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Liu W, Li G, Huang D, Qin T. AKR1C3 promotes progression and mediates therapeutic resistance by inducing epithelial-mesenchymal transition and angiogenesis in small cell lung cancer. Transl Oncol 2024; 47:102027. [PMID: 38954974 DOI: 10.1016/j.tranon.2024.102027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/30/2024] [Accepted: 06/03/2024] [Indexed: 07/04/2024] Open
Abstract
OBJECTIVE Small cell lung cancer (SCLC) is a high-grade neuroendocrine tumor characterized by initial sensitivity to chemotherapy, followed by the development of drug resistance. The underlying mechanisms of resistance in SCLC have not been fully elucidated. Aldo-keto reductase family 1 member C3 (AKR1C3), is known to be associated with chemoradiotherapy resistance in diverse tumors. We aim to evaluate the prognostic significance and immune characteristics of AKR1C3 and investigate its potential role in promoting drug resistance in SCLC. METHODS 81 postoperative SCLC tissues were used to analyze AKR1C3 prognostic value and immune features. The tissue microarrays were employed to validate the clinical significance of AKR1C3 in SCLC. The effects of AKR1C3 on SCLC cell proliferation, migration, apoptosis and tumor angiogenesis were detected by CCK-8, wound healing assay, transwell assay, flow cytometry and tube formation assay. RESULTS AKR1C3 demonstrated the highest expression level compared to other AKR1C family genes, and multivariate cox regression analysis identified it as an independent prognostic factor for SCLC. High AKR1C3 expression patients who underwent chemoradiotherapy experienced significantly shorter overall survival (OS). Furthermore, AKR1C3 was involved in the regulation of the tumor immune microenvironment in SCLC. Silencing of AKR1C3 led to the inhibition of cell proliferation and migration, while simultaneously promoting apoptosis and reducing epithelial-mesenchymal transition (EMT) in SCLC. CONCLUSION AKR1C3 promotes cell growth and metastasis, leading to drug resistance through inducing EMT and angiogenesis in SCLC.
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Affiliation(s)
- Wenting Liu
- Department of Thoracic Oncology, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China; Department of Respiratory Medicine, Beijing Friendship Hospital, Capital Medical University, Beijing 100050, China
| | - Guoli Li
- Department of Clinical Laboratory, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Dingzhi Huang
- Department of Thoracic Oncology, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.
| | - Tingting Qin
- Department of Thoracic Oncology, National Clinical Research Center for Cancer, Tianjin Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, China.
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Li M, Zhang L, Yu J, Wang X, Cheng L, Ma Z, Chen X, Wang L, Goh BC. AKR1C3 in carcinomas: from multifaceted roles to therapeutic strategies. Front Pharmacol 2024; 15:1378292. [PMID: 38523637 PMCID: PMC10957692 DOI: 10.3389/fphar.2024.1378292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
Aldo-Keto Reductase Family 1 Member C3 (AKR1C3), also known as type 5 17β-hydroxysteroid dehydrogenase (17β-HSD5) or prostaglandin F (PGF) synthase, functions as a pivotal enzyme in androgen biosynthesis. It catalyzes the conversion of weak androgens, estrone (a weak estrogen), and PGD2 into potent androgens (testosterone and 5α-dihydrotestosterone), 17β-estradiol (a potent estrogen), and 11β-PGF2α, respectively. Elevated levels of AKR1C3 activate androgen receptor (AR) signaling pathway, contributing to tumor recurrence and imparting resistance to cancer therapies. The overexpression of AKR1C3 serves as an oncogenic factor, promoting carcinoma cell proliferation, invasion, and metastasis, and is correlated with unfavorable prognosis and overall survival in carcinoma patients. Inhibiting AKR1C3 has demonstrated potent efficacy in suppressing tumor progression and overcoming treatment resistance. As a result, the development and design of AKR1C3 inhibitors have garnered increasing interest among researchers, with significant progress witnessed in recent years. Novel AKR1C3 inhibitors, including natural products and analogues of existing drugs designed based on their structures and frameworks, continue to be discovered and developed in laboratories worldwide. The AKR1C3 enzyme has emerged as a key player in carcinoma progression and therapeutic resistance, posing challenges in cancer treatment. This review aims to provide a comprehensive analysis of AKR1C3's role in carcinoma development, its implications in therapeutic resistance, and recent advancements in the development of AKR1C3 inhibitors for tumor therapies.
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Affiliation(s)
- Mengnan Li
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Limin Zhang
- Jingzhou Hospital of Traditional Chinese Medicine, Jingzhou, China
- The Third Clinical Medical College of Yangtze University, Jingzhou, China
| | - Jiahui Yu
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Xiaoxiao Wang
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Le Cheng
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Zhaowu Ma
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Xiaoguang Chen
- School of Basic Medicine, Health Science Center, Yangtze University, Jingzhou, China
| | - Lingzhi Wang
- Department of Haematology–Oncology, National University Cancer Institute, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Department of Haematology–Oncology, National University Cancer Institute, Singapore, Singapore
- NUS Center for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Wu QN, Qi J, Liu ZK, Luo XJ, Yu K, Lu YX, Wang Y, Jin Y, Liu J, Huang LY, Zeng ZL, Zheng Y, Xu RH, Liu ZX. HIPK3 maintains sensitivity to platinum drugs and prevents disease progression in gastric cancer. Cancer Lett 2024; 584:216643. [PMID: 38246220 DOI: 10.1016/j.canlet.2024.216643] [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: 09/17/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/23/2024]
Abstract
In the realm of cancer therapeutics and resistance, kinases play a crucial role, particularly in gastric cancer (GC). Our study focused on platinum-based chemotherapy resistance in GC, revealing a significant reduction in homeodomain-interacting protein kinase 3 (HIPK3) expression in platinum-resistant tumors through meticulous analysis of transcriptome datasets. In vitro and in vivo experiments demonstrated that HIPK3 knockdown enhanced tumor proliferation and metastasis, while upregulation had the opposite effect. We identified the myocyte enhancer factor 2C (MEF2C) as a transcriptional regulator of HIPK3 and uncovered HIPK3's role in downregulating the morphogenesis regulator microtubule-associated protein (MAP7) through ubiquitination. Phosphoproteome profiling revealed HIPK3's inhibitory effects on mTOR and Wnt pathways crucial in cell proliferation and movement. A combined treatment strategy involving oxaliplatin, rapamycin, and IWR1-1-endo effectively overcame platinum resistance induced by reduced HIPK3 expression. Monitoring HIPK3 levels could serve as a GC malignancy and platinum resistance indicator, with our proposed treatment strategy offering novel avenues for reversing resistance in gastric cancer.
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Affiliation(s)
- Qi-Nian Wu
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Jingjing Qi
- Tumor Epigenetics Laboratory, Johannes Kepler University Linz, Altenbergerstraße 69, 4040, Linz, Austria
| | - Ze-Kun Liu
- Department of Radiology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Xiao-Jing Luo
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Kai Yu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Yun-Xin Lu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Yun Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Ying Jin
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Jia Liu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Li-Yun Huang
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Zhao-Lei Zeng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Yongqiang Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China
| | - Rui-Hua Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China; Research Unit of Precision Diagnosis and Treatment for Gastrointestinal Cancer, Chinese Academy of Medical Sciences, Guangzhou, 510060, PR China.
| | - Ze-Xian Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, 510060, PR China.
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Liu H, Yao Z, Sun M, Zhang C, Huang YY, Luo HB, Wu D, Zheng X. Inhibition of AKR1Cs by liquiritigenin and the structural basis. Chem Biol Interact 2023; 385:110654. [PMID: 37666442 DOI: 10.1016/j.cbi.2023.110654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/27/2023] [Accepted: 08/09/2023] [Indexed: 09/06/2023]
Abstract
In vivo and in vitro studies have confirmed that liquiritigenin (LQ), the primary active component of licorice, acts as an antitumor agent. However, how LQ diminishes or inhibits tumor growth is not fully understood. Here, we report the enzymatic inhibition of LQ and six other flavanone analogues towards AKR1Cs (AKR1C1, AKR1C2 and AKR1C3), which are involved in prostate cancer, breast cancer, and resistance of anticancer drugs. Crystallographic studies revealed AKR1C3 inhibition of LQ is related to its complementarity with the active site and the hydrogen bonds net in the catalytic site formed through C7-OH, aided by its nonplanar and compact structure due to the saturation of the C2C3 double bond. Comparison of the LQ conformations in the structures of AKR1C1 and AKR1C3 revealed the induced-fit conformation changes, which explains the lack of isoform selectivity of LQ. Our findings will be helpful for better understanding the antitumor effects of LQ on hormonally dependent cancers and the rational design of selective AKR1Cs inhibitors.
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Affiliation(s)
- Huan Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
| | - Ziqing Yao
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
| | - Mingna Sun
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
| | - Chao Zhang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China
| | - Yi-You Huang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Hai-Bin Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China
| | - Deyan Wu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan, China.
| | - Xuehua Zheng
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou, 511436, China.
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Li W, Xu H, Li Y, Shi X, Ma Z, Yang F, Chen W. Identifying Ferroptosis-Related Genes Associated with Weight Loss Outcomes and Regulation of Adipocyte Microenvironment. Mol Nutr Food Res 2023; 67:e2300168. [PMID: 37599272 DOI: 10.1002/mnfr.202300168] [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: 03/22/2023] [Revised: 07/16/2023] [Indexed: 08/22/2023]
Abstract
SCOPE The study is about the influence of ferroptosis-related genes combined with the immune microenvironment exerted on weight control outcomes and systematic analysis. METHODS AND RESULTS Subcutaneous adipose tissue (sWAT) samples from 11 subjects with good outcome and 10 subjects with poor outcome in weight management are obtained from the Gene Expression Omnibus database. The results are validated in vivo in animal models with different weight loss outcomes. The CIBERSORT algorithm is used to evaluate the differences in immune cell infiltration in each sample. Patients with poor outcome have higher levels of ferroptosis in the adipose tissue. Remarkable differences in cytokine production, nuclear factor kappa-B(NF-κB) transcription factor activity, leukocyte migration involved in the inflammatory response, and other biological processes are also observed compared to that in the well-controlled group. Aldo-keto reductase family 1-member C1(AKR1C1), nuclear receptor coactivator 4(NCOA4), and glutamate-cysteine ligase catalytic subunit(GCLC) are identified as core predictive markers and their expression patterns are confirmed in animal models. CONCLUSIONS Ferroptosis and its mediated inflammation play an important role in long-term weight control, and analyses of the role of ferroptosis-related genes(FRGs) in weight control may provide new potential therapeutic targets for long-term weight control. Anti-inflammatory diets that mitigate inflammatory responses and affect ferroptosis may be considered in the future to improve weight control.
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Affiliation(s)
- Wanyang Li
- Department of Clinical Nutrition, Chinese Academy of Medical Sciences-Peking Union Medical College, Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Hanyuan Xu
- Department of Clinical Nutrition, Chinese Academy of Medical Sciences-Peking Union Medical College, Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Yao Li
- College of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, Shandong, 250355, China
| | - Xiaodong Shi
- Department of Clinical Nutrition, Chinese Academy of Medical Sciences-Peking Union Medical College, Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
| | - Zhaotian Ma
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
- Institute of Ethnic Medicine, Beijing University of Traditional Chinese Medicine, Beijing, 100029, China
| | - Fan Yang
- College of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
- National Institute of TCM Constitution and Preventive Medicine, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Wei Chen
- Department of Clinical Nutrition, Chinese Academy of Medical Sciences-Peking Union Medical College, Peking Union Medical College Hospital (Dongdan campus), No.1 Shuaifuyuan Wangfujing Dongcheng District, Beijing, 100730, China
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Graziosi L, Marino E, Natalizi N, Donini A. Prognostic Survival Significance of Signet Ring Cell (SRC) Gastric Cancer: Retrospective Analysis from a Single Western Center. J Pers Med 2023; 13:1157. [PMID: 37511770 PMCID: PMC10382060 DOI: 10.3390/jpm13071157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023] Open
Abstract
INTRODUCTION Signet ring cell carcinoma accounts for 35% to 45% of all gastric cancer. Despite the acknowledgment of its more aggressive pathological features, various controversies surrounding this topic still exist. Thus, we investigate the clinical pathological characteristics and survival prognostic significance of signet ring cell components in patients affected by gastric cancer. METHODS From January 2004 to December 2020, in a retrospective study, we enrolled 404 patients with gastric cancer who were curatively treated in our department. The male-to-female ratio was 249/142, and the median age was 75 (range 37-94). We dichotomized patients into two groups (75 patients vs. 316 patients) based on the signet ring cell presence; according to preoperative, operative, and postoperative characteristics, we performed a univariate and multivariate analysis for overall survival. RESULTS Signet ring cell carcinoma indicated an increasing incidence trend over the time analyzed. Overall median survival of signet ring cell and non-signet ring cell carcinoma were, respectively, 16 vs. 35 months, p < 0.05. In early gastric cancer, the prognosis of the signet ring cell is better than that of the non-signet ring cell, as opposed to advanced cancer. Among the entire population in the multivariate analysis, the only independent factors were preoperative serum albumin level, complete surgical resection, level of lymphadenectomy, and pathological stage. Recurrence occurred more frequently in patients affected by signet ring cell, but in our data, we could not identify a peculiar site of recurrence. CONCLUSIONS Signet ring cell carcinoma has a specific oncogenetic phenotype and treatment resistance heterogeneity; however, it is not always associated with poor prognosis. According to our results, a radical surgical procedure associated with an adequate lymphadenectomy should be advocated to improve patients survival. Gastric cancer patients with signet ring cell components should draw clinicians' attention.
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Affiliation(s)
- Luigina Graziosi
- General and Emergency Surgery of Santa Maria della Misericordia Hospital, University of Perugia, 06132 Perugia, Italy
| | - Elisabetta Marino
- General and Emergency Surgery of Santa Maria della Misericordia Hospital, University of Perugia, 06132 Perugia, Italy
| | - Nicola Natalizi
- General and Emergency Surgery of Santa Maria della Misericordia Hospital, University of Perugia, 06132 Perugia, Italy
| | - Annibale Donini
- General and Emergency Surgery of Santa Maria della Misericordia Hospital, University of Perugia, 06132 Perugia, Italy
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Zhen N, Zhu J, Mao S, Zhang Q, Gu S, Ma J, Zhang Y, Yin M, Li H, Huang N, Wu H, Sun F, Ying B, Zhou L, Pan Q. Alternative Splicing of lncRNAs From SNHG Family Alters snoRNA Expression and Induces Chemoresistance in Hepatoblastoma. Cell Mol Gastroenterol Hepatol 2023; 16:735-755. [PMID: 37478905 PMCID: PMC10520360 DOI: 10.1016/j.jcmgh.2023.07.007] [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: 09/23/2022] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND & AIMS Hepatoblastoma (HB) is a common pediatric malignant liver tumor that is characterized by a low level of genetic mutations. Alternative splicing (AS) has been shown to be closely associated with cancer progression, especially in tumors with a low mutational burden. However, the role of AS in HB remains unknown. METHODS Transcriptome sequencing was performed on 5 pairs of HB tissues and matched non-tumor tissues to delineate the AS landscape in HB. AS events were validated in 92 samples from 46 patients. RNA pull-down and RNA immunoprecipitation assays were carried out to identify splicing factors that regulate the AS of small nucleolar RNA host genes (SNHG). Patient-derived organoids (PDOs) were established to investigate the role of the splicing factor polyadenylate-binding nuclear protein 1 (PABPN1). RESULTS This study uncovered aberrant alternative splicing in HB, including lncRNAs from SNHG family that undergo intron retention in HB. Further investigations revealed that PABPN1, a significantly upregulated RNA binding protein, interacts with splicing machinery in HB, inducing the intron retention of these SNHG RNAs and the downregulation of intronic small nucleolar RNAs (snoRNAs). Functionally, PABPN1 acts as an oncofetal splicing regulator in HB by promoting cell proliferation and DNA damage repair via inducing the intron retention of SNHG19. Knock-down of PABPN1 increases the cisplatin sensitivity of HB PDOs. CONCLUSIONS Our findings revealed the role of intron retention in regulating snoRNA expression in hepatoblastoma, explained detailed regulatory mechanism between PABPN1 and the intron retention of SNHG RNAs, and provided insight into the development of new HB treatment options.
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Affiliation(s)
- Ni Zhen
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiabei Zhu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Siwei Mao
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Zhang
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Song Gu
- Department of Surgery, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ji Ma
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yue Zhang
- Department of Central Laboratory, Clinical Medicine Scientific and Technical Innovation Park, Shanghai Tenth People's Hospital, Shanghai, China
| | - Minzhi Yin
- Department of Pathology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Haojie Li
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Nan Huang
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Han Wu
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fenyong Sun
- Department of Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
| | - Lin Zhou
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China.
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China; Shanghai Key Laboratory of Clinical Molecular Diagnostics for Pediatrics, Shanghai, China; Sanya Women and Children's Hospital Managed by Shanghai Children's Medical Center, Hainan, China.
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Ismailov ZB, Belykh ES, Chernykh AA, Udoratina AM, Kazakov DV, Rybak AV, Kerimova SN, Velegzhaninov IO. Systematic review of comparative transcriptomic studies of cellular resistance to genotoxic stress. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108467. [PMID: 37657754 DOI: 10.1016/j.mrrev.2023.108467] [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: 01/07/2023] [Revised: 08/19/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
The development of resistance by tumor cells to various types of therapy is a significant problem that decreases the effectiveness of oncology treatments. For more than two decades, comparative transcriptomic studies of tumor cells with different sensitivities to ionizing radiation and chemotherapeutic agents have been conducted in order to identify the causes and mechanisms underlying this phenomenon. However, the results of such studies have little in common and often contradict each other. We have assumed that a systematic analysis of a large number of such studies will provide new knowledge about the mechanisms of development of therapeutic resistance in tumor cells. Our comparison of 123 differentially expressed gene (DEG) lists published in 98 papers suggests a very low degree of consistency between the study results. Grouping the data by type of genotoxic agent and tumor type did not increase the similarity. The most frequently overexpressed genes were found to be those encoding the transport protein ABCB1 and the antiviral defense protein IFITM1. We put forward a hypothesis that the role played by the overexpression of the latter in the development of resistance may be associated not only with the stimulation of proliferation, but also with the limitation of exosomal communication and, as a result, with a decrease in the bystander effect. Among down regulated DEGs, BNIP3 was observed most frequently. The expression of BNIP3, together with BNIP3L, is often suppressed in cells resistant to non-platinum genotoxic chemotherapeutic agents, whereas it is increased in cells resistant to ionizing radiation. These observations are likely to be mediated by the binary effects of these gene products on survival, and regulation of apoptosis and autophagy. The combined data also show that even such obvious mechanisms as inhibition of apoptosis and increase of proliferation are not universal but show multidirectional changes.
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Affiliation(s)
- Z B Ismailov
- Institute of Biology of Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia
| | - E S Belykh
- Institute of Biology of Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia
| | - A A Chernykh
- Institute of Physiology of Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, 50 Pervomaiskaya St., Syktyvkar 167982, Russia
| | - A M Udoratina
- Lobachevsky State University of Nizhny Novgorod, 23 Gagarin Avenue, Nizhny Novgorod 603022, Russia
| | - D V Kazakov
- Institute of Physics and Mathematics of Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, 4 Oplesnina St., Syktyvkar 167982, Russia
| | - A V Rybak
- Institute of Biology of Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia
| | - S N Kerimova
- State Medical Institution Komi Republican Oncology Center, 46 Nyuvchimskoe highway, Syktyvkar 167904, Russia
| | - I O Velegzhaninov
- Institute of Biology of Komi Science Centre of the Ural Branch of the Russian Academy of Sciences, 28b Kommunisticheskaya St., Syktyvkar 167982, Russia.
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Zhou Y, Lin Y, Li W, Liu Q, Gong H, Li Y, Luo D. Expression of AKRs superfamily and prognostic in human gastric cancer. Medicine (Baltimore) 2023; 102:e33041. [PMID: 36827074 DOI: 10.1097/md.0000000000033041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
The human aldo-keto reductase (AKRs) superfamily is involved in the development of various tumors. However, the different expression patterns of AKRs and their prognostic value in gastric cancer (GC) have not been clarified. In this study, we analyzed the gene expression and gene methylation level of AKRs in GC patients and the survival data and immune infiltration based on AKRs expression, using data from different databases. We found that the expression levels of AKR1B10, AKR1C1, AKR1C2, and AKR7A3 in GC tissues were lower and the expression level of AKR6A5 was higher in GC tissues than in normal tissue. These differentially expressed genes (AKR1B10, AKR1C1, AKR1C2, AKR7A3, and AKR6A5) were significantly correlated with the infiltration level. The expression of SPI1 and AKR6A5 in GC was positively correlated. Survival analysis showed that GC levels of AKR6A5 reduced or increased mRNA levels of AKR7A3, and AKR1B10 was expected to have higher overall survival (OS), first progression (FP) survival, and postprogression survival (PPS) rates and a better prognosis. Moreover, the expression of AKR1B1 was found to be correlated with the staging of GC. The methylation of AKR6A5 (KCNAB2) at cg05307871 and cg01907457 was significantly associated with the classification of GC. Meta-analysis and ROC curve analysis show that the expression level of AKR1B1 and the methylation of cg16156182 (KCNAB1), cg11194299 (KCNAB2), cg16132520 (AKR1B1), and cg13801416 (AKR1B1) had a high hazard ratio and a good prognostic value. These data suggest that the expression and methylation of AKR1B1 and AKR6A5 are significantly related to the prognosis.
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Affiliation(s)
- Yujin Zhou
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
- Laboratory Medicine Center of Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Yi Lin
- Laboratory Medicine Center of Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Wenjing Li
- Laboratory Medicine Center of Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Quan Liu
- Laboratory Medicine Center of Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Hui Gong
- Laboratory Medicine Center of Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Yifan Li
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University, Yinchuan, China
- Laboratory Medicine Center of Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Dixian Luo
- Laboratory Medicine Center of Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
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10
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Park H, Imoto S, Miyano S. Gene Regulatory Network-Classifier: Gene Regulatory Network-Based Classifier and Its Applications to Gastric Cancer Drug (5-Fluorouracil) Marker Identification. J Comput Biol 2023; 30:223-243. [PMID: 36450117 DOI: 10.1089/cmb.2022.0181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The complex mechanisms of diseases involve the disturbance of the molecular network, rather than disorder in a single gene, implying that single gene-based analysis is insufficient to understand these mechanisms. Gene regulatory networks (GRNs) have attracted a lot of interest and various approaches have been developed for their statistical inference and gene network-based analysis. Although various computational methods have been developed, relatively little attention has been paid to incorporation of biological knowledge into the computational approaches. Furthermore, existing studies on network-based analysis perform prediction/classification of status of cell lines based on preconstructed GRNs, implying that we cannot extract prediction/classification-specific gene networks, leading to difficulty in interpretation of biological mechanisms and marker identification related to the status of cancer cell lines. We developed a novel strategy to build a GRN-based classifier, called a GRN-classifier. The proposed GRN-classifier estimates GRNs and classifies cell lines simultaneously, where the gene network is estimated to minimize error in gene network estimation and the negative log-likelihood for classifying cell lines. Thus, we can identify biological status-specific gene regulatory systems, enabling us to achieve biologically reliable interpretation of the classification. We also propose an algorithm to implement the GRN-classifier based on coordinate descent update. Monte Carlo simulations were conducted to examine performance of the GRN-classifier. Results: Our strategy provides effective results in feature selection in the classification model and edge selection in gene network estimation. The GRN-classifier also shows outstanding classification accuracy. We apply the GRN-classifier to classify cancer cell lines into anticancer drug-related status, that is, 5-fluorouracil (5-FU)-sensitive/resistant and 5-FU target/nontarget cancer cell lines. We then identified 5-FU markers based on 5-FU-related status classification-specific gene networks. The mechanisms of the identified markers were verified through literature survey. Our results suggest that the molecular interplay between MYOF and AHNAK2 may play a crucial role in drug resistance and can provide information on the chemotherapy efficiency of 5-FU. It is also suggested that suppression of the identified 5-FU markers, including MYOF/AHNAK2 and AKR1C1/AKR1C3 may improve 5-FU resistance of cancer cell lines.
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Affiliation(s)
- Heewon Park
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seiya Imoto
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan.,Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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11
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Yue P, Han B, Zhao Y. Focus on the molecular mechanisms of cisplatin resistance based on multi-omics approaches. Mol Omics 2023; 19:297-307. [PMID: 36723121 DOI: 10.1039/d2mo00220e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cisplatin is commonly used in combination with other cytotoxic agents as a standard treatment regimen for a variety of solid tumors, such as lung, ovarian, testicular, and head and neck cancers. However, the effectiveness of cisplatin is accompanied by toxic side effects, for instance, nephrotoxicity and neurotoxicity. The response of tumors to cisplatin treatment involves multiple physiological processes, and the efficacy of chemotherapy is limited by the intrinsic and acquired resistance of tumor cells. Although enormous efforts have been made toward molecular mechanisms of cisplatin resistance, the development of omics provides new insights into the understanding of cisplatin resistance at genome, transcriptome, proteome, metabolome and epigenome levels. Mechanism studies using different omics approaches revealed the necessity of multi-omics applications, which provide information at different cellular function levels and expand our recognition of the peculiar genetic and phenotypic heterogeneity of cancer. The present work systematically describes the underlying mechanisms of cisplatin resistance in different tumor types using multi-omics approaches. In addition to the classical mechanisms such as enhanced drug efflux, increased DNA damage repair and changes in the cell cycle and apoptotic pathways, other changes like increased protein damage clearance, increased protein glycosylation, enhanced glycolytic process, dysregulation of the oxidative phosphorylation pathway, ferroptosis suppression and mRNA m6A methylation modification can also induce cisplatin resistance. Therefore, utilizing the integrated omics to identify key signaling pathways, target genes and biomarkers that regulate chemoresistance are essential for the development of new drugs or strategies to restore tumor sensitivity to cisplatin.
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Affiliation(s)
- Ping Yue
- Department of Translational Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China. .,Academy of Medical Science, Henan Medical College of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Bingjie Han
- Department of Translational Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
| | - Yi Zhao
- Department of Translational Medical Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China.
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12
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SUN TINGTING, SUN XUE, WANG XIN, GUO RUI, YU YUANHUA, GAO LE. Analysis of the mechanism of aldo-keto reductase dependent cis-platin resistance in HepG2 cells based on transcriptomic and NADH metabolic state. BIOCELL 2023. [DOI: 10.32604/biocell.2023.026229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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13
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Zhang T, Liu M, Liu Q, Xiao GG. Wogonin increases gemcitabine sensitivity in pancreatic cancer by inhibiting Akt pathway. Front Pharmacol 2022; 13:1068855. [PMID: 36618921 PMCID: PMC9816391 DOI: 10.3389/fphar.2022.1068855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Pancreatic cancer has a high degree of malignancy and a low 5-year survival rate, and drug resistance is one of the main factors leading to poor prognosis of pancreatic cancer. Wogonin is a flavonoid drug isolated from Scutellaria baicalensis, which has certain antitumor activity. Hence the purpose of this study was to investigate whether wogonin can be used to enhance the sensitivity of pancreatic cancer to gemcitabine chemotherapy, and investigate its possible sensitization mechanism. In vitro, MTT assay showed that wogonin increased gemcitabine cytotoxicity in gemcitabine-resistant pancreatic cancer cells. In vivo, Wogonin combined with gemcitabine was found to inhibit tumor growth in orthotopic pancreatic cancer mouse model. In order to explore the sensitization mechanism, the differentially expressed genes (DEGs) of the gemcitabine-resistant cell line Panc-1 and the gemcitabine-sensitive cell line Bxpc-3 were screened through the GEO database, and 15 differentially expressed genes were obtained by intersecting with the potential targets of wogonin. Gene Ontology and KEGG enrichment analysis was performed. Bioinformatics results predicted that wogonin promoted pancreatic cancer cell apoptosis by inhibiting protein kinase B (Akt) signaling, thereby enhancing the sensitivity of gemcitabine to Pancreatic cancer. The above results were also verified by flow cytometry and Western blotting experiments. In conclusion, wogonin may enhance the sensitivity of gemcitabine by inhibiting Akt pathway.
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14
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Lae Lae Phoo N, Sukhamwang A, Dejkriengkraikul P, Yodkeeree S. Diclofenac Sensitizes Signet Ring Cell Gastric Carcinoma Cells to Cisplatin by Activating Autophagy and Inhibition of Survival Signal Pathways. Int J Mol Sci 2022; 23:ijms232012066. [PMID: 36292923 PMCID: PMC9602524 DOI: 10.3390/ijms232012066] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/16/2022] Open
Abstract
Gastric cancer has one of the highest incidence rates of cancer worldwide while also contributing to increased drug resistance among patients in clinical practice. Herein, we have investigated the role of diclofenac (DCF) on sensitizing cisplatin resistance in signet ring cell gastric carcinoma cells (SRCGC). Non-toxic concentrations of DCF significantly augmented cisplatin-induced cell death in cisplatin-resistant SRCGC cells (KATO/DDP) but not in cisplatin-sensitive SRCGC cells (KATOIII). Consistently, concomitant treatment of DCF and cisplatin significantly enhanced autophagic cell death due to overproduction of intracellular reactive oxygen species (ROS). At the molecular level, the induction of ROS has been associated with a reduction in antioxidant enzymes expression while inhibiting nuclear factor erythroid 2-related factor 2 (Nrf2) activity. Moreover, the combination of DCF and cisplatin also inhibited the expression of survival proteins including Bcl-2, Bcl-xL, cIAP1 and cyclin D1 in KATO/DDP cells when compared with cisplatin alone. This was due, at least in part, to reduce MAPKs, Akt, NF-κB, AP-1 and STAT-3 activation. Taken together, our results suggested that DCF potentiated the anticancer effect of cisplatin in SRCGC via the regeneration of intracellular ROS, which in turn promoted cell death as an autophagy mechanism and potentially modulated the cell survival signal transduction pathway.
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Affiliation(s)
- Nang Lae Lae Phoo
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Amonnat Sukhamwang
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Pornngarm Dejkriengkraikul
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Center for Research and Development of Natural Products for Health, Chiang Mai University, Chiang Mai 50200, Thailand
- Anticarcinogenesis and Apoptosis Research Cluster, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Supachai Yodkeeree
- Department of Biochemistry, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Center for Research and Development of Natural Products for Health, Chiang Mai University, Chiang Mai 50200, Thailand
- Anticarcinogenesis and Apoptosis Research Cluster, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
- Correspondence:
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15
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Peri S, Ruzzolini J, Urciuoli S, Versienti G, Biagioni A, Andreucci E, Peppicelli S, Bianchini F, Bottari A, Calorini L, Nediani C, Magnelli L, Papucci L. An Oleocanthal-Enriched EVO Oil Extract Induces the ROS Production in Gastric Cancer Cells and Potentiates the Effect of Chemotherapy. Antioxidants (Basel) 2022; 11:antiox11091762. [PMID: 36139836 PMCID: PMC9495378 DOI: 10.3390/antiox11091762] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/26/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
Oleocanthal, a minor polar compound in extra-virgin olive (EVO) oil, contains anticancer properties, which should be encouraged in its use in oncology. Gastric Cancer (GC), a very aggressive human cancer, is often diagnosed at advanced stages, when surgery is substituted or supported by chemotherapy (CT). However, CT frequently fails due to the patient’s resistance to the treatment. Thus, the aim of this study is to verify whether an OC-enriched EVO oil extract fraction (OCF) may be useful in order to overcome a resistance to GC. We evaluated the OCF effects on an AGS gastric adenocarcinoma cell line wild type (AGS wt) and on its subpopulations resistant to 5-fluorouracil (5FUr), Paclitaxel (TAXr) or cisplatin (CISr). We found that a 60 µM dose of the OCF acts on the AGS wt, 5FUr and TAXr, leading to the cell cycle inhibition and to a ROS production, but not on CISr cells. Resistance of CISr to the OCF seems to be due to higher levels of antioxidant-enzymes that can counteract the OCF-induced ROS production. Moreover, using the OCF plus 5-fluorouracil, Paclitaxel or cisplatin, we found a potentiating effect compared with a mono-treatment in all resistant GC cells, including CISr. In conclusion, the use of the OCF in the management of GC has shown very interesting advantages, opening-up the possibility to evaluate the efficacy of the OCF in vivo, as a valid adjuvant in the treatment of resistant GC.
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Affiliation(s)
- Sara Peri
- Department of Experimental and Clinical Medicine, University of Florence, 50134 Florence, Italy
| | - Jessica Ruzzolini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Silvia Urciuoli
- PHYTOLAB (Pharmaceutical, Cosmetic, Food Supplement, Technology and Analysis)-DiSIA, University of Florence, Via U. Schiff, 6, 50019 Florence, Italy
| | - Giampaolo Versienti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Alessio Biagioni
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Elena Andreucci
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Silvia Peppicelli
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Francesca Bianchini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Andrea Bottari
- Digestive Surgery Unit, AOU Careggi University Hospital, 50134 Florence, Italy
| | - Lido Calorini
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
- Center of Excellence for Research, Transfer, and High Education (DENOTHE), University of Florence, 50134 Florence, Italy
| | - Chiara Nediani
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
- Correspondence: ; Tel.: +39-0552751203
| | - Lucia Magnelli
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
| | - Laura Papucci
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50134 Florence, Italy
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16
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Park H, Imoto S, Miyano S. PredictiveNetwork: predictive gene network estimation with application to gastric cancer drug response-predictive network analysis. BMC Bioinformatics 2022; 23:342. [PMID: 35974335 PMCID: PMC9380306 DOI: 10.1186/s12859-022-04871-z] [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: 01/29/2022] [Accepted: 08/02/2022] [Indexed: 11/22/2022] Open
Abstract
Background Gene regulatory networks have garnered a large amount of attention to understand disease mechanisms caused by complex molecular network interactions. These networks have been applied to predict specific clinical characteristics, e.g., cancer, pathogenicity, and anti-cancer drug sensitivity. However, in most previous studies using network-based prediction, the gene networks were estimated first, and predicted clinical characteristics based on pre-estimated networks. Thus, the estimated networks cannot describe clinical characteristic-specific gene regulatory systems. Furthermore, existing computational methods were developed from algorithmic and mathematics viewpoints, without considering network biology. Results To effectively predict clinical characteristics and estimate gene networks that provide critical insights into understanding the biological mechanisms involved in a clinical characteristic, we propose a novel strategy for predictive gene network estimation. The proposed strategy simultaneously performs gene network estimation and prediction of the clinical characteristic. In this strategy, the gene network is estimated with minimal network estimation and prediction errors. We incorporate network biology by assuming that neighboring genes in a network have similar biological functions, while hub genes play key roles in biological processes. Thus, the proposed method provides interpretable prediction results and enables us to uncover biologically reliable marker identification. Monte Carlo simulations shows the effectiveness of our method for feature selection in gene estimation and prediction with excellent prediction accuracy. We applied the proposed strategy to construct gastric cancer drug-responsive networks. Conclusion We identified gastric drug response predictive markers and drug sensitivity/resistance-specific markers, AKR1B10, AKR1C3, ANXA10, and ZNF165, based on GDSC data analysis. Our results for identifying drug sensitive and resistant specific molecular interplay are strongly supported by previous studies. We expect that the proposed strategy will be a useful tool for uncovering crucial molecular interactions involved a specific biological mechanism, such as cancer progression or acquired drug resistance. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04871-z.
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Affiliation(s)
- Heewon Park
- M&D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.
| | - Seiya Imoto
- Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, Japan.,Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo, Japan
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17
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Is Autophagy Always a Barrier to Cisplatin Therapy? Biomolecules 2022; 12:biom12030463. [PMID: 35327655 PMCID: PMC8946631 DOI: 10.3390/biom12030463] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 01/10/2023] Open
Abstract
Cisplatin has long been a first-line chemotherapeutic agent in the treatment of cancer, largely for solid tumors. During the course of the past two decades, autophagy has been identified in response to cancer treatments and almost uniformly detected in studies involving cisplatin. There has been increasing recognition of autophagy as a critical factor affecting tumor cell death and tumor chemoresistance. In this review and commentary, we introduce four mechanisms of resistance to cisplatin followed by a discussion of the factors that affect the role of autophagy in cisplatin-sensitive and resistant cells and explore the two-sided outcomes that occur when autophagy inhibitors are combined with cisplatin. Our goal is to analyze the potential for the combinatorial use of cisplatin and autophagy inhibitors in the clinic.
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