1
|
Rahmatallah Y, Glazko G. Improving data interpretability with new differential sample variance gene set tests. RESEARCH SQUARE 2024:rs.3.rs-4888767. [PMID: 39315246 PMCID: PMC11419169 DOI: 10.21203/rs.3.rs-4888767/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Background Gene set analysis methods have played a major role in generating biological interpretations from omics data such as gene expression datasets. However, most methods focus on detecting homogenous pattern changes in mean expression and methods detecting pattern changes in variance remain poorly explored. While a few studies attempted to use gene-level variance analysis, such approach remains under-utilized. When comparing two phenotypes, gene sets with distinct changes in subgroups under one phenotype are overlooked by available methods although they reflect meaningful biological differences between two phenotypes. Multivariate sample-level variance analysis methods are needed to detect such pattern changes. Results We use ranking schemes based on minimum spanning tree to generalize the Cramer-Von Mises and Anderson-Darling univariate statistics into multivariate gene set analysis methods to detect differential sample variance or mean. We characterize these methods in addition to two methods developed earlier using simulation results with different parameters. We apply the developed methods to microarray gene expression dataset of prednisolone-resistant and prednisolone-sensitive children diagnosed with B-lineage acute lymphoblastic leukemia and bulk RNA-sequencing gene expression dataset of benign hyperplastic polyps and potentially malignant sessile serrated adenoma/polyps. One or both of the two compared phenotypes in each of these datasets have distinct molecular subtypes that contribute to heterogeneous differences. Our results show that methods designed to detect differential sample variance are able to detect specific hallmark signaling pathways associated with the two compared phenotypes as documented in available literature. Conclusions The results in this study demonstrate the usefulness of methods designed to detect differential sample variance in providing biological interpretations when biologically relevant but heterogeneous changes between two phenotypes are prevalent in specific signaling pathways. Software implementation of the developed methods is available with detailed documentation from Bioconductor package GSAR. The available methods are applicable to gene expression datasets in a normalized matrix form and could be used with other omics datasets in a normalized matrix form with available collection of feature sets.
Collapse
Affiliation(s)
- Yasir Rahmatallah
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| |
Collapse
|
2
|
Zhang J, Yang J, Li X, Mao L, Zhang Y, Liu Y, Bao Y. EMP1 correlated with cancer progression and immune characteristics in pan-cancer and ovarian cancer. Mol Genet Genomics 2024; 299:51. [PMID: 38743077 DOI: 10.1007/s00438-024-02146-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/19/2024] [Indexed: 05/16/2024]
Abstract
This study examines the prognostic role and immunological relevance of EMP1 (epithelial membrane protein-1) in a pan-cancer analysis, with a focus on ovarian cancer. Utilizing data from TCGA, CCLE, and GTEx databases, we assessed EMP1 mRNA expression and its correlation with tumor progression, prognosis, and immune microenvironment across various cancers. Our results indicate that EMP1 expression is significantly associated with poor prognosis in multiple cancer types, including ovarian, bladder, testicular, pancreatic, breast, brain, and uveal melanoma. Immune-related analyses reveal a positive correlation between EMP1 and immune cell infiltration, particularly neutrophils, macrophages, and dendritic cells, as well as high expression of immune checkpoint such as CD274, HAVCR2, IL10, PDCD1LG2, and TGFB1 in most tumors. In vivo experiments confirm that EMP1 promotes ovarian cancer cell proliferation, metastasis, and invasion. In conclusion, EMP1 emerges as a potential prognostic biomarker and therapeutic target in various cancers, particularly ovarian cancer, due to its influence on tumor progression and immune cell dynamics. Further research is warranted to elucidate the precise mechanisms of EMP1 in cancer biology and to translate these findings into clinical applications.
Collapse
Affiliation(s)
- Jun Zhang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jing Yang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xing Li
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Lin Mao
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yan Zhang
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Yi Liu
- Department of Obstetrics and Gynecology, Xiaogan Central Hospital, Xiaogan, Hubei, China
| | - Yindi Bao
- Department of Obstetrics and Gynecology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
3
|
Luo Y, Xiang J, Tang S, Huang S, Zhou Y, Shen H. Ursolic acid induces apoptosis and pyroptosis in Reh cells by upregulating of the JNK signalling pathway based on network pharmacology and experimental validation. Heliyon 2023; 9:e23079. [PMID: 38144346 PMCID: PMC10746475 DOI: 10.1016/j.heliyon.2023.e23079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/26/2023] Open
Abstract
Objective To explore the mechanism of ursolic acid (UA) against acute B lymphoblastic leukaemia (B-ALL) based on network pharmacological analysis, molecular docking and experimental verification. Methods The core targets, functional processes, and biological pathways of UA in B-ALL were predicted by network pharmacology and molecular docking. The efficacy and mechanism of UA against B-ALL were verified through in vitro experiments such as cell viability assays, CCK-8 assays, LDH assays, AO/EB staining, flow cytometry, and Western blot assays. Results Network pharmacology analysis of the core targets indicated that the effects of UA on B-ALL were related to programmed cell death (apoptosis and pyroptosis). Molecular docking results showed that FOS, CASP8, MAPK8, IL-1β and JUN were the key targets of UA against B-ALL. The MTS assay showed that UA decreased the viability of Reh cells in a concentration- and time-dependent manner. Cellular and Western blot experiments found that UA induced Reh cell apoptosis and pyroptosis by upregulating the JNK signalling pathway. Conclusions Our findings demonstrated that UA could induce Reh cell apoptosis and pyroptosis by activating the JNK signalling pathway to exert anti-B-ALL effects. This indicates that UA may become a potential drug for the effective treatment of B-ALL.
Collapse
Affiliation(s)
- Ying Luo
- Institute of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Critical Human Diseases Prevention of the Education Department of Hunan Province, Hengyang Medical College, University of South China, Hengyang 421001, China
| | - Jing Xiang
- Institute of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Critical Human Diseases Prevention of the Education Department of Hunan Province, Hengyang Medical College, University of South China, Hengyang 421001, China
| | - Shuangyang Tang
- Institute of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Critical Human Diseases Prevention of the Education Department of Hunan Province, Hengyang Medical College, University of South China, Hengyang 421001, China
| | - Shiting Huang
- Institute of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Critical Human Diseases Prevention of the Education Department of Hunan Province, Hengyang Medical College, University of South China, Hengyang 421001, China
| | - Yishan Zhou
- Institute of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Critical Human Diseases Prevention of the Education Department of Hunan Province, Hengyang Medical College, University of South China, Hengyang 421001, China
| | - Haiyan Shen
- Institute of Biochemistry and Molecular Biology, The Key Laboratory of Environment and Critical Human Diseases Prevention of the Education Department of Hunan Province, Hengyang Medical College, University of South China, Hengyang 421001, China
| |
Collapse
|
4
|
Alves-Hanna FS, Crespo-Neto JA, Nogueira GM, Pereira DS, Lima AB, Ribeiro TLP, Santos VGR, Fonseca JRF, Magalhães-Gama F, Sadahiro A, Costa AG. Insights Regarding the Role of Inflammasomes in Leukemia: What Do We Know? J Immunol Res 2023; 2023:5584492. [PMID: 37577033 PMCID: PMC10421713 DOI: 10.1155/2023/5584492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/02/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023] Open
Abstract
Inflammation is a physiological mechanism of the immune response and has an important role in maintaining the hematopoietic cell niche in the bone marrow. During this process, the participation of molecules produced by innate immunity cells in response to a variety of pathogen-associated molecular patterns and damage-associated molecular patterns is observed. However, chronic inflammation is intrinsically associated with leukemogenesis, as it induces DNA damage in hematopoietic stem cells and contributes to the creation of the preleukemic clone. Several factors influence the malignant transformation within the hematopoietic microenvironment, with inflammasomes having a crucial role in this process, in addition to acting in the regulation of hematopoiesis and its homeostasis. Inflammasomes are intracellular multimeric complexes responsible for the maturation and secretion of the proinflammatory cytokines interleukin-1β and interleukin-18 and the cell death process via pyroptosis. Therefore, dysregulation of the activation of these complexes may be a factor in triggering several diseases, including leukemias, and this has been the subject of several studies in the area. In this review, we summarized the current knowledge on the relationship between inflammation and leukemogenesis, in particular, the role of inflammasomes in different types of leukemias, and we describe the potential therapeutic targets directed at inflammasomes in the leukemic context.
Collapse
Affiliation(s)
- Fabíola Silva Alves-Hanna
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
| | - Juniel Assis Crespo-Neto
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
| | - Glenda Menezes Nogueira
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, AM, Brazil
| | - Daniele Sá Pereira
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, AM, Brazil
| | - Amanda Barros Lima
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
| | - Thaís Lohana Pereira Ribeiro
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, AM, Brazil
| | | | - Joey Ramone Ferreira Fonseca
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
| | - Fábio Magalhães-Gama
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ-Minas), Belo Horizonte, MG, Brazil
| | - Aya Sadahiro
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
| | - Allyson Guimarães Costa
- Programa de Pós-Graduação em Imunologia Básica e Aplicada, Instituto de Ciências Biológicas, Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
- Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (HEMOAM), Manaus, AM, Brazil
- Programa de Pós-Graduação em Ciências Aplicadas à Hematologia, Universidade do Estado do Amazonas (UEA), Manaus, AM, Brazil
- Programa de Pós-Graduação em Ciências da Saúde, Instituto René Rachou, Fundação Oswaldo Cruz (FIOCRUZ-Minas), Belo Horizonte, MG, Brazil
- Escola de Enfermagem de Manaus, Universidade Federal do Amazonas (UFAM), Manaus, AM, Brazil
| |
Collapse
|
5
|
Drug-tolerant persister B-cell precursor acute lymphoblastic leukemia cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.28.530540. [PMID: 36909619 PMCID: PMC10002708 DOI: 10.1101/2023.02.28.530540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
Abstract
Reduced responsiveness of precursor B-acute lymphoblastic leukemia (BCP-ALL) to chemotherapy can be inferred when leukemia cells persist after 28 days of initial treatment. Survival of these long-term persister (LTP) / minimal residual disease (MRD) cells is partly due to bone marrow stromal cells that protect them under conditions of chemotherapy stress. We used RNA-seq to analyse BCP-ALL cells that survived a long-term, 30-day vincristine chemotherapy treatment while in co-culture with bone marrow stromal cells. RNAs of as many as 10% of the protein-encoding genes were differentially expressed. There was substantial overlap with genes associated with MRD cell persistence reported in other studies. The top pathway regulated in the LTP cells was that involving p53, a master regulator of a spectrum of responses relevant to drug resistance and cytotoxic drug exposure including control of autophagy. We tested a select number of genes for contribution to BCP-ALL cell survival using Cas9/CRISPR in a 2-step selection, initially for overall effect on cell fitness, followed by 21 days of exposure to vincristine. Many genes involved in autophagy and lysosomal function were found to contribute to survival both at steady-state and during drug treatment. We also identified MYH9, NCSTN and KIAA2013 as specific genes contributing to fitness of BCP-ALL cells. CD44 was not essential for growth under steady state conditions but was needed for survival of vincristine treatment. Finally, although the drug transporter ABCC1/MRP1 is not overexpressed in BCP-ALL, a functional gene was needed for DTP cells to survive treatment with vincristine. This suggests that addition of possible ABCC1 inhibitors during induction therapy could provide benefit in eradication of minimal residual disease in patients treated with a chemotherapy regimen that includes vincristine.
Collapse
|
6
|
Kumari S, Ali MS, Singh J, Arora M, Verma D, Pandey AK, Benjamin M, Bakhshi S, Palanichamy JK, Sharma A, Singh I, Tanwar P, Singh AR, Pushpam D, Qamar I, Chopra A. Prognostic utility of key copy number alterations in T cell acute lymphoblastic leukemia. Hematol Oncol 2022; 40:577-587. [DOI: 10.1002/hon.3030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/26/2022] [Accepted: 05/21/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Sarita Kumari
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
- School of Biotechnology Gautam Buddha University Uttar Pradesh201312 India
| | - Md Shadab Ali
- Department of Pulmonary Medicine and Sleep Disorders All India Institute of Medical Sciences New Delhi New Delhi110029 India
| | - Jay Singh
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Mohit Arora
- Department of Biochemistry All India Institute of Medical Sciences New Delhi110029 India
| | - Deepak Verma
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Avanish Kumar Pandey
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Mercilena Benjamin
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Sameer Bakhshi
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | | | - Atul Sharma
- Department of Medical Oncology Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Inder Singh
- Department of Neurology All India Institute of Medical Sciences New Delhi New Delhi110029 India
| | - Pranay Tanwar
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Amar Ranjan Singh
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Deepam Pushpam
- Department of Medical Oncology Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| | - Imteyaz Qamar
- School of Biotechnology Gautam Buddha University Uttar Pradesh201312 India
| | - Anita Chopra
- Laboratory Oncology Unit Dr. BRA‐IRCH All India Institute of Medical Sciences New Delhi110029 India
| |
Collapse
|
7
|
The Impact of NLRP3 Activation on Hematopoietic Stem Cell Transplantation. Int J Mol Sci 2021; 22:ijms222111845. [PMID: 34769275 PMCID: PMC8584591 DOI: 10.3390/ijms222111845] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 01/12/2023] Open
Abstract
NLR family pyrin domain-containing 3 (NLRP3) is an intracellular protein that after recognizing a broad spectrum of stressors, such as microbial motifs and endogenous danger signals, promotes the activation and release of the pro-inflammatory cytokines IL-1β and IL-18, thus playing an essential role in the innate immune response. Several blood cell types, including macrophages, dendritic cells, and hematopoietic stem and progenitor cells (HSPCs), express NLRP3, where it has been implicated in various physiological and pathological processes. For example, NLRP3 participates in the development and expansion of HSPCs, and their release from bone marrow into the peripheral blood has been implicated in certain hematological disorders including various types of leukemia. In addition, accumulating evidence indicates that activation of NLRP3 plays a pivotal role in the development of transplant complications in patients receiving hematopoietic stem cell transplantation (HSCT) including graft versus host disease, severe infections, and transplant-related mortality. The majority of these complications are triggered by the severe tissue damage derived from the conditioning regimens utilized in HSCT which, in turn, activates NLRP3 and, ultimately, promotes the release of proinflammatory cytokines such as IL-1β and IL-18. Here, we summarize the implications of NLRP3 in HSCT with an emphasis on the involvement of this inflammasome component in transplant complications.
Collapse
|