Tumor-specific antigens,also known as neoantigens,have potential utility in anti-cancer immunotherapy,including immune checkpoint blockade(ICB),neoantigen-specific T cell receptor-engineered T(TCR-T),chimeric antigen ...Tumor-specific antigens,also known as neoantigens,have potential utility in anti-cancer immunotherapy,including immune checkpoint blockade(ICB),neoantigen-specific T cell receptor-engineered T(TCR-T),chimeric antigen receptor T(CAR-T),and therapeutic cancer vaccines(TCVs).After recognizing presented neoantigens,the immune system becomes activated and triggers the death of tumor cells.Neoantigens may be derived from multiple origins,including somatic mutations(single nucleotide variants,insertions/deletions,and gene fusions),circular RNAs,alternative splicing,RNA editing,and polymorphic microbiomes.An increasing amount of bioinformatics tools and algorithms are being developed to predict tumor neoantigens derived from different sources,which may require inputs from different multi-omics data.In addition,calculating the peptide-major histocompatibility complex(MHC)affinity can aid in selecting putative neoantigens,as high binding affinities facilitate antigen presentation.Based on these approaches and previous experiments,many resources have been developed to reveal the landscape of tumor neoantigens across multiple cancer types.Herein,we summarize these tools,algorithms,and resources to provide an overview of computational analysis for neoantigen discovery and prioritization,as well as the future development of potential clinical utilities in this field.展开更多
Precision application in orchards enhancing deposition uniformity and environmental sustainability by accurately matching nozzle output with canopy parameters.This study provides a pipeline for creating 3D prescriptio...Precision application in orchards enhancing deposition uniformity and environmental sustainability by accurately matching nozzle output with canopy parameters.This study provides a pipeline for creating 3D prescription maps using a UAV and performing offline variable application.It also evaluates the accuracy of ground altitude measurements at various flight heights.At a flight height of 30 m,with a three-dimensional reconstruction method without phase-control points,the root mean square error(RMSE)for ground altitude measurement was 0.214 m and the mean absolute error(MAE)was 0.211 m;for the canopy area,these values were 0.591 m and 0.541 m,respectively.As flight height increased,the accuracy of altitude measurements declined and tended to be underestimated.Moreover,during offline variable spraying,the shape of the spray area influenced deposition accuracy,with collision detection area of a line segment achieving greater precision than conical ones.Field tests showed that the offline variable application method reduced pesticide usage by 32.43%and enhanced spray uniformity.This newly developed process does not require costly sensors on each sprayer and has potential for field applications.展开更多
Immune checkpoint blockade(ICB)therapies exhibit substantial clinical benefit in different cancers,but relatively low response rates in the majority of patients highlight the need to understand mutual relationships am...Immune checkpoint blockade(ICB)therapies exhibit substantial clinical benefit in different cancers,but relatively low response rates in the majority of patients highlight the need to understand mutual relationships among immune features.Here,we reveal overall positive correlations among immune checkpoints and immune cell populations.Clinically,patients benefiting from ICB exhibited increases for both immune stimulatory and inhibitory features after initiation of therapy,suggesting that the activation of the immune microenvironment might serve as the biomarker to predict immune response.As proof-of-concept,we demonstrated that the immune activation score(ISD)based on dynamic alteration of interleukins in patient plasma as early as two cycles(4-6 weeks)after starting immunotherapy can accurately predict immunotherapy efficacy.Our results reveal a systematic landscape of associations among immune features and provide a noninvasive,cost-effective,and time-efficient approach based on dynamic profiling of pre-and on-treatment plasma to predict immunotherapy efficacy.展开更多
Dear Editor,As an illuminating cancer hallmark,polymorphic microbiomes profoundly impact cancer phenotypes by promoting or repressing cancer initiation and progression.1 Diversity and composition in the gut microbiome...Dear Editor,As an illuminating cancer hallmark,polymorphic microbiomes profoundly impact cancer phenotypes by promoting or repressing cancer initiation and progression.1 Diversity and composition in the gut microbiome are significantly associated with the response rate of anti-PD1 immunotherapy in melanoma.2 In addition to the gut microbiome,a large number of microbiomes colonizing in human tumors have been shown to play significant roles in cancer development.3 However,a comprehensive understanding of intratumor microbiomes in cancer immunotherapy is lacking,largely due to the challenge of investigating intratumor microbiomes in anti-cancer immunotherapy.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.32270708 and 82203195)supported by the Medical Science Data Center at Shanghai Medical College of Fudan University,China.
文摘Tumor-specific antigens,also known as neoantigens,have potential utility in anti-cancer immunotherapy,including immune checkpoint blockade(ICB),neoantigen-specific T cell receptor-engineered T(TCR-T),chimeric antigen receptor T(CAR-T),and therapeutic cancer vaccines(TCVs).After recognizing presented neoantigens,the immune system becomes activated and triggers the death of tumor cells.Neoantigens may be derived from multiple origins,including somatic mutations(single nucleotide variants,insertions/deletions,and gene fusions),circular RNAs,alternative splicing,RNA editing,and polymorphic microbiomes.An increasing amount of bioinformatics tools and algorithms are being developed to predict tumor neoantigens derived from different sources,which may require inputs from different multi-omics data.In addition,calculating the peptide-major histocompatibility complex(MHC)affinity can aid in selecting putative neoantigens,as high binding affinities facilitate antigen presentation.Based on these approaches and previous experiments,many resources have been developed to reveal the landscape of tumor neoantigens across multiple cancer types.Herein,we summarize these tools,algorithms,and resources to provide an overview of computational analysis for neoantigen discovery and prioritization,as well as the future development of potential clinical utilities in this field.
基金supported by the earmarked fund for CARS(CARS-28)the 2115 talent development program of China Agricultural University and Sanya Institute of China Agricultural University Guiding Fund Project,Grant No.SYND-2021-06.
文摘Precision application in orchards enhancing deposition uniformity and environmental sustainability by accurately matching nozzle output with canopy parameters.This study provides a pipeline for creating 3D prescription maps using a UAV and performing offline variable application.It also evaluates the accuracy of ground altitude measurements at various flight heights.At a flight height of 30 m,with a three-dimensional reconstruction method without phase-control points,the root mean square error(RMSE)for ground altitude measurement was 0.214 m and the mean absolute error(MAE)was 0.211 m;for the canopy area,these values were 0.591 m and 0.541 m,respectively.As flight height increased,the accuracy of altitude measurements declined and tended to be underestimated.Moreover,during offline variable spraying,the shape of the spray area influenced deposition accuracy,with collision detection area of a line segment achieving greater precision than conical ones.Field tests showed that the offline variable application method reduced pesticide usage by 32.43%and enhanced spray uniformity.This newly developed process does not require costly sensors on each sprayer and has potential for field applications.
基金supported by grants from the National Key Research and Development Program of China(no.2019YFA0111600 and no.2019YFE0120800 to H.L.)the National Natural Science Foundation of China(no.82073145 to Y.Y.,no.31800979 to H.L.,no.81902149 to Q.G.,and no.82102891 to X.K.)+5 种基金the Natural Science Foundation of China for outstanding Young Scholars(no.82022060 to H.L.)the Shanghai Pujiang Program(no.20PJ1412800 to Y.Y.)the Natural Science Foundation of Shanghai(no.20ZR1472900 to Y.Y.)the Natural Science Foundation of Hunan Province for outstanding Young Scholars(no.2019JJ30040 to H.L.)the Natural Science Foundation of Hunan Province of China(no.2018SK2082 to H.L.)the Scientific Research Project of Hunan Health and Family Planning Commission(no.B20180855 to H.L.).
文摘Immune checkpoint blockade(ICB)therapies exhibit substantial clinical benefit in different cancers,but relatively low response rates in the majority of patients highlight the need to understand mutual relationships among immune features.Here,we reveal overall positive correlations among immune checkpoints and immune cell populations.Clinically,patients benefiting from ICB exhibited increases for both immune stimulatory and inhibitory features after initiation of therapy,suggesting that the activation of the immune microenvironment might serve as the biomarker to predict immune response.As proof-of-concept,we demonstrated that the immune activation score(ISD)based on dynamic alteration of interleukins in patient plasma as early as two cycles(4-6 weeks)after starting immunotherapy can accurately predict immunotherapy efficacy.Our results reveal a systematic landscape of associations among immune features and provide a noninvasive,cost-effective,and time-efficient approach based on dynamic profiling of pre-and on-treatment plasma to predict immunotherapy efficacy.
基金National Key Research and Development Program of China(2019YFE0120800,2019YFA0111600)Natural Science Foundation of China for outstanding Young Scholars(82022060)+7 种基金National Natural Science Foundation of China(81902149,81874242,31800979,82073145)Natural Science Foundation of Hunan Province for outstanding Young Scholars(2019JJ30040)Talent Young Scholars of Hunan Province(2019RS2009)Natural Science Foundation of Hunan Province(2020JJ5892)Shanghai Pujiang Program(21PJ1401700)Natural Science Foundation of Hunan Province for outstanding Young Scholars(2019JJ30040)Talent Young Scholars of Hunan Province(2019RS2009)We regret that page limitations have prevented us from including all the relevant studies in this letter.
文摘Dear Editor,As an illuminating cancer hallmark,polymorphic microbiomes profoundly impact cancer phenotypes by promoting or repressing cancer initiation and progression.1 Diversity and composition in the gut microbiome are significantly associated with the response rate of anti-PD1 immunotherapy in melanoma.2 In addition to the gut microbiome,a large number of microbiomes colonizing in human tumors have been shown to play significant roles in cancer development.3 However,a comprehensive understanding of intratumor microbiomes in cancer immunotherapy is lacking,largely due to the challenge of investigating intratumor microbiomes in anti-cancer immunotherapy.
