Genome engineering of Rhodococcus opacus PD630,an important microorganism used for the bioconversion of lignin,is currently dependent on inefficient homologous recombination.Although a CRISPR interference procedure fo...Genome engineering of Rhodococcus opacus PD630,an important microorganism used for the bioconversion of lignin,is currently dependent on inefficient homologous recombination.Although a CRISPR interference procedure for gene repression has previously been developed for R.opacus PD630,a CRISPR/Cas9 system for gene knockout has yet to be reported for the strain.In this study,we found that the cytotoxicity of Cas9 and the deficiency in pathways for repairing DNA double-strand breaks(DSBs)were the major causes of the failure of conventional CRISPR/Cas9 technologies in R.opacus,even when augmented with the recombinases Che9c60 and Che9c61.We successfully developed an efficient single-stranded DNA(ssDNA)recombineering system coupled with CRISPR/Cas9 counter-selection,which facilitated rapid and scarless editing of the R.opacus genome.A two-plasmid system,comprising Cas9 driven by a weak Rhodococcus promoter Pniami,designed to prevent cytotoxicity,and a single-guide RNA(sgRNA)under the control of a strong constitutive promoter,was proven to be appropriate with respect to cleavage function.A novel recombinase,RrRecT derived from a Rhodococcus ruber prophage,was identified for the first time,which facilitated recombination of short ssDNA donors(40-80 nt)targeted to the lagging strand and enabled us to obtain a recombination efficiency up to 103-fold higher than that of endogenous pathways.Finally,by incorporating RrRecT and Cas9 into a single plasmid and then co-transforming cells with sgRNA plasmids and short ssDNA donors,we efficiently achieved gene disruption and base mutation in R.opacus,with editing efficiencies ranging from 22%to 100%.Simultaneous disruption of double genes was also confirmed,although at a lower efficiency.This effective genome editing tool will accelerate the engineering of R.opacus metabolism.展开更多
Iron is essential for bacterial survival,and most bacteria capture iron by producing siderophores.Burkholde-riales bacteria produce various types of bioactive secondary metabolites,such as ornibactin and malleobactin ...Iron is essential for bacterial survival,and most bacteria capture iron by producing siderophores.Burkholde-riales bacteria produce various types of bioactive secondary metabolites,such as ornibactin and malleobactin siderophores.In this study,the genome analysis of Burkholderiales genomes showed a putative novel siderophore gene cluster crb,which is highly similar to the ornibactin and malleobactin gene clusters but does not have pvdF,a gene encoding a formyltransferase for N-δ-hydroxy-ornithine formylation.Establishing the bacteriophage recom-binase Redγ-Redδβ7029 mediated genome editing system in a non-model Burkholderiales strain Paraburkholderia caribensis CICC 10960 allowed the rapid identification of the products of crb gene cluster,caribactins A-F(1-6).Caribactins contain a special amino acid residue N-δ-hydroxy-N-δ-acetylornithine(haOrn),which differs from the counterpart N-δ-hydroxy-N-δ-formylornithine(hOrn)in ornibactin and malleobactin,owing to the absence of pvdF.Gene inactivation showed that the acetylation of hOrn is catalyzed by CrbK,whose homologs proba-bly not be involved in the biosynthesis of ornibactin and malleobactin,showing possible evolutionary clues of these siderophore biosynthetic pathways from different genera.Caribactins promote biofilm production and en-hance swarming and swimming abilities,suggesting that they may play crucial roles in biofilm formation.This study also revealed that recombineering has the capability to mine novel secondary metabolites from non-model Burkholderiales species.展开更多
Recombineering is an essential tool for molecular biologists,allowing for the facile and efficient manipulation of bacterial genomes directly in cells without the need for costly and laborious in vitro manipulations i...Recombineering is an essential tool for molecular biologists,allowing for the facile and efficient manipulation of bacterial genomes directly in cells without the need for costly and laborious in vitro manipulations involving restriction enzymes.The main workhorses behind recombineering are bacteriophage proteins that promote the single-strand annealing(SSA)homologous recombination pathway to repair double-stranded DNA breaks.While there have been several reviews examining recombineering methods and applications,comparatively few have focused on the mechanisms of the proteins that are the key players in the SSA pathway:a 5′→3′exonuclease and a single-strand annealing protein(SSAP or“annealase”).This review dives into the structures and functions of the two SSA recombination systems that were the first to be developed for recombineering in E.coli:the RecET system from E.coli Rac prophage and the𝜆Red system from bacteriophageλ.By comparing the structures of the RecT and Red𝛽annealases,and the RecE and𝜆Exo exonucleases,we provide new insights into how the structures of these proteins dictate their function.Examining the sequence conservation of the𝜆λExo and RecE exonucleases gives more profound insights into their critical functional features.Ultimately,as recombineering accelerates and evolves in the laboratory,a better understanding of the mechanisms of the proteins behind this powerful technique will drive the development of improved and expanded capabilities in the future.展开更多
Recombineering is a valuable technique for generating recombinant DNA in vivo,primarily in bacterial cells,and is based on homologous recombination using phage-encoded homologous recombinases,such as Red βγ from the...Recombineering is a valuable technique for generating recombinant DNA in vivo,primarily in bacterial cells,and is based on homologous recombination using phage-encoded homologous recombinases,such as Red βγ from the lambda phage and RecET from the Rac prophage.The recombineering technique can efficiently mediate homol-ogous recombination using short homologous arms(∼50 bp)and is unlimited by the size of the DNA molecules or positions of restriction sites.In this review,we summarize characteristics of recombinases,mechanism of recombineering,and advances in recombineering for DNA manipulation in Escherichia coli and other bacteria.Furthermore,the broad applications of recombineering for mining new bioactive microbial natural products,and for viral mutagenesis,phage genome engineering,and understanding bacterial metabolism are also reviewed.展开更多
This article uses a real-life example to illustrate the concept and methodology of recombineering, arevolutionary genetic engineering technique based on phage-mediated homologous recombination. A step-by-step approach...This article uses a real-life example to illustrate the concept and methodology of recombineering, arevolutionary genetic engineering technique based on phage-mediated homologous recombination. A step-by-step approach is presented along with a flow diagram, from obtaining gene-harboring BACs to the in vitro generation of a conditional null allele. This method can be used to target any gene at any position, without the knowledge or use of any restriction site. The extensive applicability of recombineering to gene manipulation is discussed.展开更多
Electron–hole(e–h)recombination is a fundamental process that governs energy dissipation and device efficiency in semiconductors.In two-dimensional(2D)materials,the formation of tightly bound excitons makes exciton-...Electron–hole(e–h)recombination is a fundamental process that governs energy dissipation and device efficiency in semiconductors.In two-dimensional(2D)materials,the formation of tightly bound excitons makes exciton-mediated e–h recombination the dominant decay pathway.In this work,nonradiative e–h recombination within excitons in monolayer MoS_(2) is investigated using first-principles simulations that combine nonadiabatic molecular dynamics with GW and real-time Bethe–Salpeter equation(BSE)propagation.A two-step process is identified:rapid intervalley redistribution induced by exchange interaction,followed by slower phonon-assisted recombination facilitated by exciton binding.By selectively removing the screened Coulomb and exchange terms from the BSE Hamiltonian,their respective contributions are disentangled—exchange interaction is found to increase the number of accessible recombination pathways,while binding reduces the excitation energy and enhances nonradiative decay.A reduction in recombination lifetime by over an order of magnitude is observed due to the excitonic many-body effects.These findings provide microscopic insights for understanding and tuning exciton lifetimes in 2D transition-metal dichalcogenides.展开更多
The published article titled“Truncated Bid Overexpression Induced by Recombinant Adenovirus Cre/LoxP System Suppresses the Tumorigenic Potential of CD133+Ovarian Cancer Stem Cells”has been retracted from Oncology Re...The published article titled“Truncated Bid Overexpression Induced by Recombinant Adenovirus Cre/LoxP System Suppresses the Tumorigenic Potential of CD133+Ovarian Cancer Stem Cells”has been retracted from Oncology Research,Vol.25,No.4,2017,pp.595–603.展开更多
Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastom...Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastome structural variation,which is induced by one pair of small inverted repeats,can also result in leaf variegation.Here we show a complex plastome structural variation caused by intermolecular and intramolecular recombination across three pairs of small inverted repeats accounts for leaf variegation in a widely cultivated shrub Heptapleurum ellipticum(Araliaceae).This plastome structural variation contains two deletions and two duplications,resulting in dramatic expansion of IRs,substantial contraction of LSC and loss of 11 genes that essential for photosynthesis.Plastome heteroplasmy was detected in both green and albino sectors of variegated leaves.Relative to green sectors,albino sectors in the variegated leaves exhibit significantly reduced expression for the 11 genes lost in the mutated plastome as well as 26 other genes,but significantly increased expression for one gene related to translation apparatus.Optical and transmission electron microscopy observations showed that mesophyll cells of albino sectors possess plastids lacking grana lamellae,which likely carry the mutated plastome and contribute to albinism.In both sectors,the first layer of spongy mesophyll cells beneath the lower epidermis contains normal chloroplasts,suggesting periclinal division of the lower epidermis during development.Our study demonstrates that multiple small repeats can collectively mediate intra-and inter-molecular recombination in plastome and offers a new mechanism accounting for leaf variegation in plants.展开更多
All-inorganic lead-free perovskite solar cells have emerged as environmentally benign candidates;however,their device performance is still constrained by pronounced carrier recombination losses in the bulk and at inte...All-inorganic lead-free perovskite solar cells have emerged as environmentally benign candidates;however,their device performance is still constrained by pronounced carrier recombination losses in the bulk and at interfaces.By combining energy band alignment analysis with detailed modeling of recombination mechanisms,a systematic strategy for optimizing hole transport layers is developed.The results reveal that a negative valence band offset produces a cliff-like interface,which facilitates hole extraction while also accounting for the observed variations in open-circuit voltage.Furthermore,short-circuit current losses are quantitatively attributed to different recombination pathways,modeled by incorporating radiative,Shockley–Read–Hall,Auger,and interface recombination processes.This comprehensive approach not only clarifies the correlation between energy level alignment and recombination dynamics but also highlights the competing roles of band offset and interface defects in determining device performance.The optimized device architecture,based on Ge-based lead-free perovskites,achieves a power conversion efficiency of 25.1%,with an open-circuit voltage of 1.29 V,a short-circuit current density of 22.5 mA·cm^(-2),and a fill factor of 86.3%.These findings provide theoretical guidance for designing stable,high-performance,and environmentally friendly lead-free perovskite solar cells.展开更多
Bacillus subtilis plays an important role in fundamental and applied research,and it has been widely used as a cell factory for the production of enzymes,antimicrobial materials,and chemicals for agriculture,medicine,...Bacillus subtilis plays an important role in fundamental and applied research,and it has been widely used as a cell factory for the production of enzymes,antimicrobial materials,and chemicals for agriculture,medicine,and industry.However,genetic manipulation tools for B.subtilis have low efficiency.In this work,our goal was to develop a simple recombineering system for B.subtilis.We showed that genome editing can be achieved in B.subtiliis 1A751 through co-expression of YqaJ/YqaK,a native phage recombinase pair found in B.sub-tilis 168,and the competence master regulator ComK using a double-stranded DNA substrate with short ho-mology arms(100 bp)and a phosphorothioate modification at the 5′-end.Efficient gene knockouts and large DNA insertions were achieved using this new recombineering system in B.subtilis 1A751.As far as we know,this is the first recombineering system using the native phage recombinase pair YqaJ/YqaK in B.subtilis.In conclusion,this new recombineering system provides a simple and fast tool for genetic manipulation of B.sub-tilis,and it will promote studies of genome function,construction of production strains,and genome mining in B.subtilis.展开更多
Magnetic resonance imaging(MRI)is a powerful tool for diagnosing and monitoring brain diseases,but its low sensitivity can hinder early detection.To address this challenge,we utilized chemical exchange saturation tran...Magnetic resonance imaging(MRI)is a powerful tool for diagnosing and monitoring brain diseases,but its low sensitivity can hinder early detection.To address this challenge,we utilized chemical exchange saturation transfer(CEST)MRI,which greatly enhances sensitivity for detecting low-concentration compounds.In this study,we developed a CEST contrast agent based on a recombinant adeno-associated viruses(rAAVs)encoding the protamine-1(PRM1)MRI reporter gene.CEST MRI revealed that PRM1 contrast agent effectively highlighted caudate putamen region after injection of the rAAVs into the mouse brain,clearly distinguishing it from the surrounding tissue,with no observable damage.This method provides a sensitive,metal-free CEST contrast agent for in vivo brain cell detection,demonstrating potential for both diagnostic and therapeutic applications in brain diseases.展开更多
NADC34-like porcine reproductive and respiratory syndrome virus(PRRSV),which first appeared in China in 2017,is currently one of the main epidemic strains in China.In this study,we found that a new variant of NADC34-l...NADC34-like porcine reproductive and respiratory syndrome virus(PRRSV),which first appeared in China in 2017,is currently one of the main epidemic strains in China.In this study,we found that a new variant of NADC34-like PRRSV evolved,named the L1A variant.The phylogenetics,epidemic status,and pathogenicity of the LA variants were subsequently comprehensively evaluated.Based on the results of the ORF5 phylogenetic analysis,the L1A variants were classified as NADC34-like PPRSV.All the strains had the same discontinuous 131-aa deletion in the NSP2 region(similar to that in the NADC30).Recombination analysis revealed that the L1A variants were recombinant viruses that contained an NADC30-like PRRSV skeleton,a nonstructural protein-encoding gene region obtained in part from JXA1-like PRRSV and a ORF2-ORF6 gene region partly obtained from NADC34-like PRRSV and that exhibited similar recombination patterns.We successfully isolated the L1A variant TZJ2756 from PAMs and Marc-145 cells.In animal experiments,TZJ2756 exhibited moderate pathogenicity in piglets,causing obvious clinical symptoms,namely,persistent fever,significantly reduced body weight,interstitial edema and severe interstitial pneumonia in the lungs,and prolonged high-load viremia.L1A variants have been detected in at least 12 provinces in China and share many similar epidemiological characteristics with the American L1C variant.This research will enhance our understanding of the prevalence of L1A variants and furnish valuable data for the ongoing monitoring of NADC34-like PRRSV in China.展开更多
Recombinant tissue plasminogen activator is commonly used for hematoma evacuation in minimally invasive surgery following intracerebral hemorrhage.However,during minimally invasive surgery,recombinant tissue plasminog...Recombinant tissue plasminogen activator is commonly used for hematoma evacuation in minimally invasive surgery following intracerebral hemorrhage.However,during minimally invasive surgery,recombinant tissue plasminogen activator may come into contact with brain tissue.Therefore,a thorough assessment of its safety is required.In this study,we established a mouse model of intracerebral hemorrhage induced by type VII collagenase.We observed that the administration of recombinant tissue plasminogen activator without hematoma aspiration significantly improved the neurological function of mice with intracerebral hemorrhage,reduced pathological damage,and lowered the levels of apoptosis and autophagy in the tissue surrounding the hematoma.In an in vitro model of intracerebral hemorrhage using primary cortical neurons induced by hemin,the administration of recombinant tissue plasminogen activator suppressed neuronal apoptosis,autophagy,and endoplasmic reticulum stress.Transcriptome sequencing analysis revealed that recombinant tissue plasminogen activator upregulated the phosphoinositide 3-kinase/RAC-alpha serine/threonine-protein kinase/mammalian target of rapamycin pathway in neurons.Moreover,the phosphoinositide 3-kinase inhibitor LY294002 abrogated the neuroprotective effects of recombinant tissue plasminogen activator in inhibiting excessive apoptosis,autophagy,and endoplasmic reticulum stress.Furthermore,to specify the domain of recombinant tissue plasminogen activator responsible for its neuroprotective effects,various inhibitors were used to target distinct domains.It has been revealed that the epidermal growth factor receptor inhibitor AG-1478 reversed the effect of recombinant tissue plasminogen activator on the phosphoinositide 3-kinase/RAC-alpha serine/threonineprotein kinase/mammalian target of rapamycin pathway.These findings suggest that recombinant tissue plasminogen activator exerts a direct neuroprotective effect on neurons following intracerebral hemorrhage,possibly through activation of the phosphoinositide 3-kinase/RAC-alpha serine/threonine-protein kinase/mammalian target of rapamycin pathway.展开更多
Adenoviruses typically cause mild illnesses,but severe diseases may occur primarily in immunodeficient individuals,particularly children.Recently,adenoviruses have garnered significant interest as a versatile tool in ...Adenoviruses typically cause mild illnesses,but severe diseases may occur primarily in immunodeficient individuals,particularly children.Recently,adenoviruses have garnered significant interest as a versatile tool in gene therapy,tumor treatment,and vaccine vector development.Over the past two decades,the advent of recombineering,a method based on homologous recombination,has notably enhanced the utility of adenoviral vectors in therapeutic applications.This review summarizes recent advancements in the use of human adenoviral vectors in medicine and discusses the pivotal role of recombineering in the development of these vectors.Additionally,it highlights the current achievements and potential future impact of therapeutic adenoviral vectors.展开更多
BACKGROUND Patients with acute-on-chronic liver failure(ACLF)have a high mortality rate,poor prognosis,and often experience concurrent thrombocytopenia and bleeding events.AIM To evaluate the efficacy and safety of re...BACKGROUND Patients with acute-on-chronic liver failure(ACLF)have a high mortality rate,poor prognosis,and often experience concurrent thrombocytopenia and bleeding events.AIM To evaluate the efficacy and safety of recombinant human thrombopoietin(rhTPO)in patients with ACLF with concomitant severe thrombocytopenia.METHODS This was a prospective,open-label study.We assigned 70 ACLF patients with severe thrombocytopenia into the rhTPO group and control group,with 35 patients in each group.Patients in the rhTPO group received subcutaneous injections of rhTPO at a dose of 15000 IU/day for 7 consecutive days,while patients in the control group did not receive rhTPO treatment.The primary endpoint was the proportion of patients with platelet count>50×10^(9)/L on day 14.RESULTS The proportion of patients with platelet count>50×10^(9)/L on day 14 was 60.7%in the rhTPO group,which was significantly higher than that(12.0%)in the control group(P<0.001).The platelet count in the rhTPO group on day 14 was 64×10^(9)/L,exceeding the baseline of 28×10^(9)/L.Compared to the control group,the rhTPO group exhibited a significant increase in platelet count from baseline(P<0.05).Model for end-stage liver disease score,albumin level and international normalized ratio improved significantly from baseline on day 14 after rhTPO injection.The concentrations of serum thrombopoietin and hepatocyte growth factor in the rhTPO group after 7 days were 143.7 and 195.4 pg/mL,respectively,showing a significant increase from baseline(P<0.05).Eight(22.9%)patients had bleeding events in the control group compared with four(11.4%)in the rhTPO group.The incidence of 90-day mortality was also higher in the control group(6,17.1%)than that in the rhTPO group(3,8.6%).CONCLUSION rhTPO significantly increased the platelet count in ACLF patients with thrombocytopenia and reduce the occurrence of bleeding events,with a good safety profile.展开更多
Objective Poxviruses are zoonotic pathogens that infect humans,mammals,vertebrates,and arthropods.However,the specific role of ticks in transmission and evolution of these viruses remains unclear.Methods Transcriptomi...Objective Poxviruses are zoonotic pathogens that infect humans,mammals,vertebrates,and arthropods.However,the specific role of ticks in transmission and evolution of these viruses remains unclear.Methods Transcriptomic and metatranscriptomic raw data from 329 sampling pools of seven tick species across five continents were mined to assess the diversity and abundance of poxviruses.Chordopoxviral sequences were assembled and subjected to phylogenetic analysis to trace the origins of the unblasted fragments within these sequences.Results Fifty-eight poxvirus species,representing two subfamilies and 20 genera,were identified,with 212 poxviral sequences assembled.A substantial proportion of AT-rich fragments were detected in the assembled poxviral genomes.These genomic sequences contained fragments originating from rodents,archaea,and arthropods.Conclusion Our findings indicate that ticks play a significant role in the transmission and evolution of poxviruses.These viruses demonstrate the capacity to modulate virulence and adaptability through horizontal gene transfer,gene recombination,and gene mutations,thereby promoting co-existence and co-evolution with their hosts.This study advances understanding of the ecological dynamics of poxvirus transmission and evolution and highlights the potential role of ticks as vectors and vessels in these processes.展开更多
Objective:Patients with homologous recombination deficiency(HRD)demonstrate distinct clinicopathological and prognostic features.However,standardised and clinically validated HRD detection methodologies specifically t...Objective:Patients with homologous recombination deficiency(HRD)demonstrate distinct clinicopathological and prognostic features.However,standardised and clinically validated HRD detection methodologies specifically tailored for non-small cell lung cancer(NSCLC)have yet to be established.Further research is needed to clarify the precise role and clinical implications of HRD in NSCLC.Methods:A cohort of 580 treatment-naive NSCLC patients was retrospectively enrolled.Comprehensive genomic profiling(CGP)was performed for all patients,and HRD status was evaluated using two genomic scar score(GSS)-based algorithms:a machine learning-based GSS(ML-GSS)and a continuous linear regression-based GSS(CLR-GSS).To assess the diagnostic performance(sensitivity and specificity)of the ML-GSS and CLR-GSS algorithms for HRD detection,immunohistochemical(IHC)staining was conducted for two HRD-related biomarkers:Schlafen 11(SLFN11)and RAD51.Survival analysis,including progression-free survival(PFS),along with multivariable Cox proportional hazards models,was performed to compare the prognostic value of the two HRD algorithms.Results:Among all patients,146(25.2%)and 46(7.9%)were classified as HRD-positive(HRD+)by ML-GSS and CLR-GSS,respectively.Using SLFN11 IHC expression as the reference standard,comparative analysis demonstrated that ML-GSS exhibited significantly higher sensitivity but lower specificity than CLR-GSS.This trend was consistently observed in RAD51 staining analysis.Compared to HRD-negative(HRD-)patients,MLGSS-defined HRD+cases displayed distinct clinicopathological and genomic features,including a higher prevalence of homologous recombination(HR)-related genes mutations,BRCA1/2 mutations,TP53 mutations,elevated tumor mutation burden(TMB),and increased copy number variations(CNVs).In contrast,CLR-GSSdefined HRD+patients were only enriched for BRCA1/2 mutations,TP53 mutations,and elevated TMB.Furthermore,ML-GSS-defined HRD+status was associated with significantly worse prognosis following first-line therapy compared to HRD-patients.Univariate and multivariable Cox analyses identified ML-GSS-defined HRD+and TP53 mutations as significant predictors and independent risk factors,respectively.No such associations were observed in the CLR-GSS-defined HRD+cohort.Conclusions:ML-GSS demonstrated superior performance to CLR-GSS in assessing chromosomal instability(CIN)and showed greater clinical utility.We recommend the ML-GSS algorithm as a robust and clinically validated tool for HRD/CIN evaluation in NSCLC.Furthermore,ML-GSS-defined HRD+status was identified as both a significant predictor and an independent risk factor.展开更多
Objective:Triple-negative breast cancer(TNBC)is a highly aggressive subtype that lacks targeted therapies,leading to a poorer prognosis.However,some patients achieve long-term recurrence-free survival(RFS),offering va...Objective:Triple-negative breast cancer(TNBC)is a highly aggressive subtype that lacks targeted therapies,leading to a poorer prognosis.However,some patients achieve long-term recurrence-free survival(RFS),offering valuable insights into tumor biology and potential treatment strategies.Methods:We conducted a comprehensive multi-omics analysis of 132 patients with American Joint Committee on Cancer(AJCC)stage III TNBC,comprising 36 long-term survivors(RFS≥8 years),62 moderate-term survivors(RFS:3-8 years),and 34 short-term survivors(RFS<3 years).Analyses investigated clinicopathological factors,whole-exome sequencing,germline mutations,copy number alterations(CNAs),RNA sequences,and metabolomic profiles.Results:Long-term survivors exhibited fewer metastatic regional lymph nodes,along with tumors showing reduced stromal fibrosis and lower Ki67 index.Molecularly,these tumors exhibited multiple alterations in genes related to homologous recombination repair,with higher frequencies of germline mutations and somatic CNAs.Additionally,tumors from long-term survivors demonstrated significant downregulation of the RTK-RAS signaling pathway.Metabolomic profiling revealed decreased levels of lipids and carbohydrate,particularly those involved in glycerophospholipid,fructose,and mannose metabolism,in long-term survival group.Multivariate Cox analysis identified fibrosis[hazard ratio(HR):12.70,95%confidence interval(95%CI):2.19-73.54,P=0.005]and RAC1copy number loss/deletion(HR:0.22,95%CI:0.06-0.83,P=0.026)as independent predictors of RFS.Higher fructose/mannose metabolism was associated with worse overall survival(HR:1.30,95%CI:1.01-1.68,P=0.045).Our findings emphasize the association between biological determinants and prolonged survival in patients with TNBC.Conclusions:Our study systematically identified the key molecular and metabolic features associated with prolonged survival in AJCC stage III TNBC,suggesting potential therapeutic targets to improve patient outcomes.展开更多
Cu_(2)ZnSn(S,Se)_(4)(CZTSSe)is considered to be the most potential light-absorbing material to replace CuInGaSe_(2)(CIGS),but the actual photoelectric conversion efficiency of such cells is much lower than that of CIG...Cu_(2)ZnSn(S,Se)_(4)(CZTSSe)is considered to be the most potential light-absorbing material to replace CuInGaSe_(2)(CIGS),but the actual photoelectric conversion efficiency of such cells is much lower than that of CIGS.One of the reasons is the high recombination rate of carriers at the interface.In this paper,in order to reduce the carrier recombination,a new solar cell structure with double absorber layers of Al-doped ZnO(AZO)/intrinsic(i)-ZnO/CdS/CZTS_(x1)Se_(1−x1)(CZTSSe_(1))/CZTS_(x2)Se_(1−x2)(CZTSSe_(2))/Mo was proposed,and the optimal conduction band offsets(CBOs)of CdS/CZTSSe_(1) interface and CZTSSe_(1)/CZTSSe_(2) interface were determined by changing the S ratio in CZTSSe_(1) and CZTSSe_(2),and the effect of thickness of CZTSSe_(1) on the performance of the cell was studied.The efficiencies of the optimized single and double absorber layers reached 17.97%and 23.4%,respectively.Compared with the single absorber layer structure,the proposed structure with double absorber layers has better cell performance.展开更多
BACKGROUND Valvular heart disease affects more than 100 million people worldwide and is associated with significant morbidity and mortality.The prevalence of at least moderate valvular heart disease is 2.5%across all ...BACKGROUND Valvular heart disease affects more than 100 million people worldwide and is associated with significant morbidity and mortality.The prevalence of at least moderate valvular heart disease is 2.5%across all age groups,but its prevalence increases with age.Mitral regurgitation and aortic stenosis are the most frequent types of valvular heart disease in the community and hospital context,res-pectively.Surgical valve replacement(or mitral valve repair)is the standard of care for treating heart valve disease.However,the replacement of a prosthetic heart valve can lead to complications,either in the peri-procedural phase or in the long-term follow-up period.CASE SUMMARY We present a case of a 71-year-old female patient with a history of mitral valve replacement and warfarin anti-coagulation therapy.She was admitted to the intensive care unit due to spontaneously reperfused ischemic stroke of probable cardioembolic etiology.A dysfunctional mitral prosthesis was identified due to malfunction of one of the fixed discs.Furthermore,a possible microthrombotic lesion was suspected.Therefore,systemic thrombolysis was performed with subsequent normalization of mitral disc opening and closing.CONCLUSION This case underscores the critical importance of a multidisciplinary approach for timely decision-making in critically ill patients with prosthetic valve complications.展开更多
基金supported by the National Key R&D Program of China(2018YFA0902200)Natural Science Foundation of China(No.21776157,No.22078173)。
文摘Genome engineering of Rhodococcus opacus PD630,an important microorganism used for the bioconversion of lignin,is currently dependent on inefficient homologous recombination.Although a CRISPR interference procedure for gene repression has previously been developed for R.opacus PD630,a CRISPR/Cas9 system for gene knockout has yet to be reported for the strain.In this study,we found that the cytotoxicity of Cas9 and the deficiency in pathways for repairing DNA double-strand breaks(DSBs)were the major causes of the failure of conventional CRISPR/Cas9 technologies in R.opacus,even when augmented with the recombinases Che9c60 and Che9c61.We successfully developed an efficient single-stranded DNA(ssDNA)recombineering system coupled with CRISPR/Cas9 counter-selection,which facilitated rapid and scarless editing of the R.opacus genome.A two-plasmid system,comprising Cas9 driven by a weak Rhodococcus promoter Pniami,designed to prevent cytotoxicity,and a single-guide RNA(sgRNA)under the control of a strong constitutive promoter,was proven to be appropriate with respect to cleavage function.A novel recombinase,RrRecT derived from a Rhodococcus ruber prophage,was identified for the first time,which facilitated recombination of short ssDNA donors(40-80 nt)targeted to the lagging strand and enabled us to obtain a recombination efficiency up to 103-fold higher than that of endogenous pathways.Finally,by incorporating RrRecT and Cas9 into a single plasmid and then co-transforming cells with sgRNA plasmids and short ssDNA donors,we efficiently achieved gene disruption and base mutation in R.opacus,with editing efficiencies ranging from 22%to 100%.Simultaneous disruption of double genes was also confirmed,although at a lower efficiency.This effective genome editing tool will accelerate the engineering of R.opacus metabolism.
基金supported by the National Key R&D Program of China(2019YFA0905700)National Natural Science Foundation of China(32070060).
文摘Iron is essential for bacterial survival,and most bacteria capture iron by producing siderophores.Burkholde-riales bacteria produce various types of bioactive secondary metabolites,such as ornibactin and malleobactin siderophores.In this study,the genome analysis of Burkholderiales genomes showed a putative novel siderophore gene cluster crb,which is highly similar to the ornibactin and malleobactin gene clusters but does not have pvdF,a gene encoding a formyltransferase for N-δ-hydroxy-ornithine formylation.Establishing the bacteriophage recom-binase Redγ-Redδβ7029 mediated genome editing system in a non-model Burkholderiales strain Paraburkholderia caribensis CICC 10960 allowed the rapid identification of the products of crb gene cluster,caribactins A-F(1-6).Caribactins contain a special amino acid residue N-δ-hydroxy-N-δ-acetylornithine(haOrn),which differs from the counterpart N-δ-hydroxy-N-δ-formylornithine(hOrn)in ornibactin and malleobactin,owing to the absence of pvdF.Gene inactivation showed that the acetylation of hOrn is catalyzed by CrbK,whose homologs proba-bly not be involved in the biosynthesis of ornibactin and malleobactin,showing possible evolutionary clues of these siderophore biosynthetic pathways from different genera.Caribactins promote biofilm production and en-hance swarming and swimming abilities,suggesting that they may play crucial roles in biofilm formation.This study also revealed that recombineering has the capability to mine novel secondary metabolites from non-model Burkholderiales species.
基金the National Science Foundation Grant MCB-2212951(to CEB)and NHMRC Ideas grant APP1184012/GNT1184012(to GT).
文摘Recombineering is an essential tool for molecular biologists,allowing for the facile and efficient manipulation of bacterial genomes directly in cells without the need for costly and laborious in vitro manipulations involving restriction enzymes.The main workhorses behind recombineering are bacteriophage proteins that promote the single-strand annealing(SSA)homologous recombination pathway to repair double-stranded DNA breaks.While there have been several reviews examining recombineering methods and applications,comparatively few have focused on the mechanisms of the proteins that are the key players in the SSA pathway:a 5′→3′exonuclease and a single-strand annealing protein(SSAP or“annealase”).This review dives into the structures and functions of the two SSA recombination systems that were the first to be developed for recombineering in E.coli:the RecET system from E.coli Rac prophage and the𝜆Red system from bacteriophageλ.By comparing the structures of the RecT and Red𝛽annealases,and the RecE and𝜆Exo exonucleases,we provide new insights into how the structures of these proteins dictate their function.Examining the sequence conservation of the𝜆λExo and RecE exonucleases gives more profound insights into their critical functional features.Ultimately,as recombineering accelerates and evolves in the laboratory,a better understanding of the mechanisms of the proteins behind this powerful technique will drive the development of improved and expanded capabilities in the future.
基金supported by the National Key R&D Program of China(2019YFA0904000)the National Natural Science Foundation of China(31570094,81502962,32170038,32270088)+1 种基金the Taishan Scholar Pro-gram of Shandong Province,the Shandong Provincial Natural Science Foundation of China(ZR2020MC015,ZR2022MC142)the Funda-mental Research Funds of Shandong University(2018GN021).
文摘Recombineering is a valuable technique for generating recombinant DNA in vivo,primarily in bacterial cells,and is based on homologous recombination using phage-encoded homologous recombinases,such as Red βγ from the lambda phage and RecET from the Rac prophage.The recombineering technique can efficiently mediate homol-ogous recombination using short homologous arms(∼50 bp)and is unlimited by the size of the DNA molecules or positions of restriction sites.In this review,we summarize characteristics of recombinases,mechanism of recombineering,and advances in recombineering for DNA manipulation in Escherichia coli and other bacteria.Furthermore,the broad applications of recombineering for mining new bioactive microbial natural products,and for viral mutagenesis,phage genome engineering,and understanding bacterial metabolism are also reviewed.
文摘This article uses a real-life example to illustrate the concept and methodology of recombineering, arevolutionary genetic engineering technique based on phage-mediated homologous recombination. A step-by-step approach is presented along with a flow diagram, from obtaining gene-harboring BACs to the in vitro generation of a conditional null allele. This method can be used to target any gene at any position, without the knowledge or use of any restriction site. The extensive applicability of recombineering to gene manipulation is discussed.
基金supported by the National Key Research and Development Program of China (Grant Nos.2024YFA1409800 for J.Z.and2024YFA1408603 for Q.Z.)the National Natural Science Foundation of China (Grant Nos.12125408,12334004for J.Z.,and 12174363 for Q.Z.)+1 种基金the Innovation Program for Quantum Science and Technology (Grant No.2021ZD0303306 for J.Z.)the Strategic Priority Research Program of the Chinese Academy of Sciences(Grant No.XDB0450101 for J.Z.)。
文摘Electron–hole(e–h)recombination is a fundamental process that governs energy dissipation and device efficiency in semiconductors.In two-dimensional(2D)materials,the formation of tightly bound excitons makes exciton-mediated e–h recombination the dominant decay pathway.In this work,nonradiative e–h recombination within excitons in monolayer MoS_(2) is investigated using first-principles simulations that combine nonadiabatic molecular dynamics with GW and real-time Bethe–Salpeter equation(BSE)propagation.A two-step process is identified:rapid intervalley redistribution induced by exchange interaction,followed by slower phonon-assisted recombination facilitated by exciton binding.By selectively removing the screened Coulomb and exchange terms from the BSE Hamiltonian,their respective contributions are disentangled—exchange interaction is found to increase the number of accessible recombination pathways,while binding reduces the excitation energy and enhances nonradiative decay.A reduction in recombination lifetime by over an order of magnitude is observed due to the excitonic many-body effects.These findings provide microscopic insights for understanding and tuning exciton lifetimes in 2D transition-metal dichalcogenides.
文摘The published article titled“Truncated Bid Overexpression Induced by Recombinant Adenovirus Cre/LoxP System Suppresses the Tumorigenic Potential of CD133+Ovarian Cancer Stem Cells”has been retracted from Oncology Research,Vol.25,No.4,2017,pp.595–603.
基金supported financially by the National Natural Science Foundation of China(31811530297 and 32170217).
文摘Plastome variation,including single spontaneous nucleotide substitutions and single insertions/deletions,is the major source of leaf variegation in plants.Additionally,one recent study has showed that a simple plastome structural variation,which is induced by one pair of small inverted repeats,can also result in leaf variegation.Here we show a complex plastome structural variation caused by intermolecular and intramolecular recombination across three pairs of small inverted repeats accounts for leaf variegation in a widely cultivated shrub Heptapleurum ellipticum(Araliaceae).This plastome structural variation contains two deletions and two duplications,resulting in dramatic expansion of IRs,substantial contraction of LSC and loss of 11 genes that essential for photosynthesis.Plastome heteroplasmy was detected in both green and albino sectors of variegated leaves.Relative to green sectors,albino sectors in the variegated leaves exhibit significantly reduced expression for the 11 genes lost in the mutated plastome as well as 26 other genes,but significantly increased expression for one gene related to translation apparatus.Optical and transmission electron microscopy observations showed that mesophyll cells of albino sectors possess plastids lacking grana lamellae,which likely carry the mutated plastome and contribute to albinism.In both sectors,the first layer of spongy mesophyll cells beneath the lower epidermis contains normal chloroplasts,suggesting periclinal division of the lower epidermis during development.Our study demonstrates that multiple small repeats can collectively mediate intra-and inter-molecular recombination in plastome and offers a new mechanism accounting for leaf variegation in plants.
基金supported by the National Natural Science Foundation of China(Grant Nos.52102165 and 62474056)the Natural Science Foundation of Nanjing University of Posts and Telecommunications(Grant Nos.NY221029 and NY222165)。
文摘All-inorganic lead-free perovskite solar cells have emerged as environmentally benign candidates;however,their device performance is still constrained by pronounced carrier recombination losses in the bulk and at interfaces.By combining energy band alignment analysis with detailed modeling of recombination mechanisms,a systematic strategy for optimizing hole transport layers is developed.The results reveal that a negative valence band offset produces a cliff-like interface,which facilitates hole extraction while also accounting for the observed variations in open-circuit voltage.Furthermore,short-circuit current losses are quantitatively attributed to different recombination pathways,modeled by incorporating radiative,Shockley–Read–Hall,Auger,and interface recombination processes.This comprehensive approach not only clarifies the correlation between energy level alignment and recombination dynamics but also highlights the competing roles of band offset and interface defects in determining device performance.The optimized device architecture,based on Ge-based lead-free perovskites,achieves a power conversion efficiency of 25.1%,with an open-circuit voltage of 1.29 V,a short-circuit current density of 22.5 mA·cm^(-2),and a fill factor of 86.3%.These findings provide theoretical guidance for designing stable,high-performance,and environmentally friendly lead-free perovskite solar cells.
基金supported by the National Key R&D Program of China(2019YFA0904000)the National Natural Science Foundation of China(31570094,81502962,32270088)+6 种基金the 111 Project(B16030)the Shan-dong Provincial Natural Science Foundation of China(ZR2020MC015,ZR2018ZC2261)the Taishan Scholar Program of Shandong Provincethe Fundamental Research Funds of Shandong University(2018GN021)the Open Project Program of the State Key Laboratory of Bio-based Material and Green Papermaking(KF201825)the Science and Technology Project of Hunan Province(2021NK1040)Natural Science Foundation of Changsha(KQ2208130).
文摘Bacillus subtilis plays an important role in fundamental and applied research,and it has been widely used as a cell factory for the production of enzymes,antimicrobial materials,and chemicals for agriculture,medicine,and industry.However,genetic manipulation tools for B.subtilis have low efficiency.In this work,our goal was to develop a simple recombineering system for B.subtilis.We showed that genome editing can be achieved in B.subtiliis 1A751 through co-expression of YqaJ/YqaK,a native phage recombinase pair found in B.sub-tilis 168,and the competence master regulator ComK using a double-stranded DNA substrate with short ho-mology arms(100 bp)and a phosphorothioate modification at the 5′-end.Efficient gene knockouts and large DNA insertions were achieved using this new recombineering system in B.subtilis 1A751.As far as we know,this is the first recombineering system using the native phage recombinase pair YqaJ/YqaK in B.subtilis.In conclusion,this new recombineering system provides a simple and fast tool for genetic manipulation of B.sub-tilis,and it will promote studies of genome function,construction of production strains,and genome mining in B.subtilis.
基金financially supported by the National Natural Science Foundation of China(82127802,22374157)Strategic Priority Research Program,CAS(XDB0540000,XDC0170000)CAS Youth Interdisciplinary Team(JCTD-2022-13).In addition,Xin Zhou acknowledges the support from the Tencent Foundation through the XPLORER PRIZE.
文摘Magnetic resonance imaging(MRI)is a powerful tool for diagnosing and monitoring brain diseases,but its low sensitivity can hinder early detection.To address this challenge,we utilized chemical exchange saturation transfer(CEST)MRI,which greatly enhances sensitivity for detecting low-concentration compounds.In this study,we developed a CEST contrast agent based on a recombinant adeno-associated viruses(rAAVs)encoding the protamine-1(PRM1)MRI reporter gene.CEST MRI revealed that PRM1 contrast agent effectively highlighted caudate putamen region after injection of the rAAVs into the mouse brain,clearly distinguishing it from the surrounding tissue,with no observable damage.This method provides a sensitive,metal-free CEST contrast agent for in vivo brain cell detection,demonstrating potential for both diagnostic and therapeutic applications in brain diseases.
基金supported by grants from the National Natural Science Foundation of China(32172890 and 32002315)the National Key Research and Development Program of China(2022YFF0711004)+3 种基金the Natural Science Foundation of Heilongjiang Province,China(YQ2022C042)the State Key Laboratory of Veterinary Biotechnology Foundation of China(SKLVBF202208)the Postdoctoral Fellowship Program of CPSF,China(GZC20233062)the National Center of Technology Innovation for Pigs,China(NCTIP-XD/C09)。
文摘NADC34-like porcine reproductive and respiratory syndrome virus(PRRSV),which first appeared in China in 2017,is currently one of the main epidemic strains in China.In this study,we found that a new variant of NADC34-like PRRSV evolved,named the L1A variant.The phylogenetics,epidemic status,and pathogenicity of the LA variants were subsequently comprehensively evaluated.Based on the results of the ORF5 phylogenetic analysis,the L1A variants were classified as NADC34-like PPRSV.All the strains had the same discontinuous 131-aa deletion in the NSP2 region(similar to that in the NADC30).Recombination analysis revealed that the L1A variants were recombinant viruses that contained an NADC30-like PRRSV skeleton,a nonstructural protein-encoding gene region obtained in part from JXA1-like PRRSV and a ORF2-ORF6 gene region partly obtained from NADC34-like PRRSV and that exhibited similar recombination patterns.We successfully isolated the L1A variant TZJ2756 from PAMs and Marc-145 cells.In animal experiments,TZJ2756 exhibited moderate pathogenicity in piglets,causing obvious clinical symptoms,namely,persistent fever,significantly reduced body weight,interstitial edema and severe interstitial pneumonia in the lungs,and prolonged high-load viremia.L1A variants have been detected in at least 12 provinces in China and share many similar epidemiological characteristics with the American L1C variant.This research will enhance our understanding of the prevalence of L1A variants and furnish valuable data for the ongoing monitoring of NADC34-like PRRSV in China.
基金supported by the National Natural Science Foundation of China,Nos.92148206,82071330(both to ZT)a grant from the Major Program of Hubei Province,No.2023BAA005(to ZT)+1 种基金a grant from the Key Research and Discovery Program of Hubei Province,No.2021BCA109(to ZT)the Research Foundation of Tongji Hospital,No.2022B37(to PZ)。
文摘Recombinant tissue plasminogen activator is commonly used for hematoma evacuation in minimally invasive surgery following intracerebral hemorrhage.However,during minimally invasive surgery,recombinant tissue plasminogen activator may come into contact with brain tissue.Therefore,a thorough assessment of its safety is required.In this study,we established a mouse model of intracerebral hemorrhage induced by type VII collagenase.We observed that the administration of recombinant tissue plasminogen activator without hematoma aspiration significantly improved the neurological function of mice with intracerebral hemorrhage,reduced pathological damage,and lowered the levels of apoptosis and autophagy in the tissue surrounding the hematoma.In an in vitro model of intracerebral hemorrhage using primary cortical neurons induced by hemin,the administration of recombinant tissue plasminogen activator suppressed neuronal apoptosis,autophagy,and endoplasmic reticulum stress.Transcriptome sequencing analysis revealed that recombinant tissue plasminogen activator upregulated the phosphoinositide 3-kinase/RAC-alpha serine/threonine-protein kinase/mammalian target of rapamycin pathway in neurons.Moreover,the phosphoinositide 3-kinase inhibitor LY294002 abrogated the neuroprotective effects of recombinant tissue plasminogen activator in inhibiting excessive apoptosis,autophagy,and endoplasmic reticulum stress.Furthermore,to specify the domain of recombinant tissue plasminogen activator responsible for its neuroprotective effects,various inhibitors were used to target distinct domains.It has been revealed that the epidermal growth factor receptor inhibitor AG-1478 reversed the effect of recombinant tissue plasminogen activator on the phosphoinositide 3-kinase/RAC-alpha serine/threonineprotein kinase/mammalian target of rapamycin pathway.These findings suggest that recombinant tissue plasminogen activator exerts a direct neuroprotective effect on neurons following intracerebral hemorrhage,possibly through activation of the phosphoinositide 3-kinase/RAC-alpha serine/threonine-protein kinase/mammalian target of rapamycin pathway.
基金the DFG grant EH 192/5-3(to AE),the internal grant program(project IFF 2024-91)f the Faculty of Health at Witten/Herdecke University(WZ and KS)and the PhD program at Witten/Herdecke University(LK).
文摘Adenoviruses typically cause mild illnesses,but severe diseases may occur primarily in immunodeficient individuals,particularly children.Recently,adenoviruses have garnered significant interest as a versatile tool in gene therapy,tumor treatment,and vaccine vector development.Over the past two decades,the advent of recombineering,a method based on homologous recombination,has notably enhanced the utility of adenoviral vectors in therapeutic applications.This review summarizes recent advancements in the use of human adenoviral vectors in medicine and discusses the pivotal role of recombineering in the development of these vectors.Additionally,it highlights the current achievements and potential future impact of therapeutic adenoviral vectors.
基金Supported by Tianjin Key Medical Discipline(Specialty)Construction Project,No.TJYXZDXK-034A.
文摘BACKGROUND Patients with acute-on-chronic liver failure(ACLF)have a high mortality rate,poor prognosis,and often experience concurrent thrombocytopenia and bleeding events.AIM To evaluate the efficacy and safety of recombinant human thrombopoietin(rhTPO)in patients with ACLF with concomitant severe thrombocytopenia.METHODS This was a prospective,open-label study.We assigned 70 ACLF patients with severe thrombocytopenia into the rhTPO group and control group,with 35 patients in each group.Patients in the rhTPO group received subcutaneous injections of rhTPO at a dose of 15000 IU/day for 7 consecutive days,while patients in the control group did not receive rhTPO treatment.The primary endpoint was the proportion of patients with platelet count>50×10^(9)/L on day 14.RESULTS The proportion of patients with platelet count>50×10^(9)/L on day 14 was 60.7%in the rhTPO group,which was significantly higher than that(12.0%)in the control group(P<0.001).The platelet count in the rhTPO group on day 14 was 64×10^(9)/L,exceeding the baseline of 28×10^(9)/L.Compared to the control group,the rhTPO group exhibited a significant increase in platelet count from baseline(P<0.05).Model for end-stage liver disease score,albumin level and international normalized ratio improved significantly from baseline on day 14 after rhTPO injection.The concentrations of serum thrombopoietin and hepatocyte growth factor in the rhTPO group after 7 days were 143.7 and 195.4 pg/mL,respectively,showing a significant increase from baseline(P<0.05).Eight(22.9%)patients had bleeding events in the control group compared with four(11.4%)in the rhTPO group.The incidence of 90-day mortality was also higher in the control group(6,17.1%)than that in the rhTPO group(3,8.6%).CONCLUSION rhTPO significantly increased the platelet count in ACLF patients with thrombocytopenia and reduce the occurrence of bleeding events,with a good safety profile.
基金financially supported by the Shanghai New Three-Year Action Plan for Public Health(Grant No.GWVI-11.1-03)National Natural Science Foundation of China(Grant No.81872673).
文摘Objective Poxviruses are zoonotic pathogens that infect humans,mammals,vertebrates,and arthropods.However,the specific role of ticks in transmission and evolution of these viruses remains unclear.Methods Transcriptomic and metatranscriptomic raw data from 329 sampling pools of seven tick species across five continents were mined to assess the diversity and abundance of poxviruses.Chordopoxviral sequences were assembled and subjected to phylogenetic analysis to trace the origins of the unblasted fragments within these sequences.Results Fifty-eight poxvirus species,representing two subfamilies and 20 genera,were identified,with 212 poxviral sequences assembled.A substantial proportion of AT-rich fragments were detected in the assembled poxviral genomes.These genomic sequences contained fragments originating from rodents,archaea,and arthropods.Conclusion Our findings indicate that ticks play a significant role in the transmission and evolution of poxviruses.These viruses demonstrate the capacity to modulate virulence and adaptability through horizontal gene transfer,gene recombination,and gene mutations,thereby promoting co-existence and co-evolution with their hosts.This study advances understanding of the ecological dynamics of poxvirus transmission and evolution and highlights the potential role of ticks as vectors and vessels in these processes.
基金supported by the National High Level Hospital Clinical Research Funding(No.BJ-2019-195)the National High Level Hospital Clinical Research Funding(No.BJ-2023-090)。
文摘Objective:Patients with homologous recombination deficiency(HRD)demonstrate distinct clinicopathological and prognostic features.However,standardised and clinically validated HRD detection methodologies specifically tailored for non-small cell lung cancer(NSCLC)have yet to be established.Further research is needed to clarify the precise role and clinical implications of HRD in NSCLC.Methods:A cohort of 580 treatment-naive NSCLC patients was retrospectively enrolled.Comprehensive genomic profiling(CGP)was performed for all patients,and HRD status was evaluated using two genomic scar score(GSS)-based algorithms:a machine learning-based GSS(ML-GSS)and a continuous linear regression-based GSS(CLR-GSS).To assess the diagnostic performance(sensitivity and specificity)of the ML-GSS and CLR-GSS algorithms for HRD detection,immunohistochemical(IHC)staining was conducted for two HRD-related biomarkers:Schlafen 11(SLFN11)and RAD51.Survival analysis,including progression-free survival(PFS),along with multivariable Cox proportional hazards models,was performed to compare the prognostic value of the two HRD algorithms.Results:Among all patients,146(25.2%)and 46(7.9%)were classified as HRD-positive(HRD+)by ML-GSS and CLR-GSS,respectively.Using SLFN11 IHC expression as the reference standard,comparative analysis demonstrated that ML-GSS exhibited significantly higher sensitivity but lower specificity than CLR-GSS.This trend was consistently observed in RAD51 staining analysis.Compared to HRD-negative(HRD-)patients,MLGSS-defined HRD+cases displayed distinct clinicopathological and genomic features,including a higher prevalence of homologous recombination(HR)-related genes mutations,BRCA1/2 mutations,TP53 mutations,elevated tumor mutation burden(TMB),and increased copy number variations(CNVs).In contrast,CLR-GSSdefined HRD+patients were only enriched for BRCA1/2 mutations,TP53 mutations,and elevated TMB.Furthermore,ML-GSS-defined HRD+status was associated with significantly worse prognosis following first-line therapy compared to HRD-patients.Univariate and multivariable Cox analyses identified ML-GSS-defined HRD+and TP53 mutations as significant predictors and independent risk factors,respectively.No such associations were observed in the CLR-GSS-defined HRD+cohort.Conclusions:ML-GSS demonstrated superior performance to CLR-GSS in assessing chromosomal instability(CIN)and showed greater clinical utility.We recommend the ML-GSS algorithm as a robust and clinically validated tool for HRD/CIN evaluation in NSCLC.Furthermore,ML-GSS-defined HRD+status was identified as both a significant predictor and an independent risk factor.
基金supported by grants from the Medical Engineering Jiont Fund of the Fudan University(No.IDH2310117)。
文摘Objective:Triple-negative breast cancer(TNBC)is a highly aggressive subtype that lacks targeted therapies,leading to a poorer prognosis.However,some patients achieve long-term recurrence-free survival(RFS),offering valuable insights into tumor biology and potential treatment strategies.Methods:We conducted a comprehensive multi-omics analysis of 132 patients with American Joint Committee on Cancer(AJCC)stage III TNBC,comprising 36 long-term survivors(RFS≥8 years),62 moderate-term survivors(RFS:3-8 years),and 34 short-term survivors(RFS<3 years).Analyses investigated clinicopathological factors,whole-exome sequencing,germline mutations,copy number alterations(CNAs),RNA sequences,and metabolomic profiles.Results:Long-term survivors exhibited fewer metastatic regional lymph nodes,along with tumors showing reduced stromal fibrosis and lower Ki67 index.Molecularly,these tumors exhibited multiple alterations in genes related to homologous recombination repair,with higher frequencies of germline mutations and somatic CNAs.Additionally,tumors from long-term survivors demonstrated significant downregulation of the RTK-RAS signaling pathway.Metabolomic profiling revealed decreased levels of lipids and carbohydrate,particularly those involved in glycerophospholipid,fructose,and mannose metabolism,in long-term survival group.Multivariate Cox analysis identified fibrosis[hazard ratio(HR):12.70,95%confidence interval(95%CI):2.19-73.54,P=0.005]and RAC1copy number loss/deletion(HR:0.22,95%CI:0.06-0.83,P=0.026)as independent predictors of RFS.Higher fructose/mannose metabolism was associated with worse overall survival(HR:1.30,95%CI:1.01-1.68,P=0.045).Our findings emphasize the association between biological determinants and prolonged survival in patients with TNBC.Conclusions:Our study systematically identified the key molecular and metabolic features associated with prolonged survival in AJCC stage III TNBC,suggesting potential therapeutic targets to improve patient outcomes.
基金supported by the Science and Technology Innovation Development Program(No.70304901).
文摘Cu_(2)ZnSn(S,Se)_(4)(CZTSSe)is considered to be the most potential light-absorbing material to replace CuInGaSe_(2)(CIGS),but the actual photoelectric conversion efficiency of such cells is much lower than that of CIGS.One of the reasons is the high recombination rate of carriers at the interface.In this paper,in order to reduce the carrier recombination,a new solar cell structure with double absorber layers of Al-doped ZnO(AZO)/intrinsic(i)-ZnO/CdS/CZTS_(x1)Se_(1−x1)(CZTSSe_(1))/CZTS_(x2)Se_(1−x2)(CZTSSe_(2))/Mo was proposed,and the optimal conduction band offsets(CBOs)of CdS/CZTSSe_(1) interface and CZTSSe_(1)/CZTSSe_(2) interface were determined by changing the S ratio in CZTSSe_(1) and CZTSSe_(2),and the effect of thickness of CZTSSe_(1) on the performance of the cell was studied.The efficiencies of the optimized single and double absorber layers reached 17.97%and 23.4%,respectively.Compared with the single absorber layer structure,the proposed structure with double absorber layers has better cell performance.
文摘BACKGROUND Valvular heart disease affects more than 100 million people worldwide and is associated with significant morbidity and mortality.The prevalence of at least moderate valvular heart disease is 2.5%across all age groups,but its prevalence increases with age.Mitral regurgitation and aortic stenosis are the most frequent types of valvular heart disease in the community and hospital context,res-pectively.Surgical valve replacement(or mitral valve repair)is the standard of care for treating heart valve disease.However,the replacement of a prosthetic heart valve can lead to complications,either in the peri-procedural phase or in the long-term follow-up period.CASE SUMMARY We present a case of a 71-year-old female patient with a history of mitral valve replacement and warfarin anti-coagulation therapy.She was admitted to the intensive care unit due to spontaneously reperfused ischemic stroke of probable cardioembolic etiology.A dysfunctional mitral prosthesis was identified due to malfunction of one of the fixed discs.Furthermore,a possible microthrombotic lesion was suspected.Therefore,systemic thrombolysis was performed with subsequent normalization of mitral disc opening and closing.CONCLUSION This case underscores the critical importance of a multidisciplinary approach for timely decision-making in critically ill patients with prosthetic valve complications.
