Polygenic risk score predicts all-cause death in East Asian patients with prior coronary artery disease

IntroductionCoronary artery disease (CAD) is a highly heritable and multifactorial disease. Numerous genome-wide association studies (GWAS) facilitated the construction of polygenic risk scores (PRS) for predicting future incidence of CAD, however, exclusively in European populations. Furthermore, identifying CAD patients with elevated risks of all-cause death presents a critical challenge in secondary prevention, which will contribute largely to reducing the burden for public healthcare.MethodsWe recruited a cohort of 1,776 Chinese CAD patients and performed medical follow-up for up to 11 years. A pruning and thresholding method was used to calculate PRS of CAD and its 14 risk factors. Their correlations with all-cause death were computed via Cox regression.Results and discussionWe found that the PRS for CAD and its seven risk factors, namely myocardial infarction, ischemic stroke, angina, heart failure, low-density lipoprotein cholesterol, total cholesterol and C-reaction protein, were significantly associated with death (P ≤ 0.05), whereas the PRS of body mass index displayed moderate association (P < 0.1). Elastic-net Cox regression with 5-fold cross-validation was used to integrate these nine PRS models into a meta score, metaPRS, which performed well in stratifying patients at different risks for death (P < 0.0001). Combining metaPRS with clinical risk factors further increased the discerning power and a 4% increase in sensitivity. The metaPRS generated from the genetic susceptibility to CAD and its risk factors can well stratify CAD patients by their risks of death. Integrating metaPRS and clinical risk factors may contribute to identifying patients at higher risk of poor prognosis

Community Attributes Predict the Relationship between Habitat Invasibility and Land Use Types in an Agricultural and Forest Landscape

Finding ecosystem or community level indicators for habitat invasibility may provide natural resource managers with environmentally friendly measures to control alien plant invasion; yet, ecosystem invasibility remains understudied. Here, we investigated alien plant invasion into various ecosystems representing different land use types in a subtropical peri-urban area of south China. Four invasive alien species were found from five out of the six ecosystems. Lower plant diversity in both the overstory and understory was consistently associated with more severe alien plant invasion to the ecosystems. The highest total abundance and plot occurrence of the invasive plants were found in the agroforestry ecosystem representing the highest disturbance. At plot scale, an increase in invasion severity was associated with a significant decrease in overstory stem density, species richness, and diversity, but with a significant increase in overstory plant dominance. The understory community attributes in response to the increase in invasion severity followed similar patterns, except that the stem density increased with invasion severity. Higher canopy openness and thus lower leaf area index and greater understory radiation were associated with higher invasion severity of invasive plants to the understory habitat. For predicting total abundance of the invasive species, the most important variable is land use type, while for the abundance of Lantana camara and Mikania micrantha, the most important predictor variable is overstory Berger–Parker index and canopy openness, respectively. Canopy structure and understory gap light regimes were among the most important factors determining the abundance of the worst invasive plant Mikania micrantha. Our results demonstrate that land use types with varying disturbance regimes determine the spatial heterogeneity in plant diversity and community structure, which predicts alien plant invasion and habitat invasibility; and that the severity of alien plant invasion in turn is a good indicator of habitat disturbance across the ecosystems

Table1_Polygenic risk score predicts all-cause death in East Asian patients with prior coronary artery disease.docx

IntroductionCoronary artery disease (CAD) is a highly heritable and multifactorial disease. Numerous genome-wide association studies (GWAS) facilitated the construction of polygenic risk scores (PRS) for predicting future incidence of CAD, however, exclusively in European populations. Furthermore, identifying CAD patients with elevated risks of all-cause death presents a critical challenge in secondary prevention, which will contribute largely to reducing the burden for public healthcare.MethodsWe recruited a cohort of 1,776 Chinese CAD patients and performed medical follow-up for up to 11 years. A pruning and thresholding method was used to calculate PRS of CAD and its 14 risk factors. Their correlations with all-cause death were computed via Cox regression.Results and discussionWe found that the PRS for CAD and its seven risk factors, namely myocardial infarction, ischemic stroke, angina, heart failure, low-density lipoprotein cholesterol, total cholesterol and C-reaction protein, were significantly associated with death (P ≤ 0.05), whereas the PRS of body mass index displayed moderate association (P < 0.1). Elastic-net Cox regression with 5-fold cross-validation was used to integrate these nine PRS models into a meta score, metaPRS, which performed well in stratifying patients at different risks for death (P < 0.0001). Combining metaPRS with clinical risk factors further increased the discerning power and a 4% increase in sensitivity. The metaPRS generated from the genetic susceptibility to CAD and its risk factors can well stratify CAD patients by their risks of death. Integrating metaPRS and clinical risk factors may contribute to identifying patients at higher risk of poor prognosis.</p

Root-centric β diversity reveals functional homogeneity while phylogenetic heterogeneity in a subtropical forest

&lt;p&gt;Root-centric studies have revealed fast taxonomic turnover across root neighborhoods, but how such turnover is accompanied by changes in species functions and phylogeny (i.e. β diversity), which can reflect the degree of community-wide biotic homogenization, remains largely unknown, hindering better inference of below-ground assembly rules, community structuring, and ecosystem processes. We collected 2480 root segments from 625 0–30 cm soil profiles in a subtropical forest in China. Root segments were identified into 143 species with DNA-barcoding with six root morphological and architectural traits measured per species. By using the mean pairwise (Dpw) and mean nearest neighbor distance (Dnn) to quantify species ecological differences, we tested the non-random functional and phylogenetic turnover of root neighborhoods that would lend more support to deterministic over stochastic community assembly processes, examined the distance-decay pattern of β diversity, and finally partitioned β diversity into geographical and environmental components to infer their potential drivers of environmental filtering, dispersal limitation, and biotic interactions. We found that functional turnover was often lower than expected given the taxonomic turnover, whereas phylogenetic turnover was often higher than expected. Both functional and phylogenetic Dpw (e.g. interfamily species) turnover exhibited a distance-decay pattern, likely reflecting limited dispersal or abiotic filtering that leads to the spatial aggregation of specific plant lineages. Conversely, phylogenetic Dnn (e.g. intrageneric species) exhibited an inverted distance-decay pattern, likely reflecting strong biotic interactions among spatially and phylogenetically close species leading to phylogenetic divergence. While the spatial distance was generally a better predictor of β diversity than environmental distance, the joint effect of environmental and spatial distance usually overrode their respective pure effects. These findings suggest that root neighborhood functional homogeneity may somewhat increase forest resilience after disturbance by exhibiting an insurance effect. Likewise, root neighborhood phylogenetic heterogeneity may enhance plant fitness by hindering the transmission of host-specific pathogens through root networks or by promoting interspecific niche complementarity not captured by species functions. Our study highlights the potential role of root-centric β diversity in mediating community structures and functions largely ignored in previous studies.&lt;/p&gt;&lt;p&gt;These datasets were collected in the Guangdong Heishiding Dynamic Forest Plot in Southern China (2016). Details for each dataset are provided in the README file.&lt;/p&gt;&lt;p&gt;Funding provided by: National Natural Science Foundation of China&lt;br&gt;Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809&lt;br&gt;Award Number: 31925027&lt;/p&gt;&lt;p&gt;Funding provided by: China Postdoctoral Science Foundation&lt;br&gt;Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002858&lt;br&gt;Award Number: 2021M70375&lt;/p&gt;&lt;p&gt;Funding provided by: Basic and Applied Basic Research Foundation of Guangdong Province&lt;br&gt;Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100021171&lt;br&gt;Award Number: 2021A1515110362&lt;/p&gt;&lt;p&gt;Funding provided by: National Natural Science Foundation of China&lt;br&gt;Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100001809&lt;br&gt;Award Number: 32301341&lt;/p&gt

Expression and Prognostic Significance of Macrophage Inflammatory Protein-3 Alpha and Cystatin A in Nasopharyngeal Carcinoma

This study aims to investigate the expression of macrophage inflammatory protein-3 alpha (MIP-3α) and cystatin A in nasopharyngeal carcinoma (NPC) and their association with clinical characteristics and prognosis. Primary tumor specimens from 114 NPC patients and associated clinical follow-up data were collected, and the expression of MIP-3α and cystatin A proteins was investigated by immunohistochemistry. Expression of MIP-3α was significantly associated with TNM stage in patients with NPC (P<0.05). NPC patients with positive expression of MIP-3α exhibited shorter median overall survival (OS) and distant metastasis-free survival (DMFS), compared with patients with negative expression (OS: 50.5 months versus 59.0 months, P=0.013; DMFS: 50.1 months versus 60.2 months, P=0.003). NPC patients with positive expression of cystatin A exhibited shorter median OS, local recurrence-free survival (LRFS), and DMFS, compared with patients with negative expression (OS: 51.1 months versus 60.0 months, P=0.004; LRFS: 54.5 months versus 59.5 months, P=0.036; DMFS: 52.3 months versus 58.8 months, P=0.036). Both MIP-3α and cystatin A overexpressions in NPC tumor tissues were strong independent factors of poor prognosis in NPC patients. MIP-3α and cystatin A expressions may be valuable prognostic markers in NPC patients

Prognostic Significance of Neutrophil to Lymphocyte Ratio, Lymphocyte to Monocyte Ratio, and Platelet to Lymphocyte Ratio in Patients with Nasopharyngeal Carcinoma

The peripheral blood neutrophil to lymphocyte ratio (NLR), lymphocyte to monocyte ratio (LMR), and platelet to lymphocyte ratio (PLR) have been reported to correlate with the prognosis of many malignancies. This study evaluated the prognostic value of pretreatment NLR, LMR, and PLR in nasopharyngeal carcinoma (NPC). A retrospective analysis of clinical and pathological data of 140 NPC patients without distant metastasis during initial treatment was conducted to identify correlations between NLR, LMR, and PLR and clinicopathological features, overall survival, and progression-free survival. Cox proportional hazard regression analysis was used to reveal the independent factors affecting the prognosis of NPC patients. NLR was associated with T staging, N staging, and overall clinical stage grouping of the NPC patients (P<0.05). NLR ≥ 2.28, LMR < 2.26, and PLR ≥ 174 were significantly associated with a relatively short overall survival (P<0.05). In addition, NLR ≥ 2.28 was significantly associated with a relatively short progression-free survival (P<0.05). Cox proportional hazard regression analysis showed that NLR was an independent prognostic factor in NPC. Pretreatment NLR, LMR, and PLR might be a useful complement to TNM staging in the prognostic assessment of NPC patients