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Hossain MM, Khalid A, Akhter Z, Parveen S, Ayaz MO, Bhat AQ, Badesra N, Showket F, Dar MS, Ahmed F, Dhiman S, Kumar M, Singh U, Hussain R, Keshari P, Mustafa G, Nargorta A, Taneja N, Gupta S, Mir RA, Kshatri AS, Nandi U, Khan N, Ramajayan P, Yadav G, Ahmed Z, Singh PP, Dar MJ. Discovery of a novel and highly selective JAK3 inhibitor as a potent hair growth promoter. J Transl Med 2024; 22:370. [PMID: 38637842 PMCID: PMC11025159 DOI: 10.1186/s12967-024-05144-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/23/2024] [Indexed: 04/20/2024] Open
Abstract
JAK-STAT signalling pathway inhibitors have emerged as promising therapeutic agents for the treatment of hair loss. Among different JAK isoforms, JAK3 has become an ideal target for drug discovery because it only regulates a narrow spectrum of γc cytokines. Here, we report the discovery of MJ04, a novel and highly selective 3-pyrimidinylazaindole based JAK3 inhibitor, as a potential hair growth promoter with an IC50 of 2.03 nM. During in vivo efficacy assays, topical application of MJ04 on DHT-challenged AGA and athymic nude mice resulted in early onset of hair regrowth. Furthermore, MJ04 significantly promoted the growth of human hair follicles under ex-vivo conditions. MJ04 exhibited a reasonably good pharmacokinetic profile and demonstrated a favourable safety profile under in vivo and in vitro conditions. Taken together, we report MJ04 as a highly potent and selective JAK3 inhibitor that exhibits overall properties suitable for topical drug development and advancement to human clinical trials.
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Affiliation(s)
- Md Mehedi Hossain
- Laboratory of Cell and Molecular Biology, Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Arfan Khalid
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Zaheen Akhter
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Sabra Parveen
- Laboratory of Cell and Molecular Biology, Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Mir Owais Ayaz
- Laboratory of Cell and Molecular Biology, Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Aadil Qadir Bhat
- Laboratory of Cell and Molecular Biology, Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Neetu Badesra
- Laboratory of Cell and Molecular Biology, Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Farheen Showket
- Laboratory of Cell and Molecular Biology, Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohmmad Saleem Dar
- Laboratory of Cell and Molecular Biology, Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
| | - Farhan Ahmed
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India
| | - Sumit Dhiman
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Mukesh Kumar
- Medicinal Product Chemistry, Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Umed Singh
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Razak Hussain
- Department of Entomology, University of Illinois Urbana-Champaign, Urbana, IL, 61801, USA
| | - Pankaj Keshari
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Ghulam Mustafa
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Amit Nargorta
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Neha Taneja
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - Somesh Gupta
- Department of Dermatology and Venereology, All India Institute of Medical Sciences, New Delhi, India
| | - Riyaz A Mir
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Aravind Singh Kshatri
- Division of Neuroscience and Ageing Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow, 226031, India
| | - Utpal Nandi
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Nooruddin Khan
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500046, India
| | - P Ramajayan
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Govind Yadav
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Zabeer Ahmed
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India
- Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India
| | - Parvinder Pal Singh
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
- Natural Products and Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India.
| | - Mohd Jamal Dar
- Laboratory of Cell and Molecular Biology, Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, Jammu and Kashmir, 180001, India.
- Academy of Scientific & Innovative Research, Ghaziabad, Uttar Pradesh, 201002, India.
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Lone M, Shadang M, Akhter Q, Kumar M, Mallick S, Gogia A, Nilima N, Chauhan SS, Mir RA. The Expression of the RUVBL1 Component of the R2TP Complex Correlates with Poor Prognosis in DLBCL. Pathobiology 2022; 89:146-156. [PMID: 35078195 DOI: 10.1159/000520723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 11/01/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Diffuse large B-cell lymphoma (DLBCL) is the most prevalent subtype of non-Hodgkin's lymphoma (NHL) accounting for 30% of adult NHL worldwide and 50% in developing countries like India. DNA damage and Myc-induced transformation are well-known contributing factors towards development of DLBCL. A recently identified HSP90 co-chaperone complex R2TP has been shown to contribute towards DNA damage and Myc-induced transformation. This study aimed to analyse the immunohistochemical (IHC) expression of R2TP complex components RUVBL1, PIH1D1, and RPAP3 in DLBCL patients and correlate with prognosis. METHODS DLBCL (n = 54) histological slides were retrieved from archives, and detailed histomorphological and clinical features were noted. IHC staining of R2TP complex components RUVBL1, PIH1D1, and RPAP3 was performed on 54 cases (FFPE) of DLBCL. Expression data were correlated with survival and clinical features. RESULTS Out of the 54 DLBCL cases, 59.26% (n = 32) stained positive for RUVBL1. The RUVBL1 expression was associated with poor prognosis in both progression-free survival (PFS) (p = 0.0146) and overall survival (OS) (p = 0.0328). The expression was positively correlated with bone marrow involvement (p = 0.0525). The expression of PIH1D1 was observed in 68.51% (n = 32) of DLBCL cases, and positive correlation was observed with international prognostic index score (p = 0.0246); however, no correlation was observed with PFS or OS. Finally, RPAP3 was found immunopositive in only 1 case of DLBCL. CONCLUSIONS Immunopositivity for RUVBL1 is associated with poor prognosis along with a higher relapse rate amongst the DLBCL patients. PIH1D1 immunopositivity correlated with a higher IPI score.
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Affiliation(s)
- Moien Lone
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Mahaiwon Shadang
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Qulsum Akhter
- Government College for Women, Nawakadal, Srinagar, India
| | - Mithilesh Kumar
- School of Life Sciences, Jaipur National University, Jaipur, India
| | - Saumyaranjan Mallick
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Ajay Gogia
- Department of Medical Oncology, Institute of Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Nilima Nilima
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - Shyam S Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Riyaz A Mir
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
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Sharma R, Kumar V, Logani A, Chawla A, Mir RA, Sharma S, Kalaivani M. Association between concentration of active MMP-9 in pulpal blood and pulpotomy outcome in permanent mature teeth with irreversible pulpitis - a preliminary study. Int Endod J 2020; 54:479-489. [PMID: 33128238 DOI: 10.1111/iej.13437] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 12/11/2022]
Abstract
AIM To investigate the correlation between the concentration of active-matrix metalloproteinases-9 (aMMP-9) in pulpal blood and the outcome of pulpotomy in mature permanent teeth with symptomatic irreversible pulpitis (SIP). METHODOLOGY Forty permanent molar teeth with a clinical diagnosis of SIP and normal apical tissues with periapical index (PAI) score ≤ 2 and ten permanent teeth (8 molars and two premolars) with a diagnosis of normal pulp that required root canal treatment for prosthetic reasons from patients between the ages of 15-35 years were recruited. All clinical procedures were performed under local anaesthesia and rubber dam isolation. After access opening, the coronal pulp tissue was amputated up to the canal orifice. A 100 μL volume of the pulpal blood was collected using a micropipette and transported to the laboratory. Sodium hypochlorite (2.5 %) was used as a haemostatic agent, and mineral trioxide aggregate (MTA) was used as the pulp capping material. The tooth was restored with composite at the same visit. Teeth with normal pulps were treated with single-visit root canal treatment. Patients with pulpotomy were recalled at 6 and 12 months. Outcome assessment of teeth with pulpotomy was carried out at 12 months and was categorized as success (asymptomatic patients with PAI score ≤ 2) or failure (symptomatic patients or PAI score ≥ 3). Quantification of aMMP-9 in pulpal blood was achieved using a fluorometric assay. The following statistical analyses were performed to assess the data: t-test, Fisher's exact test, kappa coefficient, non-parametric test, Wilcoxon rank-sum test, Spearman rank correlation test and receiver operating characteristic curve (ROC). RESULT The success rate of pulpotomy was 88 % at 12-months. There was a significant difference between the median concentrations of aMMP-9 in pulpal blood of teeth with normal pulps (52 (12-96) ng mL-1 :) and SIP (193.3 (25.8-607.7) ng mL-1 :) (P = 0.0003) and successful (132.3 (25.8-548.3) ng mL-1 :) and failed cases (512.4 (334.8-607.7 ng mL-1 :) (P = 0.0015) of MTA pulpotomy. A significant association was established between aMMP-9 concentration and outcome of pulpotomy. The area under the receiver operating characteristics curve (0.9484, 95%CI) suggested excellent discriminatory power of aMMP-9 concentration in pulpal blood to predict the pulpotomy outcome. CONCLUSION The pulpal blood concentration of aMMP-9 was significantly associated with the outcome of pulpotomy in teeth with symptomatic irreversible pulpitis, where it may be used as a potential prognostic biomarker.
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Affiliation(s)
- R Sharma
- Division of Conservative Dentistry and Endodontics, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - V Kumar
- Division of Conservative Dentistry and Endodontics, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - A Logani
- Division of Conservative Dentistry and Endodontics, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - A Chawla
- Division of Conservative Dentistry and Endodontics, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - R A Mir
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - S Sharma
- Division of Conservative Dentistry and Endodontics, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - M Kalaivani
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
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Yadav VS, Mir RA, Bhatia A, Yadav R, Shadang M, Chauhan SS, Dhingra K, Kharbanda OP, Yadav R, Garg R. Metallothionein levels in gingival crevicular fluid, saliva and serum of smokers and non-smokers with chronic periodontitis. J Periodontol 2020; 92:1329-1338. [PMID: 33107036 DOI: 10.1002/jper.20-0314] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/03/2020] [Accepted: 10/20/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND Metallothionein (MT), a cysteine rich protein is involved as a radical scavenger in several pathological conditions associated with oxidative stress; however, its role in periodontal disease still remains elusive. The aim of this cross-sectional study is to determine the serum, saliva and gingival crevicular fluid (GCF) levels of MT in smokers (S) and non-smokers (NS) with chronic periodontitis (CP), and compare them with those of periodontally healthy (PH) individuals. METHODS A total of 85 participants were enrolled: 45 patients with CP (23 S [CP+S] and 22 NS [CP+NS]) and 40 PH individuals (20 S [PH+S] and 20 NS [PH+NS]). In all the study participants, clinical periodontal parameters (plaque index, gingival index, sulcus bleeding index, probing depth, and clinical attachment level) were recorded and samples of serum, saliva and GCF were collected. Enzyme-linked immunosorbent assay was used to determine the levels of MT in the samples. RESULTS All periodontal clinical parameters were significantly higher in the CP groups as compared to PH groups (P < 0.05). MT levels in CP+S group were significantly raised in comparison to other three groups. There was no statistically significant difference in MT levels among CP+NS and PH+S groups (P > 0.05); however, relatively higher levels were observed in GCF and saliva in CP+NS group. When all the study groups were observed together, MT levels were positively correlated with clinical parameters. CONCLUSIONS Results of present study suggest that smoking and CP can induce the synthesis of MT owing to increased oxidative stress and heavy metals intoxication. Further longitudinal studies with large sample size and an interventional arm are needed to substantiate the role of MT as a potential biomarker in periodontitis.
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Affiliation(s)
- Vikender S Yadav
- Division of Periodontics, Centre for Dental Education and Research, All India Institute of Medical, Sciences, New Delhi, India
| | - Riyaz A Mir
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Anu Bhatia
- Division of Periodontics, Centre for Dental Education and Research, All India Institute of Medical, Sciences, New Delhi, India
| | - Rakhee Yadav
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Mahaiwon Shadang
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Shyam S Chauhan
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Kunaal Dhingra
- Division of Periodontics, Centre for Dental Education and Research, All India Institute of Medical, Sciences, New Delhi, India
| | - Om P Kharbanda
- Division of Orthodontics, Centre for Dental Education and Research, All India Institute of Medical, Sciences, New Delhi, India
| | - Renu Yadav
- Department of Prosthodontics, Surendera Dental College and Research Institute, Sriganganagar, Rajasthan, India
| | - Rahul Garg
- Department of Dental Surgery, Haryana Civil Dental Services, General Hospital, Sirsa, Haryana, India
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Dar MS, Singh P, Mir RA, Dar MJ. Βeta-catenin N-terminal domain: An enigmatic region prone to cancer causing mutations. Mutat Res Rev Mutat Res 2017; 773:122-133. [PMID: 28927523 DOI: 10.1016/j.mrrev.2017.06.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 05/29/2017] [Accepted: 06/05/2017] [Indexed: 12/21/2022]
Abstract
The Wnt/β-catenin is a highly conserved signaling pathway involved in cell fate decisions during various stages of development. Dysregulation of canonical Wnt/β-catenin signaling has been associated with various diseases including cancer. β-Catenin, the central component of canonical Wnt signaling pathway, is a multi-functional protein playing both structural and signaling roles. β-Catenin is composed of three distinct domains: N-terminal domain, C-terminal domain and a central armadillo repeat domain. N-terminal domain of β-catenin harbours almost all of the cancer causing mutations, thus deciphering its critical structural and functional roles offers great potential in cancer detection and therapy. Here, in this review, we have collected information from pharmacological analysis, bio-physical and structural studies, molecular modeling, in-vivo and in-vitro assays, and transgenic animal experiments employing various N-terminal domain variants of β-catenin to discuss the interaction of β-catenin with its binding partners that specifically interact with this domain and the implications of these interactions on signaling, cell fate determination, and in tumorigenesis. A thorough understanding of interactions between β-catenin and its binding partners will enable us to more effectively understand how β-catenin switches between its multiple roles, and will lead to the development of specific assays for the identification of small molecules as chemotherapeutic agents to treat diseases, including cancer and neurological disorders, where Wnt/β-catenin signaling is dysregulated.
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Affiliation(s)
- Mohd Saleem Dar
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India; Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, J&K, India
| | - Paramjeet Singh
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India; Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, J&K, India
| | - Riyaz A Mir
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Ansari Nagar, New Delhi, India
| | - Mohd Jamal Dar
- Academy of Scientific and Innovative Research (AcSIR), New Delhi, India; Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Jammu, J&K, India.
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Mir RA, Lovelace J, Schafer NP, Simone PD, Kellezi A, Kolar C, Spagnol G, Sorgen PL, Band H, Band V, Borgstahl GEO. Biophysical characterization and modeling of human Ecdysoneless (ECD) protein supports a scaffolding function. AIMS Biophys 2016; 3:195-208. [PMID: 28492064 PMCID: PMC5421643 DOI: 10.3934/biophy.2016.1.195] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The human homolog of Drosophila ecdysoneless protein (ECD) is a p53 binding protein that stabilizes and enhances p53 functions. Homozygous deletion of mouse Ecd is early embryonic lethal and Ecd deletion delays G1-S cell cycle progression. Importantly, ECD directly interacts with the Rb tumor suppressor and competes with the E2F transcription factor for binding to Rb. Further studies demonstrated ECD is overexpressed in breast and pancreatic cancers and its overexpression correlates with poor patient survival. ECD overexpression together with Ras induces cellular transformation through upregulation of autophagy. Recently we demonstrated that CK2 mediated phosphorylation of ECD and interaction with R2TP complex are important for its cell cycle regulatory function. Considering that ECD is a component of multiprotein complexes and its crystal structure is unknown, we characterized ECD structure by circular dichroism measurements and sequence analysis software. These analyses suggest that the majority of ECD is composed of α-helices. Furthermore, small angle X-ray scattering (SAXS) analysis showed that deletion fragments, ECD(1-432) and ECD(1-534), are both well-folded and reveals that the first 400 residues are globular and the next 100 residues are in an extended cylindrical structure. Taking all these results together, we speculate that ECD acts like a structural hub or scaffolding protein in its association with its protein partners. In the future, the hypothetical model presented here for ECD will need to be tested experimentally.
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Affiliation(s)
- Riyaz A Mir
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jeff Lovelace
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nicholas P Schafer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Peter D Simone
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Admir Kellezi
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Carol Kolar
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Gaelle Spagnol
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Paul L Sorgen
- Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Hamid Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Gloria E O Borgstahl
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
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Chaturvedi NK, Mir RA, Band V, Joshi SS, Guda C. Experimental validation of predicted subcellular localizations of human proteins. BMC Res Notes 2014; 7:912. [PMID: 25510246 PMCID: PMC4301851 DOI: 10.1186/1756-0500-7-912] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 12/10/2014] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Computational methods have been widely used for the prediction of protein subcellular localization. However, these predictions are rarely validated experimentally and as a result remain questionable. Therefore, experimental validation of the predicted localizations is needed to assess the accuracy of predictions so that such methods can be confidently used to annotate the proteins of unknown localization. Previously, we published a method called ngLOC that predicts the localization of proteins targeted to ten different subcellular organelles. In this short report, we describe the accuracy of these predictions using experimental validations. FINDINGS We have experimentally validated the predicted subcellular localizations of 114 human proteins corresponding to nine different organelles in normal breast and breast cancer cell lines using live cell imaging/confocal microscopy. Target genes were cloned into expression vectors as GFP fusions and cotransfected with RFP-tagged organelle-specific gene marker into normal breast epithelial and breast cancer cell lines. Subcellular localization of each target protein is confirmed by colocalization with a co-expressed organelle-specific protein marker. Our results showed that about 82.5% of the predicted subcellular localizations coincided with the experimentally validated localizations. The highest agreement was found in the endoplasmic reticulum proteins, while the cytoplasmic location showed the least concordance. With the exclusion of cytoplasmic location, the average prediction accuracy increased to 90.4%. In addition, there was no difference observed in the protein subcellular localization between normal and cancer breast cell lines. CONCLUSIONS The experimentally validated accuracy of ngLOC method with (82.5%) or without cytoplasmic location (90.4%) nears the prediction accuracy of 89%. These results demonstrate that the ngLOC method can be very useful for large-scale annotation of the unknown subcellular localization of proteins.
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Affiliation(s)
- Nagendra K Chaturvedi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198 USA
| | - Riyaz A Mir
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198 USA
| | - Vimla Band
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198 USA
- Fred and Pamela Buffet Cancer Center, Omaha, USA
| | - Shantaram S Joshi
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198 USA
| | - Chittibabu Guda
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, 985870 Nebraska Medical Center, Omaha, NE 68198 USA
- Fred and Pamela Buffet Cancer Center, Omaha, USA
- Eppley Institute for Cancer Research, Omaha, USA
- Bioinformatics and Systems Biology Core, University of Nebraska Medical Center, Omaha, NE 68198-5805 USA
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Khan FA, Das GK, Pande M, Mir RA, Shankar U. Changes in biochemical composition of follicular fluid during reproductive acyclicity in water buffalo (Bubalus bubalis). Anim Reprod Sci 2011; 127:38-42. [PMID: 21840653 DOI: 10.1016/j.anireprosci.2011.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 07/09/2011] [Accepted: 07/25/2011] [Indexed: 11/25/2022]
Abstract
This study describes the changes in biochemical composition of follicular fluid during reproductive acyclicity in buffalo. A total of 73 pairs of ovaries collected from 26 reproductively acyclic and 47 reproductively cyclic buffaloes were used in the investigation. Ovarian follicles were classified into small (5.0-6.9 mm), medium (7.0-9.9 mm) and large (≥10.0 mm) sized categories depending upon their diameter. Follicular fluid was aspirated, processed and assayed for glucose, cholesterol, total protein, acid phosphatase and alkaline phosphatase. Glucose concentration was lesser in reproductively acyclic compared to cyclic buffaloes (19.3 ± 2.59 mg/dl compared to 32.6 ± 2.60 mg/dl; P<0.05), mainly due to difference in concentration between small sized follicles (12.4 ± 2.59 mg/dl compared to 28.0 ± 3.32 mg/dl; P<0.05). Cholesterol concentration was also lesser in reproductively acyclic compared to cyclic buffaloes (32.2 ± 2.14 mg/dl compared to 35.5 ± 2.16 mg/dl; P<0.05) and this was related to the lesser concentration found in large follicles (13.8 ± 3.45 mg/dl compared to 37.2 ± 4.10mg/dl; P<0.001). Total protein and acid phosphatase levels were not affected by either the reproductive cyclicity status or the follicular size (4.9 ± 1.07 g/dl to 6.0 ± 0.28 g/dl and 1.2 ± 0.17 U/dl to 2.5 ± 1.22 U/dl, respectively). An increased alkaline phosphatase activity was, however, observed in reproductively acyclic compared to cyclic buffaloes (27.5 ± 3.08 U/dl compared to 14.0 ± 1.09 U/dl; P<0.0001). In conclusion, results of the present study indicate an alteration in the biochemical composition of follicular fluid during reproductive acyclicity in buffalo. The findings provide further support to the notion that poor nutrition is an important factor triggering reproductive acyclicity in buffalo.
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Affiliation(s)
- F A Khan
- Animal Reproduction Division, Indian Veterinary Research Institute, Izatnagar, India.
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Katara R, Mir RA, Shukla AA, Tiwari A, Singh N, Chauhan SS. Wild type p53-dependent transcriptional upregulation of cathepsin L expression is mediated by C/EBPα in human glioblastoma cells. Biol Chem 2011; 391:1031-40. [PMID: 20536385 DOI: 10.1515/bc.2010.103] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Mutations in the tumor suppressor gene p53 are frequent in human glioblastomas. Similarly cathepsin L, a lysosomal cysteine protease, is overexpressed and secreted by most human tumors including glioblastomas. However, hitherto there is no information on whether or not the mutation(s) in the p53 gene affect(s) expression of this protease. Using human glioblastoma cell lines harboring wild type and mutant p53, we demonstrate here for the first time that only the wild type but not the mutant p53 upregulates cathepsin L expression. By transfection of promoter reporter constructs, site-directed mutagenesis and chip assays we have established that wild type p53 elevates the levels of cathepsin L in these cells. It does so directly by binding to the cathepsin L promoter and also indirectly by inducing the expression of C/EBPα, which is crucial for the transcription of this protease. In view of its role in tumorigenesis, angiogenesis and tumor cell invasion, increased expression of cathepsin L in glioblastoma cells harboring wild type p53 might confer invasive ability and growth advantage to these cells. Therefore, use of cathepsin L inhibitors could prove useful in the management of these tumors.
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Affiliation(s)
- Rahul Katara
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
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Abstract
The expression of cathepsin L, a lysosomal protease, is known to be elevated in cancer and other pathologies. Multiple splice variants of human cathepsin L with variable 5'UTRs exist, which encode for the same protein. Previously we have observed that variant hCATL A (bearing the longest 5'UTR) was translated in vitro with significantly lower efficiency than variant hCATL AIII (bearing the shortest 5'UTR). Contrary to these findings, results of the present study reveal that in cancer cells, hCATL A mRNA exhibits higher translatability in spite of having lower stability than AIII. This is the first report demonstrating a highly contrasting trend in translation efficiencies of hCATL variants in rabbit reticulocytes and live cells. Expression from chimeric mRNAs containing 5'UTRs of A or AIII upstream to luciferase reporter cDNA established the A UTR to be the sole determinant for this effect. Transient transfections of bicistronic plasmids and mRNAs confirmed the presence of a functional Internal Ribosome Entry Site in this UTR. Our data suggest that differential stability and translation initiation modes mediated by the 5'UTRs of human cathepsin L variants are involved in regulating its expression.
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Affiliation(s)
- Shivani Mittal
- Department of Biochemistry, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, India
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