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Wei W, Geer MJ, Guo X, Dolgalev I, Sanjana NE, Neel BG. Genome-wide CRISPR/Cas9 screens reveal shared and cell-specific mechanisms of resistance to SHP2 inhibition. J Exp Med 2023; 220:e20221563. [PMID: 36820830 PMCID: PMC9998968 DOI: 10.1084/jem.20221563] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/14/2022] [Accepted: 01/20/2023] [Indexed: 02/24/2023] Open
Abstract
SHP2 (PTPN11) acts upstream of SOS1/2 to enable RAS activation. Allosteric SHP2 inhibitors (SHP2i) in the clinic prevent SHP2 activation, block proliferation of RTK- or cycling RAS mutant-driven cancers, and overcome "adaptive resistance." To identify SHP2i resistance mechanisms, we performed genome-wide CRISPR/Cas9 knockout screens on two SHP2i-sensitive cell lines, recovering genes expected to cause resistance (NF1, PTEN, CDKN1B, LZTR1, and RASA2) and novel targets (INPPL1, MAP4K5, epigenetic modifiers). We screened 14 additional lines with a focused CRISPR library targeting common "hits" from the genome-wide screens. LZTR1 deletion conferred resistance in 12/14 lines, followed by MAP4K5 (8/14), SPRED2/STK40 (6/14), and INPPL1 (5/14). INPPL1, MAP4K5, or LZTR1 deletion reactivated ERK signaling. INPPL1-mediated sensitization to SHP2i required its NPXY motif but not lipid phosphatase activity. MAP4K5 acted upstream of MEK through a kinase-dependent target(s); LZTR1 had cell-dependent effects on RIT and RAS stability. INPPL1, MAP4K5, or LZTR1 deletion also conferred SHP2i resistance in vivo. Defining the SHP2i resistance landscape could suggest effective combination approaches.
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Affiliation(s)
- Wei Wei
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Mitchell J. Geer
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Xinyi Guo
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Igor Dolgalev
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
| | - Neville E. Sanjana
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
- Department of Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Benjamin G. Neel
- Laura and Isaac Perlmutter Cancer Center, NYU Grossman School of Medicine, NYU Langone Health, New York, NY, USA
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The Structure, Function and Regulation of Protein Tyrosine Phosphatase Receptor Type J and Its Role in Diseases. Cells 2022; 12:cells12010008. [PMID: 36611803 PMCID: PMC9818648 DOI: 10.3390/cells12010008] [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: 10/26/2022] [Revised: 12/08/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022] Open
Abstract
Protein tyrosine phosphatase receptor type J (PTPRJ), also known as DEP-1, HPTPη, or CD148, belongs to the R3 subfamily of receptor protein tyrosine phosphatases (RPTPs). It was first identified as an antioncogene due to its protein level being significantly downregulated in most epithelial tumors and cancer cell lines (e.g., colon, lung, thyroid, breast, and pancreas). PTPRJ regulates mouse optic nerve projection by inhibiting the phosphorylation of the erythropoietin-producing hepatocellular carcinoma (Eph) receptor and abelson murine leukemia viral oncogene homolog 1 (c-Abl). PTPRJ is crucial for metabolism. Recent studies have demonstrated that PTPRJ dephosphorylates JAK2 at positions Y813 and Y868 to inhibit leptin signaling. Akt is more phosphorylated at the Ser473 and Thr308 sites in Ptprj-/- mice, suggesting that PTPRJ may be a novel negative regulator of insulin signaling. PTPRJ also plays an important role in balancing the pro- and anti-osteoclastogenic activity of the M-CSF receptor (M-CSFR), and in maintaining NFATc1 expression during the late stages of osteoclastogenesis to promote bone-resorbing osteoclast (OCL) maturation. Furthermore, multiple receptor tyrosine kinases (RTKs) as substrates of PTPRJ are probably a potential therapeutic target for many types of diseases, such as cancer, neurodegenerative diseases, and metabolic diseases, by inhibiting their phosphorylation activity. In light of the important roles that PTPRJ plays in many diseases, this review summarizes the structural features of the protein, its expression pattern, and the physiological and pathological functions of PTPRJ, to provide new ideas for treating PTPRJ as a potential therapeutic target for related metabolic diseases and cancer.
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Schwarz M, Rizzo S, Paz WE, Kresinsky A, Thévenin D, Müller JP. Disrupting PTPRJ transmembrane-mediated oligomerization counteracts oncogenic receptor tyrosine kinase FLT3 ITD. Front Oncol 2022; 12:1017947. [PMID: 36452504 PMCID: PMC9701752 DOI: 10.3389/fonc.2022.1017947] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/25/2022] [Indexed: 11/15/2022] Open
Abstract
The receptor protein tyrosine phosphatase (RPTP) PTPRJ (also known as DEP-1) has been identified as a negative regulator of the receptor tyrosine kinase FLT3 signalling in vitro. The inactivation of the PTPRJ gene in mice expressing the constitutively active, oncogenic receptor tyrosine kinase FLT3 ITD aggravated known features of leukaemogenesis, revealing PTPRJ's antagonistic role. FLT3 ITD mutations resulting in constitutively kinase activity and cell transformation frequently occur in patients with acute myeloid leukaemia (AML). Thus, in situ activation of PTPRJ could be used to abrogate oncogenic FLT3 signalling. The activity of PTPRJ is suppressed by homodimerization, which is mediated by transmembrane domain (TMD) interactions. Specific Glycine-to-Leucine mutations in the TMD disrupt oligomerization and inhibit the Epidermal Growth Factor Receptor (EGFR) and EGFR-driven cancer cell phenotypes. To study the effects of PTPRJ TMD mutant proteins on FLT3 ITD activity in cell lines, endogenous PTPRJ was inactivated and replaced by stable expression of PTPRJ TMD mutants. Autophosphorylation of wild-type and ITD-mutated FLT3 was diminished in AML cell lines expressing the PTPRJ TMD mutants compared to wild-type-expressing cells. This was accompanied by reduced FLT3-mediated global protein tyrosine phosphorylation and downstream signalling. Further, PTPRJ TMD mutant proteins impaired the proliferation and in vitro transformation of leukemic cells. Although PTPRJ's TMD mutant proteins showed impaired self-association, the specific phosphatase activity of immunoprecipitated proteins remained unchanged. In conclusion, this study demonstrates that the destabilization of PTPRJ TMD-mediated self-association increases the activity of PTPRJ in situ and impairs FLT3 activity and FLT3-driven cell phenotypes of AML cells. Thus, disrupting the oligomerization of PTPRJ in situ could prove a valuable therapeutic strategy to restrict oncogenic FLT3 activity in leukemic cells.
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Affiliation(s)
- Marie Schwarz
- Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Jena, Germany
| | - Sophie Rizzo
- Department of Chemistry, Lehigh University, Bethlehem, PA, United States
| | | | - Anne Kresinsky
- Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Jena, Germany,Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA, United States
| | - Jörg P. Müller
- Institute for Molecular Cell Biology, CMB - Center for Molecular Biomedicine, University Hospital Jena, Jena, Germany,*Correspondence: Jörg P. Müller,
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A Bioinformatics View on Acute Myeloid Leukemia Surface Molecules by Combined Bayesian and ABC Analysis. Bioengineering (Basel) 2022; 9:bioengineering9110642. [DOI: 10.3390/bioengineering9110642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/18/2022] [Accepted: 10/22/2022] [Indexed: 11/06/2022] Open
Abstract
“Big omics data” provoke the challenge of extracting meaningful information with clinical benefit. Here, we propose a two-step approach, an initial unsupervised inspection of the structure of the high dimensional data followed by supervised analysis of gene expression levels, to reconstruct the surface patterns on different subtypes of acute myeloid leukemia (AML). First, Bayesian methodology was used, focusing on surface molecules encoded by cluster of differentiation (CD) genes to assess whether AML is a homogeneous group or segregates into clusters. Gene expressions of 390 patient samples measured using microarray technology and 150 samples measured via RNA-Seq were compared. Beyond acute promyelocytic leukemia (APL), a well-known AML subentity, the remaining AML samples were separated into two distinct subgroups. Next, we investigated which CD molecules would best distinguish each AML subgroup against APL, and validated discriminative molecules of both datasets by searching the scientific literature. Surprisingly, a comparison of both omics analyses revealed that CD339 was the only overlapping gene differentially regulated in APL and other AML subtypes. In summary, our two-step approach for gene expression analysis revealed two previously unknown subgroup distinctions in AML based on surface molecule expression, which may guide the differentiation of subentities in a given clinical–diagnostic context.
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Novel Approaches to Target Mutant FLT3 Leukaemia. Cancers (Basel) 2020; 12:cancers12102806. [PMID: 33003568 PMCID: PMC7600363 DOI: 10.3390/cancers12102806] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/24/2020] [Accepted: 09/25/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary Acute myeloid leukemia (AML) is a haematologic disease in which oncogenic mutations in the receptor tyrosine kinase FLT3 frequently lead to leukaemic development. Potent treatment of AML patients is still hampered by inefficient targeting of leukemic stem cells expressing constitutive active FLT3 mutants. This review summarizes the current knowledge about the regulation of FLT3 activity at cellular level and discusses therapeutical options to affect the tumor cells and the microenvironment to impair the haematological aberrations. Abstract Fms-like tyrosine kinase 3 (FLT3) is a member of the class III receptor tyrosine kinases (RTK) and is involved in cell survival, proliferation, and differentiation of haematopoietic progenitors of lymphoid and myeloid lineages. Oncogenic mutations in the FLT3 gene resulting in constitutively active FLT3 variants are frequently found in acute myeloid leukaemia (AML) patients and correlate with patient’s poor survival. Targeting FLT3 mutant leukaemic stem cells (LSC) is a key to efficient treatment of patients with relapsed/refractory AML. It is therefore essential to understand how LSC escape current therapies in order to develop novel therapeutic strategies. Here, we summarize the current knowledge on mechanisms of FLT3 activity regulation and its cellular consequences. Furthermore, we discuss how aberrant FLT3 signalling cooperates with other oncogenic lesions and the microenvironment to drive haematopoietic malignancies and how this can be harnessed for therapeutical purposes.
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Waldt N, Scharnetzki D, Kesseler C, Kirches E, Stroscher N, Böhmer FD, Mawrin C. Loss of PTPRJ/DEP-1 enhances NF2/Merlin-dependent meningioma development. J Neurol Sci 2019; 408:116553. [PMID: 31715329 DOI: 10.1016/j.jns.2019.116553] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 10/17/2019] [Accepted: 10/24/2019] [Indexed: 11/18/2022]
Abstract
INTRODUCTION Meningiomas are common tumors in adults, which develop from the meningeal coverings of the brain and spinal cord. Loss-of-function mutations or deletion of the NF2 gene, resulting in loss of the encoded Merlin protein, lead to Neurofibromatosis type 2 (NF2), but also cause the formation of sporadic meningiomas. It was shown that inactivation of Nf2 in mice caused meningioma formation. Another meningioma tumor-suppressor candidate is the receptor-like density-enhanced phosphatase-1 (DEP-1), encoded by PTPRJ. Loss of DEP-1 enhances meningioma cell motility in vitro and invasive growth in an orthotopic xenograft model. Ptprj-deficient mice develop normally and do not show spontaneous tumorigenesis. Another genetic lesion may be required to interact with DEP-1 loss in meningioma genesis. METHODS In the present study we investigated in vitro and in vivo whether the losses of DEP-1 and Merlin/NF2 may have a combined effect. RESULTS Human meningioma cells deficient for DEP-1, Merlin/NF2 or both showed no statistically significant changes in cell proliferation, while DEP-1 or DEP1/NF2 deficiency led to moderately increased colony size in clonogenicity assays. In addition, the loss of any of the two genes was sufficient to induce a significant reduction of cell size (p < .05) and profound morphological changes. Most important, in Ptprj knockout mice Cre/lox mediated meningeal Nf2 knockout elicited a four-fold increased rate of meningioma formation within one year compared with mice with Ptprj wild type alleles (25% vs 6% tumor incidence). CONCLUSIONS Our data suggest that loss of DEP-1 and Merlin/NF2 synergize during meningioma genesis.
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Affiliation(s)
- Natalie Waldt
- Department of Neuropathology, Otto-von-Guericke-University, D-39120 Magdeburg, Germany
| | - David Scharnetzki
- Department of Neuropathology, Otto-von-Guericke-University, D-39120 Magdeburg, Germany
| | - Christoph Kesseler
- Department of Neuropathology, Otto-von-Guericke-University, D-39120 Magdeburg, Germany
| | - Elmar Kirches
- Department of Neuropathology, Otto-von-Guericke-University, D-39120 Magdeburg, Germany
| | - Nele Stroscher
- Department of Neuropathology, Otto-von-Guericke-University, D-39120 Magdeburg, Germany
| | - Frank-D Böhmer
- Institute of Molecular Cell Biology, CMB, Jena University Hospital, D-07745 Jena, Germany
| | - Christian Mawrin
- Department of Neuropathology, Otto-von-Guericke-University, D-39120 Magdeburg, Germany.
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Zheng J, Song Y, Li Z, Tang A, Fei Y, He W. The implication of lncRNA expression pattern and potential function of lncRNA RP4-576H24.2 in acute myeloid leukemia. Cancer Med 2019; 8:7143-7160. [PMID: 31568697 PMCID: PMC6885877 DOI: 10.1002/cam4.2518] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/26/2019] [Accepted: 08/13/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Recent studies have revealed that long noncoding RNAs (lncRNAs) may hold crucial triggers of the pathogenesis of hematological malignancies, while the studies evaluating the expression pattern of lncRNA in acute myeloid leukemia (AML) are few. Thus, this study aimed to investigate the implication of lncRNA expression pattern in AML development and progression. METHODS Bone marrow samples from four AML patients and four controls were subjected to lncRNA sequencing. Then, bone marrow samples from 110 AML patients and 40 controls were proposed to real-time quantitative polymerase chain reaction (RT-qPCR) validation for 10 candidate lncRNAs. Clinical data and survival profiles were recorded in AML patients. Furthermore, lncRNA RP4-576H24.2 expression in AML cell lines and its effect on AML cell proliferation and apoptosis were detected. RESULTS LncRNA expression pattern by sequencing clearly distinguished AML patients from controls, and 630 upregulated and 621 downregulated lncRNAs were identified in AML patients compared to controls, which were mainly enriched in AML oncogene-related biological process and pathways (such as neutrophil degranulation, leukocyte transendothelial migration, and hematopoietic cell lineage). RT-qPCR validation observed that six lncRNAs correlated with AML risk, one lncRNA associated with risk stratification, and three lncRNAs correlated with survivals, among which lncRNA RP4-576H24.2 was the only one correlated with AML susceptibility, risk stratification, and survivals. Further in vitro experiments showed that lncRNA RP4-576H24.2 was upregulated in AML cell lines compared to normal bone marrow mononuclear cells (BMMCs), and promoted proliferation while inhibited apoptosis in HL-60 and KG-1 cells. CONCLUSIONS LncRNA expression pattern is closely involved in the development and progression of AML, and several specific lncRNAs exhibit potential to be biomarkers for AML risk and prognosis. Besides, lncRNA RP4-576H24.2 might be a potential oncogene in AML pathogenesis.
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Affiliation(s)
- Jifu Zheng
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yuan Song
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenjiang Li
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Aiping Tang
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yan Fei
- Key Laboratory of Hematology of Jiangxi Province, Department of Hematology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wenfeng He
- Key Laboratory of Molecular Medicine of Jiangxi, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Kazi JU, Rönnstrand L. FMS-like Tyrosine Kinase 3/FLT3: From Basic Science to Clinical Implications. Physiol Rev 2019; 99:1433-1466. [PMID: 31066629 DOI: 10.1152/physrev.00029.2018] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
FMS-like tyrosine kinase 3 (FLT3) is a receptor tyrosine kinase that is expressed almost exclusively in the hematopoietic compartment. Its ligand, FLT3 ligand (FL), induces dimerization and activation of its intrinsic tyrosine kinase activity. Activation of FLT3 leads to its autophosphorylation and initiation of several signal transduction cascades. Signaling is initiated by the recruitment of signal transduction molecules to activated FLT3 through binding to specific phosphorylated tyrosine residues in the intracellular region of FLT3. Activation of FLT3 mediates cell survival, cell proliferation, and differentiation of hematopoietic progenitor cells. It acts in synergy with several other cytokines to promote its biological effects. Deregulated FLT3 activity has been implicated in several diseases, most prominently in acute myeloid leukemia where around one-third of patients carry an activating mutant of FLT3 which drives the disease and is correlated with poor prognosis. Overactivity of FLT3 has also been implicated in autoimmune diseases, such as rheumatoid arthritis. The observation that gain-of-function mutations of FLT3 can promote leukemogenesis has stimulated the development of inhibitors that target this receptor. Many of these are in clinical trials, and some have been approved for clinical use. However, problems with acquired resistance to these inhibitors are common and, furthermore, only a fraction of patients respond to these selective treatments. This review provides a summary of our current knowledge regarding structural and functional aspects of FLT3 signaling, both under normal and pathological conditions, and discusses challenges for the future regarding the use of targeted inhibition of these pathways for the treatment of patients.
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Affiliation(s)
- Julhash U Kazi
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University , Lund , Sweden ; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University , Lund , Sweden ; and Division of Oncology, Skåne University Hospital , Lund , Sweden
| | - Lars Rönnstrand
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University , Lund , Sweden ; Lund Stem Cell Center, Department of Laboratory Medicine, Lund University , Lund , Sweden ; and Division of Oncology, Skåne University Hospital , Lund , Sweden
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Lu H, Deng S, Zheng M, Hu K. iTRAQ plasma proteomics analysis for candidate biomarkers of type 2 incipient diabetic nephropathy. Clin Proteomics 2019; 16:33. [PMID: 31384238 PMCID: PMC6668123 DOI: 10.1186/s12014-019-9253-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 07/22/2019] [Indexed: 12/11/2022] Open
Abstract
Background Diabetic nephropathy is the most frequent cause of end-stage renal disease worldwide. Identification of biomarkers for diabetic nephropathy for early diagnosis may be the key to avoiding damage from this condition. Methods Proteomic iTRAQ technology was first used to identify differentially expressed plasma proteins in type 2 incipient diabetic nephropathy (IDN) using a Q-Exactive mass spectrometer. Results Compared with controls, 57 proteins (32 upregulated and 25 downregulated proteins) were identified. Furthermore, the gelsolin, collectin-11, PTPRJ, and AKAP-7 proteins were confirmed by Western blots as candidate biomarkers for type 2 IDN through ROC analysis. Conclusions These findings offer a theoretical basis for the early treatment of diabetic nephropathy.
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Affiliation(s)
- Hongmei Lu
- 1The Second Clinical Medical College, Guangdong Medical University, Dongguan, 523808 China
| | - Shaodong Deng
- 1The Second Clinical Medical College, Guangdong Medical University, Dongguan, 523808 China
| | - Minghui Zheng
- 2Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital of Sun Yat-sen University, Guangzhou, 510120 China
| | - Kunhua Hu
- 3Proteomics Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080 China
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