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Bhatia S, Gunter JH, Burgess JT, Adams MN, O'Byrne K, Thompson EW, Duijf PH. Stochastic epithelial-mesenchymal transitions diversify non-cancerous lung cell behaviours. Transl Oncol 2023; 37:101760. [PMID: 37611490 PMCID: PMC10466920 DOI: 10.1016/j.tranon.2023.101760] [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: 05/15/2023] [Revised: 07/23/2023] [Accepted: 08/07/2023] [Indexed: 08/25/2023] Open
Abstract
Epithelial-mesenchymal plasticity (EMP) is a hallmark of cancer. By enabling cells to shift between different morphological and functional states, EMP promotes invasion, metastasis and therapy resistance. We report that near-diploid non-cancerous human epithelial lung cells spontaneously shift along the EMP spectrum without genetic changes. Strikingly, more than half of single cell-derived clones adopt a mesenchymal morphology. We independently characterise epithelial-like and mesenchymal-like clones. Mesenchymal clones lose epithelial markers, display larger cell aspect ratios and lower motility, with mostly unaltered proliferation rates. Stemness marker expression and metabolic rewiring diverge independently of phenotypes. In 3D culture, more epithelial clones become mesenchymal-like. Thus, non-cancerous epithelial cells may acquire cancer metastasis-associated features prior to genetic alterations and cancerous transformation.
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Affiliation(s)
- Sugandha Bhatia
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia.
| | - Jennifer H Gunter
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Australian Prostate Cancer Research Centre-Queensland (APCRC-Q), Queensland University of Technology, Woolloongabba 4102, Australia
| | - Joshua T Burgess
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Mark N Adams
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Kenneth O'Byrne
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Princess Alexandra Hospital, Woolloongabba 4102, QLD, Australia
| | - Erik W Thompson
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia
| | - Pascal Hg Duijf
- Queensland University of Technology (QUT), School of Biomedical Sciences, Centre for Genomics and Personalised Health at the Translational Research Institute, Woolloongabba 4102, QLD, Australia; Centre for Cancer Biology, Clinical and Health Sciences, University of South Australia and SA Pathology, Adelaide SA, 5001, Australia; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway; Department of Medical Genetics, Oslo University Hospital, Oslo, Norway.
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2
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Hancock JL, Kalimutho M, Straube J, Lim M, Gresshoff I, Saunus JM, Lee JS, Lakhani SR, Simpson KJ, Bush AI, Anderson RL, Khanna KK. COMMD3 loss drives invasive breast cancer growth by modulating copper homeostasis. J Exp Clin Cancer Res 2023; 42:90. [PMID: 37072858 PMCID: PMC10111822 DOI: 10.1186/s13046-023-02663-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 04/05/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Despite overall improvement in breast cancer patient outcomes from earlier diagnosis and personalised treatment approaches, some patients continue to experience recurrence and incurable metastases. It is therefore imperative to understand the molecular changes that allow transition from a non-aggressive state to a more aggressive phenotype. This transition is governed by a number of factors. METHODS As crosstalk with extracellular matrix (ECM) is critical for tumour cell growth and survival, we applied high throughput shRNA screening on a validated '3D on-top cellular assay' to identify novel growth suppressive mechanisms. RESULTS A number of novel candidate genes were identified. We focused on COMMD3, a previously poorly characterised gene that suppressed invasive growth of ER + breast cancer cells in the cellular assay. Analysis of published expression data suggested that COMMD3 is normally expressed in the mammary ducts and lobules, that expression is lost in some tumours and that loss is associated with lower survival probability. We performed immunohistochemical analysis of an independent tumour cohort to investigate relationships between COMMD3 protein expression, phenotypic markers and disease-specific survival. This revealed an association between COMMD3 loss and shorter survival in hormone-dependent breast cancers and in particularly luminal-A-like tumours (ER+/Ki67-low; 10-year survival probability 0.83 vs. 0.73 for COMMD3-positive and -negative cases, respectively). Expression of COMMD3 in luminal-A-like tumours was directly associated with markers of luminal differentiation: c-KIT, ELF5, androgen receptor and tubule formation (the extent of normal glandular architecture; p < 0.05). Consistent with this, depletion of COMMD3 induced invasive spheroid growth in ER + breast cancer cell lines in vitro, while Commd3 depletion in the relatively indolent 4T07 TNBC mouse cell line promoted tumour expansion in syngeneic Balb/c hosts. Notably, RNA sequencing revealed a role for COMMD3 in copper signalling, via regulation of the Na+/K+-ATPase subunit, ATP1B1. Treatment of COMMD3-depleted cells with the copper chelator, tetrathiomolybdate, significantly reduced invasive spheroid growth via induction of apoptosis. CONCLUSION Overall, we found that COMMD3 loss promoted aggressive behaviour in breast cancer cells.
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Affiliation(s)
- Janelle L Hancock
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Murugan Kalimutho
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Jasmin Straube
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Malcolm Lim
- The University of Queensland Faculty of Medicine, UQ Centre for Clinical Research and Anatomical Pathology, Pathology Queensland, Herston, QLD, 4029, Australia
| | - Irma Gresshoff
- The University of Queensland Faculty of Medicine, UQ Centre for Clinical Research and Anatomical Pathology, Pathology Queensland, Herston, QLD, 4029, Australia
| | - Jodi M Saunus
- The University of Queensland Faculty of Medicine, UQ Centre for Clinical Research and Anatomical Pathology, Pathology Queensland, Herston, QLD, 4029, Australia
- Mater Research Institute-The University of Queensland, Translational Research Institute, Woolloongabba, QLD, 4102, Australia
| | - Jason S Lee
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia
| | - Sunil R Lakhani
- The University of Queensland Faculty of Medicine, UQ Centre for Clinical Research and Anatomical Pathology, Pathology Queensland, Herston, QLD, 4029, Australia
| | - Kaylene J Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, VIC, 3010, Australia
- Sir Peter MacCallum Department of Oncology and the Department of Biochemistry and Pharmacology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Ashley I Bush
- Florey Institute of Neuroscience and Mental Health, Parkville, VIC, 3052, Australia
| | - Robin L Anderson
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia.
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia.
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, QLD, 4006, Australia.
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3
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Qin X, Wang J, Wang X, Huang T, Fang Z, Yan L, Fan Y, Xu D. Widespread genomic/molecular alterations of DNA helicases and their clinical/therapeutic implications across human cancer. Biomed Pharmacother 2023; 158:114193. [PMID: 36586240 DOI: 10.1016/j.biopha.2022.114193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
DNA helicases are essential to genomic stability by regulating DNA metabolisms and their loss-of-function mutations lead to genomic instability and predisposition to cancer. Paradoxically, overexpression of DNA helicases is observed in several cancers. Here we analyzed genomic and molecular alterations in 12 important DNA helicases in TCGA pan-cancers to provide an overview of their aberrations. Significant expression heterogeneity of 12 DNA helicases was observed. We calculated DNA helicase score (DHS) based on their expression, and categorized tumors into high, low and intermediate subtypes. High DHS subtypes were robustly associated with stemness, proliferation, hyperactivated oncogenic signaling, longer telomeres, total mutation burden, copy number alterations (CNAs) and shorter survival. Importantly, tumors with high DHSs exhibited stronger expression of alternative end-join (alt-EJ) factors, indicative of sensitivity to chemo- and radio-therapies. High DHSs were also associated with homologous recombination deficiency (HRD), BRCA1/2 mutations and sensitivity to PARP inhibitors. Moreover, several drugs are identified to inhibit DNA helicases, with the Auror A kinase inhibitor Danusertib as the strongest candidate that was confirmed experimentally. The aberrant expression of DNA helicases was associated with CNAs, DNA methylation and m6A regulators. Our findings thus reveal widespread dysregulation of DNA helicases and their broad connection with featured oncogenic aberrations across human cancers. The close association of DHS with the alt-EJ pathway and HRD, and identification of Danusertib as a putative DNA helicase inhibitor have translational significance. Taken together, these findings will contribute to DNA helicase-based cancer therapy.
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Affiliation(s)
- Xin Qin
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Jing Wang
- Department of Urologic Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, China
| | - Xing Wang
- Department of Urology Surgery, The First Affiliated Hospital of USTC, Wannan Medical College, Wuhu 241000, China
| | - Tao Huang
- Department of Urologic Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, China
| | - Zhiqing Fang
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China
| | - Lei Yan
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Yidong Fan
- Department of Urology, Qilu Hospital of Shandong University, Jinan 250012, China.
| | - Dawei Xu
- Department of Medicine, Division of Hematology, Bioclinicum and Center for Molecular Medicine, Karolinska Institutet and Karolinska University Hospital Solna, Stockholm 171 76, Sweden.
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Peng H, Shen J, Long X, Zhou X, Zhang J, Xu X, Huang T, Xu H, Sun S, Li C, Lei P, Wu H, Zhao J. Local Release of TGF-β Inhibitor Modulates Tumor-Associated Neutrophils and Enhances Pancreatic Cancer Response to Combined Irreversible Electroporation and Immunotherapy. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2105240. [PMID: 35128843 PMCID: PMC8981446 DOI: 10.1002/advs.202105240] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/11/2022] [Indexed: 05/09/2023]
Abstract
Pancreatic cancer is a deadly disease with little response to standard therapies. Irreversible electroporation (IRE) has emerged as a novel ablative technique for the clinical treatment of pancreatic cancer. Combinations of IRE and immunotherapies, including anti-programmed death 1 (αPD1) immune checkpoint blockade, have shown promising efficacy in both preclinical and clinical studies. However, tumor recurrence remains an obstacle that needs to be overcome. It herein is shown that IRE induces a substantial infiltration of neutrophils into pancreatic tumors. These neutrophils are then polarized into a protumor phenotype by immunosuppressive cues, in particular transforming growth factor β (TGF-β). Using glutathione-responsive degradable mesoporous silica nanoparticles loaded with SB525334, an inhibitor of TGF-β1 receptor, it is demonstrated that local inhibition of TGF-β within the tumor microenvironment promotes neutrophil polarization into an antitumor phenotype, enhances pancreatic cancer response to combined IRE and αPD1 therapy, and induces long-term antitumor memory. The therapeutic efficacy is also attributed to tumor infiltration by CD8+ cytotoxic T cells, depletion of regulatory T cells, and maturation of antigen-presenting dendritic cells. Thus, modulating neutrophil polarization with nanomedicine is a promising strategy for treating pancreatic cancer.
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Affiliation(s)
- Huiming Peng
- Department of AnatomySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Jian Shen
- Department of Pancreatic SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Xin Long
- Department of Histology and EmbryologySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Xiaoqi Zhou
- Department of ImmunologySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Jiaqi Zhang
- Department of AnatomySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Xina Xu
- Department of AnatomySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Teng Huang
- Department of AnatomySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Hui Xu
- Ultrastructural Pathology LaboratoryDepartment of PathologySchool of Basic MedicineTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Shuguo Sun
- Department of AnatomySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Chun Li
- Department of Cancer Systems ImagingUniversity of Texas MD Anderson CancerHoustonTX77030USA
| | - Ping Lei
- Department of ImmunologySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
| | - Heshui Wu
- Department of Pancreatic SurgeryUnion HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430022China
| | - Jun Zhao
- Department of AnatomySchool of Basic MedicineHuazhong University of Science and TechnologyWuhanHubei Province430030China
- Department of Nuclear Medicine and PETTongji HospitalTongji Medical CollegeHuazhong University of Science and TechnologyWuhanHubei Province430030China
- Cell Architecture Research CenterHuazhong University of Science and TechnologyWuhanHubei Province430030China
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5
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Barkovskaya A, Goodwin CM, Seip K, Hilmarsdottir B, Pettersen S, Stalnecker C, Engebraaten O, Briem E, Der CJ, Moestue SA, Gudjonsson T, Maelandsmo GM, Prasmickaite L. Detection of phenotype-specific therapeutic vulnerabilities in breast cells using a CRISPR loss-of-function screen. Mol Oncol 2021; 15:2026-2045. [PMID: 33759347 PMCID: PMC8333781 DOI: 10.1002/1878-0261.12951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 02/18/2021] [Accepted: 03/19/2021] [Indexed: 12/09/2022] Open
Abstract
Cellular phenotype plasticity between the epithelial and mesenchymal states has been linked to metastasis and heterogeneous responses to cancer therapy, and remains a challenge for the treatment of triple-negative breast cancer (TNBC). Here, we used isogenic human breast epithelial cell lines, D492 and D492M, representing the epithelial and mesenchymal phenotypes, respectively. We employed a CRISPR-Cas9 loss-of-function screen targeting a 2240-gene 'druggable genome' to identify phenotype-specific vulnerabilities. Cells with the epithelial phenotype were more vulnerable to the loss of genes related to EGFR-RAS-MAPK signaling, while the mesenchymal-like cells had increased sensitivity to knockout of G2 -M cell cycle regulators. Furthermore, we discovered knockouts that sensitize to the mTOR inhibitor everolimus and the chemotherapeutic drug fluorouracil in a phenotype-specific manner. Specifically, loss of EGFR and fatty acid synthase (FASN) increased the effectiveness of the drugs in the epithelial and mesenchymal phenotypes, respectively. These phenotype-associated genetic vulnerabilities were confirmed using targeted inhibitors of EGFR (gefitinib), G2 -M transition (STLC), and FASN (Fasnall). In conclusion, a CRISPR-Cas9 loss-of-function screen enables the identification of phenotype-specific genetic vulnerabilities that can pinpoint actionable targets and promising therapeutic combinations.
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Affiliation(s)
- Anna Barkovskaya
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway
| | - Craig M Goodwin
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, USA
| | - Kotryna Seip
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Bylgja Hilmarsdottir
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Biomedical Center, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Pathology, Landspitali University Hospital, Reykjavik, Iceland
| | - Solveig Pettersen
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Clint Stalnecker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, USA
| | - Olav Engebraaten
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.,Department of Oncology, Oslo University Hospital, Norway
| | - Eirikur Briem
- Biomedical Center, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Genetics and Molecular Medicine, Landspitali University Hospital, Reykjavik, Iceland
| | - Channing J Der
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, USA
| | - Siver A Moestue
- Department of Circulation and Medical Imaging, Norwegian University of Science and Technology, Trondheim, Norway.,Department of Health Sciences, Nord University, Bodø, Norway
| | - Thorarinn Gudjonsson
- Biomedical Center, School of Health Sciences, University of Iceland, Reykjavik, Iceland.,Department of Laboratory Hematology, Landspitali University Hospital, Reykjavik, Iceland
| | - Gunhild M Maelandsmo
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway.,Faculty of Health Sciences, Institute of Medical Biology, The Arctic University of Norway - University of Tromsø, Norway
| | - Lina Prasmickaite
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
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6
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Yang H, Xu F, Chen Y, Tian Z. Putative N-glycoprotein markers of MCF-7/ADR cancer stem cells from N-glycoproteomics characterization of the whole cell lysate. Talanta 2021; 232:122437. [PMID: 34074422 DOI: 10.1016/j.talanta.2021.122437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 04/10/2021] [Accepted: 04/17/2021] [Indexed: 12/01/2022]
Abstract
Breast cancer is one of the most malignant diseases among females. N-glycoproteomics studies have shown that N-glycosylation alteration of tumor cells is the key player of cancer progression, multidrug resistance (MDR) and high mortality. Cancer stem cells (CSCs) have the remarkable potential of self-renewing and differentiation which leads to drug resistance and metastasis. To investigate the differentially expressed N-glycosylation in adriamycin-resistant breast cancer stem cells MCF-7/ADR CSCs (relative to MCF-7 CSCs) and find the putative biomarkers, 1:1 paired ZIC-HILIC-enriched and stable isotopic diethyl labelled (SIDE) intact N-glycopeptides from MCF-7/ADR CSCs and MCF-7 CSCs were analyzed with C18-RPLC-ESI-MS/MS (HCD with stepped NCE); differentially expressed intact N-glycopeptides (DEGPs) were identified and quantified via search engine GPSeeker. With control of spectrum-level FDR≤1%, 5515 intact N-glycopeptides were identified (1737 N-glycosites, 1705 peptide backbones and 1516 intact N-glycoproteins; 181 putative N-glycan linkages and 68 monosaccharide compositions). Among 5515 intact N-glycopeptide IDs, 3864 were identified with glycoform score≥1, i.e., one or more structure-diagnostic fragment ions were observed to distinguish sequence isomers. With the three technical replicates and the criteria of fold change≥1.5 and p value<0.05, 380 DEGPs (corresponding to 153 intact N-glycoproteins) were found along with 293 down-regulated and 87 up-regulated. For these 153 intact N-glycoproteins, the molecular functions and biological processes of were comprehensively discussed, and side-to-side comparison of differential expression results with other method were also made.
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Affiliation(s)
- Hailun Yang
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China
| | - Feifei Xu
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China
| | - Yun Chen
- School of Pharmacy, Nanjing Medical University, Nanjing, 211166, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, 200092, China.
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