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Ojha A, Zhao SJ, Zhang JT, Simo KA, Liu JY. Gap-App: A sex-distinct AI-based predictor for pancreatic ductal adenocarcinoma survival as a web application open to patients and physicians. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597246. [PMID: 38895246 PMCID: PMC11185613 DOI: 10.1101/2024.06.04.597246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
In this study, using RNA-Seq gene expression data and advanced machine learning techniques, we identified distinct gene expression profiles between male and female pancreatic ductal adenocarcinoma (PDAC) patients. Building upon this insight, we developed sex-specific 3-year survival predictive models, which achieved accuracies of 88.47% for males and 88.94% for females, respectively. These models outperformed a single general model despite the smaller sample sizes, highlighting the value of sex-specific analysis. Based on these findings, we created Gap-App, a web application that enables the use of individual gene expression profiles combined with sex information for personalized survival predictions. Gap-App, the first online tool aiming to bridge the gap between complex genomic data and clinical application and facilitating more precise and individualized cancer care, marks a significant advancement in personalized prognosis. The study not only underscores the importance of acknowledging sex differences in personalized prognosis, but also sets the stage for the shift from traditional one-size-fits-all to more personalized and targeted medicine. The GAP-App service is freely available at www.gap-app.org.
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Affiliation(s)
- Anuj Ojha
- Department of Medicine, College of Medicine, University of Toledo, Toledo, OH, USA
- Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, USA
| | - Shu-Jun Zhao
- Department of Medicine, College of Medicine, University of Toledo, Toledo, OH, USA
- Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, USA
| | - Jian-Ting Zhang
- Department of Cell and Cancer Biology, College of Medicine, University of Toledo, Toledo, OH, USA
| | - Kerri A. Simo
- Department of Surgery, College of Medicine, University of Toledo, Toledo, OH, USA
- ProMedica Health System, ProMedica Cancer Institute, Toledo, OH, USA
| | - Jing-Yuan Liu
- Department of Medicine, College of Medicine, University of Toledo, Toledo, OH, USA
- Department of Cell and Cancer Biology, College of Medicine, University of Toledo, Toledo, OH, USA
- Department of Bioengineering, College of Engineering, University of Toledo, Toledo, OH, USA
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2
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Li T, Yao J. Unveiling the hub genes in the SIGLECs family in colon adenocarcinoma with machine learning. Front Genet 2024; 15:1375100. [PMID: 38650859 PMCID: PMC11033367 DOI: 10.3389/fgene.2024.1375100] [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: 01/23/2024] [Accepted: 03/25/2024] [Indexed: 04/25/2024] Open
Abstract
Background Despite the recognized roles of Sialic acid-binding Ig-like lectins (SIGLECs) in endocytosis and immune regulation across cancers, their molecular intricacies in colon adenocarcinoma (COAD) are underexplored. Meanwhile, the complicated interactions between different SIGLECs are also crucial but open questions. Methods We investigate the correlation between SIGLECs and various properties, including cancer status, prognosis, clinical features, functional enrichment, immune cell abundances, immune checkpoints, pathways, etc. To fully understand the behavior of multiple SIGLECs' co-evolution and subtract its leading effect, we additionally apply three unsupervised machine learning algorithms, namely, Principal Component Analysis (PCA), Self-Organizing Maps (SOM), K-means, and two supervised learning algorithms, Least Absolute Shrinkage and Selection Operator (LASSO) and neural network (NN). Results We find significantly lower expression levels in COAD samples, together with a systematic enhancement in the correlations between distinct SIGLECs. We demonstrate SIGLEC14 significantly affects the Overall Survival (OS) according to the Hazzard ratio, while using PCA further enhances the sensitivity to both OS and Disease Free Interval (DFI). We find any single SIGLEC is uncorrelated to the cancer stages, which can be significantly improved by using PCA. We further identify SIGLEC-1,15 and CD22 as hub genes in COAD through Differentially Expressed Genes (DEGs), which is consistent with our PCA-identified key components PC-1,2,5 considering both the correlation with cancer status and immune cell abundance. As an extension, we use SOM for the visualization of the SIGLECs and show the similarities and differences between COAD patients. SOM can also help us define subsamples according to the SIGLECs status, with corresponding changes in both immune cells and cancer T-stage, for instance. Conclusion We conclude SIGLEC-1,15 and CD22 as the most promising hub genes in the SIGLECs family in treating COAD. PCA offers significant enhancement in the prognosis and clinical analyses, while using SOM further unveils the transition phases or potential subtypes of COAD.
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Affiliation(s)
- Tiantian Li
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Yao
- Department of Astronomy, School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Astronomical Observatory, Shanghai, China
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3
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Liu M, Bertolazzi G, Sridhar S, Lee RX, Jaynes P, Mulder K, Syn N, Hoppe MM, Fan S, Peng Y, Thng J, Chua R, Jayalakshmi, Batumalai Y, De Mel S, Poon L, Chan EHL, Lee J, Hue SSS, Chang ST, Chuang SS, Chandy KG, Ye X, Pan-Hammarström Q, Ginhoux F, Chee YL, Ng SB, Tripodo C, Jeyasekharan AD. Spatially-resolved transcriptomics reveal macrophage heterogeneity and prognostic significance in diffuse large B-cell lymphoma. Nat Commun 2024; 15:2113. [PMID: 38459052 PMCID: PMC10923916 DOI: 10.1038/s41467-024-46220-z] [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: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/10/2024] Open
Abstract
Macrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Macrophage estimation by immunohistochemistry shows varying prognostic significance across studies in DLBCL, and does not provide a comprehensive analysis of macrophage subtypes. Here, using digital spatial profiling with whole transcriptome analysis of CD68+ cells, we characterize macrophages in distinct spatial niches of reactive lymphoid tissues (RLTs) and DLBCL. We reveal transcriptomic differences between macrophages within RLTs (light zone /dark zone, germinal center/ interfollicular), and between disease states (RLTs/ DLBCL), which we then use to generate six spatially-derived macrophage signatures (MacroSigs). We proceed to interrogate these MacroSigs in macrophage and DLBCL single-cell RNA-sequencing datasets, and in gene-expression data from multiple DLBCL cohorts. We show that specific MacroSigs are associated with cell-of-origin subtypes and overall survival in DLBCL. This study provides a spatially-resolved whole-transcriptome atlas of macrophages in reactive and malignant lymphoid tissues, showing biological and clinical significance.
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Affiliation(s)
- Min Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Radiation Oncology, Chongqing University Cancer Hospital, Chongqing, PR China
- Department of Immunology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, PR China
| | - Giorgio Bertolazzi
- Department of Economics, Business and Statistics, University of Palermo, Palermo, Italy
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Shruti Sridhar
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Rui Xue Lee
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Patrick Jaynes
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Kevin Mulder
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Nicholas Syn
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Biomedical Informatics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Michal Marek Hoppe
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Shuangyi Fan
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Yanfen Peng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Jocelyn Thng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Reiya Chua
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Jayalakshmi
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Yogeshini Batumalai
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
| | - Sanjay De Mel
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Limei Poon
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Esther Hian Li Chan
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Joanne Lee
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Susan Swee-Shan Hue
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Sheng-Tsung Chang
- Department of Pathology, Chi-Mei Medical Center, Tainan City, Taiwan, ROC
| | - Shih-Sung Chuang
- Department of Pathology, Chi-Mei Medical Center, Tainan City, Taiwan, ROC
| | - K George Chandy
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, Singapore, Singapore
| | - Xiaofei Ye
- Kindstar Global Precision Medicine Institute, Wuhan, PR China
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Florent Ginhoux
- Singapore Immunology Network, Agency for Science, Technology and Research, Singapore, Singapore
- Institut National de la Santé Et de la Recherche Medicale (INSERM) U1015, Equipe Labellisée-Ligue Nationale contre le Cancer, Villejuif, France
- Université Paris-Saclay, Gustave Roussy, Villejuif, France
| | - Yen Lin Chee
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Siok-Bian Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Claudio Tripodo
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
- Histopathology Unit, Institute of Molecular Oncology Foundation (IFOM) ETS - The AIRC Institute of Molecular Oncology, Milan, Italy.
| | - Anand D Jeyasekharan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
- Department of Haematology-Oncology, National University Health System, Singapore, Singapore.
- NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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Wang TG, Shang JL, Liu JX, Li F, Yuan S, Wang J. Joint L 2,p-norm and random walk graph constrained PCA for single-cell RNA-seq data. Comput Methods Biomech Biomed Engin 2024; 27:498-511. [PMID: 36912759 DOI: 10.1080/10255842.2023.2188106] [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: 09/19/2022] [Accepted: 03/02/2023] [Indexed: 03/14/2023]
Abstract
The development and widespread utilization of high-throughput sequencing technologies in biology has fueled the rapid growth of single-cell RNA sequencing (scRNA-seq) data over the past decade. The development of scRNA-seq technology has significantly expanded researchers' understanding of cellular heterogeneity. Accurate cell type identification is the prerequisite for any research on heterogeneous cell populations. However, due to the high noise and high dimensionality of scRNA-seq data, improving the effectiveness of cell type identification remains a challenge. As an effective dimensionality reduction method, Principal Component Analysis (PCA) is an essential tool for visualizing high-dimensional scRNA-seq data and identifying cell subpopulations. However, traditional PCA has some defects when used in mining the nonlinear manifold structure of the data and usually suffers from over-density of principal components (PCs). Therefore, we present a novel method in this paper called joint L 2 , p -norm and random walk graph constrained PCA (RWPPCA). RWPPCA aims to retain the data's local information in the process of mapping high-dimensional data to low-dimensional space, to more accurately obtain sparse principal components and to then identify cell types more precisely. Specifically, RWPPCA combines the random walk (RW) algorithm with graph regularization to more accurately determine the local geometric relationships between data points. Moreover, to mitigate the adverse effects of dense PCs, the L 2 , p -norm is introduced to make the PCs sparser, thus increasing their interpretability. Then, we evaluate the effectiveness of RWPPCA on simulated data and scRNA-seq data. The results show that RWPPCA performs well in cell type identification and outperforms other comparison methods.
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Affiliation(s)
- Tai-Ge Wang
- School of Computer Science, Qufu Normal University, Rizhao 276826, China
| | - Jun-Liang Shang
- School of Computer Science, Qufu Normal University, Rizhao 276826, China
| | - Jin-Xing Liu
- School of Computer Science, Qufu Normal University, Rizhao 276826, China
| | - Feng Li
- School of Computer Science, Qufu Normal University, Rizhao 276826, China
| | - Shasha Yuan
- School of Computer Science, Qufu Normal University, Rizhao 276826, China
| | - Juan Wang
- School of Computer Science, Qufu Normal University, Rizhao 276826, China
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5
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Smolle MA, Herbsthofer L, Goda M, Granegger B, Brcic I, Bergovec M, Scheipl S, Prietl B, El-Heliebi A, Pichler M, Gerger A, Posch F, Tomberger M, López-García P, Feichtinger J, Baumgartner C, Leithner A, Liegl-Atzwanger B, Szkandera J. Influence of tumor-infiltrating immune cells on local control rate, distant metastasis, and survival in patients with soft tissue sarcoma. Oncoimmunology 2021; 10:1896658. [PMID: 33763294 PMCID: PMC7954425 DOI: 10.1080/2162402x.2021.1896658] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Soft tissue sarcomas (STS) are considered non-immunogenic, although distinct entities respond to anti-tumor agents targeting the tumor microenvironment. This study’s aims were to investigate relationships between tumor-infiltrating immune cells and patient/tumor-related factors, and assess their prognostic value for local recurrence (LR), distant metastasis (DM), and overall survival (OS). One-hundred-eighty-eight STS-patients (87 females [46.3%]; median age: 62.5 years) were retrospectively analyzed. Tissue microarrays (in total 1266 cores) were stained with multiplex immunohistochemistry and analyzed with multispectral imaging. Seven cell types were differentiated depending on marker profiles (CD3+, CD3+ CD4+ helper, CD3+ CD8+ cytotoxic, CD3+ CD4+ CD45RO+ helper memory, CD3+ CD8+ CD45RO+ cytotoxic memory T-cells; CD20 + B-cells; CD68+ macrophages). Correlations between phenotype abundance and variables were analyzed. Uni- and multivariate Fine&Gray and Cox-regression models were constructed to investigate prognostic variables. Model calibration was assessed with C-index. IHC-findings were validated with TCGA-SARC gene expression data of genes specific for macrophages, T- and B-cells. B-cell percentage was lower in patients older than 62.5 years (p = .013), whilst macrophage percentage was higher (p = .002). High B-cell (p = .035) and macrophage levels (p = .003) were associated with increased LR-risk in the univariate analysis. In the multivariate setting, high macrophage levels (p = .014) were associated with increased LR-risk, irrespective of margins, age, gender or B-cells. Other immune cells were not associated with outcome events. High macrophage levels were a poor prognostic factor for LR, irrespective of margins, B-cells, gender and age. Thus, anti-tumor, macrophage-targeting agents may be applied more frequently in tumors with enhanced macrophage infiltration.
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Affiliation(s)
- Maria A Smolle
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | | | - Mark Goda
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Barbara Granegger
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Iva Brcic
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Marko Bergovec
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Susanne Scheipl
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Barbara Prietl
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria.,Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria
| | - Amin El-Heliebi
- Center for Biomarker Research in Medicine (CBmed), Graz, Austria.,Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Martin Pichler
- Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Armin Gerger
- Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Florian Posch
- Division of Clinical Oncology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | | | | | - Julia Feichtinger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Claudia Baumgartner
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Andreas Leithner
- Department of Orthopaedics and Trauma, Medical University of Graz, Graz, Austria
| | - Bernadette Liegl-Atzwanger
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
| | - Joanna Szkandera
- Division of Cell Biology, Histology and Embryology, Gottfried Schatz Research Center, Medical University of Graz, Graz, Austria
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6
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Andrysik Z, Bender H, Galbraith MD, Espinosa JM. Multi-omics analysis reveals contextual tumor suppressive and oncogenic gene modules within the acute hypoxic response. Nat Commun 2021; 12:1375. [PMID: 33654095 PMCID: PMC7925689 DOI: 10.1038/s41467-021-21687-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022] Open
Abstract
Cellular adaptation to hypoxia is a hallmark of cancer, but the relative contribution of hypoxia-inducible factors (HIFs) versus other oxygen sensors to tumorigenesis is unclear. We employ a multi-omics pipeline including measurements of nascent RNA to characterize transcriptional changes upon acute hypoxia. We identify an immediate early transcriptional response that is strongly dependent on HIF1A and the kinase activity of its cofactor CDK8, includes indirect repression of MYC targets, and is highly conserved across cancer types. HIF1A drives this acute response via conserved high-occupancy enhancers. Genetic screen data indicates that, in normoxia, HIF1A displays strong cell-autonomous tumor suppressive effects through a gene module mediating mTOR inhibition. Conversely, in advanced malignancies, expression of a module of HIF1A targets involved in collagen remodeling is associated with poor prognosis across diverse cancer types. In this work, we provide a valuable resource for investigating context-dependent roles of HIF1A and its targets in cancer biology. The response to hypoxia can significantly impact oncogenic processes. Here, the authors define the early transcriptional response to acute hypoxia and identify HIF1A target genes as part of this acute response, providing a resource for investigating context-dependent roles of HIF1A in the biology of cancer.
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Affiliation(s)
- Zdenek Andrysik
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Heather Bender
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.,Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Matthew D Galbraith
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. .,Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.
| | - Joaquin M Espinosa
- Department of Pharmacology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. .,Linda Crnic Institute for Down Syndrome, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA. .,Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, USA.
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7
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de Torrenté L, Zimmerman S, Suzuki M, Christopeit M, Greally JM, Mar JC. The shape of gene expression distributions matter: how incorporating distribution shape improves the interpretation of cancer transcriptomic data. BMC Bioinformatics 2020; 21:562. [PMID: 33371881 PMCID: PMC7768656 DOI: 10.1186/s12859-020-03892-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND In genomics, we often assume that continuous data, such as gene expression, follow a specific kind of distribution. However we rarely stop to question the validity of this assumption, or consider how broadly applicable it may be to all genes that are in the transcriptome. Our study investigated the prevalence of a range of gene expression distributions in three different tumor types from the Cancer Genome Atlas (TCGA). RESULTS Surprisingly, the expression of less than 50% of all genes was Normally-distributed, with other distributions including Gamma, Bimodal, Cauchy, and Lognormal also represented. Most of the distribution categories contained genes that were significantly enriched for unique biological processes. Different assumptions based on the shape of the expression profile were used to identify genes that could discriminate between patients with good versus poor survival. The prognostic marker genes that were identified when the shape of the distribution was accounted for reflected functional insights into cancer biology that were not observed when standard assumptions were applied. We showed that when multiple types of distributions were permitted, i.e. the shape of the expression profile was used, the statistical classifiers had greater predictive accuracy for determining the prognosis of a patient versus those that assumed only one type of gene expression distribution. CONCLUSIONS Our results highlight the value of studying a gene's distribution shape to model heterogeneity of transcriptomic data and the impact on using analyses that permit more than one type of gene expression distribution. These insights would have been overlooked when using standard approaches that assume all genes follow the same type of distribution in a patient cohort.
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Affiliation(s)
- Laurence de Torrenté
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Samuel Zimmerman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Maximilian Christopeit
- Internal Medicine II, Hematology, Oncology, Clinical Immunology and Rheumatology, University Hospital Tuebingen, Otfried-Mueller-Strasse 10, 72076, Tuebingen, Germany
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jessica C Mar
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.
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8
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Li Y, Xu Q, Wu D, Chen G. Exploring Additional Valuable Information From Single-Cell RNA-Seq Data. Front Cell Dev Biol 2020; 8:593007. [PMID: 33335900 PMCID: PMC7736616 DOI: 10.3389/fcell.2020.593007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/26/2020] [Indexed: 12/28/2022] Open
Abstract
Single-cell RNA-seq (scRNA-seq) technologies are broadly applied to dissect the cellular heterogeneity and expression dynamics, providing unprecedented insights into single-cell biology. Most of the scRNA-seq studies mainly focused on the dissection of cell types/states, developmental trajectory, gene regulatory network, and alternative splicing. However, besides these routine analyses, many other valuable scRNA-seq investigations can be conducted. Here, we first review cell-to-cell communication exploration, RNA velocity inference, identification of large-scale copy number variations and single nucleotide changes, and chromatin accessibility prediction based on single-cell transcriptomics data. Next, we discuss the identification of novel genes/transcripts through transcriptome reconstruction approaches, as well as the profiling of long non-coding RNAs and circular RNAs. Additionally, we survey the integration of single-cell and bulk RNA-seq datasets for deconvoluting the cell composition of large-scale bulk samples and linking single-cell signatures to patient outcomes. These additional analyses could largely facilitate corresponding basic science and clinical applications.
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Affiliation(s)
- Yunjin Li
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Qiyue Xu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
| | - Duojiao Wu
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Geng Chen
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, China
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9
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Valihrach L, Androvic P, Kubista M. Circulating miRNA analysis for cancer diagnostics and therapy. Mol Aspects Med 2020; 72:100825. [DOI: 10.1016/j.mam.2019.10.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 12/12/2022]
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