1
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Hou Y, Fu Z, Wang C, Kucharzewska P, Guo Y, Zhang S. 27-Hydroxycholesterol in cancer development and drug resistance. J Enzyme Inhib Med Chem 2025; 40:2507670. [PMID: 40401382 PMCID: PMC12100970 DOI: 10.1080/14756366.2025.2507670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2025] [Revised: 04/25/2025] [Accepted: 05/13/2025] [Indexed: 05/23/2025] Open
Abstract
27-Hydroxycholesterol (27HC), a cholesterol metabolite, functions both as a selective oestrogen receptor (ER) modulator and a ligand for liver X receptors (LXRs). The discovery of 27HC involvement in carcinogenesis has unveiled new research avenues, yet its precise role remains controversial and context-dependent. In this review, we provide an overview of the biosynthesis and metabolism of 27HC and explore its cancer-associated signalling, with a particular focus on ER- and LXR-mediated pathways. Given the tissue-specific dual role of 27HC, we discuss its differential impact across various cancer types. Furthermore, we sort out 27HC-contributed drug resistance mechanisms from the perspectives of drug efflux, cellular proliferation, apoptosis, epithelial-mesenchymal transition (EMT), antioxidant defence, epigenetic modification, and metabolic reprogramming. Finally, we highlight the chemical inhibitors to mitigate 27HC-driven cancer progression and drug resistance. This review offers an updated role of 27HC in cancer biology, setting the stage for future research and the development of targeted therapeutics.
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Affiliation(s)
- Yaxin Hou
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Zhiguang Fu
- Department of Tumor Radiotherapy, Air Force Medical Center, People’s Liberation Army of China (PLA), Beijing, China
| | - Chenhui Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Paulina Kucharzewska
- Center of Cellular Immunotherapies, Warsaw University of Life Sciences, Warsaw, Poland
| | - Yuan Guo
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin, China
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2
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Jiang H, Ye J. The Warburg effect: The hacked mitochondrial-nuclear communication in cancer. Semin Cancer Biol 2025; 112:93-111. [PMID: 40147702 DOI: 10.1016/j.semcancer.2025.03.006] [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: 07/31/2024] [Revised: 02/23/2025] [Accepted: 03/17/2025] [Indexed: 03/29/2025]
Abstract
Mitochondrial-nuclear communication is vital for maintaining cellular homeostasis. This communication begins with mitochondria sensing environmental cues and transmitting signals to the nucleus through the retrograde cascade, involving metabolic signals such as substrates for epigenetic modifications, ATP and AMP levels, calcium flux, etc. These signals inform the nucleus about the cell's metabolic state, remodel epigenome and regulate gene expression, and modulate mitochondrial function and dynamics through the anterograde feedback cascade to control cell fate and physiology. Disruption of this communication can lead to cellular dysfunction and disease progression, particularly in cancer. The Warburg effect is the metabolic hallmark of cancer, characterized by disruption of mitochondrial respiration and increased lactate generation from glycolysis. This metabolic reprogramming rewires retrograde signaling, leading to epigenetic changes and dedifferentiation, further reprogramming mitochondrial function and promoting carcinogenesis. Understanding these processes and their link to tumorigenesis is crucial for uncovering tumorigenesis mechanisms. Therapeutic strategies targeting these disrupted pathways, including metabolic and epigenetic components, provide promising avenues for cancer treatment.
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Affiliation(s)
- Haowen Jiang
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jiangbin Ye
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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3
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Ji K, Chen G, Wang Y, Li Y, Chen J, Feng M. YEATS2: a novel cancer epigenetic reader and potential therapeutic target. Cancer Cell Int 2025; 25:162. [PMID: 40287757 PMCID: PMC12034173 DOI: 10.1186/s12935-025-03797-9] [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: 09/28/2024] [Accepted: 04/21/2025] [Indexed: 04/29/2025] Open
Abstract
YEATS2, an evolutionarily conserved reader of histone acylation marks (H3K27ac, H3K27cr, H3K27bz), functions as a central oncogenic driver in diverse cancers, including non-small cell lung cancer (NSCLC), pancreatic ductal adenocarcinoma (PDAC), and hepatocellular carcinoma (HCC). Its structurally plastic YEATS domain bridges acyl-CoA metabolism to chromatin remodeling, amplifying transcription of survival genes such as MYC, BCL2, and PD-L1. YEATS2 orchestrates malignancy-specific programs-sustaining ribosome biogenesis in NSCLC through ATAC complex recruitment, enhancing NF-κB-dependent immune evasion in PDAC, and activating PI3K/AKT-driven metabolic rewiring in HCC. Structural studies demonstrate a unique aromatic cage architecture that selectively engages diverse acylated histones. Although pyrazolopyridine-based inhibitors targeting the YEATS domain show preclinical efficacy, developing isoform-selective agents remains challenging. Clinically, YEATS2 overexpression correlates with therapy resistance and may synergize with immune checkpoint blockade. This review integrates mechanistic insights into the role of YEATS2 in epigenetic regulation, evaluates its therapeutic potential, and proposes future directions: elucidating full-length complex topologies, mapping synthetic lethal interactors, and optimizing selective inhibitors. Disrupting YEATS2-mediated epigenetic adaptation presents novel opportunities for precision cancer therapy.
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Affiliation(s)
- Kangkang Ji
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- Department of Clinical Medical Research, Binhai County People's Hospital, Clinical Medical College of Yangzhou University, Yancheng, 224500, Jiangsu, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Guoping Chen
- Department of Clinical Medical Research, Binhai County People's Hospital, Clinical Medical College of Yangzhou University, Yancheng, 224500, Jiangsu, China
| | - Yan Wang
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Yunyi Li
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Jian Chen
- Department of Head and Neck Surgery, Tongji Medical College, Hubei Cancer Hospital, Huazhong University of Science and Technology, Wuhan, Hubei, 430070, China.
| | - Mingqian Feng
- College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.
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4
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Gao YX, Guo XJ, Lin B, Huang XB, Tu RH, Lin M, Cao LL, Chen QY, Wang JB, Xie JW, Li P, Zheng CH, Yang YH, Huang CM, Lin JX. Targeting LHPP in neoadjuvant chemotherapy resistance of gastric cancer: insights from single-cell and multi-omics data on tumor immune microenvironment and stemness characteristics. Cell Death Dis 2025; 16:306. [PMID: 40240758 PMCID: PMC12003742 DOI: 10.1038/s41419-025-07614-z] [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: 12/08/2024] [Revised: 03/24/2025] [Accepted: 03/31/2025] [Indexed: 04/18/2025]
Abstract
Gastric cancer (GC) is a highly heterogeneous and complex malignancy, often characterized by tumor stemness and immune evasion mechanisms, which contribute to a poor response to neoadjuvant chemotherapy (NAC) and treatment resistance. In this study, we performed a comprehensive analysis using single-cell and multi-omics approaches on 375 GC samples from The Cancer Genome Atlas database, along with 141 clinical samples from patients who underwent NAC. We identified key gene modules associated with stemness and immune traits, and developed a novel stem cell-immune risk score. This score effectively distinguished responders from non-responders to chemotherapy, and was significantly associated with overall survival. Through multi-omics analysis, we further elucidated the role of phospholysine phosphohistidine inorganic pyrophosphatase (LHPP) in the tumor immune microenvironment. Our findings showed that high LHPP expression was closely linked to the increased infiltration of antitumor immune cells, such as CD8+ T cells, and significantly suppressed the development of stemness characteristics in GC. Additionally, single-cell sequencing data revealed that tumor epithelial cells with low LHPP expression exhibited heightened stemness and demonstrated the strongest communication with CD8+-exhausted T cells. We also observed that LHPP inhibited stemness and chemotherapy resistance in GC cells by regulating the phosphorylation of GSK-3β. In conclusion, LHPP plays a critical regulatory role in the stemness features and tumor immune microenvironment of GC, presenting a promising biomarker and potential therapeutic target for personalized treatment of GC.
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Affiliation(s)
- You-Xin Gao
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Xiao-Jing Guo
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Bin Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Xiao-Bo Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Ru-Hong Tu
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Mi Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Long-Long Cao
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Qi-Yue Chen
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Jia-Bin Wang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Jian-Wei Xie
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Ping Li
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Chao-Hui Zheng
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Ying-Hong Yang
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, China.
- Gastrointestinal Cancer Institute, Fujian Medical University, Fuzhou, 350001, China.
| | - Chang-Ming Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China.
| | - Jian-Xian Lin
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, China.
- Key Laboratory of Ministry of Education of Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China.
- Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China.
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5
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Mierke CT. Softness or Stiffness What Contributes to Cancer and Cancer Metastasis? Cells 2025; 14:584. [PMID: 40277910 PMCID: PMC12026216 DOI: 10.3390/cells14080584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2025] [Revised: 04/08/2025] [Accepted: 04/08/2025] [Indexed: 04/26/2025] Open
Abstract
Beyond the genomic and proteomic analysis of bulk and single cancer cells, a new focus of cancer research is emerging that is based on the mechanical analysis of cancer cells. Therefore, several biophysical techniques have been developed and adapted. The characterization of cancer cells, like human cancer cell lines, started with their mechanical characterization at mostly a single timepoint. A universal hypothesis has been proposed that cancer cells need to be softer to migrate and invade tissues and subsequently metastasize in targeted organs. Thus, the softness of cancer cells has been suggested to serve as a universal physical marker for the malignancy of cancer types. However, it has turned out that there exists the opposite phenomenon, namely that stiffer cancer cells are more migratory and invasive and therefore lead to more metastases. These contradictory results question the universality of the role of softness of cancer cells in the malignant progression of cancers. Another problem is that the various biophysical techniques used can affect the mechanical properties of cancer cells, making it even more difficult to compare the results of different studies. Apart from the instrumentation, the culture and measurement conditions of the cancer cells can influence the mechanical measurements. The review highlights the main advances of the mechanical characterization of cancer cells, discusses the strength and weaknesses of the approaches, and questions whether the passive mechanical characterization of cancer cells is still state-of-the art. Besides the cell models, conditions and biophysical setups, the role of the microenvironment on the mechanical characteristics of cancer cells is presented and debated. Finally, combinatorial approaches to determine the malignant potential of tumors, such as the involvement of the ECM, the cells in a homogeneous or heterogeneous association, or biological multi-omics analyses, together with the dynamic-mechanical analysis of cancer cells, are highlighted as new frontiers of research.
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Affiliation(s)
- Claudia Tanja Mierke
- Faculty of Physics and Earth System Sciences, Peter Debye Institute of Soft Matter Physics, Biological Physics Division, Leipzig University, 04103 Leipzig, Germany
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6
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Petrova B, Guler AT. Recent Developments in Single-Cell Metabolomics by Mass Spectrometry─A Perspective. J Proteome Res 2025; 24:1493-1518. [PMID: 39437423 PMCID: PMC11976873 DOI: 10.1021/acs.jproteome.4c00646] [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: 07/28/2024] [Revised: 10/07/2024] [Accepted: 10/15/2024] [Indexed: 10/25/2024]
Abstract
Recent advancements in single-cell (sc) resolution analyses, particularly in sc transcriptomics and sc proteomics, have revolutionized our ability to probe and understand cellular heterogeneity. The study of metabolism through small molecules, metabolomics, provides an additional level of information otherwise unattainable by transcriptomics or proteomics by shedding light on the metabolic pathways that translate gene expression into functional outcomes. Metabolic heterogeneity, critical in health and disease, impacts developmental outcomes, disease progression, and treatment responses. However, dedicated approaches probing the sc metabolome have not reached the maturity of other sc omics technologies. Over the past decade, innovations in sc metabolomics have addressed some of the practical limitations, including cell isolation, signal sensitivity, and throughput. To fully exploit their potential in biological research, however, remaining challenges must be thoroughly addressed. Additionally, integrating sc metabolomics with orthogonal sc techniques will be required to validate relevant results and gain systems-level understanding. This perspective offers a broad-stroke overview of recent mass spectrometry (MS)-based sc metabolomics advancements, focusing on ongoing challenges from a biologist's viewpoint, aimed at addressing pertinent and innovative biological questions. Additionally, we emphasize the use of orthogonal approaches and showcase biological systems that these sophisticated methodologies are apt to explore.
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Affiliation(s)
- Boryana Petrova
- Medical
University of Vienna, Vienna 1090, Austria
- Department
of Pathology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
| | - Arzu Tugce Guler
- Department
of Pathology, Boston Children’s Hospital, Boston, Massachusetts 02115, United States
- Institute
for Experiential AI, Northeastern University, Boston, Massachusetts 02115, United States
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7
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Taylor H, Spruill L, Jensen-Smith H, Rujchanarong D, Hulahan T, Ivey A, Siougiannis A, Bethard JR, Ball LE, Sandusky GE, Hollingsworth MA, Barth JL, Mehta AS, Drake RR, Marks JR, Nakshatri H, Ford M, Angel PM. Spatial localization of collagen hydroxylated proline site variation as an ancestral trait in the breast cancer microenvironment. Matrix Biol 2025; 136:71-86. [PMID: 39863086 DOI: 10.1016/j.matbio.2025.01.006] [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: 06/16/2024] [Revised: 12/27/2024] [Accepted: 01/22/2025] [Indexed: 01/27/2025]
Abstract
Collagen stroma interactions within the extracellular microenvironment of breast tissue play a significant role in breast cancer, including risk, progression, and outcomes. Hydroxylation of proline (HYP) is a common post-translational modification directly linked to breast cancer survival and progression. Changes in HYP status lead to alterations in epithelial cell signaling, extracellular matrix remodeling, and immune cell recruitment. In the present study, we test the hypothesis that the breast cancer microenvironment presents unique PTMs of collagen, which form bioactive domains at these sites that are associated with spatial histopathological characteristics and influence breast epithelial cell signaling. Mass spectrometry imaging proteomics targeting collagens were paired with comprehensive proteomic methods to identify novel breast cancer-related collagen domains based on spatial localization and regulation in 260 breast tissue samples. As ancestry plays a significant role in breast cancer outcomes, these methods were performed on ancestry diverse breast cancer tissues. Lumpectomies from the Cancer Genome Atlas (TCGA; n=10) reported increased levels of prolyl 4-hydroxylase subunit alpha-3 (P4HA3) accompanied by spatial regulation of fibrillar collagen protein sequences. A concise set of triple negative breast cancer lumpectomies (n=10) showed spatial regulation of specific domain sites from collagen alpha-1(I) chain. Tissue microarrays identified proteomic alterations around post-translationally modified collagen sites in healthy breast (n=81) and patient matched normal adjacent (NAT; n=76) and invasive ductal carcinoma (n=83). A collagen alpha-1(I) chain domain encompassing amino acids 506-514 with site-specific proline hydroxylation reported significant alteration between patient matched normal adjacent tissue and invasive breast cancer. Functional testing of domain 506-514 on breast cancer epithelial cells showed proliferation, chemotaxis and cell signaling response dependent on site localization of proline hydroxylation within domain 506-514 variants. These findings support site localized collagen HYP forms novel bioactive domains that are spatially distributed within the breast cancer microenvironment and may play a role in ancestral traits of breast cancer.
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Affiliation(s)
- Harrison Taylor
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States
| | - Laura Spruill
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Heather Jensen-Smith
- Eppley Institute for Cancer Research & Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States
| | - Denys Rujchanarong
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States
| | - Taylor Hulahan
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States
| | - Ashlyn Ivey
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States
| | - Alex Siougiannis
- College of Medicine, Medical University of South Carolina, Charleston, SC, United States
| | - Jennifer R Bethard
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States
| | - Lauren E Ball
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States
| | - George E Sandusky
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States; Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, United States
| | - M A Hollingsworth
- Eppley Institute for Cancer Research & Allied Diseases, University of Nebraska Medical Center, Omaha, NE, United States
| | - Jeremy L Barth
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, United States
| | - Anand S Mehta
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States
| | - Richard R Drake
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States
| | - Jeffrey R Marks
- Department of Surgery, Duke Cancer Institute, Duke University, Durham, NC, United States
| | - Harikrishna Nakshatri
- Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, United States; Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, United States
| | - Marvella Ford
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, United States
| | - Peggi M Angel
- Department of Pharmacology & Immunology, Proteomics Center, Medical University of South Carolina, Charleston, SC, United States.
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8
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Kang T, Wang Y, Jiang Y, Chen S, Lin N, Guo M, Zhu H, Tang D, Ding X, He M. The SGK3/GSK3β/β-catenin signaling promotes breast cancer stemness and confers resistance to alpelisib therapy. Int J Biol Sci 2025; 21:2462-2475. [PMID: 40303291 PMCID: PMC12035905 DOI: 10.7150/ijbs.104850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Accepted: 03/09/2025] [Indexed: 05/02/2025] Open
Abstract
Drug resistance is the leading cause of death in patients with advanced tumors. Alpelisib, a selective PIK3CA inhibitor, has been recently approved for treating advanced breast cancer. However, drug resistance is inevitable, and the mechanisms behind alpelisib-associated resistance remain elusive. To address this problem, we established an alpelisib-resistant breast cancer cell model and confirmed that the resistant cells exhibited enhanced abilities in colony formation, migration, anti-apoptosis, spheroidization, tumor formation and metastasis. Further analysis revealed that SGK3 was significantly upregulated in alpelisib-resistant cells, which was strongly associated with tumor stemness. Additionally, we observed that SGK3 promoted tumor cell stemness by activating GSK3β/β-catenin signaling pathway, leading to the resistance to alpelisib in breast cancer. Finally, we demonstrated that SGK3 inhibitor could restore the sensitivity of resistant cells to alpelisib. Collectively, these findings suggest that SGK3 could be a novel therapeutic target for breast cancer patients who developed resistance to alpelisib.
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Affiliation(s)
- Tingting Kang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yuanfang Wang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Yaxin Jiang
- Department of General Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Shunjie Chen
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Na Lin
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Minyan Guo
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Haotu Zhu
- Department of Oncology, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Di Tang
- Department of General Surgery, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
| | - Xiaofan Ding
- Faculty of Health Sciences, University of Macau, Macau SAR, China
- MOE Frontiers Science Center for Precision Oncology, University of Macau, Macau SAR, China
| | - Mian He
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, China
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9
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Shen D, Min J, Chen J, Yan D, Han J, Liu H, Yu X, Nie Z, Li B. Study on the Material Basis and Mechanisms of Achyrocline satureioides in the Treatment of Nonsmall Cell Lung Cancer Based on Network Pharmacology and Spatial Metabolomics. Anal Chem 2025; 97:5688-5697. [PMID: 40036484 DOI: 10.1021/acs.analchem.4c06682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2025]
Abstract
Achyrocline satureioides have good therapeutic effects on nonsmall cell lung cancer (NSCLC). Nevertheless, it is still challenging to elucidate the active ingredients and mechanism of action due to their complex chemical composition. To address this, we innovatively combined network pharmacology with spatial metabolomics to comprehensively investigate the active components and the action mechanism in the present study. First, metabolomics of cells treated with the methanol extract of A. satureioides (ASM) utilizing high-resolution ultrahigh-performance liquid chromatography tandem mass spectrometry (HR-UHPLC-MS/MS) revealed 32 changed metabolites and 7 enriched metabolic pathways, confirming the anti-NSCLC effect of ASM and its impact on endogenous metabolites at the cellular level. Then, 69 chemical components in the ASM were identified using HR-UHPLC-MS/MS, followed by the screening of 6 core components and 10 core targets of anti-NSCLC with the help of network pharmacology and molecular docking. Lastly, quercetin, the most abundant compound among the six core active ingredients, was chosen for evaluating its anti-NSCLC effect and the potential mechanism using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). 51 altered endogenous metabolites were screened, and pathway enrichment analysis results were consistent with cell metabolomics, corroborating our network pharmacology predictions. In addition, we also observed the accumulation of three metabolites of quercetin in the tumor tissues. Network pharmacology combined with MSI elucidated the metabolic mechanisms by which A. satureioides treats NSCLC, offering new insights into herbal cancer therapies.
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Affiliation(s)
- Duo Shen
- Academician Workstation, Jiangxi University of Chinese Medicine, Nanchang 330004, Jiangxi, China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Jianxin Min
- Academician Workstation, Jiangxi University of Chinese Medicine, Nanchang 330004, Jiangxi, China
| | - Jie Chen
- Academician Workstation, Jiangxi University of Chinese Medicine, Nanchang 330004, Jiangxi, China
| | - Dongmei Yan
- Academician Workstation, Jiangxi University of Chinese Medicine, Nanchang 330004, Jiangxi, China
| | - Jing Han
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Huihui Liu
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xi Yu
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Zongxiu Nie
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Bin Li
- Academician Workstation, Jiangxi University of Chinese Medicine, Nanchang 330004, Jiangxi, China
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10
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Goleij P, Heidari MM, Tabari MAK, Hadipour M, Rezaee A, Javan A, Sanaye PM, Larsen DS, Daglia M, Khan H. Polycomb repressive complex 2 (PRC2) pathway's role in cancer cell plasticity and drug resistance. Funct Integr Genomics 2025; 25:53. [PMID: 40048009 DOI: 10.1007/s10142-025-01563-8] [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: 10/29/2024] [Revised: 02/17/2025] [Accepted: 02/23/2025] [Indexed: 05/13/2025]
Abstract
Polycomb Repressive Complex 2 (PRC2) is a central regulator of gene expression via the trimethylation of histone H3 on lysine 27. This epigenetic modification plays a crucial role in maintaining cell identity and controlling differentiation, while its dysregulation is closely linked to cancer progression. PRC2 silences tumor suppressor genes, promoting cell proliferation, metastasis, epithelial-mesenchymal transition, and cancer stem cell plasticity. Enhancement of zeste homolog 2 (EZH2) overexpression or gain-of-function mutations have been observed in several cancers, including lymphoma, breast, and prostate cancers, driving aggressive tumor behavior and drug resistance. In addition to EZH2, other PRC2 components, such as embryonic ectoderm development (EED) and suppressor of zeste 12, are essential for complex stability and function. EED, in particular, enhances EZH2 activity and has emerged as a therapeutic target. Inhibitors like MAK683 and EED226 disrupt EED's ability to maintain PRC2 activity, thereby reducing H3K27me3 levels and reactivating tumor suppressor genes. Valemetostat, a dual inhibitor of both EZH2 and EED, has shown promising results in aggressive cancers like diffuse large B-cell lymphoma and small-cell lung cancer, underlining the therapeutic potential of targeting multiple PRC2 components. PRC2's role extends beyond gene repression, as it contributes to metabolic reprogramming in tumors, regulating glycolysis and lipid synthesis to fuel cancer growth. Furthermore, PRC2 is implicated in chemoresistance, particularly by modulating DNA damage response and immune evasion. Tazemetostat, a selective EZH2 inhibitor, has demonstrated significant clinical efficacy in EZH2-mutant cancers, such as non-Hodgkin lymphomas and epithelioid sarcoma. However, the compensatory function of enhancer of zeste homolog 1 (EZH1) in some cancers requires dual inhibition strategies, as seen with agents like UNC1999 and Tulmimetostat, which target both EZH1 and EZH2. Given PRC2's multifaceted role in cancer biology, its inhibition represents a promising avenue for therapeutic intervention. The continued development of PRC2 inhibitors and exploration of their use in combination with standard chemotherapy or immunotherapy has great potential for improving patient outcomes in cancers driven by PRC2 dysregulation.
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Affiliation(s)
- Pouya Goleij
- USERN Office, Kermanshah University of Medical Sciences, Kermanshah, 6715847141, Iran.
- Immunology Board for Transplantation and Cell-Based Therapeutics (Immunotact), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Mohammad Mahdi Heidari
- Department of Pediatrics, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Khazeei Tabari
- Student Research Committee, School of Medicine, Mazandaran University of Medical Sciences, Mazandaran, 4815733971, Iran
| | - Mahboube Hadipour
- Department of Biochemistry, School of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7919693116, Iran
| | - Aryan Rezaee
- School of Medicine, Iran University of Medical Sciences, Tehran, 1449614535, Iran
| | - Alireza Javan
- School of Medicine, Iran University of Medical Sciences, Tehran, 1449614535, Iran
| | - Pantea Majma Sanaye
- School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, 4513956184, Iran
| | - Danaé S Larsen
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland, 1010, New Zealand
| | - Maria Daglia
- Department of Pharmacy, University of Naples "Federico II", Via D. Montesano 49, 80131, Naples, Italy
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang, 212013, China
| | - Haroon Khan
- Department of Pharmacy, Faculty of Chemical and Life Sciences, Abdul Wali Khan University Mardan, Mardan, 23200, Pakistan.
- Department of Pharmacy, Korea University, Sejong, 20019, South Korea.
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11
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Tahghighi A, Seyedhashemi E, Mohammadi J, Moradi A, Esmaeili A, Pornour M, Jafarifar K, Ganji SM. Epigenetic marvels: exploring the landscape of colorectal cancer treatment through cutting-edge epigenetic-based drug strategies. Clin Epigenetics 2025; 17:34. [PMID: 39987205 PMCID: PMC11847397 DOI: 10.1186/s13148-025-01844-w] [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: 09/01/2024] [Accepted: 02/14/2025] [Indexed: 02/24/2025] Open
Abstract
Epigenetics is currently considered the investigation of inheritable changes in gene expression that do not rely on DNA sequence alteration. Significant epigenetic procedures are involved, such as DNA methylations, histone modifications, and non-coding RNA actions. It is confirmed through several investigations that epigenetic changes are associated with the formation, development, and metastasis of various cancers, such as colorectal cancer (CRC). The difference between epigenetic changes and genetic mutations is that the former could be reversed or prevented; therefore, cancer treatment and prevention could be achieved by restoring abnormal epigenetic events within the neoplastic cells. These treatments, consequently, cause the anti-tumour effects augmentation, drug resistance reduction, and host immune response stimulation. In this article, we begin our survey by exploring basic epigenetic mechanisms to understand epigenetic tools and strategies for treating colorectal cancer in monotherapy and combination with chemotherapy or immunotherapy.
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Affiliation(s)
- Azar Tahghighi
- Medicinal Chemistry Laboratory, Clinical Research Department, Pasteur Institute of Iran, Tehran, Iran
| | - Effat Seyedhashemi
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran
| | - Javad Mohammadi
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
| | - Arash Moradi
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran
| | - Aria Esmaeili
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran
| | - Majid Pornour
- Department of Biochemistry and Molecular Biology, University of Maryland, Baltimore, MD, USA
| | - Kimia Jafarifar
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Shahla Mohammad Ganji
- Department of Molecular Medicine, Department of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-E Pajoohesh, Km 15, P.O. Box 14965/161, Tehran, Iran.
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12
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Cremin K, Meloni GN, Soyer OS, Unwin PR. Single-Cell Analysis with Spatiotemporal Control of Local pH. ACS MEASUREMENT SCIENCE AU 2025; 5:120-129. [PMID: 39991028 PMCID: PMC11843512 DOI: 10.1021/acsmeasuresciau.4c00079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 12/16/2024] [Accepted: 12/16/2024] [Indexed: 02/25/2025]
Abstract
This work presents an experimental platform combining scanning ion conductance microscopy (SICM) with confocal laser scanning microscopy (CLSM), using intra- and extracellular pH indicator dyes to study the impact of acid delivery on individual HeLa cells within a population. The proton gradient generated by the SICM delivery is highly confined by the action of the media buffer, making the challenge local. Temporal and spatial aspects of the delivery are modeled by simulations, allowing for pH gradients across individual cells, even within a group, to be calculated. We find a strong dependency between the intracellular pH and the extracellular pH gradient imposed by local acid delivery. Postdelivery intracellular pH recovery depends on the extent of the acid challenge, with cells exposed to lower pH not returning to basal intracellular pH values after the extracellular pH recovers. This is a unique method for concentration-gradient challenge studies of cell populations that will have broad applications in cell biology. SICM can be used to deliver different chemicals and enables a wide range of local conditions to be applied across a cell population, for which the effects can be investigated at the single-cell level.
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Affiliation(s)
- Kelsey Cremin
- Bio-Electrical
Engineering Innovation Hub, University of
Warwick, Coventry CV4 7AL, United
Kingdom
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Molecular
Analytical Science Centre for Doctoral Training, University of Warwick, Coventry CV4 7AL, United
Kingdom
- School of
Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Gabriel N. Meloni
- Bio-Electrical
Engineering Innovation Hub, University of
Warwick, Coventry CV4 7AL, United
Kingdom
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- Institute
of Chemistry, Department of Chemistry, University
of São Paulo, São
Paulo, São Paulo 05508-000, Brazil
| | - Orkun S. Soyer
- Bio-Electrical
Engineering Innovation Hub, University of
Warwick, Coventry CV4 7AL, United
Kingdom
- School of
Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Patrick R. Unwin
- Bio-Electrical
Engineering Innovation Hub, University of
Warwick, Coventry CV4 7AL, United
Kingdom
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
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13
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Dai Z, Lin B, Qin M, Lin Y, Wang L, Liao K, Xie G, Wang F, Zhang J. METTL3-mediated m6A modification of SLC7A11 enhances nasopharyngeal carcinoma radioresistance by inhibiting ferroptosis. Int J Biol Sci 2025; 21:1837-1851. [PMID: 39990661 PMCID: PMC11844296 DOI: 10.7150/ijbs.100518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2024] [Accepted: 01/14/2025] [Indexed: 02/25/2025] Open
Abstract
Radiotherapy is the primary treatment for nasopharyngeal carcinoma (NPC); nonetheless, radioresistance remains the leading cause of localized recurrence. Our study demonstrates a significant increase in the N6-methyladenosine (m6A) methylase METTL3 in NPC and other tumors. Mechanistically, METTL3 acts as an m6A methylase, enhancing the m6A modification of the solute carrier family 7 member 11 (SLC7A11) transcript, which increases its stability and expression, thereby inhibiting radiation-induced ferroptosis and ultimately inducing radioresistance in NPC. Furthermore, silencing SLC7A11 or employing the ferroptosis inducer Erastin negated the promoting effect of METTL3 on NPC cell radioresistance. These findings suggest that METTL3 could be a novel therapeutic target for overcoming radiotherapy resistance in NPC.
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Affiliation(s)
- Zili Dai
- Department of Radiation Oncology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou 510095, China
| | - Baisheng Lin
- Department of Radiation Oncology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou 510095, China
| | - Maohua Qin
- Department of Radiation Oncology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou 510095, China
| | - Yunen Lin
- Department of pathology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou, China
| | - Li Wang
- Department of Radiation Oncology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou 510095, China
| | - Kai Liao
- Department of Radiation Oncology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou 510095, China
| | - Guofeng Xie
- Department of Radiation Oncology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou 510095, China
| | - Feixiang Wang
- Department of Thoracic Surgery, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Radiation Oncology, Guangzhou Institute of Cancer Research, the Affiliated Cancer Hospital, Guangzhou Medical University, Guangzhou 510095, China
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14
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Lombardi O, Li R, Jabbar F, Evans H, Halim S, Lima JDCC, Browning L, Byrne HM, Choudhry H, Ratcliffe PJ, Mole DR. Conserved patterns of transcriptional dysregulation, heterogeneity, and cell states in clear cell kidney cancer. Cell Rep 2025; 44:115169. [PMID: 39792555 DOI: 10.1016/j.celrep.2024.115169] [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: 07/26/2024] [Revised: 11/13/2024] [Accepted: 12/17/2024] [Indexed: 01/12/2025] Open
Abstract
Clear cell kidney cancers are characterized both by conserved oncogenic driver events and by marked intratumor genetic and phenotypic heterogeneity, which help drive tumor progression, metastasis, and resistance to therapy. How these are reflected in transcriptional programs within the cancer and stromal cell components remains an important question with the potential to drive novel therapeutic approaches to treating cancer. To better understand these programs, we perform single-cell transcriptomics on 75 multi-regional biopsies from kidney tumors and normal kidney. We identify conserved patterns of transcriptional dysregulation and their upstream regulators within the tumor and associated vasculature. We describe recurrent subclonal transcriptional consequences of Chr14q loss linked to metastatic potential. We identify prognostically significant conserved patterns of intratumor transcriptional heterogeneity. These reflect co-existing cell states found in both cancer cells and normal kidney cells, indicating that rather than arising from genetic heterogeneity they are a consequence of lineage plasticity.
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Affiliation(s)
- Olivia Lombardi
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Ran Li
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Faiz Jabbar
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Hannah Evans
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Silvia Halim
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK
| | - Joanna D C C Lima
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK; Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Headington, Oxford OX3 7DQ, UK
| | - Lisa Browning
- Department of Cellular Pathology, Oxford University Hospitals NHS Foundation Trust, Headington, Oxford OX3 9DU, UK
| | - Helen M Byrne
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford OX2 6GG, UK; Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Headington, Oxford OX3 7DQ, UK
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, Center of Innovation in Personalized Medicine, King Fahd Center for Medical Research, King Abdulaziz University, Jeddah 3270, Saudi Arabia
| | - Peter J Ratcliffe
- Ludwig Institute for Cancer Research, University of Oxford, Old Road Campus, Headington, Oxford OX3 7DQ, UK; The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - David R Mole
- NDM Research Building, University of Oxford, Old Road Campus, Headington, Oxford OX3 7FZ, UK.
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15
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Gao Y, Shaw VR, Amos CI. Alternative polyadenylation shapes the molecular and clinical features of lung adenocarcinoma. Hum Mol Genet 2025; 34:1-10. [PMID: 39487796 DOI: 10.1093/hmg/ddae150] [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: 06/14/2024] [Revised: 08/14/2024] [Indexed: 11/04/2024] Open
Abstract
Alternative polyadenylation (APA) is a major mechanism of post-transcriptional regulation that affects mRNA stability, localization and translation efficiency. Previous pan-cancer studies have revealed that APA is frequently disrupted in cancer and is associated with patient outcomes. Yet, little is known about cancer type-specific APA alterations. Here, we integrated RNA-sequencing data from a Korean cohort (GEO: GSE40419) and The Cancer Genome Atlas (TCGA) to comprehensively analyze APA alterations in lung adenocarcinomas (LUADs). Comparing expression levels of core genes involved in polyadenylation, we find that overall, the set of 28 of 31 genes are upregulated, with CSTF2 particularly upregulated. We observed broad and recurrent APA changes in LUAD growth-promoting genes. In addition, we find enrichment of APA events in genes associated with known LUAD pathways and an increased heterogeneity in polyadenylation (polyA) site usage of proliferation-associated genes. Upon further investigation, we report smoking-specific APA changes are also highly relevant to LUAD development. Overall, our in-depth analysis reveals APA as an important driver for the molecular and clinical features of lung adenocarcinoma.
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Affiliation(s)
- Yipeng Gao
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Vikram R Shaw
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, United States
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16
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Womersley HJ, Muliaditan D, DasGupta R, Cheow LF. Single-nucleus CUT&RUN elucidates the function of intrinsic and genomics-driven epigenetic heterogeneity in head and neck cancer progression. Genome Res 2025; 35:162-177. [PMID: 39622638 PMCID: PMC11789629 DOI: 10.1101/gr.279105.124] [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: 02/14/2024] [Accepted: 11/25/2024] [Indexed: 01/11/2025]
Abstract
Interrogating regulatory epigenetic alterations during tumor progression at the resolution of single cells has remained an understudied area of research. Here we developed a highly sensitive single-nucleus CUT&RUN (snCUT&RUN) assay to profile histone modifications in isogenic primary, metastatic, and cisplatin-resistant head and neck squamous cell carcinoma (HNSCC) patient-derived tumor cell lines. We find that the epigenome can be involved in diverse modes to contribute toward HNSCC progression. First, we demonstrate that gene expression changes during HNSCC progression can be comodulated by alterations in both copy number and chromatin activity, driving epigenetic rewiring of cell states. Furthermore, intratumor epigenetic heterogeneity (ITeH) may predispose subclonal populations within the primary tumor to adapt to selective pressures and foster the acquisition of malignant characteristics. In conclusion, snCUT&RUN serves as a valuable addition to the existing toolkit of single-cell epigenomic assays and can be used to dissect the functionality of the epigenome during cancer progression.
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Affiliation(s)
- Howard J Womersley
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore
| | - Daniel Muliaditan
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Lih Feng Cheow
- Institute for Health Innovation and Technology, National University of Singapore, Singapore 117599, Singapore;
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore
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17
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Hajipour Keyvani A, Mohammadnejad P, Pazoki-Toroudi H, Perez Gilabert I, Chu T, Manshian BB, Soenen SJ, Sohrabi B. Advancements in Cancer Treatment: Harnessing the Synergistic Potential of Graphene-Based Nanomaterials in Combination Therapy. ACS APPLIED MATERIALS & INTERFACES 2025; 17:2756-2790. [PMID: 39745785 DOI: 10.1021/acsami.4c15536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2025]
Abstract
Combination therapy, which involves using multiple therapeutic modalities simultaneously or sequentially, has become a cornerstone of modern cancer treatment. Graphene-based nanomaterials (GBNs) have emerged as versatile platforms for drug delivery, gene therapy, and photothermal therapy. These materials enable a synergistic approach, improving the efficacy of treatments while reducing side effects. This review explores the roles of graphene, graphene oxide (GO), and graphene quantum dots (GQDs) in combination therapies and highlights their potential to enhance immunotherapy and targeted cancer therapies. The large surface area and high drug-loading capacity of graphene facilitate the codelivery of multiple therapeutic agents, promoting targeted and sustained release. GQDs, with their unique optical properties, offer real-time imaging capabilities, adding another layer of precision to treatment. However, challenges such as biocompatibility, long-term toxicity, and scalability need to be addressed to ensure clinical safety. Preclinical studies show promising results for GBNs, suggesting their potential to revolutionize cancer treatment through innovative combination therapies.
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Affiliation(s)
- Armin Hajipour Keyvani
- Surface Chemistry Research Laboratory, Faculty of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Parizad Mohammadnejad
- Surface Chemistry Research Laboratory, Faculty of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
| | - Hamidreza Pazoki-Toroudi
- Physiology Research Center, Faculty of Medicine, Iran University of Medical Sciences, Tehran 14496-14535, Iran
| | - Irati Perez Gilabert
- NanoHealth and Optical Imaging Group, Department of Imaging and Pathology, KU Leuven, Rellis Research Group, Gaston Geenslaan 3 - Box 901, 3001 Leuven, Belgium
| | - Tianjiao Chu
- NanoHealth and Optical Imaging Group, Department of Imaging and Pathology, KU Leuven, Rellis Research Group, Gaston Geenslaan 3 - Box 901, 3001 Leuven, Belgium
| | - Bella B Manshian
- Translational Cell and Tissue Research Unit, Department of Imaging and Pathology, KU Leuven, RK-Herestraat 49 - Box 505,3000 Leuven, Belgium
| | - Stefaan J Soenen
- NanoHealth and Optical Imaging Group, Department of Imaging and Pathology, KU Leuven, Rellis Research Group, Gaston Geenslaan 3 - Box 901, 3001 Leuven, Belgium
- Leuven Cancer Institute, Faculty of Medicine, KU Leuven, Rellis Research Group, Gaston Geenslaan 3 - Box 901, 3001 Leuven, Belgium
| | - Beheshteh Sohrabi
- Surface Chemistry Research Laboratory, Faculty of Chemistry, Iran University of Science and Technology, Tehran 16846-13114, Iran
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18
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Bhat AA, Altamimi ASA, Goyal A, Goyal K, Kaur I, Kumar S, Sharma N, Kumar MR, Ali H, Thapa R, Negi P, Singh SK, Gupta G. The role of CD95 in modulating CAR T-cell therapy: Challenges and therapeutic opportunities in oncology. Int Immunopharmacol 2025; 144:113675. [PMID: 39608172 DOI: 10.1016/j.intimp.2024.113675] [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: 09/26/2024] [Revised: 11/07/2024] [Accepted: 11/17/2024] [Indexed: 11/30/2024]
Abstract
CAR T cell therapy has revolutionized how we deliver cancer treatment, most notably for hematologic cancers, by compelling T cells to recognize and kill tumor cells. Nevertheless, current obstacles to utilizing this therapy in solid tumors and overcoming cancer resistance include radicalization. This review discusses how CD95 modulation can boost CAR T cell efficacy. Traditionally, CD95 was known to execute apoptosis induction, but it plays a dual role in induced cell death or in supporting cancer cell survival. Recent data have demonstrated that cancer cells escape CD95-mediated apoptosis via the downregulation of CD95, caspase 8 mutation, or the expression of the inhibition protein cFLIP. Additionally, the immunosuppressive tumor microenvironment, containing CD95L expressing immune cells, explains CAR T cell therapy resistance. Furthermore, we characterize the therapeutic potential of CD95 targeted approaches, including CD95L inhibition (APG101) and alterations in CAR T cell manufacturing (tyrosine kinase inhibitors to mitigate fratricide). In this review, we highlight the importance of multi-path way strategies combining CD95 modulation with CAR T cell engineering to overcome resistance, specifically to target tumor cells better and sustain CAR T cell persistence to enhance treatment efficacy in solid tumors.
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Affiliation(s)
- Asif Ahmad Bhat
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | | | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| | - Kavita Goyal
- Department of Biotechnology, Graphic Era (Deemed to be University), Clement Town, Dehradun 248002, India
| | - Irwanjot Kaur
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Sachin Kumar
- NIMS Institute of Pharmacy, NIMS University Rajasthan, Jaipur, India
| | - Naveen Sharma
- Chandigarh Pharmacy College, Chandigarh Group of College, Jhanjeri, Mohali 140307, Punjab, India
| | - M Ravi Kumar
- Department of Chemistry, Raghu Engineering College, Visakhapatnam, Andhra Pradesh 531162, India
| | - Haider Ali
- Centre for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India
| | - Riya Thapa
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Poonam Negi
- School of Pharmaceutical Sciences, Shoolini University of Biotechnology and Management Sciences, Solan, HP 173212, India
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India; Faculty of Health, Australian Research Centre in Complementary and Integrative Medicine, University of Technology Sydney, Ultimo, Australia; School of Medical and Life Sciences, Sunway University, 47500, Sunway City, Malaysia
| | - Gaurav Gupta
- Centre for Research Impact & Outcome, Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab 140401, India; Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates.
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19
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Narain R, Muncie-Vasic JM, Weaver VM. Forcing the code: tension modulates signaling to drive morphogenesis and malignancy. Genes Dev 2025; 39:163-181. [PMID: 39638568 PMCID: PMC11789492 DOI: 10.1101/gad.352110.124] [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] [Indexed: 12/07/2024]
Abstract
Development and disease are regulated by the interplay between genetics and the signaling pathways stimulated by morphogens, growth factors, and cytokines. Experimental data highlight the importance of mechanical force in regulating embryonic development, tissue morphogenesis, and malignancy. Force not only sculpts tissue movements to drive embryogenesis and morphogenesis but also modifies the context of biochemical signaling and gene expression to regulate cell and tissue fate. Not surprisingly, experiments have demonstrated that perturbations in cell tension drive malignancy and metastasis by altering biochemical signaling and gene expression through modifications in cytoskeletal tension, transmembrane receptor structure and function, and organelle phenotype that enhance cell growth and survival, alter metabolism, and foster cell migration and invasion. At the tissue level, tumor-associated forces disrupt cell-cell adhesions to perturb tissue organization, compromise vascular integrity to induce hypoxia, and interfere with antitumor immunity to foster metastasis and treatment resistance. Exciting new approaches now exist with which to clarify the relationship between mechanotransduction, biochemical signaling, and gene expression in development and disease. Indeed, gaining insight into these interactions is essential to unravel molecular mechanisms that regulate development and clarify the molecular basis of cancer.
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Affiliation(s)
- Radhika Narain
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, California 94143, USA
- Graduate Program in Bioengineering, University of California, San Francisco and University of California, Berkeley, Berkeley, California 94720, USA
| | | | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, California 94143, USA;
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, USA
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, California 94143, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, San Francisco, California 94143
- UCSF Helen Diller Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California 94143, USA
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20
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Lica JJ, Jakóbkiewicz-Banecka J, Hellmann A. In Vitro models of leukemia development: the role of very small leukemic stem-like cells in the cellular transformation cascade. Front Cell Dev Biol 2025; 12:1463807. [PMID: 39830209 PMCID: PMC11740207 DOI: 10.3389/fcell.2024.1463807] [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: 07/15/2024] [Accepted: 11/28/2024] [Indexed: 01/22/2025] Open
Abstract
Recent experimental findings indicate that cancer stem cells originate from transformed very small embryonic-like stem cells. This finding represents an essential advancement in uncovering the processes that drive the onset and progression of cancer. In continuously growing cell lines, for the first time, our team's follow-up research on leukemia, lung cancer, and healthy embryonic kidney cells revealed stages that resembles very small precursor stem cells. This review explores the origin of leukemic stem-like cells from very small leukemic stem-like cells establish from transformed very small embryonic-like stem cells. We explore theoretical model of acute myeloid leukemia initiation and progresses through various stages, as well basing the HL60 cell line, present its hierarchical stage development in vitro, highlighting the role of these very small precursor primitive stages. We also discuss the potential implications of further research into these unique cellular stages for advancing leukemia and cancer treatment and prevention.
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Affiliation(s)
- Jan Jakub Lica
- Department Medical Biology and Genetics, Faculty of Biology, University of Gdansk, Gdansk, Poland
- Department Health Science; Powiśle University, Gdańsk, Poland
| | | | - Andrzej Hellmann
- Department of Hematology and Transplantology, Faculty of Medicine, Medical University of Gdansk, Gdańsk, Poland
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21
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Wu X, Ma L, Zhang Y, Liu S, Cheng L, You C, Dong Z. Application progress of nanomaterials in the treatment of prostate cancer. ANNALES PHARMACEUTIQUES FRANÇAISES 2025; 83:1-12. [PMID: 39187009 DOI: 10.1016/j.pharma.2024.08.009] [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: 07/12/2024] [Revised: 08/21/2024] [Accepted: 08/21/2024] [Indexed: 08/28/2024]
Abstract
Prostate cancer is one of the most common malignant tumors in men, which seriously threatens the survival and quality of life of patients. At present, there are serious limitations in the treatment of prostate cancer, such as drug tolerance, drug resistance and easy recurrence. Sonodynamic therapy and chemodynamic therapy are two emerging tumor treatment methods, which activate specific drugs or sonosensitizers through sound waves or chemicals to produce reactive oxygen species and kill tumor cells. Nanomaterials are a kind of nanoscale materials with many excellent physical properties such as high targeting, drug release regulation and therapeutic monitoring. Sonodynamic therapy and chemodynamic therapy combined with the application of nanomaterials can improve the therapeutic effect of prostate cancer, reduce side effects and enhance tumor immune response. This article reviews the application progress of nanomaterials in the treatment of prostate cancer, especially the mechanism, advantages and challenges of nanomaterials in sonodynamic therapy and chemodynamic therapy, which provides new ideas and prospects for research in this field.
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Affiliation(s)
- Xuewu Wu
- The Second Hospital & Clinical Medical School, Lanzhou University, Gansu 730030, China
| | - Longtu Ma
- The Second Hospital & Clinical Medical School, Lanzhou University, Gansu 730030, China
| | - Yang Zhang
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Shandong, China
| | - Shuai Liu
- The Second Hospital & Clinical Medical School, Lanzhou University, Gansu 730030, China
| | - Long Cheng
- The Second Hospital & Clinical Medical School, Lanzhou University, Gansu 730030, China
| | - Chengyu You
- The Second Hospital & Clinical Medical School, Lanzhou University, Gansu 730030, China
| | - Zhilong Dong
- The Second Hospital & Clinical Medical School, Lanzhou University, Gansu 730030, China.
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22
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Singh V, Shirbhate E, Kore R, Vishwakarma S, Parveen S, Veerasamy R, Tiwari AK, Rajak H. Microbial Metabolites-induced Epigenetic Modifications for Inhibition of Colorectal Cancer: Current Status and Future Perspectives. Mini Rev Med Chem 2025; 25:76-93. [PMID: 38982701 DOI: 10.2174/0113895575320344240625080555] [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: 04/17/2024] [Revised: 06/05/2024] [Accepted: 06/05/2024] [Indexed: 07/11/2024]
Abstract
Globally, one of the most prevalent cancers is colorectal cancer (CRC). Chemotherapy and surgery are two common conventional CRC therapies that are frequently ineffective and have serious adverse effects. Thus, there is a need for complementary and different therapeutic approaches. The use of microbial metabolites to trigger epigenetic alterations as a way of preventing CRC is one newly emerging field of inquiry. Small chemicals called microbial metabolites, which are made by microbes and capable of altering host cell behaviour, are created. Recent research has demonstrated that these metabolites can lead to epigenetic modifications such as histone modifications, DNA methylation, and non-coding RNA regulation, which can control gene expression and affect cellular behaviour. This review highlights the current knowledge on the epigenetic modification for cancer treatment, immunomodulatory and anti-carcinogenic attributes of microbial metabolites, gut epigenetic targeting system, and the role of dietary fibre and gut microbiota in cancer treatment. It also focuses on short-chain fatty acids, especially butyrates (which are generated by microbes), and their cancer treatment perspective, challenges, and limitations, as well as state-of-the-art research on microbial metabolites-induced epigenetic changes for CRC inhibition. In conclusion, the present work highlights the potential of microbial metabolites-induced epigenetic modifications as a novel therapeutic strategy for CRC suppression and guides future research directions in this dynamic field.
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Affiliation(s)
- Vaibhav Singh
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya, Bilaspur (C.G.), 495 009, India
| | - Ekta Shirbhate
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya, Bilaspur (C.G.), 495 009, India
| | - Rakesh Kore
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya, Bilaspur (C.G.), 495 009, India
| | - Subham Vishwakarma
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya, Bilaspur (C.G.), 495 009, India
| | - Shadiya Parveen
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya, Bilaspur (C.G.), 495 009, India
| | - Ravichandran Veerasamy
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, AIMST University, Semeling, Bedong, Kedah Darul Aman, 08100, Malaysia
| | - Amit K Tiwari
- UAMS College of Pharmacy; UAMS - University of Arkansas for Medical Sciences, AR 72205, USA
| | - Harish Rajak
- Department of Pharmacy, Guru Ghasidas Vishwavidyalaya, Bilaspur (C.G.), 495 009, India
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23
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Miniere HJM, Lima EABF, Lorenzo G, Hormuth II DA, Ty S, Brock A, Yankeelov TE. A mathematical model for predicting the spatiotemporal response of breast cancer cells treated with doxorubicin. Cancer Biol Ther 2024; 25:2321769. [PMID: 38411436 PMCID: PMC11057790 DOI: 10.1080/15384047.2024.2321769] [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: 05/11/2023] [Accepted: 02/18/2024] [Indexed: 02/28/2024] Open
Abstract
Tumor heterogeneity contributes significantly to chemoresistance, a leading cause of treatment failure. To better personalize therapies, it is essential to develop tools capable of identifying and predicting intra- and inter-tumor heterogeneities. Biology-inspired mathematical models are capable of attacking this problem, but tumor heterogeneity is often overlooked in in-vivo modeling studies, while phenotypic considerations capturing spatial dynamics are not typically included in in-vitro modeling studies. We present a data assimilation-prediction pipeline with a two-phenotype model that includes a spatiotemporal component to characterize and predict the evolution of in-vitro breast cancer cells and their heterogeneous response to chemotherapy. Our model assumes that the cells can be divided into two subpopulations: surviving cells unaffected by the treatment, and irreversibly damaged cells undergoing treatment-induced death. MCF7 breast cancer cells were previously cultivated in wells for up to 1000 hours, treated with various concentrations of doxorubicin and imaged with time-resolved microscopy to record spatiotemporally-resolved cell count data. Images were used to generate cell density maps. Treatment response predictions were initialized by a training set and updated by weekly measurements. Our mathematical model successfully calibrated the spatiotemporal cell growth dynamics, achieving median [range] concordance correlation coefficients of > .99 [.88, >.99] and .73 [.58, .85] across the whole well and individual pixels, respectively. Our proposed data assimilation-prediction approach achieved values of .97 [.44, >.99] and .69 [.35, .79] for the whole well and individual pixels, respectively. Thus, our model can capture and predict the spatiotemporal dynamics of MCF7 cells treated with doxorubicin in an in-vitro setting.
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Affiliation(s)
- Hugo J. M. Miniere
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
| | - Ernesto A. B. F. Lima
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
| | - Guillermo Lorenzo
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Department of Civil Engineering and Architecture, University of Pavia, Lombardy, Italy
| | - David A. Hormuth II
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
| | - Sophia Ty
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
| | - Amy Brock
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
| | - Thomas E. Yankeelov
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, USA
- Oden Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, USA
- Livestrong Cancer Institutes, The University of Texas at Austin, Austin, USA
- Department of Diagnostic Medicine, The University of Texas at Austin, Austin, USA
- Department of Oncology, The University of Texas at Austin, Austin, USA
- Division of Diagnostic Imaging, The University of Texas M.D. Anderson Cancer Center, Houston, USA
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24
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Bell CC, Faulkner GJ, Gilan O. Chromatin-based memory as a self-stabilizing influence on cell identity. Genome Biol 2024; 25:320. [PMID: 39736786 DOI: 10.1186/s13059-024-03461-x] [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: 07/24/2024] [Accepted: 12/16/2024] [Indexed: 01/01/2025] Open
Abstract
Cell types are traditionally thought to be specified and stabilized by gene regulatory networks. Here, we explore how chromatin memory contributes to the specification and stabilization of cell states. Through pervasive, local, feedback loops, chromatin memory enables cell states that were initially unstable to become stable. Deeper appreciation of this self-stabilizing role for chromatin broadens our perspective of Waddington's epigenetic landscape from a static surface with islands of stability shaped by evolution, to a plasticine surface molded by experience. With implications for the evolution of cell types, stabilization of resistant states in cancer, and the widespread plasticity of complex life.
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Affiliation(s)
- Charles C Bell
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia.
| | - Geoffrey J Faulkner
- Mater Research Institute, University of Queensland, TRI Building, Woolloongabba, QLD, 4102, Australia
- Queensland Brain Institute, University of Queensland, Brisbane, QLD, 4169, Australia
| | - Omer Gilan
- Australian Centre for Blood Diseases, Monash University, Melbourne, VIC, 3004, Australia
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25
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Liu S. The RNA N 6-Methyladenosine MethylomeCoordinates Long Non-Coding RNAs to MediateCancer Drug Resistance by Activating PI3KSignaling. RESEARCH SQUARE 2024:rs.3.rs-5663230. [PMID: 39764125 PMCID: PMC11702776 DOI: 10.21203/rs.3.rs-5663230/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2025]
Abstract
Long non-coding RNAs (lncRNAs) and RNA N6-methyladenosine (m6A) have been linked to leukemia drug resistance. However, whether and how lncRNAs and m6A coordinately regulate resistance remain elusive. Here, we show that many differentially expressed lncRNAs enrich m6A, and more lncRNAs tend to have higher m6A content in CML cells resistant to tyrosine kinase inhibitors (TKIs). We demonstrate broad clinical relevance of our findings, showing that upregulation of top-ranked lncRNAs (e.g., SENCR, PROX1-AS1, LN892) in TKI resistant cell lines occurs in CML patients at the diagnostic stage, blast crisis phase or not-responding to TKIs compared to chronic phase or TKI responders, respectively. Higher lncRNAs predict drug resistance and shorter survival duration. Knockdown of SENCR, PROX1-AS1 or LN892 restores TKI sensitivity. Mechanistically, upregulation of PROX1-AS1, SENCR and LN892 results from FTO-dependent m6A hypomethylation that stabilizes lncRNA transcripts, and empowers resistant cell growth through overexpression of PI3K signaling mediators (e.g., ITGA2, F2R, COL6A1). Treatment with PI3K inhibitor alpelisib eradicates resistant cells in vitro and in vivo with prolonged survival of leukemic mice through downregulation of F2R, ITGA2 and COL6A1. Thus, the lncRNA-m6A-PI3K cascade represents a new non-genetic predictor for drug resistance and poorer prognosis in cancer, and a pan-cancer mechanism underlying TKI resistance.
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Affiliation(s)
- Shujun Liu
- The Metrohealth System, Case Western Reser
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26
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Wang H, Wang Z, Hu L, Yang B, Zong L, Xu D, Yu B, Kong X, Wang M. Discovery of KW0113 as a First and Effective PROTAC Degrader of DNMT1 Protein. ChemMedChem 2024; 19:e202400467. [PMID: 39302251 DOI: 10.1002/cmdc.202400467] [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: 06/14/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/22/2024]
Abstract
DNA methyltransferase 1 (DNMT1) is an attractive therapeutic target for acute myelocytic leukemia (AML) and other malignancies. It has been reported that the genetic depletion of DNMT1 inhibited AML cell proliferation through reversing DNA methylation abnormalities. However, no DNMT1-targeted PROTAC degraders have been reported yet. Herein, a series of proteolysis-targeting chimera (PROTAC) degrader of DNMT1 based on dicyanopyridine scaffold and VHL E3 ubiquitin ligase ligand was developed. Among them, KW0113 (DC50=643/899 nM in MV4-11/MOLM-13 cells) exhibited optimal DNMT1 degradation. KW0113 induced DNMT1-selective degradation in a dose- and time-dependent manner through VHL engagement. Moreover, KW0113 inhibited AML cell growth by reversing promoter DNA hypermethylation and tumor-suppressor genes silencing. In conclusion, these findings proved the capability of PROTAC strategy for inducing DNMT1 degradation, demonstrated the therapeutic potential of DNMT1-targeted PROTACs. This work also provided a convenient chemical knockdown tool for DNMT1-related studies.
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Affiliation(s)
- Huihui Wang
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
| | - Zhaoliang Wang
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linghao Hu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Bingjie Yang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Liangyi Zong
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dounan Xu
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
| | - Bo Yu
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, 330031, China
| | - Xiangqian Kong
- State Key Laboratory of Respiratory Disease, China-New Zealand Joint Laboratory on Biomedicine and Health, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingliang Wang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, 528400, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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27
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Shaik R, Malik MS, Basavaraju S, Qurban J, Al-Subhi FMM, Badampudi S, Peddapaka J, Shaik A, Abd-El-Aziz A, Moussa Z, Ahmed SA. Cellular and molecular aspects of drug resistance in cancers. Daru 2024; 33:4. [PMID: 39652186 PMCID: PMC11628481 DOI: 10.1007/s40199-024-00545-8] [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: 05/01/2024] [Accepted: 10/09/2024] [Indexed: 12/12/2024] Open
Abstract
OBJECTIVES Cancer drug resistance is a multifaceted phenomenon. The present review article aims to comprehensively analyze the cellular and molecular aspects of drug resistance in cancer and the strategies employed to overcome it. EVIDENCE ACQUISITION A systematic search of relevant literature was conducted using electronic databases such as PubMed, Scopus, and Web of Science using appropriate key words. Original research articles and secondary literature were taken into consideration in reviewing the development in the field. RESULTS AND CONCLUSIONS Cancer drug resistance is a pervasive challenge that causes many treatments to fail therapeutically. Despite notable advances in cancer treatment, resistance to traditional chemotherapeutic agents and novel targeted medications remains a formidable hurdle in cancer therapy leading to cancer relapse and mortality. Indeed, a majority of patients with metastatic cancer experience are compromised on treatment efficacy because of drug resistance. The multifaceted nature of drug resistance encompasses various factors, such as tumor heterogeneity, growth kinetics, immune system, microenvironment, physical barriers, and the emergence of undruggable cancer drivers. Additionally, alterations in drug influx/efflux transporters, DNA repair mechanisms, and apoptotic pathways further contribute to resistance, which may manifest as either innate or acquired traits, occurring prior to or following therapeutic intervention. Several strategies such as combination therapy, targeted therapy, development of P-gp inhibitors, PROTACs and epigenetic modulators are developed to overcome cancer drug resistance. The management of drug resistance is compounded by the patient and tumor heterogeneity coupled with cancer's ability to evade treatment. Gaining further insight into the mechanisms underlying medication resistance is imperative for the development of effective therapeutic interventions and improved patient outcomes.
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Affiliation(s)
- Rahaman Shaik
- Department of Pharmacology, School of Pharmaceutical Education & Research, Jamia Hamdard, New Delhi, India
| | - M Shaheer Malik
- Department of Chemistry, Faculty of Science, Umm Al-Qura University, Makkah, 21955, Saudi Arabia.
| | | | - Jihan Qurban
- Department of Chemistry, Faculty of Science, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Fatimah M M Al-Subhi
- Department of Environmental and Occupational Health, College of Public Health and Health Informatics, Umm Al-Qura University, Makkah, 21955, Saudi Arabia
| | - Sathvika Badampudi
- Department of Pharmacology, St.Pauls College of Pharmacy, Turkayamjal, Hyderabad, India
| | - Jagruthi Peddapaka
- Department of Pharmaceutical Chemistry, St.Paul's College of Pharmacy, Turkayamjal, Hyderabad, India
| | - Azeeza Shaik
- Research&Development Department, KVB Asta Life sciences, Hyderabad, India
| | - Ahmad Abd-El-Aziz
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao, 266400, China
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Saleh A Ahmed
- Department of Chemistry, Faculty of Science, Umm Al-Qura University, Makkah, 21955, Saudi Arabia.
- Department of Chemistry, Faculty of Science, Assiut University, Assiut, 71516, Egypt.
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28
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Chan FF, Kwan KKL, Seoung DH, Chin DWC, Ng IOL, Wong CCL, Wong CM. N6-Methyladenosine modification activates the serine synthesis pathway to mediate therapeutic resistance in liver cancer. Mol Ther 2024; 32:4435-4447. [PMID: 39489921 PMCID: PMC11638877 DOI: 10.1016/j.ymthe.2024.10.025] [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: 06/06/2024] [Revised: 09/15/2024] [Accepted: 10/24/2024] [Indexed: 11/05/2024] Open
Abstract
Metabolic adaptation serves as a significant driving force for cancer growth and poses a substantial obstacle for cancer therapies. Herein, we unraveled the role of m6A-mediated serine synthesis pathway (SSP) regulation in both hepatocellular carcinoma (HCC) development and therapeutic resistance. We demonstrated that treatment of highly specific m6A inhibitor (STM2457) effectively inhibited HCC cell line growth and suppressed spontaneous HCC formation in mice driven by liver-specific Tp53 knockout and Myc overexpression. Using GLORI-seq, we delineated a single-base-resolution m6A landscape in human HCC cell lines. Interestingly, we identified three core enzymes in the SSP (PHGDH, PSAT1, and PSPH) as novel targets of METTL3-mediated m6A modification. In these SSP genes, m6A modification recruited m6A reader IGF2BP3 to stabilize their mRNA transcripts, thereby enhancing their mRNA and protein expression in HCC cells. Most importantly, our GLORI-seq data revealed that sorafenib-resistant HCC cells elevated m6A modification in SSP genes to promote protein expression and antioxidant production. STM2457 treatment attenuated the serine synthesis pathway, induced oxidative stress, and sensitized HCC cells to sorafenib and lenvatinib treatments. In conclusion, our findings suggest that targeting m6A could be a potential therapeutic strategy for HCC treatment.
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Affiliation(s)
- For-Fan Chan
- State Key Laboratory of Liver Research and Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Kenneth Kin-Leung Kwan
- State Key Laboratory of Liver Research and Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Do-Hyun Seoung
- State Key Laboratory of Liver Research and Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Don Wai-Ching Chin
- State Key Laboratory of Liver Research and Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research and Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Carmen Chak-Lui Wong
- State Key Laboratory of Liver Research and Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong; Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Chun-Ming Wong
- State Key Laboratory of Liver Research and Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong.
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29
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Wang Q, Yin X, Ding Y, Zhao H, Luo Y. Application of biomechanics in tumor epigenetic research. MECHANOBIOLOGY IN MEDICINE 2024; 2:100093. [PMID: 40395222 PMCID: PMC12082163 DOI: 10.1016/j.mbm.2024.100093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 06/26/2024] [Accepted: 08/14/2024] [Indexed: 05/22/2025]
Abstract
The field of cancer research is increasingly recognizing the complex interplay between biomechanics and tumor epigenetics. Biomechanics plays a significant role in the occurrence, development, and metastasis of cancer and may exert influence by impacting the epigenetic modifications of tumors. In this review, we investigate a spectrum of biomechanical tools, including computational models, measurement instruments, and in vitro simulations. These tools not only assist in deciphering the mechanisms behind these epigenetic changes but also provide novel methods for characterizing tumors, which are significant for diagnosis and treatment. Finally, we discuss the potential of new therapies that target the biomechanical properties of the tumor microenvironment. There is hope that by altering factors such as the stiffness of the extracellular matrix or interfering with mechano-sensing pathways, we can halt tumor progression through epigenetic mechanisms. We emphasize the necessity for multidisciplinary efforts to integrate biomechanics with tumor epigenetics more comprehensively. Such collaboration is anticipated to advance therapeutic strategies and enhance our understanding of cancer biology, signaling the dawn of a new era in cancer treatment and research.
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Affiliation(s)
- Qi Wang
- School of Mechanical Engineering, Zhejiang University, Hangzhou, 310058, China
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou 310053, China
| | - Xiaohong Yin
- School of Mechanical Engineering, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Fluid Power & Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
| | - Yunyi Ding
- Department of Emergency Medicine, The Second Affiliated Hospital of Zhejiang University, Hangzhou 310009, China
| | - Hong Zhao
- Department of Breast Surgery, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), Hangzhou 310006, China
| | - Yichen Luo
- School of Mechanical Engineering, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Fluid Power & Mechatronic Systems, Zhejiang University, Hangzhou 310058, China
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30
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Masciale V, Banchelli F, Grisendi G, Samarelli AV, Raineri G, Rossi T, Zanoni M, Cortesi M, Bandini S, Ulivi P, Martinelli G, Stella F, Dominici M, Aramini B. The molecular features of lung cancer stem cells in dedifferentiation process-driven epigenetic alterations. J Biol Chem 2024; 300:107994. [PMID: 39547513 PMCID: PMC11714729 DOI: 10.1016/j.jbc.2024.107994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 10/30/2024] [Accepted: 11/05/2024] [Indexed: 11/17/2024] Open
Abstract
Cancer stem cells (CSCs) may be dedifferentiated somatic cells following oncogenic processes, representing a subpopulation of cells able to promote tumor growth with their capacities for proliferation and self-renewal, inducing lineage heterogeneity, which may be a main cause of resistance to therapies. It has been shown that the "less differentiated process" may have an impact on tumor plasticity, particularly when non-CSCs may dedifferentiate and become CSC-like. Bidirectional interconversion between CSCs and non-CSCs has been reported in other solid tumors, where the inflammatory stroma promotes cell reprogramming by enhancing Wnt signaling through nuclear factor kappa B activation in association with intracellular signaling, which may induce cells' pluripotency, the oncogenic transformation can be considered another important aspect in the acquisition of "new" development programs with oncogenic features. During cell reprogramming, mutations represent an initial step toward dedifferentiation, in which tumor cells switch from a partially or terminally differentiated stage to a less differentiated stage that is mainly manifested by re-entry into the cell cycle, acquisition of a stem cell-like phenotype, and expression of stem cell markers. This phenomenon typically shows up as a change in the form, function, and pattern of gene and protein expression, and more specifically, in CSCs. This review would highlight the main epigenetic alterations, major signaling pathways and driver mutations in which CSCs, in tumors and specifically, in lung cancer, could be involved, acting as key elements in the differentiation/dedifferentiation process. This would highlight the main molecular mechanisms which need to be considered for more tailored therapies.
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Affiliation(s)
- Valentina Masciale
- Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Federico Banchelli
- Department of Statistical Sciences "Paolo Fortunati", Alma Mater Studiorum- University of Bologna, Bologna, Italy
| | - Giulia Grisendi
- Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Anna Valeria Samarelli
- Laboratory of and Respiratory Medicine, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Giulia Raineri
- Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy
| | - Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michele Zanoni
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Michela Cortesi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Sara Bandini
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Paola Ulivi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Giovanni Martinelli
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Franco Stella
- Thoracic Surgery Unit, Department of Medical and Surgical Sciences-DIMEC of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni-L. Pierantoni Hospital, Forlì, Italy
| | - Massimo Dominici
- Laboratory of Cellular Therapies, Department of Medical and Surgical Sciences for Children & Adults, University Hospital of Modena, Modena, Italy; Division of Oncology, University Hospital of Modena and Reggio Emilia, University of Modena and Reggio Emilia, Modena, Italy
| | - Beatrice Aramini
- Thoracic Surgery Unit, Department of Medical and Surgical Sciences-DIMEC of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni-L. Pierantoni Hospital, Forlì, Italy.
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Bomsztyk K, Mar D, Denisenko O, Powell S, Vishnoi M, Yin Z, Delegard J, Hadley C, Tandon N, Patel AJ, Patel AP, Ellenbogen RG, Ramakrishna R, Rostomily RC. Analysis of DNA Methylation in Gliomas: Assessment of Preanalytical Variables. J Transl Med 2024; 104:102160. [PMID: 39426568 PMCID: PMC11709230 DOI: 10.1016/j.labinv.2024.102160] [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: 04/08/2024] [Revised: 10/01/2024] [Accepted: 10/09/2024] [Indexed: 10/21/2024] Open
Abstract
Precision oncology is driven by biomarkers. For glioblastoma multiforme (GBM), the most common malignant adult primary brain tumor, O6-methylguanine-DNA methyltransferase (MGMT) gene promoter methylation is an important prognostic and treatment clinical biomarker. Time-consuming preanalytical steps such as biospecimen storage, fixation, sampling, and processing are sources of data irreproducibility, and all these preanalytical variables are confounded by intratumor heterogeneity of MGMT promoter methylation. To assess the effect of preanalytical variables on GBM DNA methylation, tissue storage/sampling (CryoGrid), sample preparation multisonicator (PIXUL), and 5-methylcytosine DNA immunoprecipitation (Matrix-MeDIP-qPCR/seq) platforms were used. MGMT promoter methylation status assayed by MeDIP-qPCR was validated with methylation-specific polymerase chain reaction. MGMT promoter methylation levels in frozen and formalin-fixed paraffin-embedded sample pairs were not statistically different, confirming the reliability of formalin-fixed paraffin-embedded for MGMT promoter methylation analysis. Warm ex vivo ischemia (up to 4 hours at 37 °C) and 3 cycles of repeated sample thawing and freezing did not statistically impact 5-methylcytosine at MGMT promoter, exon, and enhancer regions, indicating the resistance of DNA methylation to common variations in sample processing conditions that might be encountered in research and clinical settings. Twenty-six percent to 34% of specimens exhibited intratumor heterogeneity in the MGMT DNA promoter methylation. These data demonstrate that variations in sample fixation, ischemia duration and temperature, and DNA methylation assay technique do not have a statistically significant impact on MGMT promoter methylation assessment. However, intratumor methylation heterogeneity underscores the value of multiple biopsies at different GBM geographic tumor sites in the evaluation of MGMT promoter methylation status. Matrix-MeDIP-seq analysis revealed that MGMT promoter methylation status clustered with other differentially methylated genomic loci (eg, HOXA and lncRNAs) that are resilient to variation in the above preanalytical conditions. These observations offer new opportunities to develop more granular data-based epigenetic GBM biomarkers. In this regard, the high-throughput CryoGrid-PIXUL-Matrix toolbox could be useful.
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Affiliation(s)
- Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, Washington; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington; Matchstick Technologies, Inc, Kirkland, Washington.
| | - Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, Washington; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, Washington
| | - Suzanne Powell
- Department of Neuropathology, Houston Methodist Hospital, Houston, Texas
| | - Monika Vishnoi
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, Texas
| | - Zheng Yin
- Department of Systems Medicine and Bioengineering, Houston Methodist Neil Cancer Center, Houston, Texas
| | - Jennifer Delegard
- Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Caroline Hadley
- Department of Neurosurgery, University of New Mexico, Albuquerque, New Mexico
| | - Nitin Tandon
- Department of Neurosurgery, McGovern Medical School at UT Health, Houston, Texas
| | - Akash J Patel
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas
| | - Anoop P Patel
- Department of Neurosurgery, Duke University, Durham, North Carolina
| | - Richard G Ellenbogen
- Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Rohan Ramakrishna
- Department of Neurological Surgery, Weill Cornell Medicine, New York, New York
| | - Robert C Rostomily
- Department of Neurosurgery, Houston Methodist Research Institute, Houston, Texas; Department of Neurological Surgery, University of Washington, Seattle, Washington; Department of Neurological Surgery, Weill Cornell Medicine, New York, New York
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Zhao Y, O'Keefe CM, Hu J, Allan CM, Cui W, Lei H, Chiu A, Hsieh K, Joyce SC, Herman JG, Pisanic TR, Wang TH. Multiplex digital profiling of DNA methylation heterogeneity for sensitive and cost-effective cancer detection in low-volume liquid biopsies. SCIENCE ADVANCES 2024; 10:eadp1704. [PMID: 39576863 PMCID: PMC11584010 DOI: 10.1126/sciadv.adp1704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 10/22/2024] [Indexed: 11/24/2024]
Abstract
Molecular alterations in cancerous tissues exhibit intercellular genetic and epigenetic heterogeneity, complicating the performance of diagnostic assays, particularly for early cancer detection. Conventional liquid biopsy methods have limited sensitivity and/or ability to assess epigenetic heterogeneity of rare epiallelic variants cost-effectively. We report an approach, named REM-DREAMing (Ratiometric-Encoded Multiplex Discrimination of Rare EpiAlleles by Melt), which leverages a digital microfluidic platform that incorporates a ratiometric fluorescence multiplex detection scheme and precise digital high-resolution melt analysis to enable low-cost, parallelized analysis of heterogeneous methylation patterns on a molecule-by-molecule basis for the detection of cancer in liquid biopsies. We applied the platform to simultaneously assess intermolecular epigenetic heterogeneity in five methylation biomarkers for improved, blood-based screening for early-stage non-small cell lung cancer. In a cohort of 48 low-volume liquid biopsy specimens from patients with indeterminant pulmonary nodules, we show that assessment of intermolecular methylation density distributions can notably improve the performance of multigene methylation biomarker panels for the early detection of cancer.
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Affiliation(s)
- Yang Zhao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Christine M O'Keefe
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Jiumei Hu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Conor M Allan
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Weiwen Cui
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hanran Lei
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Allyson Chiu
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sonali C Joyce
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
| | - James G Herman
- Division of Hematology and Oncology, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA 15261, USA
| | - Thomas R Pisanic
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21287, USA
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Li Q, He G, Yu Y, Li X, Peng X, Yang L. Exosome crosstalk between cancer stem cells and tumor microenvironment: cancer progression and therapeutic strategies. Stem Cell Res Ther 2024; 15:449. [PMID: 39578849 PMCID: PMC11583673 DOI: 10.1186/s13287-024-04061-z] [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: 09/27/2024] [Accepted: 11/10/2024] [Indexed: 11/24/2024] Open
Abstract
Cancer stem cells (CSCs) represent a small yet pivotal subset of tumor cells endowed with self-renewal capabilities. These cells are intricately linked to tumor progression and are central to drug resistance, metastasis, and recurrence. The tumor microenvironment (TME) encompasses the cancer cells and their surrounding milieu, including immune and inflammatory cells, cancer-associated fibroblasts, adjacent stromal tissues, tumor vasculature, and a variety of cytokines and chemokines. Within the TME, cells such as immune and inflammatory cells, endothelial cells, adipocytes, and fibroblasts release growth factors, cytokines, chemokines, and exosomes, which can either sustain or disrupt CSCs, thereby influencing tumor progression. Conversely, CSCs can also secrete cytokines, chemokines, and exosomes, affecting various components of the TME. Exosomes, a subset of extracellular vesicles (EVs), carry a complex cargo of nucleic acids, proteins, and lipids, playing a crucial role in the communication between CSCs and the TME. This review primarily focuses on the impact of exosomes secreted by CSCs (CSC-exo) on tumor progression, including their roles in maintaining stemness, promoting angiogenesis, facilitating metastasis, inducing immune suppression, and contributing to drug resistance. Additionally, we discuss how exosomes secreted by different cells within the TME affect CSCs. Finally, we explore the potential of utilizing exosomes to mitigate the detrimental effects of CSCs or to target and eliminate them. A thorough understanding of the exosome-mediated crosstalk between CSCs and the TME could provide valuable insights for developing targeted therapies against CSCs.
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Affiliation(s)
- Qi Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Guangpeng He
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Yifan Yu
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xinyu Li
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China
| | - Xueqiang Peng
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
| | - Liang Yang
- Department of General Surgery, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110032, China.
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Feng Z, Zheng Y, Pei J, Huang L. Potential mechanism of Laportea bulbifera on treating inflammation and tumor via metabolomics, network pharmacology and molecular docking. J Biomol Struct Dyn 2024:1-17. [PMID: 39522167 DOI: 10.1080/07391102.2024.2426077] [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: 08/25/2023] [Accepted: 03/26/2024] [Indexed: 11/16/2024]
Abstract
This study aimed to utilize metabolomics, network pharmacology, and molecular docking techniques to identify the major active components of Laportea bulbifera and investigate their anti-inflammatory and potential anti-tumor mechanisms. The metabolic constituents of L. bulbifera were examined utilizing UPLC-ESI-MS/MS. PPI networks and compound-target-pathway networks were established using resources such as TCMSP, Swiss Target Prediction, DAVID, STRING database, and Cytoscape software. Molecular docking analysis of the most important compounds and targets was conducted using Autodock4, followed by validation of the molecular docking results' stability using GROMACS. The UPLC-ESI-MS/MS analysis identified a total of 798 compounds. A network pharmacology-based analysis was conducted, revealing that eight compounds and four molecular targets-namely, TNF, IL6, PIK3CA, and HDAC1-were enriched in the network. Pathway analysis of the identified targets demonstrated enrichment in 217 KEGG pathways. Molecular docking analysis and molecular dynamics simulations demonstrated strong therapeutic potential of N-feruloyltyramine, N-feruloylagmatine, and Ellagic acid against various inflammatory and tumor diseases. This study, for the first time, employed an integrated strategy of metabolomics, network pharmacology, molecular docking, and molecular dynamics, elucidating the mechanisms underlying the anti-inflammatory and potential anti-tumor effects of L. bulbifera, laying the foundation for subsequent drug development endeavors.
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Affiliation(s)
- Zhan Feng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yan Zheng
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Linfang Huang
- Key Laboratory of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People's Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Nazaret A, Fan JL, Lavallée VP, Burdziak C, Cornish AE, Kiseliovas V, Bowman RL, Masilionis I, Chun J, Eisman SE, Wang J, Hong J, Shi L, Levine RL, Mazutis L, Blei D, Pe’er D, Azizi E. Joint representation and visualization of derailed cell states with Decipher. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.11.566719. [PMID: 38014231 PMCID: PMC10680623 DOI: 10.1101/2023.11.11.566719] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Biological insights often depend on comparing conditions such as disease and health, yet we lack effective computational tools for integrating single-cell genomics data across conditions or characterizing transitions from normal to deviant cell states. Here, we present Decipher, a deep generative model that characterizes derailed cell-state trajectories. Decipher jointly models and visualizes gene expression and cell state from normal and perturbed single-cell RNA-seq data, revealing shared and disrupted dynamics. We demonstrate its superior performance across diverse contexts, including in pancreatitis with oncogene mutation, acute myeloid leukemia, and gastric cancer.
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Affiliation(s)
- Achille Nazaret
- Department of Computer Science, Columbia University, New York, NY 10027, USA
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Joy Linyue Fan
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Vincent-Philippe Lavallée
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Centre Hospitalier Universitaire Sainte-Justine Research Center, Montréal, QC, Canada
- Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Cassandra Burdziak
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andrew E. Cornish
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Vaidotas Kiseliovas
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Robert L. Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ignas Masilionis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jaeyoung Chun
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Shira E. Eisman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - James Wang
- Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Justin Hong
- Department of Computer Science, Columbia University, New York, NY 10027, USA
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Lingting Shi
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Linas Mazutis
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Alan and Sandra Gerry Metastasis and Tumor Ecosystems Center, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Institute of Biotechnology Vilnius University, Life Sciences Centre, Vilnius 02158, Lithuania
| | - David Blei
- Department of Computer Science, Columbia University, New York, NY 10027, USA
- Department of Statistics, Columbia University, New York, NY 10027, USA
- Data Science Institute, Columbia University, New York, NY 10027, USA
| | - Dana Pe’er
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York 10027, NY 10065, USA
| | - Elham Azizi
- Department of Computer Science, Columbia University, New York, NY 10027, USA
- Irving Institute for Cancer Dynamics, Columbia University, New York, NY 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
- Data Science Institute, Columbia University, New York, NY 10027, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY 10032, USA
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Zhu H, Xie Z. Therapeutic potential of tLyp-1-EV-shCTCF in inhibiting liver cancer stem cell self-renewal and immune escape via SALL3 modulation in hepatocellular carcinoma. Transl Oncol 2024; 49:102048. [PMID: 39186862 PMCID: PMC11388803 DOI: 10.1016/j.tranon.2024.102048] [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: 11/09/2023] [Revised: 06/12/2024] [Accepted: 07/01/2024] [Indexed: 08/28/2024] Open
Abstract
The progression of hepatocellular carcinoma (HCC) is influenced by disrupted metabolic processes, presenting challenges in prognostic outcomes. Hepatocellular carcinoma (HCC), a leading cause of cancer-related mortality, is closely associated with metabolic reprogramming and stem cell-like properties in liver cancer stem cells (LCSCs). This study explored the potential molecular mechanisms by which tLyP-1-modified extracellular vesicles (EVs) delivering CTCF shRNA (tLyp-1-EV-shCTCF) regulate mitochondrial DNA methylation-induced glycolytic metabolic reprogramming and LCSC self-renewal. Through a series of methods, including Western blot, nanoparticle tracking analysis, and immunofluorescence, we demonstrated the successful delivery and internalization of tLyp-1-EV in HCC cells. Our results identified SALL3 as a critical factor underexpressed in HCC and LCSCs, while CTCF was overexpressed. Overexpression of SALL3 inhibited LCSC self-renewal and immune evasion by blocking the CTCF-DNMT3A interaction, thus repressing DNMT3A methyltransferase activity and subsequent mitochondrial DNA methylation-mediated glycolytic metabolic reprogramming. In vivo experiments further supported these findings, showing that tLyp-1-EV-shCTCF treatment significantly reduced tumor growth by upregulating SALL3 expression, thereby inhibiting glycolytic metabolic reprogramming and enhancing the immune response against HCC cells. This study provides novel insights into the role of SALL3 and mitochondrial DNA methylation in HCC progression, offering potential therapeutic targets for combating HCC and its stem cell-like properties.
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Affiliation(s)
- Heng Zhu
- Department of Gastroenterology, The Fourth People's Hospital of Jinan, No.50, Normal Road, Tianqiao District, Jinan, Shandong Province 250031, P R China.
| | - Zhihui Xie
- Department of infectious diseases, Zibo Central Hospital, Zibo 255000, P R China
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Khan MA, Mishra D, Kumar R, Siddique HR. Revisiting epigenetic regulation in cancer: Evolving trends and translational implications. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 390:1-24. [PMID: 39864892 DOI: 10.1016/bs.ircmb.2024.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Cancer is a leading cause of mortality worldwide. The evolving role of epigenetics and tumor microenvironments of cancer pose significant challenges to the management of cancer. Besides genetics, epigenetic changes play a crucial role in the alteration of cellular machinery, progression, metastasis, epithelial-mesenchymal transition, and chemoresistance. Epigenetic changes such as DNA and RNA methylation, histone modifications, and chromatin modeling directly or indirectly influence the different stages of cancer from initiation to chemoresistant phenotype. In addition, alterations in the epigenetic machinery, such as hypo- or hyperactivation of proteins involved in epigenetic modifications, can lead to different health complications, including cancer. Recently, epi-drugs or epigenetic drugs offer emerging hope for the treatment and management of this deadly disease. Various epigenetic drugs targeting factors responsible for epigenetic modifications in cancer are currently under clinical trials. This chapter provides an overview of epigenetic modifications, their clinical implications, and the potential of epigenetic drugs for cancer treatment.
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Affiliation(s)
- Mohammad Afsar Khan
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, India
| | - Dhruv Mishra
- Department of Zoology, DAV College (PG), Maa Shakumbhari University, Muzaffarnagar, India
| | - Ranjan Kumar
- School of Life Science, Jawaharlal Nehru University (JNU), New Delhi, India
| | - Hifzur R Siddique
- Molecular Cancer Genetics & Translational Research Lab, Section of Genetics, Department of Zoology, Aligarh Muslim University, Aligarh, India.
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Ming Y, Gong Y, Fu X, Ouyang X, Peng Y, Pu W. Small-molecule-based targeted therapy in liver cancer. Mol Ther 2024; 32:3260-3287. [PMID: 39113358 PMCID: PMC11489561 DOI: 10.1016/j.ymthe.2024.08.001] [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] [Revised: 03/13/2024] [Accepted: 08/02/2024] [Indexed: 08/23/2024] Open
Abstract
Liver cancer is one of the most prevalent malignant tumors worldwide. According to the Barcelona Clinic Liver Cancer staging criteria, clinical guidelines provide tutorials to clinical management of liver cancer at their individual stages. However, most patients diagnosed with liver cancer are at advanced stage; therefore, many researchers conduct investigations on targeted therapy, aiming to improve the overall survival of these patients. To date, small-molecule-based targeted therapies are highly recommended (first line: sorafenib and lenvatinib; second line: regorafenib and cabozantinib) by current the clinical guidelines of the American Society of Clinical Oncology, European Society for Medical Oncology, and National Comprehensive Cancer Network. Herein, we summarize the small-molecule-based targeted therapies in liver cancer, including the approved and preclinical therapies as well as the therapies under clinical trials, and introduce their history of discovery, clinical trials, indications, and molecular mechanisms. For drug resistance, the revealed mechanisms of action and the combination therapies are also discussed. In fact, the known small-molecule-based therapies still have limited clinical benefits to liver cancer patients. Therefore, we analyze the current status and give our ideas for the urgent issues and future directions in this field, suggesting clues for novel techniques in liver cancer treatment.
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Affiliation(s)
- Yue Ming
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China
| | - Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xuewen Fu
- Jinhua Huanke Environmental Technology Co., Ltd., Jinhua 321000, China
| | - Xinyu Ouyang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; West China School of Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu 610212, China.
| | - Wenchen Pu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610064, China; West China School of Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
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Wang G, Xu XN, Zhi-Min Z, Wang K, Li F. Prediction and verification of targets for α-hederin/oxaliplatin dual-loaded rHDL modified liposomes: Reversing effector T-cells dysfunction and improving anti-COAD efficiency in vitro and in vivo. Int J Pharm 2024; 662:124512. [PMID: 39067547 DOI: 10.1016/j.ijpharm.2024.124512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 07/04/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
This study tried to develop the α-Hederin/Oxaliplatin (OXA) dual-loaded rHDL (α-Hederin-OXA-rHDL) modified liposomes to improve the therapeutic index on colon adenocarcinoma (COAD). The α-Hederin-OXA-rHDL were prepared and evaluated for characterizations, accumulate to tumor tissues, and antitumor activity. A thorough investigation into oxaliplatin resistant and KRAS-mutant related hub keg genes were identified and performed to assess the prognosis role of the genetic signature in COAD. The potential immune signatures and molecular docking for verifing the predicted targets of α-Hederin-OXA-rHDL in tumor-bearing mice. Results suggested that α-Hederin-OXA-rHDL could enhance the sensitivity of oxaliplatin in HCT116/L-OHP cells via the regulation of KEAP1/NRF2 -mediated signaling and HO1 or GPX4 proteins. Furthermore, α-Hederin-OXA-rHDL regulated the predicted targets of PRDM1 interaction with miR-140-5p, efficient activing CD8 T cell to improve therapeutic response in vivo. Collectively, this work provides drug delivery with rHDL dual-loaded α-Hederin and oxaliplatin synergistically targets cancer cells and effectory T cells combating COAD.
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Affiliation(s)
- Gang Wang
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai 200235, China; Department of Pharmaceutics, Shanghai Anda Hospital, 200000 Shanghai, China.
| | - Xiao-Na Xu
- Department of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province 212001, China
| | - Zhu Zhi-Min
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai 200235, China
| | - Kun Wang
- Department of Medicine, Jiangsu University, Zhenjiang City, Jiangsu Province 212001, China
| | - Fei Li
- Department of Pharmaceutics, Shanghai Eighth People's Hospital, Jiangsu University, Shanghai 200235, China.
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Liu Z, Fan Y, Cui M, Wang X, Zhao P. Investigation of tumour environments through advancements in microtechnology and nanotechnology. Biomed Pharmacother 2024; 178:117230. [PMID: 39116787 DOI: 10.1016/j.biopha.2024.117230] [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: 06/05/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 08/10/2024] Open
Abstract
Cancer has a significant negative social and economic impact on both developed and developing countries. As a result, understanding the onset and progression of cancer is critical for developing therapies that can improve the well-being and health of individuals with cancer. With time, study has revealed, the tumor microenvironment has great influence on this process. Micro and nanoscale engineering techniques can be used to study the tumor microenvironment. Nanoscale and Microscale engineering use Novel technologies and designs with small dimensions to recreate the TME. Knowing how cancer cells interact with one another can help researchers develop therapeutic approaches that anticipate and counteract cancer cells' techniques for evading detection and fighting anti-cancer treatments, such as microfabrication techniques, microfluidic devices, nanosensors, and nanodevices used to study or recreate the tumor microenvironment. Nevertheless, a complicated action just like the growth and in cancer advancement, and their intensive association along the environment around it that has to be studied in more detail.
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Affiliation(s)
- Zhen Liu
- Department of Radiology, Shengjing Hospital of China Medical University, China
| | - Yan Fan
- Department of Pediatrics, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Mengyao Cui
- Department of Surgical Oncology, Breast Surgery, General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xu Wang
- Department of Surgical Oncology, Breast Surgery, General Surgery, The First Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Pengfei Zhao
- Department of Radiology, Shengjing Hospital of China Medical University, China.
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Bhattacharya A, Chatterji U. Exosomal misfolded proteins released by cancer stem cells: dual functions in balancing protein homeostasis and orchestrating tumor progression. Discov Oncol 2024; 15:392. [PMID: 39215782 PMCID: PMC11365921 DOI: 10.1007/s12672-024-01262-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024] Open
Abstract
Cancer stem cells (CSCs), the master regulators of tumor heterogeneity and progression, exert profound influence on cancer metastasis, via various secretory vesicles. Emerging from CSCs, the exosomes serve as pivotal mediators of intercellular communication within the tumor microenvironment, modulating invasion, angiogenesis, and immune responses. Moreover, CSC-derived exosomes play a central role in sculpting a dynamic landscape, contributing to the malignant phenotype. Amidst several exosomal cargoes, misfolded proteins have recently gained attention for their dual functions in maintaining protein homeostasis and promoting tumor progression. Disrupting these communication pathways could potentially prevent the maintenance and expansion of CSCs, overcome treatment resistance, and inhibit the supportive environment created by the tumor microenvironment, thereby improving the effectiveness of cancer therapies and reducing the risk of tumor recurrence and metastasis. Additionally, exosomes have also shown potential therapeutic applications, such as in drug delivery or as biomarkers for cancer diagnosis and prognosis. Therefore, comprehending the biology of exosomes derived from CSCs is a multifaceted area of research with implications in both basic sciences and clinical applications. This review explores the intricate interplay between exosomal misfolded proteins released by CSCs, the potent contributor in tumor heterogeneity, and their impact on cellular processes, shedding light on their role in cancer progression.
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Affiliation(s)
- Anuran Bhattacharya
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, West Bengal, 700019, India.
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Koirala M, DiPaola M. Overcoming Cancer Resistance: Strategies and Modalities for Effective Treatment. Biomedicines 2024; 12:1801. [PMID: 39200265 PMCID: PMC11351918 DOI: 10.3390/biomedicines12081801] [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: 07/11/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Resistance to cancer drugs is a complex phenomenon that poses a significant challenge in the treatment of various malignancies. This review comprehensively explores cancer resistance mechanisms and discusses emerging strategies and modalities to overcome this obstacle. Many factors contribute to cancer resistance, including genetic mutations, activation of alternative signaling pathways, and alterations in the tumor microenvironment. Innovative approaches, such as targeted protein degradation, immunotherapy combinations, precision medicine, and novel drug delivery systems, hold promise for improving treatment outcomes. Understanding the intricacies of cancer resistance and leveraging innovative modalities are essential for advancing cancer therapy.
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Karatkevich D, Losmanova T, Zens P, Deng H, Dubey C, Zhang T, Casty C, Gao Y, Neppl C, Berezowska S, Wang W, Peng RW, Schmid RA, Dorn P, Marti TM. Chemotherapy increases CDA expression and sensitizes malignant pleural mesothelioma cells to capecitabine treatment. Sci Rep 2024; 14:18206. [PMID: 39107509 PMCID: PMC11303810 DOI: 10.1038/s41598-024-69347-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 08/03/2024] [Indexed: 08/10/2024] Open
Abstract
The combination of cisplatin and pemetrexed remains the gold standard chemotherapy for malignant pleural mesothelioma (MPM), although resistance and poor response pose a significant challenge. Cytidine deaminase (CDA) is a key enzyme in the nucleotide salvage pathway and is involved in the adaptive stress response to chemotherapy. The cytidine analog capecitabine and its metabolite 5'-deoxy-5-fluorocytidine (5'-DFCR) are converted via CDA to 5-fluorouracil, which affects DNA and RNA metabolism. This study investigated a schedule-dependent treatment strategy, proposing that initial chemotherapy induces CDA expression, sensitizing cells to subsequent capecitabine treatment. Basal CDA protein expression was low in different mesothelioma cell lines but increased in the corresponding xenografts. Standard chemotherapy increased CDA protein levels in MPM cells in vitro and in vivo in a schedule-dependent manner. This was associated with epithelial-to-mesenchymal transition and with HIF-1alpha expression at the transcriptional level. In addition, pretreatment with cisplatin and pemetrexed in combination sensitized MPM xenografts to capecitabine. Analysis of a tissue microarray (TMA) consisting of samples from 98 human MPM patients revealed that most human MPM samples had negative CDA expression. While survival curves based on CDA expression in matched samples clearly separated, significance was not reached due to the limited sample size. In non-matched samples, CDA expression before but not after neoadjuvant therapy was significantly associated with worse overall survival. In conclusion, chemotherapy increases CDA expression in xenografts, which is consistent with our in vitro results in MPM and lung cancer. A subset of matched patient samples showed increased CDA expression after therapy, suggesting that a schedule-dependent treatment strategy based on chemotherapy and capecitabine may benefit a selected MPM patient population.
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Affiliation(s)
- Darya Karatkevich
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Tereza Losmanova
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Philipp Zens
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
| | - Haibin Deng
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland
- 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Clinical Medical Research Center of Accurate Diagnosis and Treatment for Esophageal Carcinoma, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Christelle Dubey
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Tuo Zhang
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland
- Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Corsin Casty
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Yanyun Gao
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland
| | - Christina Neppl
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
- Institute of Pathology, Heinrich-Heine University and University Hospital of Duesseldorf, Duesseldorf, Germany
| | - Sabina Berezowska
- Institute of Tissue Medicine and Pathology, University of Bern, Bern, Switzerland
- Department of Laboratory Medicine and Pathology, Institute of Pathology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Wenxiang Wang
- 2nd Department of Thoracic Surgery, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
- Hunan Clinical Medical Research Center of Accurate Diagnosis and Treatment for Esophageal Carcinoma, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013, Hunan, China
| | - Ren-Wang Peng
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland.
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland.
| | - Ralph Alexander Schmid
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland.
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland.
| | - Patrick Dorn
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland.
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland.
| | - Thomas Michael Marti
- Department of General Thoracic Surgery, Inselspital, Bern University Hospital, University of Bern, Murtenstrasse 28, 3008, Bern, Switzerland.
- Oncology-Thoracic Malignancies, Department for BioMedical Research, University of Bern, Bern, Switzerland.
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Xu H, Long S, Xu C, Li Z, Chen J, Yang B, He Y, Xu Z, Li Z, Wei W, Li X. TNC upregulation promotes glioma tumourigenesis through TDG-mediated active DNA demethylation. Cell Death Discov 2024; 10:347. [PMID: 39090080 PMCID: PMC11294444 DOI: 10.1038/s41420-024-02098-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024] Open
Abstract
Gliomas represent the most predominant primary malignant tumor in central nervous system. Thymine DNA glycosylase (TDG) is a central component in active DNA demethylation. However, the specific mechanisms of TDG-mediated active DNA demethylation in gliomas remain unclear. This research indicates TDG expression is overexpressed in gliomas and correlated with poor prognosis. TDG knockdown suppressed the malignant phenotype of gliomas both in vitro and vivo. Notably, RNA-seq analysis revealed a strong association between TDG and tenascin-C (TNC). ChIP-qPCR and MeDIP-qPCR assays were undertaken to confirm that TDG participates in TNC active DNA demethylation process, revealing decreased DNA methylation levels and elevated TNC expression as a result. Silencing TNC expression also suppressed the tumor malignant phenotype in both in vitro and in vivo experiments. Additionally, simultaneous silencing of TNC reduced or even reversed the glioma promotion caused by TDG overexpression. Based on our findings, we conclude that TDG exerts an indispensable role in TNC active DNA demethylation in gliomas. The DNA demethylation process leads to alternations in TNC methylation levels and promotes its expression, thereby contributing to the development of gliomas. These results suggest a novel epigenetic therapeutic strategy targeting active DNA demethylation in gliomas.
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Affiliation(s)
- Hongyu Xu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shengrong Long
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Chengshi Xu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhengwei Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jincao Chen
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Bin Yang
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yongze He
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ziyue Xu
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zhiqiang Li
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Wei Wei
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
| | - Xiang Li
- Brain Research Center, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China.
- Medical Research Institute, Wuhan University, Wuhan, China.
- Sino-Italian Ascula Brain Science Joint Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, China.
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Saw PE, Liu Q, Wong PP, Song E. Cancer stem cell mimicry for immune evasion and therapeutic resistance. Cell Stem Cell 2024; 31:1101-1112. [PMID: 38925125 DOI: 10.1016/j.stem.2024.06.003] [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: 06/15/2023] [Revised: 03/11/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024]
Abstract
Cancer stem cells (CSCs) are heterogeneous, possess self-renewal attributes, and orchestrate important crosstalk in tumors. We propose that the CSC state represents "mimicry" by cancer cells that leads to phenotypic plasticity. CSC mimicry is suggested as CSCs can impersonate immune cells, vasculo-endothelia, or lymphangiogenic cells to support cancer growth. CSCs facilitate both paracrine and juxtracrine signaling to prime tumor-associated immune and stromal cells to adopt pro-tumoral phenotypes, driving therapeutic resistance. Here, we outline the ingenuity of CSCs' mimicry in their quest to evade immune detection, which leads to immunotherapeutic resistance, and highlight CSC-mimicry-targeted therapeutic strategies for robust immunotherapy.
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Affiliation(s)
- Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan, China
| | - Qiang Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ping-Pui Wong
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan, China
| | - Erwei Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China; Nanhai Clinical Translational Center, Sun Yat-sen Memorial Hospital, Foshan, China; Breast Tumor Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China; Zenith Institute of Medical Sciences, Guangzhou 510120, China.
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Visuddho V, Halim P, Helen H, Muhar AM, Iqhrammullah M, Mayulu N, Surya R, Tjandrawinata RR, Ribeiro RIMA, Tallei TE, Taslim NA, Kim B, Syahputra RA, Nurkolis F. Modulation of Apoptotic, Cell Cycle, DNA Repair, and Senescence Pathways by Marine Algae Peptides in Cancer Therapy. Mar Drugs 2024; 22:338. [PMID: 39195454 DOI: 10.3390/md22080338] [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: 05/25/2024] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/29/2024] Open
Abstract
Marine algae, encompassing both macroalgae and microalgae, have emerged as a promising and prolific source of bioactive compounds with potent anticancer properties. Despite their significant therapeutic potential, the clinical application of these peptides is hindered by challenges such as poor bioavailability and susceptibility to enzymatic degradation. To overcome these limitations, innovative delivery systems, particularly nanocarriers, have been explored. Nanocarriers, including liposomes, nanoparticles, and micelles, have demonstrated remarkable efficacy in enhancing the stability, solubility, and bioavailability of marine algal peptides, ensuring controlled release and prolonged therapeutic effects. Marine algal peptides encapsulated in nanocarriers significantly enhance bioavailability, ensuring more efficient absorption and utilization in the body. Preclinical studies have shown promising results, indicating that nanocarrier-based delivery systems can significantly improve the pharmacokinetic profiles and therapeutic outcomes of marine algal peptides. This review delves into the diverse anticancer mechanisms of marine algal peptides, which include inducing apoptosis, disrupting cell cycle progression, and inhibiting angiogenesis. Further research focused on optimizing nanocarrier formulations, conducting comprehensive clinical trials, and continued exploration of marine algal peptides holds great promise for developing innovative, effective, and sustainable cancer therapies.
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Affiliation(s)
- Visuddho Visuddho
- Faculty of Medicine, Universitas Airlangga, Surabaya 60132, Indonesia
| | - Princella Halim
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Indonesia
| | - Helen Helen
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Indonesia
| | - Adi Muradi Muhar
- Faculty of Medicine, Universitas Sumatera Utara, Medan 20155, Indonesia
| | - Muhammad Iqhrammullah
- Postgraduate Program of Public Health, Universitas Muhammadiyah Aceh, Banda Aceh 23123, Indonesia
| | - Nelly Mayulu
- Department of Nutrition, Faculty of Health Science, Muhammadiyah Manado University, Manado 95249, Indonesia
| | - Reggie Surya
- Department of Food Technology, Faculty of Engineering, Bina Nusantara University, Jakarta 11480, Indonesia
| | - Raymond Rubianto Tjandrawinata
- Department of Biotechnology, Faculty of Biotechnology, Atma Jaya Catholic University of Indonesia, Jakarta 12930, Indonesia
| | | | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
| | - Nurpudji Astuti Taslim
- Division of Clinical Nutrition, Department of Nutrition, Faculty of Medicine, Hasanuddin University, Makassar 90245, Indonesia
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Rony Abdi Syahputra
- Department of Pharmacology, Faculty of Pharmacy, Universitas Sumatera Utara, Medan 20155, Indonesia
| | - Fahrul Nurkolis
- Department of Biological Sciences, Faculty of Sciences and Technology, State Islamic University of Sunan Kalijaga (UIN Sunan Kalijaga), Yogyakarta 55281, Indonesia
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Chitoran E, Rotaru V, Ionescu SO, Gelal A, Capsa CM, Bohiltea RE, Mitroiu MN, Serban D, Gullo G, Stefan DC, Simion L. Bevacizumab-Based Therapies in Malignant Tumors-Real-World Data on Effectiveness, Safety, and Cost. Cancers (Basel) 2024; 16:2590. [PMID: 39061228 PMCID: PMC11274419 DOI: 10.3390/cancers16142590] [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: 06/30/2024] [Revised: 07/08/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Overall, it is estimated that more than 3,500,000 patients have received Bevacizumab as part of systemic oncologic treatment. Bevacizumab and its biosimilars are currently marketed in over 130 countries. Given the wide usage of Bevacizumab in current oncological practice, it is very important to compare the "real-world" results to those obtained in controlled clinical trials. This study aims to describe the clinical experience of using Bevacizumab in a large cohort of cancer patients in "non-controlled real-world" conditions with regard to effectiveness, safety, and cost of therapy. METHODS For this purpose, we conducted an open, observational, retrospective study involving all patients treated for solid malignant tumors in the Bucharest Institute of Oncology with "Prof. Dr. Al. Trestioreanu" with Bevacizumab-based systemic therapy, between 2017 and 2021. RESULTS The study consisted of 657 treatment episodes in 625 patients (F/B = 1.62/1, with a median age of 57.6 years) which were treated for malignant tumors (majority colorectal, non-small cell lung, ovarian, and breast cancer). First-line treatment was administered in 229 patients, and the rest received Bevacizumab as second or subsequent lines of treatment. The overall response rate to Bevacizumab-based therapies was around 60-65% across all indication except for subsequent treatment lines in colorectal and ovarian cancers, where lower values were recorded (27.1%, and 31.5% respectively). Median PFS for the entire cohort was 8.2 months (95% CI 6.8-9.6), and the median OS was 13.2 months (95% CI 11.5-14.9). Usual bevacizumab-related toxicities were observed, including bleeding, hypertension, wound-healing complications, gastrointestinal perforation, other types of fistulas, septic complications, and thromboembolic events. Although the clinical benefits are undeniable, the addition of Bevacizumab to standard chemotherapy increased the overall treatment cost by 213%. CONCLUSIONS Bevacizumab remains a high-cost therapy, but it can add to clinical benefits (like overall survival, progression-free survival, and response rate) when used in conjunction with standard chemotherapy. Similar results as those presented in various controlled trials are observable even on unselected cohorts of patients in the uncontrolled conditions of "real-world" oncological practice. Off-label usage is encountered in clinical practice, and this aspect should be monitored given the potential adverse effects of the therapy.
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Affiliation(s)
- Elena Chitoran
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- General Surgery and Surgical Oncology Department I, Bucharest Institute of Oncology “Prof. Dr. Al. Trestioreanu”, 022328 Bucharest, Romania
| | - Vlad Rotaru
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- General Surgery and Surgical Oncology Department I, Bucharest Institute of Oncology “Prof. Dr. Al. Trestioreanu”, 022328 Bucharest, Romania
| | - Sinziana-Octavia Ionescu
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- General Surgery and Surgical Oncology Department I, Bucharest Institute of Oncology “Prof. Dr. Al. Trestioreanu”, 022328 Bucharest, Romania
| | - Aisa Gelal
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- General Surgery and Surgical Oncology Department I, Bucharest Institute of Oncology “Prof. Dr. Al. Trestioreanu”, 022328 Bucharest, Romania
| | - Cristina-Mirela Capsa
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Radiology Department, Bucharest Institute of Oncology “Prof. Dr. Al. Trestioreanu”, 022328 Bucharest, Romania
| | - Roxana-Elena Bohiltea
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Obstetrics and Gynecology Department, “Filantropia” Clinical Hospital, 011132 Bucharest, Romania
| | - Madalina-Nicoleta Mitroiu
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Obstetrics and Gynecology Department, “Filantropia” Clinical Hospital, 011132 Bucharest, Romania
| | - Dragos Serban
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- Surgery Department 4, Bucharest University Emergency Hospital, 050098 Bucharest, Romania
| | - Giuseppe Gullo
- Department of Obstetrics and Gynecology, Villa Sofia Cervello Hospital, University of Palermo, 90146 Palermo, Italy
| | - Daniela-Cristina Stefan
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
| | - Laurentiu Simion
- Medicine School, “Carol Davila” University of Medicine and Pharmacy, 050474 Bucharest, Romania
- General Surgery and Surgical Oncology Department I, Bucharest Institute of Oncology “Prof. Dr. Al. Trestioreanu”, 022328 Bucharest, Romania
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Koudonas A, Dimitriadis G, Anastasiadis A, Papaioannou M. DNA Methylation as Drug Sensitivity Marker in RCC: A Systematic Review. EPIGENOMES 2024; 8:28. [PMID: 39051186 PMCID: PMC11270435 DOI: 10.3390/epigenomes8030028] [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: 03/27/2024] [Revised: 05/16/2024] [Accepted: 06/07/2024] [Indexed: 07/27/2024] Open
Abstract
Patient response after treatment of renal cell cancer (RCC) with systemic agents, which include various drug categories, is generally poor and unpredictable. In this context, the ideal drug administration includes tools to predict the sensitivity of the disease to therapy. The aim of this study was to systematically summarize the reports on the predictive value of the methylation status in the systemic therapy of RCC. Only original articles reporting on the association of promoter methylation with the response of patients or cell lines to systemic agents were included in this review. We applied PRISMA recommendations to the structure and methodology of this systematic review. Our literature search concluded with 31 articles conducted on RCC cell lines and patient tissues. The majority of the studies demonstrated a methylation-dependent response to systemic agents. This correlation suggests that the methylation pattern can be used as a predictive tool in the management of RCC with various classes of systemic agents. However, although methylation biomarkers show promise for predicting response, the evidence of such correlation is still weak. More studies on the gene methylation pattern in patients under systemic therapy and its correlation with different degrees of response are needed.
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Affiliation(s)
- Antonios Koudonas
- First Department of Urology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (A.K.); (G.D.); (A.A.)
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
- Department of Urology, 424 Military Hospital, 564 29 Thessaloniki, Greece
| | - Georgios Dimitriadis
- First Department of Urology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (A.K.); (G.D.); (A.A.)
| | - Anastasios Anastasiadis
- First Department of Urology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (A.K.); (G.D.); (A.A.)
| | - Maria Papaioannou
- First Department of Urology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece; (A.K.); (G.D.); (A.A.)
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, 541 24 Thessaloniki, Greece
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Zheng J, Lu W, Wang C, Chen S, Zhang Q, Su C. Unfolding the mysteries of heterogeneity from a high-resolution perspective: integration analysis of single-cell multi-omics and spatial omics revealed functionally heterogeneous cancer cells in ccRCC. Aging (Albany NY) 2024; 16:10943-10971. [PMID: 38944814 PMCID: PMC11272124 DOI: 10.18632/aging.205974] [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: 09/19/2023] [Accepted: 05/16/2024] [Indexed: 07/01/2024]
Abstract
The genomic landscape of clear cell renal cell carcinoma (ccRCC) has a considerable intra-tumor heterogeneity, which is a significant obstacle in the field of precision oncology and plays a pivotal role in metastasis, recurrence, and therapeutic resistance of cancer. The mechanisms of intra-tumor heterogeneity in ccRCC have yet to be fully established. We integrated single-cell RNA sequencing (scRNA-seq) and transposase-accessible chromatin sequencing (scATAC-seq) data from a single-cell multi-omics perspective. Based on consensus non-negative matrix factorization (cNMF) algorithm, functionally heterogeneous cancer cells were classified into metabolism, inflammatory, and EMT meta programs, with spatial transcriptomics sequencing (stRNA-seq) providing spatial information of such disparate meta programs of cancer cells. The bulk RNA sequencing (RNA-seq) data revealed high clinical prognostic values of functionally heterogeneous cancer cells of three meta programs, with transcription factor regulatory network and motif activities revealing the key transcription factors that regulate functionally heterogeneous ccRCC cells. The interactions between varying meta programs and other cell subpopulations in the microenvironment were investigated. Finally, we assessed the sensitivity of cancer cells of disparate meta programs to different anti-cancer agents. Our findings inform on the intra-tumor heterogeneity of ccRCC and its regulatory networks and offers new perspectives to facilitate the designs of rational therapeutic strategies.
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Affiliation(s)
- Jie Zheng
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Wenhao Lu
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Chengbang Wang
- Department of Urology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Shaohua Chen
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Qingyun Zhang
- Department of Urology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Cheng Su
- Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
- Center for Genomic and Personalized Medicine, Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
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Pang L, Zhou F, Liu Y, Ali H, Khan F, Heimberger AB, Chen P. Epigenetic regulation of tumor immunity. J Clin Invest 2024; 134:e178540. [PMID: 39133578 PMCID: PMC11178542 DOI: 10.1172/jci178540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024] Open
Abstract
Although cancer has long been considered a genetic disease, increasing evidence shows that epigenetic aberrations play a crucial role in affecting tumor biology and therapeutic response. The dysregulated epigenome in cancer cells reprograms the immune landscape within the tumor microenvironment, thereby hindering antitumor immunity, promoting tumor progression, and inducing immunotherapy resistance. Targeting epigenetically mediated tumor-immune crosstalk is an emerging strategy to inhibit tumor progression and circumvent the limitations of current immunotherapies, including immune checkpoint inhibitors. In this Review, we discuss the mechanisms by which epigenetic aberrations regulate tumor-immune interactions and how epigenetically targeted therapies inhibit tumor progression and synergize with immunotherapy.
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