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Single-cell analysis reveals the chemotherapy-induced cellular reprogramming and novel therapeutic targets in relapsed/refractory acute myeloid leukemia. Leukemia 2023; 37:308-325. [PMID: 36543880 PMCID: PMC9898038 DOI: 10.1038/s41375-022-01789-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 12/01/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022]
Abstract
Chemoresistance and relapse are the leading cause of AML-related deaths. Utilizing single-cell RNA sequencing (scRNA-seq), we dissected the cellular states of bone marrow samples from primary refractory or short-term relapsed AML patients and defined the transcriptional intratumoral heterogeneity. We found that compared to proliferating stem/progenitor-like cells (PSPs), a subpopulation of quiescent stem-like cells (QSCs) were involved in the chemoresistance and poor outcomes of AML. By performing longitudinal scRNA-seq analyses, we demonstrated that PSPs were reprogrammed to obtain a QSC-like expression pattern during chemotherapy in refractory AML patients, characterized by the upregulation of CD52 and LGALS1 expression. Flow cytometric analysis further confirmed that the preexisting CD99+CD49d+CD52+Galectin-1+ (QSCs) cells at diagnosis were associated with chemoresistance, and these cells were further enriched in the residual AML cells of refractory patients. Interaction of CD52-SIGLEC10 between QSCs and monocytes may contribute to immune evading and poor outcomes. Furthermore, we identified that LGALS1 was a promising target for chemoresistant AML, and LGALS1 inhibitor could help eliminate QSCs and enhance the chemotherapy in patient-derived primary AML cells, cell lines, and AML xenograft models. Our results will facilitate a better understanding of the AML chemoresistance mechanism and the development of novel therapeutic strategies for relapsed/refractory AML patients.
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2
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Integrative epigenomic and transcriptomic analysis reveals the requirement of JUNB for hematopoietic fate induction. Nat Commun 2022; 13:3131. [PMID: 35668082 PMCID: PMC9170695 DOI: 10.1038/s41467-022-30789-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 05/18/2022] [Indexed: 11/08/2022] Open
Abstract
Human pluripotent stem cell differentiation towards hematopoietic progenitor cell can serve as an in vitro model for human embryonic hematopoiesis, but the dynamic change of epigenome and transcriptome remains elusive. Here, we systematically profile the chromatin accessibility, H3K4me3 and H3K27me3 modifications, and the transcriptome of intermediate progenitors during hematopoietic progenitor cell differentiation in vitro. The integrative analyses reveal sequential opening-up of regions for the binding of hematopoietic transcription factors and stepwise epigenetic reprogramming of bivalent genes. Single-cell analysis of cells undergoing the endothelial-to-hematopoietic transition and comparison with in vivo hemogenic endothelial cells reveal important features of in vitro and in vivo hematopoiesis. We find that JUNB is an essential regulator for hemogenic endothelium specialization and endothelial-to-hematopoietic transition. These studies depict an epigenomic roadmap from human pluripotent stem cells to hematopoietic progenitor cells, which may pave the way to generate hematopoietic progenitor cells with improved developmental potentials.
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3
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Wang D, Tanaka-Yano M, Meader E, Kinney MA, Morris V, Lummertz da Rocha E, Liu N, Liu T, Zhu Q, Orkin SH, North TE, Daley GQ, Rowe RG. Developmental maturation of the hematopoietic system controlled by a Lin28b-let-7-Cbx2 axis. Cell Rep 2022; 39:110587. [PMID: 35385744 PMCID: PMC9029260 DOI: 10.1016/j.celrep.2022.110587] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 12/13/2021] [Accepted: 03/08/2022] [Indexed: 01/06/2023] Open
Abstract
Hematopoiesis changes over life to meet the demands of maturation and aging. Here, we find that the definitive hematopoietic stem and progenitor cell (HSPC) compartment is remodeled from gestation into adulthood, a process regulated by the heterochronic Lin28b/let-7 axis. Native fetal and neonatal HSPCs distribute with a pro-lymphoid/erythroid bias with a shift toward myeloid output in adulthood. By mining transcriptomic data comparing juvenile and adult HSPCs and reconstructing coordinately activated gene regulatory networks, we uncover the Polycomb repressor complex 1 (PRC1) component Cbx2 as an effector of Lin28b/let-7's control of hematopoietic maturation. We find that juvenile Cbx2-/- hematopoietic tissues show impairment of B-lymphopoiesis, a precocious adult-like myeloid bias, and that Cbx2/PRC1 regulates developmental timing of expression of key hematopoietic transcription factors. These findings define a mechanism of regulation of HSPC output via chromatin modification as a function of age with potential impact on age-biased pediatric and adult blood disorders.
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Affiliation(s)
- Dahai Wang
- Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Mayuri Tanaka-Yano
- Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Eleanor Meader
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Melissa A Kinney
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Vivian Morris
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA
| | - Edroaldo Lummertz da Rocha
- Department of Microbiology, Immunology, and Parasitology, Federal University of Santa Catarina, Florianopolis 88040-900, Brazil
| | - Nan Liu
- Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Tianxin Liu
- Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Qian Zhu
- Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Stuart H Orkin
- Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA
| | - Trista E North
- Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - George Q Daley
- Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - R Grant Rowe
- Department of Hematology/Oncology, Boston Children's Hospital, Boston, MA 02115, USA; Stem Cell Program, Boston Children's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02115, USA; Stem Cell Transplantation Program, Boston Children's Hospital, Boston, MA 02115, USA.
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4
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Mayer IM, Hoelbl-Kovacic A, Sexl V, Doma E. Isolation, Maintenance and Expansion of Adult Hematopoietic Stem/Progenitor Cells and Leukemic Stem Cells. Cancers (Basel) 2022; 14:cancers14071723. [PMID: 35406494 PMCID: PMC8996967 DOI: 10.3390/cancers14071723] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Transplantation of adult hematopoietic stem cells is an important therapeutic tool to help patients suffering from diverse hematological disorders. All types of blood cells can develop from a single hematopoietic stem cell underlining their enormous potential. Intense efforts are ongoing to generate “engraftable” human hematopoietic stem cells to treat hematopoietic diseases and to understand the molecular machinery driving them. Leukemic stem cells represent a low frequency subpopulation of leukemia cells that possess stem cell properties. They can instigate, maintain, and serially propagate leukemia in vivo, while they retain the capacity to differentiate into committed progenitors. Leukemic stem cells are unaffected by many therapeutic strategies and represent the major cause of relapse. We here describe all methods to maintain and expand murine and human hematopoietic cells in culture and describe their specific advantages. These methods are also employed to understand the biology of leukemic stem cells and to identify novel therapeutic strategies. Abstract Hematopoietic stem cells (HSCs) are rare, self-renewing cells that perch on top of the hematopoietic tree. The HSCs ensure the constant supply of mature blood cells in a tightly regulated process producing peripheral blood cells. Intense efforts are ongoing to optimize HSC engraftment as therapeutic strategy to treat patients suffering from hematopoietic diseases. Preclinical research paves the way by developing methods to maintain, manipulate and expand HSCs ex vivo to understand their regulation and molecular make-up. The generation of a sufficient number of transplantable HSCs is the Holy Grail for clinical therapy. Leukemia stem cells (LSCs) are characterized by their acquired stem cell characteristics and are responsible for disease initiation, progression, and relapse. We summarize efforts, that have been undertaken to increase the number of long-term (LT)-HSCs and to prevent differentiation towards committed progenitors in ex vivo culture. We provide an overview and compare methods currently available to isolate, maintain and enrich HSC subsets, progenitors and LSCs and discuss their individual advantages and drawbacks.
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5
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Chen TC, Chang SW. Repeated cell sorting ensures the homogeneity of ocular cell populations expressing a transgenic protein. PLoS One 2022; 17:e0265183. [PMID: 35333876 PMCID: PMC8956163 DOI: 10.1371/journal.pone.0265183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 02/25/2022] [Indexed: 11/19/2022] Open
Abstract
Transgenic proteins can be routinely expressed in various mammalian cell types via different transgenic systems, but the efficiency of transgene expression is constrained by the complex interplay among factors such as the temporal consistency of expression and compatibility with specific cell types, including ocular cells. Here, we report a more efficient way to express an enhanced green fluorescent protein (EGFP) in human corneal fibroblasts, corneal epithelial cells, and conjunctival epithelial cells through a lentiviral expression system. The relative transducing unit criterion for EGFP-expressing pseudovirions was first determined in HEK-293T cells. Homogeneous populations of EGFP-positive and EGFP-negative cells could be isolated by cell sorting. The half-maximal inhibitory concentration (IC50) value for puromycin was calculated according to viability curves for each cell type. The results revealed that cell types differed with respect to EGFP expression efficiency after transduction with the same amount of EGFP-encoding pseudovirions. Using a cell sorter, the homogeneity of EGFP-positive cells reached >95%. In the initial sorting stage, however, the efficiency of EGFP expression in the sorted cells was noticeably reduced after two rounds of sequential culture, but repeated sorting for up to four rounds yielded homogeneous EGFP-positive human corneal fibroblasts that could be maintained in continuous culture in vitro. The sorted EGFP-positive cells retained their proper morphology and cell type-specific protein expression patterns. Puromycin resistance was found to depend on cell type, indicating that the IC50 for puromycin must be determined for each cell type to ensure the isolation of homogeneous EGFP-positive cells. Taken together, repeated cell sorting is an efficient means of obtaining homogeneous populations of ocular cells expressing a transgenic protein during continuous culture without the potential confounding effects of antibiotics.
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Affiliation(s)
- Tsan-Chi Chen
- Department of Ophthalmology, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Shu-Wen Chang
- Department of Ophthalmology, Far Eastern Memorial Hospital, New Taipei City, Taiwan
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- * E-mail:
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6
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Morgan R, Hunter K, Pandha HS. Downstream of the HOX genes: explaining conflicting tumour suppressor and oncogenic functions in cancer. Int J Cancer 2022; 150:1919-1932. [PMID: 35080776 PMCID: PMC9304284 DOI: 10.1002/ijc.33949] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/24/2021] [Accepted: 01/07/2022] [Indexed: 11/07/2022]
Abstract
The HOX genes are a highly conserved group of transcription factors that have key roles in early development, but which are also highly expressed in most cancers. Many studies have found strong associative relationships between the expression of individual HOX genes in tumours and clinical parameters including survival. For the majority of HOX genes, high tumour expression levels seem to be associated with a worse outcome for patients, and in some cases this has been shown to result from the activation of pro-oncogenic genes and pathways. However, there are also many studies that indicate a tumour suppressor role for some HOX genes, sometimes with conclusions that contradict earlier work. In this review, we have attempted to clarify the role of HOX genes in cancer by focusing on their downstream targets as identified in studies that provide experimental evidence for their activation or repression. On this basis, the majority of HOX genes would appear to have a pro-oncogenic function, with the notable exception of HOXD10, which acts exclusively as a tumour suppressor. HOX proteins regulate a wide range of target genes involved in metastasis, cell death, proliferation, and angiogenesis, and activate key cell signalling pathways. Furthermore, for some functionally related targets, this regulation is achieved by a relatively small subgroup of HOX genes.
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Affiliation(s)
- Richard Morgan
- School of Biomedical SciencesUniversity of West LondonLondonUK
| | - Keith Hunter
- Unit of Oral and Maxillofacial Pathology, School of Clinical DentistryUniversity of SheffieldSheffieldUK
| | - Hardev S. Pandha
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
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7
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Casamassimi A, Rienzo M, Di Zazzo E, Sorrentino A, Fiore D, Proto MC, Moncharmont B, Gazzerro P, Bifulco M, Abbondanza C. Multifaceted Role of PRDM Proteins in Human Cancer. Int J Mol Sci 2020; 21:ijms21072648. [PMID: 32290321 PMCID: PMC7177584 DOI: 10.3390/ijms21072648] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/29/2020] [Accepted: 04/08/2020] [Indexed: 12/15/2022] Open
Abstract
The PR/SET domain family (PRDM) comprise a family of genes whose protein products share a conserved N-terminal PR [PRDI-BF1 (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1)] homologous domain structurally and functionally similar to the catalytic SET [Su(var)3-9, enhancer-of-zeste and trithorax] domain of histone methyltransferases (HMTs). These genes are involved in epigenetic regulation of gene expression through their intrinsic HMTase activity or via interactions with other chromatin modifying enzymes. In this way they control a broad spectrum of biological processes, including proliferation and differentiation control, cell cycle progression, and maintenance of immune cell homeostasis. In cancer, tumor-specific dysfunctions of PRDM genes alter their expression by genetic and/or epigenetic modifications. A common characteristic of most PRDM genes is to encode for two main molecular variants with or without the PR domain. They are generated by either alternative splicing or alternative use of different promoters and play opposite roles, particularly in cancer where their imbalance can be often observed. In this scenario, PRDM proteins are involved in cancer onset, invasion, and metastasis and their altered expression is related to poor prognosis and clinical outcome. These functions strongly suggest their potential use in cancer management as diagnostic or prognostic tools and as new targets of therapeutic intervention.
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Affiliation(s)
- Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
| | - Monica Rienzo
- Department of Environmental, Biological, and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, 81100 Caserta, Italy;
| | - Erika Di Zazzo
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Anna Sorrentino
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
| | - Donatella Fiore
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maria Chiara Proto
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Bruno Moncharmont
- Department of Medicine and Health Sciences “V. Tiberio”, University of Molise, 86100 Campobasso, Italy;
| | - Patrizia Gazzerro
- Department of Pharmacy, University of Salerno, 84084 Fisciano (SA), Italy; (D.F.); (M.C.P.); (P.G.)
| | - Maurizio Bifulco
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples “Federico II”, 80131 Naples, Italy;
| | - Ciro Abbondanza
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (E.D.Z.); (A.S.)
- Correspondence: (A.C.); (C.A.); Tel.: +39-081-566-7579 (A.C.); +39-081-566-7568 (C.A.)
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8
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Synergy of NUP98-HOXA10 Fusion Gene and NrasG12D Mutation Preserves the Stemness of Hematopoietic Stem Cells on Culture Condition. Cells 2019; 8:cells8090951. [PMID: 31443434 PMCID: PMC6770072 DOI: 10.3390/cells8090951] [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: 07/10/2019] [Revised: 08/08/2019] [Accepted: 08/16/2019] [Indexed: 12/21/2022] Open
Abstract
Natural hematopoietic stem cells (HSC) are susceptible and tend to lose stemness, differentiate, or die on culture condition in vitro, which adds technical challenge for maintaining bona fide HSC-like cells, if ever generated, in protocol screening from pluripotent stem cells. It remains largely unknown whether gene-editing of endogenous genes can genetically empower HSC to endure the culture stress and preserve stemness. In this study, we revealed that both NUP98-HOXA10HD fusion and endogenous Nras mutation modifications (NrasG12D) promoted the engraftment competitiveness of HSC. Furthermore, the synergy of these two genetic modifications endowed HSC with super competitiveness in vivo. Strikingly, single NAV-HSC successfully maintained its stemness and showed robust multi-lineage engraftments after undergoing the in vitro culture. Mechanistically, NUP98-HOXA10HD fusion and NrasG12D mutation distinctly altered multiple pathways involving the cell cycle, cell division, and DNA replication, and distinctly regulated stemness-related genes including Hoxa9, Prdm16, Hoxb4, Trim27, and Smarcc1 in the context of HSC. Thus, we develop a super-sensitive transgenic model reporting the existence of HSC at the single cell level on culture condition, which could be beneficial for protocol screening of bona fide HSC regeneration from pluripotent stem cells in vitro.
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9
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Reprogramming mechanisms influence the maturation of hematopoietic progenitors from human pluripotent stem cells. Cell Death Dis 2018; 9:1090. [PMID: 30356076 PMCID: PMC6200746 DOI: 10.1038/s41419-018-1124-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 08/26/2018] [Accepted: 10/01/2018] [Indexed: 12/28/2022]
Abstract
Somatic cell nuclear transfer (SCNT) or the forced expression of transcription factors can be used to generate autologous pluripotent stem cells (PSCs). Although transcriptomic and epigenomic comparisons of isogenic human NT-embryonic stem cells (NT-ESCs) and induced PSCs (iPSCs) in the undifferentiated state have been reported, their functional similarities and differentiation potentials have not been fully elucidated. Our study showed that NT-ESCs and iPSCs derived from the same donors generally displayed similar in vitro commitment capacity toward three germ layer lineages as well as proliferative activity and clonogenic capacity. However, the maturation capacity of NT-ESC-derived hematopoietic progenitors was significantly greater than the corresponding capacity of isogenic iPSC-derived progenitors. Additionally, donor-dependent variations in hematopoietic specification and commitment capacity were observed. Transcriptome and methylome analyses in undifferentiated NT-ESCs and iPSCs revealed a set of genes that may influence variations in hematopoietic commitment and maturation between PSC lines derived using different reprogramming methods. Here, we suggest that genetically identical iPSCs and NT-ESCs could be functionally unequal due to differential transcription and methylation levels acquired during reprogramming. Our proof-of-concept study indicates that reprogramming mechanisms and genetic background could contribute to diverse functionalities between PSCs.
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10
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Ren S, Gaykalova D, Wang J, Guo T, Danilova L, Favorov A, Fertig E, Bishop J, Khan Z, Flam E, Wysocki PT, DeJong P, Ando M, Liu C, Sakai A, Fukusumi T, Haft S, Sadat S, Califano JA. Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma. Int J Cancer 2018; 143:2425-2436. [PMID: 30070359 DOI: 10.1002/ijc.31778] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 05/30/2018] [Accepted: 07/04/2018] [Indexed: 12/15/2022]
Abstract
Human papillomavirus (HPV)-related oropharyngeal squamous cell carcinoma (OPSCC) exhibits a different composition of epigenetic alterations. In this study, we identified differentially methylated regions (DMRs) with potential utility in screening for HPV-positive OPSCC. Genome wide DNA methylation was measured using methyl-CpG binding domain protein-enriched genome sequencing (MBD-seq) in 50 HPV-positive OPSCC tissues and 25 normal tissues. Fifty-one DMRs were defined with maximal methylation specificity to cancer samples. The Cancer Genome Atlas (TCGA) methylation array data was used to evaluate the performance of the proposed candidates. Supervised hierarchical clustering of 51 DMRs found that HPV-positive OPSCC had significantly higher DNA methylation levels compared to normal samples, and non-HPV-related head and neck squamous cell carcinoma (HNSCC). The methylation levels of all top 20 DNA methylation biomarkers in HPV-positive OPSCC were significantly higher than those in normal samples. Further confirmation using quantitative methylation specific PCR (QMSP) in an independent set of 24 HPV-related OPSCCs and 22 controls showed that 16 of the 20 candidates had significant higher methylation levels in HPV-positive OPSCC samples compared with controls. One candidate, OR6S1, had a sensitivity of 100%, while 17 candidates (KCNA3, EMBP1, CCDC181, DPP4, ITGA4, BEND4, ELMO1, SFMBT2, C1QL3, MIR129-2, NID2, HOXB4, ZNF439, ZNF93, VSTM2B, ZNF137P and ZNF773) had specificities of 100%. The prediction accuracy of the 20 candidates rang from 56.2% to 99.8% by receiver operating characteristic analysis. We have defined 20 highly specific DMRs in HPV-related OPSCC, which can potentially be applied to molecular-based detection tests and improve disease management.
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Affiliation(s)
- Shuling Ren
- Moores Cancer Center, University of California San Diego, La Jolla, CA.,Department of Otolaryngology - Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Daria Gaykalova
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Jennifer Wang
- Department of Head and Neck Surgery, MD Anderson Cancer Center, Houston, TX
| | - Theresa Guo
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Ludmila Danilova
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russia
| | - Alexander Favorov
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD.,Laboratory of Systems Biology and Computational Genetics, Vavilov Institute of General Genetics, RAS, Moscow, Russia
| | - Elana Fertig
- Division of Oncology Biostatistics, Department of Oncology, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Justin Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Zubair Khan
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Emily Flam
- Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD
| | - Piotr T Wysocki
- Laboratory of Human Cancer Genetics, Center of New Technologies, University of Warsaw, Warsaw, Poland.,The Maria Sklodowska-Curie Institute Oncology Center, Warsaw, Poland
| | - Peter DeJong
- Moores Cancer Center, University of California San Diego, La Jolla, CA.,College of Human Medicine, Michigan State University, East Lansing, MI
| | - Mizuo Ando
- Moores Cancer Center, University of California San Diego, La Jolla, CA.,Department of Otolaryngology-Head and Neck Surgery, Tokyo University, Tokyo, Japan
| | - Chao Liu
- Moores Cancer Center, University of California San Diego, La Jolla, CA.,Department of Otolaryngology - Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Akihiro Sakai
- Moores Cancer Center, University of California San Diego, La Jolla, CA.,Department of Otolaryngology, Center of Head and Neck Surgery, Tokai University, Isehara, Japan
| | - Takahito Fukusumi
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Sunny Haft
- Moores Cancer Center, University of California San Diego, La Jolla, CA.,Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, CA
| | - Sayed Sadat
- Moores Cancer Center, University of California San Diego, La Jolla, CA
| | - Joseph A Califano
- Moores Cancer Center, University of California San Diego, La Jolla, CA.,Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins Medical Institutions, Baltimore, MD.,Division of Otolaryngology - Head and Neck Surgery, Department of Surgery, University of California San Diego, La Jolla, CA
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11
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Corrigan DJ, Luchsinger LL, Justino de Almeida M, Williams LJ, Strikoudis A, Snoeck HW. PRDM16 isoforms differentially regulate normal and leukemic hematopoiesis and inflammatory gene signature. J Clin Invest 2018; 128:3250-3264. [PMID: 29878897 DOI: 10.1172/jci99862] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/31/2018] [Indexed: 12/13/2022] Open
Abstract
PRDM16 is a transcriptional coregulator involved in translocations in acute myeloblastic leukemia (AML), myelodysplastic syndromes, and T acute lymphoblastic leukemia that is highly expressed in and required for the maintenance of hematopoietic stem cells (HSCs), and can be aberrantly expressed in AML. Prdm16 is expressed as full-length (fPrdm16) and short (sPrdm16) isoforms, the latter lacking the N-terminal PR domain. The role of both isoforms in normal and malignant hematopoiesis is unclear. We show here that fPrdm16 was critical for HSC maintenance, induced multiple genes involved in GTPase signaling, and repressed inflammation, while sPrdm16 supported B cell development biased toward marginal zone B cells and induced an inflammatory signature. In a mouse model of human MLL-AF9 leukemia, fPrdm16 extended latency, while sPrdm16 shortened latency and induced a strong inflammatory signature, including several cytokines and chemokines that are associated with myelodysplasia and with a worse prognosis in human AML. Finally, in human NPM1-mutant and in MLL-translocated AML, high expression of PRDM16, which negatively impacts outcome, was associated with inflammatory gene expression, thus corroborating the mouse data. Our observations demonstrate distinct roles for Prdm16 isoforms in normal HSCs and AML, and identify sPrdm16 as one of the drivers of prognostically adverse inflammation in leukemia.
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Affiliation(s)
- David J Corrigan
- Columbia Center of Human Development.,Department of Microbiology and Immunology
| | | | | | - Linda J Williams
- Columbia Center of Human Development.,Department of Medicine, and
| | | | - Hans-Willem Snoeck
- Columbia Center of Human Development.,Department of Microbiology and Immunology.,Department of Medicine, and.,Columbia Center for Translational Immunology, Columbia University Medical Center, New York, New York, USA
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12
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The IRX1/HOXA connection: insights into a novel t(4;11)- specific cancer mechanism. Oncotarget 2018; 7:35341-52. [PMID: 27175594 PMCID: PMC5085233 DOI: 10.18632/oncotarget.9241] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/16/2016] [Indexed: 01/01/2023] Open
Abstract
One hallmark of MLL-r leukemia is the highly specific gene expression signature indicative for commonly deregulated target genes. An usual read-out for this transcriptional deregulation is the HOXA gene cluster, where upregulated HOXA genes are detected in MLL-r AML and ALL patients. In case of t(4;11) leukemia, this simple picture becomes challenged, because these patients separate into HOXAhi- and HOXAlo-patients. HOXAlo-patients showed a reduced HOXA gene transcription, but instead overexpressed the homeobox gene IRX1. This transcriptional pattern was associated with a higher relapse rate and worse outcome. Here, we demonstrate that IRX1 binds to the MLL-AF4 complex at target gene promotors and counteract its promotor activating function. In addition, IRX1 induces transcription of HOXB4 and EGR family members. HOXB4 is usually a downstream target of c-KIT, WNT and TPO signaling pathways and necessary for maintaining and expanding in hematopoietic stem cells. EGR proteins control a p21-dependent quiescence program for hematopoietic stem cells. Both IRX1-dependend actions may help t(4;11) leukemia cells to establish a stem cell compartment. We also demonstrate that HDACi administration is functionally interfering with IRX1 and MLL-AF4, a finding which could help to improve new treatment options for t(4;11) patients.
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Ng Y, Tan SX, Chia SY, Tan HYA, Gun SY, Sun L, Hong W, Han W. HOXC10 suppresses browning of white adipose tissues. Exp Mol Med 2017; 49:e292. [PMID: 28186086 PMCID: PMC5336557 DOI: 10.1038/emm.2016.144] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 09/16/2016] [Accepted: 09/22/2016] [Indexed: 12/25/2022] Open
Abstract
Given that increased thermogenesis in white adipose tissue, also known as browning, promotes energy expenditure, significant efforts have been invested to determine the molecular factors involved in this process. Here we show that HOXC10, a homeobox domain-containing transcription factor expressed in subcutaneous white adipose tissue, is a suppressor of genes involved in browning white adipose tissue. Ectopic expression of HOXC10 in adipocytes suppresses brown fat genes, whereas the depletion of HOXC10 in adipocytes and myoblasts increases the expression of brown fat genes. The protein level of HOXC10 inversely correlates with brown fat genes in subcutaneous white adipose tissue of cold-exposed mice. Expression of HOXC10 in mice suppresses cold-induced browning in subcutaneous white adipose tissue and abolishes the beneficial effect of cold exposure on glucose clearance. HOXC10 exerts its effect, at least in part, by suppressing PRDM16 expression. The results support that HOXC10 is a key negative regulator of the process of browning in white adipose tissue.
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Affiliation(s)
- Yvonne Ng
- Metabolism in Human Diseases Unit, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Shi-Xiong Tan
- Metabolism in Human Diseases Unit, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sook Yoong Chia
- Cardiovascular and Metabolic Disorder Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Hwee Yim Angeline Tan
- Laboratory of Metabolic Medicine, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sin Yee Gun
- Laboratory of Metabolic Medicine, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lei Sun
- Metabolism in Human Diseases Unit, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Cardiovascular and Metabolic Disorder Program, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Wanjin Hong
- Metabolism in Human Diseases Unit, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Weiping Han
- Metabolism in Human Diseases Unit, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Laboratory of Metabolic Medicine, Singapore Bioimaging Consortium, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
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LECT2 drives haematopoietic stem cell expansion and mobilization via regulating the macrophages and osteolineage cells. Nat Commun 2016; 7:12719. [PMID: 27596364 PMCID: PMC5025878 DOI: 10.1038/ncomms12719] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/26/2016] [Indexed: 12/12/2022] Open
Abstract
Haematopoietic stem cells (HSCs) can differentiate into cells of all lineages in the blood. However, the mechanisms by which cytokines in the blood affect HSC homeostasis remain largely unknown. Here we show that leukocyte cell-derived chemotaxin 2 (LECT2), a multifunctional cytokine, induces HSC expansion and mobilization. Recombinant LECT2 administration results in HSC expansion in the bone marrow and mobilization to the blood via CD209a. The effect of LECT2 on HSCs is reduced after specific depletion of macrophages or reduction of osteolineage cells. LECT2 treatment reduces the tumour necrosis factor (TNF) expression in macrophages and osteolineage cells. In TNF knockout mice, the effect of LECT2 on HSCs is reduced. Moreover, LECT2 induces HSC mobilization in irradiated mice, while granulocyte colony-stimulating factor does not. Our results illustrate that LECT2 is an extramedullar cytokine that contributes to HSC homeostasis and may be useful to induce HSC mobilization.
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PRDM16 Suppresses MLL1r Leukemia via Intrinsic Histone Methyltransferase Activity. Mol Cell 2016; 62:222-236. [PMID: 27151440 DOI: 10.1016/j.molcel.2016.03.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 12/10/2015] [Accepted: 03/07/2016] [Indexed: 12/22/2022]
Abstract
PRDM16 is a transcription co-factor that plays critical roles in development of brown adipose tissue, as well as maintenance of adult hematopoietic and neural stem cells. Here we report that PRDM16 is a histone H3K4 methyltransferase on chromatin. Mutation in the N-terminal PR domain of PRDM16 abolishes the intrinsic enzymatic activity of PRDM16. We show that the methyltransferase activity of PRDM16 is required for specific suppression of MLL fusion protein-induced leukemogenesis both in vitro and in vivo. Mechanistic studies show that PRDM16 directly activates the SNAG family transcription factor Gfi1b, which in turn downregulates the HOXA gene cluster. Knockdown Gfi1b represses PRDM16-mediated tumor suppression, while Gfi1b overexpression mimics PRDM16 overexpression. In further support of the tumor suppressor function of PRDM16, silencing PRDM16 by DNA methylation is concomitant with MLL-AF9-induced leukemic transformation. Taken together, our study reveals a previously uncharacterized function of PRDM16 that depends on its PR domain activity.
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Evaluating the Safety of Retroviral Vectors Based on Insertional Oncogene Activation and Blocked Differentiation in Cultured Thymocytes. Mol Ther 2016; 24:1090-1099. [PMID: 26957223 PMCID: PMC4923324 DOI: 10.1038/mt.2016.55] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 02/24/2016] [Indexed: 12/20/2022] Open
Abstract
Insertional oncogenesis due to retroviral (RV) vector integration has caused recurrent leukemia in multiple gene therapy trials, predominantly due to vector integration effects at the LMO2 locus. While currently available preclinical safety models have been used for evaluating vector safety, none have predicted or reproduced the recurrent LMO2 integrations seen in previous X-linked severe combined immunodeficiency (X-SCID) and Wiskott–Aldrich clinical gene therapy trials. We now describe a new assay for assessing vector safety that recapitulates naturally occurring insertions into Lmo2 and other T-cell proto-oncogenes leading to a preleukemic developmental arrest in primary murine thymocytes cultured in vitro. This assay was used to compare the relative oncogenic potential of a variety of gamma-RV and lentiviral vectors and to assess the risk conferred by various transcriptional elements contained in these genomes. Gamma-RV vectors that contained full viral long-terminal repeats were most prone to causing double negative 2 (DN2) arrest and led to repeated cases of Lmo2 pathway activation, while lentiviral vectors containing these same elements were significantly less prone to activate proto-oncogenes or cause DN2 arrest. This work provides a new preclinical assay that is especially relevant for assessing safety in SCID disorders and provides a new tool for designing safer RV vectors.
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Xin C, Zhao C, Yin X, Wu S, Su Z. Bioinformatics analysis of molecular mechanism of the expansion of hematopoietic stem cell transduced by HOXB4/HOXC4. Hematology 2016; 21:462-9. [PMID: 26923762 DOI: 10.1080/10245332.2015.1101978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Affiliation(s)
- Chunlei Xin
- Department of Hematology, The Affiliated Hospital of Qingdao University, No. 16, Jiangsu Road, Qingdao City, Shandong Province, 266003, P.R. China
- Department of Hematology, Jining No. 1 People's Hospital, No. 6, Jiankang Road, Jining City, Shandong Province, 272011, P.R. China
| | - Chunting Zhao
- Department of Hematology, The Affiliated Hospital of Qingdao University, No. 16, Jiangsu Road, Qingdao City, Shandong Province, 266003, P.R. China
| | - Xiangcong Yin
- Department of Hematology, The Affiliated Hospital of Qingdao University, No. 16, Jiangsu Road, Qingdao City, Shandong Province, 266003, P.R. China
| | - Shaoling Wu
- Department of Hematology, The Affiliated Hospital of Qingdao University, No. 16, Jiangsu Road, Qingdao City, Shandong Province, 266003, P.R. China
| | - Zhan Su
- Department of Hematology, The Affiliated Hospital of Qingdao University, No. 16, Jiangsu Road, Qingdao City, Shandong Province, 266003, P.R. China
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Chi J, Cohen P. The Multifaceted Roles of PRDM16: Adipose Biology and Beyond. Trends Endocrinol Metab 2016; 27:11-23. [PMID: 26688472 DOI: 10.1016/j.tem.2015.11.005] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/07/2023]
Abstract
The PRDM [PRDI-BFI (positive regulatory domain I-binding factor 1) and RIZ1 (retinoblastoma protein-interacting zinc finger gene 1) homologous domain containing] protein family is involved in a spectrum of biological processes including cell fate determination and development. These proteins regulate transcription through intrinsic chromatin-modifying activity or by complexing with histone-modifying or other nuclear proteins. Studies have indicated crucial roles for PRDM16 in the determination and function of brown and beige fat as well as in hematopoiesis and cardiac development, highlighting the importance of PRDM16 in developmental processes in different tissues. More recently, PRDM16 mutations were also identified in humans. The substantial progress in understanding the mechanism underlying the action of PRDM16 in adipose biology may have relevance to other PRDM family members, and this new knowledge has the potential to be exploited for therapeutic benefit.
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Affiliation(s)
- Jingyi Chi
- The Rockefeller University, Laboratory of Molecular Metabolism, New York, NY 10065, USA
| | - Paul Cohen
- The Rockefeller University, Laboratory of Molecular Metabolism, New York, NY 10065, USA.
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