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Nisa KU, Tarfeen N, Humaira, Wani S, Nisa Q, Ali S, Wali AF. Proteomic approaches in the study of cancers. Proteomics 2023. [DOI: 10.1016/b978-0-323-95072-5.00002-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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2
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Cerrizuela S, Vega-Lopez GA, Méndez-Maldonado K, Velasco I, Aybar MJ. The crucial role of model systems in understanding the complexity of cell signaling in human neurocristopathies. WIREs Mech Dis 2022; 14:e1537. [PMID: 35023327 DOI: 10.1002/wsbm.1537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 08/26/2021] [Accepted: 08/30/2021] [Indexed: 11/07/2022]
Abstract
Animal models are useful to study the molecular, cellular, and morphogenetic mechanisms underlying normal and pathological development. Cell-based study models have emerged as an alternative approach to study many aspects of human embryonic development and disease. The neural crest (NC) is a transient, multipotent, and migratory embryonic cell population that generates a diverse group of cell types that arises during vertebrate development. The abnormal formation or development of the NC results in neurocristopathies (NCPs), which are characterized by a broad spectrum of functional and morphological alterations. The impaired molecular mechanisms that give rise to these multiphenotypic diseases are not entirely clear yet. This fact, added to the high incidence of these disorders in the newborn population, has led to the development of systematic approaches for their understanding. In this article, we have systematically reviewed the ways in which experimentation with different animal and cell model systems has improved our knowledge of NCPs, and how these advances might contribute to the development of better diagnostic and therapeutic tools for the treatment of these pathologies. This article is categorized under: Congenital Diseases > Genetics/Genomics/Epigenetics Congenital Diseases > Stem Cells and Development Congenital Diseases > Molecular and Cellular Physiology Neurological Diseases > Genetics/Genomics/Epigenetics.
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Affiliation(s)
- Santiago Cerrizuela
- Division of Molecular Neurobiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina
| | - Guillermo A Vega-Lopez
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Karla Méndez-Maldonado
- Instituto de Fisiología Celular - Neurociencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Departamento de Fisiología y Farmacología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Iván Velasco
- Instituto de Fisiología Celular - Neurociencias, Universidad Nacional Autónoma de México, Ciudad de México, Mexico.,Laboratorio de Reprogramación Celular del Instituto de Fisiología Celular, UNAM en el Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suárez", Ciudad de México, Mexico
| | - Manuel J Aybar
- Instituto Superior de Investigaciones Biológicas (INSIBIO, CONICET-UNT), Tucumán, Argentina.,Instituto de Biología "Dr. Francisco D. Barbieri", Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Tucumán, Argentina
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3
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Penatzer JA, Prince N, Miller JV, Newman M, Lynch C, Hobbs GR, Boyd JW. Corticosterone and chlorpyrifos oxon exposure elicits spatiotemporal MAPK phosphoprotein signaling in a mouse brain. Food Chem Toxicol 2021; 155:112421. [PMID: 34280473 DOI: 10.1016/j.fct.2021.112421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/26/2022]
Abstract
Chlorpyrifos (CPF) is one of the most widely-used pesticides globally for agricultural purposes. Certain occupations (e.g., farmers, military) are at an increased risk for high-dose exposure to CPF, which can lead to seizures and irreversible brain injury. Workers with the highest risk of exposure typically experience increased circulating cortisol levels, which is related to physiological stress. To better represent this exposure scenario, a mouse model utilized exogenous administration of corticosterone (CORT; high physiologic stress mimic) in combination with chlorpyrifos oxon (CPO; oxon metabolite of CPF); this combination increases neuroinflammation post-exposure. In the present study adult male C57BL/6J mice were given CORT (200 μg/mL) in drinking water for seven days followed by a single intraperitoneal injection of CPO (8.0 mg/kg) on day eight, and euthanized 0.5, 2, and 24 h post-injection. Ten post-translationally modified proteins were measured in the frontal cortex and striatum to evaluate brain region-specific effects. The spatiotemporal response to CORT + CPO sequentially activated phosphoproteins (p-ERK1/2, p-MEK1/2, p-JNK) involved in mitogen-activated protein kinase (MAPK) signaling. Observed p-ZAP70 responses further integrated MAPK signaling and provided a spatiotemporal connection between protein phosphorylation and neuroinflammation. This study provides insight into the spatiotemporal cellular signaling cascade following CORT + CPO exposure that represent these vulnerable populations.
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Affiliation(s)
- Julia A Penatzer
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Nicole Prince
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | | | - Mackenzie Newman
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Cayla Lynch
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA; Cellular and Integrative Physiology Department, West Virginia University School of Medicine, Morgantown, WV, USA
| | - Gerald R Hobbs
- Department of Statistics, West Virginia University, Morgantown, WV, USA
| | - Jonathan W Boyd
- Department of Orthopaedics, West Virginia University School of Medicine, Morgantown, WV, USA.
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Bougen-Zhukov NM, Lee YY, Lee JYJ, Lee P, Loo LH. PI3K Catalytic Subunits α and β Modulate Cell Death and IL-6 Secretion Induced by Talc Particles in Human Lung Carcinoma Cells. Am J Respir Cell Mol Biol 2020; 62:331-341. [PMID: 31513749 DOI: 10.1165/rcmb.2019-0050oc] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hydrated magnesium silicate (or "talc" particles) is a sclerosis agent commonly used in the management of malignant pleural effusions, a common symptom of metastatic diseases, including lung cancers. However, the direct effects of talc particles to lung carcinoma cells, which can be found in the malignant pleural effusion fluids from patients with lung cancer, are not fully understood. Here, we report a study of the signaling pathways that can modulate the cell death and IL-6 secretion induced by talc particles in human lung carcinoma cells. We found that talc-sensitive cells have higher mRNA and protein expression of PI3K catalytic subunits α and β. Further experiments confirmed that modulation (inhibition or activation) of the PI3K pathway reduces or enhances cellular sensitivity to talc particles, respectively, independent of the inflammasome. By knocking down specific PI3K isoforms, we also confirmed that both PI3Kα and -β mediate the observed talc effects. Our results suggest a novel role of the PI3K pathway in talc-induced cell death and IL-6 secretion in lung carcinoma cells. These cellular events are known to drive fibrosis, and thus further studies of the PI3K pathway may provide a better understanding of the mechanisms of talc sclerosis in the malignant pleural space.
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Affiliation(s)
| | - Yin Yeng Lee
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Jia-Ying Joey Lee
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore, Singapore
| | - Pyng Lee
- Division of Respiratory and Critical Care, National University Hospital, National University Health System, Singapore, Singapore; and
| | - Lit-Hsin Loo
- Bioinformatics Institute, Agency for Science, Technology, and Research, Singapore, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Taverna JA, Hung CN, DeArmond DT, Chen M, Lin CL, Osmulski PA, Gaczynska ME, Wang CM, Lucio ND, Chou CW, Chen CL, Nazarullah A, Lampkin SR, Qiu L, Bearss DJ, Warner S, Whatcott CJ, Mouritsen L, Wade M, Weitman S, Mesa RA, Kirma NB, Chao WT, Huang THM. Single-Cell Proteomic Profiling Identifies Combined AXL and JAK1 Inhibition as a Novel Therapeutic Strategy for Lung Cancer. Cancer Res 2020; 80:1551-1563. [PMID: 31992541 PMCID: PMC7127959 DOI: 10.1158/0008-5472.can-19-3183] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/10/2019] [Accepted: 01/23/2020] [Indexed: 12/15/2022]
Abstract
Cytometry by time-of-flight (CyTOF) simultaneously measures multiple cellular proteins at the single-cell level and is used to assess intertumor and intratumor heterogeneity. This approach may be used to investigate the variability of individual tumor responses to treatments. Herein, we stratified lung tumor subpopulations based on AXL signaling as a potential targeting strategy. Integrative transcriptome analyses were used to investigate how TP-0903, an AXL kinase inhibitor, influences redundant oncogenic pathways in metastatic lung cancer cells. CyTOF profiling revealed that AXL inhibition suppressed SMAD4/TGFβ signaling and induced JAK1-STAT3 signaling to compensate for the loss of AXL. Interestingly, high JAK1-STAT3 was associated with increased levels of AXL in treatment-naïve tumors. Tumors with high AXL, TGFβ, and JAK1 signaling concomitantly displayed CD133-mediated cancer stemness and hybrid epithelial-to-mesenchymal transition features in advanced-stage patients, suggesting greater potential for distant dissemination. Diffusion pseudotime analysis revealed cell-fate trajectories among four different categories that were linked to clinicopathologic features for each patient. Patient-derived organoids (PDO) obtained from tumors with high AXL and JAK1 were sensitive to TP-0903 and ruxolitinib (JAK inhibitor) treatments, supporting the CyTOF findings. This study shows that single-cell proteomic profiling of treatment-naïve lung tumors, coupled with ex vivo testing of PDOs, identifies continuous AXL, TGFβ, and JAK1-STAT3 signal activation in select tumors that may be targeted by combined AXL-JAK1 inhibition. SIGNIFICANCE: Single-cell proteomic profiling of clinical samples may facilitate the optimal selection of novel drug targets, interpretation of early-phase clinical trial data, and development of predictive biomarkers valuable for patient stratification.
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Affiliation(s)
- Josephine A Taverna
- Division of Hematology and Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Chia-Nung Hung
- Department of Life Science, Tunghai University, Taichung, Taiwan
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Daniel T DeArmond
- Department of Cardiothoracic Surgery, University of Texas Health Science Center, San Antonio, Texas
| | - Meizhen Chen
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Chun-Lin Lin
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Pawel A Osmulski
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Maria E Gaczynska
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Chiou-Miin Wang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Nicholas D Lucio
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Chih-Wei Chou
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Chun-Liang Chen
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Alia Nazarullah
- Department of Pathology, University of Texas Health Science Center, San Antonio, Texas
| | - Shellye R Lampkin
- Department of Pathology, University of Texas Health Science Center, San Antonio, Texas
| | - Lianqun Qiu
- Department of Pathology, University of Texas Health Science Center, San Antonio, Texas
| | - David J Bearss
- Tolero Pharmaceuticals, Department of Biomarker and Drug Discovery, Lehi, Utah
| | - Steven Warner
- Tolero Pharmaceuticals, Department of Biomarker and Drug Discovery, Lehi, Utah
| | - Clifford J Whatcott
- Tolero Pharmaceuticals, Department of Biomarker and Drug Discovery, Lehi, Utah
| | - Lars Mouritsen
- Tolero Pharmaceuticals, Department of Biomarker and Drug Discovery, Lehi, Utah
| | - Mark Wade
- Tolero Pharmaceuticals, Department of Biomarker and Drug Discovery, Lehi, Utah
| | - Steven Weitman
- Institute for Drug Development, University of Texas Health Science Center, San Antonio, Texas
| | - Ruben A Mesa
- Division of Hematology and Oncology, Department of Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Nameer B Kirma
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas
| | - Wei-Ting Chao
- Department of Life Science, Tunghai University, Taichung, Taiwan.
| | - Tim H-M Huang
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas.
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Lee JYJ, Miller JA, Basu S, Kee TZV, Loo LH. Building predictive in vitro pulmonary toxicity assays using high-throughput imaging and artificial intelligence. Arch Toxicol 2018; 92:2055-2075. [PMID: 29705884 PMCID: PMC6002469 DOI: 10.1007/s00204-018-2213-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 04/25/2018] [Indexed: 01/22/2023]
Abstract
Human lungs are susceptible to the toxicity induced by soluble xenobiotics. However, the direct cellular effects of many pulmonotoxic chemicals are not always clear, and thus, a general in vitro assay for testing pulmonotoxicity applicable to a wide variety of chemicals is not currently available. Here, we report a study that uses high-throughput imaging and artificial intelligence to build an in vitro pulmonotoxicity assay by automatically comparing and selecting human lung-cell lines and their associated quantitative phenotypic features most predictive of in vivo pulmonotoxicity. This approach is called “High-throughput In vitro Phenotypic Profiling for Toxicity Prediction” (HIPPTox). We found that the resulting assay based on two phenotypic features of a human bronchial epithelial cell line, BEAS-2B, can accurately classify 33 reference chemicals with human pulmonotoxicity information (88.8% balance accuracy, 84.6% sensitivity, and 93.0% specificity). In comparison, the predictivity of a standard cell-viability assay on the same set of chemicals is much lower (77.1% balanced accuracy, 84.6% sensitivity, and 69.5% specificity). We also used the assay to evaluate 17 additional test chemicals with unknown/unclear human pulmonotoxicity, and experimentally confirmed that many of the pulmonotoxic reference and predicted-positive test chemicals induce DNA strand breaks and/or activation of the DNA-damage response (DDR) pathway. Therefore, HIPPTox helps us to uncover these common modes-of-action of pulmonotoxic chemicals. HIPPTox may also be applied to other cell types or models, and accelerate the development of predictive in vitro assays for other cell-type- or organ-specific toxicities.
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Affiliation(s)
- Jia-Ying Joey Lee
- Bioinformatics Institute, Agency for Science, Technology, and Research, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - James Alastair Miller
- Bioinformatics Institute, Agency for Science, Technology, and Research, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Sreetama Basu
- Bioinformatics Institute, Agency for Science, Technology, and Research, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Ting-Zhen Vanessa Kee
- Bioinformatics Institute, Agency for Science, Technology, and Research, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore
| | - Lit-Hsin Loo
- Bioinformatics Institute, Agency for Science, Technology, and Research, 30 Biopolis Street, #07-01 Matrix, Singapore, 138671, Singapore.
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DRUG-NEM: Optimizing drug combinations using single-cell perturbation response to account for intratumoral heterogeneity. Proc Natl Acad Sci U S A 2018; 115:E4294-E4303. [PMID: 29654148 PMCID: PMC5939057 DOI: 10.1073/pnas.1711365115] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Single-cell high-throughput technologies enable the ability to identify combination cancer therapies that account for intratumoral heterogeneity, a phenomenon that has been shown to influence the effectiveness of cancer treatment. We developed and applied an approach that identifies top-ranking drug combinations based on the single-cell perturbation response when an individual tumor sample is screened against a panel of single drugs. This approach optimizes drug combinations by choosing the minimum number of drugs that produce the maximal intracellular desired effects for an individual sample. An individual malignant tumor is composed of a heterogeneous collection of single cells with distinct molecular and phenotypic features, a phenomenon termed intratumoral heterogeneity. Intratumoral heterogeneity poses challenges for cancer treatment, motivating the need for combination therapies. Single-cell technologies are now available to guide effective drug combinations by accounting for intratumoral heterogeneity through the analysis of the signaling perturbations of an individual tumor sample screened by a drug panel. In particular, Mass Cytometry Time-of-Flight (CyTOF) is a high-throughput single-cell technology that enables the simultaneous measurements of multiple (>40) intracellular and surface markers at the level of single cells for hundreds of thousands of cells in a sample. We developed a computational framework, entitled Drug Nested Effects Models (DRUG-NEM), to analyze CyTOF single-drug perturbation data for the purpose of individualizing drug combinations. DRUG-NEM optimizes drug combinations by choosing the minimum number of drugs that produce the maximal desired intracellular effects based on nested effects modeling. We demonstrate the performance of DRUG-NEM using single-cell drug perturbation data from tumor cell lines and primary leukemia samples.
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Abstract
The Lush Science Prize 2016 was awarded to Daniele Zink and Lit-Hsin Loo for the interdisciplinary and collaborative work between their research groups in developing alternative methods for the prediction of nephrotoxicity in humans. The collaboration has led to the establishment of a series of pioneering alternative methods for nephrotoxicity prediction, which includes: predictive gene expression markers based on pro-inflammatory responses; predictive in vitro cellular models based on pluripotent stem cell-derived proximal tubular-like cells; and predictive cellular phenotypic markers based on chromatin and cytoskeletal changes. A high-throughput method was established for chemical testing, which is currently being used to predict the potential human nephrotoxicity of ToxCast compounds in collaboration with the US Environmental Protection Agency. Similar high-throughput imaging-based methodologies are currently being developed and adapted by the Zink and Loo groups, to include other human organs and cell types. The ultimate goal is to develop a portfolio of methods accepted for the accurate prediction of human organ-specific toxicity and the consequent replacement of animal experiments.
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Affiliation(s)
- Lit-Hsin Loo
- Bioinformatics Institute (BII), Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Daniele Zink
- Institute of Bioengineering and Nanotechnology (IBN), Singapore
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The emergence of dynamic phenotyping. Cell Biol Toxicol 2017; 33:507-509. [DOI: 10.1007/s10565-017-9413-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 09/18/2017] [Indexed: 02/07/2023]
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