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Shin MG, Pico AR. Using published pathway figures in enrichment analysis and machine learning. BMC Genomics 2023; 24:713. [PMID: 38007419 PMCID: PMC10676589 DOI: 10.1186/s12864-023-09816-1] [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: 08/15/2023] [Accepted: 11/18/2023] [Indexed: 11/27/2023] Open
Abstract
Pathway Figure OCR (PFOCR) is a novel kind of pathway database approaching the breadth and depth of Gene Ontology while providing rich, mechanistic diagrams and direct literature support. Here, we highlight the utility of PFOCR in disease research in comparison with popular pathway databases through an assessment of disease coverage and analytical applications. In addition to common pathway analysis use cases, we present two advanced case studies demonstrating unique advantages of PFOCR in terms of cancer subtype and grade prediction analyses.
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Affiliation(s)
- Min-Gyoung Shin
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA
| | - Alexander R Pico
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA, USA.
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2
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Chen S, Liu Y, Fong DYT, Zhou J, Chen H, Wan C. Health-related quality of life and its influencing factors in patients with breast cancer based on the scale QLICP-BR. Sci Rep 2023; 13:15176. [PMID: 37704676 PMCID: PMC10499782 DOI: 10.1038/s41598-023-41809-8] [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: 03/24/2022] [Accepted: 08/31/2023] [Indexed: 09/15/2023] Open
Abstract
Breast cancer is the most common cancer and the leading cause of cancer death among females worldwide. During the past 15 years, quality of life (QOL) has become an important aspect of breast cancer treatment. The purpose of this study was to evaluate QOL of breast cancer patients in China, and investigate its associations with sociodemographic and clinical variables. A cross-sectional study was conducted in 246 breast cancer patients in China. Recruited patients were surveyed for QOL using the QOL instruments for cancer patients-breast cancer QLICP-BR (V2.0). We assessed the associations between potential influencing factors and QOL using multiple linear regression models. The general mean QOL score for our population was 70.24 with SD = 8.70. Results indicated that medical insurance, drinking history, alkaline phosphatase, serum chloride ion level, serum calcium ion level, serum phosphorus ion level, mean corpuscular volume, mean corpuscular hemoglobin, red cell volume distribution width and platelet had significant associations with QOL of breast cancer patients. Our results emphasized that many factors are affecting QOL of breast cancer patients, which may provide a reference for targeted management or intervention strategies of breast cancer patients to improve their QOL.
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Affiliation(s)
- Shu Chen
- The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan, China
- Key Laboratory for Quality of Life and Psychological Assessment and Intervention, Research Center for Quality of Life and Applied Psychology, Guangdong Medical University, Dongguan, China
| | - Yuxi Liu
- The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan, China
| | | | - Jiali Zhou
- Key Laboratory for Quality of Life and Psychological Assessment and Intervention, Research Center for Quality of Life and Applied Psychology, Guangdong Medical University, Dongguan, China
| | - Huanwei Chen
- Central Hospital of Guangdong Nongken, Zhanjiang, China
| | - Chonghua Wan
- The First Dongguan Affiliated Hospital of Guangdong Medical University, Dongguan, China.
- Key Laboratory for Quality of Life and Psychological Assessment and Intervention, Research Center for Quality of Life and Applied Psychology, Guangdong Medical University, Dongguan, China.
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3
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Shin MG, Pico A. Using Published Pathway Figures in Enrichment Analysis and Machine Learning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.06.548037. [PMID: 37461614 PMCID: PMC10350053 DOI: 10.1101/2023.07.06.548037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Pathway Figure OCR (PFOCR) is a novel kind of pathway database approaching the breadth and depth of Gene Ontology while providing rich, mechanistic diagrams and direct literature support. PFOCR content is extracted from published pathway figures currently emerging at a rate of 1000 new pathways each month. Here, we compare the pathway information contained in PFOCR against popular pathway databases with respect to overall and disease-specific coverage. In addition to common pathways analysis use cases, we present two advanced case studies demonstrating unique advantages of PFOCR in terms of cancer subtype and grade prediction analyses.
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Eustace AJ, Lee MJ, Colley G, Roban J, Downing T, Buchanan PJ. Aberrant calcium signalling downstream of mutations in TP53 and the PI3K/AKT pathway genes promotes disease progression and therapy resistance in triple negative breast cancer. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2022; 5:560-576. [PMID: 36176752 PMCID: PMC9511797 DOI: 10.20517/cdr.2022.41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/04/2022] [Accepted: 05/25/2022] [Indexed: 06/16/2023]
Abstract
Triple-negative breast cancer (TNBC) is characterized as an aggressive form of breast cancer (BC) associated with poor patient outcomes. For the majority of patients, there is a lack of approved targeted therapies. Therefore, chemotherapy remains a key treatment option for these patients, but significant issues around acquired resistance limit its efficacy. Thus, TNBC has an unmet need for new targeted personalized medicine approaches. Calcium (Ca2+) is a ubiquitous second messenger that is known to control a range of key cellular processes by mediating signalling transduction and gene transcription. Changes in Ca2+ through altered calcium channel expression or activity are known to promote tumorigenesis and treatment resistance in a range of cancers including BC. Emerging evidence shows that this is mediated by Ca2+ modulation, supporting the function of tumour suppressor genes (TSGs) and oncogenes. This review provides insight into the underlying alterations in calcium signalling and how it plays a key role in promoting disease progression and therapy resistance in TNBC which harbours mutations in tumour protein p53 (TP53) and the PI3K/AKT pathway.
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Affiliation(s)
- Alex J. Eustace
- DCU Cancer Research, Dublin City University, Dublin D9, Ireland
- National Institute Cellular Biotechnology, Dublin City University, Dublin D9, Ireland
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Min Jie Lee
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Grace Colley
- National Institute Cellular Biotechnology, Dublin City University, Dublin D9, Ireland
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Jack Roban
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Tim Downing
- DCU Cancer Research, Dublin City University, Dublin D9, Ireland
- School of Biotechnology, Dublin City University, Dublin D9, Ireland
| | - Paul J. Buchanan
- DCU Cancer Research, Dublin City University, Dublin D9, Ireland
- National Institute Cellular Biotechnology, Dublin City University, Dublin D9, Ireland
- School of Nursing, Psychotherapy, and Community Health, Dublin City University, Dublin D9, Ireland
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Zhou Z, Zhang C, Ma Z, Wang H, Tuo B, Cheng X, Liu X, Li T. Pathophysiological role of ion channels and transporters in HER2-positive breast cancer. Cancer Gene Ther 2022; 29:1097-1104. [PMID: 34997219 DOI: 10.1038/s41417-021-00407-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/21/2021] [Accepted: 11/08/2021] [Indexed: 11/09/2022]
Abstract
The incidence of breast cancer (BC) has been increasing each year, and BC is now the most common malignant tumor in women. Among the numerous BC subtypes, HER2-positive BC can be treated with a variety of strategies based on targeting HER2. Although there has been great progress in the treatment of HER2-positive BC, recurrence, metastasis and drug resistance remain considerable challenges. The dysfunction of ion channels and transporters can affect the development and progression of HER2-positive BC, so these entities are expected to be new therapeutic targets. This review summarizes various ion channels and transporters associated with HER2-positive BC and suggests potential targets for the development of new and effective therapies.
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Affiliation(s)
- Zhengxing Zhou
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou Province, China
| | - Chengmin Zhang
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou Province, China
| | - Zhiyuan Ma
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou Province, China
| | - Hu Wang
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou Province, China
| | - Biguang Tuo
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou Province, China
| | - Xiaoming Cheng
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou Province, China
| | - Xuemei Liu
- Department of Gastroenterology, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou Province, China.
| | - Taolang Li
- Department of Thyroid and Breast Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, 563003, Guizhou Province, China.
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Becskeházi E, Korsós MM, Gál E, Tiszlavicz L, Hoyk Z, Deli MA, Köhler ZM, Keller-Pintér A, Horváth A, Csekő K, Helyes Z, Hegyi P, Venglovecz V. Inhibition of NHE-1 Increases Smoke-Induced Proliferative Activity of Barrett's Esophageal Cell Line. Int J Mol Sci 2021; 22:10581. [PMID: 34638919 PMCID: PMC8509038 DOI: 10.3390/ijms221910581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 01/22/2023] Open
Abstract
Several clinical studies indicate that smoking predisposes its consumers to esophageal inflammatory and malignant diseases, but the cellular mechanism is not clear. Ion transporters protect esophageal epithelial cells by maintaining intracellular pH at normal levels. In this study, we hypothesized that smoking affects the function of ion transporters, thus playing a role in the development of smoking-induced esophageal diseases. Esophageal cell lines were treated with cigarettesmoke extract (CSE), and the viability and proliferation of the cells, as well as the activity, mRNA and protein expression of the Na+/H+ exchanger-1 (NHE-1), were studied. NHE-1 expression was also investigated in human samples. For chronic treatment, guinea pigs were exposed to tobacco smoke, and NHE-1 activity was measured. Silencing of NHE-1 was performed by using specific siRNA. CSE treatment increased the activity and protein expression of NHE-1 in the metaplastic cells and decreased the rate of proliferation in a NHE-1-dependent manner. In contrast, CSE increased the proliferation of dysplastic cells independently of NHE-1. In the normal cells, the expression and activity of NHE-1 decreased due to in vitro and in vivo smoke exposure. Smoking enhances the function of NHE-1 in Barrett's esophagus, and this is presumably a compensatory mechanism against this toxic agent.
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Affiliation(s)
- Eszter Becskeházi
- Department of Pharmacology and Pharmacotherapy, University of Szeged, H-6721 Szeged, Hungary; (E.B.); (M.M.K.); (E.G.)
| | - Marietta Margaréta Korsós
- Department of Pharmacology and Pharmacotherapy, University of Szeged, H-6721 Szeged, Hungary; (E.B.); (M.M.K.); (E.G.)
| | - Eleonóra Gál
- Department of Pharmacology and Pharmacotherapy, University of Szeged, H-6721 Szeged, Hungary; (E.B.); (M.M.K.); (E.G.)
| | - László Tiszlavicz
- Department of Pathology, University of Szeged, H-6725 Szeged, Hungary;
| | - Zsófia Hoyk
- Biological Research Centre, Institute of Biophysics, H-6726 Szeged, Hungary; (Z.H.); (M.A.D.)
| | - Mária A. Deli
- Biological Research Centre, Institute of Biophysics, H-6726 Szeged, Hungary; (Z.H.); (M.A.D.)
| | - Zoltán Márton Köhler
- Department of Biochemistry, University of Szeged, H-6720 Szeged, Hungary; (Z.M.K.); (A.K.-P.)
| | - Anikó Keller-Pintér
- Department of Biochemistry, University of Szeged, H-6720 Szeged, Hungary; (Z.M.K.); (A.K.-P.)
| | - Attila Horváth
- Department of Pharmacognosy, University of Szeged, H-6720 Szeged, Hungary;
| | - Kata Csekő
- Department of Pharmacology and Pharmacotherapy, Medical School & Szentágothai Research Centre, University of Pécs, H-7624 Pécs, Hungary; (K.C.); (Z.H.)
- PharmInVivo Ltd., H-7629 Pécs, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, Medical School & Szentágothai Research Centre, University of Pécs, H-7624 Pécs, Hungary; (K.C.); (Z.H.)
- PharmInVivo Ltd., H-7629 Pécs, Hungary
| | - Péter Hegyi
- First Department of Medicine, University of Szeged, H-6720 Szeged, Hungary;
- Medical School & Szentágothai Research Centre, Institute for Translational Medicine, University of Pécs, H-7624 Pécs, Hungary
- Division of Gastroenterology, First Department of Medicine, Medical School, University of Pécs, H-7624 Pécs, Hungary
| | - Viktória Venglovecz
- Department of Pharmacology and Pharmacotherapy, University of Szeged, H-6721 Szeged, Hungary; (E.B.); (M.M.K.); (E.G.)
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Murtadha AH, Azahar IIM, Sharudin NA, Has ATC, Mokhtar NF. Influence of nNav1.5 on MHC class I expression in breast cancer. J Biosci 2021. [DOI: 10.1007/s12038-021-00196-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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AQP3 and AQP5-Potential Regulators of Redox Status in Breast Cancer. Molecules 2021; 26:molecules26092613. [PMID: 33947079 PMCID: PMC8124745 DOI: 10.3390/molecules26092613] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/22/2021] [Accepted: 04/27/2021] [Indexed: 12/23/2022] Open
Abstract
Breast cancer is still one of the leading causes of mortality in the female population. Despite the campaigns for early detection, the improvement in procedures and treatment, drastic improvement in survival rate is omitted. Discovery of aquaporins, at first described as cellular plumbing system, opened new insights in processes which contribute to cancer cell motility and proliferation. As we discover new pathways activated by aquaporins, the more we realize the complexity of biological processes and the necessity to fully understand the pathways affected by specific aquaporin in order to gain the desired outcome-remission of the disease. Among the 13 human aquaporins, AQP3 and AQP5 were shown to be significantly upregulated in breast cancer indicating their role in the development of this malignancy. Therefore, these two aquaporins will be discussed for their involvement in breast cancer development, regulation of oxidative stress and redox signalling pathways leading to possibly targeting them for new therapies.
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Harguindey S, Alfarouk K, Polo Orozco J, Fais S, Devesa J. Towards an Integral Therapeutic Protocol for Breast Cancer Based upon the New H +-Centered Anticancer Paradigm of the Late Post-Warburg Era. Int J Mol Sci 2020; 21:E7475. [PMID: 33050492 PMCID: PMC7589677 DOI: 10.3390/ijms21207475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/13/2022] Open
Abstract
A brand new approach to the understanding of breast cancer (BC) is urgently needed. In this contribution, the etiology, pathogenesis, and treatment of this disease is approached from the new pH-centric anticancer paradigm. Only this unitarian perspective, based upon the hydrogen ion (H+) dynamics of cancer, allows for the understanding and integration of the many dualisms, confusions, and paradoxes of the disease. The new H+-related, wide-ranging model can embrace, from a unique perspective, the many aspects of the disease and, at the same time, therapeutically interfere with most, if not all, of the hallmarks of cancer known to date. The pH-related armamentarium available for the treatment of BC reviewed here may be beneficial for all types and stages of the disease. In this vein, we have attempted a megasynthesis of traditional and new knowledge in the different areas of breast cancer research and treatment based upon the wide-ranging approach afforded by the hydrogen ion dynamics of cancer. The concerted utilization of the pH-related drugs that are available nowadays for the treatment of breast cancer is advanced.
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Affiliation(s)
- Salvador Harguindey
- Department of Oncology, Institute of Clinical Biology and Metabolism, 01004 Vitoria, Spain;
| | - Khalid Alfarouk
- Department of Pharmacology, Al-Ghad International Colleges for Applied Medical Sciences, Al-Madinah Al-Munawarah 42316, Saudi Arabia and Alfarouk Biomedical Research LLC, Tampa, FL 33617, USA;
| | - Julián Polo Orozco
- Department of Oncology, Institute of Clinical Biology and Metabolism, 01004 Vitoria, Spain;
| | - Stefano Fais
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità (National Institute of Health), 00161 Rome, Italy;
| | - Jesús Devesa
- Scientific Direction, Foltra Medical Centre, 15886 Teo, Spain;
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