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Santana-Hernández J, Corona-Rivera A, Mendoza-Maldonado L, Santana-Bejarano UF, Cuero-Quezada I, Marquez-Mora A, Serafín-Saucedo G, Brukman-Jiménez SA, Corona-Rivera R, Ortuño-Sahagún D, Cruz-Osorio RM, Sánchez-Zubieta FA, Bobadilla-Morales L. Acute promyelocytic leukemia with PML/RARA (bcr1, bcr2 and bcr3) transcripts in a pediatric patient. Oncol Lett 2024; 27:114. [PMID: 38304177 PMCID: PMC10831402 DOI: 10.3892/ol.2024.14246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 10/16/2023] [Indexed: 02/03/2024] Open
Abstract
Patients with acute promyelocytic leukemia (APL) exhibit the t(15;17)(q24.1;q21.2) translocation that produces the promyelocytic leukemia (PML)/retinoic acid receptor α (RARA) fusion gene. Different PML breakpoints yield three alternative molecular transcripts, bcr1, bcr2 and bcr3. The present study reports the simultaneous presence of three PML/RARA transcripts in a pediatric female patient diagnosed with APL, according to the clinical characteristics, immunophenotype and karyotype of the patient. The simultaneous presence of the PML/RARA transcripts were detected using reverse transcription-quantitative PCR (RT-qPCR). This was confirmed with HemaVision-28N Multiplex RT-qPCR, HemaVision-28Q qualitative RT-qPCR and the AmpliSeq RNA Myeloid Panel. To the best of our knowledge, the pediatric patient described in the present study is the first case found to exhibit all three PML/RARA transcripts (bcr1, bcr2 and bcr3). Additionally, a microarray analysis was performed to determine the expression profile, potential predictive biomarkers and the implications of this uncommon finding. According to the information obtained from molecular monitoring, the results reported in the present study were associated with a good patient prognosis. In addition, upregulated genes that are rare in acute myeloid leukemia were identified, and these genes may be promising diagnostic biomarkers for further study. For example, CCL-1 is present in leukemic stem cells, causing treatment failure and relapse, and α- and β-defensins have been reported exclusively in chronic myeloid leukemia. However, the results of the present study confirmed that they may also be present in APL. Thus, these findings suggested a possible signaling pathway that involves the PML/RARA oncoprotein in APL.
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Affiliation(s)
- Jennifer Santana-Hernández
- Department of Molecular Biology and Genomics, Human Genetics Institute ‘Dr. Enrique Corona-Rivera’, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
- Cytogenetics Unit, Civil Hospital of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | - Alfredo Corona-Rivera
- Department of Molecular Biology and Genomics, Human Genetics Institute ‘Dr. Enrique Corona-Rivera’, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
- Cytogenetics Unit, Civil Hospital of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | | | | | - Idalid Cuero-Quezada
- Department of Molecular Biology and Genomics, Human Genetics Institute ‘Dr. Enrique Corona-Rivera’, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
- Cytogenetics Unit, Civil Hospital of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | - Aurea Marquez-Mora
- Cytogenetics Unit, Civil Hospital of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | | | | | - Román Corona-Rivera
- Department of Molecular Biology and Genomics, Human Genetics Institute ‘Dr. Enrique Corona-Rivera’, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
- Cytogenetics Unit, Civil Hospital of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | - Daniel Ortuño-Sahagún
- Molecular Neuroimmunobiology Laboratory, Biomedical Sciences Research Institute, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | - Rosa Margarita Cruz-Osorio
- Oncohematology Service, Pediatric Division, Civil Hospital of Guadalajara, Guadalajara, Jalisco 44340, Mexico
| | | | - Lucina Bobadilla-Morales
- Department of Molecular Biology and Genomics, Human Genetics Institute ‘Dr. Enrique Corona-Rivera’, University of Guadalajara, Guadalajara, Jalisco 44340, Mexico
- Cytogenetics Unit, Civil Hospital of Guadalajara, Guadalajara, Jalisco 44340, Mexico
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2
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Wu S, Coureuil M, Nassif X, Tautz L. Enzyme mechanistic studies of NMA1982, a protein tyrosine phosphatase and potential virulence factor in Neisseria meningitidis. Sci Rep 2023; 13:22015. [PMID: 38086986 PMCID: PMC10716126 DOI: 10.1038/s41598-023-49561-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 12/09/2023] [Indexed: 12/18/2023] Open
Abstract
Protein phosphorylation is an integral part of many cellular processes, not only in eukaryotes but also in bacteria. The discovery of both prokaryotic protein kinases and phosphatases has created interest in generating antibacterial therapeutics that target these enzymes. NMA1982 is a putative phosphatase from Neisseria meningitidis, the causative agent of meningitis and meningococcal septicemia. The overall fold of NMA1982 closely resembles that of protein tyrosine phosphatases (PTPs). However, the hallmark C(X)5R PTP signature motif, containing the catalytic cysteine and invariant arginine, is shorter by one amino acid in NMA1982. This has cast doubt about the catalytic mechanism of NMA1982 and its assignment to the PTP superfamily. Here, we demonstrate that NMA1982 indeed employs a catalytic mechanism that is specific to PTPs. Mutagenesis experiments, transition state inhibition, pH-dependence activity, and oxidative inactivation experiments all support that NMA1982 is a genuine PTP. Importantly, we show that NMA1982 is secreted by N. meningitidis, suggesting that this protein is a potential virulence factor. Future studies will need to address whether NMA1982 is indeed essential for N. meningitidis survival and virulence. Based on its unique active site conformation, NMA1982 may become a suitable target for developing selective antibacterial drugs.
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Affiliation(s)
- Shuangding Wu
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA, 92037, USA
| | - Mathieu Coureuil
- Université Paris CitéUFR de Médecine, 15 Rue de l'École de Médecine, 75006, Paris, France
- Institut Necker Enfants-MaladesInserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015, Paris, France
| | - Xavier Nassif
- Université Paris CitéUFR de Médecine, 15 Rue de l'École de Médecine, 75006, Paris, France
- Institut Necker Enfants-MaladesInserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015, Paris, France
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA, 92037, USA.
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Tojjari A, Saeed A, Sadeghipour A, Kurzrock R, Cavalcante L. Overcoming Immune Checkpoint Therapy Resistance with SHP2 Inhibition in Cancer and Immune Cells: A Review of the Literature and Novel Combinatorial Approaches. Cancers (Basel) 2023; 15:5384. [PMID: 38001644 PMCID: PMC10670368 DOI: 10.3390/cancers15225384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 10/13/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
SHP2 (Src Homology 2 Domain-Containing Phosphatase 2) is a protein tyrosine phosphatase widely expressed in various cell types. SHP2 plays a crucial role in different cellular processes, such as cell proliferation, differentiation, and survival. Aberrant activation of SHP2 has been implicated in multiple human cancers and is considered a promising therapeutic target for treating these malignancies. The PTPN11 gene and functions encode SHP2 as a critical signal transduction regulator that interacts with key signaling molecules in both the RAS/ERK and PD-1/PD-L1 pathways; SHP2 is also implicated in T-cell signaling. SHP2 may be inhibited by molecules that cause allosteric (bind to sites other than the active site and attenuate activation) or orthosteric (bind to the active site and stop activation) inhibition or via potent SHP2 degraders. These inhibitors have anti-proliferative effects in cancer cells and suppress tumor growth in preclinical models. In addition, several SHP2 inhibitors are currently in clinical trials for cancer treatment. This review aims to provide an overview of the current research on SHP2 inhibitors, including their mechanism of action, structure-activity relationships, and clinical development, focusing on immune modulation effects and novel therapeutic strategies in the immune-oncology field.
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Affiliation(s)
- Alireza Tojjari
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Anwaar Saeed
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15232, USA
| | - Arezoo Sadeghipour
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modarres University, Tehran P.O. Box 14115-175, Iran
| | - Razelle Kurzrock
- Department of Medicine, Genome Sciences and Precision Medicine Center, Medical College of Wisconsin Cancer Center, Milwaukee, WI 53226, USA
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4
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Wu S, Coureuil M, Nassif X, Tautz L. Enzyme Mechanistic Studies of NMA1982, a Protein Tyrosine Phosphatase and Potential Virulence Factor in Neisseria meningitidis. RESEARCH SQUARE 2023:rs.3.rs-3098138. [PMID: 37693380 PMCID: PMC10491346 DOI: 10.21203/rs.3.rs-3098138/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Protein phosphorylation is an integral part of many cellular processes, not only in eukaryotes but also in bacteria. The discovery of both prokaryotic protein kinases and phosphatases has created interest in generating antibacterial therapeutics that target these enzymes. NMA1982 is a putative phosphatase from Neisseria meningitidis, the causative agent of meningitis and meningococcal septicemia. The overall fold of NMA1982 closely resembles that of protein tyrosine phosphatases (PTPs). However, the hallmark C(X)5R PTP signature motif, containing the catalytic cysteine and invariant arginine, is shorter by one amino acid in NMA1982. This has cast doubt about the catalytic mechanism of NMA1982 and its assignment to the PTP superfamily. Here, we demonstrate that NMA1982 indeed employs a catalytic mechanism that is specific to PTPs. Mutagenesis experiments, transition state inhibition, pH-dependence activity, and oxidative inactivation experiments all support that NMA1982 is a genuine PTP. Importantly, we show that NMA1982 is secreted by N. meningitidis, suggesting that this protein is a potential virulence factor. Future studies will need to address whether NMA1982 is indeed essential for N. meningitidis survival and virulence. Based on its unique active site conformation, NMA1982 may become a suitable target for developing selective antibacterial drugs.
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Affiliation(s)
| | | | | | - Lutz Tautz
- Sanford Burnham Prebys Medical Discovery Institute
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5
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Wu S, Coureuil M, Nassif X, Tautz L. NMA1982 is a Novel Phosphatase and Potential Virulence Factor in Neisseria meningitidis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.23.541968. [PMID: 37292688 PMCID: PMC10245925 DOI: 10.1101/2023.05.23.541968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein phosphorylation is an integral part of many cellular processes, not only in eukaryotes but also in bacteria. The discovery of both prokaryotic protein kinases and phosphatases has created interest in generating antibacterial therapeutics that target these enzymes. NMA1982 is a putative phosphatase from Neisseria meningitidis, the causative agent of meningitis and meningococcal septicemia. The overall fold of NMA1982 closely resembles that of protein tyrosine phosphatases (PTPs). However, the hallmark C(X)5R PTP signature motif, containing the catalytic cysteine and invariant arginine, is shorter by one amino acid in NMA1982. This has cast doubt about the catalytic mechanism of NMA1982 and its assignment to the PTP superfamily. Here, we demonstrate that NMA1982 indeed employs a catalytic mechanism that is specific to PTPs. Mutagenesis experiments, transition state inhibition, pH-dependence activity, and oxidative inactivation experiments all support that NMA1982 is a genuine phosphatase. Importantly, we show that NMA1982 is secreted by N. meningitidis, suggesting that this protein is a potential virulence factor. Future studies will need to address whether NMA1982 is indeed essential for N. meningitidis survival and virulence. Based on its unique active site conformation, NMA1982 may become a suitable target for developing selective antibacterial drugs.
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Affiliation(s)
- Shuangding Wu
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Mathieu Coureuil
- Université Paris Cité, UFR de Médecine, 15 Rue de l’École de Médecine, 75006 Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015 Paris, France
| | - Xavier Nassif
- Université Paris Cité, UFR de Médecine, 15 Rue de l’École de Médecine, 75006 Paris, France
- Institut Necker Enfants-Malades, Inserm U1151, CNRS UMR 8253, 160 Rue de Vaugirard, 75015 Paris, France
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
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6
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Hou Y, Lu X, Xu Z, Qu J, Huang J. How a single mutation alters the protein structure: a simulation investigation on protein tyrosine phosphatase SHP2. RSC Adv 2023; 13:4263-4274. [PMID: 36760301 PMCID: PMC9891203 DOI: 10.1039/d2ra07472a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 01/23/2023] [Indexed: 02/04/2023] Open
Abstract
Protein tyrosine phosphatase SHP2 is a key regulator modulating several signaling pathways. The oncogenic mutation E76K in SHP2 releases the enzyme from an autoinhibited, closed conformation into an active, open conformation. Here, we investigated the conformational dynamics of SHP2 and the effect of the E76K mutation on its conformational ensemble via extensive molecular dynamics (MD) and metadynamics (MetaD) simulations. Our simulations provide atomistic details on how the E76K mutated SHP2 prefers the open state and also reveal that the transition between the closed and the open states is highly collective. Several intermediate metastable states during the conformational transition between the closed and the open states were also investigated. Understanding how the single E76K mutation induces the conformational change in SHP2 could facilitate the further design of SHP2 inhibitors.
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Affiliation(s)
- Yingnan Hou
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
| | - Xiaoli Lu
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
| | - Ziyao Xu
- BioMap2 Kexueyuan South RoadBeijing 100000China
| | - Jiarun Qu
- BioMap2 Kexueyuan South RoadBeijing 100000China
| | - Jing Huang
- Westlake AI Therapeutics Lab, Westlake Laboratory of Life Sciences and Biomedicine 18 Shilongshan Road Hangzhou 310024 Zhejiang China .,Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University 18 Shilongshan Road Hangzhou 310024 Zhejiang China
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7
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Baranowski MR, Wu J, Han YN, Lambert LJ, Cosford NDP, Tautz L. Protein Tyrosine Phosphatase Biochemical Inhibition Assays. Bio Protoc 2022; 12:e4510. [PMID: 36248604 PMCID: PMC9516250 DOI: 10.21769/bioprotoc.4510] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/13/2022] [Accepted: 07/20/2022] [Indexed: 12/29/2022] Open
Abstract
Disturbance of the dynamic balance between protein tyrosine phosphorylation and dephosphorylation, modulated by protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs), is known to be crucial for the development of many human diseases. The discovery of agents that restore this balance has been the subject of many drug research efforts, most of which have focused on tyrosine kinase inhibitors (TKIs), resulting in the development of more than 50 FDA-approved TKIs during the past two decades. More recently, accumulating evidence has suggested that members of the PTP superfamily are also promising drug targets, and efforts to discover tyrosine phosphatase inhibitors (TPIs) have increased dramatically. Here, we provide protocols for determining the potency of TPIs in vitro. We focus on the use of fluorescence-based substrates, which exhibit a dramatic increase in fluorescence emission when dephosphorylated by the PTP, and thus allow setting up highly sensitive and miniaturized phosphatase activity assays using 384-well or 1536-well microplates and a continuous (kinetic) assay format. The protocols cover PTP specific activity assays, Michaelis-Menten kinetics, dose-response inhibition assays, and dose-response data analysis for determining IC 50 values. Potential pitfalls are also discussed. While advanced instrumentation is utilized for compound spotting and liquid dispensing, all the assays can be adapted to existing equipment in most laboratories. Assays are described for selected PTP drug targets, including SHP2 ( PTPN11 ), PTP1B ( PTPN1 ), STEP ( PTPN5 ), and VHR ( DUSP3 ). However, all protocols are applicable to members of the PTP enzyme family in general. Graphical abstract.
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Affiliation(s)
- Marek R. Baranowski
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Ludwika Pasteura 5, 02-093 Warsaw, Poland
| | - Jiaqian Wu
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Ye Na Han
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Lester J. Lambert
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Nicholas D. P. Cosford
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
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