1
|
Hu L, Zhang M, Hu P, Zhang J, Niu C, Lu X, Jiang X, Ma Y. Dual-channel hypergraph convolutional network for predicting herb-disease associations. Brief Bioinform 2024; 25:bbae067. [PMID: 38426326 PMCID: PMC10939431 DOI: 10.1093/bib/bbae067] [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: 09/11/2023] [Revised: 01/26/2024] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Herbs applicability in disease treatment has been verified through experiences over thousands of years. The understanding of herb-disease associations (HDAs) is yet far from complete due to the complicated mechanism inherent in multi-target and multi-component (MTMC) botanical therapeutics. Most of the existing prediction models fail to incorporate the MTMC mechanism. To overcome this problem, we propose a novel dual-channel hypergraph convolutional network, namely HGHDA, for HDA prediction. Technically, HGHDA first adopts an autoencoder to project components and target protein onto a low-dimensional latent space so as to obtain their embeddings by preserving similarity characteristics in their original feature spaces. To model the high-order relations between herbs and their components, we design a channel in HGHDA to encode a hypergraph that describes the high-order patterns of herb-component relations via hypergraph convolution. The other channel in HGHDA is also established in the same way to model the high-order relations between diseases and target proteins. The embeddings of drugs and diseases are then aggregated through our dual-channel network to obtain the prediction results with a scoring function. To evaluate the performance of HGHDA, a series of extensive experiments have been conducted on two benchmark datasets, and the results demonstrate the superiority of HGHDA over the state-of-the-art algorithms proposed for HDA prediction. Besides, our case study on Chuan Xiong and Astragalus membranaceus is a strong indicator to verify the effectiveness of HGHDA, as seven and eight out of the top 10 diseases predicted by HGHDA for Chuan-Xiong and Astragalus-membranaceus, respectively, have been reported in literature.
Collapse
Affiliation(s)
- Lun Hu
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi China
- University of Chinese Academy of Sciences, Beijing, China
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
| | - Menglong Zhang
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi China
- University of Chinese Academy of Sciences, Beijing, China
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
| | - Pengwei Hu
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi China
- University of Chinese Academy of Sciences, Beijing, China
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
| | - Jun Zhang
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi China
- University of Chinese Academy of Sciences, Beijing, China
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
| | - Chao Niu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Key Laboratory of Chemistry of Plant Resources in Arid Regions, Xinjiang Technical Institute of Physicsand Chemistry,Chinese Academy of Sciences Urumqi, China
| | - Xueying Lu
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Key Laboratory of Chemistry of Plant Resources in Arid Regions, Xinjiang Technical Institute of Physicsand Chemistry,Chinese Academy of Sciences Urumqi, China
| | - Xiangrui Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica,Chinese Academy of Sciences Shanghai, China
| | - Yupeng Ma
- The Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi China
- University of Chinese Academy of Sciences, Beijing, China
- Xinjiang Laboratory of Minority Speech and Language Information Processing, Urumqi, China
| |
Collapse
|
2
|
Yin L, Ying L, Guo R, Hao M, Liang Y, Bi Y, Chen Y, Yu C, Yang Z. Ligustilide induces apoptosis and reduces proliferation in human bladder cancer cells by NFκB1 and mitochondria pathway. Chem Biol Drug Des 2023; 101:1252-1261. [PMID: 36751909 DOI: 10.1111/cbdd.14207] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Ligustilide (LIG), the bioactive constituent of Angelica sinensis, may exert potential benefits in cancer treatment. However, the potential mechanism of LIG in the suppression of bladder cancer (BC) has not been reported yet. This study uncovered the inhibitory effect of LIG on the proliferation and cell cycle arrest of BC cells (T24 and EJ-1) along with unveiling the underlying molecular mechanism. The IC50 values of LIG-treated T24 for 24 and 48 h are 39.91 μg/mL (209.8 μM) and 40.94 μg/mL (215.2 μM) separately. The same conditions, the IC50 values of EJ-1 are 45.73 μg/mL (240.4 μM) and 43.81 μg/mL (230.3 μM), separately. Additionally, LIG induced apoptosis and cycle arrest of T24 and EJ-1 cells in sub-G1 phase. Further studies showed that LIG induced apoptosis of BC cells by upregulating Caspase-8, truncated BID (tBID) and BAX proteins, and downregulating NFκB1 (p50) protein. In conclusion, LIG significantly inhibits the growth of BC cells in vitro and in vivo by inducing apoptosis and is inexpensive, making it a promising candidate for novel anti-BC drugs.
Collapse
Affiliation(s)
- Liqi Yin
- Innovation Center of Molecular Diagnostics, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Lu Ying
- Innovation Center of Molecular Diagnostics, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, College of Life Science and Technology, Tarim University, Alar, China
| | - Rui Guo
- Innovation Center of Molecular Diagnostics, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Mingxuan Hao
- Innovation Center of Molecular Diagnostics, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Youfeng Liang
- Innovation Center of Molecular Diagnostics, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Ying Bi
- Innovation Center of Molecular Diagnostics, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Yuan Chen
- Department of Urology, Dazhou Central Hospital, Dazhou, China
| | - Changyuan Yu
- Innovation Center of Molecular Diagnostics, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Zhao Yang
- Innovation Center of Molecular Diagnostics, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China.,Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin of Xinjiang Production and Construction Corps, College of Life Science and Technology, Tarim University, Alar, China
| |
Collapse
|
3
|
Dong L, Shen Z, Chi H, Wang Y, Shi Z, Fang H, Yang Y, Rong J. Research Progress of Chinese Medicine in the Treatment of Myocardial Ischemia-Reperfusion Injury. THE AMERICAN JOURNAL OF CHINESE MEDICINE 2022; 51:1-17. [PMID: 36437553 DOI: 10.1142/s0192415x23500015] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Vascular recanalization is the essential procedure in which severe coronary artery stenosis is diagnosed. However, the blood flow recovery associated with this procedure may cause myocardial ischemia-reperfusion injury (MIRI), which aggravates heart failure. Unfortunately, the mechanism of MIRI has historically been poorly understood. As we now know, calcium overloading, oxidative stress, mitochondrial dysfunction, inflammatory responses, and ferroptosis take part in the process of MIRI. Modern medicine has shown through clinical studies its own limited effects in the case of MIRI, whereas Chinese traditional medicine demonstrates a strong vitality. Multiple-target effects, such as anti-inflammatory, anti-oxidant, and cardio-protection effects, are central to this vitality. In our clinic center, Yixin formula is commonly used in patients with MIRI. This formula contains Astragalus, Ligusticum Wallichii, Salvia, Rhodiola Rosea, Radix Angelicae Sinensis, Cyperus Rotundus, and Cassia Twig. Its effects include warming yang energy, activating blood circulation, and eliminating blood stasis. In our previous laboratory studies, we have proved that it can reduce MIRI and oxidative stress injury in rats suffering from ischemia myocardiopathy. It can also inhibit apoptosis and protect myocardium. In this paper, we review the research of Yixin formula and other related herbal medicines in MIRI therapy.
Collapse
Affiliation(s)
- Li Dong
- Institute of Cardiology of Integrated Traditional, Chinese and Western Medicine, P. R. China
| | - Zhijie Shen
- Department of Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200135, P. R. China
| | - Hao Chi
- Department of Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200135, P. R. China
| | - Yingjie Wang
- Department of Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200135, P. R. China
| | - Zhaofeng Shi
- Department of Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200135, P. R. China
| | - Hongjun Fang
- Department of Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200135, P. R. China
| | - Yanling Yang
- Institute of Cardiology of Integrated Traditional, Chinese and Western Medicine, P. R. China
| | - Jingfeng Rong
- Department of Cardiology, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai 200135, P. R. China
| |
Collapse
|
4
|
Fan J, Lin B, Fan M, Niu T, Gao F, Tan B, Du X. Research progress on the mechanism of radiation enteritis. Front Oncol 2022; 12:888962. [PMID: 36132154 PMCID: PMC9483210 DOI: 10.3389/fonc.2022.888962] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 08/10/2022] [Indexed: 12/12/2022] Open
Abstract
Radiation enteritis (Re) is one of the most common complications of radiation therapy for abdominal tumors. The efficacy of cancer treatment by radiation is often limited by the side effects of Re. Re can be acute or chronic. Treatment of acute Re is essentially symptomatic. However, chronic Re usually requires surgical procedures. The underlying mechanisms of Re are complex and have not yet been elucidated. The purpose of this review is to provide an overview of the pathogenesis of Re. We reviewed the role of intestinal epithelial cells, intestinal stem cells (ISCs), vascular endothelial cells (ECs), intestinal microflora, and other mediators of Re, noting that a better understanding of the pathogenesis of Re may lead to better treatment modalities.
Collapse
Affiliation(s)
- Jinjia Fan
- Departmant of Oncology, National Health Commission Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology, Mianyang, China
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nan Chong, China
| | - Binwei Lin
- Departmant of Oncology, National Health Commission Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology, Mianyang, China
| | - Mi Fan
- Departmant of Oncology, National Health Commission Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology, Mianyang, China
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nan Chong, China
| | - Tintin Niu
- Departmant of Oncology, National Health Commission Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology, Mianyang, China
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nan Chong, China
| | - Feng Gao
- Departmant of Oncology, National Health Commission Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology, Mianyang, China
| | - Bangxian Tan
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nan Chong, China
| | - Xiaobo Du
- Departmant of Oncology, National Health Commission Key Laboratory of Nuclear Technology Medical Transformation (Mianyang Central Hospital), Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology, Mianyang, China
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nan Chong, China
- *Correspondence: Xiaobo Du,
| |
Collapse
|