Biology subjects

Chen, L.

Publications and source records attributed to Chen, L..

At least 325 records · Page 18Linked to original sources

bioRxiv2024

Phosphotyrosine Signal Profiling of Clinical CAR-T Reveals Tonic Signaling Associated with Therapeutic Efficacy

Chimeric Antigen Receptor T (CAR-T) therapies have revolutionized the treatment of cancers such as relapsed and refractory B cell malignancies. However, the precise therapeutic mechanism of CAR-T action remain to be elucidated. In this study, we systematically analyzed CAR signaling via phosphotyrosine (pTyr) proteomics in CAR-T cells from both clinical patients and healthy donors. We found that CAR-T products from clinical patients displayed heightened tyrosine phosphorylation, particularly in the JAK-STAT, MAPK and TCR signaling cascades. We also identified the significantly regulated pTyr sites in primary CAR-T cells under tonic signaling or upon stimulation by antigen-presenting CD19-K562 cells. Although both CD28{zeta} and 4-1BB{zeta} CAR-T cells exhibited comparable pTyr changes, CD28{zeta} CAR-T cells displayed a more pronounced activation in the TCR signaling pathway. Additionally, comparative analysis between clinical and primary CAR-T cells suggested that CAR-T products were subject to heightened tonic signaling, which may be related to therapeutic relapse. Our findings reveal the state of clinical CAR-T products and refine the CAR-T signal transduction network, providing comprehensive insights and informed guidance for CAR-T therapies.

immunology↗

bioRxiv2024

Neural Mechanisms of tDCS: Insights from an In-Vivo Rodent Model with Realistic Electric Field Strengths

IntroductionTranscranial direct current stimulation (tDCS) is a non-invasive neuromodulation method using low amplitude current (1-2 mA) to create weak electric fields (<1 V/m) in the brain, influencing cognition, motor skills, and behavior. However, the neural mechanisms remain unclear, as prior studies used high electric field strengths (10-40 V/m) unrepresentative of human tDCS. ObjectiveThis study aimed to develop an in-vivo rat model replicating human tDCS electric field strengths to examine effects of weak electric fields on cortical neurons. MethodCurrents of 0.005-0.3 mA were applied in 9 rats, generating electric fields of 0.5-35 V/m in the somatosensory cortex. Neural activity across cortical layers was recorded using a multichannel silicone probe. Somatosensory evoked potentials (SSEP) elicited by foot shocks assessed membrane polarization. Regular spiking (RS) and fast-spiking (FS) neurons were identified via spike shapes. Effects of tDCS on SSEP, spontaneous spiking activity (SSA), and evoked spiking activity (ESA) were analyzed. ResultsAnodal tDCS caused hyperpolarization (SSEP increase) in superficial layers and depolarization (SSEP decrease) in deeper layers, reversing asymmetrically for cathodal stimulation. Weak fields (<1 V/m) altered SSA in RS but not FS neurons, while stronger fields affected ESA in RS neurons. Effects correlated with field strength and were well described by linear mixed-effect models. Changes in SSA were correlated with changes in SSEP. ConclusionThis study demonstrates that realistic tDCS fields induce complex cortical polarization patterns linked to SSA changes. Increasing electric field strength amplifies effects, suggesting higher amplitude tDCS could enhance efficacy in humans. HighlightsO_LINewly developed in-vivo rodent model to replicate the weak electric field strengths characteristic of human tDCS, probe localized membrane polarization effects and simultaneously monitor spontaneous and evoked spiking activity. C_LIO_LIResults provide the first direct in-vivo confirmation of several tDCS mechanistic predictions derived from computational models and brain slice work. C_LIO_LIComplex Membrane Polarization Patterns: tDCS induces simultaneous hyperpolarization and depolarization in distinct neuronal compartments. C_LIO_LINeuron-Specific Effects: Weak electric fields preferentially modulate excitatory neurons, with no significant impact on inhibitory neurons at low electric field strengths. C_LIO_LIPolarity asymmetric effects: Anodic stimulation produces stronger effects than cathodic stimulation. C_LIO_LIMembrane polarization is linked to changes in spiking activity: Changes in membrane polarization are correlated with changes in spontaneous spiking activity. C_LIO_LIAll the tDCS neural mechanisms showed effects that were linearly related to electric field strength, underscoring the translational importance of novel tDCS protocols that can increase electric field strength, potentially improving the robustness and reproducibility of tDCS protocols in humans. C_LI

neuroscience↗

bioRxiv2024

Vascular endothelial growth factor-D improves lung vascular integrity during acute lung injury

Disorders in pulmonary vascular integrity are a prominent feature in many lung diseases. Paracrine signaling is highly enriched in the lung and plays a crucial role in regulating vascular homeostasis. However, the specific local cell-cell crosstalk signals that maintain pulmonary microvascular stability in adult animals and humans remain largely unexplored. In this study, we employed single-cell RNA-sequencing (scRNAseq)-based computational pipelines to systematically profile ligand-receptor (L/R) interactions within the lung microvascular niche and identified vascular endothelial growth factor-D (VEGF-D) as a key local factor with previously unrecognized barrier-protective properties in models of acute lung injury. Our scRNAseq data revealed that, under physiological conditions, soluble L/R interactions between mesenchymal cells, in particular alveolar fibroblast, and microvascular endothelial cells are predominantly associated with pathways involved in maintaining vascular integrity as compared to all other cells. Upon treatment with top identified ligands, we found that VEGF-D significantly enhanced endothelial barrier function and conferred protection against inflammatory challenges induced by tumor necrosis factor- (TNF-), interleukin-1{beta} (IL-1{beta}), and thrombin. This barrier-protective effect of VEGF-D was significantly attenuated by inhibition of VEGFR2, either through siRNA knockdown or pharmacological blockade using specific VEGFR2 inhibitors. Intravenous administration of recombinant VEGF-D in lipopolysaccharides (LPS)-induced acute lung injury models significantly reduced vascular permeability (7339 {+/-} 2510 (LPS) v.s. 5350 {+/-} 1821 (LPS + VEGF-D), p < 0.05), immune cell infiltration (0.791 {+/-} 0.199 x 106 WBC/mL (LPS) v.s. 0.540 {+/-} 0.190 x 106 WBC/mL (LPS + VEGF-D), p < 0.01), and the expression of pro-inflammatory markers TNF- and IL-6 in the lung tissue. This effect was abolished in VEGFR2iECKO mice, confirming that VEGF-D mediates its effects via VEGFR2-dependent signaling. This study demonstrates an unexpected protective role for VEGF-D in promoting lung endothelial barrier integrity and suggests that paracrine signaling from the alveolar fibroblast niche contributes critically to lung capillary homeostasis.

molecular biology↗

bioRxiv2024

Chronic Behavioral and Seizure Outcomes following Experimental Traumatic Brain Injury and Comorbid Klebsiella pneumoniae Lung Infection in Mice

Traumatic brain injury (TBI) is a leading cause of long-term disability, and infections such as pneumonia represent a common and serious complication for TBI patients in the acute and subacute post-injury period. While the acute effects of infections have been documented, their long-term consequences on neurological and behavioral recovery as well as the potential precipitation of seizures after TBI remain unclear. This study aimed to investigate the chronic effects of Klebsiella pneumoniae infection following TBI, focusing on post-traumatic seizure development and neurobehavioral changes. Using a mouse model, we assessed the long-term effects of TBI and K. pneumoniae infection both in isolation and in combination. We found that, while infection with K. pneumoniae resulted in loss of body weight and increased mortality compared to vehicle-inoculated mice, there was no additional mortality in TBI animals. Further, although TBI alone induced chronic hyperactivity and reduced anxiety-like behaviors, K. pneumoniae lung infection had no lasting effect on these long-term outcomes. Thirdly, while TBI resulted in both spontaneous and evoked seizures long-term post-injury, early post-injury K. pneumoniae infection did not affect late onset seizure susceptibility. Together with recent findings on acute outcomes in this combined insult model of TBI and K. pneumoniae infection, this study suggests that K. pneumoniae does not significantly alter long-term neurobehavioral outcomes or the development of post-traumatic epilepsy. This research highlights the need to further explore the interplay between additional immune insults such as infection that may influence long-term recovery.

neuroscience↗

bioRxiv2024

Soleus H-Reflex Up-Conditioning during Sciatic Nerve Regeneration in Rats Improves Recovery of Locomotion

Operant conditioning of the spinal stretch reflex or its electrical analog, the H-reflex, induces plasticity in the brain and spinal cord that increases (up-conditioning) or decreases (down-conditioning) the reflex elicited by primary afferent input to the spinal motoneuron. In rats in which the sciatic nerve is transected and repaired, soleus (SOL) H-reflex up-conditioning during regeneration strengthens primary afferent reinnervation of SOL motoneurons and improves recovery of the SOL H-reflex. This suggests that H-reflex up-conditioning could improve functional recovery after nerve injury and repair. To explore this possibility, we examined the impact of SOL H-reflex up- or down-conditioning during sciatic regeneration on recovery of locomotor symmetry. Sprague-Dawley rats were implanted with EMG electrodes in right SOL and a stimulating cuff on right posterior tibial nerve. After control data collection, right sciatic nerve was transected and repaired. Control EMG and H-reflex data collection continued for 20 more days. The rat was then exposed for 100 days to either: continued control data collection; SOL H-reflex up-conditioning; or SOL H-reflex down-conditioning. Locomotor EMG, H-reflex, and kinematics were assessed before nerve transection and 120 days after transection. H-reflex up-conditioning improved H-reflex recovery and also restored right/left step symmetry. H-reflex down-conditioning did not worsen H-reflex recovery or right/left step asymmetry. These results suggest that H-reflex up-conditioning might enhance functional recovery after nerve injury in humans. They also confirm previous results indicating that compensatory plasticity prevents inappropriate H-reflex conditioning (i.e., down-conditioning) from further impairing function.

neuroscience↗

bioRxiv2024

Current transcriptome database and biomarker discovery for immunotherapy by immune checkpoint blockade

Immune checkpoint blockade (ICB) has revolutionized the current immuno-oncology and significantly improved clinical outcome for cancer treatment. Despite the advancement in clinics, only a small subset of patients derives immune response to the ICB therapy. Therefore, a robust predictive biomarker that identifies potential candidate becomes increasingly crucial in delivering this technology to the public. In this review, we first discuss the biomarkers that focus on tumor genome, tumor microenvironment and tumor-host interaction. Then, we compare existing databases for biomarker discovery for ICB response. We also present IOhub - an interactive web portal that incorporates 36 bulk and 10 single-cell transcriptome datasets for benchmark analysis of the current biomarkers. Finally, we highlight the trending interest in antibody drug conjugate and combination treatment and their use in precision immuno-oncology.

bioinformatics↗

bioRxiv2024

Abnormal eNK cells contribute to endometrial fibrosis in intrauterine adhesions patients

Endometrial natural killer cells (eNK) at the proliferative phase are one of the major lymphocytes in the endometrium, but their phenotype and function remain elucidated. Here, we demonstrated that eNK cells had three subtypes and were different from peripheral blood NK (pbNK) and decidual NK (dNK) cells. They played an important role in maintaining the homeostasis of the endometrium through preventing endometrial stromal cells (ESCs) from the differentiation into myofibroblasts physiologically. However, in the fibrotic endometria of patients with intrauterine adhesions (IUA), eNK cells were significantly decreased and highly negatively correlated with an increase in myofibroblasts. In vitro experiments showed that eNK cells could inhibit the differentiation of ESCs into myofibroblasts and promote the dedifferentiation of myofibroblasts, in which the main effector molecules from eNK cells was Prostaglandin D2 (PGD2). PGD2 downregulated the expression of ZNF521 to decrease profibrotic protein synthesis. Furthermore, we confirmed the anti-endometrial fibrosis effect of eNK cells and its mechanism in an IUA-like murine model. These findings reveal an important role of eNK cells in endometrial homeostasis and provide potential therapeutic approaches for IUA patients.

immunology↗

bioRxiv2024

Extended Quality (eQual): Radial threshold clustering based on n-ary similarity

We are transforming Radial Threshold Clustering (RTC), an O(N 2) algorithm, into Extended Quality Clustering, an O(N) algorithm with several novel features. Daura et als RTC algorithm is a partitioning clustering algorithm that groups similar frames together based on their similarity to the seed configuration. Two current issues with RTC is that it scales as O(N 2) making it inefficient at high frame counts, and the clustering results are dependent on the order of the input frames. To address the first issue, we have increased the speed of the seed selection by using k-means++ to select the seeds of the available frames. To address the second issue and make the results invariant with respect to frame ordering, whenever there is a tie in the most populated cluster, the densest and most compact cluster is chosen using the extended similarity indices. The new algorithm is able to cluster in linear time and produce more compact and separate clusters.

biophysics↗

bioRxiv2024

Molecular Insights into the Regulation of GNPTAB by TMEM251

In vertebrates, newly synthesized lysosomal enzymes traffick to lysosomes through the mannose-6-phosphate (M6P) pathway. The Golgi membrane protein TMEM251 was recently discovered to regulate lysosome biogenesis by controlling the level of GlcNAc-1-phosphotransferase (GNPT). However, its precise function remained unclear. In this study, we demonstrate that TMEM251 is a two-transmembrane protein indispensable for GNPT stability, cleavage by Site-1-Protease (S1P), and enzymatic activity. We reconcile conflicting models by showing that TMEM251 enhances GNPT cleavage and prevents its mislocalization to lysosomes for degradation. We further establish that TMEM251 achieves this by interacting with GOLPH3 and retromer complexes to anchor the TMEM251-GNPT complex at the Golgi. Alanine mutagenesis identified F4XXR7 motif in TMEM251s N-tail for GOLPH3 binding. Together, our findings uncover TMEM251s multi-faceted role in stabilizing GNPT, retaining it at the Golgi, and ensuring the fidelity of the M6P pathway, thereby providing insights into its molecular function.

cell biology↗

bioRxiv2024

Sex-and Stress-Dependent Plasticity of a Corticotropin Releasing Hormone / GABA Projection from the Basolateral Amygdala to Nucleus Accumbens that Mediates Reward Behaviors

BackgroundMotivated behaviors are executed by refined brain circuits. Early-life adversity (ELA) is a risk for human affective disorders involving dysregulated reward behaviors. In mice, ELA causes anhedonia-like behaviors in males and augmented reward motivation in females, indicating sex-dependent disruption of reward circuit operations. We recently identified a corticotropin-releasing hormone (CRH) expressing GABAergic projection from basolateral amygdala (BLA) to nucleus accumbens (NAc) that governs reward-seeking deficits in adult ELA males--but not females. MethodsTo probe the sex-specific role of this projection in reward behaviors, adult male and female CRH-Cre mice raised in control or ELA conditions received excitatory or inhibitory Cre-dependent DREADDs in BLA, and then clozapine N-oxide or vehicle to NAc medial shell during reward behaviors. We determined the cell identity of the projection using immunostaining and electrophysiology. Using tissue clearing, light sheet fluorescence microscopy and deep learning pipelines, we mapped brain-wide BLA CRH+ axonal projections to uncover sex differences in innervation. ResultsChemogenetic manipulations in male mice demonstrated inhibitory effects of the CRH+ BLA-NAc projection on reward behaviors, whereas neither excitation nor inhibition influenced female behaviors. Molecular and electrophysiological cell-identities of the projection did not vary by sex. By contrast, comprehensive whole-brain mapping uncovered significant differences in NAc innervation patterns that were both sex and ELA-dependent, as well as selective changes of innervation of other brain regions. ConclusionsThe CRH/GABA BLA-NAc projection that influences reward behaviors in males differs structurally and functionally in females, uncovering potential mechanisms for the profound sex-specific impacts of ELA on reward behaviors.

neuroscience↗

bioRxiv2024

Optimizing femtosecond laser fabricating strategy of Nitinol hypotube for vascular interventional surgery

Guidewires and catheters are essential in minimally invasive procedures, particularly in accessing targets within the vascular system for neuron surgery. Femtosecond lasers can precisely cut nickel-titanium micro tubes, known as Nitinol hypotubes, serving as the heads of micro guidewires while protecting their core tips. The quality and geometry of these hypotubes depend on the focus of the laser cutting system. We evaluated the cutting efficiency and quality of Nitinol hypotubes using objective lenses with three numerical apertures (NA). Quantitative analysis indicated that higher NA objectives yield better surface quality, resulting in lower debris. Additionally, cutting with high NA objectives produced significantly lower arithmetic mean surface roughness and enhanced mechanical properties. Using a two-temperature model, we simulated the interaction between femtosecond lasers and Nitinol, showing that higher NA objectives increase electron temperatures, thus improving material removal efficiency. This study also tested the optimized Nitinol hypotube prformance in simulations of invasive neuron surgery.

neuroscience↗

bioRxiv2024

Effects of Bacterial Wilt on Community Composition and Diversity of Culturable Endophytic Fungi in Alpinia galanga

Hongdoukou plant (Alpinia galanga Willd.) is a perennial herbaceous plant that usually has a stable microflora living in the inter-root and stem and leaf tissues, which assists the host in normal growth and development. The bacterial wilt disease that had been investigated in planting bases of A. galanga, was a new soil-borne disease infected by pathogenic bacteria (Ralstonia solanacearum (Smith) Yabuuchi et al.), which disrupts the A. galanga-microbe-soil microecological balance. For this reason, it is important to study the changes of the community composition and diversity of endophytic fungi in healthy and diseased A. galanga (HDK_J and HDK_B), and to mine the active endophytic fungal resources in order to lay the foundation for exploring the functional microbial communities for artificial synthesis. All experimental materials were from the healthy and diseased plant clusters of A. galanga in the traditional planting areas in Guangdong Province. The endophytic fungi were isolated from the stems and leaves of A. galanga by separated plant tissue blocks cultured in PDA medium. The colonization rate (CR) was calculated, and the isolated strains were amplified by PCR with the ITS1/ITS4 genes as the fungal molecular markers, to identify the endophytic fungi species, and to analyze the diversity of endophytic fungi in the healthy and diseased clusters of HDK_J and HDK_B, and the indexes included: relative segregation frequency (SF), relative abundance (RA) plotted by ggplot2 under R language, Shannon-Wiener diversity index (H'), Simpson index (D), Margalef richness index (R) and Pielou uniformity index (J), and finally, a phylogenetic tree of the endophytic fungi of healthy and diseased A. galanga was constructed by MEGA. A total of 685 endophytic fungal strains were isolated from the stems and leaves of healthy (HDK_J) and diseased (HDK_B) A. galanga, of which 27 endophytic fungal species were identified in healthy A. galanga. and 8 in diseased A. galanga, which belonged to 3 Phyla, 6 Classes and 13 Families. At the genus level, the RA of HDK_B endophytic fungi were only 38.93% of HDK_J, with significant difference (P<0.05), indicating that the composition and abundance of endophytic fungi in HDK_B were lower than that in HDK_J. Meanwhile, the endophytic fungi species isolated from the stems and leaves of the HDK_J and HDK_B were the same, but the RA of leaf organs was higher than that of stems, with the RA in the leaves in HDK_J higher than that of stems by 124.23%, and the RA of leaves in HDK_B higher than that of stems by 78.23%. The RA of HDK_J leaves was 78.08% higher than that of stems. all the diversity indexes of HDK_J were higher than that of HDK_B, with significant differences (P<0.05), and the Shannon-Wiener index (H'), Simpsons index (D), and Margalefs index (R) behaved as follows: HDK_J leaves (1.16, 0.87, 5.12) > HDK_J stems (0.82, 0.72, 4.22) > HDK_B leaves (0.57, 0.24, 2.97) > HDK_B stems (0.33, 0.14, 2.25), whereas Pielous index (J) indicated that the endophytic fungal species were more uniformly distributed in HDK_J leaves, and there was not much difference in the homogeneity of the leaves of the HDK_J stems and the HDK_B stems. The mapping phylogenetic trees showed there were 4 major development branches of the species on endophytic fungi in HDK_J, and especially, there were many long development branches under the Ascomycota. The genetic relationships among different species were completely revealed in phylogenetic trees. The average genetic similarity among genera was 52.80%. Conversely, there only were1major branch (Ascomycota), and few sub-branches under the Ascomycota in HDK_B. The average genetic similarity among genera was 84.59%, and the difference was small. The bacterial wilt significantly affected the composition and RA of endophytic fungi in A. galanga. The diversity indices showed decreasing trend in A. galanga after infected by R. solanacearum. The dominant species were changed. The parts of sensitive endophytic fungi were disappeared. This result will be helpful for the study on the relationship between the artificial minimal microbial community and the role of the host as well as the study on synthetic microbiomics.

microbiology↗

bioRxiv2024

An immunomechanical checkpoint PYK2 governs monocyte-to-macrophage differentiation in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) is characterized by a fibrotic, stiff tumor microenvironment (TME), where tumor-associated macrophages (TAMs) drive ECM remodeling, progression, and immune evasion. The contribution of mechanical cues to monocyte differentiation into TAMs remains largely unexplored. Here we show that mechanical force is required for monocyte-to-macrophage differentiation. PYK2, as an innovative immunomechanical checkpoint, de facto governs this differentiation process. We demonstrated that PYK2 senses mechanical signals via Piezo1 and integrins, triggering F-actin polymerization and translocating to the nucleus to regulate mechanotransduction and differentiation genes (e.g., ACTR3, RELA). Targeted deletion of PYK2 impairs the differentiation and polarization of monocyte-derived macrophages, reshapes the PDAC microenvironment, and enhances the efficacy of anti-PD-1 immunotherapy. These findings underscore the critical role of mechanical cues in monocyte differentiation and suggest that targeting PYK2 is a promising strategy to modulate TAM function and improve immunotherapy outcomes in patients with PDAC. Statement of significanceThis study identifies PYK2 as an immunomechanical checkpoint that drives monocyte-to-macrophage differentiation in PDAC via Piezo1/integrin-mediated mechanical cues. Targeted deletion of PYK2 reshapes the PDAC microenvironment, and enhances the efficacy of anti-PD-1 immunotherapy, suggesting PYK2 as a promising therapeutic target to overcome immunotherapy resistance.

immunology↗

bioRxiv2024

Engineered mitochondrial A-to-G editors with enhanced efficiency and targeting scope

Mitochondrial base editing is a powerful technology, but the current A-to-G mitochondrial DNA (mtDNA) base editors are reluctant to achieve high efficiency, which is critical for mtDNA engineering. Through laboratory evolution, TadA-8e variants were discovered with substantially increased activity and expanded targeting compatibility, especially for previously unfavorite sequence contexts, when applied to both nuclear and mitochondrial ABEs. Further engineering of the mtDNA editors (eTd-mtABEs) dramatically reduced both DNA and RNA off-targeting effects and enhanced strand-selective A-to-G editing with substitution of DddA to DNA nickases. Moreover, the eTd-mtABEs induced up to 145-fold editing frequencies compared to previous mtDNA adenine base editors in rat cells, and installed targeted mutations in all injected rat embryos with up to 74% efficiency in founders, resulting generation of SNHL and Leigh syndrome models with severe defects. It suggests that eTd-mtABEs are promising mtDNA engineering technology for basic research and for translational studies. HighlightsO_LIEngineered TadA variants enhance nuclear and mitochondrial ABE activity in all sequence contexts. C_LIO_LIAdditional mutations in eTd-mtABEs further minimize both DNA and RNA off-targeting effects. C_LIO_LIEngineered TadA variants are compatible to DNA nickase assisted strand-selective mtDNA editing. C_LIO_LIeTd-mtABEs enable highly efficient generation of rat mtDNA disease models with severe phenotypes. C_LI

bioengineering↗

bioRxiv2024

Targeting GOF p53 and c-MYC through LZK Inhibition or Degradation Suppresses Head and Neck Tumor Growth

The worldwide frequency of head and neck squamous cell carcinoma (HNSCC) is approximately 800,000 new cases, with 430,000 deaths annually. We determined that LZK (encoded by MAP3K13) is a therapeutic target in HNSCC and showed that inhibition with small molecule inhibitors decreases the viability of HNSCC cells with amplified MAP3K13. A drug-resistant mutant of LZK blocks decreases in cell viability due to LZK inhibition, indicating on-target activity by two separate small molecules. Inhibition of LZK catalytic activity suppressed tumor growth in HNSCC PDX models with amplified MAP3K13. We found that the kinase activity of LZK stabilized c-MYC and that LZK stabilized gain-of-function (GOF) p53 through a kinase-independent mechanism. Therefore, we designed proteolysis-targeting chimeras (PROTACs) and demonstrate that our lead PROTAC promotes LZK degradation and suppresses expression of GOF p53 and c-MYC leading to impaired viability of HNSCC cell lines. This research provides a strong basis for development of therapeutics targeting LZK in HNSCCs with amplification of the gene. One Sentence SummaryThis study establishes the kinase LZK as a therapeutic target for HNSCC through regulation of c-MYC expression.

cancer biology↗

bioRxiv2024

Clair3-RNA: A deep learning-based small variant caller for long-read RNA sequencing data

Variant calling using long-read RNA sequencing (lrRNA-seq) can be applied to diverse tasks, such as capturing full-length isoforms and gene expression profiling. It poses challenges, however, due to higher error rates than DNA data, the complexities of transcript diversity, RNA editing events, etc. In this paper, we propose Clair3-RNA, the first deep learning-based variant caller tailored for lrRNA-seq data. Clair3-RNA leverages the strengths of the Clair series pipelines and incorporates several techniques optimized for lrRNA-seq data, such as uneven coverage normalization, refinement of training materials, editing site discovery, and the incorporation of phasing haplotype to enhance variant-calling performance. Clair3-RNA is available for various platforms, including PacBio and ONT complementary DNA sequencing (cDNA), and ONT direct RNA sequencing (dRNA). Our results demonstrated that Clair3-RNA achieved a [~]91% SNP F1-score on the ONT platform using the latest ONT SQK-RNA004 kit (dRNA004) and a [~]92% SNP F1-score in PacBio Iso-Seq and MAS-Seq for variants supported by at least four reads. The performance reached a [~]95% and [~]96% F1-score for ONT and PacBio, respectively, with at least ten supporting reads and disregarding the zygosity. With read phased, the performance reached [~]97% for ONT and [~]98% for PacBio. Extensive evaluation of various GIAB samples demonstrated that Clair3-RNA consistently outperformed existing callers and is capable of distinguishing RNA high-quality editing sites from variants accurately. Clair3-RNA is open-source and available at (https://github.com/HKU-BAL/Clair3-RNA).

bioinformatics↗

bioRxiv2024

Mapping Pesticide-Induced Metabolic Alterations in Human Gut Bacteria

Pesticides can modulate gut microbiota (GM) composition, but their specific effects on GM remain largely elusive. Our study demonstrated that pesticides inhibit or promote growth in various GM species, even at low concentrations, and can accumulate in GM to prolong their presence in the host. Meanwhile, the pesticide induced changes in GM composition are associated with significant alterations in gut bacterial metabolism that reflected by the changes of hundreds of metabolites. We generated a pesticide-GM-metabolites (PMM) network that not only reveals pesticide-sensitive gut bacteria species but also report specific metabolic changes in 306 pesticide-GM pairs (PGPs). Using an in vivo mice model, we further demonstrated a PGPs interactions and verified the inflammation-inducing effects of pesticides on the host through dysregulated lipid metabolism of microbes. Taken together, our findings generate a PMM interactions atlas, and shed light on the molecular level of how pesticides impact host health by modulating GM metabolism. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/623895v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@17ed5f5org.highwire.dtl.DTLVardef@10d3e0org.highwire.dtl.DTLVardef@c61b43org.highwire.dtl.DTLVardef@27d035_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2024

Delineation of Single-cell Altas Provides New Insights for Development of Coronary Artery Lesions in Kawasaki Disease: Bad and Good Signaling Molecules

BackgroundKawasaki Disease (KD) is a vasculitis syndrome featured with a high and persistent fever and mainly affects children under 5 years of age. It is the leading cause of acquired heart disease in the form of coronary artery lesions (CALs) for children in developed countries. Most KD can be relieved with the high-dosage Intravenous immunoglobulin (IVIG) therapy, but a small proportion develop CALs after IVIG treatment. MethodsWe performed the single-cell RNA sequencing for the peripheral blood mononuclear cells (PBMCs) from three KD non-CAL patients whose samples were acquired before and after IVIG treatment and three KD CAL patients whose samples were acquired only after IVIG treatment. Cell-to-cell communication patterns were also analyzed in KD CAL and non-CAL patients ResultsOverall cell expression feature analyses show immunoglobulin and adaptive immunity related genes are upregulated in KD CAL patients while B cell activation related genes are downregulated in them. Pseudo-time analyses demonstrate that both KD non-CAL patients before treatment and KD CAL patients after treatment have a dysregulated B cell developmental trajectory while the former has a mixed T and B lineage and the latter has a mixed monocyte and B lineage. The early elevated expression of SPI1 could partly explain the dysregulated B cell development in KD CAL patients. Cell communication analyses propose a disorder cell communication pattern in KD non-CAL patients before treatment and some persistent bad cell-to-cell signals in KD CAL patients after treatment. There are four signaling molecules, APP, CCL, and MCH-II, whose expression is significantly increased in the CD14 and CD16 monocytes of KD CAL patients, where the expression of RESISTIN is significantly increased in those KD non-CAL patients. ConclusionsOur results suggest that APP, CCL, and MCH-II might be the bad signals for indicating the possible development of CAL while RESISTIN is a good one for protecting from CAL.

immunology↗