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Pre-Clinical Evaluation of the Hypomethylating Agent Decitabine for the Treatment of T-Cell Lymphoblastic Lymphoma. Cancers (Basel) 2023; 15:cancers15030647. [PMID: 36765607 PMCID: PMC9913791 DOI: 10.3390/cancers15030647] [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: 11/30/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
T-cell lymphoblastic lymphoma (T-LBL) is a rare and aggressive lymphatic cancer, often diagnosed at a young age. Patients are treated with intensive chemotherapy, potentially followed by a hematopoietic stem cell transplantation. Although prognosis of T-LBL has improved with intensified treatment protocols, they are associated with side effects and 10-20% of patients still die from relapsed or refractory disease. Given this, the search toward less toxic anti-lymphoma therapies is ongoing. Here, we targeted the recently described DNA hypermethylated profile in T-LBL with the DNA hypomethylating agent decitabine. We evaluated the anti-lymphoma properties and downstream effects of decitabine, using patient derived xenograft (PDX) models. Decitabine treatment resulted in prolonged lymphoma-free survival in all T-LBL PDX models, which was associated with downregulation of the oncogenic MYC pathway. However, some PDX models showed more benefit of decitabine treatment compared to others. In more sensitive models, differentially methylated CpG regions resulted in more differentially expressed genes in open chromatin regions. This resulted in stronger downregulation of cell cycle genes and upregulation of immune response activating transcripts. Finally, we suggest a gene signature for high decitabine sensitivity in T-LBL. Altogether, we here delivered pre-clinical proof of the potential use of decitabine as a new therapeutic agent in T-LBL.
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Chen J, Huang W, Zhang H, Peng X, Yang J, Yang Y, Su J, Wang S, Zhou W. Quantitative proteomics on the cerebrospinal fluid of hydrocephalus in neonatal bacterial meningitis. Front Pediatr 2022; 10:972032. [PMID: 36052359 PMCID: PMC9424622 DOI: 10.3389/fped.2022.972032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
Objective Hydrocephalus in bacterial meningitis (BM) is a devastating infectious neurological disease and the proteins and pathways involved in its pathophysiology are not fully understood. Materials and methods Label-free quantitative (LFQ) proteomics analyses was used to identify differentially expressed proteins (DEPs) in cerebrospinal fluid (CSF) samples from infants with hydrocephalus and bacterial meningitis (HBM group, N = 8), infants with bacterial meningitis (BM group, N = 9); and healthy infants (N group, N = 11). Bioinformatics analysis was subsequently performed to investigate Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enriched signaling pathways of these DEPs. Six proteins (AZU1, COX4I1, EDF1, KRT31, MMP12, and PRG2) were selected for further validation via enzyme-linked immunosorbent assay (ELISA). Results Compared with BM group and N group, HBM group had a higher whole CSF protein level (5.6 ± 2.7 vs. 1.7 ± 1.0 vs. 1.2 ± 0.5 g/l) and lower whole CSF glucose level (0.8 ± 0.6 vs. 1.8 ± 0.7 vs. 3.3 ± 0.8 mmol/l) (both P < 0.05). Over 300 DEPs were differentially expressed in HBM group compared with BM group and BM compared with N group, of which 78% were common to both. Cluster analysis indicated that the levels of 226 proteins were increased in BM group compared with N group and were decreased in HBM group compared with BM group. Bioinformatics analysis indicated the involvement of the cell adhesion, immune response and extracellular exosome signaling were significantly enriched in HBM compared with BM group and BM compared with N group. 267 DEPs were identified between HBM group with N group, KEGG analysis indicated that DEPs mainly involved in filament cytoskeleton and immune response. The ELISA results further verified that the expression levels of AZU1 were significantly different from among three groups (both P < 0.05). Conclusion This is the first reported characterization of quantitative proteomics from the CSF of infants with HBM. Our study also demonstrated that AZU1 could be a potential biomarker for the diagnosis of hydrocephalus in bacterial meningitis.
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Affiliation(s)
- Juncao Chen
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Weiben Huang
- Department of Neonatology, The Fifth Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Hong Zhang
- Department of Neonatology, Dali Autonomous Prefecture Children’s Hospital, Dali, China
| | - Xiangwen Peng
- Department of Key Laboratory, Changsha Hospital for Maternal and Child Health Care, Changsha, China
| | - Jun Yang
- Advanced Institute of Natural Sciences, Beijing Normal University at Zhuhai, Zhuhai, China
| | - Yong Yang
- Department of Neonatology, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Jinzhen Su
- Department of Neonatology, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Siyao Wang
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
| | - Wei Zhou
- Department of Neonatology, Guangzhou Women and Children’s Medical Centre, Guangzhou Medical University, Guangzhou, China
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Schwarz A, Roeder I, Seifert M. Comparative Gene Expression Analysis Reveals Similarities and Differences of Chronic Myeloid Leukemia Phases. Cancers (Basel) 2022; 14:cancers14010256. [PMID: 35008420 PMCID: PMC8750437 DOI: 10.3390/cancers14010256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/25/2022] Open
Abstract
Chronic myeloid leukemia (CML) is a slowly progressing blood cancer that primarily affects elderly people. Without successful treatment, CML progressively develops from the chronic phase through the accelerated phase to the blast crisis, and ultimately to death. Nowadays, the availability of targeted tyrosine kinase inhibitor (TKI) therapies has led to long-term disease control for the vast majority of patients. Nevertheless, there are still patients that do not respond well enough to TKI therapies and available targeted therapies are also less efficient for patients in accelerated phase or blast crises. Thus, a more detailed characterization of molecular alterations that distinguish the different CML phases is still very important. We performed an in-depth bioinformatics analysis of publicly available gene expression profiles of the three CML phases. Pairwise comparisons revealed many differentially expressed genes that formed a characteristic gene expression signature, which clearly distinguished the three CML phases. Signaling pathway expression patterns were very similar between the three phases but differed strongly in the number of affected genes, which increased with the phase. Still, significant alterations of MAPK, VEGF, PI3K-Akt, adherens junction and cytokine receptor interaction signaling distinguished specific phases. Our study also suggests that one can consider the phase-wise CML development as a three rather than a two-step process. This is in accordance with the phase-specific expression behavior of 24 potential major regulators that we predicted by a network-based approach. Several of these genes are known to be involved in the accumulation of additional mutations, alterations of immune responses, deregulation of signaling pathways or may have an impact on treatment response and survival. Importantly, some of these genes have already been reported in relation to CML (e.g., AURKB, AZU1, HLA-B, HLA-DMB, PF4) and others have been found to play important roles in different leukemias (e.g., CDCA3, RPL18A, PRG3, TLX3). In addition, increased expression of BCL2 in the accelerated and blast phase indicates that venetoclax could be a potential treatment option. Moreover, a characteristic signaling pathway signature with increased expression of cytokine and ECM receptor interaction pathway genes distinguished imatinib-resistant patients from each individual CML phase. Overall, our comparative analysis contributes to an in-depth molecular characterization of similarities and differences of the CML phases and provides hints for the identification of patients that may not profit from an imatinib therapy, which could support the development of additional treatment strategies.
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Affiliation(s)
- Annemarie Schwarz
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
| | - Ingo Roeder
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany: German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany; Helmholtz-Zentrum Dresden—Rossendorf (HZDR), D-01328 Dresden, Germany
| | - Michael Seifert
- Institute for Medical Informatics and Biometry (IMB), Carl Gustav Carus Faculty of Medicine, Technische Universität Dresden, D-01307 Dresden, Germany; (A.S.); (I.R.)
- National Center for Tumor Diseases (NCT), D-01307 Dresden, Germany: German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany; Faculty of Medicine and University Hospital Carl Gustav Carus, Technische Universität Dresden, D-01307 Dresden, Germany; Helmholtz-Zentrum Dresden—Rossendorf (HZDR), D-01328 Dresden, Germany
- Correspondence:
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Grassi S, Palumbo S, Mariotti V, Liberati D, Guerrini F, Ciabatti E, Salehzadeh S, Baratè C, Balducci S, Ricci F, Buda G, Iovino L, Mazziotta F, Ghio F, Ercolano G, Di Paolo A, Cecchettini A, Baldini C, Mattii L, Pellegrini S, Petrini M, Galimberti S. The WNT Pathway Is Relevant for the BCR-ABL1-Independent Resistance in Chronic Myeloid Leukemia. Front Oncol 2019; 9:532. [PMID: 31293972 PMCID: PMC6601352 DOI: 10.3389/fonc.2019.00532] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/31/2019] [Indexed: 01/08/2023] Open
Abstract
Notwithstanding the introduction of Tyrosine Kinase Inhibitors (TKIs) revolutionized the outcome of Chronic Myeloid Leukemia (CML), one third of patients still suspends treatment for failure response. Recent research demonstrated that several BCR/ABL1-independent mechanisms can sustain resistance, but the relationship between these mechanisms and the outcome has not yet been fully understood. This study was designed to evaluate in a “real-life” setting if a change of expression of several genes involved in the WNT/BETA-CATENIN, JAK-STAT, and POLYCOMB pathways might condition the outcome of CML patients receiving TKIs. Thus, the expression of 255 genes, related to the aforementioned pathways, was measured by quantitative PCR after 6 months of therapy and compared with levels observed at diagnosis in 11 CML patients, in order to find possible correlations with quality of response to treatment and event-free-survival (EFS). These results were then re-analyzed by the principal component method (PCA) for tempting to better cluster resistant cases. After 12 months of therapy, 6 patients achieved an optimal response and 5 were “resistant;” after application of both statistical methods, it was evident that in all pathways a significant overall up-regulation occurred, and that WNT was the pathway mostly responsible for the TKIs resistance. Indeed, 100% of patients with a “low” up-regulation of this pathway achieved an optimal response vs. 33% of those who showed a “high” gene over-expression (p = 0.016). Analogously, the 24-months EFS resulted significantly influenced by the degree of up-regulation of the WNT signaling: all patients with a “low” up-regulation were event-free vs. 33% of those who presented a “high” gene expression (p = 0.05). In particular, the PCA analysis confirmed the role of WNT pathway and showed that the most significantly up-regulated genes with negative prognostic value were DKK, WNT6, WISP1, and FZD8. In conclusion, our results sustain the need of a wide and multitasking approach in order to understand the resistance mechanisms in CML.
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Affiliation(s)
- Susanna Grassi
- Hematology Division, University of Pisa, Pisa, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Sara Palumbo
- Department of Surgical, Medical and Molecular Pathology and Critical Care, University of Pisa, Pisa, Italy
| | - Veronica Mariotti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | | | | | | | | | | | | | | | - Gabriele Buda
- Hematology Division, University of Pisa, Pisa, Italy
| | | | - Francesco Mazziotta
- Hematology Division, University of Pisa, Pisa, Italy.,Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | | | | | - Antonello Di Paolo
- Department of Clinical and Experimental Medicine, Pharmacology Division, University of Pisa, Pisa, Italy
| | | | - Chiara Baldini
- Department of Clinical and Experimental Medicine, Rheumatology Division, University of Pisa, Pisa, Italy
| | - Letizia Mattii
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Silvia Pellegrini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Mario Petrini
- Hematology Division, University of Pisa, Pisa, Italy
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Castillo D, Galvez JM, Herrera LJ, Rojas F, Valenzuela O, Caba O, Prados J, Rojas I. Leukemia multiclass assessment and classification from Microarray and RNA-seq technologies integration at gene expression level. PLoS One 2019; 14:e0212127. [PMID: 30753220 PMCID: PMC6372182 DOI: 10.1371/journal.pone.0212127] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/27/2019] [Indexed: 12/13/2022] Open
Abstract
In more recent years, a significant increase in the number of available biological experiments has taken place due to the widespread use of massive sequencing data. Furthermore, the continuous developments in the machine learning and in the high performance computing areas, are allowing a faster and more efficient analysis and processing of this type of data. However, biological information about a certain disease is normally widespread due to the use of different sequencing technologies and different manufacturers, in different experiments along the years around the world. Thus, nowadays it is of paramount importance to attain a correct integration of biologically-related data in order to achieve genuine benefits from them. For this purpose, this work presents an integration of multiple Microarray and RNA-seq platforms, which has led to the design of a multiclass study by collecting samples from the main four types of leukemia, quantified at gene expression. Subsequently, in order to find a set of differentially expressed genes with the highest discernment capability among different types of leukemia, an innovative parameter referred to as coverage is presented here. This parameter allows assessing the number of different pathologies that a certain gen is able to discern. It has been evaluated together with other widely known parameters under assessment of an ANOVA statistical test which corroborated its filtering power when the identified genes are subjected to a machine learning process at multiclass level. The optimal tuning of gene extraction evaluated parameters by means of this statistical test led to the selection of 42 highly relevant expressed genes. By the use of minimum-Redundancy Maximum-Relevance (mRMR) feature selection algorithm, these genes were reordered and assessed under the operation of four different classification techniques. Outstanding results were achieved by taking exclusively the first ten genes of the ranking into consideration. Finally, specific literature was consulted on this last subset of genes, revealing the occurrence of practically all of them with biological processes related to leukemia. At sight of these results, this study underlines the relevance of considering a new parameter which facilitates the identification of highly valid expressed genes for simultaneously discerning multiple types of leukemia.
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Affiliation(s)
- Daniel Castillo
- Department of Computer Architecture and Computer Technology, University of Granada, Granada, Spain
| | - Juan Manuel Galvez
- Department of Computer Architecture and Computer Technology, University of Granada, Granada, Spain
| | - Luis J. Herrera
- Department of Computer Architecture and Computer Technology, University of Granada, Granada, Spain
| | - Fernando Rojas
- Department of Computer Architecture and Computer Technology, University of Granada, Granada, Spain
| | - Olga Valenzuela
- Department of Applied Mathematics, University of Granada, Granada, Spain
| | - Octavio Caba
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
| | - Jose Prados
- Institute of Biopathology and Regenerative Medicine (IBIMER), Center of Biomedical Research (CIBM), University of Granada, Granada, Spain
| | - Ignacio Rojas
- Department of Computer Architecture and Computer Technology, University of Granada, Granada, Spain
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Avilés-Vázquez S, Chávez-González A, Hidalgo-Miranda A, Moreno-Lorenzana D, Arriaga-Pizano L, Sandoval-Esquivel MÁ, Ayala-Sánchez M, Aguilar R, Alfaro-Ruiz L, Mayani H. Global gene expression profiles of hematopoietic stem and progenitor cells from patients with chronic myeloid leukemia: the effect of in vitro culture with or without imatinib. Cancer Med 2017; 6:2942-2956. [PMID: 29030909 PMCID: PMC5727298 DOI: 10.1002/cam4.1187] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 08/11/2017] [Accepted: 08/14/2017] [Indexed: 01/04/2023] Open
Abstract
In this study, we determined the gene expression profiles of bone marrow‐derived cell fractions, obtained from normal subjects and Chronic Myeloid Leukemia (CML) patients, that were highly enriched for hematopoietic stem (HSCs) and progenitor (HPCs) cells. Our results indicate that the profiles of CML HSCs and HPCs were closer to that of normal progenitors, whereas normal HSCs showed the most different expression profile of all. We found that the expression profiles of HSCs and HPCs from CML marrow were closer to each other than those of HSCs and HPCs from normal marrow. The major biologic processes dysregulated in CML cells included DNA repair, cell cycle, chromosome condensation, cell adhesion, and the immune response. We also determined the genomic changes in both normal and CML progenitor cells under culture conditions, and found that several genes involved in cell cycle, steroid biosynthesis, and chromosome segregation were upregulated, whereas genes involved in transcription regulation and apoptosis were downregulated. Interestingly, these changes were the same, regardless of the addition of Imatinib (IM) to the culture. Finally, we identified three genes—PIEZO2, RXFP1, and MAMDC2‐ that are preferentially expressed by CML primitive cells and that encode for cell membrane proteins; thus, they could be used as biomarkers for CML stem cells.
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Affiliation(s)
- Sócrates Avilés-Vázquez
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Antonieta Chávez-González
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | | | - Dafne Moreno-Lorenzana
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Lourdes Arriaga-Pizano
- Immunochemistry Research Unit, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Miguel Á Sandoval-Esquivel
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Manuel Ayala-Sánchez
- Department of Hematology, La Raza Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
| | - Rafael Aguilar
- Department of Hip Surgery, Villa Coapa General Hospital, Mexican Institute for Social Security, Mexico City, Mexico
| | | | - Hector Mayani
- Oncology Research Unit, Oncology Hospital, National Medical Center, Mexican Institute for Social Security, Mexico City, Mexico
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Differential Expression of Circadian Genes in Leukemia and a Possible Role for Sirt1 in Restoring the Circadian Clock in Chronic Myeloid Leukemia. J Circadian Rhythms 2017; 15:3. [PMID: 30210557 PMCID: PMC5624060 DOI: 10.5334/jcr.147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Disregulation of genes making up the mammalian circadian clock has been associated with different forms of cancer. This study aimed to address how the circadian clock genes behave over the course of treatment for both the acute and chronic forms of leukemia and whether any could be used as potential biomarkers as a read-out for therapeutic efficacy. Expression profiling for both core and ancillary clock genes revealed that the majority of clock genes are down-regulated in acute myeloid leukemia patients, except for Cry2, which is up-regulated towards the end of treatment. A similar process was seen in acute lymphocytic leukemia patients; however, here, Cry2 expression came back up towards control levels upon treatment completion. In addition, all of the core clock genes were down-regulated in both chronic forms of leukemia (chronic myeloid leukemia and chronic lymphocytic leukemia), except for Cry2, which was not affected when the disease was diagnosed. Furthermore, the NAD(+) - dependent protein deacetylase Sirt1 has been proposed to have a dual role in both control of circadian clock circuitry and promotion of cell survival by inhibiting apoptotic pathways in cancer. We used a pharmacological-based approach to see whether Sirt1 played a role in regulating the circadian clock circuitry in both acute and chronic forms of leukemia. Our results suggest that interfering with Sirt1 leads to a partial restoration of BMAL1 oscillation in chronic myeloid leukemia patient samples. Furthermore, interfering with Sirt1 activity led to both the induction and repression of circadian clock genes in both acute and chronic forms of leukemia, which makes it a potential therapeutic target to either augment existing therapies for chronic leukemia or to act as a means of facilitating chronotherapy in order to maximize both the effectiveness of existing therapies and to minimize therapy-associated toxicity.
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