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Wu CT, Du D, Chen L, Dai R, Liu C, Yu G, Bhardwaj S, Parker SJ, Zhang Z, Clarke R, Herrington DM, Wang Y. CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution. Bioinformatics 2024; 40:btae107. [PMID: 38407991 PMCID: PMC10924278 DOI: 10.1093/bioinformatics/btae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 01/13/2024] [Accepted: 02/25/2024] [Indexed: 02/28/2024] Open
Abstract
MOTIVATION Complex tissues are dynamic ecosystems consisting of molecularly distinct yet interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell type compositions and cell-specific expressions. With few exceptions, most existing deconvolution tools exploit supervised approaches requiring various types of references that may be unreliable or even unavailable for specific tissue microenvironments. RESULTS We previously developed a fully unsupervised deconvolution method-Convex Analysis of Mixtures (CAM), that enables estimation of cell type composition and expression from bulk tissues. We now introduce CAM3.0 tool that improves this framework with three new and highly efficient algorithms, namely, radius-fixed clustering to identify reliable markers, linear programming to detect an initial scatter simplex, and a smart floating search for the optimum latent variable model. The comparative experimental results obtained from both realistic simulations and case studies show that the CAM3.0 tool can help biologists more accurately identify known or novel cell markers, determine cell proportions, and estimate cell-specific expressions, complementing the existing tools particularly when study- or datatype-specific references are unreliable or unavailable. AVAILABILITY AND IMPLEMENTATION The open-source R Scripts of CAM3.0 is freely available at https://github.com/ChiungTingWu/CAM3/(https://github.com/Bioconductor/Contributions/issues/3205). A user's guide and a vignette are provided.
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Affiliation(s)
- Chiung-Ting Wu
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
| | - Dongping Du
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
| | - Lulu Chen
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
| | - Rujia Dai
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Chunyu Liu
- Department of Psychiatry, SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Guoqiang Yu
- Department of Automation, Tsinghua University, Beijing 100084, P. R. China
| | - Saurabh Bhardwaj
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
- Department of Electrical and Instrumentation Engineering, Thapar Institute of Engineering & Technology, Punjab 147004, India
| | - Sarah J Parker
- Advanced Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los Angeles, CA 90048, United States
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, United States
| | - Robert Clarke
- The Hormel Institute, University of Minnesota, Austin, MN 55912, United States
| | - David M Herrington
- Department of Internal Medicine, Wake Forest University, Winston-Salem, NC 27157, United States
| | - Yue Wang
- Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA 22203, United States
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Li H, Hu Y, Liu D, Wang J, Han P, Zhang N, Li Y. Bioinformatic Characterization of Whole Blood Neutrophils in Pelvic Inflammatory Disease: A Potential Prognostic Indicator for Transumbilical Single-Port Laparoscopic Pelvic Abscess Surgery. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2555603. [PMID: 35401780 PMCID: PMC8993565 DOI: 10.1155/2022/2555603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 12/19/2022]
Abstract
The purpose of this research is to determine the prognosis of patients treated with transumbilical single-port laparoscopic surgery for acute pelvic inflammatory illness. Postoperative data on 129 patients treated with laparoscopic surgery for acute pelvic inflammatory illness were obtained retrospectively. It was observed that the shorter the time required for postoperative leukocyte recovery to normal, the shorter the time required for postoperative pain and diet recovery, as well as hospital stay, in such individuals. CIBERSORT was used to examine patient data from GEO. The most significant difference between the normal and pelvic inflammatory groups was in neutrophil content. Association study found a substantial positive correlation between the quantity of neutrophils infiltrating the immune system and the abundance of monocyte M0 infiltrating the immune system. Neutrophil immune infiltration was strongly inversely linked with plasma cells, activated CD8+ Tm cells, and active CD4+ Tm cells. Four mRNAs linked with pelvic inflammatory illness were revealed to be strongly associated with neutrophil immune infiltration, notably CALML4, COQ10B, DCPS, and PPP2R1A. The ROC revealed that CALML4 (area under the curve (AUC): 0.769, 95% confidence interval (CI): 0.638-0.881), COQ10B (AUC: 0.742, 95% CI: 0.587-0.881), PPP2R1A (AUC: 0.733 95% CI: 0.593-0.857), and DCPS (AUC: 0.745, 95% CI: 0.571-0.900) were potential markers for predicting pelvic inflammatory disease. CALML4, COQ10B, PPP2R1A, and DCPS may be critical determinants determining the amount of preoperative neutrophil infiltration and the time required for leukocyte recovery after single-port laparoscopy in acute pelvic inflammatory illness.
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Affiliation(s)
- Haining Li
- General Hospital of Ningxia Medical University, China
| | | | - Dan Liu
- General Hospital of Ningxia Medical University, China
| | | | | | | | - Yan Li
- General Hospital of Ningxia Medical University, China
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Chen Z, Wu A. Progress and challenge for computational quantification of tissue immune cells. Brief Bioinform 2021; 22:6065002. [PMID: 33401306 DOI: 10.1093/bib/bbaa358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 12/28/2022] Open
Abstract
Tissue immune cells have long been recognized as important regulators for the maintenance of balance in the body system. Quantification of the abundance of different immune cells will provide enhanced understanding of the correlation between immune cells and normal or abnormal situations. Currently, computational methods to predict tissue immune cell compositions from bulk transcriptomes have been largely developed. Therefore, summarizing the advantages and disadvantages is appropriate. In addition, an examination of the challenges and possible solutions for these computational models will assist the development of this field. The common hypothesis of these models is that the expression of signature genes for immune cell types might represent the proportion of immune cells that contribute to the tissue transcriptome. In general, we grouped all reported tools into three groups, including reference-free, reference-based scoring and reference-based deconvolution methods. In this review, a summary of all the currently reported computational immune cell quantification tools and their applications, limitations, and perspectives are presented. Furthermore, some critical problems are found that have limited the performance and application of these models, including inadequate immune cell type, the collinearity problem, the impact of the tissue environment on the immune cell expression level, and the deficiency of standard datasets for model validation. To address these issues, tissue specific training datasets that include all known immune cells, a hierarchical computational framework, and benchmark datasets including both tissue expression profiles and the abundances of all the immune cells are proposed to further promote the development of this field.
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Affiliation(s)
- Ziyi Chen
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Center for Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Jiangsu, Suzhou, China
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