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Wackowski K, Zhu X, Shen S, Zhang M, Qu J, Read LK. RESC14 and RESC8 cooperate to mediate RESC function and dynamics during trypanosome RNA editing. Nucleic Acids Res 2024:gkae561. [PMID: 38967000 DOI: 10.1093/nar/gkae561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 05/16/2024] [Accepted: 06/18/2024] [Indexed: 07/06/2024] Open
Abstract
Mitochondrial transcripts in Trypanosoma brucei require extensive uridine insertion/deletion RNA editing to generate translatable open reading frames. The RNA editing substrate binding complex (RESC) serves as the scaffold that coordinates the protein-protein and protein-RNA interactions during editing. RESC broadly contains two modules termed the guide RNA binding complex (GRBC) and the RNA editing mediator complex (REMC), as well as organizer proteins. How the protein and RNA components of RESC dynamically interact to facilitate editing is not well understood. Here, we examine the roles of organizer proteins, RESC8 and RESC14, in facilitating RESC dynamics. High-throughput sequencing of editing intermediates reveals an overlapping RESC8 and RESC14 function during editing progression across multiple transcripts. Blue native PAGE analysis demonstrates that RESC14 is essential for incorporation of RESC8 into a large RNA-containing complex, while RESC8 is important in recruiting a smaller ribonucleoprotein complex (RNP) to this large complex. Proximity labeling shows that RESC14 is important for stable RESC protein-protein interactions, as well as RESC-RECC associations. Together, our data support a model in which RESC14 is necessary for assembly of editing competent RESC through recruitment of an RNP containing RESC8, GRBC and gRNA to REMC and mRNA.
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Affiliation(s)
- Katherine Wackowski
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
| | - Xiaoyu Zhu
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA and NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA and NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Ming Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA and NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 14214, USA and NYS Center of Excellence in Bioinformatics and Life Sciences, University at Buffalo, Buffalo, NY 14203, USA
| | - Laurie K Read
- Department of Microbiology and Immunology, Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY 14203, USA
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Miao X, Shen S, Koch G, Wang X, Li J, Shen X, Qu J, Straubinger RM, Jusko WJ. Systems pharmacodynamic model of combined gemcitabine and trabectedin in pancreatic cancer cells. Part I.Çô Effects on signal transduction pathways related to tumor growth. J Pharm Sci 2024; 113:214-227. [PMID: 38498417 PMCID: PMC11017371 DOI: 10.1016/j.xphs.2023.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/22/2023] [Accepted: 10/22/2023] [Indexed: 03/20/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is often chemotherapy-resistant, and novel drug combinations would fill an unmet clinical need. Previously we reported synergistic cytotoxic effects of gemcitabine and trabectedin on pancreatic cancer cells, but underlying protein-level interaction mechanisms remained unclear. We employed a reliable, sensitive, comprehensive, quantitative, high-throughput IonStar proteomic workflow to investigate the time course of gemcitabine and trabectedin effects, alone and combined, upon pancreatic cancer cells. MiaPaCa-2 cells were incubated with vehicle (controls), gemcitabine, trabectedin, and their combinations over 72 hours. Samples were collected at intervals and analyzed using the label-free IonStar liquid chromatography-mass spectrometry (LC-MS/MS) workflow to provide temporal quantification of protein expression for 4,829 proteins in four experimental groups. To characterize diverse signal transduction pathways, a comprehensive systems pharmacodynamic (SPD) model was developed. The analysis is presented in two parts. Here, Part I describes drug responses in cancer cell growth and migration pathways included in the full model: receptor tyrosine kinase- (RTK), integrin-, G-protein coupled receptor- (GPCR), and calcium-signaling pathways. The developed model revealed multiple underlying mechanisms of drug actions, provides insight into the basis of drug interaction synergism, and offers a scientific rationale for potential drug combination strategies.
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Affiliation(s)
- Xin Miao
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States
| | - Shichen Shen
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States
| | - Gilbert Koch
- Pediatric Pharmacology and Pharmacometrics Research Center, University of Basel, Children's Hospital, Basel, Switzerland
| | - Xue Wang
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States; Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - Jun Li
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States
| | - Xiaomeng Shen
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States
| | - Robert M Straubinger
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, United States; Department of Cell Stress Biology, Roswell Park Cancer Institute, Buffalo, NY, United States
| | - William J Jusko
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, United States.
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Cao Y, Harvey BP, Jin L, Westmoreland S, Wang J, Puri M, Yang Y, Robb HM, Tanriverdi S, Hu C, Wang X, Xin X, Liu Y, Macoritto MP, Smith KM, Tian Y, White K, Radstake TR, Kaymakcalan Z. Therapeutic TNF Inhibitors Exhibit Differential Levels of Efficacy in Accelerating Cutaneous Wound Healing. JID INNOVATIONS 2024; 4:100250. [PMID: 38226320 PMCID: PMC10788510 DOI: 10.1016/j.xjidi.2023.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/21/2023] [Accepted: 11/16/2023] [Indexed: 01/17/2024] Open
Abstract
Adalimumab but neither etanercept nor certolizumab-pegol has been reported to induce a wound-healing profile in vitro by regulating macrophage differentiation and matrix metalloproteinase expression, which may underlie the differences in efficacy between various TNF-α inhibitors in impaired wound healing in patients with hidradenitis suppurativa, a chronic inflammatory skin disease. To examine and compare the efficacy of various TNF inhibitors in cutaneous wound healing in vivo, a human TNF knock-in Leprdb/db mouse model was established to model the impaired cutaneous wound healing as seen in hidradenitis suppurativa. The vehicle group exhibited severe impairments in cutaneous wound healing. In contrast, adalimumab significantly accelerated healing, confirmed by both histologic assessment and a unique healing transcriptional profile. Moreover, adalimumab and infliximab showed similar levels of efficacy, but golimumab was less effective, along with etanercept and certolizumab-pegol. In line with histologic assessments, proteomics analyses from healing wounds exposed to various TNF inhibitors revealed distinct and differential wound-healing signatures that may underlie the differential efficacy of these inhibitors in accelerating cutaneous wound healing. Taken together, these data revealed that TNF inhibitors exhibited differential levels of efficacy in accelerating cutaneous wound healing in the impaired wound-healing model in vivo.
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Affiliation(s)
- Yonghao Cao
- Transformational and Translational Immunology Discovery, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Bohdan P. Harvey
- Transformational and Translational Immunology Discovery, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Liang Jin
- DMPK-BA, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Susan Westmoreland
- Phamacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Jing Wang
- Immunology Computational Biology, AbbVie Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Munish Puri
- Phamacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Yingli Yang
- Phamacology and Pathology, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Holly M. Robb
- Discovery Research, AbbVie, North Chicago, Illinois, USA
| | - Sultan Tanriverdi
- Transformational and Translational Immunology Discovery, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Chenqi Hu
- DMPK-BA, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Xue Wang
- DMPK-BA, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Xiaofeng Xin
- Global Biologics, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Yingchun Liu
- Immunology Computational Biology, AbbVie Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Michael P. Macoritto
- Immunology Computational Biology, AbbVie Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Kathleen M. Smith
- Immunology Computational Biology, AbbVie Cambridge Research Center, Cambridge, Massachusetts, USA
| | - Yu Tian
- DMPK-BA, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Kevin White
- Transformational and Translational Immunology Discovery, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Timothy R.D.J. Radstake
- Transformational and Translational Immunology Discovery, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
| | - Zehra Kaymakcalan
- Transformational and Translational Immunology Discovery, AbbVie Bioresearch Center, Worcester, Massachusetts, USA
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Miao X, Koch G, Shen S, Wang X, Li J, Shen X, Qu J, Straubinger RM, Jusko WJ. Systems Pharmacodynamic Model of Combined Gemcitabine and Trabectedin in Pancreatic Cancer Cells. Part II: Cell Cycle, DNA Damage Response, and Apoptosis Pathways. J Pharm Sci 2024; 113:235-245. [PMID: 37918792 PMCID: PMC10902796 DOI: 10.1016/j.xphs.2023.10.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/04/2023]
Abstract
Despite decades of research efforts, pancreatic adenocarcinoma (PDAC) continues to present a formidable clinical challenge, demanding innovative therapeutic approaches. In a prior study, we reported the synergistic cytotoxic effects of gemcitabine and trabectedin on pancreatic cancer cells. To investigate potential mechanisms underlying this synergistic pharmacodynamic interaction, liquid chromatography-mass spectrometry-based proteomic analysis was performed, and a systems pharmacodynamics model (SPD) was developed to capture pancreatic cancer cell responses to gemcitabine and trabectedin, alone and combined, at the proteome level. Companion report Part I describes the proteomic workflow and drug effects on the upstream portion of the SPD model related to cell growth and migration, specifically the RTK-, integrin-, GPCR-, and calcium-signaling pathways. This report presents Part II of the SPD model. Here we describe drug effects on pathways associated with cell cycle, DNA damage response (DDR), and apoptosis, and provide insights into underlying mechanisms. Drug combination effects on protein changes in the cell cycle- and apoptosis pathways contribute to the synergistic effects observed between gemcitabine and trabectedin. The SPD model was subsequently incorporated into our previously-established cell cycle model, forming a comprehensive, multi-scale quantification platform for evaluating drug effects across multiple scales, spanning the proteomic-, cellular-, and subcellular levels. This approach provides a quantitative mechanistic framework for evaluating drug-drug interactions in combination chemotherapy, and could potentially serve as a tool to predict combinatorial efficacy and assist in target selection.
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Affiliation(s)
- Xin Miao
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA
| | - Gilbert Koch
- Pediatric Pharmacology and Pharmacometrics Research Center, University of Basel, Children's Hospital, Basel, Switzerland
| | - Shichen Shen
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
| | - Xue Wang
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA; Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Jun Li
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
| | - Xiaomeng Shen
- Department of Biochemistry, School of Medicine and Biomedical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA
| | - Robert M Straubinger
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA; New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, USA; Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - William J Jusko
- Department of Pharmaceutical Sciences, University at Buffalo, SUNY, Buffalo, NY, USA.
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Rasam S, Lin Q, Shen S, Straubinger RM, Qu J. Highly Reproducible Quantitative Proteomics Analysis of Pancreatic Cancer Cells Reveals Proteome-Level Effects of a Novel Combination Drug Therapy That Induces Cancer Cell Death via Metabolic Remodeling and Activation of the Extrinsic Apoptosis Pathway. J Proteome Res 2023; 22:3780-3792. [PMID: 37906173 DOI: 10.1021/acs.jproteome.3c00463] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Pancreatic cancer patients have poor survival rates and are frequently treated using gemcitabine (Gem). However, initial tumor sensitivity often gives way to rapid development of resistance. Gem-based drug combinations are employed to increase efficacy and mitigate resistance, but our understanding of molecular-level drug interactions, which could assist in the development of more effective therapeutic regimens, is limited. Global quantitative proteomic analysis could provide novel mechanistic insights into drug combination interactions, but it is challenging to achieve high-quality quantitative proteomics analysis of the large sample sets that are typically required for drug combination studies. Here, we investigated molecular-level temporal interactions of Gem with BGJ398 (infigratinib), a recently approved pan-FGFR inhibitor, in multiple treatment groups (N = 42 samples) using IonStar, a robust large-scale proteomics method that employs well-controlled, ultrahigh-resolution MS1 quantification. A total of 5514 proteins in the sample set were quantified without missing data, requiring >2 unique peptides/protein, <1% protein false discovery rate (FDR), <0.1% peptide FDR, and CV < 10%. Functional analysis of the differentially altered proteins revealed drug-dysregulated processes such as metabolism, apoptosis, and antigen presentation pathways. These changes were validated experimentally using Seahorse metabolic assays and immunoassays. Overall, in-depth analysis of large-scale proteomics data provided novel insights into possible mechanisms by which FGFR inhibitors complement and enhance Gem activity in pancreatic cancers.
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Affiliation(s)
- Sailee Rasam
- Department of Biochemistry, University at Buffalo, Buffalo, New York 14260, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Qingxiang Lin
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14260, United States
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York 14203, United States
| | - Shichen Shen
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
| | - Robert M Straubinger
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14260, United States
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York 14203, United States
| | - Jun Qu
- Department of Biochemistry, University at Buffalo, Buffalo, New York 14260, United States
- New York State Center of Excellence in Bioinformatics and Life Sciences, 701 Ellicott Street, Buffalo, New York 14203, United States
- Department of Pharmaceutical Sciences, University at Buffalo, Buffalo, New York 14260, United States
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Elm and Carlton Streets, Buffalo, New York 14203, United States
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