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Hu C, Hu W, Tang B, Bao Q, Jiang X, Tang L, Wang H, He L, Lv M, Xiao Y, Liu C, Li X, Liu Y, Li J, Huang G, Dong Z, Li Z, Guo T, Yang S. Plasma and urine proteomics and gut microbiota analysis reveal potential factors affecting COVID-19 vaccination response. iScience 2024; 27:108851. [PMID: 38318387 PMCID: PMC10838952 DOI: 10.1016/j.isci.2024.108851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/15/2023] [Accepted: 01/03/2024] [Indexed: 02/07/2024] Open
Abstract
The efficacy of COVID-19 vaccination relies on the induction of neutralizing antibodies, which can vary among vaccine recipients. In this study, we investigated the potential factors affecting the neutralizing antibody response by combining plasma and urine proteomics and gut microbiota analysis. We found that activation of the LXR/FXR pathway in plasma was associated with the production of ACE2-RBD-inhibiting antibodies, while urine proteins related to complement system, acute phase response signaling, LXR/FXR, and STAT3 pathways were correlated with neutralizing antibody production. Moreover, we observed a correlation between the gut microbiota and plasma and urine proteins, as well as the vaccination response. Based on the above data, we built a predictive model for vaccination response (AUC = 0.85). Our study provides insights into characteristic plasma and urine proteins and gut microbiota associated with the ACE2-RBD-inhibiting antibodies, which could benefit our understanding of the host response to COVID-19 vaccination.
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Affiliation(s)
- Changjiang Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Weichao Hu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Qiyu Bao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Xingyu Jiang
- Laboratory Medicine Center, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Li Tang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - He Wang
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Lijiao He
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Moyang Lv
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Yufeng Xiao
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Cheng Liu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Xinzhe Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Yunyi Liu
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Jie Li
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Guiping Huang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Zhen Dong
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Zhongjun Li
- Laboratory Medicine Center, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Tiannan Guo
- iMarkerlab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang Province, China
- Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang, China
- Center for Infectious Disease Research, Westlake University, 18 Shilongshan Road, Hangzhou 310024, Zhejiang, China
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
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Kang CK, Kim AR. Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants. iScience 2024; 27:108747. [PMID: 38222110 PMCID: PMC10784702 DOI: 10.1016/j.isci.2023.108747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/29/2023] [Accepted: 12/12/2023] [Indexed: 01/16/2024] Open
Abstract
Massively parallel reporter assay measures transcriptional activities of various cis-regulatory modules (CRMs) in a single experiment. We developed a thermodynamic computational model framework that calculates quantitative levels of gene expression directly from regulatory DNA sequences. Using the framework, we investigated the molecular mechanisms of cis-regulatory mutations of a synthetic enhancer that cause abnormal gene expression. We found that, in a human cell line, competitive binding between family transcription factors (TFs) with slightly different binding preferences significantly increases the accuracy of recapitulating the transcriptional effects of thousands of single- or multi-mutations. We also discovered that even if various harmful mutations occurred in an activator binding site, CRM could stably maintain or even increase gene expression through a certain form of competitive binding between family TFs. These findings enhance understanding the effect of SNPs and indels on CRMs and would help building robust custom-designed CRMs for biologics production and gene therapy.
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Affiliation(s)
- Chan-Koo Kang
- School of Life Science, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Department of Advanced Convergence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
| | - Ah-Ram Kim
- School of Life Science, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Department of Advanced Convergence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- School of Applied Artificial Intelligence, Handong Global University, Pohang, Gyeong-Buk 37554, South Korea
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3
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Huang H, Pan Y, Huang J, Zhang C, Liao Y, Du Q, Qin S, Chen Y, Tan H, Chen M, Xu M, Xia M, Liu Y, Li J, Liu T, Zou Q, Zhou Y, Yuan L, Wang W, Liang Y, Pan CY, Liu J, Yao S. Patient-derived organoids as personalized avatars and a potential immunotherapy model in cervical cancer. iScience 2023; 26:108198. [PMID: 38026204 PMCID: PMC10679865 DOI: 10.1016/j.isci.2023.108198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/05/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023] Open
Abstract
Cervical cancer remains a significant health issue in developing countries. However, finding a preclinical model that accurately reproduces tumor characteristics is challenging. Therefore, we established a patient-derived organoids (PDOs) biobank containing 67 cases of heterogeneous cervical cancer that mimic the histopathological and genomic characteristics of parental tumors. The in vitro response of the organoids indicated their ability to capture the radiological heterogeneity of the patients. To model individual responses to adoptive T cell therapy (ACT), we expanded tumor-infiltrating lymphocytes (TILs) ex vivo and co-cultured them with paired organoids. The PDOs-TILs co-culture system demonstrates clear responses that correspond to established immunotherapy efficiency markers like the proportion of CTLs. This study supports the potential of the PDOs platform to guide treatment in prospective interventional trials in cervical cancer.
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Affiliation(s)
- Hua Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yuwen Pan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Jiaming Huang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Chunyu Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yuandong Liao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Qiqiao Du
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Shuhang Qin
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yili Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Hao Tan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Ming Chen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Manman Xu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Meng Xia
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yunyun Liu
- Sun Yat-Sen Memorial Hospital of Sun Yat-sen University, Guangzhou 510120, China
| | - Jie Li
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Tianyu Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Qiaojian Zou
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yijia Zhou
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Li Yuan
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Wei Wang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Yanchun Liang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Chao yun Pan
- Department of Biochemistry, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Junxiu Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
| | - Shuzhong Yao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, Guangdong, China
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Konrath F, Willenbrock M, Busse D, Scheidereit C, Wolf J. A computational model of the DNA damage-induced IKK/ NF-κB pathway reveals a critical dependence on irradiation dose and PARP-1. iScience 2023; 26:107917. [PMID: 37817938 PMCID: PMC10561052 DOI: 10.1016/j.isci.2023.107917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 06/01/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
The activation of IKK/NF-κB by genotoxic stress is a crucial process in the DNA damage response. Due to the anti-apoptotic impact of NF-κB, it can affect cell-fate decisions upon DNA damage and therefore interfere with tumor therapy-induced cell death. Here, we developed a dynamical model describing IKK/NF-κB signaling that faithfully reproduces quantitative time course data and enables a detailed analysis of pathway regulation. The approach elucidates a pathway topology with two hubs, where the first integrates signals from two DNA damage sensors and the second forms a coherent feedforward loop. The analyses reveal a critical role of the sensor protein PARP-1 in the pathway regulation. Introducing a method for calculating the impact of changes in individual components on pathway activity in a time-resolved manner, we show how irradiation dose influences pathway activation. Our results give a mechanistic understanding relevant for the interpretation of experimental and clinical studies.
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Affiliation(s)
- Fabian Konrath
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Michael Willenbrock
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Dorothea Busse
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Claus Scheidereit
- Laboratory for Signal Transduction in Tumor Cells, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jana Wolf
- Mathematical Modelling of Cellular Processes, Max Delbrueck Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Department of Mathematics and Computer Science, Free University Berlin, Germany
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5
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Shibasaki S, Mitri S. A spatially structured mathematical model of the gut microbiome reveals factors that increase community stability. iScience 2023; 26:107499. [PMID: 37670791 PMCID: PMC10475486 DOI: 10.1016/j.isci.2023.107499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 04/11/2023] [Accepted: 07/26/2023] [Indexed: 09/07/2023] Open
Abstract
Given the importance of gut microbial communities for human health, we may want to ensure their stability in terms of species composition and function. Here, we built a mathematical model of a simplified gut composed of two connected patches where species and metabolites can flow from an upstream patch, allowing upstream species to affect downstream species' growth. First, we found that communities in our model are more stable if they assemble through species invasion over time compared to combining a set of species from the start. Second, downstream communities are more stable when species invade the downstream patch less frequently than the upstream patch. Finally, upstream species that have positive effects on downstream species can further increase downstream community stability. Despite it being quite abstract, our model may inform future research on designing more stable microbial communities or increasing the stability of existing ones.
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Affiliation(s)
- Shota Shibasaki
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Mitri
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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Kim JH, Mun SJ, Kim JH, Son MJ, Kim SY. Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell-derived hepatic organoids. iScience 2023; 26:107675. [PMID: 37680467 PMCID: PMC10481365 DOI: 10.1016/j.isci.2023.107675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/30/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
To gain deeper insights into transcriptomes and epigenomes of organoids, liver organoids from two states (expandable and more differentiated) were subjected to single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) analyses. Mitochondrial gene expression was higher in differentiated than in non-differentiated hepatocytes, with ATAC-seq peaks increasing near the mitochondrial control region. Differentiation of liver organoids resulted in the expression of transcription factors that act as enhancers and repressors. In addition, epigenetic mechanisms regulating the expression of alpha-fetoprotein (AFP) and albumin (ALB) differed in liver organoids and adult liver. Knockdown of PDX1, an essential transcription factor for pancreas development, led to the hepatic maturation of liver organoids through regulation of AFP and ALB expression. This integrative analysis of the transcriptomes and epigenomes of liver organoids at the single-cell level may contribute to a better understanding of the regulatory networks during liver development and the further development of mature in vitro human liver models.
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Affiliation(s)
| | - Seon Ju Mun
- Stem Cell Convergence Research Center, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, Korea
| | - Jeong-Hwan Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Myung Jin Son
- Stem Cell Convergence Research Center, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, Korea
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seon-Young Kim
- Korean Bioinformation Center, Daejeon, Korea
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, Korea
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Bhattacharya S, Horowitz BB, Zhang J, Li X, Zhang H, Giese GE, Holdorf AD, Walhout AJ. A metabolic regulatory network for the Caenorhabditis elegans intestine. iScience 2022; 25:104688. [PMID: 35847555 PMCID: PMC9283940 DOI: 10.1016/j.isci.2022.104688] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/12/2022] [Accepted: 06/24/2022] [Indexed: 11/12/2022] Open
Abstract
Metabolic perturbations can affect gene expression, for instance to rewire metabolism. While numerous efforts have measured gene expression in response to individual metabolic perturbations, methods that determine all metabolic perturbations that affect the expression for a given gene or set of genes have not been available. Here, we use a gene-centered approach to derive a first-pass metabolic regulatory network for Caenorhabditis elegans by performing RNAi of more than 1,400 metabolic genes with a set of 19 promoter reporter strains that express a fluorescent protein in the animal's intestine. We find that metabolic perturbations generally increase promoter activity, which contrasts with transcription factor (TF) RNAi, which tends to repress promoter activity. We identify several TFs that modulate promoter activity in response to perturbations of the electron transport chain and explore complex genetic interactions among metabolic pathways. This work provides a blueprint for a systems-level understanding of how metabolism affects gene expression.
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Affiliation(s)
- Sushila Bhattacharya
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Brent B. Horowitz
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Jingyan Zhang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Xuhang Li
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Hefei Zhang
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gabrielle E. Giese
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Amy D. Holdorf
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Albertha J.M. Walhout
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA,Corresponding author
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Islam MM, Goertzen A, Singh PK, Saha R. Exploring the metabolic landscape of pancreatic ductal adenocarcinoma cells using genome-scale metabolic modeling. iScience 2022; 25:104483. [PMID: 35712079 PMCID: PMC9194136 DOI: 10.1016/j.isci.2022.104483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/08/2022] [Accepted: 05/23/2022] [Indexed: 11/18/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a major research focus because of its poor therapy response and dismal prognosis. PDAC cells adapt their metabolism to the surrounding environment, often relying on diverse nutrient sources. Because traditional experimental techniques appear exhaustive to find a viable therapeutic strategy, a highly curated and omics-informed PDAC genome-scale metabolic model was reconstructed using patient-specific transcriptomics data. From the model-predictions, several new metabolic functions were explored as potential therapeutic targets in addition to the known metabolic hallmarks of PDAC. Significant downregulation in the peroxisomal beta oxidation pathway, flux modulation in the carnitine shuttle system, and upregulation in the reactive oxygen species detoxification pathway reactions were observed. These unique metabolic traits of PDAC were correlated with potential drug combinations targeting genes with poor prognosis in PDAC. Overall, this study provides a better understanding of the metabolic vulnerabilities in PDAC and will lead to novel effective therapeutic strategies.
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Affiliation(s)
- Mohammad Mazharul Islam
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Andrea Goertzen
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
| | - Pankaj K. Singh
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Rajib Saha
- Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE 68588, USA
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Gupta S, Ray S, Khan A, China A, Das D, Mallick AI. The cost of bacterial predation via type VI secretion system leads to predator extinction under environmental stress. iScience 2021; 24:103507. [PMID: 34934926 DOI: 10.1016/j.isci.2021.103507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 10/21/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
As a common gut pathogen, Campylobacter jejuni (C. jejuni) harbors the Type VI Secretion System (T6SS) that injects toxic effectors into neighboring cells, modulating microbial competitions in the harsh gut environment. Using bile salt as a natural stressor and T6SS-positive C. jejuni as a predator, we show that T6SS activity could entail a cost during bacterial predation under environmental stress. Our data suggest bile salt influx and subsequent DNA damage due to the prey-driven activation of the T6SS. We further combined experiments and mathematical modeling to explore how the stress-induced “predation cost” determines ecological outcomes. Consistent with a population-dynamics model, we found predator extinction above a critical bile salt concentration and prey-predator coexistence below this level. Moreover, we utilized the predation cost as an effective strategy facilitating host defense against C. jejuni infection. Together, we elucidate how predator dominance versus extinction emerges from the interplay between environmental stress and the T6SS machinery. Campylobacter jejuni uses Type VI secretion system (T6SS) to kill prey bacteria Under bile salt stress, activated T6SS may promote bile salt uptake and DNA damage T6SS-dependent predation by C. jejuni thus entails a “predation cost” under stress The predation cost leads to predator extinction and host defense against C. jejuni
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Tsirvouli E, Ashcroft F, Johansen B, Kuiper M. Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes. iScience 2021; 24:103451. [PMID: 34877506 PMCID: PMC8633970 DOI: 10.1016/j.isci.2021.103451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/28/2021] [Accepted: 11/11/2021] [Indexed: 12/11/2022] Open
Abstract
Psoriasis is a chronic skin disease, in which immune cells and keratinocytes keep each other in a state of inflammation. It is believed that phospholipase A2 (PLA2)-dependent eicosanoid release plays a key role in this. T-helper (Th) 1-derived cytokines are established activators of phospholipases in keratinocytes, whereas Th17-derived cytokines have largely unknown effects. Logical model simulations describing the function of cytokine and eicosanoid signaling networks combined with experimental data suggest that Th17 cytokines stimulate proinflammatory cytokine expression in psoriatic keratinocytes via activation of cPLA2α-Prostaglandin E2-EP4 signaling, which could be suppressed using the anti-psoriatic calcipotriol. cPLA2α inhibition and calcipotriol distinctly regulate expression of key psoriatic genes, possibly offering therapeutic advantage when applied together. Model simulations additionally suggest EP4 and protein kinase cAMP-activated catalytic subunit alpha as drug targets that may restore a normal phenotype. Our work illustrates how the study of complex diseases can benefit from an integrated systems approach.
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Affiliation(s)
- Eirini Tsirvouli
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Felicity Ashcroft
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Berit Johansen
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Martin Kuiper
- Department of Biology, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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Jangid A, Selvarajan S, Ramaswamy R. A stochastic model of homeostasis: The roles of noise and nuclear positioning in deciding cell fate. iScience 2021; 24:103199. [PMID: 34703995 PMCID: PMC8524154 DOI: 10.1016/j.isci.2021.103199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/21/2021] [Accepted: 09/28/2021] [Indexed: 11/27/2022] Open
Abstract
We study a population-based cellular model that starts from a single stem cell that divides stochastically to give rise to either daughter stem cells or differentiated daughter cells. There are three main components in the model: nucleus position, the underlying gene-regulatory network, and stochastic segregation of transcription factors in the daughter cells. The proportion of self-renewal and differentiated cell lines as a function of the nucleus position which in turn decides the plane of cleavage is studied. Both nuclear position and noise play an important role in determining the stem cell genealogies. We have observed both long and short genealogies in model simulation, and these compare well with experimental results from neuroblast and B-cell division. Symmetric divisions are observed in apical nuclei, while asymmetric division occurs when the nucleus is toward the base. In this model, the number of clones decreases over time, although the average clone size increases.
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Affiliation(s)
- Amit Jangid
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Suriya Selvarajan
- Department of Theoretical Physics, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Ram Ramaswamy
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi 110016, India
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