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Qin, W.

Publications and source records attributed to Qin, W..

At least 73 records · Page 4Linked to original sources

Fusobacterium nucleatum facilitates cetuximab resistance in colorectal cancer via the PI3K/AKT and JAK/STAT3 pathways

Infectious pathogens contribute to about 20% of the total tumor burden. Fusobacterium nucleatum (Fn) has been associated with the initiation, progression, and therapy resistance in colorectal cancer (CRC). The over-abundance of Fn has been observed in patients with right-sided CRC than in those with left-sided CRC. While the KRAS/NRAS/BRAF wild-type status of the CRC conferred better response to cetuximab in patients with left-sided CRC than with right-sided CRC. However, treatment failure remains the leading cause of tumor relapse and poor clinical outcome in patients with CRC. Here, we have studied the association of Fn to cetuximab resistance. Our functional studies indicate that Fn facilitates resistance of CRC to cetuximab in vitro and in vivo. Moreover, Fn was found to target the PI3K/AKT and JAK/STAT3 pathways, which altered the response to cetuximab therapy. Therefore, assessing the levels and targeting Fn and the associated signaling pathways may allow modulating the treatment regimen and improve prognoses of CRC patients.

cancer biology↗

Functional proximity mapping of RNA binding proteins uncovers a mitochondrial mRNA anchor that promotes stress recovery

Proximity labeling (PL) with genetically-targeted promiscuous enzymes has emerged as a powerful tool for unbiased proteome discovery. By combining the spatiotemporal specificity of PL with methods for functional protein enrichment, it should be possible to map specific protein subclasses within distinct compartments of living cells. Here we demonstrate this capability for RNA binding proteins (RBPs), by combining peroxidase-based PL with organic-aqueous phase separation of crosslinked protein-RNA complexes ("APEX-PS"). We validated APEX-PS by mapping nuclear RBPs, then applied it to uncover the RBPomes of two unpurifiable subcompartments - the nucleolus and the outer mitochondrial membrane (OMM). At the OMM, we discovered the RBP SYNJ2BP, which retains specific nuclear-encoded mitochondrial mRNAs during translation stress, to promote their local translation and import of protein products into the mitochondrion during stress recovery. APEX-PS is a versatile tool for compartment-specific RBP discovery and expands the scope of PL to functional protein mapping. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=186 SRC="FIGDIR/small/387209v1_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@1223baforg.highwire.dtl.DTLVardef@7c87c6org.highwire.dtl.DTLVardef@1b5e7cdorg.highwire.dtl.DTLVardef@185449b_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

A high-affinity RBD-targeting nanobody improves fusion partner's potency against SARS-CoV-2

A key step to the SARS-CoV-2 infection is the attachment of its Spike receptor-binding domain (S RBD) to the host receptor ACE2. Considerable research have been devoted to the development of neutralizing antibodies, including llama-derived single-chain nanobodies, to target the receptor-binding motif (RBM) and to block ACE2-RBD binding. Simple and effective strategies to increase potency are desirable for such studies when antibodies are only modestly effective. Here, we identify and characterize a high-affinity synthetic nanobody (sybody, SR31) as a fusion partner to improve the potency of RBM-antibodies. Crystallographic studies reveal that SR31 binds to RBD at a conserved and greasy site distal to RBM. Although SR31 distorts RBD at the interface, it does not perturb the RBM conformation, hence displaying no neutralizing activities itself. However, fusing SR31 to two modestly neutralizing sybodies dramatically increases their affinity for RBD and neutralization activity against SARS-CoV-2 pseudovirus. Our work presents a tool protein and an efficient strategy to improve nanobody potency.

biochemistry↗

Light quality signals generated by vegetation shade facilitate acclimation to reduced light quantity in shade-avoider plants

O_LIWhen growing in search for light, plants can experience continuous or occasional shading by other plants. Plant proximity causes a decrease in the ratio of red to far red light (low R:FR) due to the preferential absorbance of red light and reflection of far red light by photosynthetic tissues of neighboring plants. This signal is often perceived before actual shading causes a reduction in photosynthetically active radiation (low PAR). C_LIO_LIHere we investigated elongation, photosynthesis and photoacclimation responses in several Brassicaceae species to explore the possible connections between low R:FR and low PAR. C_LIO_LIA negative correlation was found in shade-tolerant Cardamine hirsuta and shade-avoider Arabidopsis thaliana seedlings (e.g., shade-tolerance was associated with a good adaptation to low PAR but a poor or null response to low R:FR exposure). However, they could be genetically uncoupled. Most interestingly, exposure to low R:FR of shade-avoider plants improved their photoacclimation to low PAR by triggering changes in photosynthesis-related gene expression, pigment accumulation and chloroplast ultrastructure. C_LIO_LIThese results indicate that low R:FR signaling unleashes molecular, metabolic and developmental responses that allow shade-avoider plants (including most crops) to adjust their photosynthetic capacity in anticipation of eventual shading by nearby plants. C_LI

plant biology↗

Genome-wide association study of TP53 R249S mutation in hepatocellular carcinoma with aflatoxin B1 exposure and hepatitis B virus infection in Guangxi

Background/AimsDietary aflatoxin B1 (AFB1) exposure, which induces DNA damage and codon 249 mutation of the TP53 gene, is one of the major risk factors for hepatocellular carcinoma (HCC). Hepatitis B virus (HBV) infection and AFB1 exert synergistic effects to promote carcinogenesis and TP53 R249S mutation in HCC. MethodsA genome-wide association study (GWAS) was conducted on 485 cases of HCC with chronic HBV infection, followed by a two-stage replication study on 270 cases with chronic HBV infection. Susceptibility variants for the TP53 R249S mutation in HCC were identified based on both GWAS and replication analysis. The associations of identified variants with expression levels of their located genes were validated in 20 paired independent samples. ResultsOur results showed that TP53 R249S was significantly associated with ADAMTS18 rs9930984 (adjusted P = 4.84x10-6), WDR49 rs75218075 (adjusted P = 7.36 x 10-5) and SLC8A3 rs8022091 (adjusted P = 0.042). Additionally, ADAMTS18 mRNA expression was significantly higher in HCC tissue, compared with paired non-tumor tissue (P = 0.041) and patients carrying the TT genotype at rs9930984 showed lower ADAMTS18 expression in non-tumor tissue, compared with those carrying the GT genotype (P = 0.0028). ConclusionsTP53 expression is significantly associated with R249S mutation in HCC. Our collective results suggest that rs9930984, rs75218075 and rs8022091 are associated with susceptibility to the R249S mutation in cases of HCC exposed to AFB1 and HBV infection.

genetics↗

Potent synthetic nanobodies against SARS-CoV-2 and molecular basis for neutralization

SARS-CoV-2, the causative agent of COVID-191, recognizes host cells by attaching its receptor-binding domain (RBD) to the host receptor ACE22-7. Neutralizing antibodies that block RBD-ACE2 interaction have been a major focus for therapeutic development8-18. Llama-derived single-domain antibodies (nanobodies, [~]15 kDa) offer advantages including ease of production and possibility for direct delivery to the lungs by nebulization19, which are attractive features for bio-drugs against the global respiratory disease. Here, we generated 99 synthetic nanobodies (sybodies) by in vitro selection using three libraries. The best sybody, MR3 bound to RBD with high affinity (KD = 1.0 nM) and showed high neutralization activity against SARS-CoV-2 pseudoviruses (IC50 = 0.40 g mL-1). Structural, biochemical, and biological characterization of sybodies suggest a common neutralizing mechanism, in which the RBD-ACE2 interaction is competitively inhibited by sybodies. Various forms of sybodies with improved potency were generated by structure-based design, biparatopic construction, and divalent engineering. Among these, a divalent MR3 conjugated with the albumin-binding domain for prolonged half-life displayed highest potency (IC50 = 12 ng mL-1) and protected mice from live SARS-CoV-2 challenge. Our results pave the way to the development of therapeutic nanobodies against COVID-19 and present a strategy for rapid responses for future outbreaks.

biochemistry↗

Extensive Mammalian Germline Genome Engineering

Xenotransplantation, specifically the use of porcine organs for human transplantation, has long been sought after as an alternative for patients suffering from organ failure. However, clinical application of this approach has been impeded by two main hurdles: 1) risk of transmission of porcine endogenous retroviruses (PERVs) and 2) molecular incompatibilities between donor pigs and humans which culminate in rejection of the graft. We previously demonstrated that all 25 copies of the PERV elements in the pig genome could be inactivated and live pigs successfully generated. In this study, we improved the scale of porcine germline editing from targeting a single repetitive locus with CRISPR to engineering 13 different genes using multiple genome engineering methods. we engineered the pig genome at 42 alleles using CRISPR-Cas9 and transposon and produced PERVKO{middle dot}3KO{middle dot}9TG pigs which carry PERV inactivation, xeno-antigen KO and 9 effective human transgenes. The engineered pigs exhibit normal physiology, fertility, and germline transmission of the edited alleles. In vitro assays demonstrated that these pigs gain significant resistance to human humoral and cell mediated damage, and coagulation dysregulations, similar to that of allotransplantation. Successful creation of PERVKO{middle dot}3KO{middle dot}9TG pigs represents a significant step forward towards safe and effective porcine xenotransplantation, which also represents a synthetic biology accomplishment of engineering novel functions in a living organism. One Sentence SummaryExtensive genome engineering is applied to modify pigs for safe and immune compatible organs for human transplantation

synthetic biology↗

Satellite Imaging of Global Urbanicity relate to Adolescent Brain Development and Behavior

Urbanicity, the impact of living in urban areas, is among the greatest environmental challenges for mental health. While urbanicity might be distinct in different sociocultural conditions and geographic locations, there are likely to exist common features shared in different areas of the globe. Understanding these common and specific relations of urbanicity with human brain and behavior will enable to assess the impact of urbanicity on mental disorders, especially in childhood and adolescence, where prevention and early interventions are likely to be most effective.\n\nWe constructed from satellite-based remote sensing data a factor for urbanicity that was highly correlated with population density ground data. This factor, UrbanSat was utilized in the Chinese CHIMGEN sample (N=831) and the longitudinal European IMAGEN cohort (N=810) to investigate if exposure to urbanicity during childhood and adolescence is associated with differences in brain structure and function in young adults, and if these changes are linked to behavior.\n\nUrbanicity was found negatively correlated with medial prefrontal cortex volume and positively correlated with cerebellar vermis volume in young adults from both China and Europe. We found an increased correlation of urbanicity with functional network connectivity within- and between- brain networks in Chinese compared to European participants. Urbanicity was highly correlated with a measure of perceiving a situation from the perspective of others, as well as symptoms of depression in both datasets. These correlations were mediated by the structural and functional brain changes observed. Susceptibility to urbanicity was greatest in two developmental windows during mid-childhood and adolescence.\n\nUsing innovative technology, we were able to probe the relationship between urban upbringing with brain change and behavior in different sociocultural conditions and geographic locations. Our findings help to identify shared and distinct determinants of adolescent brain development and mental health in different regions of the world, thus contributing to targeted prevention and early-intervention programs for young people in their unique environment. Our approach may be relevant for public health, policy and urban planning globally.

neuroscience↗

Differential urine proteome analysis of a bovine IRBP induced uveitis rat model by discovery and parallel reaction monitoring proteomics

Uveitis, a group of intraocular inflammatory diseases, is one of the major causes of severe visual impairment among working age population. Urine is a promising resource for biomarker research, which could sensitively reflect the changes of the body. This study was designed to explore urinary protein biomarkers for diagnosis and/or monitoring of uveitis. Experimental autoimmune uveitis (EAU) rat model induced by bovine interphotoreceptor retinoid-binding protein (IRBP) was used to mimic the uveitis. In the discovery phase, urine samples from EAU and control rats were analyzed by data independent acquisition (DIA) approach combined with high-resolution mass spectrometry. Overall, 704 high confidential proteins were identified, of which 100 were differentially expressed (37, 33, 37, and 44 on day 5, 8, 12, and 16, respectively, after bovine IRBP immunization) (1.5-fold change, P<0.05). Gene Ontology analysis of the dysregulated proteins showed that chronic inflammatory response, neutrophil aggregation and immune system processes were significantly enriched. Finally, parallel reaction monitoring (PRM) approach was used for further validation. A total of 12 urinary proteins (MMP8, NGAL, HPT, UROM, RISC, A1AG, TTHY, KNT1, C9, PTER, CBG, and FUCA1) changed significantly, even when there is no clinical manifestations and histopathological ocular damages in the EAU rats. Our findings represent the first step towards urinary protein diagnostic biomarkers for uveitis.\n\nBiological SignificanceThis is the first study investigating urinary protein candidate biomarkers for uveitis using data independent acquisition (DIA) combined with parallel reaction monitoring (PRM) in experimental autoimmune uveitis (EAU) rats. The results revealed that urine is a promising resource for early diagnostics of uveitis. Further research including clinical urine samples is needed to determine the sensitivity and specificity of these candidate biomarkers for uveitis.

biochemistry↗

Multi-Region Brain Stimulation Optimization Using Transcranial Direct Current Stimulation

Transcranial direct current stimulation (tDCS) is a type of noninvasive transcranial electrical brain stimulation. By optimizing the current distribution of each electrode on the scalp, the stimulation can be guided to a target brain region using a tDCS dense electrode array system. However, previous studies have yielded simple results using optimization schemes in single target stimulation cases. The detailed parameter settings for each optimization scheme and the associated simulation results have not been comprehensively assessed. In this study, we investigated parameter settings of optimization schemes in detail in both single target and multi-target cases. Two optimization schemes, minimum least squares (MLS) and maximum electrical field strength (ME), were examined in this study. MLS minimizes the squared errors between the expected electrical field and the estimated electrical field, whereas ME maximizes the electrical field strength in the target region. We constructed a five layer finite-element head model with 64 electrodes placed on the scalp according to the EEG 10/10 system for simulation. We evaluated the effects of stimulation using these two schemes under three conditions, 1) single target stimulation, 2) multi-target stimulation, and 3) multi-target stimulation under specific task activation, which shown that directly using MLS and ME scheme in multi-target stimulation case may lead to a wrong result. We also reported the improved results fixed by our proposed weighted MLS and weighted ME schemes which take detailed parameter settings into consideration. Our results indicate that the parameter settings in each optimization scheme greatly affected the final stimulation results, especially in the case of multi-target stimulation, and thus, indicate that the parameter settings of each optimization scheme should be carefully considered according to the expected stimulation mode. Our results also suggest that, by calculating the parameters through our proposed methods, the weighted ME and weighted MLS scheme can precisely distribute energy into each target brain region.

bioengineering↗

Early urine proteome changes in an implanted bone cancer rat model

In this study, Walker 256 cells were implanted into rat tibiae. Urine samples were then collected on days 3, 5, 7, and 13 and were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). With label-free quantification, 25 proteins were found to change significantly in the urine of the tumor group mice compared with the proteins in the urine of the control group mice; this was even the case when there were no significant lesions identified in the Computed Tomography(CT) examination. Among these differentially proteins, 7 were reported to be associated with tumor bone metastasis. GO analysis shows that the differential proteins on day 3 were involved in several responses, including the acute phase response, the adaptive immune response and the innate immune response. The differentially proteins on day 7 were involved in the mineral absorption pathway. The differentially proteins on day 13 were involved in vitamin D binding and calcium ion binding. These processes may be associated with bone metastasis. Our results demonstrate that urine could sensitively reflect the changes in the early stage of implanted bone cancer; this provides valuable clues for future studies of urine biomarkers for tumor bone metastasis.

cancer biology↗

Genetic variation influences pluripotent ground state stability in mouse embryonic stem cells through a hierarchy of molecular phenotypes

Mouse embryonic stem cells (mESCs) cultured under controlled conditions occupy a stable ground state where pluripotency-associated transcriptional and epigenetic circuitry are highly active. However, mESCs from some genetic backgrounds exhibit metastability, where ground state pluripotency is lost in the absence of ERK1/2 and GSK3 inhibition. We dissected the genetic basis of metastability by profiling gene expression and chromatin accessibility in 185 genetically heterogeneous mESCs. We mapped thousands of loci affecting chromatin accessibility and/or transcript abundance, including eleven instances where distant QTL co-localized in clusters. For one cluster we identified Lifr transcript abundance as the causal intermediate regulating 122 distant genes enriched for roles in maintenance of pluripotency. Joint mediation analysis implicated a single enhancer variant ~10kb upstream of Lifr that alters chromatin accessibility and precipitates a cascade of molecular events affecting maintenance of pluripotency. We validated this hypothesis using reciprocal allele swaps, revealing mechanistic details underlying variability in ground state metastability in mESCs.

genomics↗

Unilateral relapse of Behcet’s disease-associated uveitis does not appear to cause asymmetric tear protein profiles

Purpose: To explore whether unilateral relapse of Bechets disease uveitis (BDU) causes differences in the tear proteome between the diseased and the contralateral quiescent eye.\n\nExperimental design: To minimize interindividual variations, bilateral tear samples were collected from the same patient (n=15) with unilateral relapse of BDU. A data-independent acquisition (DIA) strategy was used to identify proteins that differed between active and quiescent eyes.\n\nResults: A total of 1,797 confident proteins were identified in the tear samples, of which 371 are also highly expressed in various tissues and organs. Sixty-two (3.5%) proteins differed in terms of expression between tears in active and quiescent eyes, similar to the number of differentially expressed proteins (74, 4.1%) identified in a randomized grouping strategy. Furthermore, the intrapair trend of the differentially expressed proteins was not consistent and none of the proteins showed the same trend in more than 9 pairs of eyes.\n\nConclusions and clinical relevance: Unilateral relapse of BDU does not appear to cause asymmetric changes in the tear proteome between active and contralateral quiescent eyes. Tear fluid is a valuable source for biomarker studies of systemic diseases.\n\nStatement of clinical relevanceTears are an easily, noninvasively accessible body fluid that is a valuable source of biomarkers for various diseases. Behcets disease uveitis (BDU) has high potential to cause blindness and represents the leading cause of morbidity in BD patients, especially in frequently relapsing cases. Here, we adopted a method combining a \"dry\" method for tear preservation and nano-LC-DIA-MS/MS system to explore whether unilateral relapse of BDU causes differences in the tear proteome between the diseased and the contralateral quiescent eye, with the aim of evaluating tear fluid as a source for biomarker studies of uveitis relapse.

molecular biology↗

Urine proteome changes in a TNBS-induced colitis rat model

Urine is an important resource for biomarker research. Without homeostasis, urine accumulates markers of all the changes in the body. Urine proteins reflect not only renal diseases but also changes in other organs in the body. However, urine has rarely been used to reflect inflammatory bowel disease. In the present study, a trinitrobenzene sulfonic acid (TNBS)-induced colitis rat model was used to mimic the human inflammatory bowel disease Crohns disease (CD). Urine samples from a control group (n=3), a TNBS 2-day group (n=3) and a TNBS 7-day group (n=3) were analyzed for candidate biomarker discovery by label-free and TMT-labeled proteomic quantitative methods. Seventy-seven urinary proteins were significantly changed in the colitis rats compared with that in the controls. These proteins were further validated by parallel reaction monitoring (PRM) targeted proteomic quantitative methods. Urine samples from the control group (n=8), the TNBS 2-day group (n=11) and the TNBS 7-day group (n=11) were analyzed by PRM. This led to the identification of 9 significantly differential expressed urinary proteins: CAH1, G3P, MMP-8, MANBA, NGAL, RNS1G, SLC31, S6A18, and TMM27. Based on the human protein tissue atlas, CAH1, RNS1G and SLC31 are highly enriched in the gastrointestinal tract. Among the 9 PRM-validated proteins, CAH1, MMP-8 and NGAL were previously reported as IBD-associated proteins (all exhibiting consistent trends with our observation), whereas the others are newly discovered by this study. Our results provide valuable clues for future study of urine biomarker of inflammatory bowel disease and Crohns disease.

molecular biology↗

TET1 drives global DNA demethylation via DPPA3-mediated inhibition of maintenance methylation

Genome-wide DNA demethylation is a unique feature of mammalian development and naive pluripotent stem cells. So far, it was unclear how mammals specifically achieve global DNA hypomethylation, given the high conservation of the DNA (de-)methylation machinery among vertebrates. We found that DNA demethylation requires TET activity but mostly occurs at sites where TET proteins are not bound suggesting a rather indirect mechanism. Among the few specific genes bound and activated by TET proteins was the naive pluripotency and germline marker Dppa3 (Pgc7, Stella), which undergoes TDG dependent demethylation. The requirement of TET proteins for genome-wide DNA demethylation could be bypassed by ectopic expression of Dppa3. We show that DPPA3 binds and displaces UHRF1 from chromatin and thereby prevents the recruitment and activation of the maintenance DNA methyltransferase DNMT1. We demonstrate that DPPA3 alone can drive global DNA demethylation when transferred to amphibians (Xenopus) and fish (medaka), both species that naturally do not have a Dppa3 gene and exhibit no post-fertilization DNA demethylation. Our results show that TET proteins are responsible for active and - indirectly also for - passive DNA demethylation; while TET proteins initiate local and gene-specific demethylation in vertebrates, the recent emergence of DPPA3 introduced a unique means of genome-wide passive demethylation in mammals and contributed to the evolution of epigenetic regulation during early mammalian development.

developmental biology↗

Intrinsic functional reorganization of the attention network in the blind

Attention can bias visual perception by modulating the neuronal activity of visual areas. However, little is known if blindness can reshape the intrinsic functional organisation within the attention networks and between the attention and visual networks. A voxel-wise network-based functional connectivity strengthen mapping analysis was proposed to thirty congenitally, thirty early and thirty late blind subjects, and thirty sighted controls. Both the blind and sighted subjects exhibited similar spatial distributions of the intrinsic dorsal (DAN) and ventral (VAN) attention networks. Moreover, compared to the sighted controls, the blind subjects showed increased functional coupling within the DAN, and between the DAN and VAN, and between the attention sub-networks and visual areas, suggesting an increased information communication by visual deprivation. However, the onset age of blindness had little impact on the functional coupling of the attention network, indicating that non-visual sensory experience is enough for driving the development of intrinsic functional organization of the attention network. Finally, a positive correlation was identified between the duration of blindness and the functional coupling of the posterior inferior frontal gyrus with the visual network, representing an experience-dependent reorganisation after visual deprivation.

neuroscience↗

Effects of regional differences on the urinary proteomes of healthy Chinese individuals

Urine is a promising biomarker source for clinical proteomics studies. Although regional physiological differences are common in multi-center clinical studies, the presence of significant differences in the urinary proteomes of individuals from different regions remains unknown. In this study, morning urine samples were collected from healthy urban residents in three regions of China and urinary proteins were preserved using a membrane-based method (Urimem). The urine proteomes of 27 normal samples were analyzed using LC-MS/MS and compared among the three regions. We identified 1,898 proteins from Urimem samples using label-free proteome quantification, of which 62 urine proteins were differentially expressed among the three regions. Hierarchical clustering analysis showed that inter-regional differences caused less significant changes in the urine proteome than inter-sex differences. Of the 62 differentially expressed proteins, 10 have been reported to be disease biomarkers in previous clinical studies. Urimem facilitates urinary protein storage for large-scale urine sample collection, and thus accelerates biobank development and urine biomarker studies employing proteomics approaches. Regional differences are a confounding factor influencing the urine proteome and should be considered in future multi-center biomarker studies.

physiology↗

Collection And Preservation Of Urinary Proteins Using A Fluff Pulp Diaper

Change is the most fundamental property of biomarker. Contrast to the blood, which is under homeostatic controls, urine reflects changes in the body earlier and more sensitive therefore is a better biomarker source. And drawing blood from infants and toddlers is hard and less tolerated. For patients limited by language, giving chief complaint is difficult. Thus, monitoring biomarkers in urine can provide valuable clues for diagnosis of diseases, especially pediatric diseases. Collecting urine from young children and some adult patients is more challenging than collecting it from healthy adults. Here, we propose a method that uses a fluff pulp diaper to collect urine. Urinary proteins were then eluted and adsorbed onto a piece of nitrocellulose membrane, which can be dried and stored in a vacuumed bag. SDS-PAGE and LC-MS/MS analysis indicated that this method is reproducible, and similar proteins were identified as those obtained using an acetone precipitation method. With this simple economical method, it is possible to collect and preserve urine samples from infants, toddlers, and patients with special needs, even for large-scale biomarker studies.

molecular biology↗