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Ruiz-Sanmartín A, Ribas V, Suñol D, Chiscano-Camón L, Palmada C, Bajaña I, Larrosa N, González JJ, Canela N, Ferrer R, Ruiz-Rodríguez JC. Characterization of a proteomic profile associated with organ dysfunction and mortality of sepsis and septic shock. PLoS One 2022; 17:e0278708. [PMID: 36459524 PMCID: PMC9718383 DOI: 10.1371/journal.pone.0278708] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 11/21/2022] [Indexed: 12/04/2022] Open
Abstract
INTRODUCTION The search for new biomarkers that allow an early diagnosis in sepsis and predict its evolution has become a necessity in medicine. The objective of this study is to identify, through omics techniques, potential protein biomarkers that are expressed in patients with sepsis and their relationship with organ dysfunction and mortality. METHODS Prospective, observational and single-center study that included adult patients (≥ 18 years) who were admitted to a tertiary hospital and who met the criteria for sepsis. A mass spectrometry-based approach was used to analyze the plasma proteins in the enrolled subjects. Subsequently, using recursive feature elimination classification and cross-validation with a vector classifier, an association of these proteins with mortality and organ dysfunction was established. The protein-protein interaction network was analyzed with String software. RESULTS 141 patients were enrolled in this study. Mass spectrometry identified 177 proteins. Of all of them, and by recursive feature elimination, nine proteins (GPX3, APOB, ORM1, SERPINF1, LYZ, C8A, CD14, APOC3 and C1QC) were associated with organ dysfunction (SOFA > 6) with an accuracy of 0.82 ± 0.06, precision of 0.85 ± 0.093, sensitivity 0.81 ± 0.10, specificity 0.84 ± 0.10 and AUC 0.82 ± 0.06. Twenty-two proteins (CLU, LUM, APOL1, SAA1, CLEBC3B, C8A, ITIH4, KNG1, AGT, C7, SAA2, APOH, HRG, AFM, APOE, APOC1, C1S, SERPINC1, IGFALS, KLKB1, CFB and BTD) were associated with mortality with an accuracy of 0.86 ± 0.05, a precision of 0.91 ± 0.05, a sensitivity of 0.91 ± 0.05, a specificity of 0.72 ± 0.17, and an area under the curve (AUC) of 0.81 ± 0.08 with a confidence interval of 95%. CONCLUSION In sepsis there are proteomic patterns associated with organ dysfunction and mortality.
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Affiliation(s)
- Adolfo Ruiz-Sanmartín
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Vicent Ribas
- Eurecat, Centre Tecnològic de Catalunya, Digital Health Unit, Barcelona, Spain
| | - David Suñol
- Eurecat, Centre Tecnològic de Catalunya, Digital Health Unit, Barcelona, Spain
| | - Luis Chiscano-Camón
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Clara Palmada
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
| | - Iván Bajaña
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
| | - Nieves Larrosa
- Department of Clinical Microbiology, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- CIBERINFEC, ISCIII–CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Juan José González
- Department of Clinical Microbiology, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Department of Genetics and Microbiology, Universitat Autònoma de Barcelona, Barcelona, Spain
- CIBERINFEC, ISCIII–CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Núria Canela
- Eurecat, Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit URV-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), Reus, Spain
| | - Ricard Ferrer
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Carlos Ruiz-Rodríguez
- Department of Intensive Care, Vall d’Hebron University Hospital, Vall d’Hebron Barcelona Hospital Campus, Barcelona, Spain
- Shock, Organ Dysfunction and Resuscitation (SODIR) Research Group, Vall d’Hebron Research Institute, Barcelona, Spain
- Departament de Medicina, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail:
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Chauvin A, Bergeron D, Vencic J, Lévesque D, Paquette B, Scott MS, Boisvert FM. Downregulation of KRAB zinc finger proteins in 5-fluorouracil resistant colorectal cancer cells. BMC Cancer 2022; 22:363. [PMID: 35379199 PMCID: PMC8981854 DOI: 10.1186/s12885-022-09417-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 03/15/2022] [Indexed: 12/23/2022] Open
Abstract
Radio-chemotherapy with 5-flu orouracil (5-FU) is the standard of care treatment for patients with colorectal cancer, but it is only effective for a third of them. Despite our understanding of the mechanism of action of 5-FU, drug resistance remains a significant limitation to the clinical use of 5-FU, as both intrinsic and acquired chemoresistance represents the major obstacles for the success of 5-FU-based chemotherapy. In order to identify the mechanism of acquired resistance, 5-FU chemoresistance was induced in CRC cell lines by passaging cells with increasing concentrations of 5-FU. To study global molecular changes, quantitative proteomics and transcriptomics analyses were performed on these cell lines, comparing the resistant cells as well as the effect of chemo and radiotherapy. Interestingly, a very high proportion of downregulated genes were annotated as transcription factors coding for Krüppel-associated box (KRAB) domain-containing zinc-finger proteins (KZFPs), the largest family of transcriptional repressors. Among nearly 350 KRAB-ZFPs, almost a quarter were downregulated after the induction of a 5-FU-resistance including a common one between the three CRC cell lines, ZNF649, whose role is still unknown. To confirm the observations of the proteomic and transcriptomic approaches, the abundance of 20 different KZFPs and control mRNAs was validated by RT-qPCR. In fact, several KZFPs were no longer detectable using qPCR in cell lines resistant to 5-FU, and the KZFPs that were downregulated only in one or two cell lines showed similar pattern of expression as measured by the omics approaches. This proteomic, transcriptomic and genomic analysis of intrinsic and acquired resistance highlights a possible new mechanism involved in the cellular adaptation to 5-FU and therefore identifies potential new therapeutic targets to overcome this resistance.
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Affiliation(s)
- Anaïs Chauvin
- Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Danny Bergeron
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Jean Vencic
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Dominique Lévesque
- Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Benoit Paquette
- Department of Nuclear Medicine and Radiobiology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - Michelle S Scott
- Department of Biochemistry and Functional Genomics, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Jean-Mignault, Sherbrooke, Québec, J1E 4K8, Canada.
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Lacasse V, Beaudoin S, Jean S, Leyton JV. A Novel Proteomic Method Reveals NLS Tagging of T-DM1 Contravenes Classical Nuclear Transport in a Model of HER2-Positive Breast Cancer. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2020; 19:99-119. [PMID: 33024794 PMCID: PMC7522293 DOI: 10.1016/j.omtm.2020.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 08/27/2020] [Indexed: 11/01/2022]
Abstract
The next breakthrough for protein therapeutics is effective intracellular delivery and accumulation within target cells. Nuclear localization signal (NLS)-tagged therapeutics have been hindered by the lack of efficient nuclear localization due to endosome entrapment. Although development of strategies for tagging therapeutics with technologies capable of increased membrane penetration has resulted in proportional increased potency, nonspecific membrane penetration limits target specificity and, hence, widespread clinical success. There is a long-standing idea that nuclear localization of NLS-tagged agents occurs exclusively via classical nuclear transport. In the present study, we modified the antibody-drug conjugate trastuzumab-emtansine (T-DM1) with a classical NLS linked to cholic acid (cell accumulator [Accum]) that enables modified antibodies to escape endosome entrapment and increase nuclear localization efficiency without abrogating receptor targeting. In parallel, we developed a proteomics-based method to evaluate nuclear transport. Accum-modified T-DM1 significantly enhanced cytotoxic efficacy in the human epidermal growth factor receptor 2 (HER2)-positive SKBR3 breast cancer system. We discovered that efficacy was dependent on the nonclassical importin-7. Our evaluation reveals that when multiple classical NLS tagging occurs, cationic charge build-up as opposed to sequence dominates and becomes a substrate for importin-7. This study results in an effective target cell-specific NLS therapeutic and a general approach to guide future NLS-based development initiatives.
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Affiliation(s)
- Vincent Lacasse
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada
| | - Simon Beaudoin
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada
| | - Steve Jean
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, CHUS, UdeS, Sherbrooke, QC J1H 5N4, Canada
| | - Jeffrey V Leyton
- Department of Nuclear Medicine and Radiobiology, Faculty of Medicine and Health Sciences, Centre Hospitalier Universitaire de Sherbrooke (CHUS), Université de Sherbrooke (UdeS), Sherbrooke, QC J1H 5N4, Canada.,Sherbrooke Molecular Imaging Centre (CIMS), Centre de Recherche du CHUS, UdeS, Sherbrooke, QC J1H 5N4, Canada
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Proteomic Analysis of Human Endometrial Tissues Reveals the Roles of PI3K/AKT/mTOR Pathway and Tumor Angiogenesis Molecules in the Pathogenesis of Endometrial Cancer. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5273969. [PMID: 32908897 PMCID: PMC7463404 DOI: 10.1155/2020/5273969] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/07/2020] [Accepted: 07/10/2020] [Indexed: 02/06/2023]
Abstract
As one major gynecological malignancy, endometrial cancer (EC) has been widely studied recently. However, its pathogenesis is still unclear to date. In this study, we identified differentially expressed proteins between 30 endometrial cancer tissues and 30 matched normal controls using 2D LC-MS/MS quantitative proteomics. As a result, we identified 619 differentially expressed proteins among all 2521 proteins being quantified. Further analyses suggested that the changes of fat, amino acid metabolism, peroxisome, extracellular signal, cytoskeleton, and other signaling or metabolic pathways may be closely related to the development of this cancer. Particularly, the PI3K/AKT/mTOR pathway-related molecules including PI3K and mTOR, ERK (the molecule of the ERK pathway), SPP1, and ANGPT2 (angiogenesis-related molecules) are highly associated with the pathogenesis of EC, which were reconfirmed by western blot and immunohistochemistry (IHC) analysis. In summary, our study revealed that the PI3K/AKT/mTOR pathway and tumor angiogenesis molecules contribute to the pathogenesis of endometrial cancer.
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Ma Z, Chen J, Luan T, Chu C, Wu W, Zhu Y, Gu Y. Proteomic analysis of human cervical adenocarcinoma mucus to identify potential protein biomarkers. PeerJ 2020; 8:e9527. [PMID: 33194326 PMCID: PMC7394065 DOI: 10.7717/peerj.9527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 06/21/2020] [Indexed: 12/24/2022] Open
Abstract
Background Cervical cancer is the most common gynecological cancer, encompassing cervical squamous cell carcinoma, adenocarcinoma, and other epithelial tumors. There are many diagnostic methods to detect cervical cancers but no precision screening tool for cervical adenocarcinoma at present. Material and methods The cervical mucus from three normal cervices (Ctrl), three endocervical adenocarcinoma (EA), and three cervical adenocarcinoma in situ (AIS) was collected for proteomic analysis. The proteins were screened using liquid chromatography-mass spectrometry analysis (LC-MS). The biological function of the differently expressed proteins were predicted by Gene Ontology (GO). Results A total of 711 proteins were identified, including 237 differently expressed proteins identified in EA/Ctrl comparison, 256 differently expressed proteins identified in AIS/Ctrl comparison, and 242 differently expressed proteins identified in AIS/EA comparison (up-regulate ≥ 1.5 or down-regulate ≤ 0.67). Functional annotation was performed using GO analysis on 1,056 differently expressed proteins to identify those that may impact cervical cancer, such as heme protein myeloperoxidase, which is involved in the immune process, and APOA1, which is associated with lipid metabolism. Conclusion We used proteomic analysis to screen out differently expressed proteins from normal cervical mucus and cervical adenocarcinoma mucus samples. These differently expressed proteins may be potential biomarkers for the diagnosis and treatment of cervical adenocarcinoma but require additional study.
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Affiliation(s)
- Zhifang Ma
- Department of Pathology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jie Chen
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ting Luan
- Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Chengzhuo Chu
- Department of Pathology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Wangfei Wu
- Department of Pathology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yichao Zhu
- Department of Physiology, Nanjing Medical University, Nanjing, China.,State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Yun Gu
- Department of Pathology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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