1.From Gene Expression to Transcriptome-wide Association Study: Development and Comparison of Methodology
Kun FANG ; Guozhuang LI ; Linting WANG ; Qing LI ; Kexin XU ; Lina ZHAO ; Zhihong WU ; Jianguo ZHANG ; Nan WU
Medical Journal of Peking Union Medical College Hospital 2026;17(1):223-229
Over the past two decades, genome-wide association study(GWAS) has identified numerous genetic variants and loci associated with heritable diseases. With the gradual maturation and saturation of GWAS methodologies, transcriptome-wide association study(TWAS) offers a novel perspective by linkinggenetic phenotypes to gene expression levels. By integrating TWAS with other multi-omics analyses, researchers can gain a deeper understanding of heritable diseases. This article provides an overview of recent groundbreaking and representative TWAS methods and tools, analyzes their strengths and limitations, and discusses future trends in TWAS development.
2.Myocardial Metabolomics Reveals Mechanism of Shenfu Injection in Ameliorating Energy Metabolism Remodeling in Rat Model of Chronic Heart Failure
Xinyue NING ; Zhenyu ZHAO ; Mengna ZHANG ; Yang GUO ; Zhijia XIANG ; Kun LIAN ; Zhixi HU ; Lin LI
Chinese Journal of Experimental Traditional Medical Formulae 2026;32(5):178-186
ObjectiveTo examine the influences of Shenfu injection on the endogenous metabolic byproducts in the myocardium of the rat model exhibiting chronic heart failure, thus deciphering the therapeutic mechanism of the Qi-reinforcing and Yang-warming method. MethodsSD rats were randomly allocated into a control group and a modeling group. Chronic heart failure with heart-Yang deficiency syndrome in rats was modeled by multi-point subcutaneous injection of isoproterenol, and the rats were fed for 14 days after modeling. The successfully modeled rats were randomized into model, Shenfu injection (6.0 mL·kg-1), and trimetazidine (10 mg·kg-1) groups and treated with corresponding agents for 15 days. The control group and the model group were injected with equal doses of normal saline, and the samples were collected after the intervention was completed. Cardiac color ultrasound was performed. Hematoxylin-eosin (HE) staining was used to observe histopathological morphology, and the serum level of N-terminal pro-brain natriuretic peptide (NT-proBNP) was assessed by enzyme-linked immunosorbent assay (ELISA). The mitochondrial morphological and structural changes of cardiomyocytes were observed by transmission electron microscopy, and the metabolic profiling was carried out by ultra high performance liquid chromatography-quantitative exactive-mass spectrometry (UHPLC-QE-MS). Differential metabolites were screened and identified by orthogonal partial least squares-discriminant analysis (OPLS-DA) and other methods, and then the MetaboAnalyst database was used for further screening. The relevant biological pathways were obtained through pathway enrichment analysis. The receiver operating characteristic (ROC) curve was established to evaluate the diagnostic value of each potential biomarker for myocardial injury and the evaluation value for drug efficacy. ResultsThe results of color ultrasound showed that Shenfu Injection improved the cardiac function indexes of model rats (P<0.05). The results of HE staining showed that Shenfu injection effectively alleviated the pathological phenomena such as myocardial tissue structure disorder and inflammatory cell infiltration in model rats. The results of ELISA showed that Shenfu injection effectively regulated the serum NT-proBNP level in the model rats. Transmission electron microscopy (TEM) showed that Shenfu injection effectively restored the mitochondrial morphological structure. The results of metabolomics showed that the metabolic phenotypes of myocardial samples presented markedly differences between groups. Nine differential metabolites could be significantly reversed in the Shenfu injection group, involving three metabolic pathways: pyruvate metabolism, histidine metabolism, and citric acid cycle (TCA cycle). The results of ROC analysis showed that the area under the curve (AUC) values of all metabolites were between 0.75 and 1.0, indicating that the differential metabolites had high diagnostic accuracy for myocardial injury, and the changes in their expression levels could be used as potential markers for efficacy evaluation. ConclusionShenfu injection significantly alleviated the damage of cardiac function, myocardium, and mitochondrial structure in the rat model of chronic heart failure with heart-Yang deficiency syndrome by ameliorating energy metabolism remodeling. Reinforcing Qi and warming Yang is a key method for treating chronic heart failure with heart-Yang deficiency syndrome.
3.WANG Jianmin's Experience in Treating Cathartic Colon from the Perspective of "Keeping Sweet to Return Liquid"
Siyuan ZHANG ; Ming LI ; Kun TANG ; Ran TANG ; Yueyue ZHANG ; Yue ZHAO ;
Journal of Traditional Chinese Medicine 2025;66(11):1104-1108
To summarize Professor WANG Jianmin's experience in cathartic colon from "keeping sweet to return liquid". It is believed that the key to the pathogenesis of cathartic colon is fluid consumption and intestinal dryness, including yin depletion of spleen earth, and lack of sources for body fluids production; discordance of water and fire in kidneys, and irregular distribution of body fluids; and closure of the lungs and liver leads to inability of the flow of fluids. The treatment is based on the principle of "keeping sweet to return liquid", using sweet medicinals mainly, assistant with sour, bland and acrid medicinals, and self-prescribed Lipi Shengjin Decoction (理脾生津汤), Wenshen Runchang Decoction (温肾润肠汤), Kaifei Shunchang Decoction (开肺顺肠汤), Rougan Tongbian Decoction (柔肝通便汤) could be used to regulate spleen yin by the sweet and bland, and establish qi and promote fluid production; the sweet and warm medicinals can replenish water and fire, transform into qi, and distribute body fluids; the acrid and sweet can open lung depression, descend qi, and flow the body fluids; the sour and sweet can emolliate liver, move qi, and transform fluids.
4.The Role and Mechanism of Circadian Rhythm Regulation in Skin Tissue Regeneration
Ya-Qi ZHAO ; Lin-Lin ZHANG ; Xiao-Meng MA ; Zhen-Kai JIN ; Kun LI ; Min WANG
Progress in Biochemistry and Biophysics 2025;52(5):1165-1178
Circadian rhythm is an endogenous biological clock mechanism that enables organisms to adapt to the earth’s alternation of day and night. It plays a fundamental role in regulating physiological functions and behavioral patterns, such as sleep, feeding, hormone levels and body temperature. By aligning these processes with environmental changes, circadian rhythm plays a pivotal role in maintaining homeostasis and promoting optimal health. However, modern lifestyles, characterized by irregular work schedules and pervasive exposure to artificial light, have disrupted these rhythms for many individuals. Such disruptions have been linked to a variety of health problems, including sleep disorders, metabolic syndromes, cardiovascular diseases, and immune dysfunction, underscoring the critical role of circadian rhythm in human health. Among the numerous systems influenced by circadian rhythm, the skin—a multifunctional organ and the largest by surface area—is particularly noteworthy. As the body’s first line of defense against environmental insults such as UV radiation, pollutants, and pathogens, the skin is highly affected by changes in circadian rhythm. Circadian rhythm regulates multiple skin-related processes, including cyclic changes in cell proliferation, differentiation, and apoptosis, as well as DNA repair mechanisms and antioxidant defenses. For instance, studies have shown that keratinocyte proliferation peaks during the night, coinciding with reduced environmental stress, while DNA repair mechanisms are most active during the day to counteract UV-induced damage. This temporal coordination highlights the critical role of circadian rhythms in preserving skin integrity and function. Beyond maintaining homeostasis, circadian rhythm is also pivotal in the skin’s repair and regeneration processes following injury. Skin regeneration is a complex, multi-stage process involving hemostasis, inflammation, proliferation, and remodeling, all of which are influenced by circadian regulation. Key cellular activities, such as fibroblast migration, keratinocyte activation, and extracellular matrix remodeling, are modulated by the circadian clock, ensuring that repair processes occur with optimal efficiency. Additionally, circadian rhythm regulates the secretion of cytokines and growth factors, which are critical for coordinating cellular communication and orchestrating tissue regeneration. Disruptions to these rhythms can impair the repair process, leading to delayed wound healing, increased scarring, or chronic inflammatory conditions. The aim of this review is to synthesize recent information on the interactions between circadian rhythms and skin physiology, with a particular focus on skin tissue repair and regeneration. Molecular mechanisms of circadian regulation in skin cells, including the role of core clock genes such as Clock, Bmal1, Per and Cry. These genes control the expression of downstream effectors involved in cell cycle regulation, DNA repair, oxidative stress response and inflammatory pathways. By understanding how these mechanisms operate in healthy and diseased states, we can discover new insights into the temporal dynamics of skin regeneration. In addition, by exploring the therapeutic potential of circadian biology in enhancing skin repair and regeneration, strategies such as topical medications that can be applied in a time-limited manner, phototherapy that is synchronized with circadian rhythms, and pharmacological modulation of clock genes are expected to optimize clinical outcomes. Interventions based on the skin’s natural rhythms can provide a personalized and efficient approach to promote skin regeneration and recovery. This review not only introduces the important role of circadian rhythms in skin biology, but also provides a new idea for future innovative therapies and regenerative medicine based on circadian rhythms.
5.Two new taraxerane triterpenoids from mastic.
Zhi-Qiang ZHAO ; Xue-Rui AN ; Tian-Zhi LI ; Ting HE ; Hao-Kun HOU ; Wei LIU ; Tao YUAN
China Journal of Chinese Materia Medica 2025;50(13):3723-3743
Three taraxerane nortriterpenoids were isolated from mastic by using various modern chromatographic separation techniques. They were identified as(5R,8R,9R,10S,11S,12R,13S,17R,18R)-28-norlupa-11,12-epoxy-14-taraxerene-3,16-dione(1),(5R,8R,9R,10S,11S,12R,13S,17S,18S)-17-hydroxy-28-norlupa-11,12-epoxy-14-taraxerene-3-one(2), and(5R,8R,9R,10R,11S,12R,13R,14S,17S,18S)-14,17-epoxy-28-norlupa-11,12-oxidotaraxerone(3) through the high-resolution electrospray ionization mass spectrometry(HR-ESI-MS), infrared(IR), ultraviolet(UV), nuclear magnetic resonance(NMR), and single-crystal X-ray diffraction techniques as well as comparison with literature data. Compounds 1-3 were C-28 nortriterpenoids and isolated from mastic for the first time, and compounds 1-2 were new ones. In the model for RAW264.7 cell anti-inflammation induced by lipopolysaccharide(LPS), compound 1 demonstrates an inhibitory effect on nitric oxide(NO) [IC_(50)=(13.38±0.68) μmol·L~(-1)], comparable to the activity of the positive control dexamethasone [IC_(50)=(14.59±1.49) μmol·L~(-1)]. Compounds 2 and 3 exhibit weaker inhibitory effects, with IC_(50) values of(24.17±2.56) and(22.25±2.84) μmol·L~(-1), respectively.
Animals
;
Mice
;
Triterpenes/isolation & purification*
;
Drugs, Chinese Herbal/isolation & purification*
;
Mastic Resin/chemistry*
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Nitric Oxide
;
Molecular Structure
;
Macrophages/immunology*
;
RAW 264.7 Cells
6.Study on the Pathological Mechanism-Syndrome-Treatment Patterns of Approved Chinese Patent Medicines Targeting Collateral Disorders
Pengli SU ; Peng XU ; Yanhong WANG ; Yaqi ZU ; Run YUAN ; Kun LI ; Yufeng ZHAO
Journal of Traditional Chinese Medicine 2025;66(16):1711-1718
ObjectiveTo explore the pathological mechanism-syndrome-treatment patterns of approved Chinese patent medicines (CPMs) that treat collateral disorders, providing a reference for the principle of "treating different diseases with the same therapy" in collateral pathology. MethodsCPMs that apply treatment strategies based on collateral disorders were identified from the Pharmacodia database by extracting information from the "efficacy" or "indications" sections of drug package inserts. A database was established to extract the names and compositions of the CPMs, as well as their indications, related traditional Chinese medicine (TCM) symptoms, disease locations (affected areas), and pathological factors. Frequency statistics were performed. Using the Apriori algorithm, an association rule analysis was conducted on CPMs and disease-location combinations related to the top three most frequent pathological factor combinations. Core formulas for these combinations were identified and analyzed through drug network analysis and MCODE module clustering. ResultsA total of 660 CPMs targeting collateral disorders were retrieved, involving 299 indications, 323 TCM symptoms, 21 disease locations, 19 pathological factors, and 124 pathological factor combinations. The most frequent pathological factor combinations were blood stasis (involved in 109 CPMs, 16.52%), exogenous wind (外风) -cold-dampness (involved in 43 CPMs, 6.52%), and qi deficiency-blood stasis (involved in 42 CPMs, 6.36%). Analysis of the core formulas for these combinations revealed common ingredients such as Honghua (Carthami Flos), Chuanxiong (Chuanxiong Rhizoma), Danggui (Angelicae Sinensis Radix), and Dilong (Pheretima). ConclusionCollateral disorders involve a wide range of pathogenesis and represent a fundamental mechanism in the onset and development of various diseases, characterized by obstruction and stagnation. The primary therapeutic principle is unblocking of the collaterals. Blood stasis obstructing the collaterals is the core pathological basis, and the strategy of activating blood circulation and resolving stasis to unblock the collaterals should be central to the treatment. The core medication pattern involves combining blood-activating and stasis-resolving herbs with insect-derived medicinals that unblock collaterals. Exogenous wind is often the initiating patholo-gical factor in colla-teral disorders, and the appropriate addition of wind-dispelling herbs can enrich the treatment strategies for such conditions.
7.The observational chart for traumatic limb swelling enhances diagnostic accuracy for osteofascial compartment syndrome.
Zhi-Wei YANG ; Zhao-Di WANG ; Jun-Sheng YANG ; Liang-Cheng TONG ; Lei ZHAO ; Wei DAI ; Kun PANG ; Ying LI
Chinese Journal of Traumatology 2025;28(6):454-461
PURPOSE:
To evaluate the diagnostic accuracy of the observational chart for traumatic limb swelling (OCTLS) for osteofascial compartment syndrome (OCS).
METHODS:
This was a descriptive-longitudinal study. Data of 316 patients who underwent surgical treatment for tibial fractures in our department from January 2015 to December 2023 were collected. Patients with Gustilo type II or higher open fractures, vascular injury, or bilateral fractures were excluded from the study. Two groups of double-blinded investigators independently assessed patients for the presence of OCS using 2 distinct diagnostic methods. Three senior orthopedic trauma surgeons evaluated patients with post-fracture calf swelling for OCS and the need for fasciotomy based on clinical signs and their extensive clinical experience. Subsequently, fasciotomy was performed according to their judgment, followed by postoperative examination of muscle and soft tissue conditions. Additionally, a follow-up evaluation was conducted to assess for complications such as ischemic muscle contracture. Another 3 trained researchers used OCTLS to grade swelling severity and determine the need for fasciotomy. The final diagnostic gold standard of OCS was determined by referring to whether there was escape of muscles at fasciotomy and/or color change in the muscles or muscle necrosis intraoperatively, and neurological abnormality or contracture at the last follow-up. The results of the 2 diagnostic methods were compared with the final diagnostic result. Kappa consistency test, paired χ2 test (McNemar test), and receiver operating characteristic curve were used to evaluate the diagnostic efficacy of the 2 diagnostic methods.
RESULTS:
Of the 316 patients, 211 were finally included in the study, including 160 males and 51 females, with an average follow-up time of (14.5 ± 2.7) months. Among the 211 patients with tibial fracture-associated swelling, 42 were definitively diagnosed with OCS. Based on clinical symptoms and signs judgment, among the 65 fasciotomy patients, 38 were confirmed as correct, while among the 146 non-fasciotomy patients, 4 developed ischemic muscle contractures. Based on the OCTLS for assessment, fasciotomy was correctly recommended in 36 out of 43 cases, while 6 out of 168 non-fasciotomy patients developed OCS. Compared to the use of the gold standard, clinical signs judgment showed moderate consistency (McNemar's test p < 0.001, Kappa = 0.618, p < 0.001), whereas OCTLS demonstrated strong agreement (McNemar's test p = 1.000, Kappa = 0.808, p < 0.001). Receiver operating characteristic analysis revealed higher diagnostic accuracy for OCTLS (area under curve = 0.908, 95% CI: 0.843 - 0.972) compared to clinical signs judgment (area under curve = 0.872, 95% CI: 0.812 - 0.933). OCTLS achieved superior accuracy (93.8% vs. 85.3%, χ2 = 8.221, p < 0.001) and a lower fasciotomy rate (20.4% vs. 30.8%, χ2 = 6.023, p = 0.014).
CONCLUSION
Compared to clinical signs judgment, OCTLS significantly reduces unnecessary fasciotomy, improves diagnostic accuracy for OCS, and enables non-invasive, dynamic, and quantitative assessment, making it a valuable tool for clinical practice.
Humans
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Compartment Syndromes/etiology*
;
Male
;
Female
;
Adult
;
Tibial Fractures/surgery*
;
Middle Aged
;
Fasciotomy
;
Edema/etiology*
;
Longitudinal Studies
;
Aged
;
Young Adult
8.Real-world efficacy and safety of azvudine in hospitalized older patients with COVID-19 during the omicron wave in China: A retrospective cohort study.
Yuanchao ZHU ; Fei ZHAO ; Yubing ZHU ; Xingang LI ; Deshi DONG ; Bolin ZHU ; Jianchun LI ; Xin HU ; Zinan ZHAO ; Wenfeng XU ; Yang JV ; Dandan WANG ; Yingming ZHENG ; Yiwen DONG ; Lu LI ; Shilei YANG ; Zhiyuan TENG ; Ling LU ; Jingwei ZHU ; Linzhe DU ; Yunxin LIU ; Lechuan JIA ; Qiujv ZHANG ; Hui MA ; Ana ZHAO ; Hongliu JIANG ; Xin XU ; Jinli WANG ; Xuping QIAN ; Wei ZHANG ; Tingting ZHENG ; Chunxia YANG ; Xuguang CHEN ; Kun LIU ; Huanhuan JIANG ; Dongxiang QU ; Jia SONG ; Hua CHENG ; Wenfang SUN ; Hanqiu ZHAN ; Xiao LI ; Yafeng WANG ; Aixia WANG ; Li LIU ; Lihua YANG ; Nan ZHANG ; Shumin CHEN ; Jingjing MA ; Wei LIU ; Xiaoxiang DU ; Meiqin ZHENG ; Liyan WAN ; Guangqing DU ; Hangmei LIU ; Pengfei JIN
Acta Pharmaceutica Sinica B 2025;15(1):123-132
Debates persist regarding the efficacy and safety of azvudine, particularly its real-world outcomes. This study involved patients aged ≥60 years who were admitted to 25 hospitals in mainland China with confirmed SARS-CoV-2 infection between December 1, 2022, and February 28, 2023. Efficacy outcomes were all-cause mortality during hospitalization, the proportion of patients discharged with recovery, time to nucleic acid-negative conversion (T NANC), time to symptom improvement (T SI), and time of hospital stay (T HS). Safety was also assessed. Among the 5884 participants identified, 1999 received azvudine, and 1999 matched controls were included after exclusion and propensity score matching. Azvudine recipients exhibited lower all-cause mortality compared with controls in the overall population (13.3% vs. 17.1%, RR, 0.78; 95% CI, 0.67-0.90; P = 0.001) and in the severe subgroup (25.7% vs. 33.7%; RR, 0.76; 95% CI, 0.66-0.88; P < 0.001). A higher proportion of patients discharged with recovery, and a shorter T NANC were associated with azvudine recipients, especially in the severe subgroup. The incidence of adverse events in azvudine recipients was comparable to that in the control group (2.3% vs. 1.7%, P = 0.170). In conclusion, azvudine showed efficacy and safety in older patients hospitalized with COVID-19 during the SARS-CoV-2 omicron wave in China.
9.Anti-SARS-CoV-2 prodrug ATV006 has broad-spectrum antiviral activity against human and animal coronaviruses.
Tiefeng XU ; Kun LI ; Siyao HUANG ; Konstantin I IVANOV ; Sidi YANG ; Yanxi JI ; Hanwei ZHANG ; Wenbin WU ; Ye HE ; Qiang ZENG ; Feng CONG ; Qifan ZHOU ; Yingjun LI ; Jian PAN ; Jincun ZHAO ; Chunmei LI ; Xumu ZHANG ; Liu CAO ; Deyin GUO
Acta Pharmaceutica Sinica B 2025;15(5):2498-2510
Coronavirus-related diseases pose a significant challenge to the global health system. Given the diversity of coronaviruses and the unpredictable nature of disease outbreaks, the traditional "one bug, one drug" paradigm struggles to address the growing number of emerging crises. Therefore, there is an urgent need for therapeutic agents with broad-spectrum anti-coronavirus activity. Here, we provide evidence that ATV006, an anti-SARS-CoV-2 nucleoside analog targeting RNA-dependent RNA polymerase (RdRp), has broad antiviral activity against human and animal coronaviruses. Using mouse hepatitis virus (MHV) and human coronavirus NL63 (HCoV-NL63) as a model, we show that ATV006 has potent prophylactic and therapeutic activity against murine coronavirus infection in vivo. Remarkably, ATV006 successfully inhibits viral replication in mice even when administered 96 h after infection. Due to its oral bioavailability and potency against multiple coronaviruses, ATV006 has the potential to become a useful antiviral agent against SARS-CoV-2 and other circulating and emerging coronaviruses in humans and animals.
10.RXRα modulates hepatic stellate cell activation and liver fibrosis by targeting CaMKKβ-AMPKα axis.
Lijun CAI ; Meimei YIN ; Shuangzhou PENG ; Fen LIN ; Liangliang LAI ; Xindao ZHANG ; Lei XIE ; Chuanying WANG ; Huiying ZHOU ; Yunfeng ZHAN ; Gulimiran ALITONGBIEKE ; Baohuan LIAN ; Zhibin SU ; Tenghui LIU ; Yuqi ZHOU ; Zongxi LI ; Xiaohui CHEN ; Qi ZHAO ; Ting DENG ; Lulu CHEN ; Jingwei SU ; Luoyan SHENG ; Ying SU ; Ling-Juan ZHANG ; Fu-Quan JIANG ; Xiao-Kun ZHANG
Acta Pharmaceutica Sinica B 2025;15(7):3611-3631
Hepatic stellate cells (HSCs) are the primary fibrogenic cells in the liver, and their activation plays a crucial role in the development and progression of hepatic fibrosis. Here, we report that retinoid X receptor-alpha (RXRα), a unique member of the nuclear receptor superfamily, is a key modulator of HSC activation and liver fibrosis. RXRα exerts its effects by modulating calcium/calmodulin-dependent protein kinase kinase β (CaMKKβ)-mediated activation of AMP-activated protein kinase-alpha (AMPKα). In addition, we demonstrate that K-80003, which binds RXRα by a unique mechanism, effectively suppresses HSC activation, proliferation, and migration, thereby inhibiting liver fibrosis in the CCl4 and amylin liver NASH (AMLN) diet animal models. The effect is mediated by AMPKα activation, promoting mitophagy in HSCs. Mechanistically, K-80003 activates AMPKα by inducing RXRα to form condensates with CaMKKβ and AMPKα via a two-phase process. The formation of RXRα condensates is driven by its N-terminal intrinsic disorder region and requires phosphorylation by CaMKKβ. Our results reveal a crucial role of RXRα in liver fibrosis regulation through modulating mitochondrial activities in HSCs. Furthermore, they suggest that K-80003 and related RXRα modulators hold promise as therapeutic agents for fibrosis-related diseases.

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