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Huang N, Chang C, Wu L, He Q, Zhang Z, Li X, Xu F. Distinct mutation features and its clinical significance in myelodysplastic syndromes with normal karyotype. Ann Hematol 2024:10.1007/s00277-024-06005-2. [PMID: 39302466 DOI: 10.1007/s00277-024-06005-2] [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: 08/13/2024] [Accepted: 09/09/2024] [Indexed: 09/22/2024]
Abstract
Myelodysplastic syndromes (MDS) is a highly heterogeneous myeloid neoplastic disease, which needs personalized evaluation and therapy. To analyze the features and significance of gene mutations for MDS patients with normal karyotype (NK) at diagnosis, targeted sequencing was conducted on 616 MDS patients with NK, alongside 457 MDS cases with abnormal karyotype (AK). The results showed that the incidence of somatic mutation reached 70.3% and 83.8% in the NK and AK group, respectively. Initial mutation including ASXL1, DNMT3A and TET2 were common in NK group, which is the same as AK group. Some karyotype-associated gene mutations, such as TP53 and U2AF1, were relatively rare in NK group. Moreover, 34 out of 91 samples who progressed to acute myeloid leukemia (AML) underwent repeat sequencing during follow-up. 25 cases were checked out with newly emerged mutations. The AML-associated genetic alterations mainly involved with active signaling and transcription factors. In patients with NK, serial targeted sequencing was employed for minimal residual disease (MRD) monitoring, indicating the efficacy and relapse of the patients. In summary, MDS with NK showed distinct mutation features from those with AK. High-frequency gene mutations together with the mutational evolution suggested the diagnostic and monitoring significance of next generation sequencing for NK-MDS.
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Affiliation(s)
- Nanfang Huang
- Department of Hematology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chunkang Chang
- Department of Hematology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingyun Wu
- Department of Hematology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qi He
- Department of Hematology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheng Zhang
- Department of Hematology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Li
- Department of Hematology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Feng Xu
- Department of Hematology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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2
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Jin JC, Chen BY, Deng CH, Chen JN, Xu F, Tao Y, Hu CL, Xu CH, Chang BH, Wang Y, Fei MY, Liu P, Yu PC, Li ZJ, Li XY, Chen SB, Jiang YL, Chen XC, Zong LJ, Zhang JY, Ren YY, Xu FH, Liu Q, Huang XH, Guo J, He Q, Song LX, Zhou LY, Su JY, Xiao C, Zhang YM, Yan M, Zhang Z, Wu D, Chang CK, Li X, Wang L, Wu LY. ROBO1 deficiency impairs HSPC homeostasis and erythropoiesis via CDC42 and predicts poor prognosis in MDS. SCIENCE ADVANCES 2023; 9:eadi7375. [PMID: 38019913 DOI: 10.1126/sciadv.adi7375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023]
Abstract
Myelodysplastic syndrome (MDS) is a group of clonal hematopoietic neoplasms originating from hematopoietic stem progenitor cells (HSPCs). We previously identified frequent roundabout guidance receptor 1 (ROBO1) mutations in patients with MDS, while the exact role of ROBO1 in hematopoiesis remains poorly delineated. Here, we report that ROBO1 deficiency confers MDS-like disease with anemia and multilineage dysplasia in mice and predicts poor prognosis in patients with MDS. More specifically, Robo1 deficiency impairs HSPC homeostasis and disrupts HSPC pool, especially the reduction of megakaryocyte erythroid progenitors, which causes a blockage in the early stages of erythropoiesis in mice. Mechanistically, transcriptional profiling indicates that Cdc42, a member of the Rho-guanosine triphosphatase family, acts as a downstream target gene for Robo1 in HSPCs. Overexpression of Cdc42 partially restores the self-renewal and erythropoiesis of HSPCs in Robo1-deficient mice. Collectively, our result implicates the essential role of ROBO1 in maintaining HSPC homeostasis and erythropoiesis via CDC42.
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Affiliation(s)
- Jia-Cheng Jin
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Bing-Yi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chu-Han Deng
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia-Nan Chen
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Feng Xu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Ying Tao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Cheng-Long Hu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Chun-Hui Xu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Bin-He Chang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yong Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ming-Yue Fei
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ping Liu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Peng-Cheng Yu
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zi-Juan Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xi-Ya Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shu-Bei Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Lun Jiang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Xin-Chi Chen
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Li-Juan Zong
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jia-Ying Zhang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Yi Ren
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Fan-Huan Xu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Qi Liu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xin-Hui Huang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Juan Guo
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Qi He
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lu-Xi Song
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Li-Yu Zhou
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
- Department of Hematology, Shanghai Eighth People's Hospital, Shanghai, China
| | - Ji-Ying Su
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chao Xiao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Yu-Mei Zhang
- Department of Hematology, Shanghai Eighth People's Hospital, Shanghai, China
| | - Meng Yan
- Department of Hematology, Shanghai Eighth People's Hospital, Shanghai, China
| | - Zheng Zhang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Dong Wu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chun-Kang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiao Li
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Lan Wang
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ling-Yun Wu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
- Department of Hematology, Shanghai Eighth People's Hospital, Shanghai, China
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3
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Huang N, Song Y, Shi W, Guo J, Zhang Z, He Q, Wu L, Li X, Xu F. DHX9-mediated pathway contributes to the malignant phenotype of myelodysplastic syndromes. iScience 2023; 26:106962. [PMID: 37305700 PMCID: PMC10250162 DOI: 10.1016/j.isci.2023.106962] [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: 02/04/2023] [Revised: 05/06/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023] Open
Abstract
DHX9 is a member of the DEAH (Asp-Glu-Ala-His) helicase family and regulates DNA replication and RNA processing. DHX9 dysfunction promotes tumorigenesis in several solid cancers. However, the role of DHX9 in MDS is still unknown. Here, we analyzed the expression of DHX9 and its clinical significance in 120 MDS patients and 42 non-MDS controls. Lentivirus-mediated DHX9-knockdown experiments were performed to investigate its biological function. We also performed cell functional assays, gene microarray, and pharmacological intervention to investigate the mechanistic involvement of DHX9. We found that overexpression of DHX9 is frequent in MDS and associated with poor survival and high risk of acute myeloid leukemia (AML) transformation. DHX9 is essential for the maintenance of malignant proliferation of leukemia cells, and DHX9 suppression increases cell apoptosis and causes hypersensitivity to chemotherapeutic agents. Besides, knockdown of DHX9 inactivates the PI3K-AKT and ATR-Chk1 signaling, promotes R-loop accumulation, and R-loop-mediated DNA damage.
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Affiliation(s)
- Nanfang Huang
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Yang Song
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Wenhui Shi
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Juan Guo
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Zheng Zhang
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Qi He
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Lingyun Wu
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Xiao Li
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
| | - Feng Xu
- Department of Hematology, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200233, China
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4
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Li C, Wang Z, Wei B, Liu Z, Li B, Kang H, Wang J, Liu J, Wang Q, Guo H, Wu X, Liu N, Luo J. Upregulation of ROBO3 promotes proliferation, migration and adhesion of AML cells and affects the survival of AML patients. Biochem Biophys Res Commun 2023; 661:1-9. [PMID: 37084487 DOI: 10.1016/j.bbrc.2023.04.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/13/2023] [Indexed: 04/23/2023]
Abstract
Acute myeloid leukemia (AML) is a heterogeneous hematological malignancy, which is the most common and severe acute leukemia in adults. Its occurrence, development and prognosis are affected by many factors, and more research is still needed to further guide its treatment. Here, we found that roundabout3 (ROBO3) was associated with poor prognosis in AML through bioinformatics analysis. We then found that overexpression of ROBO3 promoted AML cell proliferation, adhesion and migration while knockdown of ROBO3 had opposite effects. We subsequently found that ROBO3 regulated CD34 expression in AML cells, and this regulatory effect may be achieved through the Hippo-YAP pathway. The inhibitors of this pathway, K-975 and verteporfin, showed an inhibitory effect on AML cells with high ROBO3 expression. ROBO3 was also found to be significantly increased in bone marrow samples from AML patients. Our research indicates that ROBO3 plays an important role in the development of AML, which suggests that ROBO3 can be a prognostic biomarker and potential therapeutic target for AML.
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Affiliation(s)
- Chaonan Li
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China; Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Zhen Wang
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Binghui Wei
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Zechen Liu
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Bei Li
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Hening Kang
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Jue Wang
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Junle Liu
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Qingyu Wang
- College of Basic Medicine, Hebei Medical University, Shijiazhuang, 050017, China
| | - Hongming Guo
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Xiaoli Wu
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Na Liu
- Department of Pediatrics, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Jianmin Luo
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China.
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5
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Xu F, Wu L, Guo J, He Q, Zhang Z, Li X. Somatic mutations of activating signalling, transcription factor, and tumour suppressor are a precondition for leukaemia transformation in myelodysplastic syndromes. J Cell Mol Med 2022; 26:5901-5916. [DOI: 10.1111/jcmm.17613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/13/2022] [Accepted: 11/01/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Feng Xu
- Department of Hematology Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai China
| | - Lin‐Yun Wu
- Department of Hematology Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai China
| | - Juan Guo
- Department of Hematology Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai China
| | - Qi He
- Department of Hematology Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai China
| | - Zheng Zhang
- Department of Hematology Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai China
| | - Xiao Li
- Department of Hematology Shanghai Jiao Tong University Affiliated Sixth People's Hospital Shanghai China
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Zhang TJ, Xu ZJ, Wen XM, Gu Y, Ma JC, Yuan Q, Lin J, Zhou JD, Qian J. SLIT2 promoter hypermethylation-mediated SLIT2-IT1/miR-218 repression drives leukemogenesis and predicts adverse prognosis in myelodysplastic neoplasm. Leukemia 2022; 36:2488-2498. [PMID: 35906386 DOI: 10.1038/s41375-022-01659-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/13/2022] [Accepted: 07/19/2022] [Indexed: 01/09/2023]
Abstract
Epigenetic modifications have been found to play crucial roles in myelodysplastic neoplasm (MDS) progression. Previously, we investigated genome-wide DNA methylation alterations during MDS evolution to acute myeloid leukemia (AML) by next-generation sequencing (NGS). Herein, we further determined the role and clinical implications of an evident methylation change in CpG islands at the SLIT2 promoter identified by NGS. First, increased SLIT2 promoter methylation was validated in 11 paired MDS/AML patients during disease evolution. Additionally, SLIT2 promoter methylation was markedly increased in MDS/AML patients compared with controls and was correlated with poor clinical phenotype and outcome. Interestingly, SLIT2 expression was particularly upregulated in AML patients and was not correlated with SLIT2 promoter methylation. However, the SLIT2-embedded genes SLIT2-IT1 and miR-218 were downregulated in AML patients, which was negatively associated with SLIT2 promoter methylation and further validated by demethylation studies. Functionally, SLIT2-IT1/miR-218 overexpression exhibited antileukemic effects by affecting cell proliferation, apoptosis and colony formation in vitro and in vivo. Mechanistically, SLIT2-IT1 may function as a competing endogenous RNA by sponging miR-3156-3p to regulate BMF expression, whereas miR-218 may directly target HOXA1 in MDS progression. In summary, our findings demonstrate that SLIT2 promoter hypermethylation is associated with disease evolution in MDS and predicts poor prognoses in both MDS and AML. Epigenetic inactivation of SLIT2-IT1/miR-218 by SLIT2 promoter hypermethylation could be a promising therapeutic target in MDS.
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Affiliation(s)
- Ting-Juan Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Department of Oncology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Qian Yuan
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
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7
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Zhou JD, Zhao YJ, Leng JY, Gu Y, Xu ZJ, Ma JC, Wen XM, Lin J, Zhang TJ, Qian J. DNA methylation-mediated differential expression of DLX4 isoforms has opposing roles in leukemogenesis. Cell Mol Biol Lett 2022; 27:59. [PMID: 35883028 PMCID: PMC9327205 DOI: 10.1186/s11658-022-00358-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/28/2022] [Indexed: 11/14/2022] Open
Abstract
Background Previously, we reported the expression of DLX4 isoforms (BP1 and DLX7) in myeloid leukemia, but the functional role of DLX4 isoforms remains poorly understood. In the work described herein, we further determined the underlying role of DLX4 isoforms in chronic myeloid leukemia (CML) leukemogenesis. Methods The expression and methylation of DLX4 isoforms were detected by real-time quantitative PCR (RT-qPCR) and real-time quantitative methylation-specific PCR (RT-qMSP) in patients with CML. The functional role of DLX4 isoforms was determined in vitro and in vivo. The molecular mechanism of DLX4 isoforms in leukemogenesis was identified based on chromatin immunoprecipitation with high-throughput sequencing (ChIP-Seq)/assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) and RNA sequencing (RNA-Seq). Results BP1 expression was increased in patients with CML with unmethylated promoter, but DLX7 expression was decreased with hypermethylated promoter. Functionally, overexpression of BP1 increased the proliferation rate of K562 cells with S/G2 promotion, whereas DLX7 overexpression reduced the proliferation rate of K562 cells with G1 arrest. Moreover, K562 cells with BP1 overexpression increased the tumorigenicity in NCG mice, whereas K562 cells with DLX7 overexpression decreased the tumorigenicity. Mechanistically, a total of 91 genes including 79 messenger RNAs (mRNAs) and 12 long noncoding RNAs (lncRNAs) were discovered by ChIP-Seq and RNA-Seq as direct downstream targets of BP1. Among the downstream genes, knockdown of RREB1 and SGMS1-AS1 partially revived the proliferation caused by BP1 overexpression in K562 cells. Similarly, using ATAC-Seq and RNA-Seq, a total of 282 genes including 151 mRNA and 131 lncRNAs were identified as direct downstream targets of DLX7. Knockdown of downstream genes PTPRB and NEAT1 partially revived the proliferation caused by DLX7 overexpression in K562 cells. Finally, we also identified and validated a SGMS1-AS1/miR-181d-5p/SRPK2 competing endogenous RNA (ceRNA) network caused by BP1 overexpression in K562 cells. Conclusions The current findings reveal that DNA methylation-mediated differential expression of DLX4 isoforms BP1 and DLX7 plays opposite functions in leukemogenesis. BP1 plays an oncogenic role in leukemia development, whereas DLX7 acts as a tumor suppressor gene. These results suggest DLX4 as a therapeutic target for antileukemia therapy. Supplementary Information The online version contains supplementary material available at 10.1186/s11658-022-00358-0.
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Affiliation(s)
- Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Yang-Jing Zhao
- Jiangsu Key Laboratory of Medical Science and Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, 212013, Jiangsu, People's Republic of China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Laboratory Center, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Ting-Juan Zhang
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Department of Oncology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China.
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, 212002, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, 212002, Jiangsu, People's Republic of China.
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8
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Yuan O, Ugale A, de Marchi T, Anthonydhason V, Konturek-Ciesla A, Wan H, Eldeeb M, Drabe C, Jassinskaja M, Hansson J, Hidalgo I, Velasco-Hernandez T, Cammenga J, Magee JA, Niméus E, Bryder D. A somatic mutation in moesin drives progression into acute myeloid leukemia. SCIENCE ADVANCES 2022; 8:eabm9987. [PMID: 35442741 PMCID: PMC9020775 DOI: 10.1126/sciadv.abm9987] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Acute myeloid leukemia (AML) arises when leukemia-initiating cells, defined by a primary genetic lesion, acquire subsequent molecular changes whose cumulative effects bypass tumor suppression. The changes that underlie AML pathogenesis not only provide insights into the biology of transformation but also reveal novel therapeutic opportunities. However, backtracking these events in transformed human AML samples is challenging, if at all possible. Here, we approached this question using a murine in vivo model with an MLL-ENL fusion protein as a primary molecular event. Upon clonal transformation, we identified and extensively verified a recurrent codon-changing mutation (Arg295Cys) in the ERM protein moesin that markedly accelerated leukemogenesis. Human cancer-associated moesin mutations at the conserved arginine-295 residue similarly enhanced MLL-ENL-driven leukemogenesis. Mechanistically, the mutation interrupted the stability of moesin and conferred a neomorphic activity to the protein, which converged on enhanced extracellular signal-regulated kinase activity. Thereby, our studies demonstrate a critical role of ERM proteins in AML, with implications also for human cancer.
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Affiliation(s)
- Ouyang Yuan
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Amol Ugale
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
- Department of Microbiology, Immunobiology and Genetics, Center for Molecular Biology of the University of Vienna, Max F. Perutz Laboratories, Vienna Biocenter (VBC), 1030 Vienna, Austria
| | - Tommaso de Marchi
- Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, 223 62, Lund, Sweden
| | - Vimala Anthonydhason
- Sahlgrenska Center for Cancer Research, University of Gothenburg, Medicinaregatan 1F, 413 90, Gothenburg, Sweden
| | - Anna Konturek-Ciesla
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Haixia Wan
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Mohamed Eldeeb
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Caroline Drabe
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Maria Jassinskaja
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
- York Biomedical Research Institute, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Jenny Hansson
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Isabel Hidalgo
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | | | - Jörg Cammenga
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
| | - Jeffrey A. Magee
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Emma Niméus
- Division of Surgery, Oncology, and Pathology, Department of Clinical Sciences, Lund University, Solvegatan 19, 223 62, Lund, Sweden
- Department of Surgery, Skåne University Hospital, Entrégatan 7, 222 42 Lund, Sweden
| | - David Bryder
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medical, Lund University, 221 84 Lund, Sweden
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9
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Bianchi G, Czarnecki PG, Ho M, Roccaro AM, Sacco A, Kawano Y, Gullà A, Samur AA, Chen T, Wen K, Tai YT, Moscvin M, Wu X, Camci-Unal G, Da Vià MC, Bolli N, Sewastianik T, Carrasco RD, Ghobrial IM, Anderson KC. ROBO1 Promotes Homing, Dissemination, and Survival of Multiple Myeloma within the Bone Marrow Microenvironment. Blood Cancer Discov 2021; 2:338-353. [PMID: 34268498 PMCID: PMC8265993 DOI: 10.1158/2643-3230.bcd-20-0164] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/21/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022] Open
Abstract
The bone marrow (BM) microenvironment actively promotes multiple myeloma (MM) pathogenesis and therapies targeting both cancer cells and the niche are highly effective. We were interested in identifying novel signaling pathways supporting MM-BM crosstalk. Mutations in the transmembrane receptor Roundabout 1 (ROBO1) were recently identified in MM patients, however their functional consequences are uncertain. Through protein structure-function studies, we discovered that ROBO1 is necessary for MM adhesion to BM stromal and endothelial cells and ROBO1 knock out (KO) compromises BM homing and engraftment in a disseminated mouse model. ROBO1 KO significantly decreases MM proliferation in vitro and intra- and extramedullary tumor growth, in vivo. Mechanistically, ROBO1 C-terminus is cleaved in a ligand-independent fashion and is sufficient to promote MM proliferation. Viceversa, mutants lacking the cytoplasmic domain, including the human-derived G674* truncation, act dominantly negative. Interactomic and RNA sequencing studies suggest ROBO1 may be involved in RNA processing, supporting further studies.
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Affiliation(s)
- Giada Bianchi
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.
| | - Peter G Czarnecki
- Division of Renal Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Matthew Ho
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
- Department of Medicine, Mayo Clinic, Rochester, Minnesota
| | - Aldo M Roccaro
- Clinical Research Development and Phase I Unit, CREA Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Antonio Sacco
- Clinical Research Development and Phase I Unit, CREA Laboratory, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Yawara Kawano
- Departments of Hematology, Rheumatology, and Infectious Disease, Kumamoto University Hospital, Kumamoto, Japan
| | - Annamaria Gullà
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Anil Aktas Samur
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Tianzeng Chen
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kenneth Wen
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Yu-Tzu Tai
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Maria Moscvin
- Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts
| | - Xinchen Wu
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts
| | - Gulden Camci-Unal
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts
| | - Matteo C Da Vià
- Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy
| | - Niccolo' Bolli
- Department of Oncology and Onco-Hematology, University of Milan, Milan, Italy
- Department of Clinical Oncology and Hematology, Fondazione IRCCS Istituto Nazionale Tumori, Milan, Italy
| | - Tomasz Sewastianik
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Ruben D Carrasco
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Irene M Ghobrial
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Kenneth C Anderson
- Jerome Lipper Multiple Myeloma Center, Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
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10
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Proteomic Analysis of Low-Grade, Early-Stage Endometrial Carcinoma Reveals New Dysregulated Pathways Associated with Cell Death and Cell Signaling. Cancers (Basel) 2021; 13:cancers13040794. [PMID: 33672863 PMCID: PMC7917913 DOI: 10.3390/cancers13040794] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 01/28/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Low-grade, early-stage endometrial cancer (EC) is the most frequent malignant tumor of the uterine corpus. Our study aimed to assess dysregulated pathways in this specific subset of EC through proteomic analysis. We describe and validate the dysregulation of the SLIT/ROBO signaling pathway, as well as cellular death processes such as necroptosis and ferroptosis. We identify several immune-related pathways, with a dominance of innate immune response associated pathways. Our findings reveal the singular biology of low-grade, early-stage ECs and could guide future research in the field. Abstract Low-grade, early-stage endometrial carcinoma (EC) is the most frequent malignant tumor of the uterine corpus. However, the molecular alterations that underlie these tumors are far from being fully understood. The purpose of this study is to describe dysregulated molecular pathways from EC patients. Sixteen samples of tumor tissue and paired healthy controls were collected and both were subjected to mass spectrometry (MS)/MS proteomic analysis. Gene ontology and pathway analysis was performed to discover dysregulated pathways and/or proteins using different databases and bioinformatic tools. Dysregulated pathways were cross-validated in an independent external cohort. Cell signaling, immune response, and cell death-associated pathways were robustly identified. The SLIT/ROBO signaling pathway demonstrated dysregulation at the proteomic and transcriptomic level. Necroptosis and ferroptosis were cell death-associated processes aberrantly regulated, in addition to apoptosis. Immune response-associated pathways showed a dominance of innate immune responses. Tumor immune infiltrates measured by immunofluorescence demonstrated diverse lymphoid and myeloid populations. Our results suggest a role of SLIT/ROBO, necroptosis, and ferroptosis, as well as a prominent role of innate immune response in low-grade, early-stage EC. These results could guide future research in this group of tumors.
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11
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Sengupta D, Bhattacharya G, Ganguli S, Sengupta M. Structural insights and evaluation of the potential impact of missense variants on the interactions of SLIT2 with ROBO1/4 in cancer progression. Sci Rep 2020; 10:21909. [PMID: 33318575 PMCID: PMC7736846 DOI: 10.1038/s41598-020-78882-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/01/2020] [Indexed: 02/07/2023] Open
Abstract
The cognate interaction of ROBO1/4 with its ligand SLIT2 is known to be involved in lung cancer progression. However, the precise role of genetic variants, disrupting the molecular interactions is less understood. All cancer-associated missense variants of ROBO1/4 and SLIT2 from COSMIC were screened for their pathogenicity. Homology modelling was done in Modeller 9.17, followed by molecular simulation in GROMACS. Rigid docking was performed for the cognate partners in PatchDock with refinement in HADDOCK server. Post-docking alterations in conformational, stoichiometric, as well as structural parameters, were assessed. The disruptive variants were ranked using a weighted scoring scheme. In silico prioritisation of 825 variants revealed 379 to be potentially pathogenic out of which, about 12% of the variants, i.e. ROBO1 (14), ROBO4 (8), and SLIT2 (23) altered the cognate docking. Six variants of ROBO1 and 5 variants of ROBO4 were identified as "high disruptors" of interactions with SLIT2 wild type. Likewise, 17 and 13 variants of SLIT2 were found to be "high disruptors" of its interaction with ROBO1 and ROBO4, respectively. Our study is the first report on the impact of cancer-associated missense variants on ROBO1/4 and SLIT2 interactions that might be the drivers of lung cancer progression.
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Affiliation(s)
- Debmalya Sengupta
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India
| | - Gairika Bhattacharya
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India
- Cactus Communications, Mumbai, India
| | - Sayak Ganguli
- Department of Biotechnology, St. Xavier's College (Autonomous), 30, Mother Teresa Sarani, Kolkata, 700 016, India.
| | - Mainak Sengupta
- Department of Genetics, University of Calcutta, University College of Science (UCSTA), 35, Ballygunge Circular Road, Kolkata, 700 019, India.
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12
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Sentís I, Gonzalez S, Genescà E, García-Hernández V, Muiños F, Gonzalez C, López-Arribillaga E, Gonzalez J, Fernandez-Ibarrondo L, Mularoni L, Espinosa L, Bellosillo B, Ribera JM, Bigas A, Gonzalez-Perez A, Lopez-Bigas N. The evolution of relapse of adult T cell acute lymphoblastic leukemia. Genome Biol 2020; 21:284. [PMID: 33225950 PMCID: PMC7682094 DOI: 10.1186/s13059-020-02192-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 11/03/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. A higher percentage of the adult patients relapse, compared to children. It is thus essential to study the mechanisms of relapse of adult T-ALL cases. RESULTS We profile whole-genome somatic mutations of 19 primary T-ALLs from adult patients and the corresponding relapse malignancies and analyze their evolution upon treatment in comparison with 238 pediatric and young adult ALL cases. We compare the mutational processes and driver mutations active in primary and relapse adult T-ALLs with those of pediatric patients. A precise estimation of clock-like mutations in leukemic cells shows that the emergence of the relapse clone occurs several months before the diagnosis of the primary T-ALL. Specifically, through the doubling time of the leukemic population, we find that in at least 14 out of the 19 patients, the population of relapse leukemia present at the moment of diagnosis comprises more than one but fewer than 108 blasts. Using simulations, we show that in all patients the relapse appears to be driven by genetic mutations. CONCLUSIONS The early appearance of a population of leukemic cells with genetic mechanisms of resistance across adult T-ALL cases constitutes a challenge for treatment. Improving early detection of the malignancy is thus key to prevent its relapse.
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Affiliation(s)
- Inés Sentís
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Santiago Gonzalez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 10, 08028 Barcelona, Spain
| | - Eulalia Genescà
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Violeta García-Hernández
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Ferran Muiños
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Celia Gonzalez
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Erika López-Arribillaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jessica Gonzalez
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | | | - Loris Mularoni
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- CMR[B] Center of Regenerative Medicine, Barcelona, Spain
| | - Lluís Espinosa
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Beatriz Bellosillo
- Pathology Department, CIBERONC, Hospital del Mar, IMIM, Barcelona, Spain
| | - Josep-Maria Ribera
- Hematology Departments, ICO-Hospital Germans Trias i Pujol, Josep Carreras Research Institute, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Anna Bigas
- Program in Cancer Research, Institut Hospital del Mar d’Investigacions Mèdiques, CIBERONC, Barcelona, Spain
| | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Research Program on Biomedical Informatics, Universitat Pompeu Fabra, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
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13
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Zhou JD, Zhang TJ, Xu ZJ, Deng ZQ, Gu Y, Ma JC, Wen XM, Leng JY, Lin J, Chen SN, Qian J. Genome-wide methylation sequencing identifies progression-related epigenetic drivers in myelodysplastic syndromes. Cell Death Dis 2020; 11:997. [PMID: 33219204 PMCID: PMC7679421 DOI: 10.1038/s41419-020-03213-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 10/30/2020] [Accepted: 11/03/2020] [Indexed: 02/07/2023]
Abstract
The potential mechanism of myelodysplastic syndromes (MDS) progressing to acute myeloid leukemia (AML) remains poorly elucidated. It has been proved that epigenetic alterations play crucial roles in the pathogenesis of cancer progression including MDS. However, fewer studies explored the whole-genome methylation alterations during MDS progression. Reduced representation bisulfite sequencing was conducted in four paired MDS/secondary AML (MDS/sAML) patients and intended to explore the underlying methylation-associated epigenetic drivers in MDS progression. In four paired MDS/sAML patients, cases at sAML stage exhibited significantly increased methylation level as compared with the matched MDS stage. A total of 1090 differentially methylated fragments (DMFs) (441 hypermethylated and 649 hypomethylated) were identified involving in MDS pathogenesis, whereas 103 DMFs (96 hypermethylated and 7 hypomethylated) were involved in MDS progression. Targeted bisulfite sequencing further identified that aberrant GFRA1, IRX1, NPY, and ZNF300 methylation were frequent events in an additional group of de novo MDS and AML patients, of which only ZNF300 methylation was associated with ZNF300 expression. Subsequently, ZNF300 hypermethylation in larger cohorts of de novo MDS and AML patients was confirmed by real-time quantitative methylation-specific PCR. It was illustrated that ZNF300 methylation could act as a potential biomarker for the diagnosis and prognosis in MDS and AML patients. Functional experiments demonstrated the anti-proliferative and pro-apoptotic role of ZNF300 overexpression in MDS-derived AML cell-line SKM-1. Collectively, genome-wide DNA hypermethylation were frequent events during MDS progression. Among these changes, ZNF300 methylation, a regulator of ZNF300 expression, acted as an epigenetic driver in MDS progression. These findings provided a theoretical basis for the usage of demethylation drugs in MDS patients against disease progression.
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Affiliation(s)
- Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Ting-Juan Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Zhao-Qun Deng
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China. .,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China.
| | - Su-Ning Chen
- Jiangsu Institute of Hematology, National Clinical Research Center for Hematologic Diseases, NHC Key Laboratory of Thrombosis and Hemostasis, The First Affiliated Hospital of Soochow University, Suzhou, People's Republic of China. .,Collaborative Innovation Center of Hematology, Soochow University, Suzhou, People's Republic of China.
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, People's Republic of China. .,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, Jiangsu, People's Republic of China. .,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu, People's Republic of China.
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14
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IGF‑IR promotes clonal cell proliferation in myelodysplastic syndromes via inhibition of the MAPK pathway. Oncol Rep 2020; 44:1094-1104. [PMID: 32583001 PMCID: PMC7388562 DOI: 10.3892/or.2020.7652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
Type 1 insulin-like growth factor receptor (IGF-IR) signaling is considered to serve a key role in the development of cancer. However, the effects of IGF-IR on the malignant characteristics of myelodysplastic syndrome (MDS) clonal cells remains to be determined. In the present study it was demonstrated that knockdown of IGF-IR reduced the proliferation and increased the apoptosis of MDS/leukemia cells. Integrated analysis of gene expression profiles using bioinformatics identified the MAPK signaling pathway as a critical downstream factor of IGF-IR, and this was confirmed in vitro using western blotting which revealed that IGF-IR knockdown significantly increased the expression of activated MAPK. Furthermore, IGF-IR signaling was inhibited to investigate the potential of IGF-IR as a therapeutic target of MDS. The results revealed that the IGF-IR inhibitor picropodophyllin (PPP) inhibited cell proliferation, promoted cell apoptosis and arrested the cell cycle at the G2/M phase in MDS/leukemia cells. Similar to the effects of IGF-IR knockdown, PPP treatment also increased MAPK signaling in vitro. In conclusion, IGF-IR may serve as a potential therapeutic target of MDS.
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15
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Zhang TJ, Xu ZJ, Gu Y, Wen XM, Ma JC, Zhang W, Deng ZQ, Leng JY, Qian J, Lin J, Zhou JD. Identification and validation of prognosis-related DLX5 methylation as an epigenetic driver in myeloid neoplasms. Clin Transl Med 2020; 10:e29. [PMID: 32508046 PMCID: PMC7403826 DOI: 10.1002/ctm2.29] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/04/2020] [Accepted: 04/05/2020] [Indexed: 12/12/2022] Open
Abstract
The deregulated DLX gene family members DLX1/2/3/4/5/6 (DLXs) caused by DNA methylation has been demonstrated in various cancers with therapeutic target value. However, the potential role of DLXs methylation in myeloid neoplasms such as acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) remains to be elucidated. Clinical significance of DLXs methylation/expression was analyzed in patient with AML and MDS. The functional roles of DLXs were determined in vitro. In the identification stage, we found that lower DLX5 expression was correlated with prognosis in AML among all DLXs analyzed by The Cancer Genome Atlas datasets. In the validation stage, we revealed that reduced DLX5 expression was frequently occurred, and was also correlated with promoter hypermethylation in AML evaluated by targeted bisulfite sequencing. Epigenetic studies also showed that DLX5 promoter DNA methylation was associated with its expression. By quantitative polymerase chain reaction, we also validated that DLX5 hypermethylation was frequent event in both AML and MDS, and also correlated with MDS transformation to leukemia. Moreover, DLX5 hypermethylation was associated with lower rate of complete remission and shorter time of leukemia‐free/overall survival, and was also confirmed by Logistic/Cox regression analysis. Functional studies revealed the antiproliferative and pro‐apoptotic effects of DLX5 in MDS‐derived AML cell‐line SKM‐1. Finally, bioinformatics analysis demonstrated that DLX5 functioned in leukemogenesis may be through the association with PI3K/Akt signaling pathway. Collectively, our findings demonstrated that DLX5 methylation, negatively correlated DLX5 expression, was a potential prognostic and predictive indicator in patients with AML and MDS, which could also act as an epigenetic driver in myeloid neoplasms.
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Affiliation(s)
- Ting-Juan Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Zi-Jun Xu
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Yu Gu
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Xiang-Mei Wen
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Ji-Chun Ma
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Wei Zhang
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Zhao-Qun Deng
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Jia-Yan Leng
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Jun Qian
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China.,Laboratory Center, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People's Hospital of Jiangsu University, Zhenjiang, P. R. China.,Zhenjiang Clinical Research Center of Hematology, Zhenjiang, P. R. China.,The Key Lab of Precision Diagnosis and Treatment in Hematologic Neoplasms of Zhenjiang City, Zhenjiang, P. R. China
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16
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Wu L, Li X, Xu F, Wu D, He Q, Song L, Xiao C, Zhao Y, Zhang Z, Guo J, Zhou L, Su J, Chang C. NPM1 mutation with DNMT3A wild type defines a subgroup of MDS with particularly favourable outcomes after decitabine therapy. Br J Haematol 2020; 189:982-984. [PMID: 32266961 DOI: 10.1111/bjh.16628] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/09/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Lingyun Wu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Xiao Li
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Feng Xu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Dong Wu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Qi He
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Luxi Song
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chao Xiao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Youshan Zhao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Zheng Zhang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Juan Guo
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Liyu Zhou
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Jiying Su
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
| | - Chunkang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, China
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17
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Bewicke-Copley F, Arjun Kumar E, Palladino G, Korfi K, Wang J. Applications and analysis of targeted genomic sequencing in cancer studies. Comput Struct Biotechnol J 2019; 17:1348-1359. [PMID: 31762958 PMCID: PMC6861594 DOI: 10.1016/j.csbj.2019.10.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022] Open
Abstract
Next Generation Sequencing (NGS) has dramatically improved the flexibility and outcomes of cancer research and clinical trials, providing highly sensitive and accurate high-throughput platforms for large-scale genomic testing. In contrast to whole-genome (WGS) or whole-exome sequencing (WES), targeted genomic sequencing (TS) focuses on a panel of genes or targets known to have strong associations with pathogenesis of disease and/or clinical relevance, offering greater sequencing depth with reduced costs and data burden. This allows targeted sequencing to identify low frequency variants in targeted regions with high confidence, thus suitable for profiling low-quality and fragmented clinical DNA samples. As a result, TS has been widely used in clinical research and trials for patient stratification and the development of targeted therapeutics. However, its transition to routine clinical use has been slow. Many technical and analytical obstacles still remain and need to be discussed and addressed before large-scale and cross-centre implementation. Gold-standard and state-of-the-art procedures and pipelines are urgently needed to accelerate this transition. In this review we first present how TS is conducted in cancer research, including various target enrichment platforms, the construction of target panels, and selected research and clinical studies utilising TS to profile clinical samples. We then present a generalised analytical workflow for TS data discussing important parameters and filters in detail, aiming to provide the best practices of TS usage and analyses.
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Key Words
- BAM, Binary Alignment Map
- BWA, Burrows-Wheeler Aligner
- Background error
- CLL, Chronic Lymphocytic Leukaemia
- COSMIC, Catalogue of Somatic Mutations in Cancer
- Cancer genomics
- Clinical samples
- ESP, Exome Sequencing Project
- FF, Fresh Frozen
- FFPE, Formalin Fixed Paraffin Embedded
- FL, Follicular Lymphoma
- GATK, Genome Analysis Toolkit
- ICGC, International Cancer Genome Consortium
- MBC, Molecular Barcode
- NCCN, the National Comprehensive Cancer Network®
- NGS, Next Generation Sequencing
- NHL, Non-Hodgkin Lymphoma
- NSCLC, Non-Small Cell Lung Carcinoma
- PCR duplicates
- QC, Quality Control
- SAM, Sequence Alignment Map
- TCGA, The Cancer Genome Atlas
- TS, Targeted Sequencing
- Targeted sequencing
- UMI, Unique Molecular Identifiers
- VAF, Variant Allele Frequency
- Variant calling
- WES, Whole Exome Sequencing
- WGS, Whole Genome Sequencing
- tFL, Transformed Follicular Lymphoma
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Affiliation(s)
- Findlay Bewicke-Copley
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Emil Arjun Kumar
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Giuseppe Palladino
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Koorosh Korfi
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Jun Wang
- Centre for Cancer Genomics and Computational Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
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18
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Hosokawa K, Mizumaki H, Elbadry MI, Saito C, Espinoza JL, Thi Thanh Dao A, Katagiri T, Harashima A, Kikuchi A, Kanai A, Matsui H, Inaba T, Taniwaki M, Yamamoto Y, Nakao S. Clonal hematopoiesis by SLIT1-mutated hematopoietic stem cells due to a breakdown of the autocrine loop involving Slit1 in acquired aplastic anemia. Leukemia 2019; 33:2732-2766. [PMID: 31186493 DOI: 10.1038/s41375-019-0510-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 04/23/2019] [Accepted: 05/01/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Kohei Hosokawa
- Department of Hematology & Respirology, Kanazawa University, Kanazawa, Japan
| | - Hiroki Mizumaki
- Department of Hematology & Respirology, Kanazawa University, Kanazawa, Japan
| | - Mahmoud I Elbadry
- Department of Hematology & Respirology, Kanazawa University, Kanazawa, Japan
| | - Chizuru Saito
- Department of Hematology & Respirology, Kanazawa University, Kanazawa, Japan
| | - J Luis Espinoza
- Department of Hematology & Respirology, Kanazawa University, Kanazawa, Japan
| | - An Thi Thanh Dao
- Department of Hematology & Respirology, Kanazawa University, Kanazawa, Japan
- Pediatric Department, University of Medicine and Pharmacy, Ho Chi Minh City, Vietnam
| | - Takamasa Katagiri
- Department of Clinical Laboratory Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Ai Harashima
- Department of Biochemistry, Kanazawa University, Kanazawa, Japan
| | - Akihiro Kikuchi
- Department of Endocrinology and Metabolism, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
- Division of Endocrinology and Metabolism, Department of Homeostatic Regulation, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Japan
| | - Akinori Kanai
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Hirotaka Matsui
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Toshiya Inaba
- Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Masafumi Taniwaki
- Department of Hematology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | | | - Shinji Nakao
- Department of Hematology & Respirology, Kanazawa University, Kanazawa, Japan.
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19
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Han X, Han Y, Tan Q, Huang Y, Yang J, Yang S, He X, Zhou S, Song Y, Pi J, Zuo L, Yao J, Wu D, Zhang Z, Shi Y. Tracking longitudinal genetic changes of circulating tumor DNA (ctDNA) in advanced Lung adenocarcinoma treated with chemotherapy. J Transl Med 2019; 17:339. [PMID: 31597567 PMCID: PMC6785899 DOI: 10.1186/s12967-019-2087-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023] Open
Abstract
Introduction Pemetrexed combined with platinum complexes can be used as first-line treatment for advanced non-squamous non-small cell lung cancer (NSCLC), however, the efficacy and safety is varying from individuals. There is a need to better understand the genetic variations associated with platinum response. Materials and Methods We performed next-generation sequencing (NGS) based on BGI Oseq-ctDNA panel to analyze 98 longitudinal plasma samples from 32 lung adenocarcinoma patients during platinum-based chemotherapy, and a bioinformatic pipeline was developed to detect point mutations. Results We found that mutation burden was decreased after chemotherapy, which reflected chemotherapy sensitivity, especially the frequency of C>G and C>A substitutions. Moreover, neoplastic cells carrying a specific set of somatic mutations, such as EGFR(L858R), KRAS (p.G12C) were obviously correlated with platinum treatment. In addition, the MAPK pathway was found to have a pivotal role in NSCLC and platinum based response. Finally, we found that smokers benefit less from platinum-based chemotherapy. Conclusions Collectively, this work described the dynamic changes of ctDNA mutation status during platinum-based treatment, which may contribute to advanced lung adenocarcinoma patients stratification and precision treatment.
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Affiliation(s)
- Xiaohong Han
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China.,Department of Clinical Laboratory, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Ying Han
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Qiaoyun Tan
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Yu Huang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Jianliang Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Sheng Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Xiaohui He
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Shengyu Zhou
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Yan Song
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Jinping Pi
- Beijing Chaoyang Sanhuan Cancer Hospital, Beijing, China
| | - Lijie Zuo
- Beijing Chaoyang Sanhuan Cancer Hospital, Beijing, China
| | - Jiarui Yao
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Di Wu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Zhishang Zhang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China
| | - Yuankai Shi
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, Beijing, China.
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20
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Xiu C, Li X, Wu L, Xu F, He Q, Zhang Z, Wu D, Song L, Su J, Zhou L, Zhao Y, Tao Y, Chang C. The efficacy and toxicity of the CHG priming regimen (low-dose cytarabine, homoharringtonine, and G-CSF) in higher risk MDS patients relapsed or refractory to decitabine. J Cancer Res Clin Oncol 2019; 145:3089-3097. [PMID: 31559495 DOI: 10.1007/s00432-019-03031-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022]
Abstract
PURPOSE Myelodysplastic syndromes (MDSs) refractory or relapsed after hypomethylating agents (HMAs) remain a therapeutic challenge. The CHG regimen has been demonstrated to be effective in initially treating higher risk MDS. The current study evaluated the efficacy and toxicity of the CHG regimen in patients who were resistant to decitabine. METHODS Patients with higher risk MDS relapsed or refractory to decitabine were enrolled in this study. Each patient received the CHG regimen (cytarabine (25 mg/day, days 1-14) and homoharringtonine (1 mg/day, days 1-14) intravenously with G-CSF (300 μg/day) subcutaneously from day 0 until neutrophil count recovery to 2.0 × 109 cells/L). Next gene sequencing with a 31-gene panel was carried out in patients. RESULTS Thirty-three patients were enrolled, including 12 relapsed and 21 refractory cases. The overall response rate (ORR) was 39.4% (13 of 33), with 9 (27.3%) achieving complete remission (CR), 2 having marrow CR (mCR), and 2 achieving partial remission (PR). The CR rate was higher in patients harboring fewer gene mutations (0-1) (55.6%) than in those with more gene mutations (> 1) (12.5%) (p = 0.021). The median overall survival (OS) of the 33 patients was 7.0 months. Patients who achieved a response had significantly longer survival times than were found in those without a response (21.0 M vs. 4.0 M, p < 0.0001). The regimen was endurable for most of the patients. CONCLUSIONS The CHG priming regimen provided a safe and effective salvage regimen for higher risk MDS patients who were resistant to decitabine. Further studies involving larger samples will be needed. Clinical trial No. ChiCTR-ONC-11001501.
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Affiliation(s)
- Cai Xiu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Xiao Li
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
| | - Lingyun Wu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China.
| | - Feng Xu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Qi He
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Zheng Zhang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Dong Wu
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Luxi Song
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Jiying Su
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Liyu Zhou
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Youshan Zhao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Ying Tao
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
| | - Chunkang Chang
- Department of Hematology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai, 200233, China
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21
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Iwai K, Yaguchi M, Nishimura K, Yamamoto Y, Tamura T, Nakata D, Dairiki R, Kawakita Y, Mizojiri R, Ito Y, Asano M, Maezaki H, Nakayama Y, Kaishima M, Hayashi K, Teratani M, Miyakawa S, Iwatani M, Miyamoto M, Klein MG, Lane W, Snell G, Tjhen R, He X, Pulukuri S, Nomura T. Anti-tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC-dependent vulnerability. EMBO Mol Med 2019; 10:emmm.201708289. [PMID: 29769258 PMCID: PMC5991599 DOI: 10.15252/emmm.201708289] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The modulation of pre-mRNA splicing is proposed as an attractive anti-neoplastic strategy, especially for the cancers that exhibit aberrant pre-mRNA splicing. Here, we discovered that T-025 functions as an orally available and potent inhibitor of Cdc2-like kinases (CLKs), evolutionally conserved kinases that facilitate exon recognition in the splicing machinery. Treatment with T-025 reduced CLK-dependent phosphorylation, resulting in the induction of skipped exons, cell death, and growth suppression in vitro and in vivo Further, through growth inhibitory characterization, we identified high CLK2 expression or MYC amplification as a sensitive-associated biomarker of T-025. Mechanistically, the level of CLK2 expression correlated with the magnitude of global skipped exons in response to T-025 treatment. MYC activation, which altered pre-mRNA splicing without the transcriptional regulation of CLKs, rendered cancer cells vulnerable to CLK inhibitors with synergistic cell death. Finally, we demonstrated in vivo anti-tumor efficacy of T-025 in an allograft model of spontaneous, MYC-driven breast cancer, at well-tolerated dosage. Collectively, our results suggest that the novel CLK inhibitor could have therapeutic benefits, especially for MYC-driven cancer patients.
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Affiliation(s)
- Kenichi Iwai
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Masahiro Yaguchi
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Kazuho Nishimura
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Yukiko Yamamoto
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Toshiya Tamura
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Daisuke Nakata
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Ryo Dairiki
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Yoichi Kawakita
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Ryo Mizojiri
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Yoshiteru Ito
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Moriteru Asano
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Hironobu Maezaki
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Yusuke Nakayama
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Misato Kaishima
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Kozo Hayashi
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Mika Teratani
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Shuichi Miyakawa
- Biomolecular Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Misa Iwatani
- Biomolecular Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Maki Miyamoto
- Drug Metabolism & Pharmacokinetics Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Michael G Klein
- Department of Structural Biology, Takeda California Inc., San Diego, CA, USA
| | - Wes Lane
- Department of Structural Biology, Takeda California Inc., San Diego, CA, USA
| | - Gyorgy Snell
- Department of Structural Biology, Takeda California Inc., San Diego, CA, USA
| | - Richard Tjhen
- Department of Structural Biology, Takeda California Inc., San Diego, CA, USA
| | - Xingyue He
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Sai Pulukuri
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Toshiyuki Nomura
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
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22
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Gołos A, Jesionek-Kupnicka D, Gil L, Braun M, Komarnicki M, Robak T, Wierzbowska A. The Expression of the SLIT-ROBO Family in Adult Patients with Acute Myeloid Leukemia. Arch Immunol Ther Exp (Warsz) 2019; 67:109-123. [PMID: 30820596 PMCID: PMC6420492 DOI: 10.1007/s00005-019-00535-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 11/23/2018] [Indexed: 12/13/2022]
Abstract
INTRODUCTION SLIT-ROBO is a ligand-receptor family of neuronal guidance cues that has been involved in pathological and physiological angiogenesis. SLIT-ROBO expression is altered in many tumours. However, no data exist about the role of the whole family in acute myelogenous myeloid leukemia (AML). PURPOSE Herein, we assessed the expression of all SLIT-ROBO family in bone marrow (BM) biopsy of AML patients and control group on both protein and RNA levels. METHODS The paraffin-embedded tissue blocks were subjected to immunohistochemistry for SLIT1, SLIT2, SLIT3, ROBO1, ROBO2, ROBO3, and ROBO4. Microvessel density (MVD) was evaluated by CD34 immunohistochemistry. An in silico analysis using The Cancer Genome Atlas data repository was conducted for assessment of RNA level. RESULTS Acute myeloid leukemia patients were generally high expressers of ROBO1 and ROBO2 compared to the controls (p < 0.0001, p < 0.001, respectively). In contrast, low expression of SLIT1, SLIT2, and SLIT3 ligands has been noted more commonly in AML than in control BM samples (p < 0.0001, p = 0.003, and p = 0.001, respectively). ROBO4 expression correlated with MVD. The in silico analysis showed a poor prognostic value of high ROBO3 and low SLIT2 RNA levels (p = 0.0003 and p = 0.0008, respectively), as well as high ROBO3 and ROBO4 RNA levels in cytogenetic poor risk groups of patients (p = 0.0029 and p = 0.0003, respectively). CONCLUSIONS These data indicate that SLIT-ROBO family members play a role in the biology of AML. Low expression of SLIT in BM of AML patients may suggest its expression alterations in AML. Increased expression of ROBO1 and ROBO2 in AML patients suggests their participation in AML pathogenesis.
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Affiliation(s)
- Aleksandra Gołos
- Department of Hematology, Medical University, Lodz, Poland.
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland.
| | | | - Lidia Gil
- Department of Hematology, University of Medical Sciences, Poznan, Poland
| | - Marcin Braun
- Department of Pathology, Medical University, Lodz, Poland
- Postgraduate School of Medicine, Medical University of Warsaw, Warsaw, Poland
| | | | - Tadeusz Robak
- Department of Hematology, Medical University, Lodz, Poland
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23
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Lu J, Lou H, Fu R, Lu D, Zhang F, Wu Z, Zhang X, Li C, Fang B, Pu F, Wei J, Wei Q, Zhang C, Wang X, Lu Y, Yan S, Yang Y, Jin L, Xu S. Assessing genome-wide copy number variation in the Han Chinese population. J Med Genet 2017; 54:685-692. [PMID: 28705883 DOI: 10.1136/jmedgenet-2017-104613] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 06/08/2017] [Accepted: 06/08/2017] [Indexed: 12/22/2022]
Abstract
BACKGROUND Copy number variation (CNV) is a valuable source of genetic diversity in the human genome and a well-recognised cause of various genetic diseases. However, CNVs have been considerably under-represented in population-based studies, particularly the Han Chinese which is the largest ethnic group in the world. OBJECTIVES To build a representative CNV map for the Han Chinese population. METHODS We conducted a genome-wide CNV study involving 451 male Han Chinese samples from 11 geographical regions encompassing 28 dialect groups, representing a less-biased panel compared with the currently available data. We detected CNVs by using 4.2M NimbleGen comparative genomic hybridisation array and whole-genome deep sequencing of 51 samples to optimise the filtering conditions in CNV discovery. RESULTS A comprehensive Han Chinese CNV map was built based on a set of high-quality variants (positive predictive value >0.8, with sizes ranging from 369 bp to 4.16 Mb and a median of 5907 bp). The map consists of 4012 CNV regions (CNVRs), and more than half are novel to the 30 East Asian CNV Project and the 1000 Genomes Project Phase 3. We further identified 81 CNVRs specific to regional groups, which was indicative of the subpopulation structure within the Han Chinese population. CONCLUSIONS Our data are complementary to public data sources, and the CNV map may facilitate in the identification of pathogenic CNVs and further biomedical research studies involving the Han Chinese population.
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Affiliation(s)
- Jianqi Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Haiyi Lou
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China
| | - Ruiqing Fu
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dongsheng Lu
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Feng Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China
| | - Zhendong Wu
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Xi Zhang
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Changhua Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Baijun Fang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Fangfang Pu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingning Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Qian Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Chao Zhang
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoji Wang
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yan Lu
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China
| | - Shi Yan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Yajun Yang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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24
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Appe AJ, Aggerholm A, Hansen MC, Ebbesen LH, Hokland P, Bentzen HHN, Nyvold CG. Differential expression levels and methylation status of ROBO1 in mantle cell lymphoma and chronic lymphocytic leukaemia. Int J Lab Hematol 2017; 39:e70-e73. [PMID: 28004534 DOI: 10.1111/ijlh.12615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
MESH Headings
- DNA Methylation
- DNA, Neoplasm/metabolism
- Female
- Gene Expression Regulation, Leukemic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/metabolism
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Mantle-Cell/metabolism
- Lymphoma, Mantle-Cell/pathology
- Male
- Neoplasm Proteins/biosynthesis
- Nerve Tissue Proteins/biosynthesis
- Receptors, Immunologic/biosynthesis
- Roundabout Proteins
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Affiliation(s)
- A J Appe
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - A Aggerholm
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - M C Hansen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - L H Ebbesen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - P Hokland
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - H H N Bentzen
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
| | - C G Nyvold
- Department of Haematology, Aarhus University Hospital, Aarhus, Denmark
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25
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Chi K, Li Y, Xu L, Wang X. A novel recurrent copy number loss region on 6q23.3 in MDS-related myeloid malignancy patients with stable survival conditions. Leuk Lymphoma 2017; 58:2470-2479. [PMID: 28394181 DOI: 10.1080/10428194.2017.1292357] [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: 10/19/2022]
Abstract
Metaphase cytogenetics (MC) karyotyping is a fundamental way to approach cytogenetic pathogenesis of MDS-related myeloid malignancies. However, in some patients, the results are normal while the patients often show discrepancies in survival conditions. To explain this question, we analyzed CytoScan™ HD array results of 20 MC-normal/failure patients who were followed up for three years. Exon sequencing was performed in genes RUNX1, TP53, ASXL1, and TET2. The array enabled the detection of additional aberrations in 16 (80%) patients. Eight patients were detected with cryptic copy number losses and six of them got aggressive disease conditions. RUNX1 mutations were sequenced in P110 and P114. Most importantly, two patients (P114 and P116) with copy number loss aberrations got stable survival conditions during follow-ups, and a novel recurrent copy number loss region harboring the proto-oncogene MYB was detected on chromosome 6q23.3 in both of them, which might benefit the survival of the patients.
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Affiliation(s)
- Kun Chi
- a Department of Laboratory Medicine , Qingdao Women & Children's Hospital , Qingdao , China.,b State Key Laboratory of Medical Genomics , Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Yang Li
- b State Key Laboratory of Medical Genomics , Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Lan Xu
- c Department of Hematology , Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
| | - Xuefeng Wang
- d Department of Laboratory Medicine , Ruijin Hospital, Shanghai Jiaotong University School of Medicine , Shanghai , China
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26
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Exploration of the role of gene mutations in myelodysplastic syndromes through a sequencing design involving a small number of target genes. Sci Rep 2017; 7:43113. [PMID: 28220884 PMCID: PMC5318910 DOI: 10.1038/srep43113] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/19/2017] [Indexed: 01/19/2023] Open
Abstract
Novel sequencing designs are necessary to supplement the recognized knowledge of myelodysplastic syndrome (MDS)-related genomic alterations. In this study, we sequenced 28 target genes in 320 Chinese MDS patients but obtained 77.2% of recall factors and 82.8% of genetic abnormalities (including karyotype abnormalities). In addition to known relationships among mutations, some specific chromosomal abnormalities were found to link to specific gene mutations. Trisomy 8 tended to be linked to U2AF1 and ZRSR2 mutations, and 20q- exhibited higher SRSF2/WT1 and U2AF1 mutation frequency. Chromosome 7 involvement accounted for up to 50% of RUNX1 mutations and 37.5% of SETBP1 mutations. Patients carrying a complex karyotype were prone to present TP53 mutations (36.1%). However, individuals with normal karyotypes rarely possessed mutations in the TP53, RUNX1 and U2AF1. Moreover, DNMT3A, TP53, SRSF2, STAG2, ROBO1/2 and WT1 predicted poor survival and high AML transformation. By integrating these predictors into international prognostic scoring system (IPSS) or revised IPSS, we built a set of mutation-based prognostic risk models. These models could layer different degrees of risk in patients more satisfactorily. In summary, this sequencing design was able to detect a number of gene mutations and could be used to stratify patients with varied prognostic risk.
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27
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[Identification of miR-639 expression in myelodysplastic syndrome and its target gene prediction]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2017; 38:157-159. [PMID: 28279042 PMCID: PMC7354176 DOI: 10.3760/cma.j.issn.0253-2727.2017.02.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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28
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Chang CK, Zhao YS, Xu F, Guo J, Zhang Z, He Q, Wu D, Wu LY, Su JY, Song LX, Xiao C, Li X. TP53mutations predict decitabine-induced complete responses in patients with myelodysplastic syndromes. Br J Haematol 2016; 176:600-608. [PMID: 27984642 DOI: 10.1111/bjh.14455] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/05/2016] [Indexed: 02/01/2023]
Affiliation(s)
- Chun-Kang Chang
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - You-Shan Zhao
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Feng Xu
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Juan Guo
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Zheng Zhang
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Qi He
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Dong Wu
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Ling-Yun Wu
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Ji-Ying Su
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Lu-Xi Song
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Chao Xiao
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
| | - Xiao Li
- Department of Haematology; Shanghai Jiao Tong University Affiliated Sixth People's Hospital; Shanghai China
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