The characterization of the human T-cell receptor （TCR） repertoire has made remarkable progress, with most of the work focusing on the TCRβ chains. Here, we ana- lyzed the diversity and complexity of both the TCRa ...The characterization of the human T-cell receptor （TCR） repertoire has made remarkable progress, with most of the work focusing on the TCRβ chains. Here, we ana- lyzed the diversity and complexity of both the TCRa and TCRβ repertoires of three healthy donors. We found that the diversity of the TCRα repertoire is higher than that of the TCRβ repertoire, whereas the usages of the V and J genes tended to be preferential with similar TRAV and TRAJ patterns in all three donors. The V-J pairings, like the V and J gene usages, were slightly preferential. We also found that the TRDV1 gene rearranges with the majority of TRAJ genes, suggesting that TRDV1 is a shared TRAV/DV gene （TRAV42/DV1）. Moreover, we uncovered the presence of tandem TRBD （TRB D gene） usage in -2% of the productive human TCRβ CDR3 sequences.展开更多
Chronic human immunodeficiency virus(HIV) infection not only causes a gradual loss of CD4~+T cells but also leads to a disturbance of the T cell receptor(TCR) repertoire. In people living with HIV(PLWH), monitoring TC...Chronic human immunodeficiency virus(HIV) infection not only causes a gradual loss of CD4~+T cells but also leads to a disturbance of the T cell receptor(TCR) repertoire. In people living with HIV(PLWH), monitoring TCR repertoire is challenged by the inconsistency of complementarity determining region 3(CDR3) and limited cell numbers in clinical samples. Thus, a quantitative method is necessary for monitoring the TCR repertoire in PLWH.We characterized the TCR V-J pairing profile of na?ve and memory CD4~+T cells in healthy donors, HIV-infected antiretroviral therapy(ART)-na?ve patients and long-term(over5 years) ART-experienced patients by performing TCR sequencing. We developed a V-J index with 18 parameters which were subdivided into five categories(expression coverage, cumulative percentage of the top tenth percentile, diversity, intra-individual similarity and inter-individual similarity). In ART-na?ve patients, 14 of the 18 parameters were significantly altered.Long-term ART recovered ten parameters. The four unrecovered parameters were related to inter-individual similarity.Therefore, these findings indicate that long-term ART could only partially recover TCR V-J pairs and introduce newly impacted V-J pairs. Moreover, these results provide new insights into the V-J pairing of the TCR and into the disturbance of TCR repertoire in HIV infection.展开更多
DNA double-strand breaks （DSBs） are introduced in cells by ionizing radiation and reactive oxygen species. In addition, they are commonly generated during V（D）J recombination, an essential aspect of the developing...DNA double-strand breaks （DSBs） are introduced in cells by ionizing radiation and reactive oxygen species. In addition, they are commonly generated during V（D）J recombination, an essential aspect of the developing immune system. Failure to effectively repair these DSBs can result in chromosome breakage, cell death, onset of cancer, and defects in the immune system of higher vertebrates. Fortunately, all mammalian cells possess two enzymatic pathways that mediate the repair of DSBs： homologous recombination and non-homologous end-joining （NHEJ）. The NHEJ process utilizes enzymes that capture both ends of the broken DNA molecule, bring them together in a synaptic DNA-protein complex, and finally repair the DNA break. In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented.展开更多
Cullin-RING ligases(CRLs)comprise a large group of modular eukaryotic E3 ubiquitin ligases.Within this family,the CRL4 ligase(consisting of the Cullin4[CUL4]scaffold protein,the Rbxl RING finger domain protein,the DNA...Cullin-RING ligases(CRLs)comprise a large group of modular eukaryotic E3 ubiquitin ligases.Within this family,the CRL4 ligase(consisting of the Cullin4[CUL4]scaffold protein,the Rbxl RING finger domain protein,the DNA damage-binding protein 1[DDB1],and one of many DDBl-associated substrate receptor proteins)has been intensively studied in recent years due to its involvement in regulating various cellular processes,its role in cancer development and progression,and its subversion by viral accessory proteins.Initially discovered as a target for hijacking by the human immunodeficiency virus accessory protein r,the normal targets and function of the CRL4 substrate receptor protein DDBl-Cul4-associated factor 1(DCAF1;also known as VprBP)had remained elusive,but newer studies have begun to shed light on these questions.Here,we review recent progress in understanding the diverse physiological roles of this DCAF1 in supporting various general and cell type-specific cellular processes in its context with the CRL4 E3 ligase,as well as another HECT-type E3 ligase with which DCAF1 also associates,called EDD/UBR5.We also discuss emerging questions and areas of future study to uncover the dynamic roles of DCAF1 in normal physiology.展开更多
基金We thank Dr. Christopher J. Vavrickafor and Boris Tefsen for their critical reading and revision of the manuscript and Dr. Miles P. Dav- enport for his inspiring discussions. This work is supported by the National Natural Science Foundation of China （NSFC, Grant No. 31030030）, the National Basic Research Program （973 Program） （No. 2013CB531500） and the National Natural Science Foundation of China （Grant No. 81373141 ）. G.F.G. is a leading principal investigator of the NSFC Innovative Research Group （Grant No. 81321063）.
文摘The characterization of the human T-cell receptor （TCR） repertoire has made remarkable progress, with most of the work focusing on the TCRβ chains. Here, we ana- lyzed the diversity and complexity of both the TCRa and TCRβ repertoires of three healthy donors. We found that the diversity of the TCRα repertoire is higher than that of the TCRβ repertoire, whereas the usages of the V and J genes tended to be preferential with similar TRAV and TRAJ patterns in all three donors. The V-J pairings, like the V and J gene usages, were slightly preferential. We also found that the TRDV1 gene rearranges with the majority of TRAJ genes, suggesting that TRDV1 is a shared TRAV/DV gene （TRAV42/DV1）. Moreover, we uncovered the presence of tandem TRBD （TRB D gene） usage in -2% of the productive human TCRβ CDR3 sequences.
基金supported by the National Natural Science Foundation of China(81371804,81772123 and 81672000)the Thirteen-fifth Key Project(2018ZX10715-005)+1 种基金Beijing Municipal Science and Technology Commission(Z191100006619045)Beijing Hospital authority(DFL20191801 and DFL20191802)。
文摘Chronic human immunodeficiency virus(HIV) infection not only causes a gradual loss of CD4~+T cells but also leads to a disturbance of the T cell receptor(TCR) repertoire. In people living with HIV(PLWH), monitoring TCR repertoire is challenged by the inconsistency of complementarity determining region 3(CDR3) and limited cell numbers in clinical samples. Thus, a quantitative method is necessary for monitoring the TCR repertoire in PLWH.We characterized the TCR V-J pairing profile of na?ve and memory CD4~+T cells in healthy donors, HIV-infected antiretroviral therapy(ART)-na?ve patients and long-term(over5 years) ART-experienced patients by performing TCR sequencing. We developed a V-J index with 18 parameters which were subdivided into five categories(expression coverage, cumulative percentage of the top tenth percentile, diversity, intra-individual similarity and inter-individual similarity). In ART-na?ve patients, 14 of the 18 parameters were significantly altered.Long-term ART recovered ten parameters. The four unrecovered parameters were related to inter-individual similarity.Therefore, these findings indicate that long-term ART could only partially recover TCR V-J pairs and introduce newly impacted V-J pairs. Moreover, these results provide new insights into the V-J pairing of the TCR and into the disturbance of TCR repertoire in HIV infection.
文摘DNA double-strand breaks （DSBs） are introduced in cells by ionizing radiation and reactive oxygen species. In addition, they are commonly generated during V（D）J recombination, an essential aspect of the developing immune system. Failure to effectively repair these DSBs can result in chromosome breakage, cell death, onset of cancer, and defects in the immune system of higher vertebrates. Fortunately, all mammalian cells possess two enzymatic pathways that mediate the repair of DSBs： homologous recombination and non-homologous end-joining （NHEJ）. The NHEJ process utilizes enzymes that capture both ends of the broken DNA molecule, bring them together in a synaptic DNA-protein complex, and finally repair the DNA break. In this review, all the known enzymes that play a role in the NHEJ process are discussed and a working model for the co-operation of these enzymes during DSB repair is presented.
文摘Cullin-RING ligases(CRLs)comprise a large group of modular eukaryotic E3 ubiquitin ligases.Within this family,the CRL4 ligase(consisting of the Cullin4[CUL4]scaffold protein,the Rbxl RING finger domain protein,the DNA damage-binding protein 1[DDB1],and one of many DDBl-associated substrate receptor proteins)has been intensively studied in recent years due to its involvement in regulating various cellular processes,its role in cancer development and progression,and its subversion by viral accessory proteins.Initially discovered as a target for hijacking by the human immunodeficiency virus accessory protein r,the normal targets and function of the CRL4 substrate receptor protein DDBl-Cul4-associated factor 1(DCAF1;also known as VprBP)had remained elusive,but newer studies have begun to shed light on these questions.Here,we review recent progress in understanding the diverse physiological roles of this DCAF1 in supporting various general and cell type-specific cellular processes in its context with the CRL4 E3 ligase,as well as another HECT-type E3 ligase with which DCAF1 also associates,called EDD/UBR5.We also discuss emerging questions and areas of future study to uncover the dynamic roles of DCAF1 in normal physiology.
