Biology subjects

Pan, J.

Publications and source records attributed to Pan, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2020

Machine intelligence identifies soluble TNFa as a therapeutic target for spinal cord injury

Traumatic spinal cord injury (SCI) produces a complex syndrome that is expressed across multiple endpoints ranging from molecular and cellular changes to functional behavioral deficits. Effective therapeutic strategies for CNS injury are therefore likely to manifest multi-factorial effects across a broad range of biological and functional outcome measures. Thus, multivariate analytic approaches are needed to capture the linkage between biological and neurobehavioral outcomes. Injury-induced neuroinflammation (NI) presents a particularly challenging therapeutic target, since NI is involved in both degeneration and repair1,2. Here, we used big-data integration and large-scale analytics to examine a large dataset of preclinical efficacy tests combining 5 different blinded, fully counter-balanced treatment trials for different acute anti-inflammatory treatments for cervical spinal cord injury in rats. Multi-dimensional discovery, using topological data analysis3 (TDA) and principal components analysis (PCA) revealed that only one showed consistent multidimensional syndromic benefit: intrathecal application of recombinant soluble TNF receptor 1 (sTNFR1), which showed an inverse-U dose response efficacy. Using the optimal acute dose, we showed that clinically-relevant 90 min delayed treatment profoundly affected multiple biological indices of NI in the first 48 hrs after injury, including reduction in pro-inflammatory cytokines and gene expression of a coherent complex of acute inflammatory mediators and receptors. Further, a 90 min delayed bolus dose of sTNFR1 reduced the expression of NI markers in the chronic perilesional spinal cord, and consistently improved neurological function over 6 weeks post SCI. These results provide validation of a novel strategy for precision preclinical drug discovery that is likely to improve translation in the difficult landscape of CNS trauma, and confirm the importance of TNF signaling as a therapeutic target.

neuroscience↗

bioRxiv2020

The PIF1-MIR408-Plantacyanin Repression Cascade Regulates Light Dependent Seed Germination

Light-sensing seed germination is a vital process for the seed plants. A decisive event in light-induced germination is degradation of the central repressor PHYTOCHROME INTERACTING FACTOR1 (PIF1). It is also known that the balance between gibberellic acid (GA) and abscisic acid (ABA) critically controls germination. But the cellular mechanisms linking PIF1 turnover to hormonal rebalancing remain elusive. Here, employing far-red light-induced Arabidopsis seed germination as the experimental system, we identified Plantacyanin (PLC) as an inhibitor of germination, which is a storage vacuole-associated blue copper protein highly expressed in mature seed and rapidly silenced during germination. Molecular analyses showed that PIF1 directly binds to the MIR408 promoter and represses miR408 accumulation, which in turn post-transcriptionally modulates PLC abundance, thus forming the PIF1-MIR408-PLC repression cascade for translating PIF1 turnover to PLC turnover during early germination. Genetic analysis, RNA-sequencing, and hormone quantification revealed that PLC is necessary and sufficient to maintain the PIF1-mediated seed transcriptome and the low-GA-high-ABA state. Furthermore, we found that PLC domain organization and regulation by miR408 are conserved features in seed plants. These results unraveled a cellular mechanism whereby PIF1-relayed external light signals are converted through PLC-based copper mobilization into internal hormonal profiles for controlling seed germination.

plant biology↗

bioRxiv2020

Development of follicular dendritic cells in lymph nodes depends on retinoic acid mediated signaling

Specialized stromal cells occupy and help define B- and T cell domains, which is crucial for proper functioning of our immune system. Signaling through lymphotoxin and TNF-receptors is crucial for development of different stromal subsets which are thought to arise from a common precursor. However, mechanisms that control the selective generation of the different stromal phenotypes are not known. Here we show that in mice, retinoic acid mediated signaling is important for the differentiation of precursors towards the Cxcl13pos follicular dendritic cell (FDC) lineage, while blocking lymphotoxin mediated Ccl19pos fibroblastic reticular cell (FRC) lineage differentiation. Consequently, we see at day of birth Cxcl13posCcl19neg/low and Cxcl13neg/lowCcl19pos cells within neonatal lymph nodes. Furthermore, ablation of retinoic acid receptor signaling in stromal precursors early after birth reduces Cxcl13 expression, while in addition, complete blockade of retinoic acid signaling prevents formation of FDC networks in lymph nodes.

immunology↗

bioRxiv2020

HBV pgRNA can generate a circRNA with two junction sites

To verify whether Hepatitis B virus (HBV) can form circRNA, the circRNA sequencing results of the HBV-positive HepG 2.2.15 hepatocarcinoma cell line were compared with the HBV genome. A novel circRNA, named as HBV_circ_1, was mapped to the 489-2985 nt region of the HBV genome (GenBank accession No. KU668446.1), which was derived from HBV pgRNA and has two junction sites. A partial fragment of the pgRNA (corresponding to HBV DNA genome 489-3,182-2,985nt) was resected and then connected to form a junction site of HBV_circ_1 (corresponding to HBV DNA genome 489/2985nt). The 5-terminal region (corresponding to HBV DNA genome 1,820-1,932nt) of pgRNA was repeated with the region of pgRNA at the 3-terminal region. Another junction site of HBV_circ_1 (corresponding to HBV DNA genome 1820nt) was formed in a manner similar to DNA homologous recombination mediated by repeats of pgRNA. Moreover, this RNA homologous recombination mediated by the repeats of pgRNA does not have tissue specificity and genus specificity. Reverse transcription PCR, northern blotting, and tissue in situ hybridization confirmed the existence of HBV_circ_1 in HepG2.2.15 cells and HBV related hepatocellular carcinoma (HCC) tissue. This study expands our understanding of circRNA generation mechanisms, and provide a new perspective for understanding the molecular pathogenesis of the virus.

molecular biology↗

bioRxiv2020

Functional Exploration of Heterotrimeric Kinesin-II in IFT and Ciliary Length Control in Chlamydomonas

Heterotrimeric organization of kinesin-II is essential for its function in anterograde IFT in ciliogenesis. However, the molecular basis of forming this complex for its function is not well understood. In addition, the anterograde IFT velocity varies significantly in different organisms, but how motor speed affects ciliary length is not clear. We show that Chlamydomonas kinesin-II (CrKinesin-II) involves distinct mechanisms from mammals and C. elegans in its assembly to necessitate its function in IFT. Furthermore, chimeric CrKinesin-II with human kinesin-II motor domains functioned in vitro and in vivo, leading to a ~2.8-fold reduced anterograde IFT velocity and a similar fold reduction in IFT injection rate that supposedly correlates with ciliary assembly activity. However, the ciliary length was only mildly reduced (~15%). Modelling analyses suggest that such a non-linear scaling relationship between IFT velocity and ciliary length can be accounted for by limitation of the motors and/or its ciliary cargoes, e.g. tubulin.

cell biology↗

bioRxiv2020

Single-cell analysis supports a luminal-neuroendocrine transdifferentiation in human prostate cancer

Neuroendocrine prostate cancer is one of the most aggressive subtypes of prostate tumor. Although much progress has been made in understanding the development of neuroendocrine prostate cancer, the cellular architecture associated with neuroendocrine differentiation in human prostate cancer remain incompletely understood. Here, we use single-cell RNA sequencing to profile the transcriptomes of 21,292 cells from needle biopsies of 6 castration-resistant prostate cancers. Our analyses reveal that all neuroendocrine tumor cells display a luminal-like epithelial phenotype. In particular, lineage trajectory analysis suggests that focal neuroendocrine differentiation exclusively originate from luminal-like malignant cells rather than basal compartment. Further tissue microarray analysis validates the generality of the luminal phenotype of neuroendocrine cells. Moreover, we uncover neuroendocrine differentiation-associated gene signatures that may help us to further explore novel intrinsic molecular mechanisms deriving neuroendocrine prostate cancer. In summary, our single-cell study provides direct evidence into the cellular states underlying neuroendocrine transdifferentiation in human prostate cancer.

cancer biology↗

bioRxiv2020

A molecular map of lymph node blood vascular endothelium at single cell resolution

Blood vascular endothelial cells (BECs) control the immune response by regulating immune cell recruitment, metabolite exchange and blood flow in lymphoid tissues. However, the diversity of BEC and their origins during immune angiogenesis remain poorly understood. Here we profile transcriptomes of BEC from mouse peripheral lymph nodes and map key phenotypes to the vasculature. Our analysis identifies multiple novel subsets including a venous population whose gene signature predicts an unexpectedly selective role in myeloid cell (vs lymphocyte) recruitment to the medulla, confirmed by 2 photon videomicroscopy. We define five phenotypes of capillary lining BEC including a capillary resident regenerative population (CRP) that displays stem cell and migratory gene signatures and contributes to homeostatic BEC turnover and to vascular neogenesis after immunization. Trajectory analyses reveal retention of developmental programs along a progression of cellular phenotypes from CRP to mature venous and arterial BEC subsets. Overall, our single cell atlas provides a molecular blueprint of the lymph node blood vasculature and defines subset specialization for immune cell recruitment and vascular homeostasis.

immunology↗

bioRxiv2020

Chemokine receptor 2-targeted molecular imaging in pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive, inflammatory lung disease that is monitored clinically by measures of lung function, without effective molecular markers of disease activity or therapeutic efficacy. Lung immune cells active in the pro-fibrotic process include inflammatory monocyte and interstitial macrophages that express the C-C motif chemokine receptor 2 (CCR2). CCR2+ monocyte lung influx is essential for disease phenotypes in models of fibrosis and identified in lungs from subjects with IPF. Here, we show that our peptide-based radiotracer 64Cu-DOTA-ECL1i identifies CCR2+ inflammatory monocytes and interstitial macrophages in multiple preclinical mouse models of lung fibrosis, using positron emission tomography (PET) imaging. Mice with bleomycin-induced fibrosis treated with blocking antibodies to interleukin-1{beta}, a mediator of fibrosis associated with CCR2+ cell inflammation, or with pirfenidone, an approved anti-fibrotic agent, demonstrated decreased CCR2-dependent interstitial macrophage accumulation and reduced 64Cu-DOTA-ECL1i PET uptake, compared to controls. Lung tissues from patients with fibrotic lung disease demonstrated abundant CCR2+ cells surrounding regions of fibrosis, and an ex vivo tissue-binding assay showed correlation between radiotracer localization and CCR2+ cells. In a phase 0/1 clinical study of 64Cu-DOTA-ECL1i PET, healthy volunteers showed little lung uptake, while subjects with pulmonary fibrosis exhibited increased uptake, notably in zones of subpleural fibrosis, reflecting the distribution of CCR2+ cells in the profibrotic niche. These findings support a pathologic role of inflammatory lung monocytes/macrophages in fibrotic lung disease and the translational use of 64Cu-DOTA-ECL1i PET to track CCR2-specific inflammation for image-guided therapy. One Sentence SummaryPET imaging of CCR2+ cells in lung fibrosis identifies a therapeutic response in mouse models and displays a perifibrotic signal in subjects with IPF.

cell biology↗

bioRxiv2020

An Integrated Systems Biology Approach Identifies the Proteasome as a Critical Host Machinery for ZIKV and DENV Replication

The Zika (ZIKV) and dengue (DENV) flaviviruses exhibit similar replicative processes but distinct clinical outcomes. A systematic understanding of virus-host protein-protein interaction networks can reveal cellular pathways critical to viral replication and disease pathogenesis. Here we employed three independent systems biology approaches toward this goal. First, protein array analysis of direct interactions between individual ZIKV/DENV viral proteins and 20,240 human proteins revealed multiple conserved cellular pathways and protein complexes, including proteasome complexes. Second, an RNAi screen of 10,415 druggable genes to identify host proteins required for ZIKV infection uncovered proteasome proteins. Third, a high-throughput screening of 6,016 bioactive compounds for ZIKV inhibitors yielded 134 effective compounds, including six proteasome inhibitors that suppress both ZIKV and DENV replication. Integrative analyses of these orthogonal datasets pinpoints proteasome as critical host machinery for ZIKV/DENV replication. Our study provides multi-omics datasets for further studies of flavivirus-host interactions, disease pathogenesis, and new drug targets.

microbiology↗

bioRxiv2020

Continuous detection of glucose and insulin in live animals

Real-time biosensors that can continuously measure circulating biomolecules in vivo would provide valuable insights into a patients health status and their response to therapeutics even when there is considerable variability in pharmacokinetics and pharmacodynamics across patient populations. Unfortunately, current real-time biosensors are limited to a handful of analytes (e.g. glucose and blood oxygen) and are limited in sensitivity (high nanomolar). In this work, we describe a general approach for continuously and simultaneously measuring multiple analytes with picomolar sensitivity and sub-second temporal resolution. As exemplars, we report the simultaneous detection of glucose and insulin at picomolar concentrations in live diabetic rats. Using our system, we demonstrate the capacity to resolve inter-individual differences in the pharmacokinetic responses to insulin and discriminate profiles from different insulin formulations at a high temporal resolution. Critically, our approach is general and could be readily modified to continuously and simultaneously measure other circulating analytes in vivo by swapping the affinity reagents, thus making it a versatile tool for biomedical research.

bioengineering↗

bioRxiv2020

Dual Proteome-scale Networks Reveal Cell-specific Remodeling of the Human Interactome

Thousands of interactions assemble proteins into modules that impart spatial and functional organization to the cellular proteome. Through affinity-purification mass spectrometry, we have created two proteome-scale, cell-line-specific interaction networks. The first, BioPlex 3.0, results from affinity purification of 10,128 human proteins - half the proteome - in 293T cells and includes 118,162 interactions among 14,586 proteins; the second results from 5,522 immunoprecipitations in HCT116 cells. These networks model the interactome at unprecedented scale, encoding protein function, localization, and complex membership. Their comparison validates thousands of interactions and reveals extensive customization of each network. While shared interactions reside in core complexes and involve essential proteins, cell-specific interactions bridge conserved complexes, likely rewiring each cells interactome. Interactions are gained and lost in tandem among proteins of shared function as the proteome remodels to produce each cells phenotype. Viewable interactively online through BioPlexExplorer, these networks define principles of proteome organization and enable unknown protein characterization.

systems biology↗

bioRxiv2020

A single-cell transcriptional roadmap of the mouse and human lymph node lymphatic vasculature

Single-cell transcriptomics promises to revolutionize our understanding of the vasculature. Emerging computational methods applied to high dimensional single cell data allow integration of results between samples and species, and illuminate the diversity and underlying developmental and architectural organization of cell populations. Here, we illustrate these methods in analysis of mouse lymph node (LN) lymphatic endothelial cells (LEC) at single cell resolution. Clustering identifies five well-delineated subsets, including two medullary sinus subsets not recognized previously as distinct. Nearest neighbor alignments in trajectory space position the major subsets in a sequence that recapitulates known and suggests novel features of LN lymphatic organization, providing a transcriptional map of the lymphatic endothelial niches and of the transitions between them. Differences in gene expression reveal specialized programs for (1) subcapsular ceiling endothelial interactions with the capsule connective tissue and cells, (2) subcapsular floor regulation of lymph borne cell entry into the LN parenchyma and antigen presentation, and (3) medullary subset specialization for pathogen interactions and LN remodeling. LEC of the subcapsular sinus floor and medulla, which represent major sites of cell entry and exit from the LN parenchyma respectively, respond robustly to oxazolone inflammation challenge with enriched signaling pathways that converge on both innate and adaptive immune responses. Integration of mouse and human single-cell profiles reveals a conserved cross-species pattern of lymphatic vascular niches and gene expression, as well as specialized human subsets and genes unique to each species. The examples provided demonstrate the power of single-cell analysis in elucidating endothelial cell heterogeneity, vascular organization and endothelial cell responses. We discuss the findings from the perspective of LEC functions in relation to niche formations in the unique stromal and highly immunological environment of the LN. Highlights Computational alignments ("trajectories") predict LN LEC organization in situ, revealing a continuum of phenotypes punctuated by specialized clusters Multiple intermediate phenotypes suggest LEC malleability Gene profiles define niche-specific functional specialization Medullary sinus LECs are comprised of Ptx3-LECs and Marco-LECs O_LIDistinct mechanisms for pathogen interactions and matrix modeling C_LIO_LIPtx3-LECs: paracortical and central medullary sinuses near hilus; enriched for genes driving lymphangiogenic responses and lymphocyte egress C_LIO_LIMarco-LECs: peri-follicular medullary sinuses; macrophage-associated genes, complement and coagulation cascade C_LI Niche-specific responses to inflammation O_LIIFN gene responses in SCS floor and medullary sinus LECs C_LIO_LISuppression of LEC identity genes in responding subsets C_LI Conserved and unique LEC subsets and gene programs across species O_LICore subsets common to mouse and human C_LIO_LIGreater diversity of subsets and intermediates in human LN LECs C_LI

systems biology↗

bioRxiv2019

FLS2 is a CDK-like kinase that directly binds IFT70 and is required for proper ciliary disassembly in Chlamydomonas

Intraflagellar transport (IFT) is required for ciliary assembly and maintenance. While disruption of IFT may trigger ciliary disassembly, we show here that IFT mediated transport of a CDK-like kinase ensures proper ciliary disassembly. Mutations in flagellar shortening 2 (FLS2), encoding a CDK-like kinase, lead to retardation of cilia resorption and delay of cell cycle progression. Stimulation for ciliary disassembly induces gradual dephosphorylation of FLS2 accompanied with gradual inactivation. Loss of FLS2 or its kinase activity induces early onset of kinesin13 phosphorylation in cilia. FLS2 is predominantly localized in the cell body, however, it is transported to cilia upon induction of ciliary disassembly. FLS2 directly interacts with IFT70 and loss of this interaction inhibits its ciliary transport, leading to dysregulation of kinesin13 phosphorylation and retardation of ciliary disassembly. Thus, this work demonstrates that IFT plays active roles in controlling proper ciliary disassembly by transporting a protein kinase to cilia to regulate a microtubule depolymerizer. Author SummaryCilia or eukaryotic flagella are cellular surface protrusions that function in cell motility as well as sensing. They are dynamic structures that undergo assembly and disassembly. Cilia are resorbed during cell cycle progression. Dysregulation of cilia resorption may cause delay of cell cycle progression, which underlies aberrant cell differentiation and even cancer. Ciliary resorption requires depolmerization of axonemal microtubules that is mediated by kinesin13. Using the unicellular green alga, Chlamydomonas, we have identified a CDK-like kinase FLS2 that when mutated retards cilia resorption, leading to delay of cell cycle progression. FLS2, a cell body protein, is transported to cilia via intraflagellar transport upon induction of cilia resorption. FLS2 directly interacts with IFT70 and loss of this interaction inhibits transport of FLS2 to cilia and fails to regulate proper phosphorylation of kinesin13 in cilia.

cell biology↗

bioRxiv2019

The socioeconomic burden of severe mental disorder in China, 2014-2017: a prevalence study

Mental illness is a chronic disease with high morbidity and mortality rate, resulting in heavy economic burden for family and society, especially the severe ones. Chinese government has taken a series of action on the treatment and management of severe mental disorder (SMD), but the scale of economic burden caused by SMD was still unclear. In this paper, we applied prevalence-based bottom-up approach to estimate the direct and indirect economic burden of SMD in Southwest China from 2014 to 2017. We used the sampled inpatient medical record data of patient with SMD to calculate the total direct cost and estimated the indirect economic burden using human capital approach.The total ecomonic burden of SMD was USD9,733 million and direct burden was contiributed for 7.5% as USD734.5 million in four years total. The growth rate of direct medical cost was declined due to the health policy reform and total cost control policy. The indirect cost was rapidly increased in four years when estimated with DALYs reported in GBD2010 and resulting USD8,998.6 million. We next estimated the indirect burden using sample DALYs and occupation wage cost approach as sensitive analysis. We found that the indirect burden was sensitive to the key variable and the estimation approach, but the estimates share same increasing trend but with different velocity. Our study suggests that SMD in China have posed substantial economic burden at individual and social levels, with the appropriate estimation of total economic burden, our reaserch would attract more attention and be helpful for health resources distribution.

scientific communication and education↗

bioRxiv2019

Highly diverse Asgard archaea participate in organic matter degradation in coastal sediments

Asgard is an archaeal superphylum that might hold the key to understand the origin of eukaryotes, but its diversity and ecological roles remain poorly understood. Here, we reconstructed 15 metagenomic-assembled genomes (MAGs) from coastal sediments covering most known Asgard archaea and a novel group, which is proposed as a new Asgard phylum named as the "Gerdarchaeota". Genomic analyses predict that Gerdarchaeota are facultative anaerobes in utilizing both organic and inorganic carbon. Unlike their closest relatives Heimdallarchaeota, Gerdarchaeota have genes encoding for cellulase and enzymes involving in the tetrahydromethanopterin-based Wood-Ljungdahl pathway. Transcriptomic evidence showed that all known Asgard archaea are capable of degrading organic matter, including peptides, amino acids and fatty acids, in different ecological niches in sediments. Overall, this study broadens the diversity of the mysterious Asgard archaea and provides evidence for their ecological roles in coastal sediments.

microbiology↗

bioRxiv2019

α-synuclein aggregates induce c-Abl activation and neurodegeneration by a redox stress mechanism

ObjectiveRedox stress, c-Abl activation, and -synuclein aggregates each independently contribute to neurodegeneration in Parkinsons disease. Interactions between these factors may underlie convergent and feed-forward mechanisms of disease progression. Methods-synuclein aggregate formation was induced in neuronal cultures and mouse substantia nigra by exposure to pre-formed human -synuclein fibrils or by AAV-mediated over-expression of -synuclein. Aggregate formation, c-Abl activation, redox stress, and neurodegeneration were evaluated by immunohistochemistry and Western blots, and mouse motor function was evaluated using the rota-rod and pole tests. To suppress redox stress, cultures and mice were treated with N-acetyl cysteine, a thiol repletion agent that supports neuronal glutathione metabolism. ResultsIn primary neuron cultures, the formation of -synuclein aggregates led to redox stress and c-Abl activation. Redox stress alone, in the absence of -synuclein aggregates, was also sufficient to induced c-Abl activation. N-acetyl cysteine suppressed redox stress, and likewise suppressed both c-Abl activation and -synuclein aggregation. A similar pattern was observed in the two mouse models of Parkinsons disease. In both models, -synuclein aggregates in the substantia nigra were accompanied by redox stress, c-Abl activation, dopaminergic neurodegeneration and motor impairment, all of which were attenuated in mice treated with oral N-acetyl cysteine. InterpretationThese results indicate that -synuclein aggregates induce c-Abl activation by a redox stress mechanism. c-Abl in turn promotes -synuclein aggregation, and this potentially feed-forward process can be blocked by N-acetyl cysteine. The findings thus add mechanistic support for N-acetyl cysteine as a therapeutic for Parkinsons disease.

neuroscience↗

bioRxiv2019

Lineage-Specific Epigenomic and Genomic Activation of the Oncogene HNF4A Promotes Gastrointestinal Adenocarcinomas

BackgroundsGastrointestinal adenocarcinomas (GIACs) of the tubular GI tract including esophagus, stomach, colon and rectum comprise most GI cancers and share a spectrum of genomic features. However, the unified epigenomic changes specific to GIACs are less well-characterized.We applied mathematical algorithms to large-scale DNA methylome and transcriptome profiles to reconstruct transcription factor (TF) networks using 907 GIAC samples from The Cancer Genome Atlas (TCGA). Complementary epigenomic technologies were performed to investigate HNF4A activation, including Circularized Chromosome Conformation Capture (4C), Chromatin immunoprecipitation (ChIP) sequencing, Whole Genome Bisulfite Sequencing (WGBS), and Assay for Transposase-Accessible Chromatin (ATAC) sequencing. In vitro and in vivo cellular phenotypical assays were conducted to study HNF4A functions.\n\nResultsWe identified a list of functionally hyperactive master regulator (MR)TFs shared across different GIACs. As the top candidate, HNF4A exhibited prominent genomic and epigenomic activation in a GIAC-specific manner. We further characterized a complex interplay between HNF4A promoter and three distal enhancer elements, which was coordinated by GIAC-specific MRTFs including ELF3, GATA4, GATA6 and KLF5. HNF4A also self-regulated its own promoter and enhancers. Functionally, HNF4A promoted cancer proliferation and survival by transcriptionally activating many downstream targets including HNF1A and factors of Interleukin signaling in a lineage-specific manner.\n\nConclusionWe use a large cohort of patient samples and an unbiased mathematical approach to highlight lineage-specific oncogenic MRTFs, which provide new insights into the GIAC-specific gene regulatory networks, and identify potential therapeutic strategies against these common cancers.

cancer biology↗

bioRxiv2019

The usage of six human IGHJ genes follows a particular nonrandom selection: The recombination signal sequence affects the usage frequency of six human IGHJ genes

The formation of the B cell receptor (BCR) heavy chain variable region is derived from the germline V(D)J gene rearrangement according to the \"12/23\" rule and the \"beyond 12/23\" rule. The usage frequency of each V(D)J gene in the peripheral BCR repertoires is related to the initial recombination, self-tolerance selection, and the clonal proliferative response. However, their specific differences and possible mechanisms are still unknown. We analyzed in-frame and out-of-frame BCR-H repertoires from human samples with physiological and various pathological conditions by high-throughput sequencing. Our results showed that IGHJ gene frequency follows a similar pattern where IGHJ4 is used at high frequency (>40%), IGHJ6/IGHJ3/IGHJ5 is used at medium frequencies (10%[~]20%), and IGH2/IGHJ1 is used at low frequency (<4%) under whether physiological or various pathological conditions. Furthermore, analysis of the recombination signal sequences suggested that the conserved nonamer and heptamer and certain 23 bp spacer length may affect the initial IGHD-IGHJ recombination, which results in different frequencies of IGHJ genes among the initial BCR-H repertoire. Based on this \"background repertoire\", we recommend that re-evaluation and further investigation are needed when analyzing the significance and mechanism of IGHJ gene frequency in self-tolerance selection and the clonal proliferative response.

genomics↗