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Rahmatallah Y, Glazko G. Improving data interpretability with new differential sample variance gene set tests. BMC Bioinformatics 2025; 26:103. [PMID: 40229677 PMCID: PMC11998189 DOI: 10.1186/s12859-025-06117-0] [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: 08/09/2024] [Accepted: 03/20/2025] [Indexed: 04/16/2025] Open
Abstract
BACKGROUND Gene set analysis methods have played a major role in generating biological interpretations of omics data such as gene expression datasets. However, most methods focus on detecting homogenous pattern changes in mean expression while methods detecting pattern changes in variance remain poorly explored. While a few studies attempted to use gene-level variance analysis, such approach remains under-utilized. When comparing two phenotypes, gene sets with distinct changes in subgroups under one phenotype are overlooked by available methods although they reflect meaningful biological differences between two phenotypes. Multivariate sample-level variance analysis methods are needed to detect such pattern changes. RESULTS We used ranking schemes based on minimum spanning tree to generalize the Cramer-Von Mises and Anderson-Darling univariate statistics into multivariate gene set analysis methods to detect differential sample variance or mean. We characterized the detection power and Type I error rate of these methods in addition to two methods developed earlier using simulation results with different parameters. We applied the developed methods to microarray gene expression dataset of prednisolone-resistant and prednisolone-sensitive children diagnosed with B-lineage acute lymphoblastic leukemia and bulk RNA-sequencing gene expression dataset of benign hyperplastic polyps and potentially malignant sessile serrated adenoma/polyps. One or both of the two compared phenotypes in each of these datasets have distinct molecular subtypes that contribute to within phenotype variability and to heterogeneous differences between two compared phenotypes. Our results show that methods designed to detect differential sample variance provide meaningful biological interpretations by detecting specific hallmark gene sets associated with the two compared phenotypes as documented in available literature. CONCLUSIONS The results of this study demonstrate the usefulness of methods designed to detect differential sample variance in providing biological interpretations when biologically relevant but heterogeneous changes between two phenotypes are prevalent in specific signaling pathways. Software implementation of the methods is available with detailed documentation from Bioconductor package GSAR. The available methods are applicable to gene expression datasets in a normalized matrix form and could be used with other omics datasets in a normalized matrix form with available collection of feature sets.
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Affiliation(s)
- Yasir Rahmatallah
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
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Al Amin M, Bouhenni H, Zehravi M, Sweilam SH, Durgawale TP, Qureshi MS, Durgapal S, Haque MA, Vodeti R, Urs D, Shatu MM, Rab SO, Doukani K, Emran TB. Natural compounds and programmed necrosis: pioneering a new frontier in cancer treatments. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025:10.1007/s00210-025-04050-w. [PMID: 40137962 DOI: 10.1007/s00210-025-04050-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/09/2025] [Accepted: 03/12/2025] [Indexed: 03/29/2025]
Abstract
Programmed necrosis, a controlled cell death method that bypasses resistance mechanisms that render apoptosis ineffective, is a potential cancer treatment target. Due to their diverse biological activities and low side effects, natural products are being explored as modulators of programmed necrosis pathways. This review highlights the potential of natural compounds to target cancer cells while preserving healthy tissues and their interaction with essential programmed necrosis mechanisms like ferroptosis and necroptosis. Recent developments have identified various types of programmable necrosis, including necroptosis, ferroptosis, pyroptosis, proptosis, mitochondrial permeability transition-driven necrosis, and oncosis. Natural compounds are increasingly being utilized as a primary source of anti-cancer medications, providing new cancer treatments. This review demonstrates the molecular mechanisms behind lipid peroxidation, mixed lineage kinase domain-like protein, and receptor-interacting protein kinases (RIPK1 and RIPK3) inducing cell death. Recent research has identified natural compounds like polyphenols, alkaloids, and terpenoids that can modulate pathways and benefit preclinical cancer models. The review underscores the potential of natural compounds in developing innovative cancer treatments by integrating pharmacology and cellular signaling knowledge. Integrating natural compound studies and programmed necrosis research presents a promising avenue for oncologists to overcome treatment resistance. Natural compounds have shown potential in developing programmed necrosis as a novel cancer treatment approach, enhancing therapeutic effectiveness and minimizing side effects through preclinical research, pharmacology, and molecular biology.
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Affiliation(s)
- Md Al Amin
- Department of Pharmacy, Faculty of Health and Life Sciences, Daffodil International University, Dhaka, 1216, Bangladesh.
| | - Hasna Bouhenni
- Laboratory of Agrobiotechnology and Nutrition in Semi-Arid Zones, Faculty of Nature and Life Sciences, University of Ibn Khaldoun, Tiaret, Algeria
| | - Mehrukh Zehravi
- Department of Clinical Pharmacy, College of Dentistry & Pharmacy, Buraydah Private Colleges, Buraydah, 51418, Saudi Arabia.
| | - Sherouk Hussein Sweilam
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Egyptian Russian University, Cairo-Suez Road, Badr City, Cairo, 11829, Egypt
| | - Trupti Pratik Durgawale
- Department of Pharmaceutical Chemistry, Krishna Institute of Pharmacy Krishna Vishwa Vidyapeeth (Deemed to be University), Karad, Maharashtra, India
| | - Mohammad Shamim Qureshi
- Department of Pharmacognosy & Phytochemistry, Anwarul Uloom College of Pharmacy, New Mallepally, Hyderabad, 500001, India
| | - Sumit Durgapal
- Department of Pharmaceutics, Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Premnagar, Dehradun, Uttarakhand, 248007, India
| | - M Akiful Haque
- School of Pharmacy, Anurag University, Venkatapur, Hyderabad, Telangana , 500088, India
| | - Rajeshwar Vodeti
- Deportment of Pharmaceutics, School of Pharmacy, Anurag University, Hyderabad, India
| | - Deepadarshan Urs
- Inflammation Research Laboratory, Department of Studies & Research in Biochemistry, Mangalore University, Jnana Kaveri Post Graduate Centre, Kodagu, Karnataka, 571232, India
| | - Mst Maharunnasa Shatu
- Department of Botany, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - Safia Obaidur Rab
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia
| | - Koula Doukani
- Laboratory of Agrobiotechnology and Nutrition in Semi-Arid Zones, Faculty of Nature and Life Sciences, University of Ibn Khaldoun, Tiaret, Algeria
- Laboratory of Animal Production Sciences and Techniques, Faculty of Nature and Life Sciences, University of Abdelhamid Ibn Badis, Mostaganem, Algeria
| | - Talha Bin Emran
- Department of Pharmacy, Faculty of Health and Life Sciences, Daffodil International University, Dhaka, 1216, Bangladesh.
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Wang M, Wang X. Chemoprotective Potential of Cyanidin-3-Glucoside Against 1,2-Dimethylhydrazine-Induced Colorectal Cancer: Modulation of NF-κB and Bcl-2/Bax/Caspase Pathway. J Biochem Mol Toxicol 2025; 39:e70125. [PMID: 39843995 DOI: 10.1002/jbt.70125] [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: 11/03/2024] [Revised: 11/30/2024] [Accepted: 12/21/2024] [Indexed: 01/24/2025]
Abstract
Colorectal cancer (CRC) represents a significant global health challenge, with approximately 1.8 million new cases diagnosed annually and a mortality toll exceeding 881,000 lives each year. This study aimed to evaluate the chemoprotective efficacy of Cyanidin-3-glucoside (C3G) in a rat model of CRC induced by 1,2-dimethylhydrazine (DMH). Rats were stratified into groups and administered C3G at doses of 10 and 15 mg/kg following DMH exposure to initiate CRC. Key parameters, including organ weights, tumor burdens, and biochemical markers, were meticulously assessed. Administration of C3G significantly restored body weight while reducing the weights of colon and spleen tissues. Moreover, C3G treatment substantially suppressed tumor incidence and weight in DMH-induced CRC rats. Biochemical analysis revealed that C3G markedly reduced levels of CFA, CA19.9, LDH, and nitric oxide (NO). It also modulated lipid profiles, antioxidant activities, and the expression of both Phase I and II enzymes. Inflammatory mediators, including TNF-α, IL-1β, IL-1α, IL-2, IL-4, IL-6, IL-10, IL-12, and IL-17, were significantly downregulated. Notably, C3G inhibited inflammatory markers such as COX-2, PGE2, iNOS, and NF-κB while promoting Caspase-3, -6, and -9 activity. Furthermore, it regulated the Bax/Bcl-2 apoptotic axis, reducing the Bcl-2/Bax ratio. Cyanidin-3-glucoside demonstrated potent chemopreventive effects against colorectal cancer in this experimental model. Its mechanism of action is likely mediated through modulation of NF-κB and the Bcl-2/Bax/Caspase pathway, suggesting its potential as a therapeutic agent in CRC management.
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Affiliation(s)
- Miao Wang
- Department of Gastroenterology, The Second Hospital of Heilongjiang Province, Harbin City, Heilongjiang Province, China
| | - Xiaoyong Wang
- Department of Gastroenterology, The Second Hospital of Heilongjiang Province, Harbin City, Heilongjiang Province, China
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4
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He Y, Liu F, Li Q, Jiang Z. Identification of cuproptosis and ferroptosis-related subtypes and development of a prognostic signature in colon cancer. PLoS One 2025; 20:e0307013. [PMID: 39883700 PMCID: PMC11781745 DOI: 10.1371/journal.pone.0307013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 12/25/2024] [Indexed: 02/01/2025] Open
Abstract
Colon cancer, as a highly prevalent malignant tumor globally, poses a significant threat to human health. In recent years, ferroptosis and cuproptosis, as two novel forms of cell death, have attracted widespread attention for their potential roles in the development and treatment of colon cancer. However, the investigation into the subtypes and their impact on the survival of colon cancer patients remains understudied. In this study, utilizing data from TCGA and GEO databases, we examined the expression differences of ferroptosis and cuproptosis-related genes in colon cancer and identified two subtypes. Through functional analysis and bioinformatics methods, we elucidated pathway differences and biological characteristics between these two subtypes. By leveraging differential genes between the two subtypes, we constructed a prognostic model using univariate Cox regression and multivariate Cox regression analysis as well as LASSO regression analysis. Further survival analysis and receiver operating characteristic curve analysis demonstrated the model's high accuracy. To enhance its clinical utility, we evaluated the clinical significance of the model and constructed a nomogram, significantly improving the predictive ability of the model and providing a new tool for prognostic assessment of colon cancer patients. Subsequently, through immune-related analysis, we revealed differences in immune cell infiltration and immune function between high- and low-risk groups. Further analysis of the relationship between the model and immune cells and functions revealed potential therapeutic targets. Drug sensitivity analysis revealed associations between the expression of model-related genes and drug sensitivity, suggesting their involvement in tumor resistance through certain mechanisms. AZD8055_1059, Bortezomib_1191, Dihydrorotenone_1827, and MG-132_1862 were more sensitive in the high-risk group. Finally, we analyzed differential expression of model-related genes between tumor tissues and normal tissues, validated through real-time quantitative PCR and immunohistochemistry. In summary, our study provides a relatively accurate prognostic tool for colon cancer patients, offering guidance for treatment selection and indicating the potential of immunotherapy in colon cancer.
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Affiliation(s)
- Yinghao He
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Fuqiang Liu
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Gastroenterology, The People’s Hospital of Jianyang City, Jianyang, Sichuan Province, China
| | - Qingshu Li
- Department of Pathology, College of Basic Medicine, Chongqing Medical University, Chongqing, China
- Molecular Medicine Diagnostic and Testing Center, Chongqing Medical University, Chongqing, China
- Department of Pathology, the First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zheng Jiang
- Department of Gastroenterology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
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Kong J, Dong Y, Li M, Fan J, Wang T. Protein arginine methyltransferase 5 confers the resistance of triple-negative breast cancer to nanoparticle albumin-bound paclitaxel by enhancing autophagy through the dimethylation of ULK1. Toxicol Appl Pharmacol 2024; 493:117145. [PMID: 39521146 DOI: 10.1016/j.taap.2024.117145] [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: 08/22/2024] [Revised: 10/11/2024] [Accepted: 11/02/2024] [Indexed: 11/16/2024]
Abstract
Chemotherapy remains the major strategy for treating triple-negative breast cancer (TNBC); however, frequently acquired chemoresistance greatly limits the treatment outcomes. Protein arginine methyltransferase 5 (PRMT5), which modulates arginine methylation, is important in chemoresistance acquisition across various cancers. The function of PRMT5 in the development of chemoresistance in TNBC is still not well understood. This work focused on defining PRMT5's function in contributing to the chemoresistance in TNBC and demonstrating the possible mechanisms involved. Two TNBC cell lines resistant to nanoparticle albumin-bound paclitaxel (Nab-PTX), designated MDA-MB-231/R and MDA-MB-468/R, were developed. The expression of PRMT5 was markedly elevated in the cytoplasm of Nab-PTX-resistant cells accompanied with enhanced autophagy. The depletion of PRMT5 rendered these cells sensitive to Nab-PTX-evoked cytotoxicity. The autophagic flux was upregulated in Nab-PTX-resistant cells, which was markedly repressed by PRMT5 depletion. The dimethylation of ULK1 was markedly elevated in Nab-PTX-resistant cells, which was decreased by silencing PRMT5. Re-expression of PRMT5 in PRMT5-depleted cells restored the dimethylation and activation of ULK1 as well as the autophagic flux, while the catalytically-dead PRMT5 (R368A) mutant showed no significant effects. The depletion of PRMT5 rendered the subcutaneous tumors formed by Nab-PTX-resistant TNBC cells sensitive to Nab-PTX. The findings of this work illustrate that PRMT5 confers chemoresistance of TNBC by enhancing autophagy through dimethylation and the activation of ULK1, revealing a novel mechanism for understanding the acquisition of chemoresistance in TNBC. Targeting PRMT5 could be a viable approach for overcoming chemoresistance in the treatment of TNBC.
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Affiliation(s)
- Jing Kong
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, China
| | - Yan Dong
- Department of Breast and Thyroid Surgery, Qinghai Provincial Peoples's Hospital, Xining 810000, China
| | - Mengxuan Li
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, China
| | - Jing Fan
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, China.
| | - Ting Wang
- Department of Thyroid, Breast and Vascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an 710032, China.
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6
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Ebersole JL, Kirakodu SS, Nguyen LM, Gonzalez OA. Transcriptomic features of programmed and inflammatory cell death in gingival tissues. Oral Dis 2024; 30:5274-5293. [PMID: 38623775 DOI: 10.1111/odi.14939] [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: 11/20/2023] [Revised: 03/04/2024] [Accepted: 03/09/2024] [Indexed: 04/17/2024]
Abstract
The local gingival tissue environment with homeostasis and tissue-destructive events of periodontitis demonstrates major changes in histological features and biology of the oral/sulcular epithelium, fibroblasts, vascular cells, inflammatory cell infiltration, and alveolar bone. OBJECTIVE This study used an experimental periodontitis model to detail the gingival transcriptome related to cell death processes of pyroptosis, necroptosis, ferroptosis, and cuproptosis. MATERIALS AND METHODS Healthy Macaca mulatta primates stratified by age, ≤3 years (young), 7-12 years (adolescent), 12-15 years (adult), and 17-23 years (aged), provided gingival tissue biopsies for microarray analysis focused on 257 genes representative of the four cell death processes and bacterial plaque samples for 16S rRNA gene analysis. RESULTS Age differences in the profiles of gene expression in healthy tissues were noted for cuproptosis, ferroptosis, necroptosis, and pyroptosis. Major differences were then observed with disease initiation, progression, and resolution also related to the age of the animals. Distinct bacterial families/consortia of species were significantly related to the gene expression differences for the cell death pathways. CONCLUSIONS These results emphasized age-associated differences in the gingival tissue molecular response to changes in the quality and quantity of bacteria accumulating with the disease process reflected in regulated cell death pathways that are both physiological and pathophysiological.
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Affiliation(s)
- Jeffrey L Ebersole
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Sreenatha S Kirakodu
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, Kentucky, USA
| | - Linh M Nguyen
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Octavio A Gonzalez
- Center for Oral Health Research, College of Dentistry, University of Kentucky, Lexington, Kentucky, USA
- Division of Periodontology, College of Dentistry, University of Kentucky, Lexington, Kentucky, USA
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7
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Seo JW, Lee YS, Jeon IS, Yu JE, Yoo JS, Koo JK, Son DJ, Yoon JS, Han SB, Yoon DY, Roh YS, Hong JT, Shim JH. IL-32γ Induced Autophagy Through Suppression of MET and mTOR Pathways in Liver Tumor Growth Inhibition. Int J Mol Sci 2024; 25:11678. [PMID: 39519229 PMCID: PMC11547131 DOI: 10.3390/ijms252111678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Revised: 10/18/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024] Open
Abstract
Interleukin-32γ (IL-32γ) has diverse functions in various malignancies. In this study, we investigated the role of IL-32γ in autophagy induction in liver cancer cells and delineated the underlying mechanisms. We found that the increased IL-32γ expression inhibited the growth, cell cycle progression, and migration of HepG2 and Hep3B cell lines; it also decreased the expression of related proteins. Furthermore, the IL-32γ overexpression induced autophagy, as indicated by the number of puncta, the expression of LC3, and the expression of autophagy-related markers. The expression levels of LAMP1, a protein essential for autophagosome formation, and colocalization with LC3 also increased. Big data analysis revealed that the expression of MET, a well-known target of autophagy, and the expression of mTOR and mTOR-related proteins were decreased by the IL-32γ overexpression. The combination treatment of MET inhibitor, cabozantinib (2 µM), and IL-32γ overexpression further increased the number of puncta, the colocalization of LC3 and LAMP1, and the expression of autophagy-related proteins. In vivo, liver tumor growth was suppressed in the IL-32γ-overexpressing mouse model, and autophagy induction was confirmed by the increased expression of LC3 and LAMP1 and the decreased expression of autophagy pathway markers (MET and mTOR). Autophagy was also decreased in the liver tumor sample of human patients. ROC curve and spearman analysis revealed that the expression levels of LC3 and IL-32γ were significantly correlated in human tumor serum and tissues. Therefore, IL-32γ overexpression induced autophagy in liver tumors through the suppression of MET and mTOR pathways critical for tumor growth inhibition.
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Affiliation(s)
- Ji-Won Seo
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Yong-Sun Lee
- Ministry of Food and Drug Safety, 187, Osongsaengmyeong 2-ro, Osong-eup, Heungdeok-gu, Cheongju 28159, Chungbuk, Republic of Korea;
| | - In-Sook Jeon
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Ji-Eun Yu
- College of Pharmacy, Mokpo National University, Muan 58554, Jeonnam, Republic of Korea;
- Department of Biomedicine, Health & Life Convergence Sciences, BK21 Four, Biomedical and Healthcare Research Institute, Mokpo National University, Muan 58554, Jeonnam, Republic of Korea
| | - Jun-Sang Yoo
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Ja-Keun Koo
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Dong-Ju Son
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Jae-Suk Yoon
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Sang-Bae Han
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Do-Young Yoon
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea;
| | - Yoon-Seok Roh
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Jin-Tae Hong
- College of Pharmacy and Medical Research Center, Chungbuk National University, 194-31, Osongsaengmyeong 1-ro, Osong-eup, Cheongju-si 28160, Chungbuk, Republic of Korea; (J.-W.S.); (I.-S.J.); (J.-S.Y.); (J.-K.K.); (D.-J.S.); (J.-S.Y.); (S.-B.H.); (Y.-S.R.)
| | - Jung-Hyun Shim
- College of Pharmacy, Mokpo National University, Muan 58554, Jeonnam, Republic of Korea;
- Department of Biomedicine, Health & Life Convergence Sciences, BK21 Four, Biomedical and Healthcare Research Institute, Mokpo National University, Muan 58554, Jeonnam, Republic of Korea
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Sipos F, Műzes G. Interconnection of CD133 Stem Cell Marker with Autophagy and Apoptosis in Colorectal Cancer. Int J Mol Sci 2024; 25:11201. [PMID: 39456981 PMCID: PMC11508732 DOI: 10.3390/ijms252011201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Revised: 10/09/2024] [Accepted: 10/17/2024] [Indexed: 10/28/2024] Open
Abstract
CD133 protein expression is observable in differentiated cells, stem cells, and progenitor cells within normal tissues, as well as in tumor tissues, including colorectal cancer cells. The CD133 protein is the predominant cell surface marker utilized to detect cancer cells exhibiting stem cell-like characteristics. CD133 alters common abnormal processes in colorectal cancer, such as the phosphoinositide 3-kinase (PI3K)/protein kinase B (AKT) and Wnt/β-catenin pathways. Autophagy is a cellular self-digestion mechanism that preserves the intracellular milieu and plays a dual regulatory role in cancer. In cancer cells, apoptosis is a critical cell death mechanism that can impede cancer progression. CD133 can modulate autophagy and apoptosis in colorectal cancer cells via several signaling pathways; hence, it is involved in the regulation of these intricate processes. This can be an explanation for why CD133 expression is associated with enhanced cellular self-renewal, migration, invasion, and survival under stress conditions in colorectal cancer. The purpose of this review article is to explain the complex relationship between the CD133 protein, apoptosis, and autophagy. We also want to highlight the possible ways that CD133-mediated autophagy may affect the apoptosis of colorectal cancer cells. Targeting the aforementioned mechanisms may have a significant therapeutic role in eliminating CD133-positive stem cell-phenotype colorectal cancer cells, which can be responsible for tumor recurrence.
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Affiliation(s)
- Ferenc Sipos
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
| | - Györgyi Műzes
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
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Zamanian MY, Taheri N, Ramadan MF, Mustafa YF, Alkhayyat S, Sergeevna KN, Alsaab HO, Hjazi A, Molavi Vasei F, Daneshvar S. A comprehensive view on the fisetin impact on colorectal cancer in animal models: Focusing on cellular and molecular mechanisms. Animal Model Exp Med 2024; 7:591-605. [PMID: 39136058 PMCID: PMC11528395 DOI: 10.1002/ame2.12476] [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: 05/27/2024] [Revised: 06/21/2024] [Accepted: 07/09/2024] [Indexed: 11/02/2024] Open
Abstract
Flavonoids, including fisetin, have been linked to a reduced risk of colorectal cancer (CRC) and have potential therapeutic applications for the condition. Fisetin, a natural flavonoid found in various fruits and vegetables, has shown promise in managing CRC due to its diverse biological activities. It has been found to influence key cell signaling pathways related to inflammation, angiogenesis, apoptosis, and transcription factors. The results of this study demonstrate that fisetin induces colon cancer cell apoptosis through multiple mechanisms. It impacts the p53 pathway, leading to increased levels of p53 and decreased levels of murine double minute 2, contributing to apoptosis induction. Fisetin also triggers the release of important components in the apoptotic process, such as second mitochondria-derived activator of caspase/direct inhibitor of apoptosis-binding protein with low pI and cytochrome c. Furthermore, fisetin inhibits the cyclooxygenase-2 and wingless-related integration site (Wnt)/epidermal growth factor receptor/nuclear factor kappa B signaling pathways, reducing Wnt target gene expression and hindering colony formation. It achieves this by regulating the activities of cyclin-dependent kinase 2 and cyclin-dependent kinase 4, reducing retinoblastoma protein phosphorylation, decreasing cyclin E levels, and increasing p21 levels, ultimately influencing E2 promoter binding factor 1 and cell division cycle 2 (CDC2) protein levels. Additionally, fisetin exhibits various effects on CRC cells, including inhibiting the phosphorylation of Y-box binding protein 1 and ribosomal S6 kinase, promoting the phosphorylation of extracellular signal-regulated kinase 1/2, and disrupting the repair process of DNA double-strand breaks. Moreover, fisetin serves as an adjunct therapy for the prevention and treatment of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA)-mutant CRC, resulting in a reduction in phosphatidylinositol-3 kinase (PI3K) expression, Ak strain transforming phosphorylation, mTOR activity, and downstream target proteins in CRC cells with a PIK3CA mutation. These findings highlight the multifaceted potential of fisetin in managing CRC and position it as a promising candidate for future therapy development.
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Affiliation(s)
- Mohammad Yasin Zamanian
- Department of Physiology, School of MedicineHamadan University of Medical SciencesHamadanIran
- Department of Pharmacology and Toxicology, School of PharmacyHamadan University of Medical SciencesHamadanIran
| | - Niloofar Taheri
- School of MedicineShahroud University of Medical SciencesShahroudIran
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical ChemistryCollege of Pharmacy, University of MosulMosulIraq
| | | | - Klunko Nataliya Sergeevna
- Department of Training of Scientific and Scientific‐Pedagogical PersonnelRussian New UniversityMoscowRussian Federation
| | - Hashem O. Alsaab
- Department of Pharmaceutics and Pharmaceutical TechnologyTaif UniversityTaifSaudi Arabia
| | - Ahmed Hjazi
- Department of Medical LaboratoryCollege of Applied Medical Sciences, Prince Sattam bin Abdulaziz UniversityAl‐KharjSaudi Arabia
| | - Farnoosh Molavi Vasei
- Department of Clinical Biochemistry, School of MedicineRafsanjan University of Medical SciencesRafsanjanIran
| | - Siamak Daneshvar
- Department of Surgery, School of MedicineHamadan University of Medical SciencesHamadanIran
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10
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Rahmatallah Y, Glazko G. Improving data interpretability with new differential sample variance gene set tests. RESEARCH SQUARE 2024:rs.3.rs-4888767. [PMID: 39315246 PMCID: PMC11419169 DOI: 10.21203/rs.3.rs-4888767/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/25/2024]
Abstract
Background Gene set analysis methods have played a major role in generating biological interpretations from omics data such as gene expression datasets. However, most methods focus on detecting homogenous pattern changes in mean expression and methods detecting pattern changes in variance remain poorly explored. While a few studies attempted to use gene-level variance analysis, such approach remains under-utilized. When comparing two phenotypes, gene sets with distinct changes in subgroups under one phenotype are overlooked by available methods although they reflect meaningful biological differences between two phenotypes. Multivariate sample-level variance analysis methods are needed to detect such pattern changes. Results We use ranking schemes based on minimum spanning tree to generalize the Cramer-Von Mises and Anderson-Darling univariate statistics into multivariate gene set analysis methods to detect differential sample variance or mean. We characterize these methods in addition to two methods developed earlier using simulation results with different parameters. We apply the developed methods to microarray gene expression dataset of prednisolone-resistant and prednisolone-sensitive children diagnosed with B-lineage acute lymphoblastic leukemia and bulk RNA-sequencing gene expression dataset of benign hyperplastic polyps and potentially malignant sessile serrated adenoma/polyps. One or both of the two compared phenotypes in each of these datasets have distinct molecular subtypes that contribute to heterogeneous differences. Our results show that methods designed to detect differential sample variance are able to detect specific hallmark signaling pathways associated with the two compared phenotypes as documented in available literature. Conclusions The results in this study demonstrate the usefulness of methods designed to detect differential sample variance in providing biological interpretations when biologically relevant but heterogeneous changes between two phenotypes are prevalent in specific signaling pathways. Software implementation of the developed methods is available with detailed documentation from Bioconductor package GSAR. The available methods are applicable to gene expression datasets in a normalized matrix form and could be used with other omics datasets in a normalized matrix form with available collection of feature sets.
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Affiliation(s)
- Yasir Rahmatallah
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Galina Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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11
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Gharib E, Robichaud GA. From Crypts to Cancer: A Holistic Perspective on Colorectal Carcinogenesis and Therapeutic Strategies. Int J Mol Sci 2024; 25:9463. [PMID: 39273409 PMCID: PMC11395697 DOI: 10.3390/ijms25179463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/19/2024] [Accepted: 08/24/2024] [Indexed: 09/15/2024] Open
Abstract
Colorectal cancer (CRC) represents a significant global health burden, with high incidence and mortality rates worldwide. Recent progress in research highlights the distinct clinical and molecular characteristics of colon versus rectal cancers, underscoring tumor location's importance in treatment approaches. This article provides a comprehensive review of our current understanding of CRC epidemiology, risk factors, molecular pathogenesis, and management strategies. We also present the intricate cellular architecture of colonic crypts and their roles in intestinal homeostasis. Colorectal carcinogenesis multistep processes are also described, covering the conventional adenoma-carcinoma sequence, alternative serrated pathways, and the influential Vogelstein model, which proposes sequential APC, KRAS, and TP53 alterations as drivers. The consensus molecular CRC subtypes (CMS1-CMS4) are examined, shedding light on disease heterogeneity and personalized therapy implications.
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Affiliation(s)
- Ehsan Gharib
- Département de Chimie et Biochimie, Université de Moncton, Moncton, NB E1A 3E9, Canada
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
| | - Gilles A Robichaud
- Département de Chimie et Biochimie, Université de Moncton, Moncton, NB E1A 3E9, Canada
- Atlantic Cancer Research Institute, Moncton, NB E1C 8X3, Canada
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12
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Li N, Zuo R, He Y, Gong W, Wang Y, Chen L, Luo Y, Zhang C, Liu Z, Chen P, Guo H. PD-L1 induces autophagy and primary resistance to EGFR-TKIs in EGFR-mutant lung adenocarcinoma via the MAPK signaling pathway. Cell Death Dis 2024; 15:555. [PMID: 39090096 PMCID: PMC11294607 DOI: 10.1038/s41419-024-06945-7] [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: 01/28/2024] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024]
Abstract
Resistance to epidermal growth factor receptor (EGFR)-tyrosine kinase inhibitors (TKIs) is a significant cause of treatment failure and cancer recurrence in non-small cell lung cancer (NSCLC). Approximately 30% of patients with EGFR-activating mutations exhibit primary resistance to EGFR-TKIs. However, the potential mechanisms of primary resistance to EGFR-TKIs remain poorly understood. Recent studies have shown that increased expression of programmed death ligand-1 (PD-L1) is associated with EGFR-TKIs resistance. Therefore, the present study aimed to investigate the mechanism of PD-L1 in primary resistance to EGFR-TKIs in EGFR-mutant lung adenocarcinoma (LUAD) cells. We found that PD-L1 was associated with poor prognosis in patients with EGFR-mutant LUAD, while the combination of EGFR-TKIs with chemotherapy could improve its therapeutic efficacy. In vitro and in vivo experiments revealed that PD-L1 promoted the proliferation and autophagy and inhibited the apoptosis of LUAD cells. Mechanistic studies demonstrated that upregulation of PD-L1 was critical in inducing autophagy through the mitogen-activated protein kinase (MAPK) signaling pathway, which was beneficial for tumor progression and the development of gefitinib resistance. Furthermore, we found that gefitinib combined with pemetrexed could synergistically enhance antitumor efficacy in PD-L1-overexpression LUAD cells. Overall, our study demonstrated that PD-L1 contributed to primary resistance to EGFR-TKIs in EGFR-mutant LUAD cells, which may be mediated by inducing autophagy via the MAPK signaling pathway. These findings not only help improve the prognosis of patients with EGFR-mutant LUAD but also provide a reference for the research of other cancer types.
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Affiliation(s)
- Na Li
- Department of Thoracic Oncology, Lung Cancer Diagnosis and Treatment Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Department of Oncology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, 264200, China
| | - Ran Zuo
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Department of Integrative Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Yuchao He
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Wenchen Gong
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Department of Pathology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Yu Wang
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Liwei Chen
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Yi Luo
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
- Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
| | - Cuicui Zhang
- Department of Thoracic Oncology, Lung Cancer Diagnosis and Treatment Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Zhiyong Liu
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
- Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
| | - Peng Chen
- Department of Thoracic Oncology, Lung Cancer Diagnosis and Treatment Center, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
| | - Hua Guo
- National Clinical Research Center for Cancer, State Key Laboratory of Druggability Evaluation and Systematic Translational Medicine, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China.
- Department of Tumor Cell Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, 300060, China.
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13
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Xing F, Liu N, Wang C, Wang XD. Caffeic acid phenethyl ester promotes oxaliplatin sensitization in colon cancer by inhibiting autophagy. Sci Rep 2024; 14:14624. [PMID: 38918541 PMCID: PMC11199620 DOI: 10.1038/s41598-024-65409-2] [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: 11/22/2023] [Accepted: 06/19/2024] [Indexed: 06/27/2024] Open
Abstract
Colon cancer ranks as the third most prevalent form of cancer globally, with chemotherapy remaining the primary treatment modality. To mitigate drug resistance and minimize adverse effects associated with chemotherapy, selection of appropriate adjuvants assumes paramount importance. Caffeic acid phenethyl ester (CAPE), a naturally occurring compound derived from propolis, exhibits a diverse array of biological activities. We observed that the addition of CAPE significantly augmented the drug sensitivity of colon cancer cells to oxaliplatin. In SW480 and HCT116 cells, oxaliplatin combined with 10 µM CAPE reduced the IC50 of oxaliplatin from 14.24 ± 1.03 and 84.16 ± 3.02 µM to 2.11 ± 0.15 and 3.92 ± 0.17 µM, respectively. We then used proteomics to detect differentially expressed proteins in CAPE-treated SW480 cells and found that the main proteins showing changes in expression after CAPE treatment were p62 (SQSTM1) and LC3B (MAP1LC3B). Gene ontology analysis revealed that CAPE exerted antitumor and chemotherapy-sensitization effects through the autophagy pathway. We subsequently verified the differentially expressed proteins using immunoblotting. Simultaneously, the autophagy inhibitor bafilomycin A1 and the mCherry-EGFP-LC3 reporter gene were used as controls to detect the effect of CAPE on autophagy levels. Collectively, the results indicate that CAPE may exert antitumor and chemotherapy-sensitizing effects by inhibiting autophagy, offering novel insights for the development of potential chemosensitizing agents.
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Affiliation(s)
- Fei Xing
- Department of Gastrointestinal Nutrition Surgery, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Ning Liu
- Academic Center, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Can Wang
- Department of Gastrointestinal Nutrition Surgery, The Second Hospital of Jilin University, Changchun, 130000, China
| | - Xu-Dong Wang
- Department of Gastrointestinal Nutrition Surgery, The Second Hospital of Jilin University, Changchun, 130000, China.
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14
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Műzes G, Sipos F. Inflammasomes Are Influenced by Epigenetic and Autophagy Mechanisms in Colorectal Cancer Signaling. Int J Mol Sci 2024; 25:6167. [PMID: 38892354 PMCID: PMC11173330 DOI: 10.3390/ijms25116167] [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: 04/28/2024] [Revised: 05/31/2024] [Accepted: 05/31/2024] [Indexed: 06/21/2024] Open
Abstract
Inflammasomes contribute to colorectal cancer signaling by primarily inducing inflammation in the surrounding tumor microenvironment. Its role in inflammation is receiving increasing attention, as inflammation has a protumor effect in addition to inducing tissue damage. The inflammasome's function is complex and controlled by several layers of regulation. Epigenetic processes impact the functioning or manifestation of genes that are involved in the control of inflammasomes or the subsequent signaling cascades. Researchers have intensively studied the significance of epigenetic mechanisms in regulation, as they encompass several potential therapeutic targets. The regulatory interactions between the inflammasome and autophagy are intricate, exhibiting both advantageous and harmful consequences. The regulatory aspects between the two entities also encompass several therapeutic targets. The relationship between the activation of the inflammasome, autophagy, and epigenetic alterations in CRC is complex and involves several interrelated pathways. This article provides a brief summary of the newest studies on how epigenetics and autophagy control the inflammasome, with a special focus on their role in colorectal cancer. Based on the latest findings, we also provide an overview of the latest therapeutic ideas for this complex network.
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Affiliation(s)
- Györgyi Műzes
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
| | - Ferenc Sipos
- Immunology Division, Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
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15
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Shi Y, Jiang B, Zhao J. Induction mechanisms of autophagy and endoplasmic reticulum stress in intestinal ischemia-reperfusion injury, inflammatory bowel disease, and colorectal cancer. Biomed Pharmacother 2024; 170:115984. [PMID: 38070244 DOI: 10.1016/j.biopha.2023.115984] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/19/2023] [Accepted: 12/02/2023] [Indexed: 01/10/2024] Open
Abstract
In recent years, the incidence of intestinal ischemia-reperfusion injury (II/RI), inflammatory bowel disease (IBD), and colorectal cancer (CRC) has been gradually increasing, posing significant threats to human health. Autophagy and endoplasmic reticulum stress (ERS) play important roles in II/RI. Damage caused by ischemia and cellular stress can activate ERS, which in turn initiates autophagy to clear damaged organelles and abnormal proteins, thereby alleviating ERS and maintaining the intestinal environment. In IBD, chronic inflammation damages intestinal tissues and activates autophagy and ERS. Autophagy is initiated by upregulating ATG genes and downregulating factors that inhibit autophagy, thereby clearing abnormal proteins, damaged organelles, and bacteria. Simultaneously, persistent inflammatory stimulation can also trigger ERS, leading to protein imbalance and abnormal folding in the ER lumen. The activation of ERS can maintain cellular homeostasis by initiating the autophagy process, thereby reducing inflammatory responses and cell apoptosis in the intestine. In CRC, excessive cell proliferation and protein synthesis lead to increased ERS. The activation of ERS, regulated by signaling pathways such as IRE1α and PERK, can initiate autophagy to clear abnormal proteins and damaged organelles, thereby reducing the negative effects of ERS. It can be seen that autophagy and ERS play a crucial regulatory role in the development of intestinal diseases. Therefore, the progress in targeted therapy for intestinal diseases based on autophagy and ERS provides novel strategies for managing intestinal diseases. In this paper, we review the advances in regulation of autophagy and ERS in intestinal diseases, emphasizing the potential molecular mechanisms for therapeutic applications.
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Affiliation(s)
- Yan Shi
- Department of Basic Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou 730000, Gansu, PR China
| | - Bing Jiang
- Department of Integrated Chinese and Western Medicine, Gansu University of Traditional Chinese Medicine, Lanzhou 730000, Gansu, PR China
| | - Jingwen Zhao
- Department of Proctology, Baoji Traditional Chinese Medicine Hospital, Baoji 721001, Shanxi, PR China.
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16
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El-Sayed NNE, Al-Otaibi TM, Barakat A, Almarhoon ZM, Hassan MZ, Al-Zaben MI, Krayem N, Masand VH, Ben Bacha A. Synthesis and Biological Evaluation of Some New 3-Aryl-2-thioxo-2,3-dihydroquinazolin-4(1 H)-ones and 3-Aryl-2-(benzylthio)quinazolin-4(3 H)-ones as Antioxidants; COX-2, LDHA, α-Glucosidase and α-Amylase Inhibitors; and Anti-Colon Carcinoma and Apoptosis-Inducing Agents. Pharmaceuticals (Basel) 2023; 16:1392. [PMID: 37895863 PMCID: PMC10610505 DOI: 10.3390/ph16101392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/29/2023] Open
Abstract
Oxidative stress, COX-2, LDHA and hyperglycemia are interlinked contributing pathways in the etiology, progression and metastasis of colon cancer. Additionally, dysregulated apoptosis in cells with genetic alternations leads to their progression in malignant transformation. Therefore, quinazolinones 3a-3h and 5a-5h were synthesized and evaluated as antioxidants, enzymes inhibitors and cytotoxic agents against LoVo and HCT-116 cells. Moreover, the most active cytotoxic derivatives were evaluated as apoptosis inducers. The results indicated that 3a, 3g and 5a were efficiently scavenged DPPH radicals with lowered IC50 values (mM) ranging from 0.165 ± 0.0057 to 0.191 ± 0.0099, as compared to 0.245 ± 0.0257 by BHT. Derivatives 3h, 5a and 5h were recognized as more potent dual inhibitors than quercetin against α-amylase and α-glucosidase, in addition to 3a, 3c, 3f and 5b-5f against α-amylase. Although none of the compounds demonstrated a higher efficiency than the reference inhibitors against COX-2 and LDHA, 3a and 3g were identified as the most active derivatives. Molecular docking studies were used to elucidate the binding affinities and binding interactions between the inhibitors and their target proteins. Compounds 3a and 3f showed cytotoxic activities, with IC50 values (µM) of 294.32 ± 8.41 and 383.5 ± 8.99 (LoVo), as well as 298.05 ± 13.26 and 323.59 ± 3.00 (HCT-116). The cytotoxicity mechanism of 3a and 3f could be attributed to the modulation of apoptosis regulators (Bax and Bcl-2), the activation of intrinsic and extrinsic apoptosis pathways via the upregulation of initiator caspases-8 and -9 as well as executioner caspase-3, and the arrest of LoVo and HCT-116 cell cycles in the G2/M and G1 phases, respectively. Lastly, the physicochemical, medicinal chemistry and ADMET properties of all compounds were predicted.
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Affiliation(s)
| | - Taghreed M. Al-Otaibi
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (T.M.A.-O.); (A.B.); (M.I.A.-Z.)
| | - Assem Barakat
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (T.M.A.-O.); (A.B.); (M.I.A.-Z.)
| | - Zainab M. Almarhoon
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (T.M.A.-O.); (A.B.); (M.I.A.-Z.)
| | - Mohd. Zaheen Hassan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha 62529, Saudi Arabia;
| | - Maha I. Al-Zaben
- Department of Chemistry, College of Sciences, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia; (T.M.A.-O.); (A.B.); (M.I.A.-Z.)
| | - Najeh Krayem
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, ENIS, Université de Sfax, Route de Soukra 3038, Sfax BP 1173, Tunisia;
| | - Vijay H. Masand
- Department of Chemistry, Vidya Bharati College, Camp, Amravati, Maharashtra 444602, India;
| | - Abir Ben Bacha
- Biochemistry Department, College of Sciences, King Saud University, P.O. Box 22452, Riyadh 11495, Saudi Arabia;
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