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"Zhang, Pan-Pan"
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Development and validation of a gene expression-based signature to predict distant metastasis in locoregionally advanced nasopharyngeal carcinoma: a retrospective, multicentre, cohort study
2018
Gene expression patterns can be used as prognostic biomarkers in various types of cancers. We aimed to identify a gene expression pattern for individual distant metastatic risk assessment in patients with locoregionally advanced nasopharyngeal carcinoma.
In this multicentre, retrospective, cohort analysis, we included 937 patients with locoregionally advanced nasopharyngeal carcinoma from three Chinese hospitals: the Sun Yat-sen University Cancer Center (Guangzhou, China), the Affiliated Hospital of Guilin Medical University (Guilin, China), and the First People's Hospital of Foshan (Foshan, China). Using microarray analysis, we profiled mRNA gene expression between 24 paired locoregionally advanced nasopharyngeal carcinoma tumours from patients at Sun Yat-sen University Cancer Center with or without distant metastasis after radical treatment. Differentially expressed genes were examined using digital expression profiling in a training cohort (Guangzhou training cohort; n=410) to build a gene classifier using a penalised regression model. We validated the prognostic accuracy of this gene classifier in an internal validation cohort (Guangzhou internal validation cohort, n=204) and two external independent cohorts (Guilin cohort, n=165; Foshan cohort, n=158). The primary endpoint was distant metastasis-free survival. Secondary endpoints were disease-free survival and overall survival.
We identified 137 differentially expressed genes between metastatic and non-metastatic locoregionally advanced nasopharyngeal carcinoma tissues. A distant metastasis gene signature for locoregionally advanced nasopharyngeal carcinoma (DMGN) that consisted of 13 genes was generated to classify patients into high-risk and low-risk groups in the training cohort. Patients with high-risk scores in the training cohort had shorter distant metastasis-free survival (hazard ratio [HR] 4·93, 95% CI 2·99–8·16; p<0·0001), disease-free survival (HR 3·51, 2·43–5·07; p<0·0001), and overall survival (HR 3·22, 2·18–4·76; p<0·0001) than patients with low-risk scores. The prognostic accuracy of DMGN was validated in the internal and external cohorts. Furthermore, among patients with low-risk scores in the combined training and internal cohorts, concurrent chemotherapy improved distant metastasis-free survival compared with those patients who did not receive concurrent chemotherapy (HR 0·40, 95% CI 0·19–0·83; p=0·011), whereas patients with high-risk scores did not benefit from concurrent chemotherapy (HR 1·03, 0·71–1·50; p=0·876). This was also validated in the two external cohorts combined. We developed a nomogram based on the DMGN and other variables that predicted an individual's risk of distant metastasis, which was strengthened by adding Epstein–Barr virus DNA status.
The DMGN is a reliable prognostic tool for distant metastasis in patients with locoregionally advanced nasopharyngeal carcinoma and might be able to predict which patients benefit from concurrent chemotherapy. It has the potential to guide treatment decisions for patients at different risk of distant metastasis.
The National Natural Science Foundation of China, the National Science & Technology Pillar Program during the Twelfth Five-year Plan Period, the Natural Science Foundation of Guang Dong Province, the National Key Research and Development Program of China, the Innovation Team Development Plan of the Ministry of Education, the Health & Medical Collaborative Innovation Project of Guangzhou City, China, and the Program of Introducing Talents of Discipline to Universities.
Journal Article
Single-cell transcriptomics reveals regulators underlying immune cell diversity and immune subtypes associated with prognosis in nasopharyngeal carcinoma
2020
Nasopharyngeal carcinoma (NPC) is an aggressive malignancy with extremely skewed ethnic and geographic distributions. Increasing evidence indicates that targeting the tumor microenvironment (TME) represents a promising therapeutic approach in NPC, highlighting an urgent need to deepen the understanding of the complex NPC TME. Here, we generated single-cell transcriptome profiles for 7581 malignant cells and 40,285 immune cells from fifteen primary NPC tumors and one normal sample. We revealed malignant signatures capturing intratumoral transcriptional heterogeneity and predicting aggressiveness of malignant cells. Diverse immune cell subtypes were identified, including novel subtypes such as
CLEC9A
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dendritic cells (DCs). We further revealed transcriptional regulators underlying immune cell diversity, and cell–cell interaction analyses highlighted promising immunotherapeutic targets in NPC. Moreover, we established the immune subtype-specific signatures, and demonstrated that the signatures of macrophages, plasmacytoid dendritic cells (pDCs),
CLEC9A
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DCs, natural killer (NK) cells, and plasma cells were significantly associated with improved survival outcomes in NPC. Taken together, our findings represent a unique resource providing in-depth insights into the cellular heterogeneity of NPC TME and highlight potential biomarkers for anticancer treatment and risk stratification, laying a new foundation for precision therapies in NPC.
Journal Article
Happiness inequality has a Kuznets-style relation with economic growth in China
2022
Happiness studies generally investigate average levels of happiness rather than happiness inequality between regions, and studies of social inequality usually measure it based on the distribution of life opportunities (e.g., income) rather than life results (e.g., happiness). Inspired by the Kuznets curve, which illustrates the inverted U-shaped correlation between income inequality and economic growth, this study investigates whether there is a subjective wellbeing Kuznets curve. It uses data from ten waves of the Chinese General Social Survey to construct a panel data set and runs panel data models to investigate the hypothesized curvilinear relationship between happiness inequality and economic growth. The results show that happiness inequality, measured as the standard deviations of respondents’ self-reported happiness, first increases and then decreases as per-capita GDP increases in Chinese provinces. These findings strongly support the subjective wellbeing Kuznets curve hypothesis and suggest that strategies for reducing happiness inequality must consider stages of economic development.
Journal Article
Biological Activities and Secondary Metabolites from Sophora tonkinensis and Its Endophytic Fungi
2022
The roots of Sophora tonkinensis Gagnep., a traditional Chinese medicine, is known as Shan Dou Gen in the Miao ethnopharmacy. A large number of previous studies have suggested the usage of S. tonkinensis in the folk treatment of lung, stomach, and throat diseases, and the roots of S. tonkinensis have been produced as Chinese patent medicines to treat related diseases. Existing phytochemical works reported more than 300 compounds from different parts and the endophytic fungi of S. tonkinensis. Some of the isolated extracts and monomer compounds from S. tonkinensis have been proved to exhibit diverse biological activities, including anti-tumor, anti-inflammatory, antibacterial, antiviral, and so on. The research progress on the phytochemistry and pharmacological activities of S. tonkinensis have been systematically summarized, which may be useful for its further research.
Journal Article
Thermodynamic bounce effect in quantum BTZ black hole
by
Xu, Zhen-Ming
,
Zhang, Pan-Pan
,
Wu, Bin
in
Black Holes
,
Brownian motion
,
Classical and Quantum Gravitation
2024
A
bstract
A novel thermodynamic phenomenon has been observed in the quantum Bañados-Teitelboim-Zanelli (qBTZ) black hole, utilizing generalized free energy and Kramers escape rate. This phenomenon also reveals the unique property of the quantum black hole. The stochastic thermal motion of various thermodynamic states within the black hole system induces phase transitions, under the influence of generalized free energy which obtained by extending Maxwell’s construction. Through the analysis of Kramers escape rate, it is discovered that the qBTZ black hole thermodynamic system exhibits a bounce effect. It originates from the non-monotonicity of entropy in black hole thermodynamic systems. Furthermore, the overall thermodynamic picture of the qBTZ black hole has been obtained under different quantum backreactions.
Journal Article
A Zoonotic Henipavirus in Febrile Patients in China
2022
In this report, investigators in China identified a new henipavirus associated with a febrile human illness. This virus was also found in shrews.
Journal Article
AR-induced long non-coding RNA LINC01503 facilitates proliferation and metastasis via the SFPQ-FOSL1 axis in nasopharyngeal carcinoma
2020
Increasing evidence indicates that long non-coding RNAs (lncRNAs) play vital roles in the tumorigenesis and progression of cancers. However, the functions and regulatory mechanisms of lncRNAs in nasopharyngeal carcinoma (NPC) are still largely unknown. Our previous lncRNA expression profiles identified that LINC01503 was overexpressed in NPC. Here, we verified that LINC01503 was highly expressed in NPC and correlated with poor prognosis. LINC01503 promoted NPC cell proliferation, migration, and invasion in vitro, and facilitated tumor growth and metastasis in vivo. Mechanistically, LINC01503 recruited splicing factor proline-and glutamine-rich (SFPQ) to activate Fos like 1 (FOSL1) transcription, and ectopic expression of FOSL1 reversed the suppressive effect of LINC01503 knockdown on NPC progression. Moreover, androgen receptor (AR)-mediated transcription activation was responsible for the overexpression of LINC01503, and AR ligand-dependent cell growth, migration, and invasion in NPC cells. Taken together, our findings reveal that AR-induced LINC01503 can promote NPC progression through the SFPQ-FOSL1 axis, which represents a novel prognostic biomarker and therapeutic target for NPC patients.
Journal Article
Scalable detection of statistically significant communities and hierarchies, using message passing for modularity
2014
Modularity is a popular measure of community structure. However, maximizing the modularity can lead to many competing partitions, with almost the same modularity, that are poorly correlated with each other. It can also produce illusory ‘‘communities’’ in random graphs where none exist. We address this problem by using the modularity as a Hamiltonian at finite temperature and using an efficient belief propagation algorithm to obtain the consensus of many partitions with high modularity, rather than looking for a single partition that maximizes it. We show analytically and numerically that the proposed algorithm works all of the way down to the detectability transition in networks generated by the stochastic block model. It also performs well on real-world networks, revealing large communities in some networks where previous work has claimed no communities exist. Finally we show that by applying our algorithm recursively, subdividing communities until no statistically significant subcommunities can be found, we can detect hierarchical structure in real-world networks more efficiently than previous methods.
Significance Most work on community detection does not address the issue of statistical significance, and many algorithms are prone to overfitting. We address this using tools from statistical physics. Rather than trying to find the partition of a network that maximizes the modularity, our approach seeks the consensus of many high-modularity partitions. We do this with a scalable message-passing algorithm, derived by treating the modularity as a Hamiltonian and applying the cavity method. We show analytically that our algorithm succeeds all the way down to the detectability transition in the stochastic block model; it also performs well on real-world networks. It also provides a principled method for determining the number of groups or hierarchies of communities and subcommunities.
Journal Article
Learning nonequilibrium statistical mechanics and dynamical phase transitions
by
Zhang, Pan
,
Zhang, Jiang
,
Liu, Jing
in
639/766/530/2795
,
639/766/530/2804
,
Chemical reactions
2024
Nonequilibrium statistical mechanics exhibit a variety of complex phenomena far from equilibrium. It inherits challenges of equilibrium, including accurately describing the joint distribution of a large number of configurations, and also poses new challenges as the distribution evolves over time. Characterizing dynamical phase transitions as an emergent behavior further requires tracking nonequilibrium systems under a control parameter. While a number of methods have been proposed, such as tensor networks for one-dimensional lattices, we lack a method for arbitrary time beyond the steady state and for higher dimensions. Here, we develop a general computational framework to study the time evolution of nonequilibrium systems in statistical mechanics by leveraging variational autoregressive networks, which offer an efficient computation on the dynamical partition function, a central quantity for discovering the phase transition. We apply the approach to prototype models of nonequilibrium statistical mechanics, including the kinetically constrained models of structural glasses up to three dimensions. The approach uncovers the active-inactive phase transition of spin flips, the dynamical phase diagram, as well as new scaling relations. The result highlights the potential of machine learning dynamical phase transitions in nonequilibrium systems.
Variational autoregressive networks have been employed in the study of equilibrium statistical mechanics, chemical reaction networks and quantum many-body systems. Using these tools, Tang et al. develop a general approach to nonequilibrium statistical mechanics problems, such as dynamical phase transitions.
Journal Article