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Sinkala M, Naran K, Ramamurthy D, Mungra N, Dzobo K, Martin D, Barth S. Machine learning and bioinformatic analyses link the cell surface receptor transcript levels to the drug response of breast cancer cells and drug off-target effects. PLoS One 2024; 19:e0296511. [PMID: 38306344 PMCID: PMC10836680 DOI: 10.1371/journal.pone.0296511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Accepted: 12/13/2023] [Indexed: 02/04/2024] Open
Abstract
Breast cancer responds variably to anticancer therapies, often leading to significant off-target effects. This study proposes that the variability in tumour responses and drug-induced adverse events is linked to the transcriptional profiles of cell surface receptors (CSRs) in breast tumours and normal tissues. We analysed multiple datasets to compare CSR expression in breast tumours with that in non-cancerous human tissues. Our findings correlate the drug responses of breast cancer cell lines with the expression levels of their targeted CSRs. Notably, we identified distinct differences in CSR expression between primary breast tumour subtypes and corresponding cell lines, which may influence drug response predictions. Additionally, we used clinical trial data to uncover associations between CSR gene expression in healthy tissues and the incidence of adverse drug reactions. This integrative approach facilitates the selection of optimal CSR targets for therapy, leveraging cell line dose-responses, CSR expression in normal tissues, and patient adverse event profiles.
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Affiliation(s)
- Musalula Sinkala
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine & Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Krupa Naran
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, Medical Biotechnology & Immunotherapy Research Unit, University of Cape Town, Cape Town, South Africa
| | - Dharanidharan Ramamurthy
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, Medical Biotechnology & Immunotherapy Research Unit, University of Cape Town, Cape Town, South Africa
| | - Neelakshi Mungra
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, Medical Biotechnology & Immunotherapy Research Unit, University of Cape Town, Cape Town, South Africa
| | - Kevin Dzobo
- Faculty of Health Sciences, Department of Medicine, Division of Dermatology, Medical Research Council-SA Wound Healing Unit, Hair and Skin Research Laboratory, Groote Schuur Hospital, University of Cape Town, Anzio Road, Observatory, Cape Town, South Africa
| | - Darren Martin
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine & Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Stefan Barth
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, Medical Biotechnology & Immunotherapy Research Unit, University of Cape Town, Cape Town, South Africa
- Faculty of Health Sciences, Department of Integrative Biomedical Sciences, South African Research Chair in Cancer Biotechnology, University of Cape Town, Cape Town, South Africa
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2
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Di Benedetto C, Khan T, Serrano-Saenz S, Rodriguez-Lemus A, Klomsiri C, Beutel TM, Thach A, Walczak H, Betancur P. Enhancer Clusters Drive Type I Interferon-Induced TRAIL Overexpression in Cancer, and Its Intracellular Protein Accumulation Fails to Induce Apoptosis. Cancers (Basel) 2023; 15:967. [PMID: 36765925 PMCID: PMC9913803 DOI: 10.3390/cancers15030967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 01/14/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) is a cytokine produced and secreted by immune cells in response to an infection, often in response to interferon (IFN) stimulation. In cancer, it has also been shown that IFN stimulates the production of TRAIL, and it has been proposed that this TRAIL can induce apoptosis in an autocrine or paracrine manner in different cancer cells. Yet, the mechanism mediating TRAIL upregulation and the implications of TRAIL as an apoptotic molecule in cancer cells are still poorly understood. We show here that in certain cancer cells, TRAIL is upregulated by enhancer clusters, potent genomic regulatory regions containing densely packed enhancers that have combinatorial and additive activity and that are usually found to be associated with cancer-promoting genes. Moreover, we found that TRAIL upregulation by IFNα is mediated by these enhancer clusters in breast and lung cancer cells. Surprisingly, IFNα stimulation leads to the intracellular accumulation of TRAIL protein in these cancer cells. Consequently, this TRAIL is not capable of inducing apoptosis. Our study provides novel insights into the mechanism behind the interferon-mediated upregulation of TRAIL and its protein accumulation in cancer cells. Further investigation is required to understand the role of intracellular TRAIL or depict the mechanisms mediating its apoptosis impairment in cancer cells.
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Affiliation(s)
- Carolina Di Benedetto
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Taimoor Khan
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Santiago Serrano-Saenz
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Anthony Rodriguez-Lemus
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Chananat Klomsiri
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Tim-Mathis Beutel
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
| | - Alysia Thach
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
| | - Henning Walczak
- CECAD Cluster of Excellence, University of Cologne, 50931 Cologne, Germany
- Center for Biochemistry, Medical Faculty, University of Cologne, 50931 Cologne, Germany
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London WC1E 6DD, UK
| | - Paola Betancur
- Department of Radiation Oncology, University of California, San Francisco (UCSF), San Francisco, CA 94143, USA
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3
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Targeting TRAIL Death Receptors in Triple-Negative Breast Cancers: Challenges and Strategies for Cancer Therapy. Cells 2022; 11:cells11233717. [PMID: 36496977 PMCID: PMC9739296 DOI: 10.3390/cells11233717] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
The tumor necrosis factor (TNF) superfamily member TNF-related apoptosis-inducing ligand (TRAIL) induces apoptosis in cancer cells via death receptor (DR) activation with little toxicity to normal cells or tissues. The selectivity for activating apoptosis in cancer cells confers an ideal therapeutic characteristic to TRAIL, which has led to the development and clinical testing of many DR agonists. However, TRAIL/DR targeting therapies have been widely ineffective in clinical trials of various malignancies for reasons that remain poorly understood. Triple negative breast cancer (TNBC) has the worst prognosis among breast cancers. Targeting the TRAIL DR pathway has shown notable efficacy in a subset of TNBC in preclinical models but again has not shown appreciable activity in clinical trials. In this review, we will discuss the signaling components and mechanisms governing TRAIL pathway activation and clinical trial findings discussed with a focus on TNBC. Challenges and potential solutions for using DR agonists in the clinic are also discussed, including consideration of the pharmacokinetic and pharmacodynamic properties of DR agonists, patient selection by predictive biomarkers, and potential combination therapies. Moreover, recent findings on the impact of TRAIL treatment on the immune response, as well as novel strategies to address those challenges, are discussed.
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4
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Bozkurt E, Düssmann H, Salvucci M, Cavanagh BL, Van Schaeybroeck S, Longley DB, Martin SJ, Prehn JHM. TRAIL signaling promotes entosis in colorectal cancer. J Cell Biol 2021; 220:212649. [PMID: 34546352 PMCID: PMC8563286 DOI: 10.1083/jcb.202010030] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 07/14/2021] [Accepted: 08/31/2021] [Indexed: 11/22/2022] Open
Abstract
Entosis is a form of nonphagocytic cell-in-cell (CIC) interaction where a living cell enters into another. Tumors show evidence of entosis; however, factors controlling entosis remain to be elucidated. Here, we find that besides inducing apoptosis, TRAIL signaling is a potent activator of entosis in colon cancer cells. Initiation of both apoptosis and entosis requires TRAIL receptors DR4 and DR5; however, induction of apoptosis and entosis diverges at caspase-8 as its structural presence is sufficient for induction of entosis but not apoptosis. Although apoptosis and entosis are morphologically and biochemically distinct, knockout of Bax and Bak, or inhibition of caspases, also inhibits entotic cell death and promotes survival and release of inner cells. Analysis of colorectal cancer tumors reveals a significant association between TRAIL signaling and CIC structures. Finally, the presence of CIC structures in the invasive front regions of colorectal tumors shows a strong correlation with adverse patient prognosis.
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Affiliation(s)
- Emir Bozkurt
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland.,Department of Genetics and Bioengineering, Faculty of Engineering, Izmir University of Economics, Balcova, Izmir, Turkey
| | - Heiko Düssmann
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Brenton L Cavanagh
- Cellular and Molecular Imaging Core, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Sandra Van Schaeybroeck
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Daniel B Longley
- Centre for Cancer Research and Cell Biology, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, Belfast, UK
| | - Seamus J Martin
- Molecular Cell Biology Laboratory, Department of Genetics, The Smurfit Institute, Trinity College, Dublin, Ireland
| | - Jochen H M Prehn
- Department of Physiology and Medical Physics, Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
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5
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Lim B, Greer Y, Lipkowitz S, Takebe N. Novel Apoptosis-Inducing Agents for the Treatment of Cancer, a New Arsenal in the Toolbox. Cancers (Basel) 2019; 11:cancers11081087. [PMID: 31370269 PMCID: PMC6721450 DOI: 10.3390/cancers11081087] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/11/2019] [Accepted: 07/17/2019] [Indexed: 02/06/2023] Open
Abstract
Evasion from apoptosis is an important hallmark of cancer cells. Alterations of apoptosis pathways are especially critical as they confer resistance to conventional anti-cancer therapeutics, e.g., chemotherapy, radiotherapy, and targeted therapeutics. Thus, successful induction of apoptosis using novel therapeutics may be a key strategy for preventing recurrence and metastasis. Inhibitors of anti-apoptotic molecules and enhancers of pro-apoptotic molecules are being actively developed for hematologic malignancies and solid tumors in particular over the last decade. However, due to the complicated apoptosis process caused by a multifaceted connection with cross-talk pathways, protein–protein interaction, and diverse resistance mechanisms, drug development within the category has been extremely challenging. Careful design and development of clinical trials incorporating predictive biomarkers along with novel apoptosis-inducing agents based on rational combination strategies are needed to ensure the successful development of these molecules. Here, we review the landscape of currently available direct apoptosis-targeting agents in clinical development for cancer treatment and update the related biomarker advancement to detect and validate the efficacy of apoptosis-targeted therapies, along with strategies to combine them with other agents.
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Affiliation(s)
- Bora Lim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Yoshimi Greer
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Stanley Lipkowitz
- Women's Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Naoko Takebe
- Early Clinical Trials Development, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA.
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6
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Quantitative single cell analysis uncovers the life/death decision in CD95 network. PLoS Comput Biol 2018; 14:e1006368. [PMID: 30256782 PMCID: PMC6175528 DOI: 10.1371/journal.pcbi.1006368] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 10/08/2018] [Accepted: 07/16/2018] [Indexed: 11/20/2022] Open
Abstract
CD95/Fas/APO-1 is a member of the death receptor family that triggers apoptotic and anti-apoptotic responses in particular, NF-κB. These responses are characterized by a strong heterogeneity within a population of cells. To determine how the cell decides between life and death we developed a computational model supported by imaging flow cytometry analysis of CD95 signaling. Here we show that CD95 stimulation leads to the induction of caspase and NF-κB pathways simultaneously in one cell. The related life/death decision strictly depends on cell-to-cell variability in the formation of the death-inducing complex (DISC) on one side (extrinsic noise) vs. stochastic gene expression of the NF-κB pathway on the other side (intrinsic noise). Moreover, our analysis has uncovered that the stochasticity in apoptosis and NF-kB pathways leads not only to survival or death of a cell, but also causes a third type of response to CD95 stimulation that we termed ambivalent response. Cells in the ambivalent state can undergo cell death or survive which was subsequently validated by experiments. Taken together, we have uncovered how these two competing pathways control the fate of a cell, which in turn plays an important role for development of anti-cancer therapies. Activation of death receptor (DR) family has been reported to activate both apoptotic as well as anti-apoptotic responses. Molecular mechanisms underlying the intricate details of this crosstalk have not been established yet. Here we show that these pathways are triggered simultaneously in one cell. Furthermore, using stochastic computational modeling we uncovered how an individual cell undergoes apoptosis, while other cells survive upon the same DR activation conditions. This was only possible by combination of computational modeling supported by experimental validation based on the state of the art single cell analysis. The latter included cutting edge technology of imaging flow cytometry, which combines microscopy and flow cytometry in one measurement circuit enabling quantitative analysis of endogenous cellular protein levels estimated from a large number of cells simultaneously. This allowed to shed the light on the question how a single cell possibly avoids apoptosis, which is a highly actual topic in the field of cancer research and development of efficient anti-cancer therapies.
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7
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Davies AE, Albeck JG. Microenvironmental Signals and Biochemical Information Processing: Cooperative Determinants of Intratumoral Plasticity and Heterogeneity. Front Cell Dev Biol 2018; 6:44. [PMID: 29732370 PMCID: PMC5921997 DOI: 10.3389/fcell.2018.00044] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 04/03/2018] [Indexed: 12/25/2022] Open
Abstract
Intra-tumor cellular heterogeneity is a major challenge in cancer therapy. Tumors are composed of multiple phenotypic subpopulations that vary in their ability to initiate metastatic tumors and in their sensitivity to chemotherapy. In many cases, cells can transition between these subpopulations, not by genetic mutation, but instead through reversible changes in signal transduction or gene expression programs. This plasticity begins at the level of the microenvironment where local autocrine and paracrine signals, exosomes, tumor–stroma interactions, and extracellular matrix (ECM) composition create a signaling landscape that varies over space and time. The integration of this complex array of signals engages signaling pathways that control gene expression. The resulting modulation of gene expression programs causes individual cells to sample a wide array of phenotypic states that support tumor growth, dissemination, and therapeutic resistance. In this review, we discuss how information flows dynamically within the microenvironmental landscape to inform cell state decisions and to create intra-tumoral heterogeneity. We address the role of plasticity in the acquisition of transient and prolonged drug resistant states and discuss how targeted pharmacological modification of the signaling landscape may be able to constrain phenotypic plasticity, leading to improved treatment responses.
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Affiliation(s)
- Alexander E Davies
- Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA, United States
| | - John G Albeck
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA, United States
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8
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Jana S, Hsieh AC, Gupta R. Reciprocal amplification of caspase-3 activity by nuclear export of a putative human RNA-modifying protein, PUS10 during TRAIL-induced apoptosis. Cell Death Dis 2017; 8:e3093. [PMID: 28981101 PMCID: PMC5682645 DOI: 10.1038/cddis.2017.476] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/18/2017] [Accepted: 08/24/2017] [Indexed: 02/07/2023]
Abstract
Pus10 is a pseudouridine synthase present in Archaea and Eukarya, but not in Bacteria and yeast. It has been suggested that the human PUS10 (DOBI) gene is needed during TRAIL-induced apoptosis. We analyzed the role of PUS10 in TRAIL-induced apoptosis by immunofluorescence, immunoblotting and several indicators of apoptosis. We examined several TRAIL-sensitive cell lines and we also examined some resistant cell lines after treatment with cycloheximide. PUS10 is mainly present in the nucleus. Early during apoptosis, PUS10 translocates to mitochondria via CRM1-mediated export with the concurrent release of cytochrome c and SMAC. Caspase-3 is required for PUS10 translocation, which reciprocally amplifies the activity of caspase-3 through the intrinsic/mitochondrial pathway. This suggests that in addition to cytoplasmic factors, nuclear factors also have a direct role in the major apoptosis pathways. However, p53 is not involved in TRAIL-induced PUS10 movement. The caspase-3-mediated movement of PUS10 and the release of mitochondrial contents enhancing caspase-3 activity creates a feedback amplification loop for caspase-3 action. Therefore, any defect in the movement or interactions of PUS10 would reduce the TRAIL sensitivity of tumor cells.
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Affiliation(s)
- Sujata Jana
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, IL 62901-4413, USA
| | - Andrew C Hsieh
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Ramesh Gupta
- Department of Biochemistry and Molecular Biology, Southern Illinois University, Carbondale, IL 62901-4413, USA
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9
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Abstract
Recent studies across multiple tumour types are starting to reveal a recurrent regulatory architecture in which genomic alterations cluster upstream of functional master regulator (MR) proteins, the aberrant activity of which is both necessary and sufficient to maintain tumour cell state. These proteins form small, hyperconnected and autoregulated modules (termed tumour checkpoints) that are increasingly emerging as optimal biomarkers and therapeutic targets. Crucially, as their activity is mostly dysregulated in a post-translational manner, rather than by mutations in their corresponding genes or by differential expression, the identification of MR proteins by conventional methods is challenging. In this Opinion article, we discuss novel methods for the systematic analysis of MR proteins and of the modular regulatory architecture they implement, including their use as a valuable reductionist framework to study the genetic heterogeneity of human disease and to drive key translational applications.
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Affiliation(s)
- Andrea Califano
- Department of Systems Biology, Columbia University, and the Departments of Biomedical Informatics, Biochemistry and Molecular Biophysics, JP Sulzberger Columbia Genome Center, Herbert Irving Comprehensive Cancer Center, Columbia University, New York, New York 10032, USA
| | - Mariano J Alvarez
- DarwinHealth, Inc., 3960 Broadway, Suite 540, New York, New York 10032, USA
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10
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Stage-Specific Changes in the Water, Na+, Cl- and K+ Contents of Organelles during Apoptosis, Demonstrated by a Targeted Cryo Correlative Analytical Approach. PLoS One 2016; 11:e0148727. [PMID: 26866363 PMCID: PMC4807926 DOI: 10.1371/journal.pone.0148727] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2015] [Accepted: 12/21/2015] [Indexed: 01/05/2023] Open
Abstract
Many studies have demonstrated changes in the levels of several ions during apoptosis, but a few recent studies have reported conflicting results concerning the changes in water content in apoptotic cells. We used a correlative light and cryo-scanning transmission electron microscopy method to quantify water and ion/element contents simultaneously at a nanoscale resolution in the various compartments of cells, from the onset to the end of apoptosis. We used stably transfected HeLa cells producing H2B-GFP to identify the stages of apoptosis in cells and for a targeted elemental analysis within condensed chromatin, nucleoplasm, mitochondria and the cytosol. We found that the compartments of apoptotic cells contained, on average, 10% more water than control cells. During mitochondrial outer membrane permeabilization, we observed a strong increase in the Na+ and Cl- contents of the mitochondria and a strong decrease in mitochondrial K+ content. During the first step in apoptotic volume decrease (AVD), Na+ and Cl- levels decreased in all cell compartments, but remained higher than those in control cells. Conversely, during the second step of AVD, Na+ and Cl- levels increased considerably in the nucleus and mitochondria. During these two steps of AVD, K+ content decreased steadily in all cell compartments. We also determined in vivo ion status during caspase-3 activity and chromatin condensation. Finally, we found that actinomycin D-tolerant cells had water and K+ contents similar to those of cells entering apoptosis but lower Na+ and Cl- contents than both cells entering apoptosis and control cells.
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11
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Flusberg DA, Sorger PK. Surviving apoptosis: life-death signaling in single cells. Trends Cell Biol 2015; 25:446-58. [PMID: 25920803 PMCID: PMC4570028 DOI: 10.1016/j.tcb.2015.03.003] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 03/19/2015] [Accepted: 03/19/2015] [Indexed: 12/16/2022]
Abstract
Tissue development and homeostasis are regulated by opposing pro-survival and pro-death signals. An interesting feature of the Tumor Necrosis Factor (TNF) family of ligands is that they simultaneously activate opposing signals within a single cell via the same ligand-receptor complex. The magnitude of pro-death events such as caspase activation and pro-survival events such as Nuclear Factor (NF)-κB activation vary not only from one cell type to the next but also among individual cells of the same type due to intrinsic and extrinsic noise. The molecules involved in these pro-survival and/or pro-death pathways, and the different phenotypes that result from their activities, have been recently reviewed. Here we focus on the impact of cell-to-cell variability in the strength of these opposing signals on shaping cell fate decisions.
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Affiliation(s)
- Deborah A Flusberg
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Peter K Sorger
- Laboratory of Systems Pharmacology, Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA.
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12
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Ramji R, Wong VC, Chavali AK, Gearhart LM, Miller-Jensen K. A passive-flow microfluidic device for imaging latent HIV activation dynamics in single T cells. Integr Biol (Camb) 2015; 7:998-1010. [PMID: 26138068 DOI: 10.1039/c5ib00094g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Quantifying cell-to-cell variability in drug response dynamics is important when evaluating therapeutic efficacy. For example, optimizing latency reversing agents (LRAs) for use in a clinical "activate-and-kill" strategy to purge the latent HIV reservoir in patients requires minimizing heterogeneous viral activation dynamics. To evaluate how heterogeneity in latent HIV activation varies across a range of LRAs, we tracked drug-induced response dynamics in single cells via live-cell imaging using a latent HIV-GFP reporter virus in a clonal Jurkat T cell line. To enable these studies in suspension cells, we designed a simple method to capture an array of single Jurkat T cells using a passive-flow microfluidic device. Our device, which does not require external pumps or tubing, can trap hundreds of cells within minutes with a high retention rate over 12 hours of imaging. Using this device, we quantified heterogeneity in viral activation stimulated by transcription factor (TF) activators and histone deacetylase (HDAC) inhibitors. Generally, TF activators resulted in both faster onset of viral activation and faster rates of production, while HDAC inhibitors resulted in more uniform onset times, but more heterogeneous rates of production. Finally, we demonstrated that while onset time of viral gene expression and rate of viral production together predict total HIV activation, rate and onset time were not correlated within the same individual cell, suggesting that these features are regulated independently. Overall, our results reveal drug-specific patterns of noisy HIV activation dynamics not previously identified in static single-cell assays, which may require consideration for the most effective activate-and-kill regime.
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Affiliation(s)
- Ramesh Ramji
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511
| | - Victor C Wong
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511
| | - Arvind K Chavali
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511
| | - Larisa M Gearhart
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511.,Department of Biology, Mills College, Oakland, CA 94613
| | - Kathryn Miller-Jensen
- Department of Biomedical Engineering, Yale University, New Haven, CT 06511.,Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511
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13
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Bertaux F, Stoma S, Drasdo D, Batt G. Modeling dynamics of cell-to-cell variability in TRAIL-induced apoptosis explains fractional killing and predicts reversible resistance. PLoS Comput Biol 2014; 10:e1003893. [PMID: 25340343 PMCID: PMC4207462 DOI: 10.1371/journal.pcbi.1003893] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 09/04/2014] [Indexed: 12/22/2022] Open
Abstract
Isogenic cells sensing identical external signals can take markedly different decisions. Such decisions often correlate with pre-existing cell-to-cell differences in protein levels. When not neglected in signal transduction models, these differences are accounted for in a static manner, by assuming randomly distributed initial protein levels. However, this approach ignores the a priori non-trivial interplay between signal transduction and the source of this cell-to-cell variability: temporal fluctuations of protein levels in individual cells, driven by noisy synthesis and degradation. Thus, modeling protein fluctuations, rather than their consequences on the initial population heterogeneity, would set the quantitative analysis of signal transduction on firmer grounds. Adopting this dynamical view on cell-to-cell differences amounts to recast extrinsic variability into intrinsic noise. Here, we propose a generic approach to merge, in a systematic and principled manner, signal transduction models with stochastic protein turnover models. When applied to an established kinetic model of TRAIL-induced apoptosis, our approach markedly increased model prediction capabilities. One obtains a mechanistic explanation of yet-unexplained observations on fractional killing and non-trivial robust predictions of the temporal evolution of cell resistance to TRAIL in HeLa cells. Our results provide an alternative explanation to survival via induction of survival pathways since no TRAIL-induced regulations are needed and suggest that short-lived anti-apoptotic protein Mcl1 exhibit large and rare fluctuations. More generally, our results highlight the importance of accounting for stochastic protein turnover to quantitatively understand signal transduction over extended durations, and imply that fluctuations of short-lived proteins deserve particular attention.
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Affiliation(s)
| | | | - Dirk Drasdo
- INRIA Paris-Rocquencourt, Le Chesnay, France
- Laboratoire Jacques-Louis Lions (LJLL), University of Paris 6 (UPMC) - CNRS (UMR7598), Paris, France
| | - Gregory Batt
- INRIA Paris-Rocquencourt, Le Chesnay, France
- * E-mail:
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14
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Fienberg HG, Nolan GP. Mass cytometry to decipher the mechanism of nongenetic drug resistance in cancer. Curr Top Microbiol Immunol 2014; 377:85-94. [PMID: 24578267 DOI: 10.1007/82_2014_365] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nongenetic resistance has recently been described as a major impediment to effective cancer therapy. Nongenetic resistance is challenging to study since it occurs nonuniformly, even in cell lines, and can involve the interplay of multiple survival pathways. Until recently, no technology allowed measurement of large-scale alterations in survival pathways with single-cell resolution. Mass cytometry, a flow-based technique in which the activation of up to 50 proteins can be measured simultaneously in single-cell, now provides the ability to examine nongenetic resistance on the functional level on a cell-by-cell basis. The application of mass cytometry, in combination with new bioinformatic techniques, will allow fundamental questions on nongenetic resistance to be addressed: Is resistance caused by selection of cells with a pre-existing survival phenotype or induction of a survival program? Which survival pathways are necessary for nongenetic resistance and how do they interact? Currently, mass cytometry is being used to investigate the mechanism of nongenetic resistance to TRAIL-induced apoptosis. The approaches being developed to understand resistance to TRAIL will likely be applied to elucidate the mechanisms of nongenetic resistance broadly and in the clinic.
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Affiliation(s)
- Harris G Fienberg
- Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA
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15
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Jeschke M, Baumgärtner S, Legewie S. Determinants of cell-to-cell variability in protein kinase signaling. PLoS Comput Biol 2013; 9:e1003357. [PMID: 24339758 PMCID: PMC3854479 DOI: 10.1371/journal.pcbi.1003357] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2013] [Accepted: 10/06/2013] [Indexed: 12/28/2022] Open
Abstract
Cells reliably sense environmental changes despite internal and external fluctuations, but the mechanisms underlying robustness remain unclear. We analyzed how fluctuations in signaling protein concentrations give rise to cell-to-cell variability in protein kinase signaling using analytical theory and numerical simulations. We characterized the dose-response behavior of signaling cascades by calculating the stimulus level at which a pathway responds (‘pathway sensitivity’) and the maximal activation level upon strong stimulation. Minimal kinase cascades with gradual dose-response behavior show strong variability, because the pathway sensitivity and the maximal activation level cannot be simultaneously invariant. Negative feedback regulation resolves this trade-off and coordinately reduces fluctuations in the pathway sensitivity and maximal activation. Feedbacks acting at different levels in the cascade control different aspects of the dose-response curve, thereby synergistically reducing the variability. We also investigated more complex, ultrasensitive signaling cascades capable of switch-like decision making, and found that these can be inherently robust to protein concentration fluctuations. We describe how the cell-to-cell variability of ultrasensitive signaling systems can be actively regulated, e.g., by altering the expression of phosphatase(s) or by feedback/feedforward loops. Our calculations reveal that slow transcriptional negative feedback loops allow for variability suppression while maintaining switch-like decision making. Taken together, we describe design principles of signaling cascades that promote robustness. Our results may explain why certain signaling cascades like the yeast pheromone pathway show switch-like decision making with little cell-to-cell variability. Cells sense their surroundings and respond to soluble factors in the extracellular space. Extracellular factors frequently induce heterogeneous responses, thereby restricting the biological outcome to a fraction of the cell population. However, the question arises how such cell-to-cell variability can be controlled, because some cellular systems show a very homogenous response at a defined level of an extracellular stimulus. We derived an analytical framework to systematically characterize the cell-to-cell variability of intracellular signaling pathways which transduce external signals. We analyzed how heterogeneity arises from fluctuations in the total concentrations of signaling proteins because this is the main source of variability in eukaryotic systems. We find that signaling pathways can be highly variable or inherently invariant, depending on the kinetic parameters and the structural features of the cascade. Our results indicate that the cell-to-cell variability can be reduced by negative feedback in the cascade or by signaling crosstalk between parallel pathways. We precisely define the role of negative feedback loops in variability suppression, and show that different aspects of the dose-response curve can be controlled, depending on the feedback kinetics and site of action in the cascade. This work constitutes a first step towards a systematic understanding of cell-to-cell variability in signal transduction.
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Affiliation(s)
| | | | - Stefan Legewie
- Institute of Molecular Biology (IMB), Mainz, Germany
- * E-mail:
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16
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Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR. Special section dedicated to The Sixth q-bio Conference: meeting report and preface. Phys Biol 2013; 10:030301. [DOI: 10.1088/1478-3975/10/3/030301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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17
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Flusberg DA, Roux J, Spencer SL, Sorger PK. Cells surviving fractional killing by TRAIL exhibit transient but sustainable resistance and inflammatory phenotypes. Mol Biol Cell 2013; 24:2186-200. [PMID: 23699397 PMCID: PMC3708725 DOI: 10.1091/mbc.e12-10-0737] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cells that survive fractional killing by TRAIL or FasR agonists enter a state of resistance accompanied by inflammatory phenotypes. This state is transient, decaying over the course of several days, but can be sustained by periodic TRAIL treatments. This finding has implications for optimal dosing strategies of extrinsic cell death agents. When clonal populations of human cells are exposed to apoptosis-inducing agents, some cells die and others survive. This fractional killing arises not from mutation but from preexisting, stochastic differences in the levels and activities of proteins regulating apoptosis. Here we examine the properties of cells that survive treatment with agonists of two distinct death receptors, tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) and anti-FasR antibodies. We find that “survivor” cells are highly resistant to a second ligand dose applied 1 d later. Resistance is reversible, resetting after several days of culture in the absence of death ligand. “Reset” cells appear identical to drug-naive cells with respect to death ligand sensitivity and gene expression profiles. TRAIL survivors are cross-resistant to activators of FasR and vice versa and exhibit an NF-κB–dependent inflammatory phenotype. Remarkably, reversible resistance is induced in the absence of cell death when caspase inhibitors are present and can be sustained for 1 wk or more, also without cell death, by periodic ligand exposure. Thus stochastic differences in cell state can have sustained consequences for sensitivity to prodeath ligands and acquisition of proinflammatory phenotypes. The important role played by periodicity in TRAIL exposure for induction of opposing apoptosis and survival mechanisms has implications for the design of optimal therapeutic agents and protocols.
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Affiliation(s)
- Deborah A Flusberg
- Center for Cell Decision Processes, Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
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