1
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Tran D, Beeler JS, Liu J, Wiley B, Chan IC, Xin Z, Kramer MH, Batchi-Bouyou AL, Zong X, Walter MJ, Petrone GE, Chlamydas S, Ferraro F, Oh ST, Link DC, Busby B, Cao Y, Bolton KL. Plasma Proteomic Signature Predicts Myeloid Neoplasm Risk. Clin Cancer Res 2024; 30:3220-3228. [PMID: 38446993 PMCID: PMC11292192 DOI: 10.1158/1078-0432.ccr-23-3468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/10/2024] [Accepted: 03/04/2024] [Indexed: 03/08/2024]
Abstract
PURPOSE Clonal hematopoiesis (CH) is thought to be the origin of myeloid neoplasms (MN). Yet, our understanding of the mechanisms driving CH progression to MN and clinical risk prediction of MN remains limited. The human proteome reflects complex interactions between genetic and epigenetic regulation of biological systems. We hypothesized that the plasma proteome might predict MN risk and inform our understanding of the mechanisms promoting MN development. EXPERIMENTAL DESIGN We jointly characterized CH and plasma proteomic profiles of 46,237 individuals in the UK Biobank at baseline study entry. During 500,036 person-years of follow-up, 115 individuals developed MN. Cox proportional hazard regression was used to test for an association between plasma protein levels and MN risk. RESULTS We identified 115 proteins associated with MN risk, of which 30% (N = 34) were also associated with CH. These were enriched for known regulators of the innate and adaptive immune system. Plasma proteomics improved the prediction of MN risk (AUC = 0.85; P = 5×10-9) beyond clinical factors and CH (AUC = 0.80). In an independent group (N = 381,485), we used inherited polygenic risk scores (PRS) for plasma protein levels to validate the relevance of these proteins toMNdevelopment. PRS analyses suggest that most MN-associated proteins we identified are not directly causally linked toMN risk, but rather represent downstream markers of pathways regulating the progression of CH to MN. CONCLUSIONS These data highlight the role of immune cell regulation in the progression of CH to MN and the promise of leveraging multi-omic characterization of CH to improveMN risk stratification. See related commentary by Bhalgat and Taylor, p. 3095.
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Affiliation(s)
- Duc Tran
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - J. Scott Beeler
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Jie Liu
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Brian Wiley
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Irenaeus C.C. Chan
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Zilan Xin
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Michael H. Kramer
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Armel L. Batchi-Bouyou
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Xiaoyu Zong
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.
| | - Matthew J. Walter
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Giulia E.M. Petrone
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | | | - Francesca Ferraro
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Stephen T. Oh
- Division of Hematology, Department of Medicine, WUSM, St. Louis, Missouri.
| | - Daniel C. Link
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
| | - Ben Busby
- DNAnexus, Mountain View, California.
| | - Yin Cao
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, Missouri.
| | - Kelly L. Bolton
- Division of Oncology, Department of Medicine, Washington University School of Medicine (WUSM), St. Louis, Missouri.
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2
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Bedwell L, Mavrotas M, Demchenko N, Yaa RM, Willis B, Demianova Z, Syed N, Whitwell HJ, Nott A. FANS Unfixed: Isolation and Proteomic Analysis of Mouse Cell Type-Specific Brain Nuclei. J Proteome Res 2024. [PMID: 39056441 DOI: 10.1021/acs.jproteome.4c00161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Epigenetic-mediated gene regulation orchestrates brain cell-type gene expression programs, and epigenetic dysregulation is a major driver of aging and disease-associated changes. Proteins that mediate gene regulation are mostly localized to the nucleus; however, nuclear-localized proteins are often underrepresented in gene expression studies and have been understudied in the context of the brain. To address this challenge, we have optimized an approach for nuclei isolation that is compatible with proteomic analysis. This was coupled to a mass spectrometry protocol for detecting proteins in low-concentration samples. We have generated nuclear proteomes for neurons, microglia, and oligodendrocytes from the mouse brain cortex and identified cell-type nuclear proteins associated with chromatin structure and organization, chromatin modifiers such as transcription factors, and RNA-binding proteins, among others. Our nuclear proteomics platform paves the way for assessing brain cell type changes in the nuclear proteome across health and disease, such as neurodevelopmental, aging, neurodegenerative, and neuroinflammatory conditions. Data are available via ProteomeXchange with the identifier PXD053515.
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Affiliation(s)
- Lucy Bedwell
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
| | - Myrto Mavrotas
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
| | - Nikita Demchenko
- MRC Laboratory of Medical Sciences, Du Cane Road, London W12 0NN, U.K
| | - Reuben M Yaa
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
| | - Brittannie Willis
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London W12 0NN, U.K
| | | | - Nelofer Syed
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
| | - Harry J Whitwell
- Department of Metabolism, Digestion, and Reproduction, Imperial College London, London W12 0NN, U.K
| | - Alexi Nott
- Department of Brain Sciences, Imperial College London, London W12 0NN, U.K
- UK Dementia Research Institute, Imperial College London, London W12 0NN, U.K
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3
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Zhang Z, Huang J, Zhang Z, Shen H, Tang X, Wu D, Bao X, Xu G, Chen S. Application of omics in the diagnosis, prognosis, and treatment of acute myeloid leukemia. Biomark Res 2024; 12:60. [PMID: 38858750 PMCID: PMC11165883 DOI: 10.1186/s40364-024-00600-1] [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: 03/20/2024] [Accepted: 05/17/2024] [Indexed: 06/12/2024] Open
Abstract
Acute myeloid leukemia (AML) is the most frequent leukemia in adults with a high mortality rate. Current diagnostic criteria and selections of therapeutic strategies are generally based on gene mutations and cytogenetic abnormalities. Chemotherapy, targeted therapies, and hematopoietic stem cell transplantation (HSCT) are the major therapeutic strategies for AML. Two dilemmas in the clinical management of AML are related to its poor prognosis. One is the inaccurate risk stratification at diagnosis, leading to incorrect treatment selections. The other is the frequent resistance to chemotherapy and/or targeted therapies. Genomic features have been the focus of AML studies. However, the DNA-level aberrations do not always predict the expression levels of genes and proteins and the latter is more closely linked to disease phenotypes. With the development of high-throughput sequencing and mass spectrometry technologies, studying downstream effectors including RNA, proteins, and metabolites becomes possible. Transcriptomics can reveal gene expression and regulatory networks, proteomics can discover protein expression and signaling pathways intimately associated with the disease, and metabolomics can reflect precise changes in metabolites during disease progression. Moreover, omics profiling at the single-cell level enables studying cellular components and hierarchies of the AML microenvironment. The abundance of data from different omics layers enables the better risk stratification of AML by identifying prognosis-related biomarkers, and has the prospective application in identifying drug targets, therefore potentially discovering solutions to the two dilemmas. In this review, we summarize the existing AML studies using omics methods, both separately and combined, covering research fields of disease diagnosis, risk stratification, prognosis prediction, chemotherapy, as well as targeted therapy. Finally, we discuss the directions and challenges in the application of multi-omics in precision medicine of AML. Our review may inspire both omics researchers and clinical physicians to study AML from a different angle.
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Affiliation(s)
- Zhiyu Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jiayi Huang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Zhibo Zhang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Hongjie Shen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaowen Tang
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiebing Bao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, 215123, Jiangsu, China.
- Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, 215123, Jiangsu, China.
- MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, 215123, Jiangsu Province, China.
| | - Suning Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, the First Affiliated Hospital of Soochow University, Suzhou, China.
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4
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Joshi SK, Piehowski P, Liu T, Gosline SJC, McDermott JE, Druker BJ, Traer E, Tyner JW, Agarwal A, Tognon CE, Rodland KD. Mass Spectrometry-Based Proteogenomics: New Therapeutic Opportunities for Precision Medicine. Annu Rev Pharmacol Toxicol 2024; 64:455-479. [PMID: 37738504 PMCID: PMC10950354 DOI: 10.1146/annurev-pharmtox-022723-113921] [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] [Indexed: 09/24/2023]
Abstract
Proteogenomics refers to the integration of comprehensive genomic, transcriptomic, and proteomic measurements from the same samples with the goal of fully understanding the regulatory processes converting genotypes to phenotypes, often with an emphasis on gaining a deeper understanding of disease processes. Although specific genetic mutations have long been known to drive the development of multiple cancers, gene mutations alone do not always predict prognosis or response to targeted therapy. The benefit of proteogenomics research is that information obtained from proteins and their corresponding pathways provides insight into therapeutic targets that can complement genomic information by providing an additional dimension regarding the underlying mechanisms and pathophysiology of tumors. This review describes the novel insights into tumor biology and drug resistance derived from proteogenomic analysis while highlighting the clinical potential of proteogenomic observations and advances in technique and analysis tools.
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Affiliation(s)
- Sunil K Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Paul Piehowski
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Sara J C Gosline
- Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Jason E McDermott
- Pacific Northwest National Laboratory, Richland, Washington, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Brian J Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Elie Traer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Jeffrey W Tyner
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Anupriya Agarwal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
- Department of Molecular Microbiology and Immunology, Oregon Health & Science University, Portland, Oregon, USA
| | - Cristina E Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Division of Hematology and Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, Oregon, USA
| | - Karin D Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA;
- Pacific Northwest National Laboratory, Richland, Washington, USA
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5
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Bae SG, Kim HJ, Kim MY, Kim DDH, Shin SI, Ahn JS, Park J. Identification of Cell Type-Specific Effects of DNMT3A Mutations on Relapse in Acute Myeloid Leukemia. Mol Cells 2023; 46:611-626. [PMID: 37853686 PMCID: PMC10590706 DOI: 10.14348/molcells.2023.0093] [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: 05/30/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 10/20/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by distinctive mutations in individual patients; therefore, each patient may display different cell-type compositions. Although most patients with AML achieve complete remission (CR) through intensive chemotherapy, the likelihood of relapse remains high. Several studies have attempted to characterize the genetic and cellular heterogeneity of AML; however, our understanding of the cellular heterogeneity of AML remains limited. In this study, we performed single-cell RNA sequencing (scRNAseq) of bone marrow-derived mononuclear cells obtained from same patients at different AML stages (diagnosis, CR, and relapse). We found that hematopoietic stem cells (HSCs) at diagnosis were abnormal compared to normal HSCs. By improving the detection of the DNMT3A R882 mutation with targeted scRNAseq, we identified that DNMT3A-mutant cells that mainly remained were granulocyte-monocyte progenitors (GMPs) or lymphoid-primed multipotential progenitors (LMPPs) from CR to relapse and that DNMT3A-mutant cells have gene signatures related to AML and leukemic cells. Copy number variation analysis at the single-cell level indicated that the cell type that possesses DNMT3A mutations is an important factor in AML relapse and that GMP and LMPP cells can affect relapse in patients with AML. This study advances our understanding of the role of DNMT3A in AML relapse and our approach can be applied to predict treatment outcomes.
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Affiliation(s)
- Seo-Gyeong Bae
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Hyeoung-Joon Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun 58128, Korea
| | - Mi Yeon Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Jae-Sook Ahn
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun 58128, Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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6
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Chen H, Zhao X, Pan W, Xiao H. Integrated genomic and single-cell transcriptomic analyses reveal clonal evolution and immune signature in donor cell leukemia after haploidentical allogeneic hematopoietic stem cell transplantation. Leuk Lymphoma 2023; 64:1681-1688. [PMID: 37424322 DOI: 10.1080/10428194.2023.2232493] [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: 05/06/2023] [Accepted: 06/19/2023] [Indexed: 07/11/2023]
Abstract
The pathogenesis of donor cell leukemia (DCL) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is unclear and likely multifactorial. Leukemic transformation of healthy donor HSCs in recipient's bone marrow microenvironment provides a useful in vivo model for investigating the mechanisms involved in leukemogenesis. Here, we report a rare case of late-onset DCL developing in a recipient. Whole-genome sequencing indicates that donor-derived cells harboring clonal hematopoiesis of indeterminate potential (CHIP)-associated genetic alterations expand and eventually transform to full-blown AML via acquisition of additional somatic mutations within the recipient's bone marrow microenvironment. The 10× single-cell RNA sequencing reveals the abundance of GMP-like cells with a specific transcriptional signature in DCL. Moreover, impaired immune surveillance, including dysfunction of cytotoxic T lymphocytes (CTLs) and decreased number of canonical NK cells, is discovered in DCL. Our data add valuable information to the current understanding of the mechanisms of DCL.
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Affiliation(s)
- Huiqiao Chen
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiujie Zhao
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenjue Pan
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haowen Xiao
- Department of Hematology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Institute of Hematology, Zhejiang University, Hangzhou, China
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7
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Morris VS, Ghazi H, Fletcher DM, Guinn BA. A Direct Comparison, and Prioritisation, of the Immunotherapeutic Targets Expressed by Adult and Paediatric Acute Myeloid Leukaemia Cells: A Systematic Review and Meta-Analysis. Int J Mol Sci 2023; 24:9667. [PMID: 37298623 PMCID: PMC10253696 DOI: 10.3390/ijms24119667] [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: 04/26/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Acute myeloid leukaemia (AML) is characterized by impaired myeloid differentiation resulting in an accumulation of immature blasts in the bone marrow and peripheral blood. Although AML can occur at any age, the incidence peaks at age 65. The pathobiology of AML also varies with age with associated differences in incidence, as well as the frequency of cytogenetic change and somatic mutations. In addition, 5-year survival rates in paediatrics are 60-75% but fall to 5-15% in older AML patients. This systematic review aimed to determine whether the altered genes in AML affect the same molecular pathways, indifferent of patient age, and, therefore, whether patients could benefit from the repurposing drugs or the use of the same immunotherapeutic strategies across age boundaries to prevent relapse. Using a PICO framework and PRISMA-P checklist, relevant publications were identified using five literature databases and assessed against an inclusion criteria, leaving 36 articles, and 71 targets for therapy, for further analysis. QUADAS-2 was used to determine the risk of bias and perform a quality control step. We then priority-ranked the list of cancer antigens based on predefined and pre-weighted objective criteria as part of an analytical hierarchy process used for dealing with complex decisions. This organized the antigens according to their potential to act as targets for the immunotherapy of AML, a treatment that offers an opportunity to remove residual leukaemia cells at first remission and improve survival rates. It was found that 80% of the top 20 antigens identified in paediatric AML were also within the 20 highest scoring immunotherapy targets in adult AML. To analyse the relationships between the targets and their link to different molecular pathways, PANTHER and STRING analyses were performed on the 20 highest scoring immunotherapy targets for both adult and paediatric AML. There were many similarities in the PANTHER and STRING results, including the most prominent pathways being angiogenesis and inflammation mediated by chemokine and cytokine signalling pathways. The coincidence of targets suggests that the repurposing of immunotherapy drugs across age boundaries could benefit AML patients, especially when used in combination with conventional therapies. However, due to cost implications, we would recommend that efforts are focused on ways to target the highest scoring antigens, such as WT1, NRAS, IDH1 and TP53, although in the future other candidates may prove successful.
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Affiliation(s)
- Vanessa S. Morris
- Department of Chemistry and Biochemistry, University of Hull, Kingston upon Hull HU6 7RX, UK;
| | - Hanya Ghazi
- Hull York Medical School, University of Hull, Kingston upon Hull HU6 7RX, UK;
| | - Daniel M. Fletcher
- Centre for Biomedicine, Hull York Medical School, Kingston upon Hull HU6 7RX, UK;
| | - Barbara-ann Guinn
- Centre for Biomedicine, Hull York Medical School, Kingston upon Hull HU6 7RX, UK;
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8
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Casado P, Cutillas PR. Proteomic Characterization of Acute Myeloid Leukemia for Precision Medicine. Mol Cell Proteomics 2023; 22:100517. [PMID: 36805445 PMCID: PMC10152134 DOI: 10.1016/j.mcpro.2023.100517] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 02/07/2023] [Accepted: 02/13/2023] [Indexed: 02/19/2023] Open
Abstract
Acute myeloid leukemia (AML) is a highly heterogeneous cancer of the hematopoietic system with no cure for most patients. In addition to chemotherapy, treatment options for AML include recently approved therapies that target proteins with roles in AML pathobiology, such as FLT3, BLC2, and IDH1/2. However, due to disease complexity, these therapies produce very diverse responses, and survival rates are still low. Thus, despite considerable advances, there remains a need for therapies that target different aspects of leukemic biology and for associated biomarkers that define patient populations likely to respond to each available therapy. To meet this need, drugs that target different AML vulnerabilities are currently in advanced stages of clinical development. Here, we review proteomics and phosphoproteomics studies that aimed to provide insights into AML biology and clinical disease heterogeneity not attainable with genomic approaches. To place the discussion in context, we first provide an overview of genetic and clinical aspects of the disease, followed by a summary of proteins targeted by compounds that have been approved or are under clinical trials for AML treatment and, if available, the biomarkers that predict responses. We then discuss proteomics and phosphoproteomics studies that provided insights into AML pathogenesis, from which potential biomarkers and drug targets were identified, and studies that aimed to rationalize the use of synergistic drug combinations. When considered as a whole, the evidence summarized here suggests that proteomics and phosphoproteomics approaches can play a crucial role in the development and implementation of precision medicine for AML patients.
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Affiliation(s)
- Pedro Casado
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Pedro R Cutillas
- Cell Signalling & Proteomics Group, Centre for Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom; The Alan Turing Institute, The British Library, London, United Kingdom; Digital Environment Research Institute (DERI), Queen Mary University of London, London, United Kingdom.
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9
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Rastogi N, Gonzalez JBM, Srivastava VK, Alanazi B, Alanazi RN, Hughes OM, O'Neill NS, Gilkes AF, Ashley N, Deshpande S, Andrews R, Mead A, Rodrigues NP, Knapper S, Darley RL, Tonks A. Nuclear factor I-C overexpression promotes monocytic development and cell survival in acute myeloid leukemia. Leukemia 2023; 37:276-287. [PMID: 36572750 PMCID: PMC9898032 DOI: 10.1038/s41375-022-01801-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022]
Abstract
Nuclear factor I-C (NFIC) belongs to a family of NFI transcription factors that binds to DNA through CAATT-boxes and are involved in cellular differentiation and stem cell maintenance. Here we show NFIC protein is significantly overexpressed in 69% of acute myeloid leukemia patients. Examination of the functional consequences of NFIC overexpression in HSPCs showed that this protein promoted monocytic differentiation. Single-cell RNA sequencing analysis further demonstrated that NFIC overexpressing monocytes had increased expression of growth and survival genes. In contrast, depletion of NFIC through shRNA decreased cell growth, increased cell cycle arrest and apoptosis in AML cell lines and AML patient blasts. Further, in AML cell lines (THP-1), bulk RNA sequencing of NFIC knockdown led to downregulation of genes involved in cell survival and oncogenic signaling pathways including mixed lineage leukemia-1 (MLL-1). Lastly, we show that NFIC knockdown in an ex vivo mouse MLL::AF9 pre-leukemic stem cell model, decreased their growth and colony formation and increased expression of myeloid differentiation markers Gr1 and Mac1. Collectively, our results suggest that NFIC is an important transcription factor in myeloid differentiation as well as AML cell survival and is a potential therapeutic target in AML.
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Affiliation(s)
- Namrata Rastogi
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK.
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK.
| | - Juan Bautista Menendez Gonzalez
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Vikas Kumar Srivastava
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Bader Alanazi
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Prince Mohammed Medical City, AlJouf, Saudi Arabia
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Rehab N Alanazi
- Medical Laboratory Technology Department, College of Applied Medical Sciences, Northern Border University, Arar, 91431, Saudi Arabia
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Owen M Hughes
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Niamh S O'Neill
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Amanda F Gilkes
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Neil Ashley
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Sumukh Deshpande
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Robert Andrews
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, CF14 4XN, UK
| | - Adam Mead
- Haematopoietic Stem Cell Biology Laboratory, Medical Research Council Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Neil P Rodrigues
- European Cancer Stem Cell Research Institute, School of Biosciences, Cardiff University, Cardiff, CF24 4HQ, Wales, UK
| | - Steve Knapper
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
- Cardiff Experimental and Cancer Medicine Centre (ECMC), School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Richard L Darley
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK
| | - Alex Tonks
- Department of Haematology, Division of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, CF14 4XN, Wales, UK.
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10
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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11
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Zhang W, Liu B, Wu S, Zhao L. TMT-based comprehensive proteomic profiling identifies serum prognostic signatures of acute myeloid leukemia. Open Med (Wars) 2023; 18:20220602. [PMID: 37016705 PMCID: PMC10066874 DOI: 10.1515/med-2022-0602] [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: 05/26/2022] [Revised: 09/19/2022] [Accepted: 10/16/2022] [Indexed: 04/06/2023] Open
Abstract
Acute myeloid leukemia (AML) is classified into favorable-risk, intermediate-risk, and poor-risk subtypes. This study aimed to compare the serum proteomic signatures of the three AML subtypes and identify prognostic biomarkers for AML. Serum samples from patients with favorable-risk (n = 14), intermediate-risk (n = 19), and poor-risk AMLs (n = 18) were used for the analysis of tandem mass tag (TMT) labeling-based quantitative proteomics. Comparative analysis was performed to identify differentially expressed proteins (DEPs) between groups. Prognostic proteins were screened using binary logistics regression analysis. TMT-MS/MS proteomics analysis identified 138 DEPs. Fumarate hydratase (FH), isocitrate dehydrogenase 2 (IDH2), and enolase 1 (ENO1) were significantly upregulated in poor-risk patients compared with favorable-risk patients. ELISA assay confirmed that patients with poor-risk AMLs had higher levels of IDH2, ENO1, and FH compared with intermediate-risk AML patients. Logistics analysis identified that proteins 3-hydroxyacyl-CoA dehydrogenase type-2 (HADH, odds ratio (OR) = 1.035, p = 0.010), glutamine synthetase (GLUL, OR = 1.022, p = 0.039), and lactotransferrin (LTF, OR = 1.1224, p = 0.016) were associated with poor prognosis, and proteins ENO1 (OR = 1.154, p = 0.053), FH (OR = 1.043, p = 0.059), and IDH2 (OR = 3.350, p = 0.055) were associated with AML prognosis. This study showed that AML patients had elevated levels of FH, IDH2, ENO1, LTF, and GLUL proteins and might be at high risk of poor prognosis.
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Affiliation(s)
- Wei Zhang
- Department of Central Laboratory, The First Hospital of Lanzhou University, Lanzhou 730000, Gansu Province, China
| | - Bei Liu
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Shiwen Wu
- Department of Laboratory Medicine, The First Hospital of Lanzhou University, Lanzhou 730000, China
| | - Li Zhao
- Department of Central Laboratory, The First Hospital of Lanzhou University, #1 Donggang West Road, Lanzhou 730000, Gansu Province, China
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12
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Liu L, Qiang X. Hsa_circ_0044907 promotes acute myeloid leukemia progression through upregulating oncogene KIT via sequestering miR-186-5p. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:960-970. [PMID: 36004511 DOI: 10.1080/16078454.2022.2113574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND It has been reported that circular RNA hsa_circ_0044907 (circ_0044907) expression is overtly elevated in acute myeloid leukemia (AML) patient-derived BMMCs. However, the effect of circ_0044907 on AML progression remains un-clarified. METHODS Expression of circ_0044907 in BM and AML cells were detected with real-time quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Cell viability, proliferation, apoptosis, and cycle progression were determined by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT), 5-ethynyl-2'-deoxyuridine (EDU), and flow cytometry assays. The regulatory mechanism of circ_0044907 was predicted by bioinformatics analysis and validated by dual-luciferase reporter, RNA pull-down, and RNA immunoprecipitation (RIP) assays. In vivo experiments were carried out to verify the function of circ_0044907. RESULTS Circ_0044907 was overexpressed in AML patient-derived BM and AML cells. Furthermore, circ_0044907 could distinguish AML patients from healthy controls, and high circ_0044907 expression in BM had a poor prognosis for AML patients, implying that circ_0044907 served as a diagnostic and prognostic indicator for AML. Functionally, circ_0044907 silencing reduced cell viability, restrained cell proliferation, arrested cell cycle progression, and induced cell apoptosis in AML cells in vitro. Furthermore, circ_0044907 knockdown decreased AML cell growth in xenograft mouse models. Mechanically, circ_0044907 sponged miR-186-5p to block the inhibiting effect of miR-186-5p on KIT. Silenced miR-186-5p expression weakened circ_0044907 knockdown mediated suppression on AML cell viability, proliferation, and cycle progression. Also, forced KIT expression weakened miR-186-5p upregulation mediated inhibition on AML cell viability, proliferation, and cycle progression. CONCLUSION Circ_0044907 absorbed miR-186-5p to block the inhibiting impact of miR-186-5p on KIT, thus promoting AML progression.
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Affiliation(s)
- Ling Liu
- Department of Laboratory, Liangjiang New Area First People's Hospital, Chongqing, People's Republic of China
| | - Xing Qiang
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, People's Republic of China
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13
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Nie L, Zhang Y, You Y, Lin C, Li Q, Deng W, Ma J, Luo W, He H. The signature based on seven genomic instability-related genes could predict the prognosis of acute myeloid leukemia patients. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:840-848. [PMID: 35924822 DOI: 10.1080/16078454.2022.2107970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
BACKGROUND Acute myeloid leukemia (AML) is the most common acute blood malignancy in adults. The complicated and dynamic genomic instability (GI) is the most prominent feature of AML. Our study aimed to explore the prognostic value of GI-related genes in AML patients. METHODS The mRNA data and mutation data were downloaded from the TCGA and GEO databases. Differential expression analyses were completed in limma package. GO and KEGG functional enrichment was conducted using clusterProfiler function of R. Univariate Cox and LASSO Cox regression analyses were performed to screen key genes for Risk score model construction. Nomogram was built with rms package. RESULTS We identified 114 DEGs between high TMB patients and low TMB AML patients, which were significantly enriched in 429 GO terms and 13 KEGG pathways. Based on the univariate Cox and LASSO Cox regression analyses, seven optimal genes were finally applied for Risk score model construction, including SELE, LGALS1, ITGAX, TMEM200A, SLC25A21, S100A4 and CRIP1. The Risk score could reliably predict the prognosis of AML patients. Age and Risk score were both independent prognostic indicators for AML, and the Nomogram based on them could also reliably predict the OS of AML patients. CONCLUSIONS A prognostic signature based on seven GI-related genes and a predictive Nomogram for AML patients are finally successfully constructed.
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Affiliation(s)
- Lirong Nie
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Yuming Zhang
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Yuchan You
- Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Changmei Lin
- Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Qinghua Li
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Wenbo Deng
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Jingzhi Ma
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Wenying Luo
- Department of Clinical Laboratory, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
| | - Honghua He
- Department of Hematology, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, People's Republic of China
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14
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Yao CY, Lin CC, Wang YH, Hsu CL, Kao CJ, Hou HA, Chou WC, Tien HF. The clinical and biological characterization of acute myeloid leukemia patients with S100A4 overexpression. J Formos Med Assoc 2022:S0929-6646(22)00422-3. [DOI: 10.1016/j.jfma.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 10/31/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
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15
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Xie X, Yang W, Zhang W, Qiu Y, Qiu Z, Wang H, Hu Y, Li Y, Zhou X, Li L, Chen Z, Zhao C, Lu Y, Zhang K, Lai E, Bai X. Tegaserod maleate exhibits antileukemic activity by targeting TRPM8. Biomed Pharmacother 2022; 154:113566. [PMID: 35994820 DOI: 10.1016/j.biopha.2022.113566] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/11/2022] [Accepted: 08/14/2022] [Indexed: 12/20/2022] Open
Abstract
To identify therapeutic targets in acute myeloid leukemia (AML), we conducted growth inhibition screens of 2040 small molecules from a library of FDA-approved drugs using a panel of 12 AML cell lines. Tegaserod maleate, a 5-hydroxytryptamine 4 receptor partial agonist, elicits strong anti-AML effects in vitro and in vivo by targeting transient receptor potential melastatin subtype 8 (TRPM8), which plays critical roles in several important processes. However, the role of TRPM8 remains incompletely described in AML, whose treatment is based mostly on antimitotic chemotherapy. Here, we report an unexpected role of TRPM8 in leukemogenesis. Strikingly, TRPM8 knockout inhibits AML cell survival/proliferation by promoting apoptosis. Mechanistically, TRPM8 exerts its oncogenic effect by regulating the ERK-CREB/c-Fos signaling axis. Hyperactivation of ERK signaling can be reversed by TRPM8 inhibition. Importantly, TRPM8 is overexpressed in AML patients, indicating that it is a new prognostic factor in AML. Collectively, our work demonstrates the anti-AML effects of tegaserod maleate via targeting TRPM8 and indicates that TRPM8 is a regulator of leukemogenesis with therapeutic potential in AML.
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Affiliation(s)
- Xiaoling Xie
- Shunde Hospital, Southern Medical University (The First People's Hospital of Shunde Foshan), Foshan 528308, China; Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Wanwen Yang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wuju Zhang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yingqi Qiu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Zeyou Qiu
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hao Wang
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Yuxing Hu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Yuhua Li
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China; Department of Basic Research & International Cooperation, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Xuan Zhou
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Luyao Li
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Zhuanzhuan Chen
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Chenbo Zhao
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Yao Lu
- Department of Hematology, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Keqin Zhang
- Department of Oncology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou 510999, China.
| | - Eryong Lai
- Department of Oncology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou 510999, China.
| | - Xiaochun Bai
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
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16
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Proteomic and phosphoproteomic landscapes of acute myeloid leukemia. Blood 2022; 140:1533-1548. [PMID: 35895896 PMCID: PMC9523374 DOI: 10.1182/blood.2022016033] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 07/14/2022] [Indexed: 01/21/2023] Open
Abstract
We have developed a deep-scale proteome and phosphoproteome database from 44 representative acute myeloid leukemia (AML) patients from the LAML TCGA dataset and 6 healthy bone marrow-derived controls. After confirming data quality, we orthogonally validated several previously undescribed features of AML revealed by the proteomic data. We identified examples of posttranscriptionally regulated proteins both globally (ie, in all AML samples) and also in patients with recurrent AML driver mutations. For example, samples with IDH1/2 mutations displayed elevated levels of the 2-oxoglutarate-dependent histone demethylases KDM4A/B/C, despite no changes in messenger RNA levels for these genes; we confirmed this finding in vitro. In samples with NPMc mutations, we identified several nuclear importins with posttranscriptionally increased protein abundance and showed that they interact with NPMc but not wild-type NPM1. We identified 2 cell surface proteins (CD180 and MRC1/CD206) expressed on AML blasts of many patients (but not healthy CD34+ stem/progenitor cells) that could represent novel targets for immunologic therapies and confirmed these targets via flow cytometry. Finally, we detected nearly 30 000 phosphosites in these samples; globally, AML samples were associated with the abnormal phosphorylation of specific residues in PTPN11, STAT3, AKT1, and PRKCD. FLT3-TKD samples were associated with increased phosphorylation of activating tyrosines on the cytoplasmic Src-family tyrosine kinases FGR and HCK and related signaling proteins. PML-RARA-initiated AML samples displayed a unique phosphorylation signature, and TP53-mutant samples showed abundant phosphorylation of serine-183 on TP53 itself. This publicly available database will serve as a foundation for further investigations of protein dysregulation in AML pathogenesis.
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17
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Joshi SK, Tognon CE, Druker BJ, Rodland KD. Oncoproteomic profiling of AML: moving beyond genomics. Expert Rev Proteomics 2022; 19:283-287. [PMID: 36734985 PMCID: PMC10505090 DOI: 10.1080/14789450.2023.2176757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/16/2023] [Indexed: 02/04/2023]
Affiliation(s)
- Sunil K. Joshi
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Cristina E. Tognon
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Brian J. Druker
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Division of Hematology & Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Karin D. Rodland
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
- Department of Cell, Developmental, and Cancer Biology, Oregon Health & Science University, Portland, OR, USA
- Pacific Northwest National Laboratory, Richland, WA, USA
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18
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Yang L, Gilbertsen A, Smith K, Xia H, Higgins L, Guerrero C, Henke CA. Proteomic analysis of the IPF mesenchymal progenitor cell nuclear proteome identifies abnormalities in key nodal proteins that underlie their fibrogenic phenotype. Proteomics 2022; 22:e2200018. [PMID: 35633524 PMCID: PMC9541064 DOI: 10.1002/pmic.202200018] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 11/25/2022]
Abstract
IPF is a progressive fibrotic lung disease whose pathogenesis remains incompletely understood. We have previously discovered pathologic mesenchymal progenitor cells (MPCs) in the lungs of IPF patients. IPF MPCs display a distinct transcriptome and create sustained interstitial fibrosis in immune deficient mice. However, the precise pathologic alterations responsible for this fibrotic phenotype remain to be uncovered. Quantitative mass spectrometry and interactomics is a powerful tool that can define protein alterations in specific subcellular compartments that can be implemented to understand disease pathogenesis. We employed quantitative mass spectrometry and interactomics to define protein alterations in the nuclear compartment of IPF MPCs compared to control MPCs. We identified increased nuclear levels of PARP1, CDK1, and BACH1. Interactomics implicated PARP1, CDK1, and BACH1 as key hub proteins in the DNA damage/repair, differentiation, and apoptosis signaling pathways respectively. Loss of function and inhibitor studies demonstrated important roles for PARP1 in DNA damage/repair, CDK1 in regulating IPF MPC stemness and self-renewal, and BACH1 in regulating IPF MPC viability. Our quantitative mass spectrometry studies combined with interactomic analysis uncovered key roles for nuclear PARP1, CDK1, and BACH1 in regulating IPF MPC fibrogenicity.
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Affiliation(s)
- Libang Yang
- Department of MedicineUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Adam Gilbertsen
- Department of MedicineUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Karen Smith
- Department of MedicineUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - Hong Xia
- Department of MedicineUniversity of MinnesotaMinneapolisMinnesotaUSA
| | - LeeAnn Higgins
- Center for Mass Spectrometry and ProteomicsUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Candace Guerrero
- Center for Mass Spectrometry and ProteomicsUniversity of MinnesotaSt. PaulMinnesotaUSA
| | - Craig A. Henke
- Department of MedicineUniversity of MinnesotaMinneapolisMinnesotaUSA
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19
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Yang L, Yang J, Jacobson B, Gilbertsen A, Smith K, Higgins L, Guerrero C, Xia H, Henke CA, Lin J. SFPQ Promotes Lung Cancer Malignancy via Regulation of CD44 v6 Expression. Front Oncol 2022; 12:862250. [PMID: 35707369 PMCID: PMC9190464 DOI: 10.3389/fonc.2022.862250] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
Mesenchymal stem cells (MSCs) contribute to tumor pathogenesis and elicit antitumor immune responses in tumor microenvironments. Nuclear proteins might be the main players in these processes. In the current study, combining spatial proteomics with ingenuity pathway analysis (IPA) in lung non-small cell (NSC) cancer MSCs, we identify a key nuclear protein regulator, SFPQ (Splicing Factor Proline and Glutamine Rich), which is overexpressed in lung cancer MSCs and functions to promote MSCs proliferation, chemical resistance, and invasion. Mechanistically, the knockdown of SFPQ reduces CD44v6 expression to inhibit lung cancer MSCs stemness, proliferation in vitro, and metastasis in vivo. The data indicates that SFPQ may be a potential therapeutic target for limiting growth, chemotherapy resistance, and metastasis of lung cancer.
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Affiliation(s)
- Libang Yang
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jianbo Yang
- Department of Laboratory Medicine and Pathology, School of Medicine, University of Minneapolis, Minneapolis, MN, United States.,The Cancer Center, Fujian Medical University Union Hospital, Fuzhou, China
| | - Blake Jacobson
- Hematology, Oncology and Transplantation, School of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Adam Gilbertsen
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Karen Smith
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - LeeAnn Higgins
- Center for Mass Spectrometry and Proteomics, University of Minnesota, St. Paul, MN, United States
| | - Candace Guerrero
- Center for Mass Spectrometry and Proteomics, University of Minnesota, St. Paul, MN, United States
| | - Hong Xia
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Craig A Henke
- Department of Medicine, University of Minnesota, Minneapolis, MN, United States
| | - Jizhen Lin
- The Cancer Center, Fujian Medical University Union Hospital, Fuzhou, China.,The Immunotherapy Research Laboratory, Department of Otolaryngology, Cancer Center, University of Minnesota, Minneapolis, MN, United States
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20
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Qiao X, Lu L, Zhou K, Tan L, Liu X, Ni J, Hou Y, Liang J, Dou H. The correlation between proteoglycan 2 and neuropsychiatric systemic lupus erythematosus. Clin Immunol 2022; 239:109042. [PMID: 35568106 DOI: 10.1016/j.clim.2022.109042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/09/2022] [Accepted: 05/09/2022] [Indexed: 02/06/2023]
Abstract
The proposed pathogenesis of neuropsychiatric systemic lupus erythematosus (NPSLE) mainly includes ischemia and neuroinflammation mechanisms. Protein encoded by Proteoglycan 2 (PRG2) mRNA is involved in the immune process related to eosinophils, also being found in the placenta and peripheral blood of pregnant women. We evaluated the correlation between PRG2 and NPSLE for the first time and found that PRG2 protein is overexpressed in the serum of patients with NPSLE and correlated with the SLE disease activity index (SLEDAI) subset scores of psychosis. Moreover, we investigated the correlation between hippocampal PRG2 level and hippocampally dependent learning and memory ability in MRL/lpr mice, and discovered that the number of PRG2+GFAP+ astrocytes in the cortex and hypothalamus and the number of PRG2+IBA-1+ microglia in the hippocampus and cortex significantly increased in the MRL/lpr mice. These data provided a reference for the follow-up exploration of the role of PRG2 in SLE or other diseases.
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Affiliation(s)
- Xiaoyue Qiao
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China
| | - Li Lu
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China
| | - Kangxing Zhou
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Liping Tan
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China
| | - Xuan Liu
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China
| | - Jiali Ni
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China
| | - Yayi Hou
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China.
| | - Jun Liang
- Department of Rheumatology and Immunology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China.
| | - Huan Dou
- The State Key Laboratory of Pharmaceutical Biotechnology, Division of Immunology, Medical School, Nanjing University, Nanjing 210093, China; Jiangsu Key Laboratory of Molecular Medicine, Nanjing University, Nanjing 210093, China.
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21
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Yan J, Fang X, Feng Y, Cui X, Li F, Luo W, Ma X, Liang J, Feng J. Identification of key genes associated with the progression of liver fibrosis to hepatocellular carcinoma based on iTRAQ proteomics and GEO database. Ann Hepatol 2022; 27:100681. [PMID: 35124283 DOI: 10.1016/j.aohep.2022.100681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/28/2022] [Accepted: 01/31/2022] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND OBJECTIVE Liver fibrosis (LF) often leads to cirrhosis and even hepatocellular carcinoma (HCC), but the molecular mechanism remains unclear. The aims of the present study were to identify potential biomarkers for the progression of LF to HCC and explore the associated molecular mechanisms. MATERIALS AND METHODS The isobaric tags for relative and absolute quantitation (iTRAQ) was used to detect changes in the protein expression profiles of liver tissues and to screen the differentially expressed proteins (DEPs). The differentially expressed genes (DEGs) of LF rats and patients were screened by Gene Expression Database (GEO). Subsequently, the clinicopathological analysis of the overlapping genes in different pathological stages in HCC patients based on GEPIA database was conducted. RESULTS iTRAQ proteomic analysis revealed 689, 749 and 585 DEPs in the 6W, 8W and 12W groups, respectively. ALDH2, SLC27A5 and ASNS were not only the DEPs found in rats with LF with different stages but were also the DEGs related to the pathological stages and survival in patients with HCC. CONCLUSIONS ALDH2, SLC27A5 and ASNS were the potential biomarkers associated with the progression of LF to HCC.
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Affiliation(s)
- Jiongyi Yan
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Xuewan Fang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Yinyi Feng
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Xiaojuan Cui
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Fang Li
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Weisheng Luo
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Xiaocong Ma
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China
| | - Jianqin Liang
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China; Guangxi Superior Proprietary Chinese Medicine and Ethnic Medicine Development Engineering Technology Research Centre, Guangxi University of Chinese Medicine, Nanning 530200, China.
| | - Jianfang Feng
- College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530200, China; Guangxi Superior Proprietary Chinese Medicine and Ethnic Medicine Development Engineering Technology Research Centre, Guangxi University of Chinese Medicine, Nanning 530200, China.
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22
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Reikvam H, Hemsing AL, Hernandez-Valladares M, Birkeland E. Proteomic approaches for untangling pharmacological targets in acute myeloid leukemia. Expert Rev Proteomics 2022; 19:73-76. [PMID: 35436165 DOI: 10.1080/14789450.2022.2067530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Håkon Reikvam
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Anette Lodvir Hemsing
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Biomedicine, University of Bergen, Bergen, Norway.,Department of Physical Chemistry, University of Granada, Granada, Spain
| | - Even Birkeland
- Department of Biomedicine, University of Bergen, Bergen, Norway
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23
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Mishra S, Liu J, Chai L, Tenen DG. Diverse functions of long noncoding RNAs in acute myeloid leukemia: emerging roles in pathophysiology, prognosis, and treatment resistance. Curr Opin Hematol 2022; 29:34-43. [PMID: 34854833 PMCID: PMC8647777 DOI: 10.1097/moh.0000000000000692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
PURPOSE OF REVIEW Advancements in the next-generation sequencing technologies have identified rare transcripts of long noncoding RNAs (lncRNAs) in the genome of cancers, including in acute myeloid leukemia (AML). The purpose of this review is to highlight the contribution of lncRNAs in AML pathogenesis, prognosis, and chemoresistance. RECENT FINDINGS Several studies have recently reported that deregulated lncRNAs are novel key players in the development of AML and are associated with AML pathophysiology and may serve as prognostic indicators. A few aberrantly expressed lncRNAs that correlated with the recurrent genetic mutations in AML such as NPM1 and RUNX1 have recently been characterized. Moreover, a few lncRNAs in MLL-rearranged leukemia have been described. Additionally, the involvement of lncRNAs in AML chemoresistance has been postulated. SUMMARY Investigating the functional roles of the noncoding regions including lncRNAs, may provide novel insights into the pathophysiology, refine the prognostic schema, and provide novel therapeutic treatment strategies in AML.
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Affiliation(s)
- Srishti Mishra
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
| | - Jun Liu
- Department of Pathology, Brigham & Women's Hospital
| | - Li Chai
- Department of Pathology, Brigham & Women's Hospital
| | - Daniel G Tenen
- Cancer Science Institute, National University of Singapore, Singapore, Singapore
- Harvard Stem Cell Institute, Harvard Medical School, Boston, Massachusetts, USA
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24
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Immanuel T, Li J, Green TN, Bogdanova A, Kalev-Zylinska ML. Deregulated calcium signaling in blood cancer: Underlying mechanisms and therapeutic potential. Front Oncol 2022; 12:1010506. [PMID: 36330491 PMCID: PMC9623116 DOI: 10.3389/fonc.2022.1010506] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 09/21/2022] [Indexed: 02/05/2023] Open
Abstract
Intracellular calcium signaling regulates diverse physiological and pathological processes. In solid tumors, changes to calcium channels and effectors via mutations or changes in expression affect all cancer hallmarks. Such changes often disrupt transport of calcium ions (Ca2+) in the endoplasmic reticulum (ER) or mitochondria, impacting apoptosis. Evidence rapidly accumulates that this is similar in blood cancer. Principles of intracellular Ca2+ signaling are outlined in the introduction. We describe different Ca2+-toolkit components and summarize the unique relationship between extracellular Ca2+ in the endosteal niche and hematopoietic stem cells. The foundational data on Ca2+ homeostasis in red blood cells is discussed, with the demonstration of changes in red blood cell disorders. This leads to the role of Ca2+ in neoplastic erythropoiesis. Then we expand onto the neoplastic impact of deregulated plasma membrane Ca2+ channels, ER Ca2+ channels, Ca2+ pumps and exchangers, as well as Ca2+ sensor and effector proteins across all types of hematologic neoplasms. This includes an overview of genetic variants in the Ca2+-toolkit encoding genes in lymphoid and myeloid cancers as recorded in publically available cancer databases. The data we compiled demonstrate that multiple Ca2+ homeostatic mechanisms and Ca2+ responsive pathways are altered in hematologic cancers. Some of these alterations may have genetic basis but this requires further investigation. Most changes in the Ca2+-toolkit do not appear to define/associate with specific disease entities but may influence disease grade, prognosis, treatment response, and certain complications. Further elucidation of the underlying mechanisms may lead to novel treatments, with the aim to tailor drugs to different patterns of deregulation. To our knowledge this is the first review of its type in the published literature. We hope that the evidence we compiled increases awareness of the calcium signaling deregulation in hematologic neoplasms and triggers more clinical studies to help advance this field.
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Affiliation(s)
- Tracey Immanuel
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Jixia Li
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Department of Laboratory Medicine, School of Medicine, Foshan University, Foshan City, China
| | - Taryn N. Green
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
| | - Anna Bogdanova
- Red Blood Cell Research Group, Institute of Veterinary Physiology, Vetsuisse Faculty, University of Zurich, Zürich, Switzerland
- Zurich Center for Integrative Human Physiology, University of Zurich, Zürich, Switzerland
| | - Maggie L. Kalev-Zylinska
- Blood and Cancer Biology Laboratory, Department of Molecular Medicine and Pathology, University of Auckland, Auckland, New Zealand
- Haematology Laboratory, Department of Pathology and Laboratory Medicine, Auckland City Hospital, Auckland, New Zealand
- *Correspondence: Maggie L. Kalev-Zylinska,
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25
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Zhang J, Peng Y, He Y, Xiao Y, Wang Q, Zhao Y, Zhang T, Wu C, Xie Y, Zhou J, Yu W, Lu D, Bai H, Chen T, Guo P, Zhang Q. GPX1-associated prognostic signature predicts poor survival in patients with acute myeloid leukemia and involves in immunosuppression. Biochim Biophys Acta Mol Basis Dis 2021; 1868:166268. [PMID: 34536536 DOI: 10.1016/j.bbadis.2021.166268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 08/21/2021] [Accepted: 09/04/2021] [Indexed: 01/11/2023]
Abstract
OBJECTIVE Treatment of acute myeloid leukemia (AML) remains a challenge. It is urgent to understand the microenvironment to improve therapy and prognosis. METHODS Bioinformatics methods were used to analyze transcription expression profile of AML patient samples with complete clinical information from UCSC Xena TCGA-AML datasets and validate with GEO datasets. Western blot, qPCR, RNAi and CCK8 assay were used to assay the effect of GPX1 expression on AML cell viability and the expression of genes of interest. RESULTS Our analyses revealed that highly expressed GPX1 in AML patients links to unfavorable prognosis. GPX1 expression was positively associated with not only fraction levels of myeloid-derived suppressor cells (MDSCs), monocytes and T cell exhaustion, the expression levels of MDSC markers, MDSC-promoting CCR2 and immune inhibitory checkpoints (TIM3/Gal-9, SIRPα and VISTA), but also negatively with low fraction levels of CD4+ and CD8+ T cells. Silencing GPX1 expression reduced AML cell viability and CCR2 expression. Moreover, GPX1-targetd kinases were PKC family, SRC family, SYK and PAK1, which promote AML progression and the resistance to therapy. Furthermore, Additionally, GPX1-associated prognostic signature (GPS) is an independent risk factor with high area under curve (AUC) values of receiver operating characteristic (ROC) curves. High risk group based on GPS enriched not only with endocytosis which transfers mitochondria to favor AML cell survival in response to chemotherapy, but also NOTCH, WNT and TLR signaling which promote therapy resistance. CONCLUSION Our results revealed the significant involvement of GPX1 in AML immunosuppression via and provided a prognostic signature for AML patients.
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MESH Headings
- Aged
- Antigens, Differentiation/genetics
- B7 Antigens/genetics
- Female
- Gene Expression Regulation, Leukemic/genetics
- Glutathione Peroxidase/genetics
- Hepatitis A Virus Cellular Receptor 2
- Humans
- Immune Tolerance/genetics
- Immunosuppression Therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/immunology
- Leukemia, Myeloid, Acute/pathology
- Male
- Middle Aged
- Myeloid-Derived Suppressor Cells/immunology
- Myeloid-Derived Suppressor Cells/pathology
- Prognosis
- Receptors, CCR2/genetics
- Receptors, Immunologic/genetics
- Receptors, Notch/genetics
- Risk Factors
- Syk Kinase/genetics
- Tumor Microenvironment/immunology
- Wnt Signaling Pathway/genetics
- p21-Activated Kinases/genetics
- Glutathione Peroxidase GPX1
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Affiliation(s)
- Jian Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yuhui Peng
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yan He
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yan Xiao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Qinrong Wang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yan Zhao
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Tin Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Changxue Wu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Yuan Xie
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Jianjiang Zhou
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Wenfeng Yu
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China
| | - Deqin Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hua Bai
- Medical Laboratory Center, the Third Affiliated Hospital of Guizhou Medical University, Duyun 558000, Guizhou, China.
| | - Tenxiang Chen
- Department of Pathophysiology, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, Guizhou, China; Guizhou Provincial Key Laboratory of Pathogenesis and Drug Research on Common Chronic Diseases, Guiyang 550004, Guizhou, China.
| | - Penxiang Guo
- Department of Hematology, Guizhou Provincial People's Hospital, Guizhou University, Guiyang 550002, Guizhou, China.
| | - Qifang Zhang
- Key Laboratory of Endemic and Ethnic Diseases, Ministry of Education & Key Laboratory of Medical Molecular Biology of Guizhou Province, School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, Guizhou, China.
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26
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Liu M, Wang Y, Miettinen JJ, Kumari R, Majumder MM, Tierney C, Bazou D, Parsons A, Suvela M, Lievonen J, Silvennoinen R, Anttila P, Dowling P, O'Gorman P, Tang J, Heckman CA. S100 Calcium Binding Protein Family Members Associate With Poor Patient Outcome and Response to Proteasome Inhibition in Multiple Myeloma. Front Cell Dev Biol 2021; 9:723016. [PMID: 34485305 PMCID: PMC8415228 DOI: 10.3389/fcell.2021.723016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Despite several new therapeutic options, multiple myeloma (MM) patients experience multiple relapses and inevitably become refractory to treatment. Insights into drug resistance mechanisms may lead to the development of novel treatment strategies. The S100 family is comprised of 21 calcium binding protein members with 17 S100 genes located in the 1q21 region, which is commonly amplified in MM. Dysregulated expression of S100 family members is associated with tumor initiation, progression and inflammation. However, the relationship between the S100 family and MM pathogenesis and drug response is unknown. In this study, the roles of S100 members were systematically studied at the copy number, transcriptional and protein level with patients’ survival and drug response. Copy number analysis revealed a predominant pattern of gains occurring in S100 genes clustering in the 1q21 locus. In general, gains of genes encoding S100 family members associated with worse patient survival. However, S100 gene copy number and S100 gene expression did not necessarily correlate, and high expression of S100A4 associated with poor patient survival. Furthermore, integrated analysis of S100 gene expression and ex vivo drug sensitivity data showed significant negative correlation between expression of S100 family members (S100A8, S100A9, and S100A12) and sensitivity to some drugs used in current MM treatment, including proteasome inhibitors (bortezomib, carfilzomib, and ixazomib) and histone deacetylase inhibitor panobinostat. Combined proteomic and pharmacological data exhibited significant negative association of S100 members (S100A4, S100A8, and S100A9) with proteasome inhibitors and panobinostat. Clinically, the higher expression of S100A4 and S100A10 were significantly linked to shorter progression free survival in patients receiving carfilzomib-based therapy. The results indicate an association and highlight the potential functional importance of S100 members on chromosome 1q21 in the development of MM and resistance to established myeloma drugs, including proteasome inhibitors.
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Affiliation(s)
- Minxia Liu
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juho J Miettinen
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Romika Kumari
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Muntasir Mamun Majumder
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Ciara Tierney
- Department of Hematology, Mater Misericordiae University Hospital, Dublin, Ireland.,Department of Biology, National University of Ireland, Maynooth, Ireland
| | - Despina Bazou
- Department of Hematology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Alun Parsons
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Minna Suvela
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Juha Lievonen
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Raija Silvennoinen
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Pekka Anttila
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Paul Dowling
- Department of Biology, National University of Ireland, Maynooth, Ireland
| | - Peter O'Gorman
- Department of Hematology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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27
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Guo L, Liu J, Yang Y, Zeng Y, Yuan F, Zhong F, Jin Y, Wan R, Liu W. Purple sweet potato anthocyanins elicit calcium overload-induced cell death by inhibiting the calcium-binding protein S100A4 in acute lymphoblastic leukemia. FOOD BIOSCI 2021. [DOI: 10.1016/j.fbio.2021.101214] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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28
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Su M, Zhang Z, Zhou L, Han C, Huang C, Nice EC. Proteomics, Personalized Medicine and Cancer. Cancers (Basel) 2021; 13:2512. [PMID: 34063807 PMCID: PMC8196570 DOI: 10.3390/cancers13112512] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
As of 2020 the human genome and proteome are both at >90% completion based on high stringency analyses. This has been largely achieved by major technological advances over the last 20 years and has enlarged our understanding of human health and disease, including cancer, and is supporting the current trend towards personalized/precision medicine. This is due to improved screening, novel therapeutic approaches and an increased understanding of underlying cancer biology. However, cancer is a complex, heterogeneous disease modulated by genetic, molecular, cellular, tissue, population, environmental and socioeconomic factors, which evolve with time. In spite of recent advances in treatment that have resulted in improved patient outcomes, prognosis is still poor for many patients with certain cancers (e.g., mesothelioma, pancreatic and brain cancer) with a high death rate associated with late diagnosis. In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection, surveillance, prognosis and drug monitoring, the role of the microbiome and the goals of personalized/precision medicine, discussing how emerging omics technologies can further inform on these areas. Exemplars from recent onco-proteogenomic-related publications will be given. Finally, we will address future perspectives, not only from the standpoint of perceived advances in treatment, but also from the hurdles that have to be overcome.
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Affiliation(s)
- Miao Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Chao Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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29
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Active Akt signaling triggers CLL toward Richter transformation via overactivation of Notch1. Blood 2021; 137:646-660. [PMID: 33538798 DOI: 10.1182/blood.2020005734] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/07/2020] [Indexed: 12/21/2022] Open
Abstract
Richter's transformation (RT) is an aggressive lymphoma that occurs upon progression from chronic lymphocytic leukemia (CLL). Transformation has been associated with genetic aberrations in the CLL phase involving TP53, CDKN2A, MYC, and NOTCH1; however, a significant proportion of RT cases lack CLL phase-associated events. Here, we report that high levels of AKT phosphorylation occur both in high-risk CLL patients harboring TP53 and NOTCH1 mutations as well as in patients with RT. Genetic overactivation of Akt in the murine Eµ-TCL1 CLL mouse model resulted in CLL transformation to RT with significantly reduced survival and an aggressive lymphoma phenotype. In the absence of recurrent mutations, we identified a profile of genomic aberrations intermediate between CLL and diffuse large B-cell lymphoma. Multiomics assessment by phosphoproteomic/proteomic and single-cell transcriptomic profiles of this Akt-induced murine RT revealed an S100 protein-defined subcluster of highly aggressive lymphoma cells that developed from CLL cells, through activation of Notch via Notch ligand expressed by T cells. Constitutively active Notch1 similarly induced RT of murine CLL. We identify Akt activation as an initiator of CLL transformation toward aggressive lymphoma by inducing Notch signaling between RT cells and microenvironmental T cells.
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30
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Proteomic Studies of Primary Acute Myeloid Leukemia Cells Derived from Patients Before and during Disease-Stabilizing Treatment Based on All-Trans Retinoic Acid and Valproic Acid. Cancers (Basel) 2021; 13:cancers13092143. [PMID: 33946813 PMCID: PMC8125016 DOI: 10.3390/cancers13092143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
All-trans retinoic acid (ATRA) and valproic acid (VP) have been tried in the treatment of non-promyelocytic variants of acute myeloid leukemia (AML). Non-randomized studies suggest that the two drugs can stabilize AML and improve normal peripheral blood cell counts. In this context, we used a proteomic/phosphoproteomic strategy to investigate the in vivo effects of ATRA/VP on human AML cells. Before starting the combined treatment, AML responders showed increased levels of several proteins, especially those involved in neutrophil degranulation/differentiation, M phase regulation and the interconversion of nucleotide di- and triphosphates (i.e., DNA synthesis and binding). Several among the differentially regulated phosphorylation sites reflected differences in the regulation of RNA metabolism and apoptotic events at the same time point. These effects were mainly caused by increased cyclin dependent kinase 1 and 2 (CDK1/2), LIM domain kinase 1 and 2 (LIMK1/2), mitogen-activated protein kinase 7 (MAPK7) and protein kinase C delta (PRKCD) activity in responder cells. An extensive effect of in vivo treatment with ATRA/VP was the altered level and phosphorylation of proteins involved in the regulation of transcription/translation/RNA metabolism, especially in non-responders, but the regulation of cell metabolism, immune system and cytoskeletal functions were also affected. Our analysis of serial samples during the first week of treatment suggest that proteomic and phosphoproteomic profiling can be used for the early identification of responders to ATRA/VP-based treatment.
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31
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Potluri S, Assi SA, Chin PS, Coleman DJL, Pickin A, Moriya S, Seki N, Heidenreich O, Cockerill PN, Bonifer C. Isoform-specific and signaling-dependent propagation of acute myeloid leukemia by Wilms tumor 1. Cell Rep 2021; 35:109010. [PMID: 33882316 DOI: 10.1016/j.celrep.2021.109010] [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: 08/07/2020] [Revised: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 10/21/2022] Open
Abstract
Acute myeloid leukemia (AML) is caused by recurrent mutations in members of the gene regulatory and signaling machinery that control hematopoietic progenitor cell growth and differentiation. Here, we show that the transcription factor WT1 forms a major node in the rewired mutation-specific gene regulatory networks of multiple AML subtypes. WT1 is frequently either mutated or upregulated in AML, and its expression is predictive for relapse. The WT1 protein exists as multiple isoforms. For two main AML subtypes, we demonstrate that these isoforms exhibit differential patterns of binding and support contrasting biological activities, including enhanced proliferation. We also show that WT1 responds to oncogenic signaling and is part of a signaling-responsive transcription factor hub that controls AML growth. WT1 therefore plays a central and widespread role in AML biology.
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MESH Headings
- Base Sequence
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Chromatin/chemistry
- Chromatin/metabolism
- Chromosomes, Human, Pair 21
- Chromosomes, Human, Pair 8
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Early Growth Response Protein 1/genetics
- Early Growth Response Protein 1/metabolism
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Gene Regulatory Networks
- HEK293 Cells
- Humans
- Leukemia, Myeloid, Acute/classification
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Protein Isoforms/antagonists & inhibitors
- Protein Isoforms/genetics
- Protein Isoforms/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RUNX1 Translocation Partner 1 Protein/genetics
- RUNX1 Translocation Partner 1 Protein/metabolism
- Signal Transduction
- Sp1 Transcription Factor/genetics
- Sp1 Transcription Factor/metabolism
- Translocation, Genetic
- WT1 Proteins/antagonists & inhibitors
- WT1 Proteins/genetics
- WT1 Proteins/metabolism
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/metabolism
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Affiliation(s)
- Sandeep Potluri
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
| | - Salam A Assi
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Paulynn S Chin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Dan J L Coleman
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Anna Pickin
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Shogo Moriya
- Department of Biochemistry and Genetics, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chiba 260-8670, Japan
| | - Olaf Heidenreich
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University, Herschel Building, Level 6, Brewery Lane, Newcastle upon Tyne NE1 7RU, UK; Prinses Máxima Centrum for Pediatric Oncology, Postbus 113, 3720 AC Bilthoven, Heidelberglaan 25, 3584CS Utrecht, the Netherlands
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK
| | - Constanze Bonifer
- Institute of Cancer and Genomic Sciences, College of Medicine and Dentistry, University of Birmingham, Edgbaston, Birmingham B152TT, UK.
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32
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S100A4 in the Physiology and Pathology of the Central and Peripheral Nervous System. Cells 2021; 10:cells10040798. [PMID: 33918416 PMCID: PMC8066633 DOI: 10.3390/cells10040798] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 03/27/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
S100A4 is a member of the large family of S100 proteins, exerting a broad range of intracellular and extracellular functions that vary upon different cellular contexts. While S100A4 has long been implicated mainly in tumorigenesis and metastatization, mounting evidence shows that S100A4 is a key player in promoting pro-inflammatory phenotypes and organ pro-fibrotic pathways in the liver, kidney, lung, heart, tendons, and synovial tissues. Regarding the nervous system, there is still limited information concerning S100A4 presence and function. It was observed that S100A4 exerts physiological roles contributing to neurogenesis, cellular motility and chemotaxis, cell differentiation, and cell-to cell communication. Furthermore, S100A4 is likely to participate to numerous pathological processes of the nervous system by affecting the functions of astrocytes, microglia, infiltrating cells and neurons and thereby modulating inflammation and immune reactions, fibrosis as well as neuronal plasticity and survival. This review summarizes the current state of knowledge concerning the localization, deregulation, and possible functions of S100A4 in the physiology of the central and peripheral nervous system. Furthermore, we highlight S100A4 as a gene involved in the pathogenesis of neurological disorders such as brain tumors, neurodegenerative diseases, and acute injuries.
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33
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Lyu T, Wang Y, Li D, Yang H, Qin B, Zhang W, Li Z, Cheng C, Zhang B, Guo R, Song Y. Exosomes from BM-MSCs promote acute myeloid leukemia cell proliferation, invasion and chemoresistance via upregulation of S100A4. Exp Hematol Oncol 2021; 10:24. [PMID: 33789743 PMCID: PMC8011411 DOI: 10.1186/s40164-021-00220-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/27/2021] [Indexed: 02/06/2023] Open
Abstract
Background BM-MSCs play an important role in cancer development through the release of cytokines or exosomes. Studies have shown that extracellular exosomes derived from BM-MSCs are a key pro-invasive factor. However, how BM-MSC-exos influence AML cell proliferation, invasion and chemoresistance remains poorly understood. Methods We isolated exosomes from BM-MSCs and used electron microscopy, particle size separation and western blots to identify the exosomes. The invasion of leukemia cells was observed with a transwell assay. The stemness traits and chemoresistance of the leukemia cells were detected by FCM, colony formation and CCK-8 assays. TCGA database was used to investigate the prognostic relevance of S100A4 and its potential role in AML. Results In this study, we found that BM-MSC-exos increased the metastatic potential, maintained the stemness and contributed to the chemoresistance of leukemia cells. Mechanistically, BM-MSC-exos promoted the proliferation, invasion and chemoresistance of leukemia cells via upregulation of S100A4. Downregulating S100A4 clearly suppressed the proliferation, invasion, and chemoresistance of leukemia cells after treatment with BM-MSC-exos. Bioinformatic analysis with data in TCGA database showed that S100A4 was associated with poor prognosis in AML patients, and functional enrichment revealed its involvement in the processes of cell–cell adhesion and cytokine regulation. Conclusions S100A4 is vital in the BM-MSC-exo-driven proliferation, invasion and chemoresistance of leukemia cells and may serve as a potential target for leukemia therapy.
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Affiliation(s)
- Tianxin Lyu
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China.,Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Yinuo Wang
- Translational Cancer Research Center, Peking University First Hospital, Beijing, 100034, China
| | - Ding Li
- Department of Pharmacy, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China
| | - Hui Yang
- Translational Cancer Research Center, Peking University First Hospital, Beijing, 100034, China
| | - Bin Qin
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Wenli Zhang
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China
| | - Zhiyue Li
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China
| | - Cheng Cheng
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China
| | - Binglei Zhang
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, 450052, China
| | - Rongqun Guo
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yongping Song
- Department of Hematology, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, China.
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34
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Mäkelä E, Pavic K, Varila T, Salmenniemi U, Löyttyniemi E, Nagelli SG, Ammunét T, Kähäri VM, Clark RE, Elo LL, Bachanaboyina VK, Lucas CM, Itälä-Remes M, Westermarck J. Discovery of a Novel CIP2A Variant (NOCIVA) with Clinical Relevance in Predicting TKI Resistance in Myeloid Leukemias. Clin Cancer Res 2021; 27:2848-2860. [PMID: 33674272 DOI: 10.1158/1078-0432.ccr-20-3679] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 01/08/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Cancerous inhibitor of protein phosphatase 2A (CIP2A) is an oncoprotein that inhibits the tumor suppressor PP2A-B56α. However, CIP2A mRNA variants remain uncharacterized. Here, we report the discovery of a CIP2A splicing variant, novel CIP2A variant (NOCIVA). EXPERIMENTAL DESIGN Characterization of CIP2A variants was performed by both 3' and 5' rapid amplification of cDNA ends from cancer cells. The function of NOCIVA was assessed by structural and molecular biology approaches. Its clinical relevance was studied in an acute myeloid leukemia (AML) patient cohort and two independent chronic myeloid leukemia (CML) cohorts. RESULTS NOCIVA contains CIP2A exons 1 to 13 fused to 349 nucleotides from CIP2A intron 13. Intriguingly, the first 39 nucleotides of the NOCIVA-specific sequence are in the coding frame with exon 13 of CIP2A and code for a 13-amino acid peptide tail nonhomologous to any known human protein sequence. Therefore, NOCIVA translates to a unique human protein. NOCIVA retains the capacity to bind to B56α, but, whereas CIP2A is predominantly a cytoplasmic protein, NOCIVA translocates to the nucleus. Indicative of prevalent alternative splicing from CIP2A to NOCIVA in myeloid malignancies, AML and CML patient samples overexpress NOCIVA, but not CIP2A mRNA. In AML, a high NOCIVA/CIP2A mRNA expression ratio is a marker for adverse overall survival. In CML, high NOCIVA expression is associated with inferior event-free survival among imatinib-treated patients, but not among patients treated with dasatinib or nilotinib. CONCLUSIONS We discovered a novel variant of the oncoprotein CIP2A and its clinical relevance in predicting tyrosine kinase inhibitor therapy resistance in myeloid leukemias.
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Affiliation(s)
- Eleonora Mäkelä
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
| | - Karolina Pavic
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Taru Varila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Urpu Salmenniemi
- Department of Hematology, Comprehensive Cancer Center, Helsinki University Hospital, Helsinki, Finland
| | | | - Srikar G Nagelli
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Drug Research Doctoral Programme, University of Turku, Turku, Finland
| | - Tea Ammunét
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Veli-Matti Kähäri
- Department of Dermatology, University of Turku and Turku University Hospital, Turku, Finland
| | - Richard E Clark
- Department of Molecular, Clinical and Cancer Medicine, University of Liverpool, Liverpool, England, United Kingdom
| | - Laura L Elo
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland.,Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Claire M Lucas
- Department of Molecular, Clinical and Cancer Medicine, University of Liverpool, Liverpool, England, United Kingdom.,Chester Medical School, University of Chester, Chester, England, United Kingdom
| | | | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland. .,Institute of Biomedicine, University of Turku, Turku, Finland
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35
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Fasih Ramandi N, Faranoush M, Ghassempour A, Aboul-Enein HY. Mass Spectrometry: A Powerful Method for Monitoring Various Type of Leukemia, Especially MALDI-TOF in Leukemia's Proteomics Studies Review. Crit Rev Anal Chem 2021; 52:1259-1286. [PMID: 33499652 DOI: 10.1080/10408347.2021.1871844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Recent success in studying the proteome, as a source of biomarkers, has completely changed our understanding of leukemia (blood cancer). The identification of differentially expressed proteins, such as relapse and drug resistance proteins involved in leukemia by using various ionization sources and mass analyzers of mass spectrometry techniques, has helped scientists find better diagnosis, prognosis, and treatment strategies. With the aid of this powerful analytical technique, we can investigate the qualification/quantification of proteins, protein-protein interactions, post-translational modifications, and find the correlation between proteins and their genes with the hope of finding the missing parts of the successful therapy puzzle. In this review, we followed different MS sources and analyzers which used for monitoring various type of leukemia, then focused on MALDI-TOF MS as a quick and reliable method for studying proteins. Due to several review published for other techniques, the present review is the first work in this field. Also, by classifying more than 400 proteins, we have found 42 proteins are involved in two or three different stages of leukemia. Finally, we have suggested six specific biomarkers for AML, one for ALL, three biomarkers with a role in the etiology of leukemia and 13 markers with the potential for further studies.
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Affiliation(s)
- Negin Fasih Ramandi
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Mohammad Faranoush
- Pediatric Growth and Development Research Center, Institute of Endocrinology, Iran University of Medical Sciences, Tehran, Iran
| | - Alireza Ghassempour
- Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Hassan Y Aboul-Enein
- Pharmaceutical and Medicinal Chemistry Department, Pharmaceutical and Drug Industries Research Division, National Research Center, Cairo, Egypt
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36
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Maddala R, Gao J, Mathias RT, Lewis TR, Arshavsky VY, Levine A, Backer JM, Bresnick AR, Rao PV. Absence of S100A4 in the mouse lens induces an aberrant retina-specific differentiation program and cataract. Sci Rep 2021; 11:2203. [PMID: 33500475 PMCID: PMC7838418 DOI: 10.1038/s41598-021-81611-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 01/05/2021] [Indexed: 11/21/2022] Open
Abstract
S100A4, a member of the S100 family of multifunctional calcium-binding proteins, participates in several physiological and pathological processes. In this study, we demonstrate that S100A4 expression is robustly induced in differentiating fiber cells of the ocular lens and that S100A4 (-/-) knockout mice develop late-onset cortical cataracts. Transcriptome profiling of lenses from S100A4 (-/-) mice revealed a robust increase in the expression of multiple photoreceptor- and Müller glia-specific genes, as well as the olfactory sensory neuron-specific gene, S100A5. This aberrant transcriptional profile is characterized by corresponding increases in the levels of proteins encoded by the aberrantly upregulated genes. Ingenuity pathway network and curated pathway analyses of differentially expressed genes in S100A4 (-/-) lenses identified Crx and Nrl transcription factors as the most significant upstream regulators, and revealed that many of the upregulated genes possess promoters containing a high-density of CpG islands bearing trimethylation marks at histone H3K27 and/or H3K4, respectively. In support of this finding, we further documented that S100A4 (-/-) knockout lenses have altered levels of trimethylated H3K27 and H3K4. Taken together, our findings suggest that S100A4 suppresses the expression of retinal genes during lens differentiation plausibly via a mechanism involving changes in histone methylation.
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Affiliation(s)
- Rupalatha Maddala
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA.
| | - Junyuan Gao
- Department of Physiology and Biophysics, Stony Brook University, Stony-Brook, NY, USA
| | - Richard T Mathias
- Department of Physiology and Biophysics, Stony Brook University, Stony-Brook, NY, USA
| | - Tylor R Lewis
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
| | - Vadim Y Arshavsky
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA
| | - Adriana Levine
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jonathan M Backer
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Anne R Bresnick
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Ponugoti V Rao
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC, USA.
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, USA.
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37
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Hernandez-Valladares M, Bruserud Ø, Selheim F. The Implementation of Mass Spectrometry-Based Proteomics Workflows in Clinical Routines of Acute Myeloid Leukemia: Applicability and Perspectives. Int J Mol Sci 2020; 21:ijms21186830. [PMID: 32957646 PMCID: PMC7556012 DOI: 10.3390/ijms21186830] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/10/2020] [Accepted: 09/15/2020] [Indexed: 02/08/2023] Open
Abstract
With the current reproducibility of proteome preparation workflows along with the speed and sensitivity of the mass spectrometers, the transition of the mass spectrometry (MS)-based proteomics technology from biomarker discovery to clinical implementation is under appraisal in the biomedicine community. Therefore, this technology might be implemented soon to detect well-known biomarkers in cancers and other diseases. Acute myeloid leukemia (AML) is an aggressive heterogeneous malignancy that requires intensive treatment to cure the patient. Leukemia relapse is still a major challenge even for patients who have favorable genetic abnormalities. MS-based proteomics could be of great help to both describe the proteome changes of individual patients and identify biomarkers that might encourage specific treatments or clinical strategies. Herein, we will review the advances and availability of the MS-based proteomics strategies that could already be used in clinical proteomics. However, the heterogeneity of complex diseases as AML requires consensus to recognize AML biomarkers and to establish MS-based workflows that allow their unbiased identification and quantification. Although our literature review appears promising towards the utilization of MS-based proteomics in clinical AML in a near future, major efforts are required to validate AML biomarkers and agree on clinically approved workflows.
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MESH Headings
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Computational Biology
- Humans
- Leukemia, Myeloid, Acute/diagnosis
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/therapy
- Mass Spectrometry/methods
- Prognosis
- Proteome/analysis
- Proteome/metabolism
- Proteomics/methods
- Robotics/instrumentation
- Robotics/methods
- Workflow
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Affiliation(s)
- Maria Hernandez-Valladares
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
| | - Øystein Bruserud
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
| | - Frode Selheim
- The Proteomics Facility of the University of Bergen (PROBE), Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- The Department of Biomedicine, University of Bergen, 5009 Bergen, Norway
- Correspondence: (M.H.-V.); (Ø.B.); (F.S.); Tel.: +47-55586368 (M.H.-V.); +47-55972997 (Ø.B.); +47-55586368 (F.S.)
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38
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Panuzzo C, Signorino E, Calabrese C, Ali MS, Petiti J, Bracco E, Cilloni D. Landscape of Tumor Suppressor Mutations in Acute Myeloid Leukemia. J Clin Med 2020; 9:jcm9030802. [PMID: 32188030 PMCID: PMC7141302 DOI: 10.3390/jcm9030802] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 12/11/2022] Open
Abstract
Acute myeloid leukemia is mainly characterized by a complex and dynamic genomic instability. Next-generation sequencing has significantly improved the ability of diagnostic research to molecularly characterize and stratify patients. This detailed outcome allowed the discovery of new therapeutic targets and predictive biomarkers, which led to develop novel compounds (e.g., IDH 1 and 2 inhibitors), nowadays commonly used for the treatment of adult relapsed or refractory AML. In this review we summarize the most relevant mutations affecting tumor suppressor genes that contribute to the onset and progression of AML pathology. Epigenetic modifications (TET2, IDH1 and IDH2, DNMT3A, ASXL1, WT1, EZH2), DNA repair dysregulation (TP53, NPM1), cell cycle inhibition and deficiency in differentiation (NPM1, CEBPA, TP53 and GATA2) as a consequence of somatic mutations come out as key elements in acute myeloid leukemia and may contribute to relapse and resistance to therapies. Moreover, spliceosomal machinery mutations identified in the last years, even if in a small cohort of acute myeloid leukemia patients, suggested a new opportunity to exploit therapeutically. Targeting these cellular markers will be the main challenge in the near future in an attempt to eradicate leukemia stem cells.
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Affiliation(s)
- Cristina Panuzzo
- Department of Clinical and Biological Sciences, University of Turin, 10124 Turin, Italy; (C.P.); (E.S.); (C.C.); (M.S.A.); (J.P.)
| | - Elisabetta Signorino
- Department of Clinical and Biological Sciences, University of Turin, 10124 Turin, Italy; (C.P.); (E.S.); (C.C.); (M.S.A.); (J.P.)
| | - Chiara Calabrese
- Department of Clinical and Biological Sciences, University of Turin, 10124 Turin, Italy; (C.P.); (E.S.); (C.C.); (M.S.A.); (J.P.)
| | - Muhammad Shahzad Ali
- Department of Clinical and Biological Sciences, University of Turin, 10124 Turin, Italy; (C.P.); (E.S.); (C.C.); (M.S.A.); (J.P.)
| | - Jessica Petiti
- Department of Clinical and Biological Sciences, University of Turin, 10124 Turin, Italy; (C.P.); (E.S.); (C.C.); (M.S.A.); (J.P.)
| | - Enrico Bracco
- Department of Oncology, University of Turin, 10124 Turin, Italy;
| | - Daniela Cilloni
- Department of Clinical and Biological Sciences, University of Turin, 10124 Turin, Italy; (C.P.); (E.S.); (C.C.); (M.S.A.); (J.P.)
- Correspondence: ; Tel.: +39-011-9026610; Fax: +39-011-9038636
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39
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van Dijk AD, de Bont ESJM, Kornblau SM. Targeted therapy in acute myeloid leukemia: current status and new insights from a proteomic perspective. Expert Rev Proteomics 2020; 17:1-10. [PMID: 31945303 DOI: 10.1080/14789450.2020.1717951] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Introduction: The biological heterogeneity of acute myeloid leukemia (AML) complicates personalized medicine. Individual prognosis is typically based on the presence of chromosomal and genetic lesions. Nevertheless, these classifications often lack a priori information about response to therapy. Since the protein expression landscape reflects the functional activity state of cells, we hypothesize that analyzing this can be used for the identification of protein activity markers to provide better risk stratification as well as may provide targeted therapeutic guidance in AML.Areas covered: Herein, we review recently new adopted drugs in the treatment for AML and discuss how quantitative proteomic techniques may contribute to better therapeutic selection in AML.Expert commentary: The net functional state of the cell is defined by the activity of protein within all the pathways that are active in the cell. Recognition of the proteomic profile of the leukemic blast could, therefore, complement current classification systems by providing a better a priori description of what pathways are important within a cell as a guide to the selection of therapy for the patient.
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Affiliation(s)
- Anneke D van Dijk
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Eveline S J M de Bont
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, University Medical Center Groningen, Groningen, the Netherlands
| | - Steven M Kornblau
- Department of Leukemia, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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