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Yang R, Zhang H, Chen Z, Zhang T, Wei P, Liang H, He Y, Zheng C, Wang X, Zhang Y. Drug resistance‑related gene targets and molecular mechanisms in the A2780/Taxol‑resistant epithelial ovarian cancer cell line. Oncol Lett 2024; 27:232. [PMID: 38586210 PMCID: PMC10996034 DOI: 10.3892/ol.2024.14365] [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: 10/24/2023] [Accepted: 03/08/2024] [Indexed: 04/09/2024] Open
Abstract
Epithelial ovarian cancer (EOC) is a fatal gynecological malignant tumor with a low 5-year survival rate. The use of the first-line chemotherapeutic drug, paclitaxel, for the treatment of EOC is associated with resistance, often leading to treatment failure. The present study investigated the gene targets in an A2780 paclitaxel-resistant EOC cell line (A2780/Taxol), and the potential underlying mechanisms using transcriptome sequencing technology and bioinformatics analysis. The transcriptome of the A2780/Taxol cell line was sequenced, and 498 differentially expressed genes were obtained contained in the Gene Expression Omnibus dataset. Further bioinformatics analysis revealed that matrix metalloproteinase 1 (MMP1), zyxin (ZYX) and Unc-5 netrin receptor C (UNC5C) may be gene targets related to paclitaxel resistance. Moreover, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis indicated that a potential mechanism associated with paclitaxel resistance was related to cell migration. Furthermore, the expression levels of MMP1, ZYX and UNC5C were verified using western blotting, immunofluorescence and immunohistochemistry in vitro. The results revealed that the expression levels of MMP1 and ZYX were significantly increased in A2780/Taxol cells, while UNC5C expression was significantly decreased, which was consistent with the results of the transcriptome sequencing. The present study demonstrated that MMP1, ZYX and UNC5C may be the gene targets associated with paclitaxel resistance in EOC. These genes have potential to be used as molecular markers for EOC drug therapy, targeted elimination of drug resistance, and evaluation of treatment efficacy and patient prognosis.
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Affiliation(s)
- Ruihui Yang
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Huainian Zhang
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Zexin Chen
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Tao Zhang
- Department of Laboratory, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong 510080, P.R. China
| | - Peng Wei
- Department of Physiology, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Huaguo Liang
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Yaoyao He
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Changtao Zheng
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
| | - Xicheng Wang
- Department of Oncology, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, Guangdong 510080, P.R. China
| | - Yongli Zhang
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Guangdong Pharmaceutical University, Guangzhou, Guangdong 510006, P.R. China
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2
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Shaban N, Raevskiy M, Zakharova G, Shipunova V, Deyev S, Suntsova M, Sorokin M, Buzdin A, Kamashev D. Human Blood Serum Counteracts EGFR/HER2-Targeted Drug Lapatinib Impact on Squamous Carcinoma SK-BR-3 Cell Growth and Gene Expression. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:487-506. [PMID: 38648768 DOI: 10.1134/s000629792403009x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/17/2024] [Accepted: 02/20/2024] [Indexed: 04/25/2024]
Abstract
Lapatinib is a targeted therapeutic inhibiting HER2 and EGFR proteins. It is used for the therapy of HER2-positive breast cancer, although not all the patients respond to it. Using human blood serum samples from 14 female donors (separately taken or combined), we found that human blood serum dramatically abolishes the lapatinib-mediated inhibition of growth of the human breast squamous carcinoma SK-BR-3 cell line. This antagonism between lapatinib and human serum was associated with cancelation of the drug induced G1/S cell cycle transition arrest. RNA sequencing revealed 308 differentially expressed genes in the presence of lapatinib. Remarkably, when combined with lapatinib, human blood serum showed the capacity of restoring both the rate of cell growth, and the expression of 96.1% of the genes expression of which were altered by the lapatinib treatment alone. Co-administration of EGF with lapatinib also restores the cell growth and cancels alteration of expression of 95.8% of the genes specific to lapatinib treatment of SK-BR-3 cells. Differential gene expression analysis also showed that in the presence of human serum or EGF, lapatinib was unable to inhibit the Toll-Like Receptor signaling pathway and alter expression of genes linked to the Gene Ontology term of Focal adhesion.
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Affiliation(s)
- Nina Shaban
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- The National Medical Research Center for Endocrinology, Moscow, 117036, Russia
| | - Mikhail Raevskiy
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Galina Zakharova
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, 119991, Russia.
| | - Victoria Shipunova
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Sergey Deyev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- "Biomarker" Research Laboratory, Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, 420008, Russia
| | - Maria Suntsova
- The National Medical Research Center for Endocrinology, Moscow, 117036, Russia.
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Maksim Sorokin
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, 1200, Belgium
| | - Anton Buzdin
- Moscow Institute of Physics and Technology, Dolgoprudny, 141701, Russia.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
- The National Medical Research Center for Endocrinology, Moscow, 117036, Russia
- World-Class Research Center "Digital Biodesign and Personalized Healthcare", Sechenov First Moscow State Medical University, Moscow, 119991, Russia
| | - Dmitri Kamashev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia.
- The National Medical Research Center for Endocrinology, Moscow, 117036, Russia
- Sechenov First Moscow State Medical University, Moscow, 119991, Russia
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3
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Zou H, Luo J, Guo Y, Deng L, Zeng L, Pan Y, Li P. Tyrosine phosphorylation-mediated YAP1-TFAP2A interactions coordinate transcription and trastuzumab resistance in HER2+ breast cancer. Drug Resist Updat 2024; 73:101051. [PMID: 38219531 DOI: 10.1016/j.drup.2024.101051] [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: 07/09/2023] [Revised: 12/31/2023] [Accepted: 01/05/2024] [Indexed: 01/16/2024]
Abstract
Trastuzumab resistance in HER2+ breast cancer (BC) is the major reason leading to poor prognosis of BC patients. Oncogenic gene overexpression or aberrant activation of tyrosine kinase SRC is identified to be the key modulator of trastuzumab response. However, the detailed regulatory mechanisms underlying SRC activation-associated trastuzumab resistance remain poorly understood. In the present study, we discover that SRC-mediated YAP1 tyrosine phosphorylation facilitates its interaction with transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha, TFAP2A), which in turn promotes YAP1/TEAD-TFAP2A (YTT) complex-associated transcriptional outputs, thereby conferring trastuzumab resistance in HER2+ BC. Inhibition of SRC kinase activity or disruption of YTT complex sensitizes cells to trastuzumab treatment in vitro and in vivo. Additionally, we also identify YTT complex co-occupies the regulatory regions of a series of genes related to trastuzumab resistance and directly regulates their transcriptions, including EGFR, HER2, H19 and CTGF. Moreover, YTT-mediated transcriptional regulation is coordinated by SRC kinase activity. Taken together, our study reveals that SRC-mediated YTT complex formation and transcriptions are responsible for multiple mechanisms associated with trastuzumab resistance. Therefore, targeting HER2 signaling in combination with the inhibition of YTT-associated transcriptional outputs could serve as the treatment strategy to overcome trastuzumab resistance caused by SRC activation.
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Affiliation(s)
- Hailin Zou
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China
| | - Juan Luo
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China
| | - Yibo Guo
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China
| | - Liang Deng
- Department of General Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China
| | - Leli Zeng
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China
| | - Yihang Pan
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China.
| | - Peng Li
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China; Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, No. 628 Zhenyuan Road, Shenzhen 518107, Guangdong, China.
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4
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Peippo M, Gardberg M, Kronqvist P, Carpén O, Heuser VD. Characterization of Expression and Function of the Formins FHOD1, INF2, and DAAM1 in HER2-Positive Breast Cancer. J Breast Cancer 2023; 26:525-543. [PMID: 37985384 PMCID: PMC10761758 DOI: 10.4048/jbc.2023.26.e47] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 08/31/2023] [Accepted: 10/16/2023] [Indexed: 11/22/2023] Open
Abstract
PURPOSE Human epidermal growth factor receptor 2 (HER2)-targeted therapies, such as trastuzumab, benefit patients with HER2-positive metastatic breast cancer; however, owing to traditional pathway activation or alternative signaling, resistance persists. Given the crucial role of the formin family in shaping the actin cytoskeleton during cancer progression, these proteins may function downstream of the HER2 signaling pathway. Our aim was to uncover the potential correlations between formins and HER2 expression using a combination of public databases, immunohistochemistry, and functional in vitro assays. METHODS Using online databases, we identified a negative prognostic correlation between specific formins mRNA expression in HER2-positive cancers. To validate these findings at the protein level, immunohistochemistry was performed on HER2 subtype breast cancer tumors to establish the links between staining patterns and clinical characteristics. We then knocked down individual or combined formins in MDA-MB-453 and SK-BR-3 cells and investigated their effects on wound healing, transwell migration, and proliferation. Furthermore, we investigated the effects of erb-b2 receptor tyrosine kinase 2 (ERBB2)/HER2 small interfering RNA (siRNA)-mediated knockdown on the PI3K/Akt and MEK/ERK1 pathways as well as on selected formins. RESULTS Our results revealed that correlations between INF2, FHOD1, and DAAM1 mRNA expression and ERBB2 in HER2-subtype breast cancer were associated with worse outcomes. Using immunohistochemistry, we found that high FHOD1 protein expression was linked to higher histological grades and was negatively correlated with estrogen and progesterone receptor positivity. Upon formins knockdown, we observed effects on wound healing and transwell migration, with a minimal impact on proliferation, which was evident through single and combined knockdowns in both cell lines. Notably, siRNA-mediated knockdown of HER2 affected FHOD1 and INF2 expression, along with the phosphorylated Akt/MAPK states. CONCLUSION Our study highlights the roles of FHOD1 and INF2 as downstream effectors of the HER2/Akt and HER2/MAPK pathways, suggesting that they are potential therapeutic targets in HER2-positive breast cancer.
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Affiliation(s)
- Minna Peippo
- Department of Pathology, Turku University Hospital, University of Turku, Turku, Finland
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland
| | - Maria Gardberg
- Department of Pathology, Turku University Hospital, University of Turku, Turku, Finland
| | - Pauliina Kronqvist
- Department of Pathology, Turku University Hospital, University of Turku, Turku, Finland
| | - Olli Carpén
- Department of Pathology, Turku University Hospital, University of Turku, Turku, Finland
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland
- Department of Pathology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Vanina D Heuser
- Institute of Biomedicine and FICAN West Cancer Centre, University of Turku, Turku, Finland.
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5
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Suppression of Platelet-Derived Growth Factor Receptor-Alpha Overcomes Resistance to Trastuzumab through STAT3-Dependent IL-6 Reduction in HER2-Positive Breast Cancer Cells. Biomedicines 2023; 11:biomedicines11030675. [PMID: 36979654 PMCID: PMC10045855 DOI: 10.3390/biomedicines11030675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
Platelet-derived growth factor receptor (PDGFR) plays an essential role in the proliferation and invasion of malignant cancer cells. However, the functional role of PDGFR alpha (PDGFRA) in HER2-positive (HER2+) breast cancer has not been fully clarified yet. Thus, the objective of this study was to investigate the clinical significance of PDGFRA and the therapeutic potential of PDGFR inhibitors as part of an effort to overcome trastuzumab (TRZ) resistance. Aberrant PDGFRA expression is closely associated with decreased survival in HER2+ breast cancers. Therefore, we established BT474 trastuzumab-sensitive (TRZ_S) and trastuzumab-resistant (TRZ_R) cells to investigate the association between PDGFR signaling and TRZ resistance. We found that PDGFRA was significantly upregulated in the BT474 TRZ_R cells. In addition, IL-6 expression, which was also found to be upregulated in the TRZ_R cells, was induced by PDGFC, a ligand of PDGFR. Next, we investigated the effects of ponatinib and sunitinib, PDGFR inhibitors, on the BT474 TRZ_R and HCC1954 (TRZ-resistant cell line) cells. These inhibitors decreased cell viability and migration in a dose-dependent manner. Additionally, IL-6 expression was decreased by ponatinib in both the BT474 TRZ_R and HCC1954 cells. In contrast, IL-6 was not suppressed by TRZ, implying that the PDGFRA/STAT3/IL-6 axis is associated with resistance to TRZ. In addition, we found that STAT3 and ERK phosphorylation were increased in the BT474 TRZ_R cells. IL-6 expression was suppressed by a STAT3 inhibitor, indicating that IL-6 expression is modulated downstream of STAT3. Taken together, these results suggest that PDGFRA could serve as a therapeutic target to overcome TRZ resistance.
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6
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You JY, Park KH, Lee ES, Kwon Y, Kim KT, Nam S, Kim DH, Bae JW. Determining the Factors Predicting the Response to Anti-HER2 Therapy in HER2-Positive Breast Cancer Patients. Cancer Control 2023; 30:10732748221141672. [PMID: 36814068 PMCID: PMC9950611 DOI: 10.1177/10732748221141672] [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] [Indexed: 02/24/2023] Open
Abstract
PURPOSE We aimed to identify the differently expressed genes or related pathways associated with good responses to anti-HER2 therapy and to suggest a model for predicting drug response in neoadjuvant systemic therapy with trastuzumab in HER2-positive breast cancer patients. METHODS This study was retrospectively analyzed from consecutively collected patient data. We recruited 64 women with breast cancer and categorized them into 3 groups: complete response (CR), partial response (PR), and drug resistance (DR). The final number of patients in the study was 20. RNA from 20 core needle biopsy paraffin-embedded tissues and 4 cultured cell lines (SKBR3 and BT474 breast cancer parent cells and cultured resistant cells) was extracted, reverse transcribed, and subjected to GeneChip array analysis. The obtained data were analyzed using Gene Ontology, Kyoto Gene and Genome Encyclopedia, Database for Annotation, Visualization and Integrated Discovery. RESULTS In total, 6,656 genes differentially expressed between trastuzumab-susceptible and trastuzumab-resistant cell lines were identified. Among these, 3,224 were upregulated and 3,432 were downregulated. Expression changes in 34 genes in several pathways were found to be related to the response to trastuzumab-containing treatment in HER2-type breast cancer, interfering with adhesion to other cells or tissues (focal adhesion) and regulating extracellular matrix interactions and phagosome action. Thus, decreased tumor invasiveness and enhanced drug effects might be the mechanisms explaining the better drug response in the CR group. CONCLUSIONS This multigene assay-based study provides insights into breast cancer signaling and possible predictions of therapeutic response to targeted therapies such as trastuzumab.
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Affiliation(s)
- Ji Young You
- Division of Breast and Endocrine,
Department of Surgery, Korea University Medical
Center, Seoul, Korea
| | - Kyoung Hwa Park
- Department of Medical Oncology, Korea University Medical
Center, Seoul, Korea
| | - Eun Sook Lee
- Center for Breast Cancer, Research
Institute and Hospital, National Cancer Center, Goyang, Korea
| | - Youngmee Kwon
- Center for Breast Cancer, Research
Institute and Hospital, National Cancer Center, Goyang, Korea
| | - Kyoung Tae Kim
- Department of Molecular Dynamic
Research, Research Institute and Hospital, National Cancer Center, Goyang, Korea
| | - Seungyoon Nam
- Department of Genome Medicine and
Science, Gachon University College of
Medicine, Incheon, Korea
| | - Dong Hee Kim
- Department of Surgery, Eulji Medical Center, Seoul, Korea
| | - Jeoung Won Bae
- Division of Breast and Endocrine,
Department of Surgery, Korea University Medical
Center, Seoul, Korea,Jeoung Won Bae, Division of Breast and
Endocrine, Department of Surgery, Korea University Medical Center, Inchon-ro 73,
Seongbuk-gu, Seoul 02841, Korea. ;
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7
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de Abreu Pereira D, Sandim V, Fernandes TFB, Almeida VH, Rocha MR, do Amaral RJFC, Rossi MID, Kalume DE, Zingali RB. Proteomic Analysis of HCC-1954 and MCF-7 Cell Lines Highlights Crosstalk between αv and β1 Integrins, E-Cadherin and HER-2. Int J Mol Sci 2022; 23:ijms231710194. [PMID: 36077593 PMCID: PMC9456615 DOI: 10.3390/ijms231710194] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 08/04/2022] [Accepted: 08/28/2022] [Indexed: 01/13/2023] Open
Abstract
Overexpression of human epidermal growth factor receptor-2 (HER-2) occurs in 20% of all breast cancer subtypes, especially those that present the worst prognostic outcome through a very invasive and aggressive tumour. HCC-1954 (HER-2+) is a highly invasive, metastatic cell line, whereas MCF-7 is mildly aggressive and non-invasive. We investigated membrane proteins from both cell lines that could have a pivotal biological significance in metastasis. Membrane protein enrichment for HCC-1954 and MCF-7 proteomic analysis was performed. The samples were analysed and quantified by mass spectrometry. High abundance membrane proteins were confirmed by Western blot, immunofluorescence, and flow cytometry. Protein interaction prediction and correlations with the Cancer Genome Atlas (TCGA) patient data were conducted by bioinformatic analysis. In addition, β1 integrin expression was analysed by Western blot in cells upon trastuzumab treatment. The comparison between HCC-1954 and MCF-7 membrane-enriched proteins revealed that proteins involved in cytoskeleton organisation, such as HER-2, αv and β1 integrins, E-cadherin, and CD166 were more abundant in HCC-1954. β1 integrin membrane expression was higher in the HCC-1954 cell line resistant after trastuzumab treatment. TCGA data analysis showed a trend toward a positive correlation between HER-2 and β1 integrin in HER-2+ breast cancer patients. Differences in protein profile and abundance reflected distinctive capabilities for aggressiveness and invasiveness between HCC-1954 and MCF-7 cell line phenotypes. The higher membrane β1 integrin expression after trastuzumab treatment in the HCC-1954 cell line emphasised the need for investigating the contribution of β1 integrin modulation and its effect on the mechanism of trastuzumab resistance.
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Affiliation(s)
- Denise de Abreu Pereira
- Programa de Oncobiologia Celular e Molecular (POCM), Coordenação de Pesquisa, Instituto Nacional do Câncer, Rio de Janeiro 20231-050, Brazil
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Vanessa Sandim
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Laboratório de Hemostase e Venenos (LABHEMOVEN), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Thais F. B. Fernandes
- Programa de Oncobiologia Celular e Molecular (POCM), Coordenação de Pesquisa, Instituto Nacional do Câncer, Rio de Janeiro 20231-050, Brazil
| | - Vitor Hugo Almeida
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Murilo Ramos Rocha
- Programa de Oncobiologia Celular e Molecular (POCM), Coordenação de Pesquisa, Instituto Nacional do Câncer, Rio de Janeiro 20231-050, Brazil
| | - Ronaldo J. F. C. do Amaral
- Laboratório de Proliferação e Diferenciação Celular, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
| | - Maria Isabel D. Rossi
- Instituto de Ciências Biomédicas e Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-617, Brazil
| | - Dário Eluan Kalume
- Laboratório Interdisciplinar de Pesquisas Médicas (LIPMed), Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-360, Brazil
| | - Russolina B. Zingali
- Unidade de Espectrometria de Massas e Proteômica (UEMP), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Laboratório de Hemostase e Venenos (LABHEMOVEN), Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, Brazil
- Correspondence:
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8
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Human Blood Serum Inhibits Ductal Carcinoma Cells BT474 Growth and Modulates Effect of HER2 Inhibition. Biomedicines 2022; 10:biomedicines10081914. [PMID: 36009461 PMCID: PMC9405390 DOI: 10.3390/biomedicines10081914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/27/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022] Open
Abstract
Trastuzumab, a HER2-targeted antibody, is widely used for targeted therapy of HER2-positive breast cancer (BC) patients; yet, not all of them respond to this treatment. We investigated here whether trastuzumab activity on the growth of HER2-overexpressing BT474 cells may interfere with human peripheral blood endogenous factors. Among 33 individual BC patient blood samples supplemented to the media, BT474 sensitivity to trastuzumab varied up to 14 times. In the absence of trastuzumab, human peripheral blood serum samples could inhibit growth of BT474, and this effect varied ~10 times for 50 individual samples. In turn, the epidermal growth factor (EGF) suppressed the trastuzumab effect on BT474 cell growth. Trastuzumab treatment increased the proportion of BT474 cells in the G0/G1 phases of cell cycle, while simultaneous addition of EGF decreased it, yet not to the control level. We used RNA sequencing profiling of gene expression to elucidate the molecular mechanisms involved in EGF- and human-sera-mediated attenuation of the trastuzumab effect on BT474 cell growth. Bioinformatic analysis of the molecular profiles suggested that trastuzumab acts similarly to the inhibition of PI3K/Akt/mTOR signaling axis, and the mechanism of EGF suppression of trastuzumab activity may be associated with parallel activation of PKC and transcriptional factors ETV1-ETV5.
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9
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Chu W, Xu H, Wang Y, Xie Y, Chen YL, Tan X, Huang C, Wang G, Wang Q, Luo W, Xia N, Geng M, Xie Z, Wang C. HER2/PD1 bispecific antibody in IgG4 subclass with superior anti-tumour activities. Clin Transl Med 2022; 12:e791. [PMID: 35384333 PMCID: PMC8982313 DOI: 10.1002/ctm2.791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/09/2022] [Accepted: 03/14/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Wendi Chu
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Bldg#1, 720 Cai Lun Road, Shanghai, 200126, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Hui Xu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 200126, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Yanfei Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Bldg#1, 720 Cai Lun Road, Shanghai, 200126, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Yongle Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 200126, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Yi-Li Chen
- Shanghai Mabstone Biotechnology Ltd, Shanghai, PR China
| | - Xiaorong Tan
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Bldg#1, 720 Cai Lun Road, Shanghai, 200126, PR China
| | - Chenghao Huang
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health and School of Life Science, Xiamen University, Xiamen, PR China
| | - Guifeng Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Bldg#1, 720 Cai Lun Road, Shanghai, 200126, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Qi Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Bldg#1, 720 Cai Lun Road, Shanghai, 200126, PR China
| | - Wenxin Luo
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health and School of Life Science, Xiamen University, Xiamen, PR China
| | - Ningshao Xia
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Public Health and School of Life Science, Xiamen University, Xiamen, PR China
| | - Meiyu Geng
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 200126, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Zuoquan Xie
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 200126, PR China.,University of Chinese Academy of Sciences, Beijing, PR China
| | - Chunhe Wang
- Biotherapeutics Discovery Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Bldg#1, 720 Cai Lun Road, Shanghai, 200126, PR China.,University of Chinese Academy of Sciences, Beijing, PR China.,Dartsbio Pharmaceuticals Ltd, Zhongshan, PR China
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10
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Reggiori F, Molinari M. ER-phagy: mechanisms, regulation and diseases connected to the lysosomal clearance of the endoplasmic reticulum. Physiol Rev 2022; 102:1393-1448. [PMID: 35188422 PMCID: PMC9126229 DOI: 10.1152/physrev.00038.2021] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
ER-phagy (reticulo-phagy) defines the degradation of portions of the endoplasmic reticulum (ER) within lysosomes or vacuoles. It is part of the self-digestion (i.e., auto-phagic) programs recycling cytoplasmic material and organelles, which rapidly mobilize metabolites in cells confronted with nutrient shortage. Moreover, selective clearance of ER subdomains participates to the control of ER size and activity during ER stress, the re-establishment of ER homeostasis after ER stress resolution and the removal of ER parts, in which aberrant and potentially cytotoxic material has been segregated. ER-phagy relies on the individual and/or concerted activation of the ER-phagy receptors, ER peripheral or integral membrane proteins that share the presence of LC3/Atg8-binding motifs in their cytosolic domains. ER-phagy involves the physical separation of portions of the ER from the bulk ER network, and their delivery to the endolysosomal/vacuolar catabolic district. This last step is accomplished by a variety of mechanisms including macro-ER-phagy (in which ER fragments are sequestered by double-membrane autophagosomes that eventually fuse with lysosomes/vacuoles), micro-ER-phagy (in which ER fragments are directly engulfed by endosomes/lysosomes/vacuoles), or direct fusion of ER-derived vesicles with lysosomes/vacuoles. ER-phagy is dysfunctional in specific human diseases and its regulators are subverted by pathogens, highlighting its crucial role for cell and organism life.
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Affiliation(s)
- Fulvio Reggiori
- Department of Biomedical Sciences of Cells & Systems, grid.4830.fUniversity of Groningen, Netherlands
| | - Maurizio Molinari
- Protein Folding and Quality Control, grid.7722.0Institute for Research in Biomedicine, Bellinzona, Switzerland
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11
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Jiang X, Zhang W, Li L, Xie S. Integrated Transcriptomic Analysis Revealed Hub Genes and Pathways Involved in Sorafenib Resistance in Hepatocellular Carcinoma. Pathol Oncol Res 2021; 27:1609985. [PMID: 34737677 PMCID: PMC8560649 DOI: 10.3389/pore.2021.1609985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/28/2021] [Indexed: 12/31/2022]
Abstract
Hepatocellular carcinoma (HCC), a high mortality malignancy, has become a worldwide public health concern. Acquired resistance to the multikinase inhibitor sorafenib challenges its clinical efficacy and the survival benefits it provides to patients with advanced HCC. This study aimed to identify critical genes and pathways associated with sorafenib resistance in HCC using integrated bioinformatics analysis. Differentially expressed genes (DEGs) were identified using four HCC gene expression profiles (including 34 sorafenib-resistant and 29 sorafenib-sensitive samples) based on the robust rank aggregation method and R software. Gene ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) online tool. A protein–protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING), and small molecules reversing sorafenib resistance were searched for using the connectivity map (CMAP) database. Pearson correlation and survival analyses of hub genes were performed using cBioPortal and Gene Expression Profiling and Interactive Analysis (GEPIA). Finally, the expression levels of hub genes in sorafenib-resistant HCC cells were verified using quantitative polymerase chain reaction (q-PCR). A total of 165 integrated DEGs (66 upregulated and 99 downregulated in sorafenib resistant samples compared sorafenib sensitive ones) primarily enriched in negative regulation of endopeptidase activity, extracellular exosome, and protease binding were identified. Some pathways were commonly shared between the integrated DEGs. Seven promising therapeutic agents and 13 hub genes were identified. These findings provide a strategy and theoretical basis for overcoming sorafenib resistance in HCC patients.
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Affiliation(s)
- Xili Jiang
- Department of Radiology, The Second People's Hospital of Hunan Province/Brain Hospital of Hunan Province, Changsha, China
| | - Wei Zhang
- Department of Radiology, The Second People's Hospital of Hunan Province/Brain Hospital of Hunan Province, Changsha, China
| | - Lifeng Li
- Department of Radiology, Changsha Central Hospital, Changsha, China
| | - Shucai Xie
- Department of Critical Care Medicine, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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12
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Associations of Polymorphisms Localized in the 3'UTR Regions of the KRAS, NRAS, MAPK1 Genes with Laryngeal Squamous Cell Carcinoma. Genes (Basel) 2021; 12:genes12111679. [PMID: 34828284 PMCID: PMC8625477 DOI: 10.3390/genes12111679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Background: Genetic variations, localized in the 3′ untranslated region (UTR) in mitogen-activated protein kinase (MAPK) pathway-related genes, may alter the transcription and impact the pathogenesis of laryngeal squamous cell carcinoma (LSCC). The present study investigated the associations of single-nucleotide polymorphisms (SNP), localized in the 3′UTR) of the KRAS, NRAS, and MAPK1 genes with LSCC risk and clinicopathological features. Methods: Genomic DNA and clinical data were collected from 327 adult men with LSCC. The control group was formed from 333 healthy men. Genotyping of the SNPs was performed using TaqMan SNP genotyping assays. Five KRAS, NRAS, and MAPK1 polymorphisms were analyzed. All studied genotypes were in Hardy–Weinberg equilibrium and had the same allele distribution as the 1000 Genomes project Phase 3 dataset for the European population. Results: Significant associations of the studied SNPs with reduced LSCC risk were observed between NRAS rs14804 major genotype CC. Significant associations of the studied SNPs with clinicopathologic variables were also observed between NRAS rs14804 minor T allele and advanced tumor stage and positive lymph node status. SNP of MAPK1 rs9340 was associated with distant metastasis. Moreover, haplotype analysis of two KRAS SNPs rs712 and rs7973450 revealed that TG haplotype was associated with positive lymph node status in LSCC patients. Conclusions: According to the present study, 3′UTR SNP in the NRAS and MAPK1 genes may contribute to the identifications of patients at higher risk of LSCC lymph node and distant metastasis development.
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13
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Stoessel A, Groysbeck N, Guyot L, Barret L, Nominé Y, Nguekeu-Zebaze L, Bender A, Voilquin L, Lutz T, Pallaoro N, Blocat M, Deville C, Masson M, Zuber G, Chatton B, Donzeau M. Modular Conjugation of a Potent Anti-HER2 Immunotoxin Using Coassociating Peptides. Bioconjug Chem 2020; 31:2421-2430. [PMID: 32996763 DOI: 10.1021/acs.bioconjchem.0c00482] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Immunotoxins are emerging candidates for cancer therapeutics. These biomolecules consist of a cell-targeting protein combined to a polypeptide toxin. Associations of both entities can be achieved either chemically by covalent bonds or genetically creating fusion proteins. However, chemical agents can affect the activity and/or stability of the conjugate proteins, and additional purification steps are often required to isolate the final conjugate from unwanted byproducts. As for fusion proteins, they often suffer from low solubility and yield. In this report, we describe a straightforward conjugation process to generate an immunotoxin using coassociating peptides (named K3 and E3), originating from the tetramerization domain of p53. To that end, a nanobody targeting the human epidermal growth factor receptor 2 (nano-HER2) and a protein toxin fragment from Pseudomonas aeruginosa exotoxin A (TOX) were genetically fused to the E3 and K3 peptides. Entities were produced separately in Escherichia coli in soluble forms and at high yields. The nano-HER2 fused to the E3 or K3 helixes (nano-HER2-E3 and nano-HER2-K3) and the coassembled immunotoxins (nano-HER2-K3E3-TOX and nano-HER2-E3K3-TOX) presented binding specificity on HER2-overexpressing cells with relative binding constants in the low nanomolar to picomolar range. Both toxin modules (E3-TOX and K3-TOX) and the combined immunotoxins exhibited similar cytotoxicity levels compared to the toxin alone (TOX). Finally, nano-HER2-K3E3-TOX and nano-HER2-E3K3-TOX evaluated on various breast cancer cells were highly potent and specific to killing HER2-overexpressing breast cancer cells with IC50 values in the picomolar range. Altogether, we demonstrate that this noncovalent conjugation method using two coassembling peptides can be easily implemented for the modular engineering of immunotoxins targeting different types of cancers.
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Affiliation(s)
- Audrey Stoessel
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Nadja Groysbeck
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Lucile Guyot
- IMPReSs Facility, Biotechnology and Cell Signaling, CNRS-University of Strasbourg, Illkirch, F-67412 Illkirch, France
- NovAliX, Bioparc, F-67405 Illkirch, France
| | - Lina Barret
- IMPReSs Facility, Biotechnology and Cell Signaling, CNRS-University of Strasbourg, Illkirch, F-67412 Illkirch, France
| | - Yves Nominé
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, F-67400 Illkirch, France
| | - Leonel Nguekeu-Zebaze
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Ambre Bender
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Laetitia Voilquin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, F-67400 Illkirch, France
| | - Thomas Lutz
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Nikita Pallaoro
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Marie Blocat
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Celia Deville
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, F-67400 Illkirch, France
| | - Murielle Masson
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Guy Zuber
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Bruno Chatton
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
| | - Mariel Donzeau
- Université de Strasbourg, UMR7242 Biotechnologie et Signalisation Cellulaire, Ecole Supérieure de Biotechnologie Strasbourg, F-67412 Illkirch, France
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14
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Tiron CE, Luta G, Butura M, Zugun-Eloae F, Stan CS, Coroaba A, Ursu EL, Stanciu GD, Tiron A. NHF-derived carbon dots: prevalidation approach in breast cancer treatment. Sci Rep 2020; 10:12662. [PMID: 32728167 PMCID: PMC7391642 DOI: 10.1038/s41598-020-69670-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/09/2020] [Indexed: 12/16/2022] Open
Abstract
Metastatic breast cancer dominates the female cancer-related mortality. Tumour-associated molecules represents a crucial for early disease detection and identification of novel therapeutic targets. Nanomaterial technologies provide promising novel approaches to disease diagnostics and therapeutics. In the present study we extend the investigations of antitumoral properties of Carbon Dots prepared from N-hydroxyphthalimide (CD-NHF) precursor. We evaluate the effect of CD-NHF on tumour cell migration and invasion in vitro and their impact on tumour progression using an in vivo model. Furthermore, we investigate the molecular mechanisms involved in CD-NHF antitumour effects. In vivo mammary tumours were induced in Balb/c female mice by injecting 4T1 cells into the mammary fat pad. Conditional treatment with CD-NHF significantly impair both migration and invasion of metastatic breast cancer cells. The presence of CD-NHF within the 3D cell cultures strongly inhibited the malignant phenotype of MDA-MB-231, 4T1 and MCF-7 cells in 3D culture, resulting in culture colonies lacking invasive projections and reduction of mammospheres formation. Importantly, breast tumour growth and metastasis dissemination was significantly reduced upon CD-NHF treatments in a syngeneic mouse model and is associated with down-regulation of Ki67 and HSP90 expression. CD-NHF nanostructures provide exciting perspective for improving treatment outcome in breast cancer.
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Affiliation(s)
- Crina Elena Tiron
- Regional Institute of Oncology, TRANSCEND Center, 700483, Iasi, Romania
| | - Gabriel Luta
- Regional Institute of Oncology, TRANSCEND Center, 700483, Iasi, Romania
| | - Mihail Butura
- Regional Institute of Oncology, TRANSCEND Center, 700483, Iasi, Romania
| | - Florin Zugun-Eloae
- Regional Institute of Oncology, TRANSCEND Center, 700483, Iasi, Romania
- Department of Immunology, "Gr.T.Popa" University of Medicine and Pharmacy, 700115, Iasi, Romania
| | - Corneliu S Stan
- Department of Natural and Synthetic Polymers, "Gheorghe Asachi" Technical University of Iasi, 700050, Iasi, Romania
| | - Adina Coroaba
- Department of Chemistry, "Petru Poni" Institute of Macromolecular Chemistry, 700487, Iasi, Romania
| | - Elena-Laura Ursu
- Department of Chemistry, "Petru Poni" Institute of Macromolecular Chemistry, 700487, Iasi, Romania
| | - Gabriela Dumitrita Stanciu
- Center for Advanced Research and Development in Experimental Medicine (CEMEX), "Gr.T.Popa" University of Medicine and Pharmacy, Iasi, Romania
| | - Adrian Tiron
- Regional Institute of Oncology, TRANSCEND Center, 700483, Iasi, Romania.
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15
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Conforte AJ, Alves L, Coelho FC, Carels N, da Silva FAB. Modeling Basins of Attraction for Breast Cancer Using Hopfield Networks. Front Genet 2020; 11:314. [PMID: 32318098 PMCID: PMC7154169 DOI: 10.3389/fgene.2020.00314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/16/2020] [Indexed: 12/26/2022] Open
Abstract
Cancer is a genetic disease for which traditional treatments cause harmful side effects. After two decades of genomics technological breakthroughs, personalized medicine is being used to improve treatment outcomes and mitigate side effects. In mathematical modeling, it has been proposed that cancer matches an attractor in Waddington's epigenetic landscape. The use of Hopfield networks is an attractive modeling approach because it requires neither previous biological knowledge about protein-protein interactions nor kinetic parameters. In this report, Hopfield network modeling was used to analyze bulk RNA-Seq data of paired breast tumor and control samples from 70 patients. We characterized the control and tumor attractors with respect to their size and potential energy and correlated the Euclidean distances between the tumor samples and the control attractor with their corresponding clinical data. In addition, we developed a protocol that outlines the key genes involved in tumor state stability. We found that the tumor basin of attraction is larger than that of the control and that tumor samples are associated with a more substantial negative energy than control samples, which is in agreement with previous reports. Moreover, we found a negative correlation between the Euclidean distances from tumor samples to the control attractor and patient overall survival. The ascending order of each node's density in the weight matrix and the descending order of the number of patients that have the target active only in the tumor sample were the parameters that withdrew more tumor samples from the tumor basin of attraction with fewer gene inhibitions. The combinations of therapeutic targets were specific to each patient. We performed an initial validation through simulation of trastuzumab treatment effects in HER2+ breast cancer samples. For that, we built an energy landscape composed of single-cell and bulk RNA-Seq data from trastuzumab-treated and non-treated HER2+ samples. The trajectory from the non-treated bulk sample toward the treated bulk sample was inferred through the perturbation of differentially expressed genes between these samples. Among them, we characterized key genes involved in the trastuzumab response according to the literature.
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Affiliation(s)
- Alessandra Jordano Conforte
- Laboratory of Biological Systems Modeling, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Laboratory of Computational Modeling of Biological Systems, Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Leon Alves
- Applied Math School, Getúlio Vargas Foundation, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Nicolas Carels
- Laboratory of Biological Systems Modeling, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Fabrício Alves Barbosa da Silva
- Laboratory of Computational Modeling of Biological Systems, Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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16
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Stefely JA, Zhang Y, Freiberger EC, Kwiecien NW, Thomas HE, Davis AM, Lowry ND, Vincent CE, Shishkova E, Clark NA, Medvedovic M, Coon JJ, Pagliarini DJ, Mercer CA. Mass spectrometry proteomics reveals a function for mammalian CALCOCO1 in MTOR-regulated selective autophagy. Autophagy 2020; 16:2219-2237. [PMID: 31971854 DOI: 10.1080/15548627.2020.1719746] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Macroautophagy/autophagy is suppressed by MTOR (mechanistic target of rapamycin kinase) and is an anticancer target under active investigation. Yet, MTOR-regulated autophagy remains incompletely mapped. We used proteomic profiling to identify proteins in the MTOR-autophagy axis. Wild-type (WT) mouse cell lines and cell lines lacking individual autophagy genes (Atg5 or Ulk1/Ulk2) were treated with an MTOR inhibitor to induce autophagy and cultured in media with either glucose or galactose. Mass spectrometry proteome profiling revealed an elevation of known autophagy proteins and candidates for new autophagy components, including CALCOCO1 (calcium binding and coiled-coil domain protein 1). We show that CALCOCO1 physically interacts with MAP1LC3C, a key protein in the machinery of autophagy. Genetic deletion of CALCOCO1 disrupted autophagy of the endoplasmic reticulum (reticulophagy). Together, these results reveal a role for CALCOCO1 in MTOR-regulated selective autophagy. More generally, the resource generated by this work provides a foundation for establishing links between the MTOR-autophagy axis and proteins not previously linked to this pathway. Abbreviations: ATG: autophagy-related; CALCOCO1: calcium binding and coiled-coil domain protein 1; CALCOCO2/NDP52: calcium binding and coiled-coil domain protein 2; CLIR: MAP1LC3C-interacting region; CQ: chloroquine; KO: knockout; LIR: MAP1LC3-interacting region; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MEF: mouse embryonic fibroblast; MLN: MLN0128 ATP-competitive MTOR kinase inhibitor; MTOR: mechanistic target of rapamycin kinase; reticulophagy: selective autophagy of the endoplasmic reticulum; TAX1BP1/CALCOCO3: TAX1 binding protein 1; ULK: unc 51-like autophagy activating kinase; WT: wild-type.
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Affiliation(s)
- Jonathan A Stefely
- Morgridge Institute for Research , Madison, WI, USA.,Medical Scientist Training Program, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, WI, USA.,Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Yu Zhang
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Elyse C Freiberger
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Nicholas W Kwiecien
- Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Hala Elnakat Thomas
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Alexander M Davis
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Nathaniel D Lowry
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
| | - Catherine E Vincent
- Genome Center of Wisconsin , Madison, WI, USA.,Department of Chemistry, Hartwick College , Oneonta, NY, USA
| | | | - Nicholas A Clark
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Mario Medvedovic
- Division of Biostatistics and Bioinformatics, Department of Environmental Health, University of Cincinnati , Cincinnati, OH, USA
| | - Joshua J Coon
- Morgridge Institute for Research , Madison, WI, USA.,Department of Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Department of Biomolecular Chemistry, University ofWisconsin-Madison , Madison, WI, USA.,Genome Center of Wisconsin , Madison, WI, USA
| | - David J Pagliarini
- Morgridge Institute for Research , Madison, WI, USA.,Department of Biochemistry, University ofWisconsin-Madison , Madison, Madison, WI, USA
| | - Carol A Mercer
- Division of Hematology/Oncology, Department of Internal Medicine, University of Cincinnati , Cincinnati, OH, USA
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17
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Zeng F, Wang K, Liu X, Zhao Z. Comprehensive profiling identifies a novel signature with robust predictive value and reveals the potential drug resistance mechanism in glioma. Cell Commun Signal 2020; 18:2. [PMID: 31907037 PMCID: PMC6943920 DOI: 10.1186/s12964-019-0492-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/29/2019] [Indexed: 12/13/2022] Open
Abstract
Background Gliomas are the most common and malignant brain tumors. The standard therapy is surgery combined with radiotherapy, chemotherapy, and/or other comprehensive methods. However, the emergence of chemoresistance is the main obstacle in treatment and its mechanism is still unclear. Methods We firstly developed a multi-gene signature by integrated analysis of cancer stem cell and drug resistance related genes. The Chinese Glioma Genome Atlas (CGGA, 325 samples) and The Cancer Genome Atlas (TCGA, 699 samples) datasets were then employed to verify the efficacy of the risk signature and investigate its significance in glioma prognosis. GraphPad Prism, SPSS and R language were used for statistical analysis and graphical work. Results This signature could distinguish the prognosis of patients, and patients with high risk score exhibited short survival time. The Cox regression and Nomogram model indicated the independent prognostic performance and high prognostic accuracy of the signature for survival. Combined with a well-known chemotherapy impact factor-MGMT promoter methylation status, this risk signature could further subdivide patients with distinct survival. Functional analysis of associated genes revealed signature-related biological process of cell proliferation, immune response and cell stemness. These mechanisms were confirmed in patient samples. Conclusions The signature was an independent and powerful prognostic biomarker in glioma, which would improve risk stratification and provide a more accurate assessment of personalized treatment. Additional file 8 Video abstract
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Affiliation(s)
- Fan Zeng
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No.119 South 4th Ring Road West, Fengtai District, Beijing, 100070, China
| | - Kuanyu Wang
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Xiu Liu
- Department of Neurosurgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
| | - Zheng Zhao
- Department of Molecular Neuropathology, Beijing Neurosurgical Institute, Capital Medical University, No.119 South 4th Ring Road West, Fengtai District, Beijing, 100070, China.
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18
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McGinnis CS, Patterson DM, Winkler J, Conrad DN, Hein MY, Srivastava V, Hu JL, Murrow LM, Weissman JS, Werb Z, Chow ED, Gartner ZJ. MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices. Nat Methods 2019. [PMID: 31209384 DOI: 10.1101/387241] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Sample multiplexing facilitates scRNA-seq by reducing costs and identifying artifacts such as cell doublets. However, universal and scalable sample barcoding strategies have not been described. We therefore developed MULTI-seq: multiplexing using lipid-tagged indices for single-cell and single-nucleus RNA sequencing. MULTI-seq reagents can barcode any cell type or nucleus from any species with an accessible plasma membrane. The method involves minimal sample processing, thereby preserving cell viability and endogenous gene expression patterns. When cells are classified into sample groups using MULTI-seq barcode abundances, data quality is improved through doublet identification and recovery of cells with low RNA content that would otherwise be discarded by standard quality-control workflows. We use MULTI-seq to track the dynamics of T-cell activation, perform a 96-plex perturbation experiment with primary human mammary epithelial cells and multiplex cryopreserved tumors and metastatic sites isolated from a patient-derived xenograft mouse model of triple-negative breast cancer.
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Affiliation(s)
- Christopher S McGinnis
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - David M Patterson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Juliane Winkler
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Daniel N Conrad
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Marco Y Hein
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Vasudha Srivastava
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L Hu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Lyndsay M Murrow
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Zena Werb
- Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.
- Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA.
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.
- Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA.
- Chan Zuckerberg BioHub, University of California San Francisco, San Francisco, CA, USA.
- Center for Cellular Construction, University of California San Francisco, San Francisco, CA, USA.
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19
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Buiga P, Elson A, Tabernero L, Schwartz JM. Modelling the role of dual specificity phosphatases in herceptin resistant breast cancer cell lines. Comput Biol Chem 2019; 80:138-146. [PMID: 30952040 DOI: 10.1016/j.compbiolchem.2019.03.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 03/23/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Breast cancer remains the most lethal type of cancer for women. A significant proportion of breast cancer cases are characterised by overexpression of the human epidermal growth factor receptor 2 protein (HER2). These cancers are commonly treated by Herceptin (Trastuzumab), but resistance to drug treatment frequently develops in tumour cells. Dual-specificity phosphatases (DUSPs) are thought to play a role in the mechanism of resistance, since some of them were reported to be overexpressed in tumours resistant to Herceptin. RESULTS We used a systems biology approach to investigate how DUSP overexpression could favour cell proliferation and to predict how this mechanism could be reversed by targeted inhibition of selected DUSPs. We measured the expression of 20 DUSP genes in two breast cancer cell lines following long-term (6 months) exposure to Herceptin, after confirming that these cells had become resistant to the drug. We constructed several Boolean models including specific substrates of each DUSP, and showed that our models correctly account for resistance when overexpressed DUSPs were kept activated. We then simulated inhibition of both individual and combinations of DUSPs, and determined conditions under which the resistance could be reversed. CONCLUSIONS These results show how a combination of experimental analysis and modelling help to understand cell survival mechanisms in breast cancer tumours, and crucially enable us to generate testable predictions potentially leading to new treatments of resistant tumours.
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Affiliation(s)
- Petronela Buiga
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel; School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Ari Elson
- Department of Molecular Genetics, The Weizmann Institute of Science, Rehovot, Israel
| | - Lydia Tabernero
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jean-Marc Schwartz
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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20
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Qian XL, Pan YH, Huang QY, Shi YB, Huang QY, Hu ZZ, Xiong LX. Caveolin-1: a multifaceted driver of breast cancer progression and its application in clinical treatment. Onco Targets Ther 2019; 12:1539-1552. [PMID: 30881011 PMCID: PMC6398418 DOI: 10.2147/ott.s191317] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human breast cancer is one of the most frequent cancer diseases and causes of death among female population worldwide. It appears at a high incidence and has a high malignancy, mortality, recurrence rate and poor prognosis. Caveolin-1 (Cav1) is the main component of caveolae and participates in various biological events. More and more experimental studies have shown that Cav1 plays a critical role in the progression of breast cancer including cell proliferation, apoptosis, autophagy, invasion, migration and breast cancer metastasis. Besides, Cav1 has been found to be involved in chemotherapeutics and radiotherapy resistance, which are still the principal problems encountered in clinical breast cancer treatment. In addition, stromal Cav1 may be a potential indicator for breast cancer patients’ prognosis. In the current review, we cover the state-of-the-art study, development and progress on Cav1 and breast cancer, altogether describing the role of Cav1 in breast cancer progression and application in clinical treatment, in the hope of providing a basis for further research and promoting CAV1 gene as a potential target to diagnose and treat aggressive breast cancers.
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Affiliation(s)
- Xian-Ling Qian
- Department of Pathophysiology, Basic Medical College, Nanchang University, Nanchang 330006, China, ; .,First Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Yi-Hang Pan
- Department of Pathophysiology, Basic Medical College, Nanchang University, Nanchang 330006, China, ; .,First Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Qi-Yuan Huang
- Department of Pathophysiology, Basic Medical College, Nanchang University, Nanchang 330006, China, ; .,Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Yu-Bo Shi
- Department of Pathophysiology, Basic Medical College, Nanchang University, Nanchang 330006, China, ;
| | - Qing-Yun Huang
- Department of Pathophysiology, Basic Medical College, Nanchang University, Nanchang 330006, China, ;
| | - Zhen-Zhen Hu
- Department of Pathophysiology, Basic Medical College, Nanchang University, Nanchang 330006, China, ; .,Jiangxi Province Key Laboratory of Tumor Pathogenesis and Molecular Pathology, Nanchang 330006, China, ;
| | - Li-Xia Xiong
- Department of Pathophysiology, Basic Medical College, Nanchang University, Nanchang 330006, China, ; .,Jiangxi Province Key Laboratory of Tumor Pathogenesis and Molecular Pathology, Nanchang 330006, China, ;
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21
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Ahmad A. Current Updates on Trastuzumab Resistance in HER2 Overexpressing Breast Cancers. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1152:217-228. [PMID: 31456185 DOI: 10.1007/978-3-030-20301-6_10] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Trastuzumab represents the predominant therapy to target breast cancer subtype marked by HER2 amplification. It has been in use for two decades and its continued importance is underlined by recent FDA approvals of its biosimilar and conjugated versions. Progression to an aggressive disease with acquisition of resistance to trastuzumab remains a major clinical concern. In addition to a number of cellular signaling pathways being investigated, focus in recent years has also shifted to epigenetic and non-coding RNA basis of acquired resistance against trastuzumab. This article provides a succinct discussion on the most recent advances in our understanding of such factors.
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Affiliation(s)
- Aamir Ahmad
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
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22
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Pereira PMR, Sharma SK, Carter LM, Edwards KJ, Pourat J, Ragupathi A, Janjigian YY, Durack JC, Lewis JS. Caveolin-1 mediates cellular distribution of HER2 and affects trastuzumab binding and therapeutic efficacy. Nat Commun 2018; 9:5137. [PMID: 30510281 PMCID: PMC6277446 DOI: 10.1038/s41467-018-07608-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 11/13/2018] [Indexed: 12/19/2022] Open
Abstract
Human epidermal growth factor receptor 2 (HER2) gene amplification and/or protein overexpression in tumors is a prerequisite for initiation of trastuzumab therapy. Although HER2 is a cell membrane receptor, differential rates of endocytosis and recycling engender a dynamic surface pool of HER2. Since trastuzumab must bind to the extracellular domain of HER2, a depressed HER2 surface pool hinders binding. Using in vivo biological models and cultures of fresh human tumors, we find that the caveolin-1 (CAV1) protein is involved in HER2 cell membrane dynamics within the context of receptor endocytosis. The translational significance of this finding is highlighted by our observation that temporal CAV1 depletion with lovastatin increases HER2 half-life and availability at the cell membrane resulting in improved trastuzumab binding and therapy against HER2-positive tumors. These data show the important role that CAV1 plays in the effectiveness of trastuzumab to target HER2-positive tumors. Trastuzumab binding to tumor cells depends on the availability of HER2 at the cell membrane. Here the authors show that caveolin-1 (CAV1) regulates HER2 density at the cell membranes and that CAV1 gene knockdown or protein depletion via the cholesterol modulator lovastatin, increases trastuzumab binding and anti-tumor activity.
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Affiliation(s)
- Patrícia M R Pereira
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Sai Kiran Sharma
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Lukas M Carter
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Kimberly J Edwards
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Jacob Pourat
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Ashwin Ragupathi
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jeremy C Durack
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.,Department of Radiology, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jason S Lewis
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. .,Department of Radiology, Weill Cornell Medical College, New York, NY, 10065, USA. .,Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA. .,Department of Pharmacology, Weill Cornell Medical College, New York, NY, 10065, USA. .,Radiochemistry and Molecular Imaging Probes Core, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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23
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NRF1 motif sequence-enriched genes involved in ER/PR −ve HER2 +ve breast cancer signaling pathways. Breast Cancer Res Treat 2018; 172:469-485. [DOI: 10.1007/s10549-018-4905-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 07/29/2018] [Indexed: 12/17/2022]
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24
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Wielgos ME, Zhang Z, Rajbhandari R, Cooper TS, Zeng L, Forero A, Esteva FJ, Osborne CK, Schiff R, LoBuglio AF, Nozell SE, Yang ES. Trastuzumab-Resistant HER2 + Breast Cancer Cells Retain Sensitivity to Poly (ADP-Ribose) Polymerase (PARP) Inhibition. Mol Cancer Ther 2018; 17:921-930. [PMID: 29592880 DOI: 10.1158/1535-7163.mct-17-0302] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 08/29/2017] [Accepted: 02/23/2018] [Indexed: 01/24/2023]
Abstract
HER2-targeted therapies, such as trastuzumab, have increased the survival rates of HER2+ breast cancer patients. However, despite these therapies, many tumors eventually develop resistance to these therapies. Our lab previously reported an unexpected sensitivity of HER2+ breast cancer cells to poly (ADP-ribose) polymerase inhibitors (PARPi), agents that target homologous recombination (HR)-deficient tumors, independent of a DNA repair deficiency. In this study, we investigated whether HER2+ trastuzumab-resistant (TR) breast cancer cells were susceptible to PARPi and the mechanism behind PARPi induced cytotoxicity. We demonstrate that the PARPi ABT-888 (veliparib) decreased cell survival in vitro and tumor growth in vivo of HER2+ TR breast cancer cells. PARP-1 siRNA confirmed that cytotoxicity was due, in part, to PARP-1 inhibition. Furthermore, PARP-1 silencing had variable effects on the expression of several NF-κB-regulated genes. In particular, silencing PARP-1 inhibited NF-κB activity and reduced p65 binding at the IL8 promoter, which resulted in a decrease in IL8 mRNA and protein expression. Our results provide insight in the potential mechanism by which PARPi induces cytotoxicity in HER2+ breast cancer cells and support the testing of PARPi in patients with HER2+ breast cancer resistant to trastuzumab. Mol Cancer Ther; 17(5); 921-30. ©2018 AACR.
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Affiliation(s)
- Monica E Wielgos
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Zhuo Zhang
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Rajani Rajbhandari
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Tiffiny S Cooper
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ling Zeng
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Andres Forero
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Francisco J Esteva
- Breast Medical Oncology Program, NYU Cancer Institute, New York, New York
| | - C Kent Osborne
- Lester and Sue Smith Breast Cancer, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Rachel Schiff
- Lester and Sue Smith Breast Cancer, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Medicine, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas
| | - Albert F LoBuglio
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Susan E Nozell
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Eddy S Yang
- Department of Radiation Oncology, University of Alabama at Birmingham, Birmingham, Alabama.
- Department of Cell, Developmental, and Integrative Biology, University of Alabama at Birmingham, Birmingham, Alabama
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama
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25
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Yue Z, Li HT, Yang Y, Hussain S, Zheng CH, Xia J, Chen Y. Identification of breast cancer candidate genes using gene co-expression and protein-protein interaction information. Oncotarget 2017; 7:36092-36100. [PMID: 27150055 PMCID: PMC5094985 DOI: 10.18632/oncotarget.9132] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 04/16/2016] [Indexed: 01/18/2023] Open
Abstract
Breast cancer (BC) is one of the most common malignancies that could threaten female health. As the molecular mechanism of BC has not yet been completely discovered, identification of related genes of this disease is an important area of research that could provide new insights into gene function as well as potential treatment targets. Here we used subnetwork extraction algorithms to identify novel BC related genes based on the known BC genes (seed genes), gene co-expression profiles and protein-protein interaction network. We computationally predicted seven key genes (EPHX2, GHRH, PPYR1, ALPP, KNG1, GSK3A and TRIT1) as putative genes of BC. Further analysis shows that six of these have been reported as breast cancer associated genes, and one (PPYR1) as cancer associated gene. Lastly, we developed an expression signature using these seven key genes which significantly stratified 1660 BC patients according to relapse free survival (hazard ratio [HR], 0.55; 95% confidence interval [CI], 0.46–0.65; Logrank p = 5.5e−13). The 7-genes signature could be established as a useful predictor of disease prognosis in BC patients. Overall, the identified seven genes might be useful prognostic and predictive molecular markers to predict the clinical outcome of BC patients.
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Affiliation(s)
- Zhenyu Yue
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China.,Institute of Health Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Hai-Tao Li
- College of Electrical Engineering and Automation, Anhui University, Hefei, Anhui 230601, China
| | - Yabing Yang
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Sajid Hussain
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Chun-Hou Zheng
- College of Electrical Engineering and Automation, Anhui University, Hefei, Anhui 230601, China
| | - Junfeng Xia
- Institute of Health Sciences, Anhui University, Hefei, Anhui 230601, China
| | - Yan Chen
- School of Life Sciences, Anhui University, Hefei, Anhui 230601, China
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26
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Greene MK, Richards DA, Nogueira JCF, Campbell K, Smyth P, Fernández M, Scott CJ, Chudasama V. Forming next-generation antibody-nanoparticle conjugates through the oriented installation of non-engineered antibody fragments. Chem Sci 2017; 9:79-87. [PMID: 29629076 PMCID: PMC5869316 DOI: 10.1039/c7sc02747h] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/08/2017] [Indexed: 12/15/2022] Open
Abstract
Enabling oriented installation of non-engineered antibody fragments on nanoparticle surfaces to create next-generation antibody–nanoparticle conjugates.
The successful development of targeted nanotherapeutics is contingent upon the conjugation of therapeutic nanoparticles to target-specific ligands, with particular emphasis being placed on antibody-based ligands. Thus, new methods that enable the covalent and precise installation of targeting antibodies to nanoparticle surfaces are greatly desired, especially those which do not rely on costly and time-consuming antibody engineering techniques. Herein we present a novel method for the highly controlled and oriented covalent conjugation of non-engineered antibody F(ab) fragments to PLGA–PEG nanoparticles using disulfide-selective pyridazinedione linkers and strain-promoted alkyne–azide click chemistry. Exemplification of this method with trastuzumab and cetuximab showed significant improvements in both conjugation efficiency and antigen binding capability, when compared to commonly employed strategies for antibody–nanoparticle construction. This new approach paves the way for the development of antibody-targeted nanomedicines with improved paratope availability, reproducibility and uniformity to enhance both biological activity and ease of manufacture.
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Affiliation(s)
- Michelle K Greene
- Centre for Cancer Research and Cell Biology , School of Medicine , Dentistry and Biomedical Sciences , Queen's University Belfast , Belfast , UK .
| | | | | | - Katrina Campbell
- Institute for Global Food Security , School of Biological Sciences , Queen's University Belfast , Belfast , UK
| | - Peter Smyth
- Centre for Cancer Research and Cell Biology , School of Medicine , Dentistry and Biomedical Sciences , Queen's University Belfast , Belfast , UK .
| | - Marcos Fernández
- Department of Chemistry , University College London , London , UK .
| | - Christopher J Scott
- Centre for Cancer Research and Cell Biology , School of Medicine , Dentistry and Biomedical Sciences , Queen's University Belfast , Belfast , UK .
| | - Vijay Chudasama
- Department of Chemistry , University College London , London , UK . .,Research Institute for Medicines (iMed.ULisboa) , Faculty of Pharmacy , Universidade de Lisboa , Lisbon , Portugal
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27
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Peckys DB, Korf U, Wiemann S, de Jonge N. Liquid-phase electron microscopy of molecular drug response in breast cancer cells reveals irresponsive cell subpopulations related to lack of HER2 homodimers. Mol Biol Cell 2017; 28:mbc.E17-06-0381. [PMID: 28794264 PMCID: PMC5687022 DOI: 10.1091/mbc.e17-06-0381] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/27/2017] [Accepted: 08/01/2017] [Indexed: 12/31/2022] Open
Abstract
The development of drug resistance in cancer poses a major clinical problem. An example is human epidermal growth factor receptor 2 (HER2) overexpressing breast cancer often treated with anti-HER2 antibody therapies, such as trastuzumab. Since drug resistance is rooted mainly in tumor cell heterogeneity, we examined the drug effect in different subpopulations of SKBR3 breast cancer cells, and compared the results with a drug resistant cell line, HCC1954. Correlative light microscopy and liquid-phase scanning transmission electron microscopy (STEM) were used to quantitatively analyze HER2 responses upon drug binding, whereby many tens of whole cells were imaged. Trastuzumab was found to selectively cross-link and down regulate HER2 homodimers from the plasma membranes of bulk cancer cells. In contrast, HER2 resided mainly as monomers in rare subpopulations of resting- and cancer stem cells (CSCs), and these monomers were not internalized after drug binding. The HER2 distribution was hardly influenced by trastuzumab for the HCC1954 cells. These findings show that resting cells and CSCs are irresponsive to the drug, and thus point towards a molecular explanation behind the origin of drug resistance. This analytical method is broadly applicable to study membrane protein interactions in the intact plasma membrane, while accounting for cell heterogeneity.
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Affiliation(s)
- Diana B Peckys
- Department of Biophysics, Saarland University, D-66421 Homburg, Germany
| | - Ulrike Korf
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Niels de Jonge
- INM - Leibniz Institute for New Materials, 66123 Saarbrücken, Germany
- Department of Physics, Saarland University, 66123 Saarbrücken, Germany
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28
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Zang H, Li N, Pan Y, Hao J. Identification of upstream transcription factors (TFs) for expression signature genes in breast cancer. Gynecol Endocrinol 2017; 33:193-198. [PMID: 27809618 DOI: 10.1080/09513590.2016.1239253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Breast cancer is a common malignancy among women with a rising incidence. Our intention was to detect transcription factors (TFs) for deeper understanding of the underlying mechanisms of breast cancer. Integrated analysis of gene expression datasets of breast cancer was performed. Then, functional annotation of differentially expressed genes (DEGs) was conducted, including Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment. Furthermore, TFs were identified and a global transcriptional regulatory network was constructed. Seven publically available GEO datasets were obtained, and a set of 1196 DEGs were identified (460 up-regulated and 736 down-regulated). Functional annotation results showed that cell cycle was the most significantly enriched pathway, which was consistent with the fact that cell cycle is closely related to various tumors. Fifty-three differentially expressed TFs were identified, and the regulatory networks consisted of 817 TF-target interactions between 46 TFs and 602 DEGs in the context of breast cancer. Top 10 TFs covering the most downstream DEGs were SOX10, NFATC2, ZNF354C, ARID3A, BRCA1, FOXO3, GATA3, ZEB1, HOXA5 and EGR1. The transcriptional regulatory networks could enable a better understanding of regulatory mechanisms of breast cancer pathology and provide an opportunity for the development of potential therapy.
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Affiliation(s)
- Hongyan Zang
- a Department of Breast Surgery , Yantaishan Hospital , Yantai , China and
| | - Ning Li
- b Department of Human Anatomy , School of Basic Medicine, Shandong University of Traditional Chinese Medicine , Jinan , China
| | - Yuling Pan
- b Department of Human Anatomy , School of Basic Medicine, Shandong University of Traditional Chinese Medicine , Jinan , China
| | - Jingguang Hao
- a Department of Breast Surgery , Yantaishan Hospital , Yantai , China and
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29
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Agosto-Arroyo E, Isayeva T, Wei S, Almeida JS, Harada S. Differential Gene Expression in Ductal Carcinoma In Situ of the Breast Based on ERBB2 Status. Cancer Control 2017; 24:102-110. [PMID: 28178722 DOI: 10.1177/107327481702400117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The molecular signature of ductal carcinoma in situ (DCIS) in the breast is not well understood. Erb-b2 receptor tyrosine kinase 2 (ERBB2 [formerly known as HER2/neu]) positivity in DCIS is predictive of coexistent early invasive breast carcinoma. The aim of this study is to identify the gene-expression signature profiles of estrogen receptor (ER)/progesterone receptor (PR)-positive, ERBB2, and triple-negative subtypes of DCIS. METHODS Based on ER, PR, and ERBB2 status, a total of 18 high nuclear grade DCIS cases with no evidence of invasive breast carcinoma were selected along with 6 non-neoplastic controls. The 3 study groups were defined as ER/PR-positive, ERBB2, and triple-negative subtypes. RESULTS A total of 49 genes were differentially expressed in the ERBB2 subtype compared with the ER/PR-positive and triple-negative groups. PROM1 was overexpressed in the ERBB2 subtype compared with ER/PR-positive and triple-negative subtypes. Other genes differentially expressed included TAOK1, AREG, AGR3, PEG10, and MMP9. CONCLUSIONS Our study identified unique gene signatures in ERBB2-positive DCIS, which may be associated with the development of invasive breast carcinoma. The results may enhance our understanding of the progression of breast cancer and become the basis for developing new predictive biomarkers and therapeutic targets for DCIS.
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Affiliation(s)
| | - Tatyana Isayeva
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL
| | - Shi Wei
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL
| | - Jonas S Almeida
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL
| | - Shuko Harada
- Department of Pathology, University of Alabama at Birmingham, Birmingham, AL.
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30
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The collectins CL-L1, CL-K1 and CL-P1, and their roles in complement and innate immunity. Immunobiology 2016; 221:1058-67. [DOI: 10.1016/j.imbio.2016.05.012] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 05/21/2016] [Accepted: 05/23/2016] [Indexed: 12/11/2022]
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31
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Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues. Oncotarget 2016; 6:41216-27. [PMID: 26515599 PMCID: PMC4747401 DOI: 10.18632/oncotarget.5649] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/12/2015] [Indexed: 12/13/2022] Open
Abstract
Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.
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32
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Muthukaruppan A, Lasham A, Woad KJ, Black MA, Blenkiron C, Miller LD, Harris G, McCarthy N, Findlay MP, Shelling AN, Print CG. Multimodal Assessment of Estrogen Receptor mRNA Profiles to Quantify Estrogen Pathway Activity in Breast Tumors. Clin Breast Cancer 2016; 17:139-153. [PMID: 27756582 DOI: 10.1016/j.clbc.2016.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 08/25/2016] [Accepted: 09/02/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND Molecular markers have transformed our understanding of the heterogeneity of breast cancer and have allowed the identification of genomic profiles of estrogen receptor (ER)-α signaling. However, our understanding of the transcriptional profiles of ER signaling remains inadequate. Therefore, we sought to identify the genomic indicators of ER pathway activity that could supplement traditional immunohistochemical (IHC) assessments of ER status to better understand ER signaling in the breast tumors of individual patients. MATERIALS AND METHODS We reduced ESR1 (gene encoding the ER-α protein) mRNA levels using small interfering RNA in ER+ MCF7 breast cancer cells and assayed for transcriptional changes using Affymetrix HG U133 Plus 2.0 arrays. We also compared 1034 ER+ and ER- breast tumors from publicly available microarray data. The principal components of ER activity generated from these analyses and from other published estrogen signatures were compared with ESR1 expression, ER-α IHC, and patient survival. RESULTS Genes differentially expressed in both analyses were associated with ER-α IHC and ESR1 mRNA expression. They were also significantly enriched for estrogen-driven molecular pathways associated with ESR1, cyclin D1 (CCND1), MYC (v-myc avian myelocytomatosis viral oncogene homolog), and NFKB (nuclear factor kappa B). Despite their differing constituent genes, the principal components generated from these new analyses and from previously published ER-associated gene lists were all associated with each other and with the survival of patients with breast cancer treated with endocrine therapies. CONCLUSION A biomarker of ER-α pathway activity, generated using ESR1-responsive mRNAs in MCF7 cells, when used alongside ER-α IHC and ESR1 mRNA expression, could provide a method for further stratification of patients and add insight into ER pathway activity in these patients.
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Affiliation(s)
- Anita Muthukaruppan
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand.
| | - Annette Lasham
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Kathryn J Woad
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Cherie Blenkiron
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC
| | - Gavin Harris
- Canterbury Health Laboratories, Christchurch, New Zealand
| | - Nicole McCarthy
- Discipline of Oncology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Michael P Findlay
- Discipline of Oncology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Andrew N Shelling
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand
| | - Cristin G Print
- Department of Molecular Medicine and Pathology, Faculty of Medical and Health Sciences, The University of Auckland, Auckland, New Zealand; New Zealand Bioinformatics Institute, The University of Auckland, Auckland, New Zealand; Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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