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Zhang S, Huang L, Zeng Y, Gao G, Wu H, Li D, Guo R. SLC38A3 Promotes the Proliferation and Migration of Tumor Cells and Predicts Poor Prognosis in Colorectal Cancer. ACS OMEGA 2024; 9:21116-21126. [PMID: 38764627 PMCID: PMC11097367 DOI: 10.1021/acsomega.4c00901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 04/05/2024] [Accepted: 04/24/2024] [Indexed: 05/21/2024]
Abstract
Previous studies have revealed that abnormal expressions of membrane transporters were associated with colorectal cancer (CRC). We herein performed a comprehensive bioinformatics analysis to identify the key transporter protein-related genes involved in CRC and potential mechanisms. Differentially expressed transporter protein-related genes (DE-TPRGs) were identified from CRC and normal samples using The Cancer Genome Atlas database. SLC38A3 expression was validated by immunohistochemistry and RT-qPCR, and the potential mechanism was explored. A total of 63 DE-TPRGs (29 up-regulated and 34 down-regulated) were screened. Inside, ABCC2, ABCG2, SLC4A4, SLC9A3, SLC15A1, and SLC38A3 were identified as hub genes. SLC38A3 is indeed upregulated in colorectal cancer patients. Furthermore, we found that knockdown of SLC38A3 inhibited the proliferation and migration of HCT116 cells, and Hsp70 ATPase activator could rescue it. Overall, SLC38A3 is a novel potential biomarker involved in CRC progression and promotes the proliferation and migration of tumor cells by positively regulating the function of Hsp70.
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Affiliation(s)
- Siyi Zhang
- Department
of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Lingli Huang
- Department
of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Youjie Zeng
- Department
of Anesthesiology, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Ge Gao
- Department
of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Hui Wu
- Department
of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
| | - Dai Li
- Phase
I Clinical Tria Center, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
- National
Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410005, China
| | - Ren Guo
- Department
of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, China
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2
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Mooney B, Negri GL, Shyp T, Delaidelli A, Zhang HF, Spencer Miko SE, Weiner AK, Radaoui AB, Shraim R, Lizardo MM, Hughes CS, Li A, El-Naggar AM, Rouleau M, Li W, Dimitrov DS, Kurmasheva RT, Houghton PJ, Diskin SJ, Maris JM, Morin GB, Sorensen PH. Surface and Global Proteome Analyses Identify ENPP1 and Other Surface Proteins as Actionable Immunotherapeutic Targets in Ewing Sarcoma. Clin Cancer Res 2024; 30:1022-1037. [PMID: 37812652 PMCID: PMC10905525 DOI: 10.1158/1078-0432.ccr-23-2187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/13/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
PURPOSE Ewing sarcoma is the second most common bone sarcoma in children, with 1 case per 1.5 million in the United States. Although the survival rate of patients diagnosed with localized disease is approximately 70%, this decreases to approximately 30% for patients with metastatic disease and only approximately 10% for treatment-refractory disease, which have not changed for decades. Therefore, new therapeutic strategies are urgently needed for metastatic and refractory Ewing sarcoma. EXPERIMENTAL DESIGN This study analyzed 19 unique Ewing sarcoma patient- or cell line-derived xenografts (from 14 primary and 5 metastatic specimens) using proteomics to identify surface proteins for potential immunotherapeutic targeting. Plasma membranes were enriched using density gradient ultracentrifugation and compared with a reference standard of 12 immortalized non-Ewing sarcoma cell lines prepared in a similar manner. In parallel, global proteome analysis was carried out on each model to complement the surfaceome data. All models were analyzed by Tandem Mass Tags-based mass spectrometry to quantify identified proteins. RESULTS The surfaceome and global proteome analyses identified 1,131 and 1,030 annotated surface proteins, respectively. Among surface proteins identified, both approaches identified known Ewing sarcoma-associated proteins, including IL1RAP, CD99, STEAP1, and ADGRG2, and many new cell surface targets, including ENPP1 and CDH11. Robust staining of ENPP1 was demonstrated in Ewing sarcoma tumors compared with other childhood sarcomas and normal tissues. CONCLUSIONS Our comprehensive proteomic characterization of the Ewing sarcoma surfaceome provides a rich resource of surface-expressed proteins in Ewing sarcoma. This dataset provides the preclinical justification for exploration of targets such as ENPP1 for potential immunotherapeutic application in Ewing sarcoma. See related commentary by Bailey, p. 934.
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Affiliation(s)
- Brian Mooney
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Taras Shyp
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hai-Feng Zhang
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sandra E. Spencer Miko
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Amber K. Weiner
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Alexander B. Radaoui
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Rawan Shraim
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michael M. Lizardo
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Christopher S. Hughes
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amy Li
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amal M. El-Naggar
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Rouleau
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Wei Li
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Dimiter S. Dimitrov
- Division of Infectious Diseases, Department of Medicine, Center for Antibody Therapeutics, University of Pittsburgh Medical School, Pittsburgh, Pennsylvania
| | - Raushan T. Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Peter J. Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Sharon J. Diskin
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gregg B. Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Poul H. Sorensen
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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3
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Chen DY, Zhang YY, Nie HH, Wang HZ, Qiu PS, Wang F, Peng YN, Xu F, Zhao Q, Zhang M. Comprehensive analyses of solute carrier family members identify SLC12A2 as a novel therapy target for colorectal cancer. Sci Rep 2024; 14:4459. [PMID: 38396064 PMCID: PMC10891168 DOI: 10.1038/s41598-024-55048-y] [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: 08/31/2023] [Accepted: 02/20/2024] [Indexed: 02/25/2024] Open
Abstract
As the largest transporter family impacting on tumor genesis and development, the prognostic value of solute carrier (SLC) members has not been elucidated in colorectal cancer (CRC). We aimed to identify a prognostic signature from the SLC members and comprehensively analyze their roles in CRC. Firstly, we downloaded transcriptome data and clinical information of CRC samples from GEO (GSE39582) and TCGA as training and testing dataset, respectively. We extracted the expression matrix of SLC genes and established a prognostic model by univariate and multivariate Cox regression. Afterwards, the low-risk and high-risk group were identified. Then, the differences of prognosis traits, transcriptome features, clinical characteristics, immune infiltration and drug sensitivity between the two groups were explored. Furthermore, molecular subtyping was also implemented by non-negative matrix factorization (NMF). Finally, we studied the expression of the screened SLC genes in CRC tumor tissues and normal tissues as well as investigated the role of SLC12A2 by loss of function and gain of function. As a result, we developed a prognostic risk model based on the screened 6-SLC genes (SLC39A8, SLC2A3, SLC39A13, SLC35B1, SLC4A3, SLC12A2). Both in the training and testing sets, CRC patients in the high-risk group had the poorer prognosis and were in the more advanced pathological stage. What's more, the high-risk group were enriched with CRC progression signatures and immune infiltration. Two groups showed different drug sensitivity. On the other hand, two distinct subclasses (C1 and C2) were identified based on the 6 SLC genes. CRC patients in the high-risk group and C1 subtype had a worse prognosis. Furthermore, we found and validated that SLC12A2 was steadily upregulated in CRC. A loss-of-function study showed that knockdown of SLC12A2 expression restrained proliferation and stemness of CRC cells while a gain-of-function study showed the contrary results. Hence, we provided a 6-SLC gene signature for prognosis prediction of CRC patients. At the same time, we identified that SLC12A2 could promote tumor progression in CRC, which may serve as a potential therapeutic target.
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Affiliation(s)
- Dan-Yang Chen
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Yang-Yang Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
- Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, China
| | - Hai-Hang Nie
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Hai-Zhou Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Pei-Shan Qiu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Fan Wang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Ya-Nan Peng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Fei Xu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China
| | - Qiu Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China.
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China.
| | - Meng Zhang
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, No. 169, Donghu Road, Wuchang District, Wuhan, 430071, Hubei Province, China.
- Hubei Clinical Center and Key Lab of Intestinal and Colorectal Diseases, Wuhan, 430071, China.
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Dhakne P, Pillai M, Mishra S, Chatterjee B, Tekade RK, Sengupta P. Refinement of safety and efficacy of anti-cancer chemotherapeutics by tailoring their site-specific intracellular bioavailability through transporter modulation. Biochim Biophys Acta Rev Cancer 2023; 1878:188906. [PMID: 37172652 DOI: 10.1016/j.bbcan.2023.188906] [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: 01/31/2023] [Revised: 04/20/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
Low intracellular bioavailability, off-site toxicities, and multi drug resistance (MDR) are the major constraints involved in cancer chemotherapy. Many anticancer molecules fail to become a good lead in drug discovery because of their poor site-specific bioavailability. Concentration of a molecule at target sites is largely varied because of the wavering expression of transporters. Recent anticancer drug discovery strategies are paying high attention to enhance target site bioavailability by modulating drug transporters. The level of genetic expression of transporters is an important determinant to understand their ability to facilitate drug transport across the cellular membrane. Solid carrier (SLC) transporters are the major influx transporters involved in the transportation of most anti-cancer drugs. In contrast, ATP-binding cassette (ABC) superfamily is the most studied class of efflux transporters concerning cancer and is significantly involved in efflux of chemotherapeutics resulting in MDR. Balancing SLC and ABC transporters is essential to avoid therapeutic failure and minimize MDR in chemotherapy. Unfortunately, comprehensive literature on the possible approaches of tailoring site-specific bioavailability of anticancer drugs through transporter modulation is not available till date. This review critically discussed the role of different specific transporter proteins in deciding the intracellular bioavailability of anticancer molecules. Different strategies for reversal of MDR in chemotherapy by incorporation of chemosensitizers have been proposed in this review. Targeted strategies for administration of the chemotherapeutics to the intracellular site of action through clinically relevant transporters employing newer nanotechnology-based formulation platforms have been explained. The discussion embedded in this review is timely considering the current need of addressing the ambiguity observed in pharmacokinetic and clinical outcomes of the chemotherapeutics in anti-cancer treatment regimens.
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Affiliation(s)
- Pooja Dhakne
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Opp. Airforce Station, Palaj, Gandhinagar 382355, Gujarat, India
| | - Megha Pillai
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Opp. Airforce Station, Palaj, Gandhinagar 382355, Gujarat, India
| | - Sonam Mishra
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Opp. Airforce Station, Palaj, Gandhinagar 382355, Gujarat, India
| | - Bappaditya Chatterjee
- SVKM's NMIMS School of Pharmacy and Management, Department of Pharmaceutics, Vaikunthlal Mehta Road, Vile Parle West, Mumbai, Maharashtra 400056, India
| | - Rakesh K Tekade
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Opp. Airforce Station, Palaj, Gandhinagar 382355, Gujarat, India
| | - Pinaki Sengupta
- National Institute of Pharmaceutical Education and Research-Ahmedabad (NIPER-A), An Institute of National Importance, Government of India, Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Opp. Airforce Station, Palaj, Gandhinagar 382355, Gujarat, India.
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5
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Patel OV, Partridge C, Plaut K. Space Environment Impacts Homeostasis: Exposure to Spaceflight Alters Mammary Gland Transportome Genes. Biomolecules 2023; 13:biom13050872. [PMID: 37238741 DOI: 10.3390/biom13050872] [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: 03/09/2023] [Revised: 04/22/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Membrane transporters and ion channels that play an indispensable role in metabolite trafficking have evolved to operate in Earth's gravity. Dysregulation of the transportome expression profile at normogravity not only affects homeostasis along with drug uptake and distribution but also plays a key role in the pathogenesis of diverse localized to systemic diseases including cancer. The profound physiological and biochemical perturbations experienced by astronauts during space expeditions are well-documented. However, there is a paucity of information on the effect of the space environment on the transportome profile at an organ level. Thus, the goal of this study was to analyze the effect of spaceflight on ion channels and membrane substrate transporter genes in the periparturient rat mammary gland. Comparative gene expression analysis revealed an upregulation (p < 0.01) of amino acid, Ca2+, K+, Na+, Zn2+, Cl-, PO43-, glucose, citrate, pyruvate, succinate, cholesterol, and water transporter genes in rats exposed to spaceflight. Genes associated with the trafficking of proton-coupled amino acids, Mg2+, Fe2+, voltage-gated K+-Na+, cation-coupled chloride, as well as Na+/Ca2+ and ATP-Mg/Pi exchangers were suppressed (p < 0.01) in these spaceflight-exposed rats. These findings suggest that an altered transportome profile contributes to the metabolic modulations observed in the rats exposed to the space environment.
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Affiliation(s)
- Osman V Patel
- Cell and Molecular Biology Department, Grand Valley State University, Allendale, MI 49401, USA
| | - Charlyn Partridge
- Annis Water Resources Institute, Grand Valley State University, Muskegon, MI 49441, USA
| | - Karen Plaut
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47906, USA
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6
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Chen Y, Liu S, Papageorgiou LG, Theofilatos K, Tsoka S. Optimisation Models for Pathway Activity Inference in Cancer. Cancers (Basel) 2023; 15:1787. [PMID: 36980673 PMCID: PMC10046797 DOI: 10.3390/cancers15061787] [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: 01/05/2023] [Revised: 02/24/2023] [Accepted: 03/08/2023] [Indexed: 03/18/2023] Open
Abstract
BACKGROUND With advances in high-throughput technologies, there has been an enormous increase in data related to profiling the activity of molecules in disease. While such data provide more comprehensive information on cellular actions, their large volume and complexity pose difficulty in accurate classification of disease phenotypes. Therefore, novel modelling methods that can improve accuracy while offering interpretable means of analysis are required. Biological pathways can be used to incorporate a priori knowledge of biological interactions to decrease data dimensionality and increase the biological interpretability of machine learning models. METHODOLOGY A mathematical optimisation model is proposed for pathway activity inference towards precise disease phenotype prediction and is applied to RNA-Seq datasets. The model is based on mixed-integer linear programming (MILP) mathematical optimisation principles and infers pathway activity as the linear combination of pathway member gene expression, multiplying expression values with model-determined gene weights that are optimised to maximise discrimination of phenotype classes and minimise incorrect sample allocation. RESULTS The model is evaluated on the transcriptome of breast and colorectal cancer, and exhibits solution results of good optimality as well as good prediction performance on related cancer subtypes. Two baseline pathway activity inference methods and three advanced methods are used for comparison. Sample prediction accuracy, robustness against noise expression data, and survival analysis suggest competitive prediction performance of our model while providing interpretability and insight on key pathways and genes. Overall, our work demonstrates that the flexible nature of mathematical programming lends itself well to developing efficient computational strategies for pathway activity inference and disease subtype prediction.
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Affiliation(s)
- Yongnan Chen
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Bush House, London WC2B 4BG, UK
| | - Songsong Liu
- School of Management, Harbin Institute of Technology, Harbin 150001, China
| | - Lazaros G Papageorgiou
- The Sargent Centre for Process Systems Engineering, Department of Chemical Engineering, University College London, Torrington Place, London WC1E 7JE, UK
| | - Konstantinos Theofilatos
- King's College London British Heart Foundation Centre, School of Cardiovascular and Metabolic Medicine and Sciences, London SE1 7EH, UK
| | - Sophia Tsoka
- Department of Informatics, Faculty of Natural, Mathematical and Engineering Sciences, King's College London, Bush House, London WC2B 4BG, UK
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Mallini P, Chen M, Mahkamova K, Lennard TWJ, Pan Y, Wei D, Stemke-Hale K, Kirby JA, Lash GE, Meeson A. Hypoxia-Driven TGFβ Modulation of Side Population Cells in Breast Cancer: The Potential Role of ERα. Cancers (Basel) 2023; 15:1108. [PMID: 36831452 PMCID: PMC9954173 DOI: 10.3390/cancers15041108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/31/2023] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Epithelial-to-mesenchymal transition (EMT) is known to be important in regulating the behaviour of cancer cells enabling them to acquire stem cell characteristics or by enhancing the stem cell characteristics of cancer stem cells, resulting in these cells becoming more migratory and invasive. EMT can be driven by a number of mechanisms, including the TGF-β1 signalling pathway and/or by hypoxia. However, these drivers of EMT differ in their actions in regulating side population (SP) cell behaviour, even within SPs isolated from the same tissue. In this study we examined CoCl2 exposure and TGF-β driven EMT on SP cells of the MDA-MB-231 and MCF7 breast cancer cell lines. Both TGF-β1 and CoCl2 treatment led to the depletion of MDA-MB-231 SP. Whilst TGF-β1 treatment significantly reduced the MCF7 SP cells, CoCl2 exposure led to a significant increase. Single cell analysis revealed that CoCl2 exposure of MCF7 SP leads to increased expression of ABCG2 and HES1, both associated with multi-drug resistance. We also examined the mammosphere forming efficiency in response to CoCl2 exposure in these cell lines, and saw the same effect as seen with the SP cells. We suggest that these contrasting effects are due to ERα expression and the inversely correlated expression of TGFB-RII, which is almost absent in the MCF7 cells. Understanding the EMT-mediated mechanisms of the regulation of SP cells could enable the identification of new therapeutic targets in breast cancer.
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Affiliation(s)
- Paraskevi Mallini
- Biosciences Institute, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Miaojuan Chen
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Jinsui Road, Tianhe, Guangzhou 510623, China
| | - Kamilla Mahkamova
- Biosciences Institute, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
| | - Thomas W. J. Lennard
- Northern Institute for Cancer Research, Newcastle University, 3rd Floor William Leech Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Yue Pan
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Jinsui Road, Tianhe, Guangzhou 510623, China
| | - Dan Wei
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Jinsui Road, Tianhe, Guangzhou 510623, China
| | - Katherine Stemke-Hale
- Department of Systems Biology, MD Anderson Cancer Center, University of Texas, Houston, TX 77030, USA
| | - John A. Kirby
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, 3rd Floor William Leech Building, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Gendie E. Lash
- Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Medical University, Jinsui Road, Tianhe, Guangzhou 510623, China
| | - Annette Meeson
- Biosciences Institute, International Centre for Life, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK
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8
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Puris E, Fricker G, Gynther M. The Role of Solute Carrier Transporters in Efficient Anticancer Drug Delivery and Therapy. Pharmaceutics 2023; 15:pharmaceutics15020364. [PMID: 36839686 PMCID: PMC9966068 DOI: 10.3390/pharmaceutics15020364] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 01/24/2023] Open
Abstract
Transporter-mediated drug resistance is a major obstacle in anticancer drug delivery and a key reason for cancer drug therapy failure. Membrane solute carrier (SLC) transporters play a crucial role in the cellular uptake of drugs. The expression and function of the SLC transporters can be down-regulated in cancer cells, which limits the uptake of drugs into the tumor cells, resulting in the inefficiency of the drug therapy. In this review, we summarize the current understanding of low-SLC-transporter-expression-mediated drug resistance in different types of cancers. Recent advances in SLC-transporter-targeting strategies include the development of transporter-utilizing prodrugs and nanocarriers and the modulation of SLC transporter expression in cancer cells. These strategies will play an important role in the future development of anticancer drug therapies by enabling the efficient delivery of drugs into cancer cells.
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9
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Sato K, Seki T, Mizutani A, Muranaka Y, Hirota S, Nishi K, Yamazaki K, Nishii R, Nakanishi T, Tamai I, Kawai K, Kobayashi M. A single high-dose irradiation changes accumulation of methotrexate and gene expression levels of SLC and ABC transporters in cancer cells. Front Pharmacol 2023; 13:1069321. [PMID: 36712667 PMCID: PMC9874220 DOI: 10.3389/fphar.2022.1069321] [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: 10/13/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Chemoradiotherapy is frequently used to treat cancer. Stereotactic body radiotherapy (SBRT) is a single high-dose radiotherapy used to treat a variety of cancers. The anticancer drug methotrexate (MTX) shows affinity for solute carrier (SLC) and ATP-binding cassette (ABC) transporters. This study investigated relationships between accumulation of methotrexate and gene expression levels of solute carrier and ATP-binding cassette transporters in cancer cells after a single and high-dose X-ray irradiation. Cancer cell lines were selected from lung and cervical cancer cell line that are commonly used for stereotactic body radiotherapy and effective with methotrexate. We examined expression levels of organic anion-transporting polypeptide (OATP)1B1, OATP1B3, OATP1B7, and organic anion transporter (OAT)1 as solute carrier transporters and multidrug resistance-associated protein (MRP)1 and MRP2 as ATP-binding cassette transporters, using real-time polymerase chain reaction and accumulation of 3H-MTX in cancer cells after 10-Gy irradiation, assuming stereotactic body radiotherapy. Cells were divided into three groups: Control without irradiation; 4 h after irradiation; and 24 h after irradiation. In control, gene expression levels of OAT1 in all cells was below the limit of measurement. After irradiation, gene expression levels of OATP1B1/1B3/1B7 showed changes in each cell line. Gene expression levels of MRP1/2 tended to increase after irradiation. Gene expression levels of OATP1B1/1B3/1B7 were much lower than those of MRP1/2. Accumulation of 3H-MTX tended to decrease over time after irradiation. Irradiation of cancer cells thus alters gene expression levels of both solute carrier transporters (OATP1B1/1B3/1B7) and ABC transporters (MRP1/2) and decreases accumulation of 3H-MTX in cancer cells over time due to elevated expression of MRP1/2.
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Affiliation(s)
- Kakeru Sato
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Tatsuya Seki
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Asuka Mizutani
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Yuka Muranaka
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Shiho Hirota
- Division of Health Sciences, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Kodai Nishi
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Kana Yamazaki
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Ryuichi Nishii
- Department of Molecular Imaging and Theranostics, Institute for Quantum Medical Science, Quantum Life and Medical Science Directorate, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Takeo Nakanishi
- Faculty of Pharmacy, Takasaki University of Health and Welfare, Takasaki, Gunma, Japan
| | - Ikumi Tamai
- Faculty of Pharmaceutical Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan
| | - Keiichi Kawai
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan,Biomedical Imaging Research Center, University of Fukui, Fukui, Japan
| | - Masato Kobayashi
- Faculty of Health Sciences, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Kanazawa, Japan,*Correspondence: Masato Kobayashi,
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10
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Gu Y, Xu ZJ, Zhou JD, Wen XM, Jin Y, Yuan Q, Xia PH, Feng Y, Yang L, Lin J, Qian J. SLC22A3 methylation-mediated gene silencing predicts adverse prognosis in acute myeloid leukemia. Clin Epigenetics 2022; 14:162. [PMID: 36461046 PMCID: PMC9716704 DOI: 10.1186/s13148-022-01373-w] [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: 06/01/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND We screened out several hypermethylated solute carrier (SLC) family genes in acute myeloid leukemia by reduced representation bisulfite sequencing. SLC22A3 encodes an organic cation transport protein, which is critical for drug transportation and cellular detoxification. SLC22A3 is significantly downregulated and associated with tumor progression and worse prognosis in a variety of solid tumors. However, there are no data available regarding the role of SLC22 in AML. This study aimed to explore the regulatory mechanism of DNA methylation on SLC22A3 expression, as well as its clinical significance in AML prognosis. RESULTS SLC22A3 was identified as the sole prognosis-associated gene among SLCs based on TCGA and Beat AML databases. Bone marrow mononuclear cells (BMMNCs) from AML, MDS patients, and healthy donors were enrolled in this study. SLC22A3 methylation was significantly increased in AML compared with controls and MDS patients; meanwhile, the expression level of SLC22A3 was decreased. SLC22A3 hypermethylation presented an obvious association with some specific clinical characteristics and affected the survival time of AML patients as an independent risk indicator. SLC22A3 expression changed regularly as the disease complete remissions and relapses. Demethylation drug 5-aza-2'-deoxycytidine (DAC) activated transcription and increased mRNA expression of SLC22A3 in leukemia cell lines and AML fresh BMMNCs. Knockdown of SLC22A3 in leukemia cells enhanced cell proliferation and suppressed cell apoptosis. Data from public programs were used for auxiliary screening of probable molecular mechanisms of SLC22A3 in the antileukemia effect. CONCLUSIONS Our results showed that increased methylation and decreased expression of SLC22A3 may be indicators of poor prognosis in AML. Methylation-silenced SLC22A3 expression may have potential guiding significance on antileukemia effect of DAC.
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Affiliation(s)
- Yu Gu
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Zi-jun Xu
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jing-dong Zhou
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Xiang-mei Wen
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Ye Jin
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Qian Yuan
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Pei-hui Xia
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Yuan Feng
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Lei Yang
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jiang Lin
- Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,grid.452247.2Laboratory Center, Affiliated People’s Hospital of Jiangsu University, Zhenjiang, Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
| | - Jun Qian
- grid.452247.2Department of Hematology, Affiliated People’s Hospital of Jiangsu University, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,Zhenjiang Clinical Research Center of Hematology, 8 Dianli Rd., Zhenjiang, 212002 Jiangsu People’s Republic of China ,The Key Lab of Precision Diagnosis and Treatment in Hematologic Malignancies of Zhenjiang City, Zhenjiang, Jiangsu People’s Republic of China
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Sharma P, Singh N, Sharma S. Polymorphisms in solute carrier genes (SLC19A1, SLCO1B1, and SLCO1B3) predicts survival and toxicity in North Indian lung cancer patients undergoing platinum-based doublet chemotherapy. J Clin Pharm Ther 2022; 47:2049-2067. [PMID: 35896189 DOI: 10.1111/jcpt.13748] [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: 06/19/2022] [Revised: 06/30/2022] [Accepted: 07/10/2022] [Indexed: 12/24/2022]
Abstract
WHAT IS KNOWN AND OBJECTIVE Solute Carrier (SLC) transporters are known mediators of drug disposition that facilitate the influx of substrates and various chemotherapeutic agents into cells. Polymorphisms in the SLC19A1, SLCO1B1, and SLCO1B3 gene influence the prognosis in the cancer patients, but little is known about their role in lung cancer in Asians. So, the current study aims to investigate the polymorphisms in SLC19A1, SLCO1B1, and SLCO1B3 genes in Northern Indian lung cancer patients. METHODS Patients with lung cancer who had a confirmed histology and cytology diagnosis were enrolled in the study. SLC polymorphisms were assessed by Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) for variations in SLC19A1 (G80 A), SLCO1B1 (A388 G, T521 C), and SLCO1B3 (A1683-5676 G). RESULTS AND DISCUSSION Our results showed that mutant genotype for SLC19A1 G80 A polymorphism had higher median survival time (MST) compared to wild genotype. ADCC patients with mutant genotype showed better survival compared to wild genotype for SLC19A1 G80 A. SCLC patients G80 A polymorphism showed increased survival in patients with mutant genotype (p = 0.04). In SLCO1B3, A1683-5676 G patients carrying heterozygous alleles and administered with platinum and docetaxel showed inferior survival (p = 0.006). In T521 C variant, patients with carrier genotype had reduced chances of developing anaemia (p = 0.04). Patients with SLC19A1 and SLCO1B3 variants showed lower incidence of thrombocytopenia and nephrotoxicity. WHAT IS NEW AND CONCLUSION Our findings imply that Solute Carrier gene polymorphisms modulate the overall survival in lung cancer patients undergoing platin-based doublet chemotherapy, also these polymorphisms have a modifying impact on the associated adverse events/toxicity.
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Affiliation(s)
- Parul Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
| | - Navneet Singh
- Department of Pulmonary medicine, Post Graduate Institute of Medical Education & Research, Chandigarh, India
| | - Siddharth Sharma
- Department of Biotechnology, Thapar Institute of Engineering & Technology, Patiala, India
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12
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Smorodina E, Diankin I, Tao F, Qing R, Yang S, Zhang S. Structural informatic study of determined and AlphaFold2 predicted molecular structures of 13 human solute carrier transporters and their water-soluble QTY variants. Sci Rep 2022; 12:20103. [PMID: 36418372 PMCID: PMC9684436 DOI: 10.1038/s41598-022-23764-y] [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: 07/29/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022] Open
Abstract
Solute carrier transporters are integral membrane proteins, and are important for diverse cellular nutrient transports, metabolism, energy demand, and other vital biological activities. They have recently been implicated in pancreatic cancer and other cancer metastasis, angiogenesis, programmed cell death and proliferation, cell metabolism and chemo-sensitivity. Here we report the study of 13 human solute carrier membrane transporters using the highly accurate AlphaFold2 predictions of 3D protein structures. In the native structures, there are hydrophobic amino acids leucine (L), isoleucine (I), valine (V) and phenylalanine (F) in the transmembrane alpha-helices. These hydrophobic amino acids L, I, V, F are systematically replaced by hydrophilic amino acids glutamine (Q), threonine (T) and tyrosine (Y), thus the QTY code. Therefore, these QTY variant transporters become water-soluble without requiring detergents. We present the superposed structures of these native solute carrier transporters and their water-soluble QTY variants. The superposed structures show remarkable similarity with RMSD ~ 1 Å-< 3 Å despite > 46% protein sequence substitutions in transmembrane alpha-helices. We also show the differences of surface hydrophobicity between the native solute carrier transporters and their QTY variants. Our study may further stimulate designs of water-soluble transmembrane proteins and other aggregated proteins for drug discovery and biotechnological applications.
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Affiliation(s)
- Eva Smorodina
- grid.55325.340000 0004 0389 8485Laboratory for Computational and Systems Immunology, Department of Immunology, University of Oslo, Oslo University Hospital, Oslo, Norway
| | - Igor Diankin
- grid.78780.300000 0004 0613 1044Department of Computer Science, American University of Armenia, Yerevan, Armenia
| | - Fei Tao
- grid.16821.3c0000 0004 0368 8293Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Rui Qing
- grid.16821.3c0000 0004 0368 8293Laboratory of Food Microbial Technology, State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, 200240 China
| | - Steve Yang
- PT Metiska Farma, Daerah Khusus Ibukota, Jakarta, 12220 Indonesia
| | - Shuguang Zhang
- grid.116068.80000 0001 2341 2786Laboratory of Molecular Architecture, Media Lab, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139 USA
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13
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Cao Y, Yan X, Bai X, Tang F, Si P, Bai C, Tuoheti K, Guo L, Yisha Z, Liu T, Liu T. UCHL5 Promotes Proliferation and Migration of Bladder Cancer Cells by Activating c-Myc via AKT/mTOR Signaling. Cancers (Basel) 2022; 14:cancers14225538. [PMID: 36428630 PMCID: PMC9688806 DOI: 10.3390/cancers14225538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 10/30/2022] [Accepted: 11/08/2022] [Indexed: 11/12/2022] Open
Abstract
Ubiquitin C-terminal hydrolase L5 (UCHL5) is a deubiquitinating enzyme (DUB) that removes ubiquitin from its substrates. Associations between UCHL5 and cancer have been reported in various tissues, but the effect of UCHL5 on bladder cancer has not been thoroughly investigated. This study investigates the expression and function of UCHL5 in bladder cancer. UCHL5 was shown to be abnormally expressed using IHC of tissue microarray and Western blotting. Several procedures were performed to assess the effect of UCHL5 overexpression or knockdown on bladder cancer, such as cell proliferation, colony formation, wound-healing, and Transwell assays. In addition, RNA-Seq and Western blotting experiments were used to verify the status of downstream signaling pathways. Finally, bladder cancers with knockdown or overexpression of UCHL5 were treated with either SC79 or LY294002 to examine the participation of the AKT/mTOR signaling pathway and the expression of downstream targets c-Myc, SLC25A19, and ICAM5. In contrast to adjacent tissue samples, we discovered that UCHL5 was substantially expressed in bladder cancer samples. We also found that UCHL5 downregulation significantly suppressed both tumor growth in vivo and cell proliferation and migration in vitro. According to RNA-Seq analyses and Western blotting experiments, the expression of c-Myc, SLC25A19, and ICAM5 was modified as a result of UCHL5 activating AKT/mTOR signaling in bladder cancer cells. All things considered, our findings show that increased UCHL5 expression stimulates AKT/mTOR signaling, subsequently triggering the expression of c-Myc, SLC25A19, and ICAM5, which in turn promotes carcinogenesis in bladder cancer. UCHL5 is therefore a potential target for therapy in bladder cancer patients.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Tao Liu
- Correspondence: (T.L.); (T.L.); Tel.: +86-13657246625 (T.L.); +86-027-67813104 (T.L.)
| | - Tongzu Liu
- Correspondence: (T.L.); (T.L.); Tel.: +86-13657246625 (T.L.); +86-027-67813104 (T.L.)
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14
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Nomogram Models Based on the Gene Expression in Prediction of Breast Cancer Bone Metastasis. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:8431946. [PMID: 36046013 PMCID: PMC9424032 DOI: 10.1155/2022/8431946] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 06/01/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022]
Abstract
Objective The aim of this study is to design a weighted co-expression network and build gene expression signature-based nomogram (GESBN) models for predicting the likelihood of bone metastasis in breast cancer (BC) patients. Methods Dataset GSE124647 was used as a training set, while GSE16446, GSE45255, and GSE14020 were taken as validation sets. In the training cohort, the limma package in R was adopted to obtain differentially expressed genes (DEGs) between BC nonbone metastasis and bone metastasis patients, which were used for functional enrichment analysis. After weighted co-expression network analysis (WGCNA), univariate Cox regression and Kaplan–Meier plotter analyses were performed to screen potential prognosis-related genes. Then, GESBN models were constructed and evaluated. The prognostic value of the GESBN models was investigated in the GSE124647 dataset, which was validated in GSE16446 and GSE45255 datasets. Further, the expression levels of genes in the models were explored in the training set, which was validated in GSE14020. Finally, the expression and prognostic value of hub genes in BC were explored. Results A total of 1858 DEGs were obtained. The WGCNA result showed that the blue module was most significantly related to bone metastasis and prognosis. After survival analyses, GAJ1, SLC24A3, ITGBL1, and SLC44A1 were subjected to construct a GESBN model for overall survival (OS). While GJA1, IGFBP6, MDFI, TGFBI, ANXA2, and SLC24A3 were subjected to build a GESBN model for progression-free survival (PFS). Kaplan–Meier plotter and receiver operating characteristic analyses presented the reliable prediction ability of the models. Cox regression analysis further revealed that GESBN models were independent prognostic predictors for OS and PFS in BC patients. Besides, GJA1, IGFBP6, ITGBL1, SLC44A1, and TGFBI expressions were significantly different between the two groups in GSE124647 and GSE14020. The hub genes had a significant impact on patient prognosis. Conclusion Both the four-gene signature and six-gene signature could accurately predict patient prognosis, which may provide novel treatment insights for BC bone metastasis.
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15
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Anabtawi N, Drabison T, Hu S, Sparreboom A, Talebi Z. The role of OATP1B1 and OATP1B3 transporter polymorphisms in drug disposition and response to anticancer drugs: a review of the recent literature. Expert Opin Drug Metab Toxicol 2022; 18:459-468. [PMID: 35983889 DOI: 10.1080/17425255.2022.2113380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Members of the solute carrier family of organic anion transporting polypeptides are responsible for the cellular uptake of a broad range of endogenous compounds and xenobiotics in multiple tissues. In particular, the polymorphic transporters OATP1B1 and OATP1B3 are highly expressed in the liver and have been identified as critical regulators of hepatic eliminaton. As these transporters are also expressed in cancer cells, the function alteration of these proteins have important consequences for an individual's susceptibility to certain drug-induced side effects, drug-drug interactions, and treatment efficacy. AREAS COVERED In this mini-review, we provide an update of this rapidly emerging field, with specific emphasis on the direct contribution of genetic variants in OATP1B1 and OATP1B3 to the transport of anticancer drugs, the role of these carriers in regulation of their disposition and toxicity profiles, and recent advances in attempts to integrate information on transport function in patients to derive individualized treatment strategies. EXPERT OPINION Based on currently available data, it appears imperative that different aspects of disease, physiology, and drugs of relevance should be evaluated along with an individual's genetic signature, and that tools such as biomarker levels can be implemented to achieve the most reliable prediction of clinically relevant pharmacodynamic endpoints.
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Affiliation(s)
- Nadeen Anabtawi
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Thomas Drabison
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Shuiying Hu
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio.,Division of Outcomes and Translational Sciences, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Alex Sparreboom
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
| | - Zahra Talebi
- Division of Pharmaceutics and Pharmacology, College of Pharmacy, The Ohio State University, Columbus, Ohio
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16
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Thind AS, Ashford B, Strbenac D, Mitchell J, Lee J, Mueller SA, Minaei E, Perry JR, Ch’ng S, Iyer NG, Clark JR, Gupta R, Ranson M. Whole genome analysis reveals the genomic complexity in metastatic cutaneous squamous cell carcinoma. Front Oncol 2022; 12:919118. [PMID: 35982973 PMCID: PMC9379253 DOI: 10.3389/fonc.2022.919118] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 12/13/2022] Open
Abstract
Metastatic cutaneous squamous cell carcinoma (CSCC) is a highly morbid disease requiring radical surgery and adjuvant therapy, which is associated with a poor prognosis. Yet, compared to other advanced malignancies, relatively little is known of the genomic landscape of metastatic CSCC. We have previously reported the mutational signatures and mutational patterns of CCCTC-binding factor (CTCF) regions in metastatic CSCC. However, many other genomic components (indel signatures, non-coding drivers, and structural variants) of metastatic CSCC have not been reported. To this end, we performed whole genome sequencing on lymph node metastases and blood DNA from 25 CSCC patients with regional metastases of the head and neck. We designed a multifaceted computational analysis at the whole genome level to provide a more comprehensive perspective of the genomic landscape of metastatic CSCC. In the non-coding genome, 3′ untranslated region (3′UTR) regions of EVC (48% of specimens), PPP1R1A (48% of specimens), and ABCA4 (20% of specimens) along with the tumor-suppressing long non-coding RNA (lncRNA) LINC01003 (64% of specimens) were significantly functionally altered (Q-value < 0.05) and represent potential non-coding biomarkers of CSCC. Recurrent copy number loss in the tumor suppressor gene PTPRD was observed. Gene amplification was much less frequent, and few genes were recurrently amplified. Single nucleotide variants driver analyses from three tools confirmed TP53 and CDKN2A as recurrently mutated genes but also identified C9 as a potential novel driver in this disease. Furthermore, indel signature analysis highlighted the dominance of ID signature 13 (ID13) followed by ID8 and ID9. ID9 has previously been shown to have no association with skin melanoma, unlike ID13 and ID8, suggesting a novel pattern of indel variation in metastatic CSCC. The enrichment analysis of various genetically altered candidates shows enrichment of “TGF-beta regulation of extracellular matrix” and “cell cycle G1 to S check points.” These enriched terms are associated with genetic instability, cell proliferation, and migration as mechanisms of genomic drivers of metastatic CSCC.
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Affiliation(s)
- Amarinder Singh Thind
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
| | - Bruce Ashford
- School of Medicine, University of Wollongong, Wollongong, NSW, Australia
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
- *Correspondence: Bruce Ashford,
| | - Dario Strbenac
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
| | - Jenny Mitchell
- Illawarra Shoalhaven Local Health District, Wollongong, NSW, Australia
| | - Jenny Lee
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Clinical Medicine, Macquarie University, Sydney, NSW, Australia
| | - Simon A. Mueller
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Department of Otorhinolaryngology, Head and Neck Surgery, Zurich University Hospital and University of Zurich, Zurich, Switzerland
| | - Elahe Minaei
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Jay R. Perry
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
| | - Sydney Ch’ng
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
| | - N. Gopalakrishna Iyer
- Department of Head and Neck Surgery, National Cancer Center, Singapore, Singapore
- Duke-NUS Medical School, Singapore, Singapore
| | - Jonathan R. Clark
- Sydney Medical School, Faculty of Medicine and Health, The University of Sydney, NSW, Australia
- Sydney Head and Neck Cancer Institute, Chris O’Brien Lifehouse, Sydney, NSW, Australia
- Royal Prince Alfred Institute of Academic Surgery, Sydney Local Health District, Sydney, NSW, Australia
| | - Ruta Gupta
- Anatomical Pathology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Marie Ranson
- Illawarra Health and Medical Research Institute, Wollongong, NSW, Australia
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW, Australia
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Alam MS, Sultana A, Reza MS, Amanullah M, Kabir SR, Mollah MNH. Integrated bioinformatics and statistical approaches to explore molecular biomarkers for breast cancer diagnosis, prognosis and therapies. PLoS One 2022; 17:e0268967. [PMID: 35617355 PMCID: PMC9135200 DOI: 10.1371/journal.pone.0268967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Integrated bioinformatics and statistical approaches are now playing the vital role in identifying potential molecular biomarkers more accurately in presence of huge number of alternatives for disease diagnosis, prognosis and therapies by reducing time and cost compared to the wet-lab based experimental procedures. Breast cancer (BC) is one of the leading causes of cancer related deaths for women worldwide. Several dry-lab and wet-lab based studies have identified different sets of molecular biomarkers for BC. But they did not compare their results to each other so much either computationally or experimentally. In this study, an attempt was made to propose a set of molecular biomarkers that might be more effective for BC diagnosis, prognosis and therapies, by using the integrated bioinformatics and statistical approaches. At first, we identified 190 differentially expressed genes (DEGs) between BC and control samples by using the statistical LIMMA approach. Then we identified 13 DEGs (AKR1C1, IRF9, OAS1, OAS3, SLCO2A1, NT5E, NQO1, ANGPT1, FN1, ATF6B, HPGD, BCL11A, and TP53INP1) as the key genes (KGs) by protein-protein interaction (PPI) network analysis. Then we investigated the pathogenetic processes of DEGs highlighting KGs by GO terms and KEGG pathway enrichment analysis. Moreover, we disclosed the transcriptional and post-transcriptional regulatory factors of KGs by their interaction network analysis with the transcription factors (TFs) and micro-RNAs. Both supervised and unsupervised learning's including multivariate survival analysis results confirmed the strong prognostic power of the proposed KGs. Finally, we suggested KGs-guided computationally more effective seven candidate drugs (NVP-BHG712, Nilotinib, GSK2126458, YM201636, TG-02, CX-5461, AP-24534) compared to other published drugs by cross-validation with the state-of-the-art alternatives top-ranked independent receptor proteins. Thus, our findings might be played a vital role in breast cancer diagnosis, prognosis and therapies.
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Affiliation(s)
- Md. Shahin Alam
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- * E-mail: (MNHM); (MSA)
| | - Adiba Sultana
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Center for Systems Biology, Soochow University, Suzhou, China
| | - Md. Selim Reza
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Amanullah
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Syed Rashel Kabir
- Department of Biochemistry and Molecular Biology, Rajshahi University, Rajshahi, Bangladesh
| | - Md. Nurul Haque Mollah
- Bioinformatics Lab (Dry), Department of Statistics, University of Rajshahi, Rajshahi, Bangladesh
- * E-mail: (MNHM); (MSA)
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18
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Nayak D, Weadick B, Persaud AK, Raj R, Shakya R, Li J, Campbell MJ, Govindarajan R. EMT alterations in the solute carrier landscape uncover SLC22A10/A15 imposed vulnerabilities in pancreatic cancer. iScience 2022; 25:104193. [PMID: 35479410 PMCID: PMC9036131 DOI: 10.1016/j.isci.2022.104193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 01/31/2022] [Accepted: 03/30/2022] [Indexed: 11/29/2022] Open
Abstract
The involvement of membrane-bound solute carriers (SLCs) in neoplastic transdifferentiation processes is poorly defined. Here, we examined changes in the SLC landscape during epithelial-mesenchymal transition (EMT) of pancreatic cancer cells. We show that two SLCs from the organic anion/cation transporter family, SLC22A10 and SLC22A15, favor EMT via interferon (IFN) α and γ signaling activation of receptor tyrosine kinase-like orphan receptor 1 (ROR1) expression. In addition, SLC22A10 and SLC22A15 allow tumor cell accumulation of glutathione to support EMT via the IFNα/γ-ROR1 axis. Moreover, a pan-SLC22A inhibitor lesinurad reduces EMT-induced metastasis and gemcitabine chemoresistance to prolong survival in mouse models of pancreatic cancer, thus identifying new vulnerabilities for human PDAC.
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Affiliation(s)
- Debasis Nayak
- Division of Pharmaceutics and Pharmacology, The Ohio State University College of Pharmacy, Columbus, OH 43210, USA
| | - Brenna Weadick
- Division of Pharmaceutics and Pharmacology, The Ohio State University College of Pharmacy, Columbus, OH 43210, USA
| | - Avinash K. Persaud
- Division of Pharmaceutics and Pharmacology, The Ohio State University College of Pharmacy, Columbus, OH 43210, USA
| | - Radhika Raj
- Division of Pharmaceutics and Pharmacology, The Ohio State University College of Pharmacy, Columbus, OH 43210, USA
| | - Reena Shakya
- Target Validation Shared Resource, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Junan Li
- The Ohio State University College of Pharmacy, Columbus, OH 43210, USA
| | - Moray J. Campbell
- Molecular Carcinogenesis and Chemoprevention Program, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
- Biomedical Informatics Shared Resource, The Ohio State University, Columbus, OH 43210, USA
| | - Rajgopal Govindarajan
- Division of Pharmaceutics and Pharmacology, The Ohio State University College of Pharmacy, Columbus, OH 43210, USA
- Translational Therapeutics, The Ohio State University Comprehensive Cancer Center, Columbus, OH 43210, USA
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19
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Zheng D, Wei Z, Guo W. Identification of a Solute Carrier Family-Based Signature for Predicting Overall Survival in Osteosarcoma. Front Genet 2022; 13:849789. [PMID: 35518353 PMCID: PMC9061960 DOI: 10.3389/fgene.2022.849789] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
Given the important role of SLC family in essential physiological processes including nutrient uptake, ion transport, and waste removal, and that their dysregulation was found in distinct forms of cancer, here we identified a novel gene signature of SLC family for patient risk stratification in osteosarcoma. Gene expression data and relevant clinical materials of osteosarcoma samples were retrieved from The Cancer Genome Atlas (TCGA) database. Prognosis-related SLC genes were identified by performing univariate Cox regression analysis and were utilized to construct a four-SLC gene signature in osteosarcoma. It allowed patients to be classified into high- and low-risk groups, and Kaplan-Meier survival analysis in the training, testing, entire, and external GSE21257 cohorts suggested that the overall survival of patients in high-risk group was consistently worse than that in low-risk group, suggesting the promising accuracy and generalizability of the SLC-based signature in predicting the prognosis of patients with osteosarcoma. Moreover, univariate and multivariate Cox regression analyses indicated that the derived risk score was the only independent prognostic factor for osteosarcoma patients in TCGA and GSE21257 cohorts. Besides, a prognostic nomogram comprising the derived risk score and clinical features including gender and age was developed for clinical decision-making. Functional enrichment analyses of the differentially expressed genes between high- and low-risk group revealed that immune-related biological processes and pathways were significantly enriched. Estimation of tumor immune microenvironment using ESTIMATE algorithm revealed that patients with lower risk score had higher stromal, immune, and ESTIMATE score, and lower tumor purity. ssGSEA analyses indicated that the scores of various immune subpopulations including CD8+ T cells, DCs, and TIL were lower in high-risk group than these in low-risk group in both cohorts. As for the related immune functions, the scores of APC co-inhibition, CCR, check-point, T cell co-stimulation, and Type II IFN response were lower in high-risk group than these in low-risk group in both cohorts. In all, we identified a novel prognostic signature based on four SLC family genes that accurately predicted overall survival in osteosarcoma patients. Furthermore, the signature is linked to differences in immunological status and immune cell infiltrations in the tumor microenvironment.
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Affiliation(s)
- Di Zheng
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Zhun Wei
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, China
| | - Weichun Guo
- Department of Orthopedics, Renmin Hospital of Wuhan University, Wuhan, China
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20
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Chatterton RT. Functions of dehydroepiandrosterone in relation to breast cancer. Steroids 2022; 179:108970. [PMID: 35122788 DOI: 10.1016/j.steroids.2022.108970] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/17/2022] [Accepted: 01/31/2022] [Indexed: 11/20/2022]
Abstract
Although DHEA sulfate (DS) is the most abundant steroid in the circulation, breast fluid contains an approximately 80-fold greater concentration than serum. Transport of DS into cells requires organic anion transporting polypeptides (OATPs), which are specific for cell type, cell location, and substrate, but may have a broader specificity for housekeeping functions. Specific classes, which may be modified by soluble factors including neutral steroids, have been identified in the breast. After transport, DS may be cleaved to DHEA by ubiquitous sulfatases, which may be modified by the cell milieu, or DHEA may enter by diffusion. Synthesis from cholesterol does not occur because CYP17B12 and cytochrome b5 are lacking in breast tissues. Case-control studies reveal a positive association of serum DS with risk of breast cancer. The association is even greater with DHEA, particularly in postmenopausal women with HR + invasive tumors. Metabolites of DHEA, androstenedione and testosterone, are associated with breast cancer but DHEA is likely to have an independent role as well. Mechanisms by which DHEA may promote breast cancer relate to its effect in increasing circulating IGF-I, by inhibiting the suppressive effect of glucocorticoids, and by promoting retention of pre-adipocytes with aromatase activity. In addition, DHEA may interact with the G-protein coupled receptor GPER for stimulation of miR-21 and subsequent activation of the MAPK pathway. DHEA also has antitumor properties that relate to stimulation of immunity, suppression of inflammation, and elevation of adipose tissue adiponectin synthesis. The net effect may depend on the which factors predominate.
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Affiliation(s)
- Robert T Chatterton
- Department of Obstetrics and Gynecology and the Robert H Lurie Comprehensive Cancer Center of Northwestern, Northwestern University Feinberg Medical School. Chicago, IL 60911, USA.
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21
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Zhu J, Mou Y, Ye S, Hu H, Wang R, Yang Q, Hu Y. Identification of a Six-Gene SLC Family Signature With Prognostic Value in Patients With Lung Adenocarcinoma. Front Cell Dev Biol 2022; 9:803198. [PMID: 34977043 PMCID: PMC8714960 DOI: 10.3389/fcell.2021.803198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/30/2021] [Indexed: 12/17/2022] Open
Abstract
Given the importance of solute carrier (SLC) proteins in maintaining cellular metabolic homeostasis and that their dysregulation contributes to cancer progression, here we constructed a robust SLC family signature for lung adenocarcinoma (LUAD) patient stratification. Transcriptomic profiles and relevant clinical information of LUAD patients were downloaded from the TCGA and GEO databases. SLC family genes differentially expressed between LUAD tissues and adjacent normal tissues were identified using limma in R. Of these, prognosis-related SLC family genes were further screened out and used to construct a novel SLC family-based signature in the training cohort. The accuracy of the prognostic signature was assessed in the testing cohort, the entire cohort, and the external GSE72094 cohort. Correlations between the prognostic signature and the tumor immune microenvironment and immune cell infiltrates were further explored. We found that seventy percent of SLC family genes (279/397) were differentially expressed between LUAC tissues and adjacent normal. Twenty-six genes with p-values < 0.05 in univariate Cox regression analysis and Kaplan-Meier survival analysis were regarded as prognosis-related SLC family genes, six of which were used to construct a prognostic signature for patient classification into high- and low-risk groups. Kaplan-Meier survival analysis in all internal and external cohorts revealed a better overall survival for patients in the low-risk group than those in the high-risk group. Univariate and multivariate Cox regression analyses indicated that the derived risk score was an independent prognostic factor for LUAD patients. Moreover, a nomogram based on the six-gene signature and clinicopathological factors was developed for clinical application. High-risk patients had lower stromal, immune, and ESTIMATE scores and higher tumor purities than those in the low-risk group. The proportions of infiltrating naive CD4 T cells, activated memory CD4 T cells, M0 macrophages, resting dendritic cells, resting mast cells, activated mast cells, and eosinophils were significantly different between the high- and low-risk prognostic groups. In all, the six-gene SLC family signature is of satisfactory accuracy and generalizability for predicting overall survival in patients with LUAD. Furthermore, this prognostics signature is related to tumor immune status and distinct immune cell infiltrates in the tumor microenvironment.
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Affiliation(s)
- Jing Zhu
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Mou
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shenglan Ye
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongling Hu
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rujuan Wang
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qing Yang
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yi Hu
- Department of Respiratory and Critical Care Medicine, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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22
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Zhang Q, Liu Y, Chen P, Shi X, Liu Y, Shi L, Cong P, Mao S, Tong C, Du C, Hou M. Solute carrier family 12 member 8 (SLC12A8) is a potential biomarker and related to tumor immune cell infiltration in bladder cancer. Bioengineered 2021; 12:4946-4961. [PMID: 34365894 PMCID: PMC8806707 DOI: 10.1080/21655979.2021.1962485] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 01/10/2023] Open
Abstract
The solute carrier family has been reported to play critical roles in the progression of several cancers; however, the relationship between solute carrier family 12 member 8 (SLC12A8) and bladder cancer (BC) has not been clearly confirmed. This study explores the prognostic value of SLC12A8 for BC and its correlation with immune cell infiltration. We found that the expression of SLC12A8 mRNA was significantly overexpressed in BC tissues compared with noncancerous tissues in multiple public databases, and the result was validated using real-time PCR and immunohistochemistry (IHC). The Kaplan-Meier method and Cox proportional hazards models were used to evaluate the prognostic value of SLC12A8 for BC. The high expression of SLC12A8 led to a shorter overall survival time and was an unfavorable prognostic biomarker for BC. The mechanisms of SLC12A8 promoting tumorigenesis were investigated by Gene Set Enrichment Analysis (GSEA). Moreover, the correlations of SLC12A8 expression with the tumor-infiltrating immune cells (TICs) in BC were explored using TIMER 2.0 and CIBERSORT. SLC12A8 was associated with CD4+ T cells, dendritic cells, neutrophils, and macrophages infiltration. The expression of SLC12A8 was positively correlated with crucial immune checkpoint molecules. In conclusion, SLC12A8 might be an unfavorable prognostic biomarker in BC related to tumor immune cell infiltration.
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Affiliation(s)
- Qian Zhang
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, P.R. China
| | - Yunen Liu
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Peng Chen
- Department of Urology, General Hospital of Northern Theater Command, Shenyang, Liaoning, P.R. China
| | - Xiuyun Shi
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Ying Liu
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Lin Shi
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Peifang Cong
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Shun Mao
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Cangci Tong
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
| | - Cheng Du
- Department of Oncology, General Hospital of Northern Theater Command, Shenyang, Liaoning, P.R. China
| | - Mingxiao Hou
- College of Medicine and Biological Information Engineering, Northeastern University, Shenyang, Liaoning, P.R. China
- Emergency Medicine Department of General Hospital of Northern Theater Command, Laboratory of Rescue Center of Severe Wound and Trauma PLA, Shenyang, Liaoning, P.R. China
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23
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Hiu JJ, Yap MKK. The effects of Naja sumatrana venom cytotoxin, sumaCTX on alteration of the secretome in MCF-7 breast cancer cells following membrane permeabilization. Int J Biol Macromol 2021; 184:776-786. [PMID: 34174307 DOI: 10.1016/j.ijbiomac.2021.06.145] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/21/2021] [Accepted: 06/21/2021] [Indexed: 12/24/2022]
Abstract
Naja sumatrana venom cytotoxin (sumaCTX) is a basic protein which belongs to three-finger toxin family. It has been shown to induce caspase-dependent, mitochondrial-mediated apoptosis in MCF-7 cells at lower concentrations. This study aimed to investigate the alteration of secretome in MCF-7 cells following membrane permeabilization by high concentrations of sumaCTX, using label-free quantitative (LFQ) approach. The degree of membrane permeabilization of sumaCTX was determined by lactate dehydrogenase (LDH) assay and calcein-propidium iodide (PI) assays. LDH and calcein-PI assays revealed time-dependent membrane permeabilization within a narrow concentration range. However, as toxin concentrations increased, prolonged exposure of MCF-7 cells to sumaCTX did not promote the progression of membrane permeabilization. The secretome analyses showed that membrane permeabilization was an event preceding the release of intracellular proteins. Bioinformatics analyses of the LFQ secretome revealed the presence of 105 significantly distinguished proteins involved in metabolism, structural supports, inflammatory responses, and necroptosis in MCF-7 cells treated with 29.8 μg/mL of sumaCTX. Necroptosis was presumably an initial stress response in MCF-7 cells when exposed to high sumaCTX concentration. Collectively, sumaCTX-induced the loss of membrane integrity in a concentration-dependent manner, whereby the cell death pattern of MCF-7 cells transformed from apoptosis to necroptosis with increasing toxin concentrations.
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Affiliation(s)
- Jia Jin Hiu
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia.
| | - Michelle Khai Khun Yap
- School of Science, Monash University Malaysia, Bandar Sunway, Malaysia; Tropical Medicine and Biology Multidisciplinary Platform, Monash University Malaysia, Bandar Sunway, Malaysia.
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24
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Yuan S, Tanzeel Y, Tian X, Zheng D, Wajeeha N, Xu J, Ke Y, Zhang Z, Peng X, Lu L, Sun G, Guo D, Wang M. Global analysis of HBV-mediated host proteome and ubiquitylome change in HepG2.2.15 human hepatoblastoma cell line. Cell Biosci 2021; 11:75. [PMID: 33865438 PMCID: PMC8052555 DOI: 10.1186/s13578-021-00588-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/08/2021] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) infection remains a major health issue worldwide and the leading cause of cirrhosis and hepatocellular carcinoma (HCC). It has been reported previously that HBV invasion can extensively alter transcriptome, the proteome of exosomes and host cell lipid rafts. The impact of HBV on host proteins through regulating their global post-translational modifications (PTMs), however, is not well studied. Viruses have been reported to exploit cellular processes by enhancing or inhibiting the ubiquitination of specific substrates. Nevertheless, host cell physiology in terms of global proteome and ubiquitylome has not been addressed yet. Here by using HBV-integrated HepG2.2.15 model cell line we first report that HBV significantly modify the host global ubiquitylome. As currently the most widely used HBV cell culture model, HepG2.2.15 can be cultivated for multiple generations for protein labeling, and can replicate HBV, express HBV proteins and secrete complete HBV Dane particles, which makes it a suitable cell line for ubiquitylome analysis to study HBV replication, hepatocyte immune response and HBV-related HCC progression. Our previous experimental results showed that the total ubiquitination level of HepG2.2.15 cell line was significantly higher than that of the corresponding parental HepG2 cell line. By performing a Ubiscan quantification analysis based on stable isotope labeling of amino acids in cell culture (SILAC) of HepG2.2.15 and HepG2 cell lines, we identified a total of 7188 proteins and the protein levels of nearly 19% of them were changed over 2-folds. We further identified 3798 ubiquitinated Lys sites in 1476 host proteins with altered ubiquitination in response to HBV. Our results also showed that the global proteome and ubiquitylome were negatively correlated, indicating that ubiquitination might be involved in the degradation of host proteins upon HBV integration. We first demonstrated the ubiquitination change of VAMP3, VAMP8, DNAJB6, RAB8A, LYN, VDAC2, OTULIN, SLC1A4, SLC1A5, HGS and TOLLIP. In addition, we described 5 novel host factors SLC1A4, SLC1A5, EIF4A1, TOLLIP and BRCC36 that efficiently reduced the amounts of secreted HBsAg and HBeAg. Overall, the HBV-mediated host proteome and ubiquitylome change we reported will provide a valuable resource for further investigation of HBV pathogenesis and host-virus interaction networks.
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Affiliation(s)
- Sen Yuan
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yousaf Tanzeel
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Xuezhang Tian
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Dandan Zheng
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Naz Wajeeha
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Jiaqi Xu
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Yujia Ke
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Zuopeng Zhang
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China
| | - Xiaojun Peng
- Jingjie PTM BioLab (Hangzhou) Co. Ltd., Hangzhou, People's Republic of China
| | - Long Lu
- School of Information Management, Wuhan University, Wuhan, People's Republic of China
| | - Guihong Sun
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China. .,Hubei Provincial Key Laboratory of Allergy and Immunology, Wuhan, People's Republic of China.
| | - Deyin Guo
- School of Medicine, Sun Yat-Sen University, Shenzhen, People's Republic of China.
| | - Min Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, People's Republic of China.
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25
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SLC46A1 Haplotype with Predicted Functional Impact has Prognostic Value in Breast Carcinoma. Mol Diagn Ther 2021; 25:99-110. [PMID: 33387348 DOI: 10.1007/s40291-020-00506-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND OBJECTIVE Membrane solute carrier transporters play an important role in the transport of a wide spectrum of substrates including anticancer drugs and cancer-related physiological substrates. This study aimed to assess the prognostic relevance of gene expression and genetic variability of selected solute carrier transporters in breast cancer. METHODS Gene expression was determined by quantitative real-time polymerase chain reaction. All SLC46A1 and SLCO1A2 exons and surrounding non-coding sequences in DNA extracted from the blood of patients with breast cancer (exploratory phase) were analyzed by next-generation sequencing technology. Common variants (minor allele frequency ≥ 5%) with in silico-predicted functional relevance were further analyzed in a large cohort of patients with breast cancer (n = 815) and their prognostic and predictive potential was estimated (validation phase). RESULTS A gene expression and bioinformatics analysis suggested SLC46A1 and SLCO1A2 to play a putative role in the prognosis of patients with breast cancer. In total, 135 genetic variants (20 novel) were identified in both genes in the exploratory phase. Of these variants, 130 were non-coding, three missense, and two synonymous. One common variant in SLCO1A2 and four variants in SLC46A1 were predicted to be pathogenic by in silico programs and subsequently validated. A SLC46A1 haplotype block composed of rs2239911-rs2239910-rs8079943 was significantly associated with ERBB2/HER2 status and disease-free survival of hormonally treated patients. CONCLUSIONS This study revealed the prognostic value of a SLC46A1 haplotype block for breast cancer that should be further studied.
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