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Kanyal A, Deshmukh B, Davies H, Mamatharani DV, Farheen D, Treeck M, Karmodiya K. PfHDAC1 is an essential regulator of P. falciparum asexual proliferation and host cell invasion genes with a dynamic genomic occupancy responsive to artemisinin stress. mBio 2024:e0237723. [PMID: 38709067 DOI: 10.1128/mbio.02377-23] [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: 09/01/2023] [Accepted: 03/26/2024] [Indexed: 05/07/2024] Open
Abstract
Plasmodium falciparum, the deadly protozoan parasite responsible for malaria, has a tightly regulated gene expression profile closely linked to its intraerythrocytic development cycle. Epigenetic modifiers of the histone acetylation code have been identified as key regulators of the parasite's transcriptome but require further investigation. In this study, we map the genomic distribution of Plasmodium falciparum histone deacetylase 1 (PfHDAC1) across the erythrocytic asexual development cycle and find it has a dynamic occupancy over a wide array of developmentally relevant genes. Overexpression of PfHDAC1 results in a progressive increment in parasite load over consecutive rounds of the asexual infection cycle and is associated with enhanced gene expression of multiple families of host cell invasion factors (merozoite surface proteins, rhoptry proteins, etc.) and with increased merozoite invasion efficiency. With the use of class-specific inhibitors, we demonstrate that PfHDAC1 activity in parasites is crucial for timely intraerythrocytic development. Interestingly, overexpression of PfHDAC1 results in decreased sensitivity to frontline-drug dihydroartemisinin in parasites. Furthermore, we identify that artemisinin exposure can interfere with PfHDAC1 abundance and chromatin occupancy, resulting in enrichment over genes implicated in response/resistance to artemisinin. Finally, we identify that dihydroartemisinin exposure can interrupt the in vitro catalytic deacetylase activity and post-translational phosphorylation of PfHDAC1, aspects that are crucial for its genomic function. Collectively, our results demonstrate PfHDAC1 to be a regulator of critical functions in asexual parasite development and host invasion, which is responsive to artemisinin exposure stress and deterministic of resistance to it. IMPORTANCE Malaria is a major public health problem, with the parasite Plasmodium falciparum causing most of the malaria-associated mortality. It is spread by the bite of infected mosquitoes and results in symptoms such as cyclic fever, chills, and headache. However, if left untreated, it can quickly progress to a more severe and life-threatening form. The World Health Organization currently recommends the use of artemisinin combination therapy, and it has worked as a gold standard for many years. Unfortunately, certain countries in southeast Asia and Africa, burdened with a high prevalence of malaria, have reported cases of drug-resistant infections. One of the major problems in controlling malaria is the emergence of artemisinin resistance. Population genomic studies have identified mutations in the Kelch13 gene as a molecular marker for artemisinin resistance. However, several reports thereafter indicated that Kelch13 is not the main mediator but rather hinted at transcriptional deregulation as a major determinant of drug resistance. Earlier, we identified PfGCN5 as a global regulator of stress-responsive genes, which are known to play a central role in artemisinin resistance generation. In this study, we have identified PfHDAC1, a histone deacetylase as a cell cycle regulator, playing an important role in artemisinin resistance generation. Taken together, our study identified key transcriptional regulators that play an important role in artemisinin resistance generation.
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Affiliation(s)
- Abhishek Kanyal
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India
| | - Bhagyashree Deshmukh
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India
| | - Heledd Davies
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - D V Mamatharani
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India
| | - Dilsha Farheen
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India
| | - Moritz Treeck
- Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Krishanpal Karmodiya
- Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India
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2
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Ocaña-Paredes B, Rivera-Orellana S, Ramírez-Sánchez D, Montalvo-Guerrero J, Freire MP, Espinoza-Ferrao S, Altamirano-Colina A, Echeverría-Espinoza P, Ramos-Medina MJ, Echeverría-Garcés G, Granda-Moncayo D, Jácome-Alvarado A, Andrade MG, López-Cortés A. The pharmacoepigenetic paradigm in cancer treatment. Front Pharmacol 2024; 15:1381168. [PMID: 38720770 PMCID: PMC11076712 DOI: 10.3389/fphar.2024.1381168] [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: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Epigenetic modifications, characterized by changes in gene expression without altering the DNA sequence, play a crucial role in the development and progression of cancer by significantly influencing gene activity and cellular function. This insight has led to the development of a novel class of therapeutic agents, known as epigenetic drugs. These drugs, including histone deacetylase inhibitors, histone acetyltransferase inhibitors, histone methyltransferase inhibitors, and DNA methyltransferase inhibitors, aim to modulate gene expression to curb cancer growth by uniquely altering the epigenetic landscape of cancer cells. Ongoing research and clinical trials are rigorously evaluating the efficacy of these drugs, particularly their ability to improve therapeutic outcomes when used in combination with other treatments. Such combination therapies may more effectively target cancer and potentially overcome the challenge of drug resistance, a significant hurdle in cancer therapy. Additionally, the importance of nutrition, inflammation control, and circadian rhythm regulation in modulating drug responses has been increasingly recognized, highlighting their role as critical modifiers of the epigenetic landscape and thereby influencing the effectiveness of pharmacological interventions and patient outcomes. Epigenetic drugs represent a paradigm shift in cancer treatment, offering targeted therapies that promise a more precise approach to treating a wide spectrum of tumors, potentially with fewer side effects compared to traditional chemotherapy. This progress marks a step towards more personalized and precise interventions, leveraging the unique epigenetic profiles of individual tumors to optimize treatment strategies.
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Affiliation(s)
- Belén Ocaña-Paredes
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | - David Ramírez-Sánchez
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | - María Paula Freire
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | | | | | - María José Ramos-Medina
- German Cancer Research Center (DKFZ), Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Gabriela Echeverría-Garcés
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | | | - Andrea Jácome-Alvarado
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - María Gabriela Andrade
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
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3
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Orlacchio A, Muzyka S, Gonda TA. Epigenetic therapeutic strategies in pancreatic cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 383:1-40. [PMID: 38359967 DOI: 10.1016/bs.ircmb.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid malignancies, characterized by its aggressiveness and metastatic potential, with a 5-year survival rate of only 8-11%. Despite significant improvements in PDAC treatment and management, therapeutic alternatives are still limited. One of the main reasons is its high degree of intra- and inter-individual tumor heterogeneity which is established and maintained through a complex network of transcription factors and epigenetic regulators. Epigenetic drugs, have shown promising preclinical results in PDAC and are currently being evaluated in clinical trials both for their ability to sensitize cancer cells to cytotoxic drugs and to counteract the immunosuppressive characteristic of PDAC tumor microenvironment. In this review, we discuss the current status of epigenetic treatment strategies to overcome molecular and cellular PDAC heterogeneity in order to improve response to therapy.
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Affiliation(s)
- Arturo Orlacchio
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States
| | - Stephen Muzyka
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States
| | - Tamas A Gonda
- Division of Gastroenterology and Hepatology, New York University, New York, NY, United States.
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4
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Dai D, Wu D, Ni R, Li P, Tian Z, Shui Y, Hu H, Wei Q. Novel insights into the progression and prognosis of the calpain family members in hepatocellular carcinoma: a comprehensive integrated analysis. Front Mol Biosci 2023; 10:1162409. [PMID: 37503539 PMCID: PMC10368982 DOI: 10.3389/fmolb.2023.1162409] [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: 02/09/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023] Open
Abstract
Objectives: The goal of our bioinformatics study was to comprehensively analyze the association between the whole calpain family members and the progression and prognosis of hepatocellular carcinoma (HCC). Methods: The data were collected from The Cancer Genome Atlas (TCGA). The landscape of the gene expression, copy number variation (CNV), mutation, and DNA methylation of calpain members were analyzed. Clustering analysis was performed to stratify the calpain-related groups. The least absolute shrinkage and selection operator (LASSO)-based Cox model was used to select hub survival genes. Results: We found 14 out of 16 calpain members expressed differently between tumor and normal tissues of HCC. The clustering analyses revealed high- and low-risk calpain groups which had prognostic difference. We found the high-risk calpain group had higher B cell infiltration and higher expression of immune checkpoint genes HAVCR2, PDCD1, and TIGHT. The CMap analysis found that the histone deacetylase (HDAC) inhibitor trichostatin A and the PI3K-AKT-mTOR pathway inhibitors LY-294002 and wortmannin might have a therapeutic effect on the high-risk calpain group. The DEGs between calpain groups were identified. Subsequent univariate Cox analysis of each DEG and LASSO-based Cox model obtained a calpain-related prognostic signature. The risk score model of this signature showed good ability to predict the overall survival of HCC patients in TCGA datasets and external validation datasets from the Gene Expression Omnibus database and the International Cancer Genome Consortium database. Conclusion: We found that calpain family members were associated with the progression, prognosis, and drug response of HCC. Our results require further studies to confirm.
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Affiliation(s)
- Dongjun Dai
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Dehao Wu
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Runliang Ni
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Ping Li
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhifeng Tian
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongjie Shui
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hanguang Hu
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
- Department of Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Zhejiang University School of Medicine, Hangzhou, China
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Subhan MA, Parveen F, Shah H, Yalamarty SSK, Ataide JA, Torchilin VP. Recent Advances with Precision Medicine Treatment for Breast Cancer including Triple-Negative Sub-Type. Cancers (Basel) 2023; 15:cancers15082204. [PMID: 37190133 DOI: 10.3390/cancers15082204] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023] Open
Abstract
Breast cancer is a heterogeneous disease with different molecular subtypes. Breast cancer is the second leading cause of mortality in woman due to rapid metastasis and disease recurrence. Precision medicine remains an essential source to lower the off-target toxicities of chemotherapeutic agents and maximize the patient benefits. This is a crucial approach for a more effective treatment and prevention of disease. Precision-medicine methods are based on the selection of suitable biomarkers to envision the effectiveness of targeted therapy in a specific group of patients. Several druggable mutations have been identified in breast cancer patients. Current improvements in omics technologies have focused on more precise strategies for precision therapy. The development of next-generation sequencing technologies has raised hopes for precision-medicine treatment strategies in breast cancer (BC) and triple-negative breast cancer (TNBC). Targeted therapies utilizing immune checkpoint inhibitors (ICIs), epidermal growth factor receptor inhibitor (EGFRi), poly(ADP-ribose) polymerase inhibitor (PARPi), antibody-drug conjugates (ADCs), oncolytic viruses (OVs), glucose transporter-1 inhibitor (GLUT1i), and targeting signaling pathways are potential treatment approaches for BC and TNBC. This review emphasizes the recent progress made with the precision-medicine therapy of metastatic breast cancer and TNBC.
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Affiliation(s)
- Md Abdus Subhan
- Department of Chemistry, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Farzana Parveen
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Department of Pharmacy Services, DHQ Hospital Jhang 35200, Primary and Secondary Healthcare Department, Government of Punjab, Lahore 54000, Pakistan
| | - Hassan Shah
- Department of Pharmaceutics, Faculty of Pharmacy, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- CPBN, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | | | - Janaína Artem Ataide
- CPBN, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, SP, Brazil
| | - Valdimir P Torchilin
- CPBN, Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
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6
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Tagoug A, Safra I. The Impact of Panobinostat on Cell Death in Combination with S63845 in Multiple Myeloma Cells. Indian J Hematol Blood Transfus 2023; 39:245-257. [PMID: 37006981 PMCID: PMC10064410 DOI: 10.1007/s12288-022-01584-4] [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: 06/27/2022] [Accepted: 09/13/2022] [Indexed: 01/03/2023] Open
Abstract
Multiple myeloma is a B cell neoplasm characterized by bone marrow infiltration with malignant plasma cells. The Overexpression of histone deacetylase prevents apoptosis of myeloma cells by different mechanisms. The combination of Panobinostat with a BH3 mimetic, S63845, has demonstrated significant antitumor activity in multiple myeloma. We examined the impact of Panobinostat combined with MCL-1 inhibitor on multiple myeloma cell lines in vivo and in vitro as well as on fresh human myeloma cells. Our study shows that MCL-1 remains a major resistant factor to cell death induced by Panobinostat. Therefore, the inhibition of the MCL-1 member is considered a therapeutic strategy to kill the myeloma cells. We examined that the MCL-1 inhibitor (S63845) enhanced the cytotoxic effect of Panobinostat and decreased the viability of human cell lines and primary myeloma patient cells. Mechanistically, Panobinostat/S63845 control cell death via an intrinsic pathway. Given these data, the combination can be a promising therapeutic target for myeloma patients and should be further explored in clinical trials.
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Affiliation(s)
- Arwa Tagoug
- Laboratory of Molecular and Cellular Hematology, LR6IPT07, Pasteur Institute of Tunis, 13 Place Pasteur BP 74, 1002 Tunis Belvedere, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
| | - Ines Safra
- Laboratory of Molecular and Cellular Hematology, LR6IPT07, Pasteur Institute of Tunis, 13 Place Pasteur BP 74, 1002 Tunis Belvedere, Tunisia
- University of Tunis El Manar, Tunis, Tunisia
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7
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Li X, Fu X, Li H, Gao Y, Wang W, Shen Y. Leptin differentially regulate cell apoptosis and cycle by histone acetylation in tibial and vertebral epiphyseal plates. Cell Biol Int 2023; 47:660-668. [PMID: 36453460 DOI: 10.1002/cbin.11968] [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: 06/23/2022] [Revised: 10/31/2022] [Accepted: 11/19/2022] [Indexed: 12/03/2022]
Abstract
Leptin showed different apoptosis regulation effects on the chondrocytes from tibial and vertebral epiphyseal plates. However, the mechanism is still unclear. In this study, we tested the protein profile of tibial and vertebral epiphyseal plate chondrocytes with and without leptin stimulation by mass spectrometry and found that the histone acetylation level of tibial chondrocytes was decreased after leptin treatment, while increased in vertebral epiphyseal plates. COIP assay showed that leptin promoted H3, H4 histone acetylation by recruiting CREB binding protein (CBP)/P300 to activate histone acetyl transferases (HATs) activity in vertebral disc chondrocytes. But in tibial plate cartilage cells, leptin did not recruit CBP and p300, thus differently affect the apoptosis of epiphyseal plate chondrocytes. Through explored the mechanism of histone acetylation modulated by leptin, and its effect on cartilage cell apoptosis and cell cycle regulation, This provides a novel target therapy possibility therapeutic approach to for the related disease.
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Affiliation(s)
- Xiaomiao Li
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Xiaodong Fu
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Hao Li
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yingjian Gao
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Weili Wang
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yi Shen
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
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8
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Depsipeptides Targeting Tumor Cells: Milestones from In Vitro to Clinical Trials. MOLECULES (BASEL, SWITZERLAND) 2023; 28:molecules28020670. [PMID: 36677728 PMCID: PMC9864405 DOI: 10.3390/molecules28020670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023]
Abstract
Cancer is currently considered one of the most threatening diseases worldwide. Diet could be one of the factors that can be enhanced to comprehensively address a cancer patient's condition. Unfortunately, most molecules capable of targeting cancer cells are found in uncommon food sources. Among them, depsipeptides have emerged as one of the most reliable choices for cancer treatment. These cyclic amino acid oligomers, with one or more subunits replaced by a hydroxylated carboxylic acid resulting in one lactone bond in a core ring, have broadly proven their cancer-targeting efficacy, some even reaching clinical trials and being commercialized as "anticancer" drugs. This review aimed to describe these depsipeptides, their reported amino acid sequences, determined structure, and the specific mechanism by which they target tumor cells including apoptosis, oncosis, and elastase inhibition, among others. Furthermore, we have delved into state-of-the-art in vivo and clinical trials, current methods for purification and synthesis, and the recognized disadvantages of these molecules. The information collated in this review can help researchers decide whether these molecules should be incorporated into functional foods in the near future.
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Shanmukha KD, Paluvai H, Lomada SK, Gokara M, Kalangi SK. Histone deacetylase (HDACs) inhibitors: Clinical applications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:119-152. [DOI: 10.1016/bs.pmbts.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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10
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A Comprehensive Analysis of the Effects of Key Mitophagy Genes on the Progression and Prognosis of Lung Adenocarcinoma. Cancers (Basel) 2022; 15:cancers15010057. [PMID: 36612054 PMCID: PMC9817891 DOI: 10.3390/cancers15010057] [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: 11/01/2022] [Revised: 12/17/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
The aim of our study was to perform a comprehensive analysis of the gene expression, copy number variation (CNV) and mutation of key mitophagy genes in the progression and prognosis of lung adenocarcinoma (LUAD). We obtained the data from The Cancer Genome Atlas (TCGA). Clustering analysis was performed to stratify the mitophagy related groups. The least absolute shrinkage and selection operator (LASSO) based cox model was used to select hub survival genes. An independent validation cohort was retrieved from Gene Expression Omnibus database. We found 24 out of 27 mitophagy genes were aberrantly expressed between tumor and normal samples. CNV gains were associated with higher expression of mitophagy genes in 23 of 27 mitophagy genes. The clustering analysis identified high and low risk mitophagy groups with distinct survival differences. The high risk mitophagy groups had higher tumor mutation burden, stemness phenotype, total CNVs and lower CD4+ T cells infiltration. Drugs targeted to high risk mitophagy groups were identified including the PI3K/AKT/mTOR inhibitor, HDAC inhibitor and chemotherapy agents such as cisplatin and gemcitabine. In addition, the differentially expressed genes (DEGs) were identified between mitophagy groups. Further univariate Cox analysis of each DEG and subsequent LASSO-based Cox model revealed a mitophagy-related prognostic signature. The risk score model of this signature showed a strong ability to predict the overall survival of LUAD patients in training and validation datasets. In conclusion, the mitophagy genes played an important role in the progression and prognosis of LUAD, which might provide useful information for the treatment of LUAD.
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11
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Hai R, Yang D, Zheng F, Wang W, Han X, Bode AM, Luo X. The emerging roles of HDACs and their therapeutic implications in cancer. Eur J Pharmacol 2022; 931:175216. [PMID: 35988787 DOI: 10.1016/j.ejphar.2022.175216] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/03/2022] [Accepted: 08/12/2022] [Indexed: 12/25/2022]
Abstract
Deregulation of protein post-translational modifications is intensively involved in the etiology of diseases, including degenerative diseases, inflammatory injuries, and cancers. Acetylation is one of the most common post-translational modifications of proteins, and the acetylation levels are controlled by two mutually antagonistic enzyme families, histone acetyl transferases (HATs) and histone deacetylases (HDACs). HATs loosen the chromatin structure by neutralizing the positive charge of lysine residues of histones; whereas HDACs deacetylate certain histones, thus inhibiting gene transcription. Compared with HATs, HDACs have been more intensively studied, particularly regarding their clinical significance. HDACs extensively participate in the regulation of proliferation, migration, angiogenesis, immune escape, and therapeutic resistance of cancer cells, thus emerging as critical targets for clinical cancer therapy. Compared to HATs, inhibitors of HDAC have been clinically used for cancer treatment. Here, we enumerate and integratethe mechanisms of HDAC family members in tumorigenesis and cancer progression, and address the new and exciting therapeutic implications of single or combined HDAC inhibitor (HDACi) treatment.
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Affiliation(s)
- Rihan Hai
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, PR China
| | - Deyi Yang
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, PR China
| | - Feifei Zheng
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, PR China
| | - Weiqin Wang
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, PR China
| | - Xing Han
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, PR China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Nuclear Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, 410078, PR China; Cancer Research Institute, School of Basic Medicine, Central South University, Changsha, Hunan, 410078, PR China; Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, 410078, China; Key Laboratory of Biological Nanotechnology of National Health Commission, Central South University, Changsha, Hunan, 410078, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410078, China.
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12
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Wu TY, Chen M, Chen IC, Chen YJ, Chen CY, Wang CH, Cheng JJ, Nepali K, Chuang KH, Liou JP. Rational design of synthetically tractable HDAC6/HSP90 dual inhibitors to destroy immune-suppressive tumor microenvironment. J Adv Res 2022; 46:159-171. [PMID: 35752438 PMCID: PMC10105078 DOI: 10.1016/j.jare.2022.06.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 06/06/2022] [Accepted: 06/18/2022] [Indexed: 12/18/2022] Open
Abstract
INTRODUCTION The tumor microenvironment is mainly flooded with immunosuppressive cells and inhibitory cytokines, resulting in the inability of effective immune cells to infiltrate and recognize tumors and even the loss of anti-cancer ability. OBJECTIVES We propose a novel HDAC6/HSP90 dual inhibitory strategy as well as a chemoimmunotherapeutic agent that does not only kill tumor cells but also destroys the tumor microenvironment and enhances anti-cancer immunity. METHODS A hybrid scaffold construction approach was leveraged to furnish a series of rationally designed resorcinol-based hydroxamates as dual selective HDAC6/HSP90 inhibitors. The drug design campaign commenced with a fragment recruitment process to pinpoint validated structural units to inhibit HDAC6 and HSP90, followed by their installation in flexible HDAC inhibitory templates via an efficient and facile multistep synthetic route. Subsequent evaluations identified a strikingly potent selective HDAC6/HSP90 dual inhibitor (compound 17) via molecular and biological analysis in vitro and in vivo. RESULTS Compound 17 exhibited not only direct cytotoxicity to cancer cells but also downregulated immune checkpoints (PD-L1 and IDO) expression in tumors via the inhibition of STAT1 pathway and degradation of oncogene proteins (Src, AKT, Rb, and FAK), leading to in vivo tumor growth inhibition. These multiple effects enabled the effector T cells to largely infiltrate into the tumor region and release granzyme B to kill cancer cells. In addition, compound 17 also decreased TGF-β secretion from normal cells, resulting in the systemic reduction of immunosuppressive regulatory T cells. Delightfully, a cocktail treatment of compound 17 and anti-PD-1 antibodies demonstrated synergistic efficacy to eliminate solid tumors with 83.9% of tumor growth inhibition. CONCLUSION In summary, the impressive activity profile of compound 17, as an effective anticancer agent and a potential immunosensitizer, forecasts the application of HDAC6/HSP90 dual inhibitory strategy to overcome the immunosuppressive tumor microenvironment.
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Affiliation(s)
- Tung-Yun Wu
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Michael Chen
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - I-Chung Chen
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Yi-Jou Chen
- Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Che-Yi Chen
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Chang-Hung Wang
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan
| | - Jing-Jy Cheng
- National Research Institute of Chinese Medicine, Ministry of Health and Welfare, Taipei 11221, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; TMU Research Center for Drug Discovery, Taipei Medical University, Taipei 110031, Taiwan.
| | - Kuo-Hsiang Chuang
- Ph.D. Program in Clinical Drug Development of Herbal Medicine, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; Graduate Institute of Pharmacognosy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; TMU Research Center for Drug Discovery, Taipei Medical University, Taipei 110031, Taiwan; Traditional Herbal Medicine Research Center of Taipei Medical University Hospital, Taipei 110031, Taiwan.
| | - Jing-Ping Liou
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 110031, Taiwan; TMU Research Center for Drug Discovery, Taipei Medical University, Taipei 110031, Taiwan.
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Ubiquitination-Proteasome System (UPS) and Autophagy Two Main Protein Degradation Machineries in Response to Cell Stress. Cells 2022; 11:cells11050851. [PMID: 35269473 PMCID: PMC8909305 DOI: 10.3390/cells11050851] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/17/2022] [Accepted: 02/22/2022] [Indexed: 02/07/2023] Open
Abstract
In response to environmental stimuli, cells make a series of adaptive changes to combat the injury, repair the damage, and increase the tolerance to the stress. However, once the damage is too serious to repair, the cells will undergo apoptosis to protect the overall cells through suicidal behavior. Upon external stimulation, some intracellular proteins turn into unfolded or misfolded protein, exposing their hydrophobic regions to form protein aggregation, which may ultimately produce serious damage to the cells. Ubiquitin plays an important role in the degradation of these unnatural proteins by tagging with ubiquitin chains in the ubiquitin-proteasome or autophagy system. If the two processes fail to eliminate the abnormal protein aggregates, the cells will move to apoptosis and death. Dysregulation of ubiquitin-proteasome system (UPS) and autophagy may result in the development of numerous diseases. This review focuses on the molecular mechanisms of UPS and autophagy in clearance of intracellular protein aggregates, and the relationship between dysregulation of ubiquitin network and diseases.
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14
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Peng Z, Zhao Q, Tian X, Lei T, Xiang R, Chen L, Yang Y. Discovery of Potent and Isoform‐Selective Histone Deacetylase Inhibitors Using Structure‐Based Virtual Screening and Biological Evaluation. Mol Inform 2022; 41:e2100295. [DOI: 10.1002/minf.202100295] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/26/2022] [Indexed: 11/10/2022]
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Versemann L, Hessmann E, Ulisse M. Epigenetic Therapeutic Strategies to Target Molecular and Cellular Heterogeneity in Pancreatic Cancer. Visc Med 2022; 38:11-19. [PMID: 35291698 PMCID: PMC8874235 DOI: 10.1159/000519859] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/22/2021] [Indexed: 07/25/2023] Open
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) remains a major challenge in cancer medicine and is characterized by a 5-year survival rate of <10%. Compelling evidence suggests that the devastating disease outcome of PDAC patients is linked to a high degree of intra- and interindividual tumor heterogeneity, which is predominantly installed at the level of gene transcription. The cellular and molecular complexities of the disease explain the poor efficacy of "one-size-fits-all" therapeutic approaches in PDAC treatment and strongly argue for pursuing tailored therapeutic strategies to tackle PDAC. In a highly dynamic manner, a network of transcription factors and epigenetic regulatory proteins temporally and spatially control the diverse transcriptomic states determining PDAC heterogeneity. Given the reversibility of epigenetic processes, pharmacological intervention with key epigenetic drivers of PDAC heterogeneity appeals as a promising concept to shift the transcriptomic phenotype of PDAC toward a less aggressive and more chemosensible state. SUMMARY In this review, we discuss the chances and pitfalls of epigenetic treatment strategies in overcoming and shifting molecular and cellular PDAC heterogeneities in order to combat PDAC. To this end, we utilized the keywords "pancreatic cancer," "heterogeneity," and "epigenetics" to search for relevant articles on the database PubMed and selected interventional studies enrolling PDAC patients as displayed in clinicaltrails.gov to generate a synopsis of clinical trials involving epigenetic targeting. KEY MESSAGES Targeting epigenetic regulators in PDAC represents a promising concept to reprogram molecular and cellular tumor heterogeneities in the pancreas and hence to modulate the PDAC phenotype in favor of a less aggressive and more therapy susceptible disease course. However, we just start to understand the complex interactions of epigenetic regulators in controlling PDAC plasticity, and a clinical breakthrough utilizing epigenetic targeting in PDAC patients has not been achieved yet. Nevertheless, increasing translational efforts which consider the pleiotropic effects of targeting epigenetic regulation in different cellular compartments of the tumor and that focus on the utility and sequence of combinatory treatment approaches might pave the way toward novel epigenetic treatment strategies in PDAC therapy.
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Affiliation(s)
- Lennart Versemann
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, Goettingen, Germany
| | - Elisabeth Hessmann
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, Goettingen, Germany
- Clinical Research Unit KFO5002, University Medical Center Goettingen, Goettingen, Germany
| | - Maria Ulisse
- Department of Gastroenterology, Gastrointestinal Oncology and Endocrinology, University Medical Center Goettingen, Goettingen, Germany
- Clinical Research Unit KFO5002, University Medical Center Goettingen, Goettingen, Germany
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Pu Y, Wang J, Wang S. Role of autophagy in drug resistance and regulation of osteosarcoma (Review). Mol Clin Oncol 2022; 16:72. [PMID: 35251623 DOI: 10.3892/mco.2022.2505] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 11/17/2021] [Indexed: 11/06/2022] Open
Affiliation(s)
- Yanchuan Pu
- Department of Orthopedics, Wuwei People's Hospital, Wuwei, Gansu 733000, P.R. China
| | - Jin Wang
- Department of Orthopedics, Wuwei People's Hospital, Wuwei, Gansu 733000, P.R. China
| | - Shizhong Wang
- Department of Orthopedics, Wuwei People's Hospital, Wuwei, Gansu 733000, P.R. China
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Dai D, Guo Y, Shui Y, Li J, Jiang B, Wei Q. Combination of Radiosensitivity Gene Signature and PD-L1 Status Predicts Clinical Outcome of Patients With Locally Advanced Head and Neck Squamous Cell Carcinoma: A Study Based on The Cancer Genome Atlas Dataset. Front Mol Biosci 2022; 8:775562. [PMID: 34970597 PMCID: PMC8712874 DOI: 10.3389/fmolb.2021.775562] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
Aim: The aim of our study was to investigate the potential predictive value of the combination of radiosensitivity gene signature and PD-L1 expression for the prognosis of locally advanced head and neck squamous cell carcinoma (HNSCC). Methods: The cohort was selected from The Cancer Genome Atlas (TCGA) and classified into the radiosensitive (RS) group and radioresistant (RR) group by a radiosensitivity-related gene signature. The cohort was also grouped as PD-L1-high or PD-L1-low based on PD-L1 mRNA expression. The least absolute shrinkage and selection operator (lasso)-based Cox model was used to select hub survival genes. An independent validation cohort was obtained from the Gene Expression Omnibus (GEO) database. Results: We selected 288 locally advanced HNSCC patients from TCGA. The Kaplan–Meier method found that the RR and PD-L1-high group had a worse survival than others (p = 0.033). The differentially expressed gene (DEG) analysis identified 553 upregulated genes and 486 downregulated genes (p < 0.05, fold change >2) between the RR and PD-L1-high group and others. The univariate Cox analysis of each DEG and subsequent lasso-based Cox model revealed five hub survival genes (POU4F1, IL34, HLF, CBS, and RNF165). A further hub survival gene-based risk score model was constructed, which was validated by an external cohort. We observed that a higher risk score predicted a worse prognosis (p = 0.0013). The area under the receiver operating characteristic curve (AUC) plots showed that this risk score model had good prediction value (1-year AUC = 0.684, 2-year AUC = 0.702, and 3-year AUC = 0.688). Five different deconvolution methods all showed that the B cells were lower in the RR and PD-L1-high group (p < 0.05). Finally, connectivity mapping analysis showed that the histone deacetylase (HDAC) inhibitor trichostatin A might have the potential to reverse the phenotype of RR and PD-L1-high in locally advanced HNSCC (p < 0.05, false discovery rate <0.1). Conclusion: The combination of 31-gene signature and the PD-L1 mRNA expression had a potential predictive value for the prognosis of locally advanced HNSCC who had RT. The B cells were lower in the RR and PD-L1-high group. The identified risk gene signature of locally advanced HNSCC and the potential therapeutic drug trichostatin A for the RR and PD-L1-high group are worth being further studied in a prospective homogenous cohort.
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Affiliation(s)
- Dongjun Dai
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yinglu Guo
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yongjie Shui
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinfan Li
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Biao Jiang
- Department of Radiology, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Simultaneous administration of bromodomain and histone deacetylase I inhibitors alleviates cognition deficit in Alzheimer's model of rats. Brain Res Bull 2021; 179:49-56. [PMID: 34915044 DOI: 10.1016/j.brainresbull.2021.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 12/02/2021] [Accepted: 12/07/2021] [Indexed: 01/22/2023]
Abstract
BACKGROUND Histone deacetylases (HDACs) target various genes responsible for cognitive functions. However, chromatin readers, particularly bromodomain-containing protein 4 (BRD4), are capable to change the final products of genes. The objective of this study was to evaluate the simultaneous effects of inhibition of HDACs and BRD4 on spatial and aversive memories impaired by amyloid β (Aβ) in a rat model of Alzheimer's disease (AD) considering CREB and TNF-α signaling. METHODS Forty male Wistar rats aged 3 months were randomly divided into five groups: saline +DMSO, Aβ+saline+DMSO, Aβ+JQ1, Aβ+MS-275, Aβ+JQ1+MS-275, and received the related treatments. MS-275, is the second generation of HDACs inhibitor, and JQ1 is a potent inhibitor of the BET family of bromodomain proteins in mammals. After the treatments, cognitive function was assessed by Morris water maze (MWM) and passive avoidance learning (PAL). The hippocampal level of mRNA for CREB and TNF-α, and also phosphorylated CREB were measured using real-time PCR and western blotting respectively. RESULTS Administration of JQ1 and MS-275, either separately or simultaneously, improved acquisition and retrieval of spatial and aversive memories as it was evident by decreased escape latency and increased time spent in the target quadrant (TTS) in Morris water maze (MWM), together with increase in step-through latency, but reduced time spent in the dark zone time in passive avoidance learning (PAL) compared with Aβ+saline+DMSO. Furthermore, there was a significant rise in the hippocampal level of CREB mRNA and phosphorylated CREB, but a reduction in TNF-α expression in comparison with Aβ + Saline. CONCLUSION Simultaneous administration of JQ1 and MS-275 improves acquisition and retrieval of both spatial and aversive memories partly via CREB and TNF-α signaling with no superiority to monotherapy.
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Yu X, Li M, Guo C, Wu Y, Zhao L, Shi Q, Song J, Song B. Therapeutic Targeting of Cancer: Epigenetic Homeostasis. Front Oncol 2021; 11:747022. [PMID: 34765551 PMCID: PMC8576334 DOI: 10.3389/fonc.2021.747022] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 10/11/2021] [Indexed: 12/12/2022] Open
Abstract
A large number of studies have revealed that epigenetics plays an important role in cancer development. However, the currently-developed epigenetic drugs cannot achieve a stable curative effect. Thus, it may be necessary to redefine the role of epigenetics in cancer development. It has been shown that embryonic development and tumor development share significant similarities in terms of biological behavior and molecular expression patterns, and epigenetics may be the link between them. Cell differentiation is likely a manifestation of epigenetic homeostasis at the cellular level. In this article, we introduced the importance of epigenetic homeostasis in cancer development and analyzed the shortcomings of current epigenetic treatment regimens. Understanding the dynamic process of epigenetic homeostasis in organ development can help us characterize cancer according to its differentiation stages, explore new targets for cancer treatment, and improve the clinical prognosis of patients with cancer.
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Affiliation(s)
- Xiaoyuan Yu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Menglu Li
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Chunyan Guo
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Yuesheng Wu
- Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Li Zhao
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Qinying Shi
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Jianbo Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
| | - Bin Song
- Cancer Center, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, China
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Nguyen A, Dzulko M, Murr J, Yen Y, Schneider G, Krämer OH. Class 1 Histone Deacetylases and Ataxia-Telangiectasia Mutated Kinase Control the Survival of Murine Pancreatic Cancer Cells upon dNTP Depletion. Cells 2021; 10:2520. [PMID: 34685500 PMCID: PMC8534202 DOI: 10.3390/cells10102520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/13/2021] [Accepted: 09/18/2021] [Indexed: 12/20/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with a dismal prognosis. Here, we show how an inhibition of de novo dNTP synthesis by the ribonucleotide reductase (RNR) inhibitor hydroxyurea and an inhibition of epigenetic modifiers of the histone deacetylase (HDAC) family affect short-term cultured primary murine PDAC cells. We used clinically relevant doses of hydroxyurea and the class 1 HDAC inhibitor entinostat. We analyzed the cells by flow cytometry and immunoblot. Regarding the induction of apoptosis and DNA replication stress, hydroxyurea and the novel RNR inhibitor COH29 are superior to the topoisomerase-1 inhibitor irinotecan which is used to treat PDAC. Entinostat promotes the induction of DNA replication stress by hydroxyurea. This is associated with an increase in the PP2A subunit PR130/PPP2R3A and a reduction of the ribonucleotide reductase subunit RRM2 and the DNA repair protein RAD51. We further show that class 1 HDAC activity promotes the hydroxyurea-induced activation of the checkpoint kinase ataxia-telangiectasia mutated (ATM). Unlike in other cell systems, ATM is pro-apoptotic in hydroxyurea-treated murine PDAC cells. These data reveal novel insights into a cytotoxic, ATM-regulated, and HDAC-dependent replication stress program in PDAC cells.
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Affiliation(s)
- Alexandra Nguyen
- Department of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, 55131 Mainz, Germany; (A.N.); (M.D.)
| | - Melanie Dzulko
- Department of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, 55131 Mainz, Germany; (A.N.); (M.D.)
| | - Janine Murr
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany; (J.M.); (G.S.)
| | - Yun Yen
- Ph.D. Program for Cancer Biology and Drug Discovery, Taipei Medical University, 250 Wu Hsing Street, Taipei 110, Taiwan;
| | - Günter Schneider
- Medical Clinic and Polyclinic II, Klinikum rechts der Isar, Technical University Munich, 81675 München, Germany; (J.M.); (G.S.)
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Oliver H. Krämer
- Department of Toxicology, University Medical Center, Obere Zahlbacher Str. 67, 55131 Mainz, Germany; (A.N.); (M.D.)
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Cho H, Son WC, Lee YS, Youn EJ, Kang CD, Park YS, Bae J. Differential Effects of Histone Deacetylases on the Expression of NKG2D Ligands and NK Cell-Mediated Anticancer Immunity in Lung Cancer Cells. Molecules 2021; 26:molecules26133952. [PMID: 34203519 PMCID: PMC8271929 DOI: 10.3390/molecules26133952] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 11/17/2022] Open
Abstract
Histone acetylation is an epigenetic mechanism that regulates the expression of various genes, such as natural killer group 2, member D (NKG2D) ligands. These NKG2D ligands are the key molecules that activate immune cells expressing the NKG2D receptor. It has been observed that cancer cells overexpress histone deacetylases (HDACs) and show reduced acetylation of nuclear histones. Furthermore, HDAC inhibitors are known to upregulate the expression of NKG2D ligands. Humans have 18 known HDAC enzymes that are divided into four classes. At present, it is not clear which types of HDAC are involved in the expression of NKG2D ligands. We hypothesized that specific types of HDAC genes might be responsible for altering the expression of NKG2D ligands. In this study, we monitored the expression of NKG2D ligands and major histocompatibility complex (MHC) class I molecules in lung cancer cells which were treated with six selective HDAC inhibitors and specific small interfering RNAs (siRNAs). We observed that treatment with FK228, which is a selective HDAC1/2 inhibitor, also known as Romidepsin, induced NKG2D ligand expression at the transcriptional and proteomic levels in two different lung cancer cell lines. It also caused an increase in the susceptibility of NCI-H23 cells to NK cells. Silencing HDAC1 or HDAC2 using specific siRNAs increased NKG2D ligand expression. In conclusion, it appears that HDAC1 and HDAC2 might be the key molecules regulating the expression of NKG2D ligands. These results imply that specifically inhibiting HDAC1 and HDAC2 could induce the expression of NKG2D ligands and improve the NK cell-mediated anti-cancer immunity.
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Affiliation(s)
- Haeryung Cho
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 50612, Korea; (H.C.); (Y.-S.L.); (E.J.Y.); (C.-D.K.)
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan 50612, Korea
| | - Woo-Chang Son
- Department of Research Center, Dongnam Institute of Radiological and Medical Sciences, Gijang, Busan 46033, Korea;
| | - Young-Shin Lee
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 50612, Korea; (H.C.); (Y.-S.L.); (E.J.Y.); (C.-D.K.)
| | - Eun Jung Youn
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 50612, Korea; (H.C.); (Y.-S.L.); (E.J.Y.); (C.-D.K.)
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan 50612, Korea
| | - Chi-Dug Kang
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 50612, Korea; (H.C.); (Y.-S.L.); (E.J.Y.); (C.-D.K.)
| | - You-Soo Park
- Department of Research Center, Dongnam Institute of Radiological and Medical Sciences, Gijang, Busan 46033, Korea;
- Correspondence: (Y.-S.P.); (J.B.); Tel.: +82-51-720-5114(Y.-S.P.); +82-51-510-8085 (J.B.); Fax: +82-51-510-8086 (J.B.)
| | - Jaeho Bae
- Department of Biochemistry, Pusan National University School of Medicine, Yangsan 50612, Korea; (H.C.); (Y.-S.L.); (E.J.Y.); (C.-D.K.)
- PNU GRAND Convergence Medical Science Education Research Center, Pusan National University School of Medicine, Yangsan 50612, Korea
- Correspondence: (Y.-S.P.); (J.B.); Tel.: +82-51-720-5114(Y.-S.P.); +82-51-510-8085 (J.B.); Fax: +82-51-510-8086 (J.B.)
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22
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Wang Y, Xie Q, Tan H, Liao M, Zhu S, Zheng LL, Huang H, Liu B. Targeting cancer epigenetic pathways with small-molecule compounds: Therapeutic efficacy and combination therapies. Pharmacol Res 2021; 173:105702. [PMID: 34102228 DOI: 10.1016/j.phrs.2021.105702] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/07/2021] [Accepted: 05/29/2021] [Indexed: 02/08/2023]
Abstract
Epigenetics mainly refers to covalent modifications to DNA or histones without affecting genomes, which ultimately lead to phenotypic changes in cells or organisms. Given the abundance of regulatory targets in epigenetic pathways and their pivotal roles in tumorigenesis and drug resistance, the development of epigenetic drugs holds a great promise for the current cancer therapy. However, lack of potent, selective, and clinically tractable small-molecule compounds makes the strategy to target cancer epigenetic pathways still challenging. Therefore, this review focuses on epigenetic pathways, small molecule inhibitors targeting DNA methyltransferase (DNMT) and small molecule inhibitors targeting histone modification (the main regulatory targets are histone acetyltransferases (HAT), histone deacetylases (HDACs) and histone methyltransferases (HMTS)), as well as the combination strategies of the existing epigenetic therapeutic drugs and more new therapies to improve the efficacy, which will shed light on a new clue on discovery of more small-molecule drugs targeting cancer epigenetic pathways as promising strategies in the future.
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Affiliation(s)
- Yi Wang
- Health Management Center, Sichuan Provincial People' Hospital, University of Electronic Science and Technology of China, Chengdu 610072, PR China; Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, PR China
| | - Qiang Xie
- Department of Stomatology, Sichuan Provincial People' Hospital, University of Electronic Science and Technology of China, Chengdu 610072, PR China
| | - Huidan Tan
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu 610072, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Minru Liao
- Department of Stomatology, Sichuan Provincial People' Hospital, University of Electronic Science and Technology of China, Chengdu 610072, PR China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Shiou Zhu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China
| | - Ling-Li Zheng
- Department of Pharmacy, The First Affiliated Hospital of Chengdu Medical College, No. 278, Baoguang Rd, Xindu Region, Chengdu 610500, PR China.
| | - Haixia Huang
- Oral & Maxillofacial Reconstruction and Regeneration Laboratory, Southwest Medical University, Luzhou, 646000, PR China; Department of Prosthodontics, The Affiliated Stomatology Hospital of Southwest Medical University, Luzhou, 646000, PR China.
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, PR China.
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Quantitative Proteomic Approach Reveals Altered Metabolic Pathways in Response to the Inhibition of Lysine Deacetylases in A549 Cells under Normoxia and Hypoxia. Int J Mol Sci 2021; 22:ijms22073378. [PMID: 33806075 PMCID: PMC8036653 DOI: 10.3390/ijms22073378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/24/2022] Open
Abstract
Growing evidence is showing that acetylation plays an essential role in cancer, but studies on the impact of KDAC inhibition (KDACi) on the metabolic profile are still in their infancy. Here, we analyzed, by using an iTRAQ-based quantitative proteomics approach, the changes in the proteome of KRAS-mutated non-small cell lung cancer (NSCLC) A549 cells in response to trichostatin-A (TSA) and nicotinamide (NAM) under normoxia and hypoxia. Part of this response was further validated by molecular and biochemical analyses and correlated with the proliferation rates, apoptotic cell death, and activation of ROS scavenging mechanisms in opposition to the ROS production. Despite the differences among the KDAC inhibitors, up-regulation of glycolysis, TCA cycle, oxidative phosphorylation and fatty acid synthesis emerged as a common metabolic response underlying KDACi. We also observed that some of the KDACi effects at metabolic levels are enhanced under hypoxia. Furthermore, we used a drug repositioning machine learning approach to list candidate metabolic therapeutic agents for KRAS mutated NSCLC. Together, these results allow us to better understand the metabolic regulations underlying KDACi in NSCLC, taking into account the microenvironment of tumors related to hypoxia, and bring new insights for the future rational design of new therapies.
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Peng Q, Weng K, Li S, Xu R, Wang Y, Wu Y. A Perspective of Epigenetic Regulation in Radiotherapy. Front Cell Dev Biol 2021; 9:624312. [PMID: 33681204 PMCID: PMC7930394 DOI: 10.3389/fcell.2021.624312] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 01/28/2021] [Indexed: 12/17/2022] Open
Abstract
Radiation therapy (RT) has been employed as a tumoricidal modality for more than 100 years and on 470,000 patients each year in the United States. The ionizing radiation causes genetic changes and results in cell death. However, since the biological mechanism of radiation remains unclear, there is a pressing need to understand this mechanism to improve the killing effect on tumors and reduce the side effects on normal cells. DNA break and epigenetic remodeling can be induced by radiotherapy. Hence the modulation of histone modification enzymes may tune the radiosensitivity of cancer cells. For instance, histone deacetylase (HDAC) inhibitors sensitize irradiated cancer cells by amplifying the DNA damage signaling and inhibiting double-strand DNA break repair to influence the irradiated cells’ survival. However, the combination of epigenetic drugs and radiotherapy has only been evaluated in several ongoing clinical trials for limited cancer types, partly due to a lack of knowledge on the potential mechanisms on how radiation induces epigenetic regulation and chromatin remodeling. Here, we review recent advances of radiotherapy and radiotherapy-induced epigenetic remodeling and introduce related technologies for epigenetic monitoring. Particularly, we exploit the application of fluorescence resonance energy transfer (FRET) biosensors to visualize dynamic epigenetic regulations in single living cells and tissue upon radiotherapy and drug treatment. We aim to bridge FRET biosensor, epigenetics, and radiotherapy, providing a perspective of using FRET to assess epigenetics and provide guidance for radiotherapy to improve cancer treatment. In the end, we discuss the feasibility of a combination of epigenetic drugs and radiotherapy as new approaches for cancer therapeutics.
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Affiliation(s)
- Qin Peng
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.,Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Kegui Weng
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States.,Chongqing Cancer Hospital, Chongqing Cancer Institute, Chongqing University Cancer Hospital, Chongqing, China
| | - Shitian Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Richard Xu
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Yingxiao Wang
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, United States.,Institute of Engineering in Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Yongzhong Wu
- Chongqing Cancer Hospital, Chongqing Cancer Institute, Chongqing University Cancer Hospital, Chongqing, China
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Dai D, Xie L, Shui Y, Li J, Wei Q. Identification of Tumor Microenvironment-Related Prognostic Genes in Sarcoma. Front Genet 2021; 12:620705. [PMID: 33597971 PMCID: PMC7882740 DOI: 10.3389/fgene.2021.620705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/06/2021] [Indexed: 12/16/2022] Open
Abstract
Aim Immune cells that infiltrate the tumor microenvironment (TME) are associated with cancer prognosis. The aim of the current study was to identify TME related gene signatures related to the prognosis of sarcoma (SARC) by using the data from The Cancer Genome Atlas (TCGA). Methods Immune and stromal scores were calculated by estimation of stromal and immune cells in malignant tumor tissues using expression data algorithms. The least absolute shrinkage and selection operator (lasso) based cox model was then used to select hub survival genes. A risk score model and nomogram were used to predict the overall survival of patients with SARC. Results We selected 255 patients with SARC for our analysis. The Kaplan–Meier method found that higher immune (p = 0.0018) or stromal scores (p = 0.0022) were associated with better prognosis of SARC. The estimated levels of CD4+ (p = 0.0012) and CD8+ T cells (p = 0.017) via the tumor immune estimation resource were higher in patients with SARC with better overall survival. We identified 393 upregulated genes and 108 downregulated genes (p < 0.05, fold change >4) intersecting between the immune and stromal scores based on differentially expressed gene (DEG) analysis. The univariate Cox analysis of each intersecting DEG and subsequent lasso-based Cox model identified 11 hub survival genes (MYOC, NNAT, MEDAG, TNFSF14, MYH11, NRXN1, P2RY13, CXCR3, IGLV3-25, IGHV1-46, and IGLV2-8). Then, a hub survival gene-based risk score gene signature was constructed; higher risk scores predicted worse SARC prognosis (p < 0.0001). A nomogram including the risk scores, immune/stromal scores and clinical factors showed a good prediction value for SARC overall survival (C-index = 0.716). Finally, connectivity mapping analysis identified that the histone deacetylase inhibitors trichostatin A and vorinostat might have the potential to reverse the harmful TME for patients with SARC. Conclusion The current study provided new indications for the association between the TME and SARC. Lists of TME related survival genes and potential therapeutic drugs were identified for SARC.
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Affiliation(s)
- Dongjun Dai
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lanyu Xie
- Department of Clinical Medicine, Fuzhou Medical College of Nanchang University, Jiangxi, China
| | - Yongjie Shui
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinfan Li
- Department of Pathology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qichun Wei
- Department of Radiation Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Colletti M, Ceglie D, Di Giannatale A, Nazio F. Autophagy and Exosomes Relationship in Cancer: Friends or Foes? Front Cell Dev Biol 2021; 8:614178. [PMID: 33511121 PMCID: PMC7835528 DOI: 10.3389/fcell.2020.614178] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Abstract
Autophagy is an intracellular degradation process involved in the removal of proteins and damaged organelles by the formation of a double-membrane vesicle named autophagosome and degraded through fusion with lysosomes. An intricate relationship between autophagy and the endosomal and exosomal pathways can occur at different stages with important implications for normal physiology and human diseases. Recent researches have revealed that extracellular vesicles (EVs), such as exosomes, could have a cytoprotective role by inducing intracellular autophagy; on the other hand, autophagy plays a crucial role in the biogenesis and degradation of exosomes. Although the importance of these processes in cancer is well established, their interplay in tumor is only beginning to be documented. In some tumor contexts (1) autophagy and exosome-mediated release are coordinately activated, sharing the molecular machinery and regulatory mechanisms; (2) cancer cell-released exosomes impact on autophagy in recipient cells through mechanisms yet to be determined; (3) exosome-autophagy relationship could affect drug resistance and tumor microenvironment (TME). In this review, we survey emerging discoveries relevant to the exosomes and autophagy crosstalk in the context of cancer initiation, progression and recurrence. Consequently, we discuss clinical implications by targeting autophagy-exosomal pathway interaction and how this could lay a basis for the purpose of novel cancer therapeutics.
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Affiliation(s)
- Marta Colletti
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Donatella Ceglie
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Angela Di Giannatale
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesca Nazio
- Department of Pediatric Hemato-Oncology and Cell and Gene Therapy, IRCCS, Bambino Gesù Children's Hospital, Rome, Italy
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