We comprehensively analyzed clinical, genomic, and transcriptomic data of a cohort of 465 primary triple-negative breast cancer (TNBC). PIK3CA mutations and copy-number gains of chromosome 22q11 were ...more frequent in our Chinese cohort than in The Cancer Genome Atlas. We classified TNBCs into four transcriptome-based subtypes: (1) luminal androgen receptor (LAR), (2) immunomodulatory, (3) basal-like immune-suppressed, and (4) mesenchymal-like. Putative therapeutic targets or biomarkers were identified among each subtype. Importantly, the LAR subtype showed more ERBB2 somatic mutations, infrequent mutational signature 3 and frequent CDKN2A loss. The comprehensive profile of TNBCs provided here will serve as a reference to further advance the understanding and precision treatment of TNBC.
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•We build the genomic and transcriptomic landscape of 465 primary TNBCs•Chinese TNBC cases demonstrate more PIK3CA mutations and LAR subtype•Transcriptomic data classify TNBCs into four subtypes•Multi-omics profiling identifies potential targets within specific TNBC subtypes
Jiang et al. characterize primary Chinese triple-negative breast cancer (TNBC) and classify it into four subtypes. They find that these TNBCs have more frequent PIK3CA mutations and chromosome 22q11 copy-number gains than non-Asian TNBCs and that the LAR subtype has more ERBB2 somatic mutations and CDKN2A loss.
Glaciers on the southeastern Tibetan Plateau, known as the “Asian Water Tower”, directly affect the utilization of water resources in downstream regions. The currently available instrumental climatic ...dataset covers only a short period, and the resolution of proxy-based climate reconstructions is low, and these limitations restrict the accurate exploration of glacial changes on the southeastern Tibetan Plateau within the context of long-term climate change. Here, annual-resolution tree ring samples were collected from the oldest pioneer trees (Hippophae rhamnoides subsp. yunnanensis), from the bottom of a glacial valley on the southeastern Tibetan Plateau, and used to reconstruct the glacial changes based on the relationship between the ages of the trees and their distances from the glacier terminal. Results indicate that Zepu glacier has been retreating since 1778 CE, with a total retreat distance of 2757 m and an average retreat rate of 11 m yr−1. The rate of retreat has varied over time, with a maximum of 40 m yr−1 between the 1950s CE and 1970s CE, and glacial retreat has been modulated mainly by temperature variability over interdecadal to centennial timescales. This study provides a new way to reconstruct the history of glacial retreat.
It is of great significance to study the effects of precipitation events on carbon exchange in the ecosystem for an accurate understanding of the carbon cycle. However, the response of net ecosystem ...CO
2
exchange (NEE) in the desert to precipitation events is elusive. In this study, the NEE in response to precipitation events of varying intensities in the Badain Jaran Desert (BJD) in China was continuously monitored using the eddy covariance (EC) technique. The following results were obtained: (1) The BJD ecosystem was a net CO
2
sink throughout the study period, with NEE values of -113.4, -130.7, and -175.4 g C m
-2
a
-1
in 2016, 2018, and 2019, respectively. The total precipitation yielded a higher carbon sequestration capacity in 2019 than in the other two years. In addition, the intensity, time, and frequency of precipitation had significant impacts on CO
2
; (2) the threshold value of the NEE response to precipitation was ~1.4 mm, indicating the extreme sensitivity of the BJD to precipitation events; (3) the variations in the NEE response to precipitation events conformed to a dual exponential model. The analytical results of the model indicate that precipitation intensity was positively correlated with the carbon sequestration capacity of the desert. The model revealed that the greater the precipitation intensity, the longer it takes the NEE to reach the maximum, and the lengthier the duration of the residual effects. With an increase in the total precipitation and frequency of extreme precipitation events under warm and humidification climates, the carbon sequestration capacity of the BJD will likely be enhanced. The results of this study are of great significance for revealing the carbon cycle mechanism of the desert ecosystem.
The relationship between the variation of CO2 flux and the pH of inorganic factors.
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•The difference of CO2 absorption and release is obvious during the day and night.•Yindeer Lake was ...a net sink of CO2 during the study period.•The lakes can absorb large amounts of CO2 every year to slow down global warming.•Meteorological factors controlling CO2 fluxes differed by time scale.•pH is the main influencing factor controlling CO2 absorption and release.
Carbon sequestration levels in lakes are often underestimated despite being vital for the comprehensive analysis of CO2 budget and significantly influencing inland lakesin arid areas. In this study, the eddy covariance (EC) technique was used to measure CO2 flux for six consecutive years during 2012–2017 in a small salt-lake (Yindeer Lake) replenishedby groundwater in southeastern Badain Jaran Desert, China. The results indicate that: (1) Yindeer Lake was a net sink of CO2, which led to the estimate that the lakes in the Badain Jaran Desert can absorb approximately 1.91 × 103 t of CO2 per year andhelp slow down the rate of global warming. (2) The effects of meteorological factors on the CO2 flux of the lake vary with timescales. (3) Inorganic processes, in which pH is the main influence mechanism, control CO2 absorption and releases in Yindeer Lake. Thus, the study results provide a new guide for solving the “missing sink” problem.
Nonsyndromic cleft lip with or without palate (NSCL/P) is a common birth defect involving genetic factors. We conducted this case–control study to verify the association of ten single-nucleotide ...polymorphisms (SNPs) of six genes (
VAX1
,
MAFB
,
PAX7
,
ABCA4
,
NTN1
, and
NOG
) with NSCL/P in the Chinese population. The study included 249 NSCL/P patients, 62 nonsyndromic cleft palate only (NSCPO) patients and 480 controls. Three loci, namely,
VAX1
rs7078160,
MAFB
rs11696257, and
NTN1
rs4791774, were associated with NSCL/P (Bonferroni method adjusted
p
values were 0.020, 0.00031, and 0.030, respectively). We also found that the disease risk of individuals carrying both
VAX1
rs7078160 and
NTN1
rs4791774 was higher than those carrying only one of them (
p
= 4.50 × 10
–4
and 6.03 × 10
–3
, respectively). SNPs of genes
VAX1
rs7078160,
MAFB
rs11696257, and
NTN1
rs4791774 increased NSCL/P risk in the Chinese population.
Desert ecosystems possess an astonishing biodiversity and are rich in endangered species. This study investigated characteristics of species diversity and soil environmental factors in three major ...deserts of China’s Alxa Plateau. The Alxa Desert included 183 plant species belonging to 109 genera and 35 families. The highest numbers of plant species belonged to the Compositae, Gramineae, and Chenopodiaceae families. The research area belongs to the semi-shrub and small semi-shrub deserts in temperate deserts. Species diversity was low, with the Shannon–Wiener index (H′) of shrub-herb = shrub > herb > tree. The Pielou evenness index (E) of shrub herb vegetation was the lowest, indicating more enriched species and fewer sparse species in the community, and that these types of vegetation had the characteristics of rich and obviously dominant species. Redundancy analysis (RDA) and correlations between the comprehensive plant community biodiversity index and soil factors indicated that soil-available phosphorus (NP), organic matter (SOM), and electrical conductivity (EC) had significant impacts on community species diversity. The herbaceous shrub community exhibited the highest H′, Simpson index (D), species richness index (S), soil moisture (SW), and soil nutrients. Planting Calligonum mongolicum, Ephedra membranacea, Artemisia annua, and Phragmites australis to form a typical desert shrub community for community diversity protection is recommended to effectively protect and restore desert ecosystems.
Common polymorphisms of microRNA gene MIR146A were reported as associated with different autoimmune diseases, include systemic lupus erythematosus, psoriatic arthritis, asthma and ankylosing ...spondylitis. In this study we investigated MIR146A SNPs in Chinese people with ankylosing spondylitis. Three common SNPs: rs2910164, rs2431697 and rs57095329 were selected and genotyped in 611 patients and 617 controls. We found no association between these SNPs and ankylosing spondylitis in our samples.
Proteasome is a large protein complex, which degrades most intracellular proteins. It regulates numerous cellular processes, including the removal of misfolded or unfolded proteins, cell cycle ...control, and regulation of apoptosis. However, the function of proteasome subunits in viral immunity has not been well characterized. In this study, we identified PSMB1, a member of the proteasome β subunits (PSMB) family, as a negative regulator of innate immune responses during viral infection. Knockdown of
enhanced the RNA virus-induced cytokine and chemokine production. Overexpression of PSMB1 abolished virus-induced activation of the interferon-stimulated response element (ISRE) and interferon beta (IFNβ) promoters. Mechanistically, PSMB1 inhibited the activation of RIG-I-like receptor (RLR) and Toll-like receptor 3 (TLR3) signaling pathways. PSMB1 was induced after viral infection and its interaction with IKK-ε promoted degradation of IKK-ε through the ubiquitin-proteasome system. Collectively, our study demonstrates PSMB1 is an important regulator of innate immune signaling.
Mega-dunes in the lake group area of the Badain Jaran Sand Sea, China, are generally taller than dunes in the non-lake group area. This spatial distribution of dune heights may provide a new ...perspective on the controversy regarding the dunes’ formation mechanism. In this study, we calculated the relative heights and slopes of individual dunes based on a digital elevation model, and we confirmed the height distribution of abnormally tall dunes in the lake group area of the sand sea. It was also found that slopes of more than 10° in the lake group area are more common than those in the non-lake group area. Based on meteorological observations, coupled with the measurement of water content in the sand layers, we propose a conceptual model demonstrating that moisture exchange between the lakes and soil via non-rainfall water will humidify dune slopes and form a more favorable accumulation environment for aeolian sand, thus increasing dune heights. Although long-term observations are yet to be carried out, the present study can be used as evidence for understanding the basis of dune formation in the lake group area and assessing groundwater utilization in deserts.
Wind controls the formation and development of sand dunes. Therefore, understanding the wind regimes is necessary in sand dune research. In this study, we combined the wind data from 2017 to 2019 at ...four meteorological stations (Cherigele and Wuertabulage stations in the lake basins, and Yikeri and Sumujilin stations on the top of sand dunes) in the hinterland of the Badain Jaran Desert in China, with high resolution Google Earth images to analyze the correlation between the wind energy environments and dune morphology. The results of data analysis indicated that both the wind direction and sand drift intensity exhibited notable spatial and temporal variations. The highest level of wind activity was observed in spring. Northwesterly and northeasterly winds were the dominant in the Badain Jaran Desert. At the Cherigele, Wuertabulage, and Yikeri stations, the drift potential (DP) was below 200.00 vector units (VU). The wind energy environments in most areas could be classified as low-energy environments. The resultant drift direction differed at different stations and in different seasons, but the overall direction was mainly the southeast. The resultant drift potential (RDP)/DP ratio was greater than 0.30 in most parts of the study area, suggesting that the wind regimes mainly exhibited unimodal or bimodal characteristics. Differences between the thermodynamic properties and the unique landscape settings of lakes and sand dunes could alter the local circulation and intensify the complexity of the wind regimes. The wind regimes were weaker in the lake basins than on the top of sand dunes. Transverse dunes were the most dominant types of sand dunes in the study area, and the wind regimes at most stations were consistent with sand dune types. Wind was thus the main dynamic factor affecting the formation of sand dunes in the Badain Jaran Desert BJD. The results of this study are important for understanding the relationship between the wind regimes and aeolian landforms of the dune field in the deserts.
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