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Wei PJ, Ma W, Li Y, Su Y. Disease biomarker identification based on sample network optimization. Methods 2023; 213:42-49. [PMID: 37001685 DOI: 10.1016/j.ymeth.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/12/2023] [Accepted: 03/16/2023] [Indexed: 03/31/2023] Open
Abstract
A large amount of evidence shows that biomarkers are discriminant features related to disease development. Thus, the identification of disease biomarkers has become a basic problem in the analysis of complex diseases in the medical fields, such as disease stage judgment, disease diagnosis and treatment. Research based on networks have become one of the most popular methods. Several algorithms based on networks have been proposed to identify biomarkers, however the networks of genes or molecules ignored the similarities and associations among the samples. It is essential to further understand how to construct and optimize the networks to make the identified biomarkers more accurate. On this basis, more effective strategies can be developed to improve the performance of biomarkers identification. In this study, a multi-objective evolution algorithm based on sample similarity networks has been proposed for disease biomarker identification. Specifically, we design the sample similarity networks to extract the structural characteristic information among samples, which used to calculate the influence of the sample to each class. Besides, based on the networks and the group of biomarkers we choose in every iteration, we can divide samples into different classes by the importance for each class. Then, in the process of evolution algorithm population iteration, we develop the elite guidance strategy and fusion selection strategy to select the biomarkers which make the sample classification more accurate. The experiment results on the five gene expression datasets suggests that the algorithm we proposed is superior over some state-of-the-art disease biomarker identification methods.
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Affiliation(s)
- Pi-Jing Wei
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, 111 Jiulong Road, 230601 Hefei, Anhui, China
| | - Wenwen Ma
- Key Laboratory of Intelligent Computing and Signal Processing, School of Computer Science and Technology, Anhui University, 111 Jiulong Road, 230601 Hefei, China
| | - Yanxin Li
- Department of Cardiology, The Third Hospital of Xingtai, Xingtai 054000, Hebei, China
| | - Yansen Su
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, 5089 Wangjiang West Road, 230088 Hefei, China; School of Artificial Intelligence, Anhui University, 111 Jiulong Road, 230601 Hefei, China.
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Wakasa H, Tsugami Y, Koyama T, Han L, Nishimura T, Isobe N, Kobayashi K. Adverse Effects of High Temperature On Mammary Alveolar Development In Vitro. J Mammary Gland Biol Neoplasia 2022; 27:155-170. [PMID: 35581442 DOI: 10.1007/s10911-022-09518-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/26/2022] [Indexed: 10/18/2022] Open
Abstract
In the mammary glands during pregnancy, the alveolar buds are first branched from the mammary ducts after which they form the alveolar luminal structure for milk production postparturition. Body temperature could increase for several reasons, such as infectious disease and heat stress. We have previously reported that high temperature adversely effects on the lactation capacity of mouse mammary epithelial cells (MECs). However, it remains unclear how high temperature influences mammary morophogenesis during pregnancy. In this study, we investigated the effects of high temperature on this mammary alveolar development process using two types of culture models including embedded organoids of MECs in Matrigel; these models reproduced mammary alveolar bud induction and alveolar luminal formation. Results showed that a culture temperature of 41 °C repressed alveolar bud induction and inhibited alveolar luminal formation. In addition, the treatment at 41 °C decreased the number of proliferating mammary epithelial cells but did not affect cell migration. Levels of phosphorylated Akt, -ERK1/2, -HSP90, and -HSP27 were increased in organoids cultured at 41 °C. The specific inhibitors of HSP90 and HSP27 exacerbated the disruption of organoids at 41 °C but not at 37 °C. Furthermore, the organoids precultured at 37 and 41 °C in the alveolar luminal formation model showed differences in the expression levels of caseins and tight junction proteins, which express in MECs in lactating mammary glands, after induction of MEC differentiation by prolactin and dexamethasone treatment in vitro. These results suggest that elevated temperature directly hinders mammary alveolar development; however, heat shock proteins may mitigate the adverse effects of high temperatures.
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Affiliation(s)
- Haruka Wakasa
- Laboratory of Cell and Tissue Biology, Research Faculty of Agriculture, Hokkaido University, North 9, West 9, 060-8589, Sapporo, Japan
| | - Yusaku Tsugami
- Laboratory of Animal Histophysiology, Graduate School of Integrated Science for Life Faculty of Applied Biological Science, Hiroshima University, 1-4-4, Kagamiyama, 739-8528, Higashi-Hiroshima, Japan
| | - Taku Koyama
- Laboratory of Cell and Tissue Biology, Research Faculty of Agriculture, Hokkaido University, North 9, West 9, 060-8589, Sapporo, Japan
| | - Liang Han
- Laboratory of Cell and Tissue Biology, Research Faculty of Agriculture, Hokkaido University, North 9, West 9, 060-8589, Sapporo, Japan
| | - Takanori Nishimura
- Laboratory of Cell and Tissue Biology, Research Faculty of Agriculture, Hokkaido University, North 9, West 9, 060-8589, Sapporo, Japan
| | - Naoki Isobe
- Laboratory of Animal Histophysiology, Graduate School of Integrated Science for Life Faculty of Applied Biological Science, Hiroshima University, 1-4-4, Kagamiyama, 739-8528, Higashi-Hiroshima, Japan
| | - Ken Kobayashi
- Laboratory of Cell and Tissue Biology, Research Faculty of Agriculture, Hokkaido University, North 9, West 9, 060-8589, Sapporo, Japan.
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Akhter MS, Uddin MA, Kubra KT, Barabutis N. Elucidation of the Molecular Pathways Involved in the Protective Effects of AUY-922 in LPS-Induced Inflammation in Mouse Lungs. Pharmaceuticals (Basel) 2021; 14:ph14060522. [PMID: 34072430 PMCID: PMC8226636 DOI: 10.3390/ph14060522] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 12/11/2022] Open
Abstract
Acute lung injury (ALI) and acute respiratory distress syndrome (ARDS) cause thousands of deaths every year and are associated with high mortality rates (~40%) due to the lack of efficient therapies. Understanding the molecular mechanisms associated with those diseases will most probably lead to novel therapeutics. In the present study, we investigated the effects of the Hsp90 inhibitor AUY-922 in the major inflammatory pathways of mouse lungs. Mice were treated with LPS (1.6 mg/kg) via intratracheal instillation for 24 h and were then post-treated intraperitoneally with AUY-922 (10 mg/kg). The animals were examined 48 h after AUY-922 injection. LPS activated the TLR4-mediated signaling pathways, which in turn induced the release of different inflammatory cytokines and chemokines. AUY-922 suppressed the LPS-induced inflammation by inhibiting major pro-inflammatory pathways (e.g., JAK2/STAT3, MAPKs), and downregulated the IL-1β, IL-6, MCP-1 and TNFα. The expression levels of the redox regulator APE1/Ref1, as well as the DNA-damage inducible kinases ATM and ATR, were also increased after LPS treatment. Those effects were counteracted by AUY-922. Interestingly, this Hsp90 inhibitor abolished the LPS-induced pIRE1α suppression, a major component of the unfolded protein response. Our study elucidates the molecular pathways involved in the progression of murine inflammation and supports our efforts on the development of new therapeutics against lung inflammatory diseases and sepsis.
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Zhang H, Ge F, Shui X, Xiang Y, Wang X, Liao C, Wang J. NIX protein enhances antioxidant capacity of and reduces the apoptosis induced by HSP90 inhibitor luminespib/NVP-AUY922 in PC12 cells. Cell Stress Chaperones 2021; 26:495-504. [PMID: 33629253 PMCID: PMC8065087 DOI: 10.1007/s12192-021-01193-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 11/29/2022] Open
Abstract
Pheochromocytomas and paragangliomas (PCPGs) are catecholamine-producing neuroendocrine tumors. Accumulating evidences indicate that the blockade of antioxidative pathways might be a novel therapeutic approach to the treatment of PCPG. NIX has been confirmed to play a key role in maintaining redox homeostasis in tumors, while the function of NIX in PCPG remains unclear. In this study, the analyses of the disease-free survival (DFS) showed that high NIX protein level is related to poor prognosis in patients of PCPG. Consistent with this, high level of NIX protein upregulates the level of p-NF-κB and promotes the migration of PC12 cells. In NIX-over-expressing PC12 cells, the level of reactive oxygen species (ROS) is decreased while trolox-equivalent antioxidant capacity (TEAC) increased. But in NIX-silencing cells, ROS level is increased, while TEAC reversely reduced, consequently antioxidase and phase II enzymes of NRF2 signaling were activated, and elevated endoplasmic reticulum (ER) stress was observed. Additionally, the apoptosis induced by luminespib/NVP-AUY922, an inhibitor of heat shock protein 90 (HSP90, a cellular stress response factor), was enhanced in NIX-silencing cells but reduced in the NIX-over-expressing cells. All of these results indicated that high NIX protein level enhances antioxidant capacity of PC12 cells and reduces the apoptosis caused by cell stress, such as induced by luminespib/NVP-AUY922. Therefore, luminespib/NVP-AUY922 might be effective only for PCPG with low NIX level, while targeting NIX could be a further supplement to the therapeutic treatment strategy for PCPG patients with high NIX protein level.
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Affiliation(s)
- Hong Zhang
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, 610500, Sichuan, China
| | - Fanghui Ge
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, 610500, Sichuan, China
| | - Xindong Shui
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- School of Basic Medical Sciences, Fujian Medical University, Fuzhou, 350122, Fujian, China
| | - Yuling Xiang
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, 610500, Sichuan, China
- College of Life Science and Technology, Guangxi University, Nanning, 530004, Guangxi, China
| | - Xinxin Wang
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, 610500, Sichuan, China
| | - Chang Liao
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, 610500, Sichuan, China
| | - Jiandong Wang
- School of Bioscience and Technology, Chengdu Medical College, Chengdu, 610500, Sichuan, China.
- Collaborative Innovation Center of Sichuan for Elderly Care and Health, Chengdu Medical College, Chengdu, 610500, Sichuan, China.
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Hamidi O. Metastatic pheochromocytoma and paraganglioma: recent advances in prognosis and management. Curr Opin Endocrinol Diabetes Obes 2019; 26:146-154. [PMID: 30893083 DOI: 10.1097/med.0000000000000476] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
PURPOSE OF REVIEW Metastatic pheochromocytomas and paragangliomas (PPGL) are rare neuroendocrine tumors with variable prognosis. This review highlights recent studies on outcomes and management of patients with metastatic PPGL. RECENT FINDINGS Latest advances were made in identifying predictors of favorable outcomes of patients with metastatic PPGL. Recent studies evaluated the efficacy of tyrosine kinase inhibitors, high-specific-activity radiopharmaceuticals, and peptide receptors radionuclide therapy in treatment of metastatic disease. Moreover, ongoing studies are assessing the effects of hypoxia-inducible factor 2αα and heat shock protein 90 inhibitors as potential therapies. SUMMARY Several active studies are evaluating the efficacy of systemic chemo, immuno, radiopharmaceutical, and peptide receptor radionuclide therapies to relieve local and adrenergic symptoms and provide survival benefit for patients with symptomatic and/or progressive advanced metastatic PPGL. Owing to rarity and wide-outcome variability, multidisciplinary team effort and personalized approach are central in caring for patients with metastatic PPGL.
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Affiliation(s)
- Oksana Hamidi
- Division of Endocrinology and Metabolism, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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Zhang X, Gao F, Zhong S. Combinatorial Inhibition of mTORC2 and Hsp90 Leads to a Distinctly Effective Therapeutic Strategy in Malignant Pheochromocytoma. Curr Cancer Drug Targets 2019; 19:698-706. [PMID: 30727894 DOI: 10.2174/1568009619666190206120615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Malignant pheochromocytoma (mPCC) is an uncommon tumor with poor prognosis, and no effective therapeutic strategy exists as yet. Discovering new and effective therapeutic strategies to improve prognosis is an urgent need. OBJECTIVE To investigate whether a combinatorial inhibition of both mTORC2 and Hsp90 in PC12 cells could lead to a distinct anti-tumor effect in vitro and in vivo that was greater than the inhibition of mTORC2 or Hsp90 alone. METHODS Targeting mTORC2 was assessed by knockdown of Rictor using shRNA, and 17-AAG was used to inhibit Hsp90 function. RESULTS Combinatorial inhibition of both mTORC2 and Hsp90 could lead to a distinct anti-tumor effect in vitro that was greater than the inhibition of mTORC2 or Hsp90 alone. Inhibiting Hsp90 specifically could inhibit tumor growth of sh-Rictor cells in vivo, suggesting that the combinatorial inhibition of both mTORC2 and Hsp90 could lead to a distinct anti-tumor effect in vivo. Western blotting has shown that both p-Akt Ser473 and p-Akt Thr450 showed significantly decreased expression after targeting mTORC2, while p-Akt Thr308 did not. However, all three different p-AKTs, including p-Akt Ser473, p-Akt Thr450 and p-Akt Thr308, showed a significantly decreased expression in combinatorial inhibition of both mTORC2 and Hsp90. Collectively, it revealed that combinatorial inhibition of mTORC2 and Hsp90 could destabilize the Akt signaling. CONCLUSION Our results demonstrated that combinatorial inhibition of mTORC2 and Hsp90 could increase their anti-tumor effect and destabilize the Akt signaling in PC12 cells, suggesting a combinatorial inhibition of both mTORC2 and Hsp90 which might be an effective therapeutic strategy for mPCC.
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Affiliation(s)
- Xiaohua Zhang
- Department of Urology, Huashan Hospital Affiliated to Fudan University, Shanghai, China
| | - Fengbin Gao
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Shan Zhong
- Department of Urology, Huashan Hospital Affiliated to Fudan University, Shanghai, China
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Crona J, Beuschlein F, Pacak K, Skogseid B. Advances in adrenal tumors 2018. Endocr Relat Cancer 2018; 25:R405-R420. [PMID: 29794126 PMCID: PMC5976083 DOI: 10.1530/erc-18-0138] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 04/24/2018] [Indexed: 12/14/2022]
Abstract
This review aims to provide clinicians and researchers with a condensed update on the most important studies in the field during 2017. We present the academic output measured by active clinical trials and peer-reviewed published manuscripts. The most important and contributory manuscripts were summarized for each diagnostic entity, with a particular focus on manuscripts that describe translational research that have the potential to improve clinical care. Finally, we highlight the importance of collaborations in adrenal tumor research, which allowed for these recent advances and provide structures for future success in this scientific field.
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Affiliation(s)
- J Crona
- Department of Medical SciencesUppsala University, Uppsala, Sweden
| | - F Beuschlein
- Medizinische Klinik und Poliklinik IVKlinikum der Universität München, Munich, Germany
- Klinik für EndokrinologieDiabetologie und Klinische Ernährung, UniversitätsSpital Zürich, Zürich, Switzerland
| | - K Pacak
- Section on Medical NeuroendocrinologyEunice Kennedy Shriver National Institute of Child Health & Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - B Skogseid
- Department of Medical SciencesUppsala University, Uppsala, Sweden
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Wang H, Zhang S, Zhang A, Yan C. Propofol Prevents the Progression of Malignant PheochromocytomaIn VitroandIn Vivo. DNA Cell Biol 2018; 37:308-315. [PMID: 29565198 DOI: 10.1089/dna.2017.3972] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Hua Wang
- Department of Endocrinology, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin, China
| | - Shu Zhang
- Department of Endocrinology, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin, China
| | - Aihong Zhang
- Department of Pharmaceuticals, Harbin Medical University Affiliated 3rd Hospital, Harbin, China
| | - Cunling Yan
- Department of Medicine, Harbin Medical University Affiliated 3rd Hospital, Harbin, China
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Moon HJ, Kim HB, Lee SH, Jeun SE, Kang CD, Kim SH. Sensitization of multidrug-resistant cancer cells to Hsp90 inhibitors by NSAIDs-induced apoptotic and autophagic cell death. Oncotarget 2018. [PMID: 29541415 PMCID: PMC5834263 DOI: 10.18632/oncotarget.24130] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
NSAIDs (non-steroidal anti-inflammatory drugs) have potential use as anticancer agents, either alone or in combination with other cancer therapies. We found that NSAIDs including celecoxib (CCB) and ibuprofen (IBU) significantly potentiated the cytotoxicity of Hsp90 inhibitors in human multidrug-resistant (MDR) cells expressing high levels of mutant p53 (mutp53) protein and P-glycoprotein (P-gp), and reversed Hsp90 inhibitor resistance caused by activation of heat shock factor 1 (HSF1) and by up-regulation of heat shock proteins (Hsps) and P-gp. Inhibition of Akt/mTOR and STAT3 pathways by CCB induced autophagy, which promoted the degradation of mutp53, one of Hsp90 client proteins, and subsequently down-regulated HSF1/Hsps and P-gp. Inhibition of autophagy prevented mutp53 degradation and CCB-induced apoptosis, and inhibition of caspase-3-mediated apoptotic pathway by Z-DEVD-FMK did not completely block CCB-induced cell death in MDR cells, suggesting that autophagic and apoptotic cell death may contribute to CCB-induced cytotoxicity in MDR cells. Furthermore, CCB and IBU suppressed Hsp90 inhibitor-induced HSF1/Hsp70/P-gp activity and mutp53 expression in MDR cells. Our results suggest that NSAIDs can be used as potential Hsp90 inhibitor chemosensitizers and reverse resistance of MDR cells to Hsp90 inhibitors via induction of apoptosis and autophagy. These results might enable the use of lower, less toxic doses of Hsp90 inhibitors and facilitate the design of practically applicable, novel combination therapy for the treatment of MDR cancer.
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Affiliation(s)
- Hyun-Jung Moon
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 626-870, Korea
| | - Hak-Bong Kim
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 626-870, Korea
| | - Su-Hoon Lee
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 626-870, Korea
| | - So-Eun Jeun
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 626-870, Korea
| | - Chi-Dug Kang
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 626-870, Korea
| | - Sun-Hee Kim
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 626-870, Korea
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