The growing recognition of the role of genetics in the development of amyotrophic lateral sclerosis is evident.However,there has yet to be a comprehensive analysis of the clinical characteristics and genetics of famil...The growing recognition of the role of genetics in the development of amyotrophic lateral sclerosis is evident.However,there has yet to be a comprehensive analysis of the clinical characteristics and genetics of familial amyotrophic lateral sclerosis in an Asian population.This study aimed to provide an in-depth analysis of the clinical features and genetic spectrum of familial amyotrophic lateral sclerosis over 15 years in a clinic-based cohort of patients from the Chinese mainland.Enrollment of 302 amyotrophic lateral sclerosis families from 28 provinces was undertaken from January 2008 to September 2023.A group-based trajectory model for disease progression based on amyotrophic lateral sclerosis Functional Rating Scale-Revised(ALSFRS-R)scores was validated using bootstrap internal validation in patients with familial amyotrophic lateral sclerosis,as well as patients with sporadic amyotrophic lateral sclerosis(matched at a 1:4 ratio,with replacement).DNA samples from 244 index patients were screened for variants in the pathogenic genes SOD1,FUS,TDP43,and C9ORF72,of which 146 were also subjected to genome-wide next-generation sequencing.Gene-level burden analysis was used to evaluate the distribution of rare variants in the cohort.We found that rapid dynamic disease progression was associated with an older age at onset,shorter diagnostic delay,lower body mass index,bulbar onset,and≥1 affected first-degree relative.Certain attributes,such as age at onset and time from onset to diagnosis,had comparable impacts on the clinical progression trajectories of both familial amyotrophic lateral sclerosis and sporadic amyotrophic lateral sclerosis.Harboring pathogenic/likely pathogenic variants in amyotrophic lateral sclerosis-causative genes reduced the age of onset of familial amyotrophic lateral sclerosis.Among the patients with familial amyotrophic lateral sclerosis,17.8%possessed≥2 pathogenic/likely pathogenic variants.Sequencing kernel association test analysis showed that the SOD1 rare variant burden(P=1.3e-15)was associated with a significant risk of familial amyotrophic lateral sclerosis.Our findings conclusively confirmed the clinical features and genetic spectrum of familial amyotrophic lateral sclerosis over 15 years in a clinical cohort from China,contributing to a deeper understanding of genotype-phenotype relationships in familial amyotrophic lateral sclerosis.This comprehensive evaluation of specific clinical characteristics,clinical prognosis,and genetic variants of amyotrophic lateral sclerosis based on detailed clinical and genetic information may lead to the development of genotype-specific treatment approaches.展开更多
染色质高级结构在基因调控中起到不可忽视的作用,染色质结构的形成与调控机制受到广泛关注。"相分离"理论近年来受到较多关注,异染色质与转录因子在其中的作用引人瞩目。但是,目前的相分离模型更关注结合因子与表观遗传性质,...染色质高级结构在基因调控中起到不可忽视的作用,染色质结构的形成与调控机制受到广泛关注。"相分离"理论近年来受到较多关注,异染色质与转录因子在其中的作用引人瞩目。但是,目前的相分离模型更关注结合因子与表观遗传性质,对DNA序列自身的作用理解尚较不充分。许多物种基因组的序列分布均具有多尺度的不均一性,仅基于Cp G岛(Cp G island,CGI)密度差异这一序列性质,就可以划分出基因、表观遗传、结构和转录性质都截然不同的高CGI密度"森林"和低CGI密度"草原"两种序列区域,体现了基因组自身的马赛克性。本文聚焦染色质结构的序列依赖性,讨论了染色质结构模型的研究进展,关注在序列几乎相同的不同细胞类型中的序列–结构关系及其功能调控,对发育、分化、衰老、疾病等多种过程的染色质结构变化进行了系统分析。针对基于序列的染色质相分离模型,对其物理驱动力进行了讨论,并在该模型的框架下基于相分离的物理特性,对温度、序列不均一性等物理因素对染色质结构可能造成的影响进行了探讨。展开更多
A fully convolutional encoder-decoder network(FCEDN),a deep learning model,was developed and applied to image scanning microscopy(ISM).Super-resolution imaging was achieved with a 78μm×78μm field of view and 12...A fully convolutional encoder-decoder network(FCEDN),a deep learning model,was developed and applied to image scanning microscopy(ISM).Super-resolution imaging was achieved with a 78μm×78μm field of view and 12.5 Hz-40 Hz imaging frequency.Mono and dual-color continuous super-resolution images of microtubules and cargo in cells were obtained by ISM.The signal-to-noise ratio of the obtained images was improved from 3.94 to 22.81 and the positioning accuracy of cargoes was enhanced by FCEDN from 15.83±2.79 nm to 2.83±0.83 nm.As a general image enhancement method,FCEDN can be applied to various types of microscopy systems.Application with conventional spinning disk confocal microscopy was demonstrated and significantly improved images were obtained.展开更多
Objective: Previous investigations of circulating tumor cells(CTCs) have mainly focused on their genomic or transcriptomic features, leaving their epigenetic landscape relatively uncharacterized. Here, we investigated...Objective: Previous investigations of circulating tumor cells(CTCs) have mainly focused on their genomic or transcriptomic features, leaving their epigenetic landscape relatively uncharacterized. Here, we investigated the genome-wide DNA methylome of CTCs with a view to understanding the epigenetic regulatory mechanisms underlying cancer metastasis.Methods: We evaluated single-cell DNA methylome and copy number alteration(CNA) in 196 single cells,including 107 CTCs collected from 17 cancer patients covering six different cancer types. Our single-cell bisulfite sequencing(sc BS-seq) covered on average 11.78% of all Cp G dinucleotides and accurately deduced the CNA patterns at 500 kb resolution.Results: We report distinct subclonal structures and different evolutionary histories of CTCs inferred from CNA and DNA methylation profiles. Furthermore, we demonstrate potential tumor origin classification based on the tissue-specific DNA methylation profiles of CTCs.Conclusions: Our work provides a comprehensive survey of genome-wide DNA methylome in single CTCs and reveals 5-methylcytosine(5-m C) heterogeneity in CTCs, addressing the potential epigenetic regulatory mechanisms underlying cancer metastasis and facilitating the future clinical application of CTCs.展开更多
This decade has seen remarkable advances in the field of high-throughput single cell techniques.Single-cell RNA sequencing(sc RNA-seq)has proven to be a powerful strategy to study the heterogeneity in clinical samples...This decade has seen remarkable advances in the field of high-throughput single cell techniques.Single-cell RNA sequencing(sc RNA-seq)has proven to be a powerful strategy to study the heterogeneity in clinical samples,providing an unbiased approach to uncover the characteristics in different cell subsets.To ensure the reproducibility and robustness of biological discoveries,researchers need to be aware of hidden caveats in tissue dissociation,cell capturing and transcripts measurement which may affect cell composition assessment and cellular function annotation.With measured interpretation of data and innovations in experimental and technical approaches,sc RNA-seq can greatly unravel the heterogeneity in complex system and improve our understandings in tissue homeostasis and cancer biology.展开更多
Viewing cancer as a large,evolving population of heterogeneous cells is a common perspective.Because genomic instability is one of the fundamental features of cancer,this intrinsic tendency of genomic variation leads ...Viewing cancer as a large,evolving population of heterogeneous cells is a common perspective.Because genomic instability is one of the fundamental features of cancer,this intrinsic tendency of genomic variation leads to striking intratumor heterogeneity and functions during the process of cancer formation,development,metastasis,and relapse.With the increased mutation rate and abundant diversity of the gene pool,this heterogeneity leads to cancer evolution,which is the major obstacle in the clinical treatment of cancer.Cells rely on the integrity of DNA repair machineries to maintain genomic stability,but these machineries often do not function properly in cancer cells.The deficiency of DNA repair could contribute to the generation of cancer genomic instability,and ultimately promote cancer evolution.With the rapid advance of new technologies,such as single-cell sequencing in recent years,we have the opportunity to better understand the specific processes and mechanisms of cancer evolution,and让s relationship with DNA repair.Here,we review recent findings on how DNA repair affects cancer evolution,and discuss how these mechanisms provide the basis for critical clinical challenges and therapeutic applications.展开更多
Background: Mucosal-associated invariant T(MAIT) cells are systemically depleted in human immunodeficiency virus type 1(HIV-1) infected patients and are not replenished even after successful combined antiretroviral th...Background: Mucosal-associated invariant T(MAIT) cells are systemically depleted in human immunodeficiency virus type 1(HIV-1) infected patients and are not replenished even after successful combined antiretroviral therapy(cART).This study aimed to identify the mechanism underlying MAIT cell depletion.Methods: In the present study, we applied flow cytometry, single-cell RNA sequencing and immunohistochemical staining to evaluate the characteristics of pyroptotic MAIT cells in a total of 127 HIV-1 infected individuals, including 69 treatment-naive patients, 28 complete responders, 15 immunological non-responders, and 15 elite controllers, at the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.Results: Single-cell transcriptomic profiles revealed that circulating MAIT cells from HIV-1 infected subjects were highly activated, with upregulation of pyroptosis-related genes. Further analysis revealed that increased frequencies of pyroptotic MAIT cells correlated with markers of systemic T-cell activation, microbial translocation, and intestinal damage in cART-naive patients and poor CD4+ T-cell recovery in long-term cART patients. Immunohistochemical staining revealed that MAIT cells in the gut mucosa of HIV-1 infected patients exhibited a strong active gasdermin-D(GSDMD, marker of pyroptosis) signal near the cavity side, suggesting that these MAIT cells underwent active pyroptosis in the colorectal mucosa. Increased levels of the proinflammatory cytokines interleukin-12(IL-12) and IL-18 were observed in HIV-1 infected patients. In addition, activated MAIT cells exhibited an increased pyroptotic phenotype after being triggered by HIV-1 virions, T-cell receptor signals, IL-12 plus IL-18, and combinations of these factors, in vitro.Conclusions: Activation-induced MAIT cell pyroptosis contributes to the loss of MAIT cells in HIV-1 infected patients,which could potentiate disease progression and poor immune reconstitution.展开更多
Ossifying fibroma(OF)and fibrous dysplasia(FD)are two fibro-osseous lesions with overlapping clinicopathological features,making diagnosis challenging.In this study,we applied a whole-genome shallow sequencing approac...Ossifying fibroma(OF)and fibrous dysplasia(FD)are two fibro-osseous lesions with overlapping clinicopathological features,making diagnosis challenging.In this study,we applied a whole-genome shallow sequencing approach to facilitate differential diagnosis via precise profiling of copy number alterations(CNAs)using minute amounts of DNA extracted from morphologically correlated microdissected tissue samples.Freshly frozen tissue specimens from OF(n=29)and FD(n=28)patients were obtained for analysis.Lesion fibrous tissues and surrounding normal tissues were obtained by laser capture microdissection(LCM),with~30–50 cells(5000–10000µm2)per sample.We found that the rate of recurrent CNAs in OF cases was much higher(44.8%,13 of 29)than that in FD cases(3.6%,1 of 28).Sixty-nine percent(9 of 13)of the CNA-containing OF cases involved segmental amplifications and deletions on Chrs 7 and 12.We also identified eight CNA-associated genes(HILPDA,CALD1,C1GALT1,MICALL2,PHF14,AIMP2,MDM2,and CDK4)with amplified expression,which was consistent with the copy number changes.We further confirmed a jaw lesion with a previous uncertain diagnosis due to its ambiguous morphological features and the absence of GNAS mutation as OF based on the typical Chr 12 amplification pattern in its CNA profile.Moreover,analysis of a set of longitudinal samples collected from an individual with a cellular lesion in suspicion of OF at the first surgery,recurrence and the latest malignant transformation revealed identical CNA patterns at the three time points,suggesting that copy number profiling can be used as an important tool to identify borderline lesions or lesions with malignant potential.Overall,CNA profiling of fibro-osseous lesions can greatly improve differential diagnosis between OF and FD and help predict disease progression.展开更多
Introduction Primary liver cancer, the second most common cause of cancer related death worldwide, presents ethnic, etiological, sex, and geographical diversity2 （Figure 1A）. At the histological level, liver cancer ...Introduction Primary liver cancer, the second most common cause of cancer related death worldwide, presents ethnic, etiological, sex, and geographical diversity2 （Figure 1A）. At the histological level, liver cancer includes two major types： hepatocellular carcinoma （HCC, about 80%） and cholangiocarcinoma （CCA, about 15%）. Many etiological factors contribute to HCC development, such as hepatitis B virus （HBV）, hepatitis C virus （HCV）, aflatoxin B1 （AFB1）, alcohol, and metabolic diseases3. By contrast, the major risk factors for CCA are liver flukes （Opisthorchis viverrini and Clonorchis sinensis） and primary sclerosing cholangitis4,展开更多
The Cancer Genome Atlas(TCGA) project produced RNA-Seq data for tens of thousands of cancer and non-cancer samples with clinical survival information,providing an unprecedented opportunity for analyzing prognostic gen...The Cancer Genome Atlas(TCGA) project produced RNA-Seq data for tens of thousands of cancer and non-cancer samples with clinical survival information,providing an unprecedented opportunity for analyzing prognostic genes and their isoforms.In this study,we performed the first large-scale identification of transcriptional isoforms that are specifically associated with patient prognosis,even without gene-level association.These specific isoforms are defined as Transcripts Associated with Patient Prognosis(TAPPs).Although a group of TAPPs are the principal isoforms of their genes with intact functional protein domains,another group of TAPPs lack important protein domains found in their canonical gene isoforms.This dichotomy in the distribution of protein domains may indicate different patterns of TAPPs association with cancer.TAPPs in protein-coding genes,especially those with altered protein domains,are rich in known cancer driver genes.We further identified multiple types of cancer recurrent TAPPs,such as DCAF17-201,providing a new approach for the detection of cancer-associated events.In order to make the wide research community to study prognostic isoforms,we developed a portal named GESUR(http://gesur.cancer-pku.cn/),which illustrates the detailed prognostic characteristics of TAPPs and other isoforms.Overall,our integrated analysis of gene expression and clinical parameters provides a new perspective for understanding the applications of different gene isoforms in tumor progression.展开更多
Human leukocyte antigen(HLA)disparity between donors and recipients is a key determinant triggering intense alloreactivity,leading to a lethal complication,namely,acute graft-versus-host disease(aGVHD),after allogenei...Human leukocyte antigen(HLA)disparity between donors and recipients is a key determinant triggering intense alloreactivity,leading to a lethal complication,namely,acute graft-versus-host disease(aGVHD),after allogeneic transplantation.Moreover,aGVHD remains a cause of mortality after HLA-matched allogeneic transplantation.Protocols for HLA-haploidentical hematopoietic cell transplantation(haploHCT)have been established successfully and widely applied,further highlighting the urgency of performing panoramic screening of non-HLA variations correlated with aGVHD.On the basis of our time-consecutive large haploHCT cohort(with a homogenous discovery set and an extended confirmatory set),we first delineated the genetic landscape of 1366 samples to quantitatively model aGVHD risk by assessing the contributions of HLA and non-HLA genes together with clinical factors.In addition to identifying multiple loss-of-function(LoF)risk variations in non-HLA coding genes,our data-driven study revealed that non-HLA genetic variations,independent of HLA disparity,contributed the most to the occurrence of aGVHD.This unexpected major effect was verified in an independent cohort that received HLA-identical sibling HCT.Subsequent functional experiments further revealed the roles of a representative non-HLA LoF gene and LoF gene pair in regulating the alloreactivity of primary human T cells.Our findings highlight the importance of non-HLA genetic risk in the new era of transplantation and propose a new direction to explore the immunogenetic mechanism of alloreactivity and to optimize donor selection strategies for allogeneic transplantation.展开更多
The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems.These adv...The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems.These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues.In this review,we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics.We have reviewed the breakthroughs in single-cell multi-omics technologies,spatial genomics methods,and the computational strategies employed toward the analyses of singlecell atlas data.Furthermore,we have highlighted the advances made in constructing cellular atlases and their clinical applications,particularly in the context of disease.Finally,we have discussed the emerging trends,challenges,and opportunities in this rapidly evolving field.展开更多
T-cell metabolism plays a pivotal role in defining T-cell functional states.Through analysis of a comprehensive pancancer single-cell transcriptional atlas,we identified SARDH,an enzyme involved in one-carbon(1-C)meta...T-cell metabolism plays a pivotal role in defining T-cell functional states.Through analysis of a comprehensive pancancer single-cell transcriptional atlas,we identified SARDH,an enzyme involved in one-carbon(1-C)metabolism,as a potential T-cell metabolic checkpoint.SARDH significantly impacts T-cell fate and function,leading to impaired tumor control efficacy.Knocking down SARDH resulted in sarcosine accumulation and reduced consumption of S-adenosylmethionine(SAM),a critical methyl donor for epigenetic modulation,likely due to the shift in glycine-to-sarcosine homeostasis.Deletion of SARDH increased H3K79me2 modification at NF-κB-activating genes,thereby augmenting NF-κB signaling and T-cell function.Additionally,we observed transcriptional dysregulation of 1-C metabolism within tumors across various cancer types,which was often accompanied by increased sarcosine levels.Sarcosine was found to induce SARDH upregulation,suggesting a feedback mechanism for metabolic homeostasis in T cells within tumors.These findings underscore the potential effects and mechanism of targeting 1-C metabolism,particularly SARDH,as an avenue for cancer therapy.展开更多
This article reviews recent super-resolution(SR)optical imaging techniques for cellular study,encompassing structured illumination microscopy(SIM),point-scanning super-resolution(PS-SR)microscopy,single-molecule local...This article reviews recent super-resolution(SR)optical imaging techniques for cellular study,encompassing structured illumination microscopy(SIM),point-scanning super-resolution(PS-SR)microscopy,single-molecule localization microscopy(SMLM),mathematical and deep learning(DL)SR algorithms.Historically,the resolution of traditional far-field optical imaging was constrained by the diffraction limit.The emergence of SR imaging techniques and image processing algorithms has propelled biological research into nanoscale realm.SIM enhances resolution by manipulating spatial frequency content,effectively doubling the resolution capacity of traditional microscopy.PS-SR imaging,on the other hand,offers superior optical sectioning and a high signal-to-noise ratio.SMLM has achieved a remarkable spatial resolution of approximately 20 nm and supports multi-color,wide-field-of-view(FOV),automated 3D high-throughput imaging,thus broadening the horizons for advanced biomedical investigations.Additionally,both mathematical and DL-based SR algorithms have significantly advanced the conversion of low-resolution images to high-resolution counterparts,extending the capabilities of conventional microscopes.This review underscores the principles,recent developments,and diverse applications of these cutting-edge SR imaging methodologies in biological research.展开更多
基金supported by the Natural Science Foundation of Beijing,Nos.7244428(to WZ)and 7222215(to JH)the Peking University Medicine Sailing Program forYoung Scholars’Scientific and Technological Innovation,No.BMU2023YFJHPY034(to WZ)+4 种基金the National Natural Science Foundation of China,Nos.81873784,82071426(to DF),and81974197(to JH)the Clinical Cohort Construction Program of Peking University Third Hospital,No.BYSYDL2019002(to DF)Beijing Physician-Scientist TrainingProgram,No.BJPSTP-2024-03(to JH)the China Postdoctoral Science Foundation,Nos.2022TQ0014(to LX),2022M720284(to LX)the E-Town Cooperation&Development Foundation,No.YCXJ-JZ-2023-017(to LX).
文摘The growing recognition of the role of genetics in the development of amyotrophic lateral sclerosis is evident.However,there has yet to be a comprehensive analysis of the clinical characteristics and genetics of familial amyotrophic lateral sclerosis in an Asian population.This study aimed to provide an in-depth analysis of the clinical features and genetic spectrum of familial amyotrophic lateral sclerosis over 15 years in a clinic-based cohort of patients from the Chinese mainland.Enrollment of 302 amyotrophic lateral sclerosis families from 28 provinces was undertaken from January 2008 to September 2023.A group-based trajectory model for disease progression based on amyotrophic lateral sclerosis Functional Rating Scale-Revised(ALSFRS-R)scores was validated using bootstrap internal validation in patients with familial amyotrophic lateral sclerosis,as well as patients with sporadic amyotrophic lateral sclerosis(matched at a 1:4 ratio,with replacement).DNA samples from 244 index patients were screened for variants in the pathogenic genes SOD1,FUS,TDP43,and C9ORF72,of which 146 were also subjected to genome-wide next-generation sequencing.Gene-level burden analysis was used to evaluate the distribution of rare variants in the cohort.We found that rapid dynamic disease progression was associated with an older age at onset,shorter diagnostic delay,lower body mass index,bulbar onset,and≥1 affected first-degree relative.Certain attributes,such as age at onset and time from onset to diagnosis,had comparable impacts on the clinical progression trajectories of both familial amyotrophic lateral sclerosis and sporadic amyotrophic lateral sclerosis.Harboring pathogenic/likely pathogenic variants in amyotrophic lateral sclerosis-causative genes reduced the age of onset of familial amyotrophic lateral sclerosis.Among the patients with familial amyotrophic lateral sclerosis,17.8%possessed≥2 pathogenic/likely pathogenic variants.Sequencing kernel association test analysis showed that the SOD1 rare variant burden(P=1.3e-15)was associated with a significant risk of familial amyotrophic lateral sclerosis.Our findings conclusively confirmed the clinical features and genetic spectrum of familial amyotrophic lateral sclerosis over 15 years in a clinical cohort from China,contributing to a deeper understanding of genotype-phenotype relationships in familial amyotrophic lateral sclerosis.This comprehensive evaluation of specific clinical characteristics,clinical prognosis,and genetic variants of amyotrophic lateral sclerosis based on detailed clinical and genetic information may lead to the development of genotype-specific treatment approaches.
基金supported by the National Natural Science Foundation of China(21521003,21233002)National Key Basic Research Special Foundation of China(2012CB917304)~~
文摘染色质高级结构在基因调控中起到不可忽视的作用,染色质结构的形成与调控机制受到广泛关注。"相分离"理论近年来受到较多关注,异染色质与转录因子在其中的作用引人瞩目。但是,目前的相分离模型更关注结合因子与表观遗传性质,对DNA序列自身的作用理解尚较不充分。许多物种基因组的序列分布均具有多尺度的不均一性,仅基于Cp G岛(Cp G island,CGI)密度差异这一序列性质,就可以划分出基因、表观遗传、结构和转录性质都截然不同的高CGI密度"森林"和低CGI密度"草原"两种序列区域,体现了基因组自身的马赛克性。本文聚焦染色质结构的序列依赖性,讨论了染色质结构模型的研究进展,关注在序列几乎相同的不同细胞类型中的序列–结构关系及其功能调控,对发育、分化、衰老、疾病等多种过程的染色质结构变化进行了系统分析。针对基于序列的染色质相分离模型,对其物理驱动力进行了讨论,并在该模型的框架下基于相分离的物理特性,对温度、序列不均一性等物理因素对染色质结构可能造成的影响进行了探讨。
基金Project supported by the China Postdoctoral Science Foundation,the National Key Research and Development Program of China for Y.S.(Grant No.2017YFA0505300)the National Science Foundation of China for Y.S.(Grant No.21825401)。
文摘A fully convolutional encoder-decoder network(FCEDN),a deep learning model,was developed and applied to image scanning microscopy(ISM).Super-resolution imaging was achieved with a 78μm×78μm field of view and 12.5 Hz-40 Hz imaging frequency.Mono and dual-color continuous super-resolution images of microtubules and cargo in cells were obtained by ISM.The signal-to-noise ratio of the obtained images was improved from 3.94 to 22.81 and the positioning accuracy of cargoes was enhanced by FCEDN from 15.83±2.79 nm to 2.83±0.83 nm.As a general image enhancement method,FCEDN can be applied to various types of microscopy systems.Application with conventional spinning disk confocal microscopy was demonstrated and significantly improved images were obtained.
基金financially supported by the Guangdong Province Key Research and Development Program (No. 2019B020226002)the National Science and Technology Major Project (No. 2019YFC1315702)。
文摘Objective: Previous investigations of circulating tumor cells(CTCs) have mainly focused on their genomic or transcriptomic features, leaving their epigenetic landscape relatively uncharacterized. Here, we investigated the genome-wide DNA methylome of CTCs with a view to understanding the epigenetic regulatory mechanisms underlying cancer metastasis.Methods: We evaluated single-cell DNA methylome and copy number alteration(CNA) in 196 single cells,including 107 CTCs collected from 17 cancer patients covering six different cancer types. Our single-cell bisulfite sequencing(sc BS-seq) covered on average 11.78% of all Cp G dinucleotides and accurately deduced the CNA patterns at 500 kb resolution.Results: We report distinct subclonal structures and different evolutionary histories of CTCs inferred from CNA and DNA methylation profiles. Furthermore, we demonstrate potential tumor origin classification based on the tissue-specific DNA methylation profiles of CTCs.Conclusions: Our work provides a comprehensive survey of genome-wide DNA methylome in single CTCs and reveals 5-methylcytosine(5-m C) heterogeneity in CTCs, addressing the potential epigenetic regulatory mechanisms underlying cancer metastasis and facilitating the future clinical application of CTCs.
基金supported by the National Natural Science Foundation of China(No.81988101,91942307,31991171)Beijing Municipal Science and Technology Commission(No.Z201100005320014)。
文摘This decade has seen remarkable advances in the field of high-throughput single cell techniques.Single-cell RNA sequencing(sc RNA-seq)has proven to be a powerful strategy to study the heterogeneity in clinical samples,providing an unbiased approach to uncover the characteristics in different cell subsets.To ensure the reproducibility and robustness of biological discoveries,researchers need to be aware of hidden caveats in tissue dissociation,cell capturing and transcripts measurement which may affect cell composition assessment and cellular function annotation.With measured interpretation of data and innovations in experimental and technical approaches,sc RNA-seq can greatly unravel the heterogeneity in complex system and improve our understandings in tissue homeostasis and cancer biology.
基金supported by the National Natural Science Foundation of China(Grant Nos.81672981 and 81972240).
文摘Viewing cancer as a large,evolving population of heterogeneous cells is a common perspective.Because genomic instability is one of the fundamental features of cancer,this intrinsic tendency of genomic variation leads to striking intratumor heterogeneity and functions during the process of cancer formation,development,metastasis,and relapse.With the increased mutation rate and abundant diversity of the gene pool,this heterogeneity leads to cancer evolution,which is the major obstacle in the clinical treatment of cancer.Cells rely on the integrity of DNA repair machineries to maintain genomic stability,but these machineries often do not function properly in cancer cells.The deficiency of DNA repair could contribute to the generation of cancer genomic instability,and ultimately promote cancer evolution.With the rapid advance of new technologies,such as single-cell sequencing in recent years,we have the opportunity to better understand the specific processes and mechanisms of cancer evolution,and让s relationship with DNA repair.Here,we review recent findings on how DNA repair affects cancer evolution,and discuss how these mechanisms provide the basis for critical clinical challenges and therapeutic applications.
基金supported by the Peking University Clinical Scientist Program Special(BMU2019LCKXJ013)the National Natural Science Foundation Innovation Research Group Project(81721002)+2 种基金the Sanming Project of Medicine Project in Shenzhen(SZSM201612014)the Yunnan Applied Basic Research Projects-Union Foundation by Yunnan Provincial Department of Science and Technology and Kunming Medical University(202001AY070001-154)the Scientific Research Fund of Education Department of Yunnan Province(2021J0297)。
文摘Background: Mucosal-associated invariant T(MAIT) cells are systemically depleted in human immunodeficiency virus type 1(HIV-1) infected patients and are not replenished even after successful combined antiretroviral therapy(cART).This study aimed to identify the mechanism underlying MAIT cell depletion.Methods: In the present study, we applied flow cytometry, single-cell RNA sequencing and immunohistochemical staining to evaluate the characteristics of pyroptotic MAIT cells in a total of 127 HIV-1 infected individuals, including 69 treatment-naive patients, 28 complete responders, 15 immunological non-responders, and 15 elite controllers, at the Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.Results: Single-cell transcriptomic profiles revealed that circulating MAIT cells from HIV-1 infected subjects were highly activated, with upregulation of pyroptosis-related genes. Further analysis revealed that increased frequencies of pyroptotic MAIT cells correlated with markers of systemic T-cell activation, microbial translocation, and intestinal damage in cART-naive patients and poor CD4+ T-cell recovery in long-term cART patients. Immunohistochemical staining revealed that MAIT cells in the gut mucosa of HIV-1 infected patients exhibited a strong active gasdermin-D(GSDMD, marker of pyroptosis) signal near the cavity side, suggesting that these MAIT cells underwent active pyroptosis in the colorectal mucosa. Increased levels of the proinflammatory cytokines interleukin-12(IL-12) and IL-18 were observed in HIV-1 infected patients. In addition, activated MAIT cells exhibited an increased pyroptotic phenotype after being triggered by HIV-1 virions, T-cell receptor signals, IL-12 plus IL-18, and combinations of these factors, in vitro.Conclusions: Activation-induced MAIT cell pyroptosis contributes to the loss of MAIT cells in HIV-1 infected patients,which could potentiate disease progression and poor immune reconstitution.
基金This research was supported by research grants from the National Natural Science Foundation of China(81671006,81700994,22050002,22050004)and CAMS Innovation Fund for Medical Sciences(2019-I2M-5-038).
文摘Ossifying fibroma(OF)and fibrous dysplasia(FD)are two fibro-osseous lesions with overlapping clinicopathological features,making diagnosis challenging.In this study,we applied a whole-genome shallow sequencing approach to facilitate differential diagnosis via precise profiling of copy number alterations(CNAs)using minute amounts of DNA extracted from morphologically correlated microdissected tissue samples.Freshly frozen tissue specimens from OF(n=29)and FD(n=28)patients were obtained for analysis.Lesion fibrous tissues and surrounding normal tissues were obtained by laser capture microdissection(LCM),with~30–50 cells(5000–10000µm2)per sample.We found that the rate of recurrent CNAs in OF cases was much higher(44.8%,13 of 29)than that in FD cases(3.6%,1 of 28).Sixty-nine percent(9 of 13)of the CNA-containing OF cases involved segmental amplifications and deletions on Chrs 7 and 12.We also identified eight CNA-associated genes(HILPDA,CALD1,C1GALT1,MICALL2,PHF14,AIMP2,MDM2,and CDK4)with amplified expression,which was consistent with the copy number changes.We further confirmed a jaw lesion with a previous uncertain diagnosis due to its ambiguous morphological features and the absence of GNAS mutation as OF based on the typical Chr 12 amplification pattern in its CNA profile.Moreover,analysis of a set of longitudinal samples collected from an individual with a cellular lesion in suspicion of OF at the first surgery,recurrence and the latest malignant transformation revealed identical CNA patterns at the three time points,suggesting that copy number profiling can be used as an important tool to identify borderline lesions or lesions with malignant potential.Overall,CNA profiling of fibro-osseous lesions can greatly improve differential diagnosis between OF and FD and help predict disease progression.
基金supported,in part,by the Precision Medical Research Program from Ministry of Science and Technology of China(Grant No.YL 2017YFC0908400)National Science and Technology Major Project for Infectious Disease and Funding(Grant No.YL 17-163-12-ZT-005-095-01)+2 种基金Science and Technology Commission in Ministry of National Defense of China(Grant No.YL 17-163-12-ZT-005-095-01)Xinwei Wang was supported by the intramural research program of the Center for Cancer Research,National Cancer Institute of the United StatesJunfang Ji was supported by the Thousand Young Talents Plan of China,National Natural Science Foundation of China(Grant No.81672905)
文摘Introduction Primary liver cancer, the second most common cause of cancer related death worldwide, presents ethnic, etiological, sex, and geographical diversity2 （Figure 1A）. At the histological level, liver cancer includes two major types： hepatocellular carcinoma （HCC, about 80%） and cholangiocarcinoma （CCA, about 15%）. Many etiological factors contribute to HCC development, such as hepatitis B virus （HBV）, hepatitis C virus （HCV）, aflatoxin B1 （AFB1）, alcohol, and metabolic diseases3. By contrast, the major risk factors for CCA are liver flukes （Opisthorchis viverrini and Clonorchis sinensis） and primary sclerosing cholangitis4,
基金supported by Beijing Advanced Innovation Centre for Genomics at Peking University,Key Technologies R&D Program(2016YFC0900100)National Natural Science Foundation of China(81573022,31530036,91742203 and 31601063)
文摘The Cancer Genome Atlas(TCGA) project produced RNA-Seq data for tens of thousands of cancer and non-cancer samples with clinical survival information,providing an unprecedented opportunity for analyzing prognostic genes and their isoforms.In this study,we performed the first large-scale identification of transcriptional isoforms that are specifically associated with patient prognosis,even without gene-level association.These specific isoforms are defined as Transcripts Associated with Patient Prognosis(TAPPs).Although a group of TAPPs are the principal isoforms of their genes with intact functional protein domains,another group of TAPPs lack important protein domains found in their canonical gene isoforms.This dichotomy in the distribution of protein domains may indicate different patterns of TAPPs association with cancer.TAPPs in protein-coding genes,especially those with altered protein domains,are rich in known cancer driver genes.We further identified multiple types of cancer recurrent TAPPs,such as DCAF17-201,providing a new approach for the detection of cancer-associated events.In order to make the wide research community to study prognostic isoforms,we developed a portal named GESUR(http://gesur.cancer-pku.cn/),which illustrates the detailed prognostic characteristics of TAPPs and other isoforms.Overall,our integrated analysis of gene expression and clinical parameters provides a new perspective for understanding the applications of different gene isoforms in tumor progression.
基金supported by the Major Program of the National Natural Science Foundation of China(No.82293630)the Peking University Medicine Fund for the world’s leading discipline or discipline cluster development(No.71003Y3035)+1 种基金the National Key Research and Development Program of China(Nos.2022YFA0103300,2017YFA0104500,and 2016YFC0901603)the State Key Laboratory of Gene Function and Modulation Research and the Beijing Advanced Innovation Center for Genomics(ICG)at Peking University.
文摘Human leukocyte antigen(HLA)disparity between donors and recipients is a key determinant triggering intense alloreactivity,leading to a lethal complication,namely,acute graft-versus-host disease(aGVHD),after allogeneic transplantation.Moreover,aGVHD remains a cause of mortality after HLA-matched allogeneic transplantation.Protocols for HLA-haploidentical hematopoietic cell transplantation(haploHCT)have been established successfully and widely applied,further highlighting the urgency of performing panoramic screening of non-HLA variations correlated with aGVHD.On the basis of our time-consecutive large haploHCT cohort(with a homogenous discovery set and an extended confirmatory set),we first delineated the genetic landscape of 1366 samples to quantitatively model aGVHD risk by assessing the contributions of HLA and non-HLA genes together with clinical factors.In addition to identifying multiple loss-of-function(LoF)risk variations in non-HLA coding genes,our data-driven study revealed that non-HLA genetic variations,independent of HLA disparity,contributed the most to the occurrence of aGVHD.This unexpected major effect was verified in an independent cohort that received HLA-identical sibling HCT.Subsequent functional experiments further revealed the roles of a representative non-HLA LoF gene and LoF gene pair in regulating the alloreactivity of primary human T cells.Our findings highlight the importance of non-HLA genetic risk in the new era of transplantation and propose a new direction to explore the immunogenetic mechanism of alloreactivity and to optimize donor selection strategies for allogeneic transplantation.
基金supported by the Key R&D Program of Zhejiang(2024SSYS0022)the National Natural Science Foundation of China(31930028,91842301,32370608,32250710678,32200073,32250710678)+4 种基金Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang(2021R01012)“Pioneer”R&D programs of Zhejiang Province(2024C03005)STI2030-Major Projects(2021ZD0202502)the National Key Research and Development Program of China(2022YFC3400400,2018YFA0800503,2018YFA0107804)Beijing Municipal Science and Technology Commission(Z221100007022002).
文摘The applications of single-cell and spatial technologies in recent times have revolutionized the present understanding of cellular states and the cellular heterogeneity inherent in complex biological systems.These advancements offer unprecedented resolution in the examination of the functional genomics of individual cells and their spatial context within tissues.In this review,we have comprehensively discussed the historical development and recent progress in the field of single-cell and spatial genomics.We have reviewed the breakthroughs in single-cell multi-omics technologies,spatial genomics methods,and the computational strategies employed toward the analyses of singlecell atlas data.Furthermore,we have highlighted the advances made in constructing cellular atlases and their clinical applications,particularly in the context of disease.Finally,we have discussed the emerging trends,challenges,and opportunities in this rapidly evolving field.
基金supported by funding from the National Key Research and Development Program of China(2023YFF1204700)the National Natural Science Foundation of China(L2424217,92459001,and 92259205).
文摘T-cell metabolism plays a pivotal role in defining T-cell functional states.Through analysis of a comprehensive pancancer single-cell transcriptional atlas,we identified SARDH,an enzyme involved in one-carbon(1-C)metabolism,as a potential T-cell metabolic checkpoint.SARDH significantly impacts T-cell fate and function,leading to impaired tumor control efficacy.Knocking down SARDH resulted in sarcosine accumulation and reduced consumption of S-adenosylmethionine(SAM),a critical methyl donor for epigenetic modulation,likely due to the shift in glycine-to-sarcosine homeostasis.Deletion of SARDH increased H3K79me2 modification at NF-κB-activating genes,thereby augmenting NF-κB signaling and T-cell function.Additionally,we observed transcriptional dysregulation of 1-C metabolism within tumors across various cancer types,which was often accompanied by increased sarcosine levels.Sarcosine was found to induce SARDH upregulation,suggesting a feedback mechanism for metabolic homeostasis in T cells within tumors.These findings underscore the potential effects and mechanism of targeting 1-C metabolism,particularly SARDH,as an avenue for cancer therapy.
基金supported by the National Natural Science Foundation of China(62125504,61827825,62205288)China Postdoctoral Science Foundation(2021TQ0275,2022M712734)。
文摘This article reviews recent super-resolution(SR)optical imaging techniques for cellular study,encompassing structured illumination microscopy(SIM),point-scanning super-resolution(PS-SR)microscopy,single-molecule localization microscopy(SMLM),mathematical and deep learning(DL)SR algorithms.Historically,the resolution of traditional far-field optical imaging was constrained by the diffraction limit.The emergence of SR imaging techniques and image processing algorithms has propelled biological research into nanoscale realm.SIM enhances resolution by manipulating spatial frequency content,effectively doubling the resolution capacity of traditional microscopy.PS-SR imaging,on the other hand,offers superior optical sectioning and a high signal-to-noise ratio.SMLM has achieved a remarkable spatial resolution of approximately 20 nm and supports multi-color,wide-field-of-view(FOV),automated 3D high-throughput imaging,thus broadening the horizons for advanced biomedical investigations.Additionally,both mathematical and DL-based SR algorithms have significantly advanced the conversion of low-resolution images to high-resolution counterparts,extending the capabilities of conventional microscopes.This review underscores the principles,recent developments,and diverse applications of these cutting-edge SR imaging methodologies in biological research.
