1
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Zhang Y, Zhao X, Zhang J, Zhang Y, Wei Y. Advancements in the impact of human microbiota and probiotics on leukemia. Front Microbiol 2024; 15:1423838. [PMID: 39021626 PMCID: PMC11251910 DOI: 10.3389/fmicb.2024.1423838] [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: 04/26/2024] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
The human gut microbiota is a complex ecosystem that plays a crucial role in promoting the interaction between the body and its environment. It has been increasingly recognized that the gut microbiota has diverse physiological functions. Recent studies have shown a close association between the gut microbiota and the development of certain tumors, including leukemia. Leukemia is a malignant clonal disease characterized by the uncontrolled growth of one or more types of blood cells, which is the most common cancer in children. The imbalance of gut microbiota is linked to the pathological mechanisms of leukemia. Probiotics, which are beneficial microorganisms that help maintain the balance of the host microbiome, play a role in regulating gut microbiota. Probiotics have the potential to assist in the treatment of leukemia and improve the clinical prognosis of leukemia patients. This study reviews the relationship between gut microbiota, probiotics, and the progression of leukemia based on current research. In addition, utilizing zebrafish leukemia models in future studies might reveal the specific mechanisms of their interactions, thereby providing new insights into the clinical treatment of leukemia. In conclusion, further investigation is still needed to fully understand the accurate role of microbes in leukemia.
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Affiliation(s)
| | | | | | - Yaodong Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, School of Pharmaceutical Sciences, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital Zhengzhou Children’s Hospital, Zhengzhou University, Zhengzhou, China
| | - Yongjun Wei
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, School of Pharmaceutical Sciences, Children’s Hospital Affiliated to Zhengzhou University, Henan Children’s Hospital Zhengzhou Children’s Hospital, Zhengzhou University, Zhengzhou, China
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2
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Keshavarz A, Navidinia AA, Kuhestani Dehaghi BH, Amiri V, Mohammadi MH, Allahbakhshian Farsani M. Identification of Prognostic Genes in Acute Myeloid Leukemia Microenvironment: A Bioinformatic and Experimental Analysis. Mol Biotechnol 2024:10.1007/s12033-024-01128-3. [PMID: 38714601 DOI: 10.1007/s12033-024-01128-3] [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: 08/30/2023] [Accepted: 02/27/2024] [Indexed: 05/10/2024]
Abstract
Acute myeloid leukemia (AML) is a lethal hematologic malignancy with a variable prognosis that is highly dependent on the bone marrow microenvironment. Consequently, a better understanding of the AML microenvironment is crucial for early diagnosis, risk stratification, and personalized therapy. In recent years, the role of bioinformatics as a powerful tool in clarifying the complexities of cancer has become more prominent. Gene expression profile and clinical data of 173 AML patients were downloaded from the TCGA database, and the xCell algorithm was applied to calculate the microenvironment score (MS). Then, the correlation of MS with FAB classification, and CALGB cytogenetic risk category was investigated. Differentially expressed genes (DEGs) were identified, and the correlation analysis of DEGs with patient survival was done using univariate cox. The prognostic value of candidate prognostic DEGs was confirmed based on the GEO database. In the last step, real-time PCR was used to compare the expression of the top three prognostic genes between patients and the control group. During TCGA data analysis, 716 DEGs were identified, and survival analysis results showed that 152 DEGs had survival-related changes. In addition, the prognostic value of 31 candidate prognostic genes was confirmed by GEO data analysis. Finally, the expression analysis of FLVCR2, SMO, and CREB5 genes, the most related genes to patients' survival, was significantly different between patients and control groups. In summary, we identified key microenvironment-related genes that influence the survival of AML patients and may serve as prognostic and therapeutic targets.
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Affiliation(s)
- Ali Keshavarz
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Amir Abbas Navidinia
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Bentol Hoda Kuhestani Dehaghi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
| | - Vahid Amiri
- Department of Laboratory Sciences, School of Paramedicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Mohammad Hossein Mohammadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran
- HSCT Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehdi Allahbakhshian Farsani
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, P.O. Box: 15468-15514, Tehran, Iran.
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3
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Yang T, Ke H, Liu J, An X, Xue J, Ning J, Hao F, Xiong L, Chen C, Wang Y, Zheng J, Gao B, Bao Z, Gong K, Zhang L, Zhang F, Guo S, Li QX. Narazaciclib, a novel multi-kinase inhibitor with potent activity against CSF1R, FLT3 and CDK6, shows strong anti-AML activity in defined preclinical models. Sci Rep 2024; 14:9032. [PMID: 38641704 PMCID: PMC11031590 DOI: 10.1038/s41598-024-59650-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 04/12/2024] [Indexed: 04/21/2024] Open
Abstract
CSF1R is a receptor tyrosine kinase responsible for the growth/survival/polarization of macrophages and overexpressed in some AML patients. We hypothesized that a novel multi-kinase inhibitor (TKi), narazaciclib (HX301/ON123300), with high potency against CSF1R (IC50 ~ 0.285 nM), would have anti-AML effects. We tested this by confirming HX301's high potency against CSF1R (IC50 ~ 0.285 nM), as well as other kinases, e.g. FLT3 (IC50 of ~ 19.77 nM) and CDK6 (0.53 nM). An in vitro proliferation assay showed that narazaciclib has a high growth inhibitory effect in cell cultures where CSF1R or mutant FLT3-ITD variants that may be proliferation drivers, including primary macrophages (IC50 of 72.5 nM) and a subset of AML lines (IC50 < 1.5 μM). In vivo pharmacology modeling of narazaciclib using five AML xenografts resulted in: inhibition of MV4-11 (FLT3-ITD) subcutaneous tumor growth and complete suppression of AM7577-PDX (FLT3-ITD/CSF1Rmed) systemic growth, likely due to the suppression of FLT3-ITD activity; complete suppression of AM8096-PDX (CSF1Rhi/wild-type FLT3) growth, likely due to the inhibition of CSF1R ("a putative driver"); and nonresponse of both AM5512-PDX and AM7407-PDX (wild-type FLT3/CSF1Rlo). Significant leukemia load reductions in bone marrow, where disease originated, were also achieved in both responders (AM7577/AM8096), implicating that HX301 might be a potentially more effective therapy than those only affecting peripheral leukemic cells. Altogether, narazaciclib can potentially be a candidate treatment for a subset of AML with CSF1Rhi and/or mutant FLT3-ITD variants, particularly second generation FLT3 inhibitor resistant variants.
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Affiliation(s)
- Tao Yang
- Hanx Biopharmaceuticals, Ltd., Wuhan, Hubei, PRC, China
| | - Hang Ke
- Hanx Biopharmaceuticals, Ltd., Wuhan, Hubei, PRC, China
| | - Jinping Liu
- Crown Bioscience, Inc., Taicang, Jiangsu, PRC, USA
| | - Xiaoyu An
- Crown Bioscience, Inc., Taicang, Jiangsu, PRC, USA
| | - Jia Xue
- Crown Bioscience, Inc., Taicang, Jiangsu, PRC, USA
| | | | - Feng Hao
- Kyinno Biotechnology, Ltd., Beijing, PRC, China
| | | | - Cen Chen
- Hanx Biopharmaceuticals, Ltd., Wuhan, Hubei, PRC, China
| | - Yueying Wang
- Crown Bioscience, Inc., Taicang, Jiangsu, PRC, USA
| | - Jia Zheng
- Crown Bioscience, Inc., Taicang, Jiangsu, PRC, USA
| | - Bing Gao
- Crown Bioscience, Inc., Taicang, Jiangsu, PRC, USA
| | | | - Kefeng Gong
- Crown Bioscience, Inc., Taicang, Jiangsu, PRC, USA
| | - Lei Zhang
- Hanx Biopharmaceuticals, Ltd., Wuhan, Hubei, PRC, China
| | - Faming Zhang
- Hanx Biopharmaceuticals, Ltd., Wuhan, Hubei, PRC, China
| | - Sheng Guo
- Crown Bioscience, Inc., Taicang, Jiangsu, PRC, USA
| | - Qi-Xiang Li
- Hanx Biopharmaceuticals, Ltd., Wuhan, Hubei, PRC, China.
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4
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Bae SG, Kim HJ, Kim MY, Kim DDH, Shin SI, Ahn JS, Park J. Identification of Cell Type-Specific Effects of DNMT3A Mutations on Relapse in Acute Myeloid Leukemia. Mol Cells 2023; 46:611-626. [PMID: 37853686 PMCID: PMC10590706 DOI: 10.14348/molcells.2023.0093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/27/2023] [Accepted: 08/01/2023] [Indexed: 10/20/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease caused by distinctive mutations in individual patients; therefore, each patient may display different cell-type compositions. Although most patients with AML achieve complete remission (CR) through intensive chemotherapy, the likelihood of relapse remains high. Several studies have attempted to characterize the genetic and cellular heterogeneity of AML; however, our understanding of the cellular heterogeneity of AML remains limited. In this study, we performed single-cell RNA sequencing (scRNAseq) of bone marrow-derived mononuclear cells obtained from same patients at different AML stages (diagnosis, CR, and relapse). We found that hematopoietic stem cells (HSCs) at diagnosis were abnormal compared to normal HSCs. By improving the detection of the DNMT3A R882 mutation with targeted scRNAseq, we identified that DNMT3A-mutant cells that mainly remained were granulocyte-monocyte progenitors (GMPs) or lymphoid-primed multipotential progenitors (LMPPs) from CR to relapse and that DNMT3A-mutant cells have gene signatures related to AML and leukemic cells. Copy number variation analysis at the single-cell level indicated that the cell type that possesses DNMT3A mutations is an important factor in AML relapse and that GMP and LMPP cells can affect relapse in patients with AML. This study advances our understanding of the role of DNMT3A in AML relapse and our approach can be applied to predict treatment outcomes.
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Affiliation(s)
- Seo-Gyeong Bae
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Hyeoung-Joon Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun 58128, Korea
| | - Mi Yeon Kim
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
| | - Dennis Dong Hwan Kim
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - So-I Shin
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
| | - Jae-Sook Ahn
- Department of Internal Medicine, Chonnam National University Hwasun Hospital, Chonnam National University, Hwasun 58128, Korea
- Genomic Research Center for Hematopoietic Diseases, Chonnam National University Hwasun Hospital, Hwasun 58128, Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Korea
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5
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Khalsa JK, Cha J, Utro F, Naeem A, Murali I, Kuang Y, Vasquez K, Li L, Tyekucheva S, Fernandes SM, Veronese L, Guieze R, Sasi BK, Wang Z, Machado JH, Bai H, Alasfour M, Rhrissorrakrai K, Levovitz C, Danysh BP, Slowik K, Jacobs RA, Davids MS, Paweletz CP, Leshchiner I, Parida L, Getz G, Brown JR. Genetic events associated with venetoclax resistance in CLL identified by whole-exome sequencing of patient samples. Blood 2023; 142:421-433. [PMID: 37146250 PMCID: PMC10447490 DOI: 10.1182/blood.2022016600] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 03/14/2023] [Accepted: 04/04/2023] [Indexed: 05/07/2023] Open
Abstract
Although BCL2 mutations are reported as later occurring events leading to venetoclax resistance, many other mechanisms of progression have been reported though remain poorly understood. Here, we analyze longitudinal tumor samples from 11 patients with disease progression while receiving venetoclax to characterize the clonal evolution of resistance. All patients tested showed increased in vitro resistance to venetoclax at the posttreatment time point. We found the previously described acquired BCL2-G101V mutation in only 4 of 11 patients, with 2 patients showing a very low variant allele fraction (0.03%-4.68%). Whole-exome sequencing revealed acquired loss(8p) in 4 of 11 patients, of which 2 patients also had gain (1q21.2-21.3) in the same cells affecting the MCL1 gene. In vitro experiments showed that CLL cells from the 4 patients with loss(8p) were more resistant to venetoclax than cells from those without it, with the cells from 2 patients also carrying gain (1q21.2-21.3) showing increased sensitivity to MCL1 inhibition. Progression samples with gain (1q21.2-21.3) were more susceptible to the combination of MCL1 inhibitor and venetoclax. Differential gene expression analysis comparing bulk RNA sequencing data from pretreatment and progression time points of all patients showed upregulation of proliferation, B-cell receptor (BCR), and NF-κB gene sets including MAPK genes. Cells from progression time points demonstrated upregulation of surface immunoglobulin M and higher pERK levels compared with those from the preprogression time point, suggesting an upregulation of BCR signaling that activates the MAPK pathway. Overall, our data suggest several mechanisms of acquired resistance to venetoclax in CLL that could pave the way for rationally designed combination treatments for patients with venetoclax-resistant CLL.
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MESH Headings
- Humans
- Antineoplastic Agents/pharmacology
- Bridged Bicyclo Compounds, Heterocyclic/pharmacology
- Drug Resistance, Neoplasm/genetics
- Exome Sequencing
- Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Myeloid Cell Leukemia Sequence 1 Protein/genetics
- Proto-Oncogene Proteins c-bcl-2
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Affiliation(s)
- Jasneet Kaur Khalsa
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Justin Cha
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | | | - Aishath Naeem
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Ishwarya Murali
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Yanan Kuang
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Kevin Vasquez
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | - Liang Li
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Svitlana Tyekucheva
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health, Boston, MA
| | - Stacey M. Fernandes
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Lauren Veronese
- Service de Cytogénétique Médicale, CHU Clermont-Ferrand, Clermont-Ferrand, France
- EA7453 CHELTER, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Romain Guieze
- EA7453 CHELTER, Université Clermont Auvergne, Clermont-Ferrand, France
- Service d’Hématologie clinique et thérapie cellulaire, CHU Clermont-Ferrand, Clermont-Ferrand, France
| | - Binu Kandathilparambil Sasi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Zixu Wang
- Department of Data Sciences, Dana-Farber Cancer Institute, Harvard TH Chan School of Public Health, Boston, MA
| | - John-Hanson Machado
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Harrison Bai
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | - Maryam Alasfour
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - Brian P. Danysh
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Kara Slowik
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Raquel A. Jacobs
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Matthew S. Davids
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Cloud P. Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Gad Getz
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Cancer Center, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Massachusetts General Hospital, Boston, MA
| | - Jennifer R. Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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6
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Xie JY, Wang WJ, Wang N, Dong Q, Han H, Feng YP, Yuan Y, Feng J, Chen K. A novel immune-related gene signature correlated with serum IL33 expression in acute myeloid leukemia prognosis. Am J Transl Res 2023; 15:4332-4344. [PMID: 37434810 PMCID: PMC10331686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/15/2023] [Indexed: 07/13/2023]
Abstract
PURPOSE To identify and validate the immune-related gene signature in patients with acute myeloid leukemia (AML). METHODS Differentially expressed genes (DEGs) profiles and survival data were obtained from The Cancer Genome Atlas (TCGA), following screened immune-associated genes from the InnateDB database. Subsequently, the weighted gene co-expression network analysis (WGCNA) was used to detect functional modules, and survival analysis was performed. The least absolute shrinkage and selection operator (LASSO) regression model combined with a partial likelihood-based Cox proportional hazard regression model was applied to select prognostic genes, and the ESTIMATE algorithm was used to construct an immune score-based risk assessment model. Finally, two independent datasets from the Gene Expression Omnibus (GEO) and our clinical data were used for external validation. Moreover, a subpopulation of the immune microenvironment cells was analyzed by the CIBERSORT algorithm, and its related serum indicator was identified by the enzyme-linked immunosorbent assay (ELISA) in clinical samples. RESULTS Finally, CTSD, GNB2, CDK6, and WAS were identified as the immune-related gene signature, and the risk stratification model was validated in both the GSE12417 database and our clinical cohort. Furthermore, the fraction of activated mast cells was identified. CIBERSORT algorithm showed that these cells have a positive association with prognosis. In addition, mast cell stimulator IL-33 was markedly decreased in AML patients with poor prognoses. CONCLUSION A novel immune-related gene signature (CTSD, GNB2, CDK6 and WAS) and its associated plasma indicator (mast cells activator, IL-33) were found to have prognostic value in AML patients.
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Affiliation(s)
- Jin-Ye Xie
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Wei-Jia Wang
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
- Department of Medical Research, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Nan Wang
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Qian Dong
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Hui Han
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Yan-Pin Feng
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Yong Yuan
- Department of Cardiovascular Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
- Department of Medical Research, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
| | - Juan Feng
- School of Medicine, Foshan UniversityFoshan 528225, Guangdong, China
| | - Kang Chen
- Department of Laboratory Medicine, Zhongshan City People’s HospitalZhongshan 528403, Guangdong, China
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7
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Swartzel JC, Bond MJ, Pintado-Urbanc AP, Daftary M, Krone MW, Douglas T, Carder EJ, Zimmer JT, Maeda T, Simon MD, Crews CM. Targeted Degradation of mRNA Decapping Enzyme DcpS by a VHL-Recruiting PROTAC. ACS Chem Biol 2022; 17:1789-1798. [PMID: 35749470 PMCID: PMC10367122 DOI: 10.1021/acschembio.2c00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The RNA decapping scavenger protein, DcpS, has recently been identified as a dependency in acute myeloid leukemia (AML). The potent DcpS inhibitor RG3039 attenuates AML cell viability, and shRNA knockdown of DcpS is also antiproliferative. Importantly, DcpS was found to be non-essential in normal human hematopoietic cells, which opens a therapeutic window for AML treatment by DcpS modulation. Considering this strong DcpS dependence in AML cell lines, we explored PROTAC-mediated degradation as an alternative strategy to modulate DcpS activity. Herein, we report the development of JCS-1, a PROTAC exhibiting effective degradation of DcpS at nanomolar concentrations. JCS-1 non-covalently binds DcpS with a RG3039-based warhead and recruits the E3 ligase VHL, which induces potent, rapid, and sustained DcpS degradation in several AML cell lines. JCS-1 serves as a chemical biology tool to interrogate DcpS degradation and associated changes in RNA processes in different cellular contexts, which may be an attractive strategy for the treatment of AML and other DcpS-dependent genetic disorders.
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Affiliation(s)
- Jake C Swartzel
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Michael J Bond
- Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Andreas P Pintado-Urbanc
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States
| | - Mehana Daftary
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Mackenzie W Krone
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Todd Douglas
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Evan J Carder
- Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Joshua T Zimmer
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Matthew D Simon
- Institute for Biomolecular Design and Discovery, Yale University, West Haven, Connecticut 06516, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Craig M Crews
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States.,Department of Pharmacology, Yale University, New Haven, Connecticut 06511, United States.,Department of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
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8
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Schmalzbauer BS, Thondanpallil T, Heller G, Schirripa A, Sperl CM, Mayer IM, Knab VM, Nebenfuehr S, Zojer M, Mueller AC, Fontaine F, Klampfl T, Sexl V, Kollmann K. CDK6 Degradation Is Counteracted by p16INK4A and p18INK4C in AML. Cancers (Basel) 2022; 14:cancers14061554. [PMID: 35326705 PMCID: PMC8946512 DOI: 10.3390/cancers14061554] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary CDK4/6 kinase inhibitors show promising results in various subtypes of AML, which has been primarily assigned to the inhibition of CDK6. To bypass therapeutic resistances and tackle the kinase-dependent, as well as kinase-independent, functions of CDK6, new CDK6 degraders have been developed. Here, we present insights into the mechanistic requirements for the efficacy of a CDK6-specific degrader in AML. We show that the presence and levels of the INK4 proteins p16INK4A and p18INK4C determine the extent of CDK6 degradation. Our study reveals the importance of INK4 protein levels as predictive markers for CDK6-targeted therapy in AML. Abstract Cyclin-dependent kinase 6 (CDK6) represents a novel therapeutic target for the treatment of certain subtypes of acute myeloid leukaemia (AML). CDK4/6 kinase inhibitors have been widely studied in many cancer types and their effects may be limited by primary and secondary resistance mechanisms. CDK4/6 degraders, which eliminate kinase-dependent and kinase-independent effects, have been suggested as an alternative therapeutic option. We show that the efficacy of the CDK6-specific protein degrader BSJ-03-123 varies among AML subtypes and depends on the low expression of the INK4 proteins p16INK4A and p18INK4C. INK4 protein levels are significantly elevated in KMT2A-MLLT3+ cells compared to RUNX1-RUNX1T1+ cells, contributing to the different CDK6 degradation efficacy. We demonstrate that CDK6 complexes containing p16INK4A or p18INK4C are protected from BSJ-mediated degradation and that INK4 levels define the proliferative response to CDK6 degradation. These findings define INK4 proteins as predictive markers for CDK6 degradation-targeted therapies in AML.
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Affiliation(s)
- Belinda S. Schmalzbauer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Teresemary Thondanpallil
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Gerwin Heller
- Division of Oncology, Department of Medicine I, Medical University of Vienna, 1090 Vienna, Austria;
| | - Alessia Schirripa
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Clio-Melina Sperl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Isabella M. Mayer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Vanessa M. Knab
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Sofie Nebenfuehr
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Markus Zojer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - André C. Mueller
- CeMM—Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; (A.C.M.); (F.F.)
| | - Frédéric Fontaine
- CeMM—Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; (A.C.M.); (F.F.)
| | - Thorsten Klampfl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Veronika Sexl
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
| | - Karoline Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, 1210 Vienna, Austria; (B.S.S.); (T.T.); (A.S.); (C.-M.S.); (I.M.M.); (V.M.K.); (S.N.); (M.Z.); (T.K.); (V.S.)
- Correspondence:
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Teixeira TM, Nazareno AG. One Step Away From Extinction: A Population Genomic Analysis of A Narrow Endemic, Tropical Plant Species. FRONTIERS IN PLANT SCIENCE 2021; 12:730258. [PMID: 34630476 PMCID: PMC8496504 DOI: 10.3389/fpls.2021.730258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
Intraspecific genetic variation plays a fundamental role in maintaining the evolutionary potential of wild populations. Hence, the assessment of genetic diversity patterns becomes essential to guide biodiversity conservation policies, particularly for threatened species. To inform management strategies for conservation of Mimosa catharinensis - a narrow endemic, critically endangered plant species - we identified 1,497 unlinked SNP markers derived from a reduced representation sequencing method (i.e., double digest restriction site associated DNA sequencing, or ddRADseq). This set of molecular markers was employed to assess intrapopulation genetic parameters and the demographic history of one extremely small population of M. catharinensis (N=33) located in the Brazilian Atlantic Forest. Contrary to what is expected for narrow endemic and threatened species with small population sizes, we observed a moderate level of genetic diversity for M. catharinensis [uH E(0%missing data)=0.205, 95% CI (0.160, 0.250); uH E(30%missing data)=0.233, 95% CI (0.174, 0.292)]. Interestingly, M. catharinensis, which is a lianescent shrub with no indication of seed production for at least two decades, presented high levels of outcrossing [t (0%missing data)=0.883, SE±0.0483; t (30%missing data)=0.909, SE±0.011] and an apparent absence of inbreeding [F (0%missing data)=-0.145, 95% CI (-0.189, -0.101); F (30%missing data)=-0.105, 95% CI (-0.199, -0.011)]. However, the reconstruction of demographic history of M. catharinensis indicated that the population should be suffered a recent bottleneck. Our population genomic study tackles a central issue in evolution and conservation biology and we expect that it will be useful to help safeguard the remaining genetic diversity reported for this unique genetic resource.
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Affiliation(s)
- Thais M. Teixeira
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Alison G. Nazareno
- Department of Genetics, Ecology and Evolution, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, United States
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The Prognostic Significance of the BIN1 and CCND2 Gene in Adult Patients with Acute Myeloid Leukemia. Indian J Hematol Blood Transfus 2021; 38:481-491. [DOI: 10.1007/s12288-021-01479-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/28/2021] [Indexed: 10/20/2022] Open
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