Ziada
- Research Department, Utopia Pharmaceuticals, Nasr City, 11765 Cairo, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City, 11231 Cairo, Egypt.
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Petroni M, La Monica V, Fabretti F, Augusto M, Battaglini D, Polonara F, Di Giulio S, Giannini G. The Multiple Faces of the MRN Complex: Roles in Medulloblastoma and Beyond. Cancers (Basel) 2023; 15:3599. [PMID: 37509263 PMCID: PMC10377613 DOI: 10.3390/cancers15143599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/09/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Hypomorphic mutations in MRN complex genes are frequently found in cancer, supporting their role as oncosuppressors. However, unlike canonical oncosuppressors, MRN proteins are often overexpressed in tumor tissues, where they actively work to counteract DSBs induced by both oncogene-dependent RS and radio-chemotherapy. Moreover, at the same time, MRN genes are also essential genes, since the constitutive KO of each component leads to embryonic lethality. Therefore, even though it is paradoxical, MRN genes may work as oncosuppressive, oncopromoting, and essential genes. In this review, we discussed how alterations in the MRN complex impact the physiopathology of cancer, in light of our recent discoveries on the gene-dosage-dependent effect of NBS1 in Medulloblastoma. These updates aim to understand whether MRN complex can be realistically used as a prognostic/predictive marker and/or as a therapeutic target for the treatment of cancer patients in the future.
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Affiliation(s)
- Marialaura Petroni
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Veronica La Monica
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
| | - Francesca Fabretti
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
| | - Mariaconcetta Augusto
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy
| | - Damiana Battaglini
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
| | - Francesca Polonara
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, 00161 Rome, Italy
| | - Stefano Di Giulio
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
| | - Giuseppe Giannini
- Department of Molecular Medicine, University La Sapienza, 00161 Rome, Italy
- Istituto Pasteur-Fondazione Cenci Bolognetti, 00161 Rome, Italy
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Vaclaw C, Merritt K, Griffin VP, Whitaker N, Gokhale M, Volkin DB, Ogunyankin MO, Dhar P. Comparison of Protein Particle Formation in IgG1 mAbs Formulated with PS20 Vs. PS80 When Subjected to Interfacial Dilatational Stress. AAPS PharmSciTech 2023; 24:104. [PMID: 37081185 PMCID: PMC10118229 DOI: 10.1208/s12249-023-02561-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 03/28/2023] [Indexed: 04/22/2023] Open
Abstract
Polysorbates (PS) are nonionic surfactants that are commonly included in protein formulations to mitigate the formation of interfacial stress-induced protein particles and thus increase their long-term storage stability. Nonetheless, factors that dictate the efficiency of different polysorbates in mitigating protein particle formation, especially during the application of interfacial stresses, are often ill defined. Here, we used a Langmuir trough to determine the surface activity of two IgG1 monoclonal antibodies formulated with two different polysorbates (PS20 and PS80) when subjected to interfacial dilatational stress. Interfacial properties of these formulations were then correlated with characterization of subvisible protein particles measured by micro-flow imaging (MFI). Both mAbs, when formulated in PS20, demonstrate faster adsorption kinetics and higher surface activity compared to PS80 or surfactant-free formulations. Compression/expansion results suggest that when exposed to interfacial dilatational stresses, both mAb/PS20 formulations display interfacial properties of PS20 alone. In contrast, interfacial properties of both mAb/PS80 formulations suggest mAbs and PS80 are co-adsorbed to the air-water interface. Further, MFI analysis of the interface and the bulk solution confirms that PS20 is more effective than PS80 at mitigating the formation of larger particles in the bulk solution in both mAbs. Concomitantly, the efficiency of PS to prevent interface-induced protein particle formation also depended on the protein's inherent tendency to aggregate at a surfactant-free interface. Together, the studies presented here highlight the importance of determining the interfacial properties of mAbs, surfactants, and their combinations to make informed formulation decisions about the choice of surfactant.
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Affiliation(s)
- Coleman Vaclaw
- Bioengineering Program, School of Engineering, The University of Kansas, 1530 W 15th Street, Lawrence, Kansas, 66045, USA
- Amgen, Thousand Oaks, California, USA
| | - Kimberly Merritt
- Bioengineering Program, School of Engineering, The University of Kansas, 1530 W 15th Street, Lawrence, Kansas, 66045, USA
- Hill's Pet Nutrition, Emporia, Kansas, USA
| | - Valerie P Griffin
- Department of Chemical and Petroleum Engineering, The University of Kansas, 1530 W 15th Street, Lawrence, Kansas, 66045, USA
| | - Neal Whitaker
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas, 66047, USA
- Sparks Therapeutics, Philadelphia, Pennsylvania, USA
| | - Madhushree Gokhale
- Department of Drug Product Development, Bristol-Myers Squibb, Inc., One Squibb Drive, New Brunswick, New Jersey, 08901, USA
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, 2030 Becker Drive, Lawrence, Kansas, 66047, USA
| | - Maria O Ogunyankin
- Department of Drug Product Development, Bristol-Myers Squibb, Inc., One Squibb Drive, New Brunswick, New Jersey, 08901, USA
| | - Prajnaparamita Dhar
- Bioengineering Program, School of Engineering, The University of Kansas, 1530 W 15th Street, Lawrence, Kansas, 66045, USA.
- Department of Chemical and Petroleum Engineering, The University of Kansas, 1530 W 15th Street, Lawrence, Kansas, 66045, USA.
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10
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Tao H, Yang J, Xu M, Liu Z, Liu Y, Xiong Q. MicroRNA-27a-3p targeting Vangl1 and Vangl2 inhibits cell proliferation in mouse granulosa cells. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194885. [PMID: 36288764 DOI: 10.1016/j.bbagrm.2022.194885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Mammalian folliculogenesis is the complex process through which primordial follicles develop into preovulatory follicles. The chief function of ovarian follicle granulosa cells is to play a vital role in the growth, development and atresia of ovarian follicles via gap junctions. Increasing evidence suggests that microRNAs (miRNAs) are essential regulators of granulosa cell apoptosis or proliferation. METHODS The expression level of miR-27a-3p, myogenic differentiation (MyoD), Vangl1 and Vangl2 was investigated by Real-time quantitative PCR (RT-qPCR) and Western blot. Luciferase reporter assay, bioinformatics analysis and ChIP-PCR was used to detect the binding sites between miR-27a-3p, transcription factor and target genes. KEGG pathway analyses were performed to reveal the predicted targets of miR-27a-3p. Ethynyl deoxyuridine (EdU) proliferation assay was used to measure cell proliferation. RESULTS To explore the underlying mechanisms of the miR-27a-3p function in the development of mouse granulosa cells (mGCs), we screened for the target genes of miR-27a-3p, confirmed its interaction with Vangl1 and Vangl2 and elucidated their roles in mGCs. MiR-27a-3p inhibited the proliferation of mGCs, whereas target genes Vangl1 and Vangl2 had the opposite effect. In addition, the transcription factor MYOD bound to and activated the promoter of miR-27a-3p. MiR-27a-3p suppressed Vangl1 and Vangl2 expression by targeting their 3'-untranslated region (3'-UTR). Furthermore, Vangl1 and Vangl2 suppressed the Wnt pathway by reducing the expression of β-catenin and B-cell lymphoma/leukemia-2 (Bcl-2). CONCLUSION These findings indicate a pro-survival mechanism of the MyoD/miR-27a-3p/Vangl1/Vangl2 axis for granulosa cell proliferation and suggest a novel target for the improvement of female fertility.
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Affiliation(s)
- Hu Tao
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
| | - Juan Yang
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Mingzhu Xu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Zelin Liu
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, China
| | - Yang Liu
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Qi Xiong
- Hubei Key Laboratory of Animal Embryo Engineering and Molecular Breeding, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan 430064, China.
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11
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Chen M, Dahl A. A robust model for cell type-specific interindividual variation in single-cell RNA sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529987. [PMID: 36909553 PMCID: PMC10002707 DOI: 10.1101/2023.02.24.529987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
The development of single-cell RNA sequencing (scRNA-seq) offers opportunities to characterize cellular heterogeneity at unprecedented resolution. Although scRNA-seq has been widely used to identify and characterize gene expression variation across cell types and cell states based on their average gene expression profiles, most studies ignore variation across individual donors. Modelling this inter-individual variation could improve statistical power to detect cell type-specific biology and inform the genes and cell types that underlying complex traits. We therefore develop a new model to detect and quantify cell type-specific variation across individuals called CTMM (Cell Type-specific linear Mixed Model). CTMM operates on cell type-specific pseudobulk expression and is fit with efficient methods that scale to hundreds of samples. We use extensive simulations to show that CTMM is powerful and unbiased in realistic settings. We also derive calibrated tests for cell type-specific interindividual variation, which is challenging given the modest sample sizes in scRNA-seq data. We apply CTMM to scRNA-seq data from human induced pluripotent stem cells to characterize the transcriptomic variation across donors as cells differentiate into endoderm. We find that almost 100% of transcriptome-wide variability between donors is differentiation stage-specific. CTMM also identifies individual genes with statistically significant stage-specific variability across samples, including 61 genes that do not have significant stage-specific mean expression. Finally, we extend CTMM to partition interindividual covariance between stages, which recapitulates the overall differentiation trajectory. Overall, CTMM is a powerful tool to characterize a novel dimension of cell type-specific biology in scRNA-seq.
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Affiliation(s)
- Minhui Chen
- Section of Genetic Medicine, University of Chicago, Chicago, IL 60637
| | - Andy Dahl
- Section of Genetic Medicine, University of Chicago, Chicago, IL 60637
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12
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Akram Z, Mahjabeen I, Irshad F, Ahmed MW, Rehman S, Rizwan M, Shafqat A, Kiran A, Saeed A. Expression deregulation of matrix metalloproteinases and vasoconstriction related genes in Pakistani females with abnormal uterine bleeding. BMC Womens Health 2022; 22:543. [PMID: 36564776 PMCID: PMC9784108 DOI: 10.1186/s12905-022-02132-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Abnormal uterine bleeding (AUB) is irregular menstrual bleeding which has great impact on female health and life style. Various genetic factors are involved in etiology and pathology of AUB. Present study was designed to explore the association of PTGFR, MMP9, MMP2, TGFB3 and VEGFB with AUB. METHODS Blood samples of 212 females with AUB were collected along with age-matched healthy control. Expression variation of targeted genes was evaluated using qPCR. Present study cohort was divided into different groups based on demographic parameters and all targeted genes were correlated with study demographics. RESULTS Expression of targeted genes was significantly (P < 0.001) downregulated in females with AUB compared to control. Reduced (P < 0.01) expression of targeted genes was observed in all age groups (21-30, 31-40, 41-50 year) of AUB patients compared to respective control. Expression of VEGFB increased (P < 0.05) in AUB females with > 9 days bleeding compared to AUB patient had < 9 days bleeding. AUB women with miscarriage history showed upregulation in MMP2, TGFB3 (P < 0.05), and downregulation in MMP9 and VEGFB (P < 0.05) expression compared to AUB group with no miscarriage history. Expression of MMP2 increased (P < 0.05) in AUB females with > 60 kg body weigh compared to AUB patient with < 60 kg weight. CONCLUSION Present study open a new window for diagnosis of AUB at early stages and suggested a possible involvement of PTGFR, MMP9, MMP2, TGFB3 and VEGFB as candidate biomarkers in AUB.
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Affiliation(s)
- Zertashia Akram
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Faiza Irshad
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Malik Waqar Ahmed
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sadaf Rehman
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Rizwan
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Amna Shafqat
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Aniqa Kiran
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Asma Saeed
- grid.418920.60000 0004 0607 0704Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
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13
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Li L, Zou BJ, Zhao JZ, Liang JB, She ZY, Zhou WY, Lin SX, Tian L, Luo WJ, He FZ. A novel DNA damage repair-related signature for predicting prognositc and treatment response in non-small lung cancer. Front Oncol 2022; 12:961274. [PMID: 36408135 PMCID: PMC9673481 DOI: 10.3389/fonc.2022.961274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 10/14/2022] [Indexed: 10/06/2023] Open
Abstract
DNA damage repair (DDR) is essential for maintaining genome integrity and modulating cancer risk, progression, and therapeutic response. DDR defects are common among non-small lung cancer (NSCLC), resulting in new challenge and promise for NSCLC treatment. Thus, a thorough understanding of the molecular characteristics of DDR in NSCLC is helpful for NSCLC treatment and management. Here, we systematically analyzed the relationship between DDR alterations and NSCLC prognosis, and successfully established and validated a six-DDR gene prognostic model via LASSO Cox regression analysis based on the expression of prognostic related DDR genes, CDC25C, NEIL3, H2AFX, NBN, XRCC5, RAD1. According to this model, NSCLC patients were classified into high-risk subtype and low-risk subtype, each of which has significant differences between the two subtypes in clinical features, molecular features, immune cell components, gene mutations, DDR pathway activation status and clinical outcomes. The high-risk patients was characterized with worse prognosis, lower proportion and number of DDR mutations, unique immune profile and responsive to immunetherapy. And the low-risk patients tend to have superior survival, while being less responsive to immunotherapy and more sensitive to treatment with DNA-damaging chemotherapy drugs. Overall, this molecular classification based on DDR expression profile enables hierarchical management of patients and personalized clinical treatment, and provides potential therapeutic targets for NSCLC.
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Affiliation(s)
- Ling Li
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Bao-jia Zou
- Department of Hepatobiliary Surgery, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, China
| | - Juan-zhi Zhao
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Jia-bi Liang
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Zi-yue She
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wen-ying Zhou
- Department of Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Si-xiao Lin
- Department of Central Laboratory, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Lin Tian
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Wen-ji Luo
- Department of Pharmacy, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Fa-zhong He
- Department of Quality Control, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, Guangdong, China
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14
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Cai Q, Duan J, Ding L. Prognostic model of immune-related genes for patients with hepatocellular carcinoma. Front Surg 2022; 9:819491. [PMID: 35937592 PMCID: PMC9349350 DOI: 10.3389/fsurg.2022.819491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 06/30/2022] [Indexed: 11/30/2022] Open
Abstract
Background Immune-related genes (IRGs) are closely connected to the occurrence and development of tumors. Their influence on the prognosis of patients with HCC, however, remains unclear. Methods From the TCGA database, we integrated 365 liver cancer tissues and 50 normal tissues to identify differential immune genes related to prognosis. Multivariate COX analysis was used to establish a new prognostic index on account of IRGs, whereby risk score = (Expression level of HSPA4*0.022) + (Expression level of PSMD14*0.042) + (Expression level of RBP2*0.019) + (Expression level of MAPT*0.197) + (Expression level of TRAF3*0.146) + (Expression level of NDRG1*(0.006) + (Expression level of NRAS*0.027) + (Expression level of IL17D*0.075). Results The risk score was clearly correlated with an unfavorable survival rate and with clinical characteristics. By integrating the immune-related risk score model with clinical features, a nomogram was constructed to predict the survival rate of HCC patients (1-, 3- and 5-year AUC of 0.721, 0.747 and 0.781, respectively). Conclusion We have established a valuable prognostic risk score for HCC patients that may be a better predictor of survival than the present method. With the risk score's strong predictive value for immune cells and functions, it may provide clinical guidance for the diagnosis and prognosis of different immunophenotypes, and provide multiple therapeutic targets for the treatment of HCC patients based on subtype-specific immune molecules.
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Affiliation(s)
- Qun Cai
- Department of Infectious Diseases and Liver Diseases, Ningbo Medical Center Lihuili Hospital, Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
- Correspondence: Qun Cai
| | - Jinnan Duan
- Department of Infectious Diseases, Shaoxing People's Hospital, Shaoxing, China
| | - Liang Ding
- Department of Infectious Diseases, Shaoxing People's Hospital, Shaoxing, China
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15
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Das A, Roy S, Upadhyaya G, Agarwal T, Ray S. NBS1 protein from Physcomitrium patens confers protection against oxidative damage by limiting the accumulation of cellular reactive oxygen species. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 180:81-90. [PMID: 35398654 DOI: 10.1016/j.plaphy.2022.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/30/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
Nijmegen breakage syndrome 1 (NBS1) protein is a core member of the MRE11-RAD50-NBS1 (MRN) complex that plays a crucial role in DNA damage sensing and repair in plants. Here we report that NBS1 from moss Physcomitrium patens reduces oxidative damage by lowering the cellular ROS in addition to its known role in oxidative DNA damage recovery. Real-time transcript analysis showed up-regulation of the PpNBS1 transcript under different stress conditions. Bacterial cells showed better cell survivability upon over-expressing PpNBS1 protein as compared to untransformed cells. Likewise, overexpression of PpNBS1 in tobacco plants provides improved protection against oxidative damage and exhibited a lesser amount of ROS upon exposure to oxidative stress. Moreover, PpNBS1 contributes to the antioxidant defense mechanism by positively regulating the expression of the antioxidant genes under stress conditions in transgenic tobacco plants. PpNBS1 expressing transgenic tobacco plants resulted in lesser membrane damage, lower lipid peroxidation level, and higher chlorophyll content under stress conditions. Taken together, we conclude in addition to its known role as DNA damage sensor, PpNBS1 also plays a definite role in oxidative stress mitigation by minimizing ROS accumulation in the cell.
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Affiliation(s)
- Arup Das
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Shuddhanjali Roy
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Gouranga Upadhyaya
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Tanushree Agarwal
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| | - Sudipta Ray
- Plant Functional Genomics Laboratory, Department of Botany, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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Kose A, Oncel SS. Design of melanogenesis regulatory peptides derived from phycocyanin of the microalgae Spirulina platensis. Peptides 2022; 152:170783. [PMID: 35278583 DOI: 10.1016/j.peptides.2022.170783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 12/20/2022]
Abstract
Pigmentation issues are common conditions associated with excessive or insufficient production of melanin. Recently peptides are investigated to discover novel melanogenesis regulators as low molecular weight compounds to regulate skin pigmentation. In this study, an internal library of peptides obtained through in silico enzymatic digestion of phycocyanin from microalgae S. platensis was tested to apprehend their anti-melanogenic effects. Seven peptides were investigated for their inhibitory potential against mushroom and B16-F10 murine tyrosinase enzymes. According to the results, P5 (SPSWY) and P7 (AADQRGKDKCARDIGY) were effective in lowering the activity of mushroom and B16-F10 tyrosinases. P5 was the most potent (IC50 value, 12.1 µM) in mushroom which was followed by P2 (MAACLR, 86.9 µM). Although the peptides were particularly powerful in inhibiting monophenolase activity, only moderate inhibition was observed for diphenolase activity in mushroom tyrosinase assay. Apart from tyrosinase inhibition, P2 and P3 (RCLNGRL) were efficient DPPH radical scavengers at low concentrations (IC50 < 200 µM). In the mammalian assay system, P5 and P7 were noticeably effective to decrease tyrosinase enzyme activity with IC50 values of 48.9 and 34.2 µM, respectively. However, although P4 (RYVTYAVF) was a potent mushroom tyrosinase inhibitor, it increased melanin synthesis up to 3-fold in B16-F10 cells. The results indicate that C-terminal tyrosine residue is important for tyrosinase inhibition. This study shows, for the first time, that microalgae proteins can be regarded as sources for melanogenesis regulation.
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Affiliation(s)
- Ayse Kose
- Ege University Faculty of Engineering Department of Bioengineering, 35100 Bornova, Izmir, Turkey
| | - Suphi S Oncel
- Ege University Faculty of Engineering Department of Bioengineering, 35100 Bornova, Izmir, Turkey.
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17
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Li SC, Lan KC, Hung HN, Huang WT, Lai YJ, Cheng HH, Tsai CC, Huang KL, You HL, Hsu TY. HSPA4 Is a Biomarker of Placenta Accreta and Enhances the Angiogenesis Ability of Vessel Endothelial Cells. Int J Mol Sci 2022; 23:ijms23105682. [PMID: 35628491 PMCID: PMC9143901 DOI: 10.3390/ijms23105682] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/15/2022] [Accepted: 05/17/2022] [Indexed: 12/02/2022] Open
Abstract
Placenta accreta spectrum (PAS) accounts for 7% of maternal mortality and is associated with intraoperative and postoperative morbidity caused by massive blood loss, infection, and adjacent organ damage. The aims of this study were to identify the protein biomarkers of PAS and to further explore their pathogenetic roles in PAS. For this purpose, we collected five placentas from pregnant subjects with PAS complications and another five placentas from normal pregnancy (NP) cases. Then, we enriched protein samples by specifically isolating the trophoblast villous, deeply invading into the uterine muscle layer in the PAS patients. Next, fluorescence-based two-dimensional difference gel electrophoresis (2D-DIGE) and MALDI-TOF/MS were used to identify the proteins differentially abundant between PAS and NP placenta tissues. As a result, nineteen spots were determined as differentially abundant proteins, ten and nine of which were more abundant in PAS and NP placenta tissues, respectively. Then, specific validation with western blot assay and immunohisto/cytochemistry (IHC) assay confirmed that heat shock 70 kDa protein 4 (HSPA4) and chorionic somatomammotropin hormone (CSH) were PAS protein biomarkers. Further tube formation assays demonstrated that HSPA4 promoted the in vitro angiogenesis ability of vessel endothelial cells, which is consistent with the in vivo scenario of PAS complications. In this study, we not only identified PAS protein biomarkers but also connected the promoted angiogenesis with placenta invasion, investigating the pathogenetic mechanism of PAS.
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Affiliation(s)
- Sung-Chou Li
- Center for Mitochondrial Research and Medicine and Genomics and Proteomics Core Laboratory, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan;
| | - Kuo-Chung Lan
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (K.-C.L.); (H.-N.H.); (Y.-J.L.); (H.-H.C.); (C.-C.T.); (K.-L.H.)
- Department of Obstetrics and Gynecology, Jen-Ai Hospital, Taichung 412, Taiwan
| | - Hsuan-Ning Hung
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (K.-C.L.); (H.-N.H.); (Y.-J.L.); (H.-H.C.); (C.-C.T.); (K.-L.H.)
| | - Wan-Ting Huang
- Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (W.-T.H.); (H.-L.Y.)
| | - Yun-Ju Lai
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (K.-C.L.); (H.-N.H.); (Y.-J.L.); (H.-H.C.); (C.-C.T.); (K.-L.H.)
| | - Hsin-Hsin Cheng
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (K.-C.L.); (H.-N.H.); (Y.-J.L.); (H.-H.C.); (C.-C.T.); (K.-L.H.)
| | - Chih-Chang Tsai
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (K.-C.L.); (H.-N.H.); (Y.-J.L.); (H.-H.C.); (C.-C.T.); (K.-L.H.)
| | - Kun-Long Huang
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (K.-C.L.); (H.-N.H.); (Y.-J.L.); (H.-H.C.); (C.-C.T.); (K.-L.H.)
| | - Huey-Ling You
- Department of Laboratory Medicine, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (W.-T.H.); (H.-L.Y.)
| | - Te-Yao Hsu
- Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 833, Taiwan; (K.-C.L.); (H.-N.H.); (Y.-J.L.); (H.-H.C.); (C.-C.T.); (K.-L.H.)
- Correspondence:
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18
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Wang J, Liu J, Wang J, Wang S, Li F, Li R, Liu P, Li M, Wang C. Identification of proteomic markers for prediction of the response to 5-Fluorouracil based neoadjuvant chemoradiotherapy in locally advanced rectal cancer patients. Cancer Cell Int 2022; 22:117. [PMID: 35292026 PMCID: PMC8922748 DOI: 10.1186/s12935-022-02530-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/21/2022] [Indexed: 11/10/2022] Open
Abstract
Background Neoadjuvant chemoradiotherapy (nCRT) prior to surgery is the standard treatment for patients with locally advanced rectal cancer (LARC), while parts of them show poor therapeutic response accompanied by therapy adverse effects. Predictive biomarkers for nCRT response could facilitate the guidance on treatment decisions but are still insufficient until now, which limits the clinical applications of nCRT in LARC patients. Methods In our study, 37 formalin-fixed paraffin-embedded tumor biopsies were obtained from patients with LARC before receiving 5-fluorouracil based nCRT. Proteomics analyses were conducted to identify the differentially expressed proteins (DEPs) between total responders (TR) and poor responders (PR). The DEPs were validated via ROC plotter web tool and their predictive performance was evaluated by receiver operating characteristic analysis. Functional enrichment analyses were performed to further explore the potential mechanisms underlying nCRT response. Results Among 3,998 total proteins, 91 DEPs between TR and PR were screened out. HSPA4, NIPSNAP1, and SPTB all with areas under the curve (AUC) ~ 0.8 in the internal discovery cohort were independently validated by the external mRNA datasets (AUC ~ 0.7), and their protein levels were linearly correlated with the graded responses to nCRT in the internal cohort. The combination of HSPA4 and SPTB could distinctly discriminate the TR and PR groups (AUC = 0.980, p < 0.0001). Moreover, multiple combinations of the three proteins realized increased specificity and/or sensitivity, while achieving favorable predictive value when moderate responders were introduced into the ROC analysis. Pathways including DNA damage repair, cell cycle, and epithelial mesenchymal transition were involved in nCRT response according to the enrichment analysis results. Conclusions HSPA4, SPTB and NIPSNAP1 in tumor biopsies and/or their optional combinations might be potential predictive markers for nCRT response in patients with LARC. The DEPs and their related functions have implications for the potential mechanisms of treatment response to nCRT in patients with LARC. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-022-02530-0.
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Affiliation(s)
- Jianan Wang
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China.,Medical School of Chinese PLA, Beijing, 100853, China
| | - Jiayu Liu
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China
| | - Jinyang Wang
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China.,School of Laboratory Medicine, Weifang Medical College, Weifang, 261053, Shandong, China
| | - Shijian Wang
- Nankai University School of Medicine, Nankai University, Tianjin, 300071, China
| | - Feifei Li
- Department of Pathology, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China
| | - Ruibing Li
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China
| | - Peng Liu
- Department of Pathology, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China
| | - Mianyang Li
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China.
| | - Chengbin Wang
- Department of Laboratory Medicine, The First Medical Centre of Chinese PLA General Hospital, Beijing, 100853, China.
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Shang BB, Chen J, Wang ZG, Liu H. Significant correlation between HSPA4 and prognosis and immune regulation in hepatocellular carcinoma. PeerJ 2021; 9:e12315. [PMID: 34754620 PMCID: PMC8555498 DOI: 10.7717/peerj.12315] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/24/2021] [Indexed: 12/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is an inflammation-associated tumor involved in immune tolerance and evasion in the immune microenvironment. Heat shock proteins (HSPs) are involved in the occurrence, progression, and immune regulation of tumors. Therefore, HSPs have been considered potential therapeutic targets. Here, we aimed to elucidate the value of HSP family A (Hsp70) member 4 (HSPA4) in the diagnosis and predicting prognosis of HCC, and its relationship with immune cell infiltration, immune cell biomarkers, and immune checkpoints. Gene mutation, DNA methylation, and the pathway involved in HCC were also analyzed. Methods The gene expression omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases were used to compare HSPA4 expression, and the results were confirmed by immunohistochemical staining of clinical samples. R package was used to analyze the correlation between HSPA4 and cancer stage, and to establish receiver operating characteristic (ROC) curve of diagnosis, time-dependent survival ROC curve, and a nomogram model. cBioPortal and MethSurv were used to identify genetic alterations and DNA methylation, and their effect on prognosis. The Tumor Immune Estimation Resource (TIMER) was used to analyze immune cell infiltration, immune cell biomarkers, and immune checkpoints. The STRING database was used to analyze protein-protein interaction network information. Gene Ontology (GO) analysis and the Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to investigate the functions of HSPA4 and its functional partner genes. Results Overexpression of HSPA4 was identified in 25 cancers. Overexpression of HSPA4 considerably correlated with cancer stage and alpha-fetoprotein (AFP) level in HCC. Patients with higher HSPA4 expression showed poorer prognosis. HSPA4 expression can accurately identify tumor from normal tissue (AUC = 0.957). The area under 1-, 3-, and 5-year survival ROCs were above 0.6. The HSPA4 genetic alteration rate was 1.3%. Among the 14 DNA methylation CpG sites, seven were related to the prognosis of HCC. HSPA4 was positively related to immune cell infiltration and immune checkpoints (PD-1 and CTLA-4) in HCC. The KEGG pathway enrichment analysis revealed HSPA4 enrichment in antigen processing and presentation together with HSPA8 and HSP90AA1. We verified the value of HSPA4 in the diagnosis and predicting prognosis of HCC. HSPA4 may not only participate in the occurrence and progression but also the immune regulation of HCC. Therefore, HSPA4 can be a potential diagnostic and prognostic biomarker and a therapeutic target for HCC.
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Affiliation(s)
| | - Jun Chen
- Laboratory Animal Center, Dalian Medical University, Dalian, China
| | - Zhi-Guo Wang
- Second Hospital of Dalian Medical University, Dalian, China
| | - Hui Liu
- Second Hospital of Dalian Medical University, Dalian, China
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20
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Halaby R. Natural Products Induce Lysosomal Membrane Permeabilization as an Anticancer Strategy. MEDICINES 2021; 8:medicines8110069. [PMID: 34822366 PMCID: PMC8624533 DOI: 10.3390/medicines8110069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 11/03/2021] [Accepted: 11/08/2021] [Indexed: 11/26/2022]
Abstract
Cancer is a global health and economic issue. The majority of anticancer therapies become ineffective due to frequent genomic turnover and chemoresistance. Furthermore, chemotherapy and radiation are non-specific, killing all rapidly dividing cells including healthy cells. In this review, we examine the ability of some natural products to induce lysosomal-mediated cell death in neoplastic cells as a way to kill them more specifically than conventional therapies. This list is by no means exhaustive. We postulate mechanisms to explain lysosomal membrane permeabilization and its role in triggering cell death in cancer cells.
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Affiliation(s)
- Reginald Halaby
- Department of Biology, Montclair State University, Montclair, NJ 07043, USA
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21
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Wagner KT, Radisic M. A New Role for Extracellular Vesicles in Cardiac Tissue Engineering and Regenerative Medicine. ADVANCED NANOBIOMED RESEARCH 2021; 1:2100047. [PMID: 34927167 PMCID: PMC8680295 DOI: 10.1002/anbr.202100047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cardiovascular diseases are the leading cause of death worldwide. Discovering new therapies to treat heart disease requires improved understanding of cardiac physiology at a cellular level. Extracellular vesicles (EVs) are plasma membrane-bound nano- and microparticles secreted by cells and known to play key roles in intercellular communication, often through transfer of biomolecular cargo. Advances in EV research have established techniques for EV isolation from tissue culture media or biofluids, as well as standards for quantitation and biomolecular characterization. EVs released by cardiac cells are known to be involved in regulating cardiac physiology as well as in the progression of myocardial diseases. Due to difficulty accessing the heart in vivo, advanced in vitro cardiac 'tissues-on-a-chip' have become a recent focus for studying EVs in the heart. These physiologically relevant models are producing new insight into the role of EVs in cardiac physiology and disease while providing a useful platform for screening novel EV-based therapeutics for cardiac tissue regeneration post-injury. Numerous hurdles have stalled the clinical translation of EV therapeutics for heart patients, but tissue-on-a-chip models are playing an important role in bridging the translational gap, improving mechanistic understanding of EV signalling in cardiac physiology, disease, and repair.
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Affiliation(s)
- Karl T Wagner
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
| | - Milica Radisic
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 27 King's College Circle, Toronto, Ontario, Canada M5S 1A1
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Ebenezer DL, Ramchandran R, Fu P, Mangio LA, Suryadevara V, Ha AW, Berdyshev E, Van Veldhoven PP, Kron SJ, Schumacher F, Kleuser B, Natarajan V. Nuclear Sphingosine-1-phosphate Lyase Generated ∆2-hexadecenal is A Regulator of HDAC Activity and Chromatin Remodeling in Lung Epithelial Cells. Cell Biochem Biophys 2021; 79:575-592. [PMID: 34085165 DOI: 10.1007/s12013-021-01005-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2021] [Indexed: 12/14/2022]
Abstract
Sphingosine-1-phosphate (S1P), a bioactive lipid mediator, is generated from sphingosine by sphingosine kinases (SPHKs) 1 and 2 and is metabolized to ∆2-hexadecenal (∆2-HDE) and ethanolamine phosphate by S1P lyase (S1PL) in mammalian cells. We have recently demonstrated the activation of nuclear SPHK2 and the generation of S1P in the nucleus of lung epithelial cells exposed to Pseudomonas aeruginosa. Here, we have investigated the nuclear localization of S1PL and the role of ∆2-HDE generated from S1P in the nucleus as a modulator of histone deacetylase (HDAC) activity and histone acetylation. Electron micrographs of the nuclear fractions isolated from MLE-12 cells showed nuclei free of ER contamination, and S1PL activity was detected in nuclear fractions isolated from primary lung bronchial epithelial cells and alveolar epithelial MLE-12 cells. Pseudomonas aeruginosa-mediated nuclear ∆2-HDE generation, and H3/H4 histone acetylation was attenuated by S1PL inhibitors in MLE-12 cells and human bronchial epithelial cells. In vitro, the addition of exogenous ∆2-HDE (100-10,000 nM) to lung epithelial cell nuclear preparations inhibited HDAC1/2 activity, and increased acetylation of Histone H3 and H4, whereas similar concentrations of S1P did not show a significant change. In addition, incubation of ∆2-HDE with rHDAC1 generated five different amino acid adducts as detected by LC-MS/MS; the predominant adduct being ∆2-HDE with lysine residues of HDAC1. Together, these data show an important role for the nuclear S1PL-derived ∆2-HDE in the modification of HDAC activity, histone acetylation, and chromatin remodeling in lung epithelial cells.
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Affiliation(s)
- David L Ebenezer
- Departments of Pharmacology & Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Ramaswamy Ramchandran
- Departments of Pharmacology & Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Panfeng Fu
- The Affiliated Hospital of School of Medicine, Ningbo University, Ningbo, China
| | - Lizar A Mangio
- Departments of Pharmacology & Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Vidyani Suryadevara
- Departments of Pharmacology & Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Alison W Ha
- Department of Biochemistry & Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
| | - Evgeny Berdyshev
- Department of Medicine, National Jewish Medical Center, Denver, CO, USA
| | - Paul P Van Veldhoven
- LIPIT, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Stephen J Kron
- Department of Molecular Genetics and Cell Biology and Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, USA
| | - Fabian Schumacher
- Institute of Pharmacy, Department of Pharmacology & Toxicology, Freie Universität Berlin, Berlin, Germany
| | - Burkhard Kleuser
- Institute of Pharmacy, Department of Pharmacology & Toxicology, Freie Universität Berlin, Berlin, Germany
| | - Viswanathan Natarajan
- Departments of Pharmacology & Regenerative Medicine, University of Illinois at Chicago, Chicago, IL, USA. .,Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA.
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A Brief Review on Erythropoietin and Mesenchymal Stem Cell Therapies for Paediatric Neurological Disorders. CURRENT STEM CELL REPORTS 2021. [DOI: 10.1007/s40778-021-00189-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Han Y, Cai Y, Lai X, Wang Z, Wei S, Tan K, Xu M, Xie H. lncRNA RMRP Prevents Mitochondrial Dysfunction and Cardiomyocyte Apoptosis via the miR-1-5p/hsp70 Axis in LPS-Induced Sepsis Mice. Inflammation 2021; 43:605-618. [PMID: 31900829 DOI: 10.1007/s10753-019-01141-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Both long non-coding RNA (lncRNA) RMRP and heat shock protein (HSP) 70 have been known to play crucial roles in inflammation. The present study investigated the roles of lncRNA RMRP and HSP70 protein 4 (HSPA4) in lipopolysaccharide (LPS)-induced sepsis. The C57BL/6 mice were treated with LPS, following which the cardiomyocytes were isolated for in vitro experiments. Further, a cardiac muscle cell line, HL-1 was transfected with plasmids expressing RMRP and HSPA4, si-NC, si-HSPA4, miR-1-5p mimic, and controls in vitro. Cell apoptosis, mitochondrial membrane potential (MMP), and levels of intracellular reactive oxygen species (ROS), mRNAs, and proteins were detected in the transfected mice tissues and cells. The LPS treatment significantly reduced the expression levels of RMRP, MMP, and mitochondrial cytochrome C. Moreover, it enhanced the cardiomyocyte apoptosis, intracellular ROS levels, cytoplasm cytochrome C levels, and the expression of caspase-3 and caspase-9 and nuclear factor κB (NF-κB) p65 subunit. The predicted RMRP-miR-1-5p-HSPA4 network was validated by co-transfection experiments in vitro in HL-1 cells. The transfection of miR-1-5p-treated cells with pcDNA-RMRP enhanced the levels of the protein HSPA4; however, no change at the mRNA level was observed. Moreover, miR-1-5p mimic attenuated the protective effect of pcDNA-HSPA4 against LPS-induced mitochondrial damage and apoptosis. In addition, we observed that silencing of HSPA4 increased the expression of nuclear p65; however, this effect could be reversed by co-transfection with pcDNA-RMRP. The lncRNA RMRP axis acts as a sponge for miR-1-5p. RMRP inhibits LPS-induced apoptosis of cardiomyocytes and mitochondrial damage by suppressing the post-transcriptional regulatory function of miR-1-5p on HSPA4. We believe that RMRP exhibits therapeutic potential for LPS-induced myocardial dysfunction both in vitro and in vivo.
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Affiliation(s)
- Ying Han
- Department of Hospital Infection Control, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Yixin Cai
- Department of Thoracic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Xiaoquan Lai
- Department of Hospital Infection Control, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhenling Wang
- Department of Hospital Infection Control, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Shiqing Wei
- Department of Hospital Infection Control, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Kun Tan
- Department of Hospital Infection Control, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Min Xu
- Department of Hospital Infection Control, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Hongyan Xie
- Department of Hospital Infection Control, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
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Middelkamp HHT, Verboven AHA, De Sá Vivas AG, Schoenmaker C, Klein Gunnewiek TM, Passier R, Albers CA, 't Hoen PAC, Nadif Kasri N, van der Meer AD. Cell type-specific changes in transcriptomic profiles of endothelial cells, iPSC-derived neurons and astrocytes cultured on microfluidic chips. Sci Rep 2021; 11:2281. [PMID: 33500551 PMCID: PMC7838281 DOI: 10.1038/s41598-021-81933-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 01/13/2021] [Indexed: 01/30/2023] Open
Abstract
In vitro neuronal models are essential for studying neurological physiology, disease mechanisms and potential treatments. Most in vitro models lack controlled vasculature, despite its necessity in brain physiology and disease. Organ-on-chip models offer microfluidic culture systems with dedicated micro-compartments for neurons and vascular cells. Such multi-cell type organs-on-chips can emulate neurovascular unit (NVU) physiology, however there is a lack of systematic data on how individual cell types are affected by culturing on microfluidic systems versus conventional culture plates. This information can provide perspective on initial findings of studies using organs-on-chip models, and further optimizes these models in terms of cellular maturity and neurovascular physiology. Here, we analysed the transcriptomic profiles of co-cultures of human induced pluripotent stem cell (hiPSC)-derived neurons and rat astrocytes, as well as one-day monocultures of human endothelial cells, cultured on microfluidic chips. For each cell type, large gene expression changes were observed when cultured on microfluidic chips compared to conventional culture plates. Endothelial cells showed decreased cell division, neurons and astrocytes exhibited increased cell adhesion, and neurons showed increased maturity when cultured on a microfluidic chip. Our results demonstrate that culturing NVU cell types on microfluidic chips changes their gene expression profiles, presumably due to distinct surface-to-volume ratios and substrate materials. These findings inform further NVU organ-on-chip model optimization and support their future application in disease studies and drug testing.
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Affiliation(s)
- H H T Middelkamp
- Applied Stem Cell Technologies, University of Twente, Enschede, The Netherlands.
- BIOS/Lab on a Chip, University of Twente, Enschede, The Netherlands.
| | - A H A Verboven
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands.
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands.
- Centre for Molecular and Biomolecular Informatics, Radboudumc, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands.
| | - A G De Sá Vivas
- Applied Stem Cell Technologies, University of Twente, Enschede, The Netherlands
- BIOS/Lab on a Chip, University of Twente, Enschede, The Netherlands
| | - C Schoenmaker
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
| | - T M Klein Gunnewiek
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - R Passier
- Applied Stem Cell Technologies, University of Twente, Enschede, The Netherlands
- Department of Anatomy and Embryology, Leiden University Medical Centre, Leiden, The Netherlands
| | - C A Albers
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
- Department of Molecular Developmental Biology, Radboud University, Nijmegen, The Netherlands
| | - P A C 't Hoen
- Centre for Molecular and Biomolecular Informatics, Radboudumc, Radboud Institute for Molecular Life Sciences, 6500 HB, Nijmegen, The Netherlands
| | - N Nadif Kasri
- Department of Human Genetics, Radboudumc, Nijmegen, The Netherlands
- Department of Cognitive Neurosciences, Radboudumc, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - A D van der Meer
- Applied Stem Cell Technologies, University of Twente, Enschede, The Netherlands.
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The expression profiles and prognostic values of HSPs family members in Head and neck cancer. Cancer Cell Int 2020; 20:220. [PMID: 32523426 PMCID: PMC7278206 DOI: 10.1186/s12935-020-01296-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 05/26/2020] [Indexed: 12/24/2022] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSC) ranks as the sixth most common malignancy. The identification of highly specific and sensitive prognostic markers and potential drug targets can contribute to enhanced patient prognosis and individualized treatments. Heat shock proteins (HSPs) act as molecular chaperones and play a crucial role in maintaining cell homeostasis. Recently, research has indicated that HSPs also act as "evil chaperones" in cancer development. Methods In this study, we assessed the expression of HSPs in HNSC patients using the ONCOMINE, GEPIA, and UALCAN databases. Mutations of HSP genes were also analysed using the cBioPortal database. Additionally, the expression levels of HSPs were verified using the Human Protein Altas (THPA) database. Results We found that the expression levels of HSPH1, HSPD1, SERPINH1, HSPA4, and HSP90AA1 were significantly higher in tissues from HNSC patients compared with normal tissues. Moreover, HSPH1, HSPD1, SERPINH1, HSPA4 and HSP90AA1 expressions were linked to disease progression. Survival analysis with the GEPIA and OncoLnc databases indicated that upregulation of HSPH1, HSPD1, SERPINH1, HSPA4 and HSP90AA1 was related to poor overall survival (OS). Conclusion This study suggests that the HSPH1, HSPD1, SERPINH1, HSPA4 and HSP90AA1 genes are potential clinical targets and prognostic biomarkers for patients with HNSC.
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Poppi DA, Moore SS, Wade NM, Glencross BD. Adequate supply of dietary taurine stimulates expression of molecular markers of growth and protein turnover in juvenile barramundi (Lates calcarifer). FISH PHYSIOLOGY AND BIOCHEMISTRY 2020; 46:953-969. [PMID: 31933028 DOI: 10.1007/s10695-020-00762-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 01/03/2020] [Indexed: 06/10/2023]
Abstract
A trial was conducted to investigate the effect of dietary taurine (Tau) supply on the plasma amino acid composition and hepatic expression of several genes in juvenile barramundi (Lates calcarifer) after feeding. Triplicate tanks of fish (average weight, 89.3 g) were fed diets containing either a deficient (1 g kg-1), adequate (8 g kg-1) or excessive (19 g kg-1) level of dietary Tau. Liver tissues collected before feeding, and at 2- and 4-h post-feeding, were analysed for expression of genes involved in pathways of sulphur amino acid turnover, Tau biosynthesis and transport, target of rapamycin (TOR) signalling, the somatotropic axis and protein turnover. The treatment had no significant effect on the profiles of any amino acid in plasma collected over time after feeding, other than Tau and glycine. The expression profile of cystine and Tau synthetic genes suggested an effect of Tau excess on the metabolism of cystine. Markers of two pathways of Tau biosynthesis appear to be active in this species, providing proof that this species possesses the ability to synthesise Tau from SAA precursors. A marker for the regulation of Tau transport and homeostasis was shown to be directly regulated by Tau availability, whilst a link between adequate supply of Tau and TOR pathway-mediated growth stimulation was also apparent. An observed depression in expression of genes of the somatotropic axis, coupled with upregulation of the proteolytic and TOR-suppressing genes, in response to excessive Tau supply in the diet, signalled that excessive Tau may not be conducive to optimal growth in this species.
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Affiliation(s)
- David A Poppi
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia.
- CSIRO Agriculture and Food, QLD Biosciences Precinct, Building 80, Services Road, St. Lucia, QLD, 4067, Australia.
| | - Stephen S Moore
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, 4067, Australia
| | - Nicholas M Wade
- CSIRO Agriculture and Food, QLD Biosciences Precinct, Building 80, Services Road, St. Lucia, QLD, 4067, Australia
| | - Brett D Glencross
- Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, UK
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Abstract
MicroRNAs (miRNA) are non-coding RNAs that regulate gene expression in up to 90% of the human genome through interactions with messenger RNA (mRNA). The expression of miRNAs varies and changes in diseased and healthy states, including all stages of myocardial ischemia-reperfusion and subsequent ischemia-reperfusion injury (IRI). These changes in expression make miRNAs an attractive potential therapeutic target. Herein, we review the differences in miRNA expression prior to ischemia (including remote ischemic conditioning and ischemic pre-conditioning), the changes during ischemia-reperfusion, and the changes in miRNA expression after IRI, with an emphasis on inflammatory and fibrotic pathways. Additionally, we review the effects of manipulating the levels of certain miRNAs on changes in infarct size, inflammation, remodeling, angiogenesis, and cardiac function after either ischemia-reperfusion or permanent coronary ligation. Levels of target miRNA can be increased using molecular mimics ("agomirs"), or can be decreased by using "antagomirs" which are antisense molecules that act to bind and thus inactivate the target miRNA sequence. Other non-coding RNAs, including long non-coding RNAs and circular RNAs, also regulate gene expression and have a role in the regulation of IRI pathways. We review the mechanisms and downstream effects of the miRNAs that have been studied as therapy in both permanent coronary ligation and ischemia-reperfusion models.
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Yang D, Su B, Bi Y, Zhang L, Zhang B, Song J, Lu Y, Du G. Preparation and Certification of a New Salvianolic Acid A Reference Material for Food and Drug Research. NATURAL PRODUCTS AND BIOPROSPECTING 2020; 10:67-75. [PMID: 32306209 PMCID: PMC7176770 DOI: 10.1007/s13659-020-00236-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/19/2020] [Indexed: 05/12/2023]
Abstract
Salvianolic acid A (Sal A), a water-soluble ingredient in Danshen, has various biological activities. Sal A and its impurities have similar physical and chemical properties, as well as strong reducibility; therefore, they are difficult to prepare and purify. In this study, high-purity Sal A was obtained by purification of sephadex chromatography and preparative chromatography. Furthermore, HPLC-DAD tandem ECD and HPLC-DAD tandem MS methods were used for non-volatile organic impurity analysis, ICP-MS method was used for non-volatile inorganic impurities and mass balance method and quantitative nuclear magnetic resonance were employed to certify the product. The structures of Sal A and its relative impurities were validated by nuclear magnetic resonance spectroscopy and mass spectrometry, and their contents were quantified as well. Following the principles of ISO Guides 34:2009 and 35:2005, a Sal A reference material was certified, covering homogeneity studies, stability studies, characterization, and uncertainty estimations.
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Affiliation(s)
- Dezhi Yang
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Bin Su
- Soteria Pharmaceutical Co., Ltd., Laiwu, 271100, People's Republic of China
| | - Yancai Bi
- Soteria Pharmaceutical Co., Ltd., Laiwu, 271100, People's Republic of China
| | - Li Zhang
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Baoxi Zhang
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Junke Song
- Beijing City Key Laboratory of Drug Target and Screening Research, National Center for Pharmaceutical Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, People's Republic of China
| | - Yang Lu
- Beijing City Key Laboratory of Polymorphic Drugs, Center of Pharmaceutical Polymorphs, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, People's Republic of China.
| | - Guanhua Du
- Beijing City Key Laboratory of Drug Target and Screening Research, National Center for Pharmaceutical Screening, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, People's Republic of China.
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Identification of cancer stem cell-related biomarkers in lung adenocarcinoma by stemness index and weighted correlation network analysis. J Cancer Res Clin Oncol 2020; 146:1463-1472. [PMID: 32221746 DOI: 10.1007/s00432-020-03194-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 03/20/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Accounting for tumor heterogeneity, cancer stem cells (CSC) are involved in tumor metastasis, relapse, and drug resistance. Genes regulating CSC characteristics in lung adenocarcinoma (LUAD) were explored and validated in this study. METHODS The mRNA stemness index (mRNAsi) of more than 500 LUAD cases from The Cancer Genome Atlas database were calculated using a one-class logistic regression machine learning algorithm based on the mRNA expression of pluripotent stem cells and their differentiated progeny. mRNAsi-related key genes were identified by weighted correlation network analysis. The expression levels and prognostic roles of key genes were analyzed in Oncomine, PrognoScan, and Kaplan-Meier plotter databases, and validated using data from our center. RESULTS The mRNAsi was significantly higher in LUAD compared with normal lung tissues. LUAD patients of advanced stage exhibited a higher mRNAsi and worse overall survival (OS). Eight key genes were identified: heat shock 70 kDa protein 4 (HSPA4), cell division cycle associated 7 (CDCA7), cell division cycle 20 (CDC20), cyclin-dependent kinase 1 (CDK1), CAP-GLY domain containing linker protein 1 (CLIP1), cyclin B1 (CCNB1), H2A histone family, member X (H2AFX), and Bloom syndrome, RecQ helicase-like (BLM). These genes were differentially expressed in various types of malignancies and validated in the LUAD cases. LUAD patients with low expression of CDC20, CDK1, CCNB1, H2AFX, or BLM had a significantly better OS, whereas OS was reduced for patients with low expression of CLIP1. In addition, the expression of CDCA7 did not significantly impact the OS of LUAD patients. The protein-protein interaction networks evaluated by STRING demonstrated strong relationships between these key genes, which were validated in our cases. CONCLUSIONS The mRNAsi was significantly higher in LUAD compared with normal samples. Eight mRNAsi-related key genes were associated with prognosis and the cell cycle, and were strongly correlated with each other and differentially expressed in tumor and normal samples. We provide a new strategy for exploring stemness-related genes in LUAD cases.
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Chanukuppa V, Paul D, Taunk K, Chatterjee T, Sharma S, Kumar S, Santra MK, Rapole S. XPO1 is a critical player for bortezomib resistance in multiple myeloma: A quantitative proteomic approach. J Proteomics 2019; 209:103504. [PMID: 31465861 DOI: 10.1016/j.jprot.2019.103504] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 07/26/2019] [Accepted: 08/19/2019] [Indexed: 02/07/2023]
Abstract
Among the blood cancers, 13% mortality is caused by Multiple myeloma (MM) type of hematological malignancy. In spite of therapeutic advances in chemotherapy treatment, still MM remains an incurable disease is mainly due to emergence of chemoresistance. At present time, FDA approved bortezomib is the first line drug for MM treatment. However, like other chemotherapy, MM patients are acquiring resistance against bortezomib. The present study aims to identify and validate bortezomib resistant protein targets in MM using iTRAQ and label free quantitative proteomic approaches. 112 differentially expressed proteins were commonly found in both approaches with similar differential expression pattern. Exportin-1 (XPO1) protein was selected for further validation as its significant high expression was observed in both iTRAQ and label free analysis. Bioinformatic analysis of these common differentially expressed proteins showed a clear cluster of proteins such as SMC1A, RCC2, CSE1, NUP88, NUP50, TPR, HSPA14, DYNLL1, RAD21 and RANBP2 being associated with XPO1. Functional studies like cell count assay, flow cytometry assay and soft agar assay proved that XPO1 knock down in RPMI 8226R cell line results in re-sensitization to bortezomib drug. The mass spectrometry data are available via ProteomeXchange with identifier PXD013859. BIOLOGICAL SIGNIFICANCE: Multiple myeloma (MM) is a type of hematological malignancy which constitutes about 13% of all blood cell related malignancies. Chemoresistance is one of the major obstacles for the successful treatment for MM. Bortezomib is a first proteasome inhibitor drug, widely used in MM treatment. The present study aims to identify and validate bortezomib resistant protein targets in MM. Here, we identified 112 candidate proteins to be associated with bortezomib resistance using global quantitative proteomic analysis. Among these candidate proteins, we show that XPO1 plays crucial role in emerging bortezomib resistance using functional studies like cell count assay, flow cytometry assay and soft agar assay. XPO1 could be a potential therapeutic target for MM and development of inhibitors of XPO1 might help to cure MM.
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Affiliation(s)
- Venkatesh Chanukuppa
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India; Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MH, India
| | - Debasish Paul
- Savitribai Phule Pune University, Ganeshkhind, Pune 411007, MH, India; Cancer Biology and Epigenetics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Khushman Taunk
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | | | | | - Saravanan Kumar
- Thermo Fisher Scientific India Pvt. Ltd, Whitefield, Bangalore 560066, KA, India
| | - Manas K Santra
- Cancer Biology and Epigenetics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India
| | - Srikanth Rapole
- Proteomics Lab, National Centre for Cell Science, Ganeshkhind, Pune 411007, MH, India.
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A nano-sized gel-in-oil suspension for transcutaneous protein delivery. Int J Pharm 2019; 567:118495. [DOI: 10.1016/j.ijpharm.2019.118495] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 06/20/2019] [Accepted: 07/01/2019] [Indexed: 12/31/2022]
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Chakafana G, Zininga T, Shonhai A. Comparative structure-function features of Hsp70s of Plasmodium falciparum and human origins. Biophys Rev 2019; 11:591-602. [PMID: 31280465 PMCID: PMC6682331 DOI: 10.1007/s12551-019-00563-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 06/20/2019] [Indexed: 01/18/2023] Open
Abstract
The heat shock protein 70 (Hsp70) family of molecular chaperones are crucial for the survival and pathogenicity of the main agent of malaria, Plasmodium falciparum. Hsp70 is central to cellular proteostasis and some of its isoforms are essential for survival of the malaria parasite. In addition, they are also implicated in the development of antimalarial drug resistance. For these reasons, they are thought to be potential drug targets, especially in antimalarial combination therapies. However, their high sequence conservation across species presents a hurdle with respect to their selective targeting. The human genome encodes 17 Hsp70 isoforms while P. falciparum encodes for only 6. The structural architecture of Hsp70s is typically characterized by a highly conserved N-terminal nucleotide-binding domain (NBD) and a less conserved C-terminal substrate-binding domain (SBD). The two domains are connected by a highly conserved linker. In spite of their fairly high sequence conservation, Hsp70s from various species possess unique signature motifs that appear to uniquely influence their function. In addition, their cooperation with co-chaperones further regulates their functional specificity. In the current review, bioinformatics tools were used to identify conserved and unique signature motifs in Hsp70s of P. falciparum versus their human counterparts. We discuss the common and distinctive structure-function features of these proteins. This information is important towards elucidating the prospects of selective targeting of parasite heat shock proteins as part of antimalarial design efforts.
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Affiliation(s)
- Graham Chakafana
- Department of Biochemistry, University of Venda, Private Bags X5050, Thohoyandou, 0950, South Africa
| | - Tawanda Zininga
- Department of Biochemistry, University of Venda, Private Bags X5050, Thohoyandou, 0950, South Africa
| | - Addmore Shonhai
- Department of Biochemistry, University of Venda, Private Bags X5050, Thohoyandou, 0950, South Africa.
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Shi J, Guo S, Wu Y, Chen G, Lai J, Xu X. Behaviour of cell penetrating peptide TAT-modified liposomes loaded with salvianolic acid B on the migration, proliferation, and survival of human skin fibroblasts. J Liposome Res 2019; 30:93-106. [DOI: 10.1080/08982104.2019.1593451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jun Shi
- Department of Traditional Chinese Medicine, Guangdong Pharmaceutical University of China, Guangzhou, PR China
- Guangdong Engineering & Technology Research of topical precise drug delivery system, Guangzhou Higher Education Mega Center, Guangdong, PR China
| | - Siyi Guo
- Department of Traditional Chinese Medicine, Guangdong Pharmaceutical University of China, Guangzhou, PR China
| | - Yanting Wu
- Department of Traditional Chinese Medicine, Guangdong Pharmaceutical University of China, Guangzhou, PR China
| | - Guitian Chen
- Department of Traditional Chinese Medicine, Guangdong Pharmaceutical University of China, Guangzhou, PR China
| | - Jianhui Lai
- Department of Traditional Chinese Medicine, Guangdong Pharmaceutical University of China, Guangzhou, PR China
| | - Xiaoqi Xu
- Department of Traditional Chinese Medicine, Guangdong Pharmaceutical University of China, Guangzhou, PR China
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Xu H, Yuan Y, Wu W, Zhou M, Jiang Q, Niu L, Ji J, Liu N, Zhang L, Wang X. Hypoxia stimulates invasion and migration of human cervical cancer cell lines HeLa/SiHa through the Rab11 trafficking of integrin αvβ3/FAK/PI3K pathway-mediated Rac1 activation. J Biosci 2018; 42:491-499. [PMID: 29358562 DOI: 10.1007/s12038-017-9699-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Hypoxia plays a key role in tumour cell survival, invasion, and metastasis. An increasing number of studies have attempted to characterize the tumour response to hypoxia and to identify predictive markers of disease. Here we show that hypoxia increases tumour cell invasion and migration by the modulation of Rab11, an important molecule for vesicular trafficking. In our study, we found that Rab11, together with the activation of Rac1, could stimulate invasion and migration of cervical cancer cell lines HeLa/SiHa in hypoxia. Activation of Rac1 activity by hypoxia seems to be central to carcinoma invasion. We also found that these effects could be related to the integrin αvβ3. In addition, we studied the molecular pathway for this process. Our results showed that in cervical cancer cell lines HeLa/SiHa, Rac1 activation in hypoxia could stimulate invasion and migration, and this process was mediated by integrin αvβ3-mediated FAK and PI3K phosphorylation. Furthermore, hypoxia induced a dramatic increase in αvβ3 integrin surface expression, and this increase is dependent on Rab11. In conclusion, our study might provide a new mechanism for the effect of hypoxia on stimulating cervical carcinoma invasion.
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Affiliation(s)
- Hao Xu
- Department of Radiotherapy, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
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Huebner H, Strick R, Wachter DL, Kehl S, Strissel PL, Schneider-Stock R, Hartner A, Rascher W, Horn LC, Beckmann MW, Ruebner M, Fahlbusch FB. Hypermethylation and loss of retinoic acid receptor responder 1 expression in human choriocarcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2017; 36:165. [PMID: 29169400 PMCID: PMC5701501 DOI: 10.1186/s13046-017-0634-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/13/2017] [Indexed: 01/06/2023]
Abstract
Background Human placental development resembles tumorigenesis, due to the invasive and fusogenic potential of trophoblasts. However, these features are tightly controlled in trophoblasts. Disturbance of this spatial and temporal regulation is thought to contribute to the rare formation of choriocarcinomas. Promoter hypermethylation and loss of the tumor suppressor Retinoic acid receptor responder 1 (RARRES1) were shown to contribute to cancer progression. Our study investigated the epigenetic and transcriptional regulation of RARRES1 in healthy human placenta in comparison to choriocarcinoma cell lines and cases. Methods Three choriocarcinoma cell lines (Jeg-3, JAR and BeWo) were treated with three different retinoic acid derivates (Am580, Tazarotene and all-trans retinoic acid) and 5-aza-2′-deoxycytidine. We analyzed RARRES1 promoter methylation by pyrosequencing and performed realtime-PCR quantification to determine RARRES1 expression in placental tissue and trophoblastic cell lines. Additionally, RARRES1 was stained in healthy placentas and in biopsies of choriocarcinoma cases (n = 10) as well as the first trimester trophoblast cell line Swan71 by immunofluorescence and immunohistochemistry. Results In the choriocarcinoma cell lines, RARRES1 expression could not be induced by sole retinoic acid treatment. Stimulation with 5-aza-2′-deoxycytidine significantly induced RARRES1 expression, which then could be further increased with Am580, Tazarotene and all-trans retinoic acid. In comparison to healthy placenta, choriocarcinoma cell lines showed a hypermethylation of the RARRES1 promoter, which correlated with a reduced RARRES1 expression. In concordance, RARRES1 protein expression was lost in choriocarcinoma tissue. Additionally, in the trophoblastic cell line Swan71, we found a significant induction of RARRES1 expression with increased cell density, during mitosis and in syncytial knots. Conclusions Our findings showed that RARRES1 expression is absent in choriocarcinoma due to promoter methylation. Based on our analysis, we hypothesize that RARRES1 might exert tumor suppressive functions in multiple cellular processes (e.g. cell cycle regulation, adhesion, invasion and apoptosis). Electronic supplementary material The online version of this article (10.1186/s13046-017-0634-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- H Huebner
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - R Strick
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - D L Wachter
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - S Kehl
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - P L Strissel
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - R Schneider-Stock
- Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - A Hartner
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Loschgestraße 15, 91054 Erlangen, Erlangen, Germany
| | - W Rascher
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Loschgestraße 15, 91054 Erlangen, Erlangen, Germany
| | - L C Horn
- Division Molecular Pathology, Institute of Pathology, University of Leipzig, Leipzig, Germany
| | - M W Beckmann
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - M Ruebner
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - F B Fahlbusch
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Loschgestraße 15, 91054 Erlangen, Erlangen, Germany.
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Ganaie IA, Naqvi SH, Jain SK, Wajid S. Reduced expression of SETD2 and SNX9 proteins in chemically induced mammary tumorigenesis in Wistar rats: a prognostic histological and proteomic study. PROTOPLASMA 2017; 254:1451-1466. [PMID: 27766425 DOI: 10.1007/s00709-016-1035-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 10/10/2016] [Indexed: 06/06/2023]
Abstract
Breast cancer is a major global health concern, appealing for precise prognostic approaches. Thus, the need is to have studies focusing on the identification and recognition of preliminary events leading to the disease. The present study reports the tracing of precancerous progression and serum proteomic analysis in a breast cancer model developed as a result of 7,12-dimethylbenz[a]anthracene (DMBA) administration. Mammary gland histological changes of prime importance were examined by histopathology, and immunohistochemical analysis with Ki-67 was performed to monitor enhanced cell proliferation, right from the onset of hyperplasia till neoplasia. Serum proteomics (one-dimensional (1D) and two-dimensional (2D) electrophoresis, followed by MALDI-TOF MS characterization) was performed to decipher the differentially expressed serum proteins in animals undergoing tumorigenesis vis-à-vis controls. The significance of our study lies in reporting the significantly reduced expression of two proteins: histone-lysine N-methyltransferase (SETD2) and sorting nexin-9 (SNX9) at very early stage (13 weeks) of tumorigenesis, while the full-fledged tumors developed after 6 months. The reduced expression of SETD2 and SNX9 was validated by western blotting and relative expression analysis using quantitative real-time PCR. These proteins may hence prove as potentially useful tools in search for prognostic markers for the early detection of mammary cancer.
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Affiliation(s)
- Ishfaq Ahmad Ganaie
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi, 110062, India
| | | | - Swatantra Kumar Jain
- Department of Biochemistry, Hamdard Institute of Medical Sciences and Research, Hamdard University (Jamia Hamdard), New Delhi, 110062, India
| | - Saima Wajid
- Department of Biotechnology, Faculty of Science, Hamdard University (Jamia Hamdard), New Delhi, 110062, India.
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Nowak J, Świątek-Kościelna B, Kałużna EM, Rembowska J, Dzikiewicz-Krawczyk A, Zawada M, Januszkiewicz-Lewandowska D. Effect of irradiation on DNA synthesis, NBN gene expression and chromosomal stability in cells with NBN mutations. Arch Med Sci 2017; 13:283-292. [PMID: 28261280 PMCID: PMC5332466 DOI: 10.5114/aoms.2017.65452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/22/2015] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION The NBN gene product is part of the MRE11/RAD50/NBN complex, which plays an essential role in genomic stability. In the study we try to answer the question what is the effect of irradiation on DNA synthesis, NBN gene expression and chromosomal stability in cells with homozygous c.657-661del, and heterozygous c.657-661del, p.I171V and p.R215W NBN gene mutations. MATERIAL AND METHODS Immortalized B-lymphocytes with NBN gene mutations were X-ray irradiated at doses of 1, 2, 5 and 8 Gy/min. Radioresistant DNA synthesis rate and the percentage of cells in phase S was analyzed by 3H thymidine and BrdU incorporation assays. NBN gene expression was quantified by real-time PCR with TaqMan fluorescent probe. RESULTS Increasing the irradiation dose resulted in gradual decrease of 3H thymidine incorporation in all cells, but significantly only in homo- and heterozygous c.657-661del cells (p-values < 0.0001). After irradiation the relative expression of NBN was significantly higher in homozygous c.657-661del and heterozygous p.R215W cells as compared to heterozygous c.657-661del, p.I171V and control cells (p < 0.01). All cells with NBN gene mutations showed significantly higher total number of chromosomal aberrations per metaphase as compared to control cells, with the highest number of aberrations in homozygous c.657-661del cells (p < 0.001). CONCLUSIONS The results obtained indicate that homozygous c.657-661del mutation affects cell sensitivity to irradiation. Moreover, homozygous variant is associated with disturbance in the activation of cell cycle checkpoints and with defects in DNA repair. In turn, heterozygous c.657-661del, p.R215W and p.I171V mutations do not substantially alter the radiosensitivity.
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Affiliation(s)
- Jerzy Nowak
- Department of Molecular Pathology, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Bogna Świątek-Kościelna
- Department of Molecular Pathology, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Ewelina M. Kałużna
- Department of Molecular Pathology, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Jolanta Rembowska
- Department of Molecular Pathology, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | | | - Mariola Zawada
- Department of Molecular Pathology, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Danuta Januszkiewicz-Lewandowska
- Department of Molecular Pathology, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
- Department of Paediatric Oncology, Haematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
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Shang W, Si X, Strappe P, Zhou Z, Blanchard C. Resistant starch attenuates impaired lipid biosynthesis induced by dietary oxidized oil via activation of insulin signaling pathways. RSC Adv 2017. [DOI: 10.1039/c7ra08855h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The current study found that deep-frying process led to an increased content of oxidized triacylglycerols in canola oil, 3.5 times higher than that of fresh canola oil (not used for frying).
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Affiliation(s)
- Wenting Shang
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- School of Food Engineering and Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Xu Si
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- School of Food Engineering and Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Padraig Strappe
- School of Medical and Applied Sciences
- Central Queensland University
- Rockhampton
- Australia
| | - Zhongkai Zhou
- Key Laboratory of Food Nutrition and Safety
- Ministry of Education
- School of Food Engineering and Biotechnology
- Tianjin University of Science and Technology
- Tianjin 300457
| | - Chris Blanchard
- ARC Industrial Transformation Training Centre for Functional Grains
- Charles Sturt University
- Wagga Wagga
- Australia
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Kaur M, Silakari O. Ligand-based and e-pharmacophore modeling, 3D-QSAR and hierarchical virtual screening to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3). J Biomol Struct Dyn 2016; 35:3043-3060. [PMID: 27678281 DOI: 10.1080/07391102.2016.1240108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The clinical efficacy of multiple kinase inhibitors has caught the interest of Pharmaceutical and Biotech researchers to develop potential drugs with multi-kinase inhibitory activity for complex diseases. In the present work, we attempted to identify dual inhibitors of spleen tyrosine kinase (Syk) and janus kinase 3 (JAK3), keys players in immune signaling, by developing ideal pharmacophores integrating Ligand-based pharmacophore models (LBPMs) and Structure-based pharmacophore models (SBPMs), thereby projecting the optimum pharmacophoric required for inhibition of both the kinases. The four point LBPM; ADPR.14 suggested the presence of one hydrogen bond acceptor, one hydrogen bond donor, one positive ionizable, and one ring aromatic feature for Syk inhibitory activity and AADH.54 proposed the necessity of two hydrogen bond acceptor, one hydrogen bond donor, and one hydrophobic feature for JAK3 inhibitory activity. To our interest, SBPMs identified additional ring aromatic features required for inhibition of both the kinases. For Syk inhibitory activity, the hydrogen bond acceptor feature indicated by LBPM was devoid of forming hydrogen bonding interaction with the hinge region amino acid residue (Ala451). Thus merging the information revealed by both LBPMs and SBPMs, ideal pharmacophore models i.e. ADPRR.14 (Syk) and AADHR.54 (JAK3) were generated. These models after rigorous statistical validation were used for screening of Asinex database. The systematic virtual screening protocol, including pharmacophore and docking-based screening, ADME property, and MM-GBSA energy calculations, retrieved final 10 hits as dual inhibitors of Syk and JAK3. Final 10 hits thus obtained can aid in the development of potential therapeutic agents for autoimmune disorders. Also the top two hits were evaluated against both the enzymes.
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Affiliation(s)
- Maninder Kaur
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , Punjab 147002 , India
| | - Om Silakari
- a Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research , Punjabi University , Patiala , Punjab 147002 , India
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Radons J. The human HSP70 family of chaperones: where do we stand? Cell Stress Chaperones 2016; 21:379-404. [PMID: 26865365 PMCID: PMC4837186 DOI: 10.1007/s12192-016-0676-6] [Citation(s) in RCA: 358] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 01/23/2023] Open
Abstract
The 70-kDa heat shock protein (HSP70) family of molecular chaperones represents one of the most ubiquitous classes of chaperones and is highly conserved in all organisms. Members of the HSP70 family control all aspects of cellular proteostasis such as nascent protein chain folding, protein import into organelles, recovering of proteins from aggregation, and assembly of multi-protein complexes. These chaperones augment organismal survival and longevity in the face of proteotoxic stress by enhancing cell viability and facilitating protein damage repair. Extracellular HSP70s have a number of cytoprotective and immunomodulatory functions, the latter either in the context of facilitating the cross-presentation of immunogenic peptides via major histocompatibility complex (MHC) antigens or in the context of acting as "chaperokines" or stimulators of innate immune responses. Studies have linked the expression of HSP70s to several types of carcinoma, with Hsp70 expression being associated with therapeutic resistance, metastasis, and poor clinical outcome. In malignantly transformed cells, HSP70s protect cells from the proteotoxic stress associated with abnormally rapid proliferation, suppress cellular senescence, and confer resistance to stress-induced apoptosis including protection against cytostatic drugs and radiation therapy. All of the cellular activities of HSP70s depend on their adenosine-5'-triphosphate (ATP)-regulated ability to interact with exposed hydrophobic surfaces of proteins. ATP hydrolysis and adenosine diphosphate (ADP)/ATP exchange are key events for substrate binding and Hsp70 release during folding of nascent polypeptides. Several proteins that bind to distinct subdomains of Hsp70 and consequently modulate the activity of the chaperone have been identified as HSP70 co-chaperones. This review focuses on the regulation, function, and relevance of the molecular Hsp70 chaperone machinery to disease and its potential as a therapeutic target.
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Affiliation(s)
- Jürgen Radons
- Scientific Consulting International, Mühldorfer Str. 64, 84503, Altötting, Germany.
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Discovery of a selective, safe and novel anti-malarial compound with activity against chloroquine resistant strain of Plasmodium falciparum. Sci Rep 2015; 5:13838. [PMID: 26346444 PMCID: PMC4561909 DOI: 10.1038/srep13838] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/27/2015] [Indexed: 12/19/2022] Open
Abstract
In recent years the DNA minor groove has attracted much attention for the development of anti-malarial agents. In view of this we have attempted to discover novel DNA minor groove binders through in-silico and in-vitro workflow. A rigorously validated pharmacophore model comprising of two positive ionizable (PI), one hydrophobic (HY) and one ring aromatic (RA) features was used to mine NCI chemical compound database. This led to retrieval of many hits which were screened on the basis of estimated activity, fit value and Lipinski's violation. Finally two compounds NSC639017 and NSC371488 were evaluated for their in-vitro anti-malarial activities against Plasmodium falciparum 3D7 (CQ sensitive) and K1 (CQ resistant) strains by SYBR green-I based fluorescence assay. The results revealed that out of two, NSC639017 posses excellent anti-malarial activity particularly against chloroquine resistant strain and moreover NSC639017 also appeared to be safe (CC50 126.04 μg/ml) and selective during cytotoxicity evaluation.
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Caburet S, Anttonen M, Todeschini AL, Unkila-Kallio L, Mestivier D, Butzow R, Veitia RA. Combined comparative genomic hybridization and transcriptomic analyses of ovarian granulosa cell tumors point to novel candidate driver genes. BMC Cancer 2015; 15:251. [PMID: 25884336 PMCID: PMC4407711 DOI: 10.1186/s12885-015-1283-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 03/27/2015] [Indexed: 12/23/2022] Open
Abstract
Background Ovarian granulosa cell tumors (GCTs) are the most frequent sex cord-stromal tumors. Several studies have shown that a somatic mutation leading to a C134W substitution in the transcription factor FOXL2 appears in more than 95% of adult-type GCTs. Its pervasive presence suggests that FOXL2 is the main cancer driver gene. However, other mutations and genomic changes might also contribute to tumor formation and/or progression. Methods We have performed a combined comparative genomic hybridization and transcriptomic analyses of 10 adult-type GCTs to obtain a picture of the genomic landscape of this cancer type and to identify new candidate co-driver genes. Results Our results, along with a review of previous molecular studies, show the existence of highly recurrent chromosomal imbalances (especially, trisomy 14 and monosomy 22) and preferential co-occurrences (i.e. trisomy 14/monosomy 22 and trisomy 7/monosomy 16q). In-depth analyses showed the presence of recurrently broken, amplified/duplicated or deleted genes. Many of these genes, such as AKT1, RUNX1 and LIMA1, are known to be involved in cancer and related processes. Further genomic explorations suggest that they are functionally related. Conclusions Our combined analysis identifies potential candidate genes, whose alterations might contribute to adult-type GCT formation/progression together with the recurrent FOXL2 somatic mutation. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1283-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sandrine Caburet
- Institut Jacques Monod, Paris, France. .,Université Paris Diderot/Paris, Paris, France. .,Université Paris-Diderot & Institut Jacques Monod, CNRS-UMR 7592, Bâtiment Buffon, 15 Rue Hélène Brion, Paris, Cedex 13, France.
| | - Mikko Anttonen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland. .,Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Anne-Laure Todeschini
- Institut Jacques Monod, Paris, France. .,Université Paris Diderot/Paris, Paris, France.
| | - Leila Unkila-Kallio
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | - Denis Mestivier
- Institut Jacques Monod, Paris, France. .,Université Paris Diderot/Paris, Paris, France.
| | - Ralf Butzow
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland. .,Department of pathology, University of Helsinki, and HUSLAB, Helsinki University Central Hospital, Helsinki, Finland.
| | - Reiner A Veitia
- Institut Jacques Monod, Paris, France. .,Université Paris Diderot/Paris, Paris, France. .,Université Paris-Diderot & Institut Jacques Monod, CNRS-UMR 7592, Bâtiment Buffon, 15 Rue Hélène Brion, Paris, Cedex 13, France.
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Nandy A, Roy K, Saha A. Exploring molecular fingerprints of selective PPARδ agonists through comparative and validated chemometric techniques. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2015; 26:363-382. [PMID: 25986170 DOI: 10.1080/1062936x.2015.1039576] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Peroxysome proliferator-activated receptors (PPARs) have grown greatly in importance due to their role in the metabolic profile. Among three subtypes (α, γ and δ), we here consider the least investigated δ subtype to explore the molecular fingerprints of selective PPARδ agonists. Validated QSAR models (regression based 2D-QSAR, HQSAR and KPLS) and molecular docking with dynamics analyses support the inference of classification-based Bayesian and recursive models. Chemometric studies indicate that the presence of ether linkages and heterocyclic rings has optimum influence in imparting selective bioactivity. Pharmacophore models and docking with molecular dynamics analyses postulate the occurrence of aromatic rings, HB acceptor and a hydrophobic region as crucial molecular fragments for development of PPARδ modulators. Multi-chemometric studies suggest the essential structural requirements of a molecule for imparting potent and selective PPARδ modulation.
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Affiliation(s)
- A Nandy
- a Department of Chemical Technology , University of Calcutta , Kolkata , India
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Yang Z, Zhuang L, Szatmary P, Wen L, Sun H, Lu Y, Xu Q, Chen X. Upregulation of heat shock proteins (HSPA12A, HSP90B1, HSPA4, HSPA5 and HSPA6) in tumour tissues is associated with poor outcomes from HBV-related early-stage hepatocellular carcinoma. Int J Med Sci 2015; 12:256-63. [PMID: 25798051 PMCID: PMC4366630 DOI: 10.7150/ijms.10735] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/21/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Heat shock proteins (HSPs) are overexpressed in human hepatocellular carcinoma (HCC) tissue and correlate with aggressiveness and prognosis of HCC. METHODS Using the GSE14520 microarray expression profile from Gene Expression Omnibus, we compared HSP gene expression between tumour and non-tumour tissues and correlated this with outcomes in HCC patients. RESULTS We analysed 220 hepatitis B virus (HBV)-related HCC patients and 25 HSPs in this study. With the exception of HSPA4L, HSPA12A and HSPB8, members of the HSP family, including HSPH1, HSPBP1, HSPA1A, HSPA1B, HSPA1L, HSPA2, HSPA4, HSPA5, HSPA8, HSPA9, HSPAA1, HSPAB1, HSPA14, HSPB11, HSPA13, HSP90B1 and HSPBAP1, were all overexpressed in tumour tissues (all P < 0.001). In contrast, HSPB6, HSPB7, HSPA6, HSPB2 and HSPB3 were upregulated in non-tumour tissues (all P < 0.001). Multivariate analysis showed that cirrhosis (HR = 5.282, 95% CI = 1.294-21.555, P = 0.02), Barcelona Clinic liver cancer (BCLC) staging (HR = 2.151, 95% CI = 1.682-2.750, P < 0.001), HSPA12A (HR = 1.042, 95% CI = 1.003-1.082, P = 0.033) and HSP90B1 (HR = 1.001, 95% CI = 1.000-1.001, P = 0.011) were negatively associated with survival of HBV-related HCC patients. Furthermore, advanced BCLC staging (HR = 1.797, 95% CI = 1.439-2.244, P < 0.001) was also associated with earlier recurrence of HCC. The high expression of HSPA4 (HR = 1.002, 95% CI = 1.000-1.004, P = 0.019), HSPA5 (HR = 1.0, 95% CI = 1.0-1.0, P = 0.046) and HSPA6 (HR = 1.008, 95% CI = 1.001-1.015, P = 0.021) was similarly associated with HCC recurrence. CONCLUSIONS The expression of most HSPs was higher in tumour tissues than in non-tumour tissues. High BCLC staging scores, advanced cirrhosis and the overexpression of HSPA12A and HSP90B1 might be associated with poor survival from HCC, whereas high levels of HSPA4, HSPA5 and HSPA6 might be associated with earlier recurrence of HCC.
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Affiliation(s)
- Zongguo Yang
- 1. Department of Traditional Chinese Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Liping Zhuang
- 2. Department of Integrative Medicine, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- 3. Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Peter Szatmary
- 4. NIHR Liverpool Pancreas Biomedical Research Unit, Royal Liverpool University Hospital, Liverpool L69 3GA, UK
- 5. Department of Molecular and Clinical Cancer Medicine, Institute of Translation medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Li Wen
- 4. NIHR Liverpool Pancreas Biomedical Research Unit, Royal Liverpool University Hospital, Liverpool L69 3GA, UK
- 5. Department of Molecular and Clinical Cancer Medicine, Institute of Translation medicine, University of Liverpool, Liverpool L69 3GA, UK
| | - Hua Sun
- 1. Department of Traditional Chinese Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yunfei Lu
- 1. Department of Traditional Chinese Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Qingnian Xu
- 1. Department of Traditional Chinese Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Xiaorong Chen
- 1. Department of Traditional Chinese Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- ✉ Corresponding author: Xiaorong Chen, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Jinshan District, Shanghai 201508, China. Tel: +86 21 37990333; Fax: +86 21 57248762;
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Morisaki T, Yashiro M, Kakehashi A, Inagaki A, Kinoshita H, Fukuoka T, Kasashima H, Masuda G, Sakurai K, Kubo N, Muguruma K, Ohira M, Wanibuchi H, Hirakawa K. Comparative proteomics analysis of gastric cancer stem cells. PLoS One 2014; 9:e110736. [PMID: 25379943 PMCID: PMC4224387 DOI: 10.1371/journal.pone.0110736] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Accepted: 09/16/2014] [Indexed: 02/07/2023] Open
Abstract
Cancer stem cells (CSCs) are responsible for cancer progression, metastasis, and recurrence. To date, the specific markers of CSCs remain undiscovered. The aim of this study was to identify novel biomarkers of gastric CSCs for clinical diagnosis using proteomics technology. CSC-like SP cells, OCUM-12/SP cells, OCUM-2MD3/SP cells, and their parent OCUM-12 cells and OCUM-2MD3 cells were used in this study. Protein lysates from each cell line were analyzed using QSTAR Elite Liquid Chromatography with Tandem Mass Spectrometry, coupled with isobaric tags for relative and absolute quantitation technology. Candidate proteins detected by proteomics technology were validated by immunohistochemical analysis of 300 gastric cancers. Based on the results of LC-MS/MS, eight proteins, including RBBP6, GLG1, VPS13A, DCTPP1, HSPA9, HSPA4, ALDOA, and KRT18, were up-regulated in both OCUM-12/SP cells and OCUM-2MD3/SP cells when compared to their corresponding parent cells. RT-PCR analysis indicated that the expression level of RBBP6, HSPA4, DCTPP1, HSPA9, VPS13A, ALDOA, GLG1, and CK18 was high in OCUM-12/SP and OCUM-2MD3/SP, in compared with the control of parent OCUM-12 and OCUM-2MD3. These proteins were significantly associated with advanced invasion depth, lymph node metastasis, distant metastasis, or advanced clinical stage. RBBP6, DCTPP1, HSPA4, and ALDOA expression in particular were significantly associated with a poor prognosis in the 300 gastric cancer patients. RBBP6 was determined to be an independent prognostic factor. The motility-stimulating ability of OCUM-12/SP cells and OCUM-2MD3/SP cells was inhibited by RBBP6 siRNA. These findings might suggest that the eight proteins, RBBP6, GLG1, VPS13A, DCTPP1, HSPA9, HSPA4, ALDOA, and KRT18, utilizing comparative proteomics analysis, were perceived to be potential CSC markers of gastric cancer. Of the eight candidate proteins, RBBP6 was suggested to be a promising prognostic biomarker and a therapeutic target for gastric cancer.
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Affiliation(s)
- Tamami Morisaki
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masakazu Yashiro
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
- Oncology Institute of Geriatrics and Medical Science, Osaka City University Graduate School of Medicine, Osaka, Japan
- * E-mail:
| | - Anna Kakehashi
- Department of Pathology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Azusa Inagaki
- Department of Pathology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Haruhito Kinoshita
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Tatsunari Fukuoka
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hiroaki Kasashima
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Go Masuda
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Katsunobu Sakurai
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Naoshi Kubo
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Kazuya Muguruma
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Masaichi Ohira
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Hideki Wanibuchi
- Department of Pathology, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Kosei Hirakawa
- Department of Surgical Oncology, Osaka City University Graduate School of Medicine, Osaka, Japan
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Paliwal S, Mittal A, Sharma M, pandey A, Singh A, Paliwal S. Pharmacophore and molecular docking based identification of novel structurally diverse PDE-5 inhibitors. Med Chem Res 2014. [DOI: 10.1007/s00044-014-1144-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Papageorgiou I, Abberton T, Fuller M, Tipper JL, Fisher J, Ingham E. Biological Effects of Clinically Relevant CoCr Nanoparticles in the Dura Mater: An Organ Culture Study. NANOMATERIALS 2014; 4:485-504. [PMID: 28344233 PMCID: PMC5304670 DOI: 10.3390/nano4020485] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2014] [Revised: 05/09/2014] [Accepted: 05/26/2014] [Indexed: 01/12/2023]
Abstract
Medical interventions for the treatment of spinal disc degeneration include total disc replacement and fusion devices. There are, however, concerns regarding the generation of wear particles by these devices, the majority of which are in the nanometre sized range with the potential to cause adverse biological effects in the surrounding tissues. The aims of this study were to develop an organ culture model of the porcine dura mater and to investigate the biological effects of CoCr nanoparticles in this model. A range of histological techniques were used to analyse the structure of the tissue in the organ culture. The biological effects of the CoCr wear particles and the subsequent structural changes were assessed using tissue viability assays, cytokine assays, histology, immunohistochemistry, and TEM imaging. The physiological structure of the dura mater remained unchanged during the seven days of in vitro culture. There was no significant loss of cell viability. After exposure of the organ culture to CoCr nanoparticles, there was significant loosening of the epithelial layer, as well as the underlying collagen matrix. TEM imaging confirmed these structural alterations. These structural alterations were attributed to the production of MMP-1, -3, -9, -13, and TIMP-1. ELISA analysis revealed that there was significant release of cytokines including IL-8, IL-6, TNF-α, ECP and also the matrix protein, tenascin-C. This study suggested that CoCr nanoparticles did not cause cytotoxicity in the dura mater but they caused significant alterations to its structural integrity that could lead to significant secondary effects due to nanoparticle penetration, such as inflammation to the local neural tissue.
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Affiliation(s)
- Iraklis Papageorgiou
- IMBE (Institute of Medical & Biological Engineering), School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Thomas Abberton
- IMBE (Institute of Medical & Biological Engineering), School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Martin Fuller
- IMBE (Institute of Medical & Biological Engineering), School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - Joanne L Tipper
- IMBE (Institute of Medical & Biological Engineering), School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
| | - John Fisher
- IMBE, School of Mechanical Engineering, University of Leeds, Leeds LS2 9JT, UK.
| | - Eileen Ingham
- IMBE (Institute of Medical & Biological Engineering), School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.
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Zhou GJ, Wang W, Xie XM, Qin MJ, Kuai BK, Zhou TS. Post-harvest induced production of salvianolic acids and significant promotion of antioxidant properties in roots of Salvia miltiorrhiza (Danshen). Molecules 2014; 19:7207-22. [PMID: 24886944 PMCID: PMC6271733 DOI: 10.3390/molecules19067207] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 01/17/2023] Open
Abstract
Danshen, the dried roots of Salvia miltiorrhiza, is an extremely valued Traditional Chinese Medicine. Previously, we have demonstrated that salvianolic acid B (SaB), the important bioactive ingredient in this herb, was a post-harvest product. Here, we further reported that all salvianolic acids (SAs) in the roots were post-harvest products of the drying process. In addition, the results of various radical scavenging activity assays, including lipid peroxidation (1), DPPH (2), hydroxyl (3) and superoxide (4), were significantly increased along with the accumulation of total salvianolic acids in the process. The contents of chemical targets and antioxidant activities both reached the highest value under thermal treatment at 130 °C for 80 min. In this dehydration period, contents of SaB, and sum of nine SAs increased from 0.01% to 5.51%, and 0.20% to 6.61%; and IC50 of antioxidant activity decreased from 4.85 to 2.69 (1); 7.75 to 0.43 (2); 2.57 to 1.13 (3) and 17.25 to 1.10 mg/mL. These results further supported the hypothesis that the newly harvested plant roots were still physiologically active and the secondary metabolites might be produced due to dehydration stress after harvest. Our findings supplied an important and useful theoretical basis for promoting the quality of Danshen and other medicinal plant materials.
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Affiliation(s)
- Guo-Jun Zhou
- Research Center of Natural Products, Institute of Plant Biology, Fudan University, Shanghai 200433, China
| | - Wei Wang
- Research Center of Natural Products, Institute of Plant Biology, Fudan University, Shanghai 200433, China
| | - Xiao-Mei Xie
- School of Traditional Chinese Pharmacy, Anhui University of Chinese Medicine, Hefei 230038, China
| | - Min-Jian Qin
- Department of Resources Science of Traditional Chinese Medicines & Key Laboratory of Modern Chinese Medicines (Ministry of Education), China Pharmaceutical University, Nanjing 210009, China
| | - Ben-Ke Kuai
- Research Center of Natural Products, Institute of Plant Biology, Fudan University, Shanghai 200433, China
| | - Tong-Shui Zhou
- Research Center of Natural Products, Institute of Plant Biology, Fudan University, Shanghai 200433, China.
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Mittal A, Paliwal S, Sharma M, Singh A, Sharma S, Yadav D. Pharmacophore based virtual screening, molecular docking and biological evaluation to identify novel PDE5 inhibitors with vasodilatory activity. Bioorg Med Chem Lett 2014; 24:3137-41. [PMID: 24856068 DOI: 10.1016/j.bmcl.2014.05.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 04/30/2014] [Accepted: 05/02/2014] [Indexed: 11/18/2022]
Abstract
Prompted by the role of PDE5 and its closely associated cAMP and cGMP in hypertension, we have attempted to discover novel PDE5 inhibitors through ligand based virtual screening. Rigorously validated model comprising of one HBA, one HY and one RA was used as a query to search the NCI database leading to retrieval of many compounds which were screened on the basis of estimated activity, fit value and Lipinski's violation. Selected compounds were subjected to docking studies which resulted into visualization of potential interaction capabilities of NCI compounds in line to pharmacophoric features. Finally three compounds were subjected to in vitro evaluation using the isolated rat aortic model. The results showed that all three compounds are potent and novel PDE5 inhibitors with vasodilatory activity range from 10(-2) to 10(-5) M.
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Affiliation(s)
- Anupama Mittal
- Department of Pharmacy, Banasthali University, P.O. Banasthali, Rajasthan 304022, India.
| | - Sarvesh Paliwal
- Department of Pharmacy, Banasthali University, P.O. Banasthali, Rajasthan 304022, India.
| | - Mukta Sharma
- Department of Pharmacy, Banasthali University, P.O. Banasthali, Rajasthan 304022, India.
| | - Aarti Singh
- Department of Pharmacy, Banasthali University, P.O. Banasthali, Rajasthan 304022, India.
| | - Swapnil Sharma
- Department of Pharmacy, Banasthali University, P.O. Banasthali, Rajasthan 304022, India.
| | - Divya Yadav
- Department of Pharmacy, Banasthali University, P.O. Banasthali, Rajasthan 304022, India.
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