The human microbiome plays a crucial role in human health.In the past decade,advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiom...The human microbiome plays a crucial role in human health.In the past decade,advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome.However,most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection,handling,and processing procedures,which impedes obtaining valid and timely microbial taxonomic and functional results.This protocol provides detailed operation methods of human microbial sample collection,DNA extraction,and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity,oral cavity,and skin,as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult par-ticipants.This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples.展开更多
Birth weight(BW)is a key determinant of infant mortality.Previous studies have reported seasonal fluctuation of BW.However,the responsible environmental factors remain disputable.High-altitude environment provides a g...Birth weight(BW)is a key determinant of infant mortality.Previous studies have reported seasonal fluctuation of BW.However,the responsible environmental factors remain disputable.High-altitude environment provides a great opportunity to test the current hypotheses due to its distinctive climate conditions.We collected BW data of~9000 Tibetan singletons born at Lhasa(elevation:3660 m)from 2014 to 2018.Using regression models,we analyzed BW seasonality of highland Tibetans.Multivariate models with meteorological factors as independent variables were employed to examine responsible environmental factors accounting for seasonal variation.We compared BW,low-BW prevalence and sex ratio between high-land and lowland populations,and we observed a significant seasonal pattern of BW in Tibetans,with a peak in winter and a trough in summer.Notably,there is a marked sex-biased pattern of BW seasonality(more striking in males than in females).Sunlight exposure in the 3rd trimester and barometric pressure exposure in the 2nd trimester are significantly correlated with BW,and the latter can be explained by seasonal change of oxygen partial pressure.In particular,due to the male-biased BW seasonality,we found a more serious BW reduction and higher prevalence of low-BW in males,and a skewed sex ratio in highlanders.The infant BW of highland Tibetans has a clear pattern of seasonality.The winter BW is larger than the summer BW,due to the longer sunlight exposure during the late-trimester.Male infants are more sensitive to hypoxia than female infants during the 2nd trimester,leading to more BW reduction and higher mortality.展开更多
Tau proteins accumulation and their spreading pattern were afected by gender in cognitive impairment patients,especially in the progression of Alzheimer’s disease(AD).However,it was unclear whether the gender efects ...Tau proteins accumulation and their spreading pattern were afected by gender in cognitive impairment patients,especially in the progression of Alzheimer’s disease(AD).However,it was unclear whether the gender efects for tau deposition infuenced by amyloid deposition.The aim of this study was to investigate gender diferences for tau depositions in Aβpositive(A^(+))subjects.In this study,tau and amyloid positron emission tomography images,structural magnetic resonance imaging images,and demographic information were collected from 179 subjects in Alzheimer’s Disease Neuroimaging Initiative(ADNI)database and 63 subjects from Huashan Hospital.Subjects were classifed as T^(+)or T^(-)according to the presence or absence of tau(T)biomarkers.We used two-sample t test and one-way analysis of variance test to analyze the efect of gender with adjusting for age,years of education,and Minimum Mental State Examination.In the ADNI cohort,we found diferences in Tau deposition in fusiform gyrus,inferior temporal gyrus,middle temporal gyrus and parahippocampal gyrus between the female T^(+)(FT^(+))and male T^(+)(MT^(+))groups(p<0.05).Tau deposition did not difer signifcantly between female T^(-)(FT^(-))and male T^(-)(MT^(-))subjects(p>0.05).In the Huashan Hospital cohort,there was no diference in Tau deposition between FT^(+)and MT^(+)(p>0.05).The results show that tau depositions signifcantly increased in females in above brain regions.Our fndings suggest that tau deposition is infuenced by gender in the A+subjects.This result has important clinical implications for the development of gender-guided early interventions for patients with both Tau and Amyloid depositions.展开更多
Alzheimer’s disease(AD)is the main cause of dementia,with its diagnosis and management remaining challenging.Amyloid positron emission tomography(PET)has become increasingly important in medical practice for patients...Alzheimer’s disease(AD)is the main cause of dementia,with its diagnosis and management remaining challenging.Amyloid positron emission tomography(PET)has become increasingly important in medical practice for patients with AD.To integrate and update previous guidelines in the field,a task group of experts of several disciplines from multiple countries was assembled,and they revised and approved the content related to the application of amyloid PET in the medical settings of cognitively impaired individuals,focusing on clinical scenarios,patient preparation,administered activities,as well as image acquisition,processing,interpretation and reporting.In addition,expert opinions,practices,and protocols of prominent research institutions performing research on amyloid PET of dementia are integrated.With the increasing availability of amyloid PET imaging,a complete and standard pipeline for the entire examination process is essential for clinical practice.This international consensus and practice guideline will help to promote proper clinical use of amyloid PET imaging in patients with AD.展开更多
Hemodynamically significant patent ductus arteriosus(hsPDA)is a severe condition in newborns.Ibuprofen is an effective treatment to reduce the severe complications and the need for surgical treatment.Several single-nu...Hemodynamically significant patent ductus arteriosus(hsPDA)is a severe condition in newborns.Ibuprofen is an effective treatment to reduce the severe complications and the need for surgical treatment.Several single-nucleotide polymorphisms(SNPs)were related to the ibuprofen metabolism,treatment effects,and the onset of side effects.The effects of SNPs on hsPDA response after ibuprofen treatment are unknown.Therefore,in this study,we recruited hsPDA patients with standard ibuprofen treatment.Those patients had participated in China Neonatal Genomes Project(CNGP,ClinicalTrials.gov Identifier:NCT03931707)with next-generation sequencing data.We reanalyzed the sequencing data and compared the allele frequencies of known ibuprofen-related SNPs between ibuprofen Responder and Non-responder groups.In total,185 hsPDA patients were recruited with gestational age(GA)ranging from 24 to 40 weeks.No significant differences were detected in the basic information,period of ibuprofen treatment,rate of conservative treatment,complications,and side effects between ibuprofen Responder group and Non-responder group.Totally,17 hsPDA carried CYP2C9^(*)3 and one with CYP2C9^(*)2 were detected.In the GA group of more than 30 GA weeks(GA>30 wks group),we found higher allele frequency of CYP2C9^(*)3 in Responder group than in Non-responder group(16%vs.0,p=0.0391).In the GA group of less than 30 GA weeks(GA≤30 wks group),the sum allele frequency of CYP2C9^(*)3 and CYP2C9^(*)2 had no stastical difference between two groups(Responder group vs.Non-responder group,13%vs.11%,p=0.768).Therefore,we came to conclude that genetic tests of CYP2C9^(*)3 site may benefit the prediction of ibuprofen treatment outcome for hsPDA patients with gestational age of more than 30 weeks.展开更多
The DEAD-box RNA helicase(DDX)family plays a critical role in the growth and development of multiple organisms.DDX1 is involved in mRNA/rRNA processing and mature,virus replication and transcription,hormone metabolism...The DEAD-box RNA helicase(DDX)family plays a critical role in the growth and development of multiple organisms.DDX1 is involved in mRNA/rRNA processing and mature,virus replication and transcription,hormone metabolism,tumo-rigenesis,and tumor development.However,how DDX1 functions in various cancers remains unclear.Here,we explored the potential oncogenic roles of DDX1 across 33 tumors with The Cancer Genome Atlas(TCGA)and the Genotype-Tissue Expression(GTEx)databases.DDX1 is highly expressed in breast cancer(BRCA),cholangiocarcinoma(CHOL),and colon adenocarcinoma(COAD),but it is lowly expressed in renal cancers,including kidney renal clear cell carcinoma(KIRC),kidney chromophobe(KICH),and kidney renal papillary cell carcinoma(KIRP).Low expression of DDX1 in KIRC is cor-related with a good prognosis of overall survival(OS)and disease-free survival(DFS).Highly expressed DDX1 is linked to a poor prognosis of OS for adrenocortical carcinoma(ACC),bladder urothelial carcinoma(BLCA),KICH,and liver hepatocellular carcinoma(LIHC).Also,the residue Ser481 of DDX1 had an enhanced phosphorylation level in BRCA and ovarian cancer(OV)but decreased in KIRC.Immune infiltration analysis exhibited that DDX1 expression affected CD8+T cells,and it was significantly associated with MSI(microsatellite instability),TMB(tumor mutational burden),and ICT(immune checkpoint blockade therapy)in tumors.In addition,the depletion of DDX1 dramatically affected the cell viability of human tumor-derived cell lines.DDX1 could affect the DNA repair pathway and the RNA transport/DNA replication processes during tumorigenesis by analyzing the CancerSEA database.Thus,our pan-cancer analysis revealed that DDX1 had complicated impacts on different cancers and might act as a prognostic marker for cancers such as renal cancer.展开更多
Pseudomonas aeruginosa AG1(PaeAG1)is a Costa Rican strain that was isolated in 2010 in a major Hospital.This strain has resistance to multiple antibiotics such asβ-lactams(including carbapenems),aminoglycosides,and f...Pseudomonas aeruginosa AG1(PaeAG1)is a Costa Rican strain that was isolated in 2010 in a major Hospital.This strain has resistance to multiple antibiotics such asβ-lactams(including carbapenems),aminoglycosides,and fluoroquinolones.PaeAG1 is considered critical(Priority 1)due to its resistance to carbapenems,and it was the first report of a P.aeruginosa isolate carrying both VIM-2 and IMP-18 genes encoding for metallo-β-lactamases(MBL)enzymes(both with carbapenemase activity).Owing to these traits,we have studied this model for 10 years using diverse approaches including multi-omics.In this review,we summarize the main points of the different steps that we have studied in PaeAG1:preliminary analyses of this strain at the genomic and phenomic levels revealed that this microorganism has particular features of antibiotic resistance.In the multi-omics approach,the genome assembly was the initial step to identify the genomic determinants of this strain,includ-ing virulence factors,antibiotic resistance genes,as well as a complex accessory genome.Second,a comparative genomic approach was implemented to define and update the phylogenetic relationship among complete P.aeruginosa genomes,the genomic island content in other strains,and the architecture of the two MBL-carrying integrons.Third,the proteomic profile of PaeAG1 was studied after exposure to antibiotics using 2-dimensional gel electrophoresis(2D-GE).Fourth,to study the central response to multiple perturbations in P.aeruginosa,i.e.,the core perturbome,a machine learning approach was used.The analysis revealed biological functions and determinants that are shared by different disturbances.Finally,to evaluate the effects of ciprofloxacin(CIP)on PaeAG1,a growth curve comparison,differential expression analysis(RNA-Seq),and network analysis were performed.Using the results of the core perturbome(pathways that also were found in this perturbation with CIP),it was possible to identify the“exclusive”response and determinants of PaeAG1 after exposure to CIP.Altogether,after a decade of study using a multi-omics approach(at genomics,comparative genomics,perturbomics,transcriptomics,proteomics,and phenomics levels),we have provided new insights about the genomic and transcriptomic determinants associated with antibiotic resistance in PaeAG1.These results not only partially explain the high-risk condition of this strain that enables it to conquer nosocomial environments and its multi-resistance profile,but also this information may eventually be used as part of the strategies to fight this pathogen.展开更多
The clinical manifestations of COVID-19,caused by the SARS-CoV-2,define a large spectrum of symptoms that are mainly dependent on the human host conditions.In Costa Rica,more than 169,000 cases and 2185 deaths were re...The clinical manifestations of COVID-19,caused by the SARS-CoV-2,define a large spectrum of symptoms that are mainly dependent on the human host conditions.In Costa Rica,more than 169,000 cases and 2185 deaths were reported during the year 2020,the pre-vaccination period.To describe the clinical presentations at the time of diagnosis of SARS-CoV-2 infection in Costa Rica during the pre-vaccination period,we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles at the population level among 18,974 records of positive cases.Profiles were compared based on symptoms,risk factors,viral load,and genomic features of the SARS-CoV-2 sequence.A total of 18 symptoms at time of diagnosis of SARS-CoV-2 infection were reported with a frequency>1%,and those were used to identify seven clinical profiles with a specific composition of clinical manifestations.In the comparison between clusters,a lower viral load was found for the asymptomatic group,while the risk factors and the SARS-CoV-2 genomic features were distributed among all the clusters.No other distribution patterns were found for age,sex,vital status,and hospitalization.In conclusion,during the pre-vaccination time in Costa Rica,the symptoms at the time of diagnosis of SARS-CoV-2 infection were described in clinical profiles.The host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile,rather they are present in all the groups,including asymptomatic cases.In addition,this information can be used for decision-making by the local healthcare institutions(first point of contact with health professionals,case definition,or infrastructure).In further analyses,these results will be compared against the profiles of cases during the vaccination period.展开更多
Poor adherence to standard protocols of blood pressure(BP)measurement in routine clinical practice leads to higher readings than“research-quality”measurements.Whether this phenomenon exists in periodic health examin...Poor adherence to standard protocols of blood pressure(BP)measurement in routine clinical practice leads to higher readings than“research-quality”measurements.Whether this phenomenon exists in periodic health examinations was unknown.We aimed to explore the concordance between BP measurements in periodic health examinations and those measured following a standard measurement protocol.We used data from the Kailuan Study,an ongoing longitudinal cohort study in China,of which participants received biennial health examinations in health management centers.In addition,BPs were measured following standard protocols in a workplace-based hypertension management program nested in the Kailuan Study.We compared BP readings of the same person between the two settings using generalized linear mixed-effects models.A total of 3988 men(the mean age was 44.9 years)had at least two BP measurements both in health examinations and management program with a time interval between the two settings that less than 90 days.The mean systolic blood pressures(SBP)and diastolic blood pressures(DBP)in health examinations were 4.2(95%CI 3.9–4.5)mm Hg and 3.3(95%CI 3.1–3.5)mm Hg higher than those in the management program,respectively.Bland–Altman analyses showed the wide agreement inter-vals ranging from-27.7-to 36.5-mm Hg for SBP and-18.3-to 24.7-mm Hg for DBP.In conclusion,BP measurements in periodic health examinations were generally higher than BPs measured following a standard protocol.Our findings highlight the importance of standard BP measurement to avoid overestimation of hypertension prevalence and treatment initiation.展开更多
Prostate cancer remains one of the most prevalent malignancies in men globally(Preisser et al.2020).Accurate diagnosis and diferentiation of the disease are paramount for efective treatment planning and improved patie...Prostate cancer remains one of the most prevalent malignancies in men globally(Preisser et al.2020).Accurate diagnosis and diferentiation of the disease are paramount for efective treatment planning and improved patient outcomes(Hsieh et al.2022).Traditionally,the diagnosis of prostate cancer heavily relied on invasive biopsy procedures,which,although efective,are associated with potential complications and discomfort for patients.With the advancements in medical imaging,positron emission tomography/computed tomography(PET/CT)using prostate-specifc membrane antigen(PSMA)tracers has emerged as a revolutionary diagnostic tool(Obek et al.2017).This technique,often termed as'virtual biopsy',provides a non-invasive alternative to traditional biopsy.Baseline PSMA PET/CT ofers detailed and precise imaging of prostate lesions,allowing clinicians to pinpoint not only the location but also the potential aggressiveness of the tumor.The capability of PSMA PET/CT to bind specifcally to PSMA-expressing cells gives it a unique edge in diferentiating between benign and malignant prostate lesions.展开更多
Years of intensive research has brought us extensive knowledge on the genetic and molecular factors involved in Alzheimer's disease(AD).In addition to the mutations in the three main causative genes of familial AD...Years of intensive research has brought us extensive knowledge on the genetic and molecular factors involved in Alzheimer's disease(AD).In addition to the mutations in the three main causative genes of familial AD(FAD)including presenilins and amyloid precursor protein genes,studies have identified several genes as the most plausible genes for the onset and progression of FAD,such as triggering receptor expressed on myeloid cells 2,sortilin-related receptor 1,and adenosine triphosphate-binding cassette transporter subfamily A member 7.The apolipoprotein Eε4 allele is reported to be the strongest genetic risk factor for sporadic AD(SAD),and it also plays an important role in FAD.Here,we reviewed recent developments in genetic and molecular studies that contributed to the understanding of the genetic phenotypes of FAD and compared them with SAD.We further reviewed the advancements in AD gene therapy and discussed the future perspectives based on the genetic phenotypes.展开更多
Due to inefficient diagnostic methods,inflammatory bowel disease(IBD)normally progresses into severe complications including cancer.Highly efficient extraction and identification of metabolic fingerprints are of signi...Due to inefficient diagnostic methods,inflammatory bowel disease(IBD)normally progresses into severe complications including cancer.Highly efficient extraction and identification of metabolic fingerprints are of significance for disease surveillance.In this work,we synthesized a layered titania nanosheet doped with graphitized carbon(2D-GC-mTNS)through a simple one-step assembly process for assisting laser desorption ionization mass spectrometry(LDI-MS)for metabolite analysis.Based on the synergistic effect of graphitized carbon and mesoporous titania,2D-GC-mTNS exhibits good extraction ability including high sensitivity(<1 fmolμL−1)and great repeatability toward metabolites.A total of 996 fingerprint spectra were collected from hundreds of native urine samples(including IBD patients and healthy controls),each of which contained 1220 m/z metabolite features.Diagnostic model was further established for precise discrimination of patients from healthy controls,with high area under the curve value of 0.972 and 0.981 toward discovery cohort and validation cohort,respectively.The 2D-GC-mTNS promotes LDI-MS to be close to clinical application,with rapid speed,minimum sample consumption and free of sample pretreatment.展开更多
HDAC6 is involved in several biological processes related to aging-associated diseases.However,it was unknown whether HDAC6 could directly regulate lifespan and healthspan.We found that HDAC6 knockdown induced transcr...HDAC6 is involved in several biological processes related to aging-associated diseases.However,it was unknown whether HDAC6 could directly regulate lifespan and healthspan.We found that HDAC6 knockdown induced transcriptome changes to attenuate the aging changes in the Drosophila head,particularly on the inflammation and innate immunity-related genes.Whole-body knockdown of HDAC6 extended lifespan in the fly,furthermore brain-specific knockdown of HDAC6 extended both lifespan and healthspan in the fly.Our results established HDAC6 as a lifespan regulator and provided a potential anti-aging target.展开更多
Modern Western biomedical research and clinical practice are primarily focused on disease.This disease-centric approach has yielded an impressive amount of knowledge around what goes wrong in illness.However,in compar...Modern Western biomedical research and clinical practice are primarily focused on disease.This disease-centric approach has yielded an impressive amount of knowledge around what goes wrong in illness.However,in comparison,researchers and physicians know little about health.What is health?How do we quantify it?And how do we improve it?We currently do not have good answers to these questions.Our lack of fundamental knowledge about health is partly driven by three main factors:(i)a lack of understanding of the dynamic processes that cause variations in health/disease states over time,(ii)an excessive focus on genes,and(iii)a pervasive psychological bias towards additive solutions.Here I briefly discuss potential reasons why scientists and funders have generally adopted a gene-and disease-centric framework,how medicine has ended up practicing“diseasecare”rather than healthcare,and present cursory evidence that points towards an alternative energetic view of health.Understanding the basis of human health with a similar degree of precision that has been deployed towards mapping disease processes could bring us to a point where we can actively support and promote human health across the lifespan,before disease shows up on a scan or in bloodwork.展开更多
The determinative view of mutation penetrance is a fundamental assumption for the building of molecular evolutionary theory:individuals in the population with the same genotype have the same fitness effect.Since this ...The determinative view of mutation penetrance is a fundamental assumption for the building of molecular evolutionary theory:individuals in the population with the same genotype have the same fitness effect.Since this view has been constantly challenged by experimental evidence,it is desirable to examine to what extent violation of this view could affect our under-standing of molecular evolution.To this end,the author formulated a new theory of molecular evolution under a random model of penetrance:for any individual with the same mutational genotype,the coefficient of selection is a random variable.It follows that,in addition to the conventional Ne-genetic drift(Ne is the effective population size),the variance of penetrance among individuals(ε^(2))represents a new type of genetic drift,coined by theε^(2)-genetic drift.It has been demonstrated that these two genetic drifts together provided new insights on the nearly neutral evolution:the evolutionary rate is inversely related to the log-of-Ne when theε^(2)-genetic drift is nontrivial.This log-of-Ne feature ofε^(2)-genetic drift did explain well why the dN/dS ratio(the nonsynonymous rate to the synonymous rate)in humans is only as twofold as that in mice,while the effective population size(Ne)of mice is about two-magnitude larger than that of humans.It was estimated that,for the first time,the variance of random penetrance in mammalian genes was approximatelyε^(2)≈5.89×10^(-3).展开更多
Coronavirus disease 2019(COVID-19),caused by severe acute respiratory syndrome coronavirus-2(SARS-CoV-2),has created an immense menace to public health worldwide,exerting huge effects on global economic and political ...Coronavirus disease 2019(COVID-19),caused by severe acute respiratory syndrome coronavirus-2(SARS-CoV-2),has created an immense menace to public health worldwide,exerting huge effects on global economic and political conditions.Understanding the biology and pathogenesis mechanisms of this novel virus,in large parts,relies on optimal physiological models that allow replication and propagation of SARS-CoV-2.Human organoids,derived from stem cells,are three-dimen-sional cell cultures that recapitulate the cellular organization,transcriptional and epigenetic signatures of their counterpart organs.Recent studies have indicated their great values as experimental virology platforms,making human organoid an ideal tool for investigating host-pathogen interactions.Here,we summarize research developments for SARS-CoV-2 infection of various human organoids involved in multiple systems,including lung,liver,brain,intestine,kidney and blood vessel organoids.These studies help us reveal the pathogenesis mechanism of COVID-19,and facilitate the development of effec-tive vaccines and drugs as well as other therapeutic regimes.展开更多
Age and gender are the important factors for brain metabolic declines in both normal aging and neurodegeneration,and the confounding effects may influence early and differential diagnosis of neurodegenerative diseases...Age and gender are the important factors for brain metabolic declines in both normal aging and neurodegeneration,and the confounding effects may influence early and differential diagnosis of neurodegenerative diseases based on the[^(18)F]fluorodeoxyglucose positron emission tomography([^(18)F]FDG PET).We aimed to explore the potential of the adjustment of age-and gender-related confounding factors on[^(18)F]FDG PET images in differentiation of Parkinson’s disease(PD),multiple system atrophy(MSA)and progressive supra-nuclear palsy(PSP).Eight hundred and seventy-seven clinically definitely diagnosed Parkinsonian patients from a benchmark Huashan Parkinsonian PET imaging database were included.An age-and gender-adjusted Z(AGAZ)score was established based on the gender-specific longitudinal metabolic changes on healthy subjects.AGAZ scores and standardized uptake value ratio(SUVR)values were quantified at regional-level and support vector machine-based error-correcting output codes method was applied for classification.Additional references of the classifications based on metabolic pattern scores were included.The feature-based AGAZ score showed the best performance in classification(accuracy for PD,MSA,PSP:93.1%,96.3%,94.8%).In both genders,the AGAZ score con-sistently achieved the best efficiency,and the improvements compared to the conventional SUVR value for PD,MSA,and PSP mainly laid in specificity(Male:5.7%;Female:11.1%),sensitivity(Male:7.2%;Female:7.3%),and sensitivity(Male:7.3%;Female:17.2%).Female patients benefited more from the adjustment on[^(18)F]FDG PET in MSA and PSP groups(absolute net reclassification index,p<0.001).Collectively,the adjustment of age-and gender-related confounding factors may improve the differential diagnosis of Parkinsonism.Particularly,the diagnosis of female Parkinsonian population has the best improvement from this correction.展开更多
Immunophenotyping is proving crucial to understanding the role of the immune system in health and disease.High-through-put flow cytometry has been used extensively to reveal changes in immune cell composition and func...Immunophenotyping is proving crucial to understanding the role of the immune system in health and disease.High-through-put flow cytometry has been used extensively to reveal changes in immune cell composition and function at the single-cell level.Here,we describe six optimized 11-color flow cytometry panels for deep immunophenotyping of human whole blood.A total of 51 surface antibodies,which are readily available and validated,were selected to identify the key immune cell populations and evaluate their functional state in a single assay.The gating strategies for effective flow cytometry data analysis are included in the protocol.To ensure data reproducibility,we provide detailed procedures in three parts,including(1)instrument characterization and detector gain optimization,(2)antibody titration and sample staining,and(3)data acquisition and quality checks.This standardized approach has been applied to a variety of donors for a better understanding of the complexity of the human immune system.展开更多
The immune system defends the body from infection and plays a vital role in a wide range of health conditions.Metabolism afects a series of physiological processes,including those linked to the function of human immun...The immune system defends the body from infection and plays a vital role in a wide range of health conditions.Metabolism afects a series of physiological processes,including those linked to the function of human immune system.Cellular metabolism modulates immune cell activation and cytokine production.Understanding the relationship between metabolism and immune response has important implications for the development of immune-based therapeutics.However,the deployment of large-scale functional assays to investigate the metabolic regulation of immune response has been limited by the lack of standardized procedures.Here,we present a protocol for the analysis of immune response using standardized whole-blood stimulation with metabolism modulation.Diverse immune stimuli including pattern recognition receptor(PRR)ligands and microbial stimuli were incubated with fresh human whole blood.The metabolic inhibitors were used to modulate metabolic status in the immune cells.The variable immune responses after metabolic interventions were evaluated.We described in detail the main steps involved in the whole-blood stimulation and cytokines quantifcation,namely,collection and treatment of whole blood,preparation of samples and controls,cytokines detection,and stimulation with metabolic interventions.The metabolic inhibitors for anabolic pathways and catabolic pathways exert selective efects on the production of cytokines from immune cells.In addition to a robust and accurate assessment of immune response in cohort studies,the standardized whole-blood stimulation with metabolic regulation might provide new insights for modulating immunity.展开更多
Genetic alterations are a major cause of microphthalmos,while novel-related genes and mutations in microphthalmos have rarely been explored.To identify the underlying genetic defect responsible for microphthalmos eyes...Genetic alterations are a major cause of microphthalmos,while novel-related genes and mutations in microphthalmos have rarely been explored.To identify the underlying genetic defect responsible for microphthalmos eyes in two three-generation Chinese families,we screened 425 genes involved in common inherited non-syndromic eye diseases with next-generation sequencing-based target capture sequencing of the two probands of two three-generation Chinese families diagnosed with microphthalmos.Variants were filtered and analyzed to identify possible disease-causing variants before Sanger sequencing validation.We enrolled two families with microphthalmos(Family 1:microphthalmos with congenital ocular coloboma and Family 2:simple microphthalmos).Two novel heterozygous mutations,Peroxidasin(PXDN)c.3165C>T(p.Pro1055Pro)and PXDN c.2640C>G(p.Arg880Arg),were found in Family 1,and Crystallin Beta B2(CRYBB2)c.481G>A(p.Gly161Arg)was found in Family 2,but none of the mutations were found in the unaffected individuals,who were phenotypically nor-mal.Multiple orthologous sequence alignment(MSA)revealed that the CRYBB2 p.Gly161Arg mutation was a deleterious effect mutation.In conclusion,the three novel mutations found in our study extend our current understanding of the genetic basis of microphthalmos and provide early pre-symptomatic diagnosis and emphasize the significance of genetic diagnosis of microphthalmos.展开更多
基金supported by the National Key Research and Development Program of China(2021YFA1301000)the Shanghai Municipal Science and Technology Major Project(2017SHZDZX01).
文摘The human microbiome plays a crucial role in human health.In the past decade,advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome.However,most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection,handling,and processing procedures,which impedes obtaining valid and timely microbial taxonomic and functional results.This protocol provides detailed operation methods of human microbial sample collection,DNA extraction,and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity,oral cavity,and skin,as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult par-ticipants.This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples.
基金funded by grants from the National Natural Science Foundation of China(NSFC)(91631306 to B.S,3217040584 and 32000390 to Y.H.,32070578 to X.Q and 32170629 to H.Z.)the Youth Innovation Promotion Association of CAS(to Y.H.)+2 种基金the Science and Technology General Program of Yunnan Province(202001AT070110 to Y.H.)the Provincial Natural Science Foundation of Tibet Autonomous Region(XZ2018ZRG-130 to J.L.)Tibetan Fukang Hospital(2017-04 to J.L.).
文摘Birth weight(BW)is a key determinant of infant mortality.Previous studies have reported seasonal fluctuation of BW.However,the responsible environmental factors remain disputable.High-altitude environment provides a great opportunity to test the current hypotheses due to its distinctive climate conditions.We collected BW data of~9000 Tibetan singletons born at Lhasa(elevation:3660 m)from 2014 to 2018.Using regression models,we analyzed BW seasonality of highland Tibetans.Multivariate models with meteorological factors as independent variables were employed to examine responsible environmental factors accounting for seasonal variation.We compared BW,low-BW prevalence and sex ratio between high-land and lowland populations,and we observed a significant seasonal pattern of BW in Tibetans,with a peak in winter and a trough in summer.Notably,there is a marked sex-biased pattern of BW seasonality(more striking in males than in females).Sunlight exposure in the 3rd trimester and barometric pressure exposure in the 2nd trimester are significantly correlated with BW,and the latter can be explained by seasonal change of oxygen partial pressure.In particular,due to the male-biased BW seasonality,we found a more serious BW reduction and higher prevalence of low-BW in males,and a skewed sex ratio in highlanders.The infant BW of highland Tibetans has a clear pattern of seasonality.The winter BW is larger than the summer BW,due to the longer sunlight exposure during the late-trimester.Male infants are more sensitive to hypoxia than female infants during the 2nd trimester,leading to more BW reduction and higher mortality.
基金the National Natural Science Foundation of China(82020108013,81971641,82071200,82021002)the research project of Shanghai Health Commission(2020YJZX0111)+1 种基金the Shanghai Aging and Maternal and Child Health Research Special Project(Grant 2020YJZX0111)the Clinical Research Plan of Shanghai Hospital Development Center(Grants SHDC2020CR1038B and SHDC2020CR4007).
文摘Tau proteins accumulation and their spreading pattern were afected by gender in cognitive impairment patients,especially in the progression of Alzheimer’s disease(AD).However,it was unclear whether the gender efects for tau deposition infuenced by amyloid deposition.The aim of this study was to investigate gender diferences for tau depositions in Aβpositive(A^(+))subjects.In this study,tau and amyloid positron emission tomography images,structural magnetic resonance imaging images,and demographic information were collected from 179 subjects in Alzheimer’s Disease Neuroimaging Initiative(ADNI)database and 63 subjects from Huashan Hospital.Subjects were classifed as T^(+)or T^(-)according to the presence or absence of tau(T)biomarkers.We used two-sample t test and one-way analysis of variance test to analyze the efect of gender with adjusting for age,years of education,and Minimum Mental State Examination.In the ADNI cohort,we found diferences in Tau deposition in fusiform gyrus,inferior temporal gyrus,middle temporal gyrus and parahippocampal gyrus between the female T^(+)(FT^(+))and male T^(+)(MT^(+))groups(p<0.05).Tau deposition did not difer signifcantly between female T^(-)(FT^(-))and male T^(-)(MT^(-))subjects(p>0.05).In the Huashan Hospital cohort,there was no diference in Tau deposition between FT^(+)and MT^(+)(p>0.05).The results show that tau depositions signifcantly increased in females in above brain regions.Our fndings suggest that tau deposition is infuenced by gender in the A+subjects.This result has important clinical implications for the development of gender-guided early interventions for patients with both Tau and Amyloid depositions.
基金This study was partially sponsored by the National Natural Science Foundation of China(NSFC)(81761148029,81725009,82030049,82021002,81971641)Ministry of Science and Technology of China(MOST)(2021YFA110004500,2021YFE0108300)+3 种基金Clinical Research Plan of SHDC(SHDC2020CR1038B)Science and Technology Innovation 2030 Major Projects(2022ZD0211600)Swiss National Science Foundation(project nos.185028,188355,and 169876)National Research Foundation of Korea(NRF-2017K2A9A2A10013554).
文摘Alzheimer’s disease(AD)is the main cause of dementia,with its diagnosis and management remaining challenging.Amyloid positron emission tomography(PET)has become increasingly important in medical practice for patients with AD.To integrate and update previous guidelines in the field,a task group of experts of several disciplines from multiple countries was assembled,and they revised and approved the content related to the application of amyloid PET in the medical settings of cognitively impaired individuals,focusing on clinical scenarios,patient preparation,administered activities,as well as image acquisition,processing,interpretation and reporting.In addition,expert opinions,practices,and protocols of prominent research institutions performing research on amyloid PET of dementia are integrated.With the increasing availability of amyloid PET imaging,a complete and standard pipeline for the entire examination process is essential for clinical practice.This international consensus and practice guideline will help to promote proper clinical use of amyloid PET imaging in patients with AD.
基金supported by Shanghai Municipal Science and Technology Major Project(Grant No.2017SHZDZX01).
文摘Hemodynamically significant patent ductus arteriosus(hsPDA)is a severe condition in newborns.Ibuprofen is an effective treatment to reduce the severe complications and the need for surgical treatment.Several single-nucleotide polymorphisms(SNPs)were related to the ibuprofen metabolism,treatment effects,and the onset of side effects.The effects of SNPs on hsPDA response after ibuprofen treatment are unknown.Therefore,in this study,we recruited hsPDA patients with standard ibuprofen treatment.Those patients had participated in China Neonatal Genomes Project(CNGP,ClinicalTrials.gov Identifier:NCT03931707)with next-generation sequencing data.We reanalyzed the sequencing data and compared the allele frequencies of known ibuprofen-related SNPs between ibuprofen Responder and Non-responder groups.In total,185 hsPDA patients were recruited with gestational age(GA)ranging from 24 to 40 weeks.No significant differences were detected in the basic information,period of ibuprofen treatment,rate of conservative treatment,complications,and side effects between ibuprofen Responder group and Non-responder group.Totally,17 hsPDA carried CYP2C9^(*)3 and one with CYP2C9^(*)2 were detected.In the GA group of more than 30 GA weeks(GA>30 wks group),we found higher allele frequency of CYP2C9^(*)3 in Responder group than in Non-responder group(16%vs.0,p=0.0391).In the GA group of less than 30 GA weeks(GA≤30 wks group),the sum allele frequency of CYP2C9^(*)3 and CYP2C9^(*)2 had no stastical difference between two groups(Responder group vs.Non-responder group,13%vs.11%,p=0.768).Therefore,we came to conclude that genetic tests of CYP2C9^(*)3 site may benefit the prediction of ibuprofen treatment outcome for hsPDA patients with gestational age of more than 30 weeks.
基金supported by grants from the National Natural Science Foundation of China(82071782)the Shanghai Committee of Science and Technology(20XD1400800)to JL.
文摘The DEAD-box RNA helicase(DDX)family plays a critical role in the growth and development of multiple organisms.DDX1 is involved in mRNA/rRNA processing and mature,virus replication and transcription,hormone metabolism,tumo-rigenesis,and tumor development.However,how DDX1 functions in various cancers remains unclear.Here,we explored the potential oncogenic roles of DDX1 across 33 tumors with The Cancer Genome Atlas(TCGA)and the Genotype-Tissue Expression(GTEx)databases.DDX1 is highly expressed in breast cancer(BRCA),cholangiocarcinoma(CHOL),and colon adenocarcinoma(COAD),but it is lowly expressed in renal cancers,including kidney renal clear cell carcinoma(KIRC),kidney chromophobe(KICH),and kidney renal papillary cell carcinoma(KIRP).Low expression of DDX1 in KIRC is cor-related with a good prognosis of overall survival(OS)and disease-free survival(DFS).Highly expressed DDX1 is linked to a poor prognosis of OS for adrenocortical carcinoma(ACC),bladder urothelial carcinoma(BLCA),KICH,and liver hepatocellular carcinoma(LIHC).Also,the residue Ser481 of DDX1 had an enhanced phosphorylation level in BRCA and ovarian cancer(OV)but decreased in KIRC.Immune infiltration analysis exhibited that DDX1 expression affected CD8+T cells,and it was significantly associated with MSI(microsatellite instability),TMB(tumor mutational burden),and ICT(immune checkpoint blockade therapy)in tumors.In addition,the depletion of DDX1 dramatically affected the cell viability of human tumor-derived cell lines.DDX1 could affect the DNA repair pathway and the RNA transport/DNA replication processes during tumorigenesis by analyzing the CancerSEA database.Thus,our pan-cancer analysis revealed that DDX1 had complicated impacts on different cancers and might act as a prognostic marker for cancers such as renal cancer.
基金funded by projects B8114,B8152,B7124,B5113,B4658,B4657,B4504,B4094,B4059,and B4051,Vicerrectoría de Investigación,Universidad de Costa Rica(period 2010-2020).
文摘Pseudomonas aeruginosa AG1(PaeAG1)is a Costa Rican strain that was isolated in 2010 in a major Hospital.This strain has resistance to multiple antibiotics such asβ-lactams(including carbapenems),aminoglycosides,and fluoroquinolones.PaeAG1 is considered critical(Priority 1)due to its resistance to carbapenems,and it was the first report of a P.aeruginosa isolate carrying both VIM-2 and IMP-18 genes encoding for metallo-β-lactamases(MBL)enzymes(both with carbapenemase activity).Owing to these traits,we have studied this model for 10 years using diverse approaches including multi-omics.In this review,we summarize the main points of the different steps that we have studied in PaeAG1:preliminary analyses of this strain at the genomic and phenomic levels revealed that this microorganism has particular features of antibiotic resistance.In the multi-omics approach,the genome assembly was the initial step to identify the genomic determinants of this strain,includ-ing virulence factors,antibiotic resistance genes,as well as a complex accessory genome.Second,a comparative genomic approach was implemented to define and update the phylogenetic relationship among complete P.aeruginosa genomes,the genomic island content in other strains,and the architecture of the two MBL-carrying integrons.Third,the proteomic profile of PaeAG1 was studied after exposure to antibiotics using 2-dimensional gel electrophoresis(2D-GE).Fourth,to study the central response to multiple perturbations in P.aeruginosa,i.e.,the core perturbome,a machine learning approach was used.The analysis revealed biological functions and determinants that are shared by different disturbances.Finally,to evaluate the effects of ciprofloxacin(CIP)on PaeAG1,a growth curve comparison,differential expression analysis(RNA-Seq),and network analysis were performed.Using the results of the core perturbome(pathways that also were found in this perturbation with CIP),it was possible to identify the“exclusive”response and determinants of PaeAG1 after exposure to CIP.Altogether,after a decade of study using a multi-omics approach(at genomics,comparative genomics,perturbomics,transcriptomics,proteomics,and phenomics levels),we have provided new insights about the genomic and transcriptomic determinants associated with antibiotic resistance in PaeAG1.These results not only partially explain the high-risk condition of this strain that enables it to conquer nosocomial environments and its multi-resistance profile,but also this information may eventually be used as part of the strategies to fight this pathogen.
基金This work was funded by Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud(INCIENSA,DG-of-2020-174)Vicerrectoría de Investigación-Universidad de Costa Rica,with the Project“C0196 Protocolo bioinformático y de inteligencia artificial para el apoyo de la vigilancia epidemiológica basada en laboratorio del virus SARS-CoV-2 mediante la identificación de patrones genómicos y clínico-demográficos en Costa Rica(2020-2022)”.
文摘The clinical manifestations of COVID-19,caused by the SARS-CoV-2,define a large spectrum of symptoms that are mainly dependent on the human host conditions.In Costa Rica,more than 169,000 cases and 2185 deaths were reported during the year 2020,the pre-vaccination period.To describe the clinical presentations at the time of diagnosis of SARS-CoV-2 infection in Costa Rica during the pre-vaccination period,we implemented a symptom-based clustering using machine learning to identify clusters or clinical profiles at the population level among 18,974 records of positive cases.Profiles were compared based on symptoms,risk factors,viral load,and genomic features of the SARS-CoV-2 sequence.A total of 18 symptoms at time of diagnosis of SARS-CoV-2 infection were reported with a frequency>1%,and those were used to identify seven clinical profiles with a specific composition of clinical manifestations.In the comparison between clusters,a lower viral load was found for the asymptomatic group,while the risk factors and the SARS-CoV-2 genomic features were distributed among all the clusters.No other distribution patterns were found for age,sex,vital status,and hospitalization.In conclusion,during the pre-vaccination time in Costa Rica,the symptoms at the time of diagnosis of SARS-CoV-2 infection were described in clinical profiles.The host co-morbidities and the SARS-CoV-2 genotypes are not specific of a particular profile,rather they are present in all the groups,including asymptomatic cases.In addition,this information can be used for decision-making by the local healthcare institutions(first point of contact with health professionals,case definition,or infrastructure).In further analyses,these results will be compared against the profiles of cases during the vaccination period.
基金supported by National Natural Science Foundation of China(81930124 and 82021005)Shanghai Municipal Science and Technology Major Project(Grant No.2017SHZDZX01).
文摘Poor adherence to standard protocols of blood pressure(BP)measurement in routine clinical practice leads to higher readings than“research-quality”measurements.Whether this phenomenon exists in periodic health examinations was unknown.We aimed to explore the concordance between BP measurements in periodic health examinations and those measured following a standard measurement protocol.We used data from the Kailuan Study,an ongoing longitudinal cohort study in China,of which participants received biennial health examinations in health management centers.In addition,BPs were measured following standard protocols in a workplace-based hypertension management program nested in the Kailuan Study.We compared BP readings of the same person between the two settings using generalized linear mixed-effects models.A total of 3988 men(the mean age was 44.9 years)had at least two BP measurements both in health examinations and management program with a time interval between the two settings that less than 90 days.The mean systolic blood pressures(SBP)and diastolic blood pressures(DBP)in health examinations were 4.2(95%CI 3.9–4.5)mm Hg and 3.3(95%CI 3.1–3.5)mm Hg higher than those in the management program,respectively.Bland–Altman analyses showed the wide agreement inter-vals ranging from-27.7-to 36.5-mm Hg for SBP and-18.3-to 24.7-mm Hg for DBP.In conclusion,BP measurements in periodic health examinations were generally higher than BPs measured following a standard protocol.Our findings highlight the importance of standard BP measurement to avoid overestimation of hypertension prevalence and treatment initiation.
文摘Prostate cancer remains one of the most prevalent malignancies in men globally(Preisser et al.2020).Accurate diagnosis and diferentiation of the disease are paramount for efective treatment planning and improved patient outcomes(Hsieh et al.2022).Traditionally,the diagnosis of prostate cancer heavily relied on invasive biopsy procedures,which,although efective,are associated with potential complications and discomfort for patients.With the advancements in medical imaging,positron emission tomography/computed tomography(PET/CT)using prostate-specifc membrane antigen(PSMA)tracers has emerged as a revolutionary diagnostic tool(Obek et al.2017).This technique,often termed as'virtual biopsy',provides a non-invasive alternative to traditional biopsy.Baseline PSMA PET/CT ofers detailed and precise imaging of prostate lesions,allowing clinicians to pinpoint not only the location but also the potential aggressiveness of the tumor.The capability of PSMA PET/CT to bind specifcally to PSMA-expressing cells gives it a unique edge in diferentiating between benign and malignant prostate lesions.
基金supported by the Key Project of the National Natural Science Foundation of China(U20A20354)Beijing Brain Initiative from Beijing Municipal Science&Technology Commission(Z201100005520016,Z201100005520017)+4 种基金National major R&D projects of China-Scientific technological innovation 2030(2021ZD0201802)the National Key Scientific Instrument and Equipment Development Project(31627803)the Key Project of the National Natural Science Foundation of China(81530036)Youth Program of National Natural Science Foundation of China(82101503)Beijing Postdoctoral Research Foundation.
文摘Years of intensive research has brought us extensive knowledge on the genetic and molecular factors involved in Alzheimer's disease(AD).In addition to the mutations in the three main causative genes of familial AD(FAD)including presenilins and amyloid precursor protein genes,studies have identified several genes as the most plausible genes for the onset and progression of FAD,such as triggering receptor expressed on myeloid cells 2,sortilin-related receptor 1,and adenosine triphosphate-binding cassette transporter subfamily A member 7.The apolipoprotein Eε4 allele is reported to be the strongest genetic risk factor for sporadic AD(SAD),and it also plays an important role in FAD.Here,we reviewed recent developments in genetic and molecular studies that contributed to the understanding of the genetic phenotypes of FAD and compared them with SAD.We further reviewed the advancements in AD gene therapy and discussed the future perspectives based on the genetic phenotypes.
基金This work was financially supported by National Key R&D Program of China(2018YFA0507501)the National Natural Science Foundation of China(22074019,21425518,22004017)Shanghai Sailing Program(20YF1405300).
文摘Due to inefficient diagnostic methods,inflammatory bowel disease(IBD)normally progresses into severe complications including cancer.Highly efficient extraction and identification of metabolic fingerprints are of significance for disease surveillance.In this work,we synthesized a layered titania nanosheet doped with graphitized carbon(2D-GC-mTNS)through a simple one-step assembly process for assisting laser desorption ionization mass spectrometry(LDI-MS)for metabolite analysis.Based on the synergistic effect of graphitized carbon and mesoporous titania,2D-GC-mTNS exhibits good extraction ability including high sensitivity(<1 fmolμL−1)and great repeatability toward metabolites.A total of 996 fingerprint spectra were collected from hundreds of native urine samples(including IBD patients and healthy controls),each of which contained 1220 m/z metabolite features.Diagnostic model was further established for precise discrimination of patients from healthy controls,with high area under the curve value of 0.972 and 0.981 toward discovery cohort and validation cohort,respectively.The 2D-GC-mTNS promotes LDI-MS to be close to clinical application,with rapid speed,minimum sample consumption and free of sample pretreatment.
基金This work was supported by grants from the National Natural Science Foundation of China(31771545,92049301,31821002,91329302,and 31210103916)China Ministry of Science and Technology(2015CB964803,2016YFE0108700,and 2016YFA0500600),and Max Planck fellowship to J.D.J.H.
文摘HDAC6 is involved in several biological processes related to aging-associated diseases.However,it was unknown whether HDAC6 could directly regulate lifespan and healthspan.We found that HDAC6 knockdown induced transcriptome changes to attenuate the aging changes in the Drosophila head,particularly on the inflammation and innate immunity-related genes.Whole-body knockdown of HDAC6 extended lifespan in the fly,furthermore brain-specific knockdown of HDAC6 extended both lifespan and healthspan in the fly.Our results established HDAC6 as a lifespan regulator and provided a potential anti-aging target.
基金M.P.is supported by NIH grants R01MH119336,R01MH122706,R01AG066828,R21MH123927 and the Wharton Fund.
文摘Modern Western biomedical research and clinical practice are primarily focused on disease.This disease-centric approach has yielded an impressive amount of knowledge around what goes wrong in illness.However,in comparison,researchers and physicians know little about health.What is health?How do we quantify it?And how do we improve it?We currently do not have good answers to these questions.Our lack of fundamental knowledge about health is partly driven by three main factors:(i)a lack of understanding of the dynamic processes that cause variations in health/disease states over time,(ii)an excessive focus on genes,and(iii)a pervasive psychological bias towards additive solutions.Here I briefly discuss potential reasons why scientists and funders have generally adopted a gene-and disease-centric framework,how medicine has ended up practicing“diseasecare”rather than healthcare,and present cursory evidence that points towards an alternative energetic view of health.Understanding the basis of human health with a similar degree of precision that has been deployed towards mapping disease processes could bring us to a point where we can actively support and promote human health across the lifespan,before disease shows up on a scan or in bloodwork.
基金supported by the fund from Iowa State University.
文摘The determinative view of mutation penetrance is a fundamental assumption for the building of molecular evolutionary theory:individuals in the population with the same genotype have the same fitness effect.Since this view has been constantly challenged by experimental evidence,it is desirable to examine to what extent violation of this view could affect our under-standing of molecular evolution.To this end,the author formulated a new theory of molecular evolution under a random model of penetrance:for any individual with the same mutational genotype,the coefficient of selection is a random variable.It follows that,in addition to the conventional Ne-genetic drift(Ne is the effective population size),the variance of penetrance among individuals(ε^(2))represents a new type of genetic drift,coined by theε^(2)-genetic drift.It has been demonstrated that these two genetic drifts together provided new insights on the nearly neutral evolution:the evolutionary rate is inversely related to the log-of-Ne when theε^(2)-genetic drift is nontrivial.This log-of-Ne feature ofε^(2)-genetic drift did explain well why the dN/dS ratio(the nonsynonymous rate to the synonymous rate)in humans is only as twofold as that in mice,while the effective population size(Ne)of mice is about two-magnitude larger than that of humans.It was estimated that,for the first time,the variance of random penetrance in mammalian genes was approximatelyε^(2)≈5.89×10^(-3).
基金supported by grants from the National Key Research and Development Program of China(2018YFA0109400)the National Natural Science Foundation of China(32022022).
文摘Coronavirus disease 2019(COVID-19),caused by severe acute respiratory syndrome coronavirus-2(SARS-CoV-2),has created an immense menace to public health worldwide,exerting huge effects on global economic and political conditions.Understanding the biology and pathogenesis mechanisms of this novel virus,in large parts,relies on optimal physiological models that allow replication and propagation of SARS-CoV-2.Human organoids,derived from stem cells,are three-dimen-sional cell cultures that recapitulate the cellular organization,transcriptional and epigenetic signatures of their counterpart organs.Recent studies have indicated their great values as experimental virology platforms,making human organoid an ideal tool for investigating host-pathogen interactions.Here,we summarize research developments for SARS-CoV-2 infection of various human organoids involved in multiple systems,including lung,liver,brain,intestine,kidney and blood vessel organoids.These studies help us reveal the pathogenesis mechanism of COVID-19,and facilitate the development of effec-tive vaccines and drugs as well as other therapeutic regimes.
基金supported by National Natural Science Foundation of China(81671239,81361120393,82171252,81701250,81401135,81971641,91949118,81771372,82021002)the Ministry of Science and Technology of China(2016YFC1306504)+5 种基金Shanghai Municipal Science and Technology Major Project(2017SHZDZX01,2018SHZDZX03)ZJ Lab,Shanghai Aging and Maternal and Child Health Research Special Project(2020YJZX0111)Clinical Research Plan of Shanghai Hospital Development Center(SHDC-2020CR1038B),Science and Technology Innovation 2030 Major Projects(2022ZD0211600)Youth Medical Talents-Medical Imaging Practitioner Program by Shanghai Municipal Health Commission and Shanghai Medical and Health Development Foundation(SHWRS(2020)_087)the Swiss National Science Foundation(188350)Jacques&Gloria Gossweiler Foundation and Siemens Healthineers.
文摘Age and gender are the important factors for brain metabolic declines in both normal aging and neurodegeneration,and the confounding effects may influence early and differential diagnosis of neurodegenerative diseases based on the[^(18)F]fluorodeoxyglucose positron emission tomography([^(18)F]FDG PET).We aimed to explore the potential of the adjustment of age-and gender-related confounding factors on[^(18)F]FDG PET images in differentiation of Parkinson’s disease(PD),multiple system atrophy(MSA)and progressive supra-nuclear palsy(PSP).Eight hundred and seventy-seven clinically definitely diagnosed Parkinsonian patients from a benchmark Huashan Parkinsonian PET imaging database were included.An age-and gender-adjusted Z(AGAZ)score was established based on the gender-specific longitudinal metabolic changes on healthy subjects.AGAZ scores and standardized uptake value ratio(SUVR)values were quantified at regional-level and support vector machine-based error-correcting output codes method was applied for classification.Additional references of the classifications based on metabolic pattern scores were included.The feature-based AGAZ score showed the best performance in classification(accuracy for PD,MSA,PSP:93.1%,96.3%,94.8%).In both genders,the AGAZ score con-sistently achieved the best efficiency,and the improvements compared to the conventional SUVR value for PD,MSA,and PSP mainly laid in specificity(Male:5.7%;Female:11.1%),sensitivity(Male:7.2%;Female:7.3%),and sensitivity(Male:7.3%;Female:17.2%).Female patients benefited more from the adjustment on[^(18)F]FDG PET in MSA and PSP groups(absolute net reclassification index,p<0.001).Collectively,the adjustment of age-and gender-related confounding factors may improve the differential diagnosis of Parkinsonism.Particularly,the diagnosis of female Parkinsonian population has the best improvement from this correction.
基金supported by the National Key Research and Development Program of China(2021YFA1301000)Shanghai Municipal Science and Technology Major Project(Grant No.2017SHZDZX01).
文摘Immunophenotyping is proving crucial to understanding the role of the immune system in health and disease.High-through-put flow cytometry has been used extensively to reveal changes in immune cell composition and function at the single-cell level.Here,we describe six optimized 11-color flow cytometry panels for deep immunophenotyping of human whole blood.A total of 51 surface antibodies,which are readily available and validated,were selected to identify the key immune cell populations and evaluate their functional state in a single assay.The gating strategies for effective flow cytometry data analysis are included in the protocol.To ensure data reproducibility,we provide detailed procedures in three parts,including(1)instrument characterization and detector gain optimization,(2)antibody titration and sample staining,and(3)data acquisition and quality checks.This standardized approach has been applied to a variety of donors for a better understanding of the complexity of the human immune system.
基金National Key Research and Development Program of China(2021YFA1301000)Shanghai Municipal Technology Standards Project(23DZ2202600)Shanghai Municipal Science and Technology Major Project(Grant No.2017SHZDZX01).
文摘The immune system defends the body from infection and plays a vital role in a wide range of health conditions.Metabolism afects a series of physiological processes,including those linked to the function of human immune system.Cellular metabolism modulates immune cell activation and cytokine production.Understanding the relationship between metabolism and immune response has important implications for the development of immune-based therapeutics.However,the deployment of large-scale functional assays to investigate the metabolic regulation of immune response has been limited by the lack of standardized procedures.Here,we present a protocol for the analysis of immune response using standardized whole-blood stimulation with metabolism modulation.Diverse immune stimuli including pattern recognition receptor(PRR)ligands and microbial stimuli were incubated with fresh human whole blood.The metabolic inhibitors were used to modulate metabolic status in the immune cells.The variable immune responses after metabolic interventions were evaluated.We described in detail the main steps involved in the whole-blood stimulation and cytokines quantifcation,namely,collection and treatment of whole blood,preparation of samples and controls,cytokines detection,and stimulation with metabolic interventions.The metabolic inhibitors for anabolic pathways and catabolic pathways exert selective efects on the production of cytokines from immune cells.In addition to a robust and accurate assessment of immune response in cohort studies,the standardized whole-blood stimulation with metabolic regulation might provide new insights for modulating immunity.
基金This study was supported by grants for Natural Science Foundation of China(NSFC 81670835 and NSFC 81600719)the Shanghai Science and Technology Commission(11231200602)the Visual Impairment and Reconstruction Key Laboratory of Shanghai(12DZ2260500).
文摘Genetic alterations are a major cause of microphthalmos,while novel-related genes and mutations in microphthalmos have rarely been explored.To identify the underlying genetic defect responsible for microphthalmos eyes in two three-generation Chinese families,we screened 425 genes involved in common inherited non-syndromic eye diseases with next-generation sequencing-based target capture sequencing of the two probands of two three-generation Chinese families diagnosed with microphthalmos.Variants were filtered and analyzed to identify possible disease-causing variants before Sanger sequencing validation.We enrolled two families with microphthalmos(Family 1:microphthalmos with congenital ocular coloboma and Family 2:simple microphthalmos).Two novel heterozygous mutations,Peroxidasin(PXDN)c.3165C>T(p.Pro1055Pro)and PXDN c.2640C>G(p.Arg880Arg),were found in Family 1,and Crystallin Beta B2(CRYBB2)c.481G>A(p.Gly161Arg)was found in Family 2,but none of the mutations were found in the unaffected individuals,who were phenotypically nor-mal.Multiple orthologous sequence alignment(MSA)revealed that the CRYBB2 p.Gly161Arg mutation was a deleterious effect mutation.In conclusion,the three novel mutations found in our study extend our current understanding of the genetic basis of microphthalmos and provide early pre-symptomatic diagnosis and emphasize the significance of genetic diagnosis of microphthalmos.
