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Deng J, Wei K, Fang J, Li Y. Deep self-reconstruction driven joint nonnegative matrix factorization model for identifying multiple genomic imaging associations in complex diseases. J Biomed Inform 2024; 156:104684. [PMID: 38936566 DOI: 10.1016/j.jbi.2024.104684] [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: 04/11/2024] [Revised: 06/14/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
OBJECTIVE Comprehensive analysis of histopathology images and transcriptomics data enables the identification of candidate biomarkers and multimodal association patterns. Most existing multimodal data association studies are derived from extensions of the joint nonnegative matrix factorization model for identifying complex data associations, which can make full use of clinical prior information. However, the raw data were usually taken as the input without considering the underlying complex multi-subspace structure, influencing the subsequent integration analysis results. METHODS This study proposed a deep-self reconstructed joint nonnegative matrix factorization (DSRJNMF) model to use self-expressive properties to reconstruct the raw data to characterize the similarity structure associated with clinical labels. Then, the sparsity, orthogonality, and regularization constraints constructed from prior information are added to the DSRJNMF model to determine the sparse set of biologically relevant features across modalities. RESULTS The algorithm has been applied to identify the imaging genetic association of triple negative breast cancer (TNBC). Multilevel experimental results demonstrate that the proposed algorithm better estimates potential associations between pathological image features and miRNA-gene and identifies consistent multimodal imaging genetic biomarkers to guide the interpretation of TNBC. CONCLUSION The propose method provides a novel idea of data association analysis oriented to complex diseases.
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Affiliation(s)
- Jin Deng
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Kai Wei
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jiana Fang
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou 510642, China
| | - Ying Li
- Shanghai Institute of Technology, Shanghai 201418, China.
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Liu L, He C, Liu J, Lv Z, Wang G, Gao H, Dai Y, Cooper DKC, Cai Z, Mou L. Transplant Tolerance: Current Insights and Strategies for Long-Term Survival of Xenografts. Arch Immunol Ther Exp (Warsz) 2018; 66:355-364. [PMID: 29992337 DOI: 10.1007/s00005-018-0517-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/18/2018] [Indexed: 12/20/2022]
Abstract
Xenotransplantation is an attractive solution to the problem of allograft shortage. However, transplants across discordant species barriers are subject to vigorous immunologic and pathobiologic hurdles, some of which might be overcome with the induction of immunologic tolerance. Several strategies have been designed to induce tolerance to a xenograft at both the central (including induction of mixed chimerism and thymic transplantation) and peripheral (including adoptive transfer of regulatory cells and blocking T cell costimulation) levels. Currently, xenograft tolerance has been well-established in rodent models, but these protocols have not yet achieved similar success in nonhuman primates. This review will discuss the major barriers that impede the establishment of immunological tolerance across xenogeneic barriers and the potential solution to these challenges, and provide a perspective on the future of the development of novel tolerance-inducing strategies.
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Affiliation(s)
- Lu Liu
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center' Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China.,Department of Gastroenterology' Center For Digestive Diseases, People's Hospital of Baoan District, The 8th people's Hospital of Shenzhen, Shenzhen, 518101, Guangdong, China
| | - Chen He
- Department of Ophthalmology, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, 518035, Guangdong, China
| | - Jintao Liu
- Department of Gastroenterology' Center For Digestive Diseases, People's Hospital of Baoan District, The 8th people's Hospital of Shenzhen, Shenzhen, 518101, Guangdong, China
| | - Zhiwu Lv
- Department of Gastroenterology' Center For Digestive Diseases, People's Hospital of Baoan District, The 8th people's Hospital of Shenzhen, Shenzhen, 518101, Guangdong, China
| | - Ganlu Wang
- Department of Gastroenterology' Center For Digestive Diseases, People's Hospital of Baoan District, The 8th people's Hospital of Shenzhen, Shenzhen, 518101, Guangdong, China
| | - Hanchao Gao
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center' Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China
| | - Yifan Dai
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - David K C Cooper
- Xenotransplantation Program/Department of Surgery, The University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Zhiming Cai
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center' Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China
| | - Lisha Mou
- Shenzhen Xenotransplantation Medical Engineering Research and Development Center' Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen University School of Medicine, Shenzhen University Health Science Center, Shenzhen, 518035, Guangdong, China.
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The Role of NK Cells in Pig-to-Human Xenotransplantation. J Immunol Res 2017; 2017:4627384. [PMID: 29410970 PMCID: PMC5749293 DOI: 10.1155/2017/4627384] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 10/31/2017] [Indexed: 02/07/2023] Open
Abstract
Recruitment of human NK cells to porcine tissues has been demonstrated in pig organs perfused ex vivo with human blood in the early 1990s. Subsequently, the molecular mechanisms leading to adhesion and cytotoxicity in human NK cell-porcine endothelial cell (pEC) interactions have been elucidated in vitro to identify targets for therapeutic interventions. Specific molecular strategies to overcome human anti-pig NK cell responses include (1) blocking of the molecular events leading to recruitment (chemotaxis, adhesion, and transmigration), (2) expression of human MHC class I molecules on pECs that inhibit NK cells, and (3) elimination or blocking of pig ligands for activating human NK receptors. The potential of cell-based strategies including tolerogenic dendritic cells (DC) and regulatory T cells (Treg) and the latest progress using transgenic pigs genetically modified to reduce xenogeneic NK cell responses are discussed. Finally, we present the status of phenotypic and functional characterization of nonhuman primate (NHP) NK cells, essential for studying their role in xenograft rejection using preclinical pig-to-NHP models, and summarize key advances and important perspectives for future research.
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Production of Cloned Miniature Pigs Expressing High Levels of Human Apolipoprotein(a) in Plasma. PLoS One 2015; 10:e0132155. [PMID: 26147378 PMCID: PMC4492603 DOI: 10.1371/journal.pone.0132155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 06/10/2015] [Indexed: 11/19/2022] Open
Abstract
High lipoprotein(a) [Lp(a)] levels are a major risk factor for the development of atherosclerosis. However, because apolipoprotein(a) [apo(a)], the unique component of Lp(a), is found only in primates and humans, the study of human Lp(a) has been hampered due to the lack of appropriate animal models. Using somatic cell nuclear transfer (SCNT) techniques, we produced transgenic miniature pigs expressing human apo(a) in the plasma. First, we placed the hemagglutinin (HA)-tagged cDNA of human apo(a) under the control of the β-actin promoter and cytomegalovirus enhancer, and then introduced this construct into kidney epithelial cells. Immunostaining of cells with anti-HA antibody allowed identification of cells stably expressing apo(a); one of the positive clones was used to provide donor cells for SCNT, yielding blastocysts that expressed apo(a). Immunohistochemical analysis of tissue sections and RT-PCR analysis of total RNA from organs of cloned piglet revealed that apo(a) is expressed in various tissues/organs including heart, liver, kidney, and intestine. More importantly, a transgenic line exhibited a high level (>400 mg/dL) of Lp(a) in plasma, and the transgenic apo(a) gene was transmitted to the offspring. Thus, we generated a human apo(a)–transgenic miniature pig that can be used as a model system to study advanced atherosclerosis related to human disease. The anatomical and physiological similarities between the swine and human cardiovascular systems will make this pig model a valuable source of information on the role of apo(a) in the formation of atherosclerosis, as well as the mechanisms underlying vascular health and disease.
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Vadori M, Cozzi E. Immunological challenges and therapies in xenotransplantation. Cold Spring Harb Perspect Med 2014; 4:a015578. [PMID: 24616201 DOI: 10.1101/cshperspect.a015578] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Xenotransplantation, or the transplantation of cells, tissues, or organs between different species, was proposed a long time ago as a possible solution to the worldwide shortage of human organs and tissues for transplantation. In this setting, the pig is currently seen as the most likely candidate species. In the last decade, progress in this field has been remarkable and includes a better insight into the immunological mechanisms underlying the rejection process. Several immunological hurdles nonetheless remain, such as the strong antibody-mediated and innate or adaptive cellular immune responses linked to coagulation derangements, precluding indefinite xenograft survival. This article reviews our current understanding of the immunological mechanisms involved in xenograft rejection and the potential strategies that may enable xenotransplantation to become a clinical reality in the not-too-distant future.
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Affiliation(s)
- Marta Vadori
- CORIT (Consortium for Research in Organ Transplantation), Legnaro, 35020 Padua, Italy
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Tian M, Lv Y, Zhai C, Zhu H, Yu L, Wang B. Alternative immunomodulatory strategies for xenotransplantation: CD80/CD86-CTLA4 pathway-modified immature dendritic cells promote xenograft survival. PLoS One 2013; 8:e69640. [PMID: 23922766 PMCID: PMC3726660 DOI: 10.1371/journal.pone.0069640] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Accepted: 06/10/2013] [Indexed: 12/26/2022] Open
Abstract
Background Xenotransplantation is a promising approach to circumventing the current organ shortage. However, T-cell-dependent anti-xenoresponses are a major challenge to successful xenografts. Given the advantages of the use of CTLA4-Ig in the survival of allografts, the purpose of the study was to investigate the therapeutic potential of CTLA4-IgG4 modified immature dendritic cells (imDCs) in the prevention of islets xenograft rejection. Methods CTLA4-IgG4 was constructed by the fusion of the extracellular regions of porcine CTLA4 to human the hIgG4 Fc region. The imDCs were induced and cultured from porcine peripheral blood mononuclear cells (PBMC). The CTLA4-IgG4 modified imDCs were delivered via the portal vein to the liver of diabetic mice (insulin-dependent diabetes mellitus) before islet xenografting, and mCTLA4-Ig was administered intravenously after xenotransplantation. Results The xenograft survival of mice receiving unmodified imDCs was approximately 30 days. However, following administration of CTLA4-IgG4 modified imDCs before grafting and mCTLA4-Ig after grafting, xenografts survived for more than 100 days. Flow cytometric analysis showed that the CD4+CD25+Foxp3+ Treg population was increased in spleens. The efficacy of donor CTLA4-IgG4 modified imDCs correlated partially with the amplification of Tregs. Conclusions These results confirm that selective inhibition of the direct and indirect pathways of T-cell activation by donor CTLA4-IgG4 modified imDCs and receptor CTLA4-Ig is a highly effective strategy to promote survival of xenografts.
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Affiliation(s)
- Min Tian
- Department of Hepatobiliary Surgery, First Affiliated Hospital, Medical College, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Yi Lv
- Department of Hepatobiliary Surgery, First Affiliated Hospital, Medical College, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Chao Zhai
- Department of Hepatobiliary Surgery, First Affiliated Hospital, Medical College, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Haitao Zhu
- Department of Hepatobiliary Surgery, First Affiliated Hospital, Medical College, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Liang Yu
- Department of Hepatobiliary Surgery, First Affiliated Hospital, Medical College, Xi'an Jiaotong University, Xi'an, People's Republic of China
| | - Bo Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital, Medical College, Xi'an Jiaotong University, Xi'an, People's Republic of China
- * E-mail:
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Abstract
PURPOSE OF REVIEW Immunological barriers still preclude clinical xenotransplantation. The protective role of CD4(+)CD25(+)Foxp3(+) T-regulatory cells (Treg) in allotransplantation is well described and, therefore, could represent a promising therapeutical tool for xenotransplantation. This review addresses the latest findings on Treg in xenotransplantation research. RECENT FINDINGS In vivo, costimulation blockade-based strategies including anti-CD154 monoclonal antibodies (mAbs) in combination with rapamycin or anti-LFA-1 mAb prolonged both concordant and discordant islets xenografts survival in a Treg-dependent manner. In vitro, IL-10 secretion was shown to be critical for the suppression of xenogeneic responses mediated by Treg. Moreover, transgenic expression of inducible costimulator-immunoglobulin or PD-L1 on porcine endothelial cells inhibited human T-cell proliferation in vitro and was associated with the induction of Treg and IL-10 secretion. CXCR3 mediated the recruitment of Treg to pig endothelium. Finally, the recruitment of human Treg was enhanced by the immobilization of human CCL17 on pig endothelium. SUMMARY There is increasing evidence for the potential of CD4(+)CD25(+)Foxp3(+) Treg to protect xenografts. Induction of Treg in recipients and/or recruitment of human Treg to pig endothelium may represent novel strategies to prevent cell-mediated rejection in pig-to-human xenotransplantation.
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