Biology subjects

Fang, H.

Publications and source records attributed to Fang, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

A Watershed Algorithm GUI for Personalized fMRI-guided rTMS Target

Personalized repetitive transcranial magnetic stimulation (rTMS) increasingly relies on resting-state functional magnetic resonance imaging (fMRI) to select stimulation sites, yet most pipelines depend on user-defined thresholds and atlas masks, which can shift individualized targets. We propose a watershed-based approach, implemented in a graphical user interface, that performs threshold-independent segmentation of functional images to support rTMS target localization. As a proof-of-concept, we focused on Alzheimers disease-related circuits within the default mode network, designating the posterior cingulate cortex (PCC) as the deep effective region and the inferior parietal lobule (IPL) as the superficial stimulation target. In a cohort of 21 healthy participants, quantitative comparison with a conventional threshold-based, mask-constrained peak strategy revealed high concordance for PCC peaks but a median spatial displacement of 6.0 mm (95% CI: 0.0-12.7 mm) for IPL targets. Qualitative examples further illustrate that watershed segmentation reduces bias from neighboring functional clusters, truncation by atlas boundaries, and ambiguity among multiple local peaks. By decoupling target definition from user-chosen thresholds and packaging the method in an accessible toolbox, this framework offers a generalizable tool for individualized fMRI-guided rTMS.

neuroscience↗

bioRxiv2024

CD4+ tissue resident memory Th17 cells drive IL-17A-mediated joint pathology in Spondyloarthritis

ObjectivesInterleukin (IL)-17A is a key driver of Spondyloarthritis (SpA) joint pathology. We aimed to identify its cellular source in synovial tissue from patients with two forms of SpA namely Axial SpA (AxSpA) and Psoriatic arthritis (PsA). MethodsSynovial tissue from patients with SpA was profiled using single-cell RNA sequencing (scRNA-seq: AxSpA, n=5 and PsA, n=6) or spatial RNA profiling (PsA, n=4). CellPhoneDB was used to infer cell-cell communication. Tissue resident memory Th17 (TRM17)-like cells were generated in vitro using blood memory CD4+ T cells from SpA patients. An epigenetic inhibitor library, siRNA and clustered regularly interspaced short palindromic repeats (CRISPR) were used to identify epigenetic regulator(s) for TRM17. ResultsscRNA-seq showed that CD4+CXCR6+ TRM17 cells are the predominant spontaneous IL17A producers in SpA synovium. Cell-cell communication and single-cell spatial analysis support the interaction between TRM17 and CLEC10A+ dendritic cells, which were activated in SpA. Both sublining and lining fibroblasts in SpA synovium showed evidence of IL-17A activation. In vitro-generated CD4+ TRM17-like cells phenocopied joint tissue TRM17, producing IL-17A/F upon T cell receptor (TCR) stimulation, which was further enhanced by cytokines. Perturbation of BRD1 inhibited the generation of TRM17-like cells. ConclusionsCD4+ TRM17 cells are the predominant source of IL-17A in SpA synovial tissue. TCR stimulation is essential for the secretion of IL-17A by CD4+TRM17-like cells. The epigenetic regulator BRD1 contributes to the generation of CD4+TRM17. Depleting CD4+TRM17 cells in SpA is thus a therapeutic strategy with potential to induce long-term remission. Key messagesO_ST_ABSWhat is already known on this topicC_ST_ABSInterleukin (IL)-17A plays a key role in the immunopathogenesis of Spondyloarthritis (SpA), but its cellular source in joint tissue has not been determined previously. The induction and accumulation of CD4+ tissue resident memory Th17 (TRM17) cells following the clearance of pathogens has been described in skin, lung and kidney. Whether CD4+ TRM17 cells also accumulate in the joint and contribute to the pathology of SpA is not clear. What this study addsO_LICD4+ TRM17 cells are present in SpA synovial tissue and are the predominant source of IL17A C_LIO_LICD4+ TRM17 cells in SpA joints express IL17A without any in vitro exogenous stimulation C_LIO_LIT cell receptor (TCR) rather than cytokine stimulation is essential for IL-17A production by CD4+ TRM17-like cells C_LIO_LIThe epigenetic regulator BRD1 contributes to the generation of CD4+ TRM17-like cells. C_LI How this study might affect research, practice or policyOur findings identify CD4+ TRM17 cells as the primary source of IL-17A in SpA synovium, a previously unrecognized role for these cells. Key questions remain: How do CD4+ TRM17 cells relate to IL-17A producers in synovial fluid? What mechanisms induce and maintain them in the joint? How do they interact with other cells to promote arthritis? These questions warrant further investigation. In addition, our data suggest that targeting CD4+ TRM17 cells, the "factory" of IL-17A in SpA synovial tissue, has the potential to induce long-term remission, encouraging future efforts to develop new therapies to deplete CD4+ TRM17 cells in SpA.

immunology↗

bioRxiv2024

Suppression of Visceral Nociception by Selective C-Fiber Transmission Block Using Temporal Interference Sinusoidal Stimulation

Chronic visceral pain management remains challenging due to limitations in selective targeting of C-fiber nociceptors. This study investigates temporal interference stimulation (TIS) on dorsal root ganglia (DRG) as a novel approach for selective C-fiber transmission block. We employed (1) GCaMP6 recordings in mouse whole DRG using a flexible, transparent microelectrode array for visualizing L6 DRG neuron activation, (2) ex vivo single-fiber recordings to assess sinusoidal stimulation effects on peripheral nerve axons, (3) in vivo behavioral assessment measuring visceromotor responses (VMR) to colorectal distension in mice, including a TNBS-induced visceral hypersensitivity model, and (4) immunohistological analysis to evaluate immediate immune responses in DRG following TIS. We demonstrated that TIS (2000 Hz and 2020 Hz carrier frequencies) enabled tunable activation of L6 DRG neurons, with the focal region adjustable by altering stimulation amplitude ratios. Low-frequency (20-50 Hz) sinusoidal stimulation effectively blocked C-fiber and A{delta}-fiber transmission while sparing fast-conducting A-fibers, with 20 Hz showing highest efficacy. TIS of L6 DRG reversibly suppressed VMR to colorectal distension in both control and TNBS-induced visceral hypersensitive mice. The blocking effect was fine-tunable by adjusting interfering stimulus signal amplitude ratios. No apparent immediate immune responses were observed in DRG following hours-long TIS. In conclusion, TIS on lumbosacral DRG demonstrates promise as a selective, tunable approach for managing chronic visceral pain by effectively blocking C-fiber transmission. This technique addresses limitations of current neuromodulation methods and offers potential for more targeted relief in chronic visceral pain conditions.

neuroscience↗

bioRxiv2024

STAMBPL1 activates the GRHL3/HIF1A/VEGFA axis through interaction with FOXO1 to promote angiogenesis in triple-negative breast cancer

In the clinic, anti-tumor angiogenesis is commonly employed for treating recurrent, metastatic, drug-resistant triple-negative and advanced breast cancer. Our previous research revealed that the deubiquitinase STAMBPL1 enhances the stability of MKP-1, thereby promoting cisplatin resistance in breast cancer. In this study, we discovered that STAMBPL1 could upregulate the expression of the hypoxia-inducible factor HIF1 in breast cancer cells. Therefore, we investigated whether STAMBPL1 promotes tumor angiogenesis. We demonstrated that STAMBPL1 increased HIF1A transcription in a non-enzymatic manner, thereby activating the HIF1/VEGFA signaling pathway to facilitate TNBC angiogenesis. Through RNA-seq analysis, we identified the transcription factor GRHL3 as a downstream target of STAMBPL1 that is responsible for mediating HIF1A transcription. Furthermore, we discovered that STAMBPL1 regulates GRHL3 transcription by interacting with the transcription factor FOXO1. These findings shed light on the role and mechanism of STAMBPL1 in the pathogenesis of breast cancer, offering novel targets and avenues for the treatment of triple-negative and advanced breast cancer.

cancer biology↗

bioRxiv2024

Self-association enhances early attentional selection through automatic prioritization of socially salient signals

Efficiently processing self-related information is critical for cognition, yet the earliest mechanisms enabling this self-prioritization remain unclear. By combining a temporal order judgement task with computational modelling based on the Theory of Visual Attention (TVA), we show how mere, arbitrary associations with the self can fundamentally alter attentional selection of sensory information into short-term memory/awareness, by enhancing the attentional weights and processing capacity devoted to encoding socially loaded information. This self-prioritization in attentional selection occurs automatically at early perceptual stages but reduces when active social decoding is required. Importantly, the processing benefits obtained from attentional selection via self-relatedness and via physical salience were additive, suggesting that social and perceptual salience captured attention via separate mechanisms. Furthermore, intra-individual correlations revealed an obligatory self-prioritization effect, whereby self-relatedness overpowered the contribution of perceptual salience in guiding attentional selection. Together, our findings provide evidence for the influence of self-relatedness during earlier, automatic stages of attentional section at the gateway to perception, distinct from later post-attentive processing stages.

neuroscience↗

bioRxiv2024

Trait anxiety impairs reciprocity behavior: A multi-modal and computational modeling study

Anxiety significantly impacts reciprocal behavior, crucial for positive social interactions. The neurocomputational mechanisms of anxietys effects on the core (individual propensity) and peripheral (decision context) factors shaping reciprocity remain unclear. Here, we investigated reciprocity in individuals with low and high trait anxiety using a binary trust game with gain/loss framing, combining computational modeling, eye-tracking, and event-related potentials (ERPs). Our computational model, validated by eye-tracking data, identified four psychological components driving reciprocal behavior: reward, guilt aversion, superiority aversion, and superiority attraction. Regarding the core of reciprocity, trait anxiety diminished both overall reciprocity and specific psychological components like guilt aversion and superiority attraction, irrespective of context. The reduction in guilt aversion was supported by ERP findings showing decreased P2 (selective attention) and increased LPP (emotion regulation) amplitudes in anxious individuals. Regarding the periphery of reciprocity, trait anxiety altered the contextual perception of both superiority aversion and reward. Further, trait anxiety reversed the perception of superiority aversion from gain to loss contexts, a pattern that was linked to the N2 amplitudes (cognitive control). Our findings revealed distinct effects of trait anxiety on core and peripheral factors in reciprocity, offering potential targets for interventions aimed at improving reciprocity in individuals with anxiety disorders.

neuroscience↗

bioRxiv2024

Prkra is the double-stranded RNA sensor to mediate an embryonic integrated stress response

Double-stranded RNAs (dsRNAs), known as conserved pathogen-associated molecular patterns, are recognized by interferon-induced protein kinase R (PKR) to trigger an integrated stress response, characterized by the inhibition of global translation. However, the interferon system is inactive in pluripotent cells, thus the mechanism underlying dsRNA sensing and translational control is unclear. In this study, we utilized early zebrafish embryos as a model of pluripotent cells and discovered a PKR-independent blockage of translation initiation induced by dsRNA stimulation. Prkra dimer was identified as the genuine dsRNA sensor. Upon binding to dsRNAs, the dimerized dsRNA binding domain 3 becomes activated to sequester the eIF2 complexes from the translation machinery, leading to a hindrance in global protein synthesis. This distinctive embryonic stress response restricts RNA virus SVCV replication in zebrafish embryos but is also conserved in early mouse embryos and embryonic stem cells. Therefore, the Prkra-mediated dsRNA sensing and translation blocking mechanism potentially represents a common strategy for reestablishing physiological homeostasis in response to environmental stresses.

immunology↗

bioRxiv2024

SlNAP2 promoted fruit ripening by directly binding the ACS2 promoter and interacting with EIL3

The ripening process of tomato fruit is affected by a variety of environmental factors and genetic regulators. NAC transcription factors (TFs) function in a multitude of biological processes, while the current knowledge on the participation of NAC TFs in the regulatory network of fruit ripening is relatively limited. In this study, we isolated a NAC TFs, NAP2, which acts as a positive transcription activator in tomato fruit ripening. We also observed a notable delay in the ripening process of SlNAP2 silenced and knockout mutant fruit. In particular, ethylene production was obviously inhibited in SlNAP2 mutant fruit. Y1H and DLR assays showed that SlNAP2 directly binds to the promoter of SlACS2 and activates its transcriptional activity. Furthermore, SlNAP2 and SlEIL3 physically interaction was demonstrated by yeast two-hybrid (Y2H), luciferase complementation (LUC), bimolecular fluorescence complementation (BiFC) and coimmunoprecipitation analysis (CoIP) assays. Meanwhile, the pigment content, firmness and the transcript levels of genes associated with carotenoid and chlorophyll metabolism and cell wall metabolism were also potentially affected by the SlNAP2 deletion; however, it has remained unclear whether these genes are also directly regulated by SlNAP2. Therefore, our findings indicate that SlNAP2 directly binds to SlACS2 promoter to activate its expression and promote ethylene generation, which in turn interacts with EIL3 to enhance the function of ethylene in tomato fruit ripening. Collectively, our data contribute to understanding the interaction of NAC TFs and ethylene in tomato fruit ripening, thereby enhancing our knowledge of the ripening regulatory network that governs tomato fruit maturation.

biochemistry↗

bioRxiv2024

Discovery and characterization of stereodefined PMO-gapmers targeting tau

Antisense oligonucleotides (ASOs) are an important class of therapeutics to treat genetic diseases, and expansion of this modality to neurodegenerative disorders has been an active area of research. To realize chronic administration of ASO therapeutics to treat neurogenerative diseases, new chemical modifications improving activity and safety profile are still needed. Furthermore, it is highly desirable to develop a single stereopure ASO with defined activity and safety profile to avoid any efficacy and safety concerns due to the batch-to-batch variation in the composition of diastereomers. Herein, a stereopure PMO-gapmer was developed as a new construct to improve safety and stability by installing charge-neutral PMOs at the wing region and by fully controlling phosphorus stereochemistries. The developed stereopure PMO-gapmer construct was applied to the discovery of ASO candidates for the reduction of microtubule-associated protein tau (MAPT, tau). Sequence screening targeting MAPT followed by screening of optimal phosphorus stereochemistry identified stereopure development candidates. While evaluating the stereopure PMO-gapmers, we observed a dramatic difference in safety profile among stereoisomers in which only one phosphorus stereochemistry differs. These results further highlight the benefits of developing stereopure ASOs as safe and well-characterized candidates for clinical studies.

neuroscience↗

bioRxiv2024

MGPfactXMBD: A Model-Based Factorization Method for scRNA Data Unveils Bifurcating Transcriptional Modules Underlying Cell Fate Determination

Manifold-learning is particularly useful to resolve the complex cellular state space from single-cell RNA sequences. While current manifold-learning methods provide insights into cell fate by inferring graph-based trajectory at cell level, challenges remain to retrieve interpretable biology underlying the diverse cellular states. Here, we described MGPfactXMBD, a model-based manifold-learning framework and capable to factorize complex development trajectories into independent bifurcation processes of gene sets, and thus enables trajectory inference based on relevant features. MGPfactXMBD offers more nuanced understanding of the biological processes underlying cellular trajectories with potential determinants. When bench-tested across 239 datasets, MGPfactXMBD showed advantages in major quantity-control metrics, such as branch division accuracy and trajectory topology, outperforming most established methods. In real datasets, MGPfactXMBD recovered the critical pathways and cell types in microglia development with experimentally valid regulons and markers. Furthermore, MGPfactXMBD discovered evolutionary trajectories of tumor-associated CD8+ T cells and yielded new subtypes of CD8+ T cells with gene expression signatures significantly predictive of the responses to immune checkpoint inhibitor in independent cohorts. In summary, MGPfactXMBD offers a manifold-learning framework in scRNA-seq data which enables feature selection for specific biological processes and contributing to advance our understanding of biological determination of cell fate.

bioinformatics↗

bioRxiv2024

Multi-omics discovery of hallmark protein and lipid features of circulating small extracellular vesicles in humans

Extracellular vesicles (EVs) are now being increasingly recognized as an essential signaling entity in human plasma, linking them to health and various diseases. Still, their core protein and lipid componentry, which lie at the center of EV form and function, remain poorly defined. Achieving this unmet milestone remains greatly hindered by abundant non-vesicular extracellular plasma components (non-EVs) in mass spectrometry-based analyses. Here, we performed high-resolution density gradient fractionation of over 140 human plasma samples to isolate circulating EVs, and systematically construct their quantitative proteome (4500 proteins) and lipidome (829 lipids) landscapes. This led to the discovery of a highly conserved panel of 182 proteins (ADAM10, STEAP23, STX7) and 52 lipids (PS, PIPs, Hex2Cer, PAs), providing a deep survey of hallmark molecular features and biological pathways intrinsic to circulating EVs. We also mapped the surfaceome diversity, identifying 151 proteins on the EV surface. We further establish a set of 42 proteins and 114 lipids features that served as hallmark features of non-EV particles in plasma. We submit ADAM10 and PS(36:1) as conserved EV biological markers that precisely differentiate between EV and non-EV particles. Our findings, which can be explored via an open-source Shiny web tool (evmap.shinyapps.io/evmap/) will serve as a valuable repository to the research community for a clearer understanding of circulating EV biology.

cell biology↗

bioRxiv2024

Fertilization-induced synergid cell death by RALF12-triggered ROS production and ethylene signaling

Fertilization-dependent elimination of the persistent synergid cell is essential to block supernumerary pollen tubes and thus to avoid polyspermy in flowering plants. Little is known about the molecular mechanisms ensuring timely induction and execution of synergid cell death. We analysed manually isolated maize synergid cells along their degeneration and show that they are gland cells expressing batteries of genes encoding small secreted proteins under control of the MYB98 transcription factor. This network is down-regulated after fertilization, while genes involved in reactive oxygen species (ROS) production, ethylene biosynthesis and response, senescence, and oxidative stress regulation are induced before synergid elimination and its ultimate fusion with the endosperm. We further show that fertilization-induced RALF12 peptide specifically triggers mitochondrial ROS and apoptosis, while ethylene promotes synergid degeneration. In conclusion, this study sheds light on developmental programmed cell death (dPCD) in plants and provides a unique resource to discover novel PCD regulators.

cell biology↗

bioRxiv2023

Atlas of Fshr Expression from Novel Reporter Mice

The FSH-FSHR signaling pathway has traditionally been considered an essential regulator in reproductive development and fertility. But there has been emerging evidence of FSHR expression in extragonadal tissues/organs. This poses new questions and long-term debates regarding the physiological role of the FSH-FSHR pathway, and underscores the need for reliable, in vivo analysis of FSHR expression in animal models. However, conventional methods have proven insufficient for examining FSHR expression due to limitations, such as the scarcity of reliable antibodies, rapid turnover/degradation of transcripts, and a lack of robust in vivo tools. To address this challenge, we developed Fshr-ZsGreen knockin reporter mice under the control of Fshr endogenous promoter using CRISPR/Cas9 genome-editing technology to append a P2A-ZsGreen targeting vector into a locus between the last exon and the stop codon of Fshr. With this novel genetic tool, we provide a reliable readout of Fshr expression at single-cell resolution level in vivo and in real time. Reporter animals were also subjected to additional analyses, including immunohistochemical staining, ddRT-PCR, and in situ hybridization, to define the accurate expression profile of FSHR in gonadal and extragonadal organs/tissues. Our compelling results not only demonstrated Fshr expression in intragonadal tissues but also, strikingly, unveiled notably increased expression in Leydig cells, osteoblast lineage cells, endothelial cells in vascular structures, and epithelial cells in bronchi of the lung and renal tubes. The genetic decoding of the widespread pattern of Fshr expression highlights its physiological relevance beyond reproduction and fertility, and opens new avenues for therapeutic options for age-related disorders of the bones, lungs, kidneys, and hearts, among other tissues/organs. Exploiting the power of the Fshr knockin reporter animals, this report provides the first comprehensive genetic record of the spatial distribution of FSHR expression, correcting a long-term misconception about Fshr expression and offering prospects for extensive exploration of FSH-FSHR biology.

cell biology↗

bioRxiv2023

KDM6A facilitates Xist upregulation at the onset of X inactivation

X chromosome inactivation (XCI) is a female-specific process in which one X chromosome is silenced to balance X-linked gene expression between the sexes. XCI is initiated in early development by upregulation of the lncRNA Xist on the future inactive X (Xi). A subset of X-linked genes escape silencing and thus have higher expression in females, suggesting female-specific functions. One of these genes is the highly conserved gene Kdm6a, which encodes a histone demethylase that removes methyl groups at H3K27 to facilitate gene expression. Here, we investigate the role of KDM6A in the regulation of Xist. We observed impaired upregulation of Xist during early stages of differentiation in hybrid mouse ES cells following CRISPR/Cas9 knockout of Kdm6a. This is associated with reduced Xist RNA coating of the Xi, suggesting diminished XCI potency. Indeed, Kdm6a knockout results in aberrant overexpression of genes from the Xi after differentiation. KDM6A binds to the Xist promoter and knockout cells show an increase in H3K27me3 at Xist. These results indicate that KDM6A plays a role in the initiation of XCI through histone demethylase-dependent activation of Xist during early differentiation.

molecular biology↗

bioRxiv2023

Robust Adaptive Deep Brain Stimulation Control of Non-Stationary Cortex-Basal Ganglia-Thalamus Network Models in Parkinson's Disease

Closed-loop deep brain stimulation (DBS) is a promising therapy for Parkinsons disease (PD) that works by adjusting DBS patterns in real time from the guidance of feedback neural activity. Current closed-loop DBS mainly uses threshold-crossing on-off controllers or linear time-invariant (LTI) controllers to regulate the basal ganglia (BG) beta band oscillation power. However, the critical cortex-BG-thalamus network dynamics underlying PD are nonlinear, non-stationary, and noisy, hindering the accurate and robust control of PD neural dynamics using current closed-loop DBS methods. Here, we develop a new robust adaptive closed-loop DBS method for regulating cortex-BG-thalamus network dynamics in PD. We first build an adaptive state-space model to quantify the dynamic, nonlinear, and non-stationary neural activity. We then construct an adaptive estimator to track the nonlinearity and non-stationarity in real time. We next design a robust controller to automatically determine the DBS frequency based on the estimated PD neural state while reducing the systems sensitivity to high-frequency noise. We adopt and tune a biophysical cortex-BG-thalamus network model as a testbed to simulate various nonlinear and non-stationary neural dynamics for evaluating DBS methods. We find that under different nonlinear and non-stationary neural dynamics, our robust adaptive DBS method achieved accurate regulation of the BG beta band oscillation power with small control error, bias, and deviation. Moreover, the accurate regulation generalizes across different therapeutic targets and consistently outperforms state-of-the-art on-off and LTI DBS methods. These results have implications for future designs of clinically-viable closed-loop DBS systems to treat PD and other neurological and neuropsychiatric disorders.

neuroscience↗

bioRxiv2023

Trained immunity in human monocyte enhances myeloid-T-cell pathogenic crosstalk in Ankylosing Spondylitis

Recent studies in infectious, cardiovascular and neurodegenerative diseases have established the presence of memory in innate immune cells. This "trained immunity (TI)" leads to an enhanced response to a second challenge. Monocytes in Ankylosing Spondylitis (AS), a common form of inflammatory arthritis, are known to be hyper-responsive to microbial stimulus lipopolysaccharide (LPS). We asked if TI is present in AS monocytes and, if so, how it contributes to disease pathology. Using Single-cell RNA sequencing (scRNA-seq), flow cytometry and enzyme-linked immunosorbent assays (ELISA), we identify a subset of monocytes from AS patients exhibiting features of trained immunity and being hyperresponsive to LPS stimulation. Surprisingly, both trained monocytes in AS and {beta}-glucan-trained monocytes from healthy donors are hyper-responsive to T-cell-induced activation. scRNA-seq of AS synovial mononuclear cells shows enrichment of a monocyte population with these/analogous features. Additionally, T cell-stimulated monocytes act back on T-cells to support Th17 responses (of established pathology in AS). Lastly, using genetic and chemical perturbations we show that ERN1, an AS risk gene enriched in this trained monocyte population, contributes to T-cell-induced monocyte activation. Our data provide strong evidence for the first time for the key role of TI in common human inflammatory arthritis.

molecular biology↗

bioRxiv2023

Characterisation of the genetic determinants of context specific DNA methylation in primary monocytes

DNA methylation (DNAm) has pervasive effects on gene expression and associations with ageing-related traits. Here we describe monocyte DNAm responses to inflammatory stimuli across 192 individuals. We find that, unlike the similarly widespread changes in gene expression elicited by LPS and IFN{gamma}, DNAm is markedly more sensitive to LPS. Exposure to LPS caused differential methylation at 20,858 immune-modulated CpGs (imCpGs) which display distinct genomic localisation and transcription factor usage, dependent upon whether methylation is lost or gained. Demethylated imCpGs are profoundly enriched for enhancers, and are over-represented by genes implicated in human diseases, most notably cancer. We find LPS-induced demethylation follows hydroxymethylation and for most sites the degree of demethylation correlates with baseline signal. Notably, we find LPS exposure triggers gain in epigenetic age by approximately 6 months, identifying a potential cause of accelerated epigentic aging which has diverse negative health associations. Finally, we explore the effect of genetic variation on LPS-induced changes in DNAm, identifying 209 imCpGs under genetic control. Exploring shared causal loci between LPS-induced DNAm responses and human disease traits highlights examples of human disease associated loci that also modulate imCpG formation. In summary, our findings suggest innate immune activity continually remodels DNAm in a highly punctate, enhancerenriched fashion that is under tight genetic control and predominantly involves genes commonly mutated in cancer.

genetics↗

bioRxiv2023

RealSeq2: a software integrated with UMI identification, error correction, and methylation modifications storing

High-throughput UMI technology sequencing is widely used in early tumor screening, detection, recurrence monitoring, etc. Detecting extremely low-frequency mutations is especially important for monitoring tumor recurrence, so high-precision data, as well as high-quality data, are required. We developed RealSeq2, a new integrated data-preprocessing software based on fastp and gencore, to achieve adapter removal, quality control, UMI identification, and generate consensus reads by clustering and error correction using multithreading in high-throughput next-generation sequencing background. RealSeq2 also supports methylation data of 5-methylcytosine bisulfite-free sequencing. RealSeq2 defined a new tag in SAM for storing methylation information, which is beneficial for co-identifying methylation sites and mutation sites for downstream analysis. RealSeq2 includes three submodules: ReadsProfiler, ReadsCleaner, and ReadsRecycler. In addition, the output format file (BAM or SAM) is universal for downstream analyses. RealSeq2 is the preferred upstream analysis software for the co-detection of ultra-low frequency mutations and bisulfite-free methylation data. The error profile provides data support for downstream analysis. Additionally, XM tags will become a standard protocol for recording methylation signals.

bioinformatics↗