Biology subjects

Qi, R.

Publications and source records attributed to Qi, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Root gene regulatory network analysis reveals roles for defense hormones and secondary metabolites in establishment of disease-suppressive soil

Plants recruit beneficial microbiota in their rhizosphere to alleviate stresses. In Arabidopsis thaliana, foliar infection by Hyaloperonospora arabidopsidis (Hpa) has been shown to establish a disease-suppressive microbiome that promotes protection against Hpa infection of the subsequent plant generation grown in this conditioned soil - a phenomenon known as soil-borne legacy (SBL). The root responses involved in SBL establishment have remained largely unclear. In this study, time-series RNA-seq of roots from Hpa-infected plants grown in natural soil was conducted over seven days post-inoculation. A gene regulatory network of the responding roots was constructed. The role of predicted key components was verified in follow-up assays. Root transcriptional reprogramming started within one day after foliar infection. Genes associated with salicylic acid (SA)-mediated defense were upregulated, while those linked to secondary metabolism and jasmonic acid (JA) responsiveness were downregulated. SA accumulation increased at 1 dpi, and JA decreased by 3 dpi. Transcriptional regulation occurred primarily in the tips of the roots. Mutant analyses confirmed that SA, JA, indole glucosinolates, camalexin, and flavonoids contribute to SBL establishment. Our findings reveal rapid systemic transcriptional reprogramming in roots upon foliar pathogen attack, uncovering novel roles of hormone signaling and secondary metabolism in shaping a disease-suppressive soil beyond their known defense functions.

plant biology↗

bioRxiv2026

Hyperexcitable primary somatosensory cortex in the MitoPark mouse model of Parkinson's disease

The majority of Parkinson's disease patients suffer from decreased tactile acuity or neuropathic pain, both of which contribute to low quality of life and likely exacerbate motor dysfunction. How Parkinson's disease pathology relates to altered somatosensation remains unclear. One potential contributor is the progressive degeneration of dopamine neurons. To assess the extent to which gradual dopamine neuron loss contributes to altered somatosensation, we recorded spontaneous and stimulus-evoked activity in the primary somatosensory cortex of the MitoPark mouse model of Parkinson's disease. MitoPark mice experience progressive dopamine neuron degeneration that is independent of -synuclein. We found that MitoPark layer V regular-spiking (largely pyramidal) neurons, but not fast-spiking (largely parvalbumin-expressing inhibitory) neurons, had elevated spontaneous firing rates relative to littermate controls at late stages of symptom progression. Regular-spiking neurons also became hyperresponsive to tactile stimuli -- more neurons were recruited by stimuli across a wide range of intensities, and these neurons responded with higher firing rates. Fast-spiking neurons, but not regular-spiking neurons, became desynchronized at late stages of symptom progression. These physiological changes coincided with pronounced degeneration of dopamine neurons and axons, which we measured with tyrosine hydroxylase immunostaining in the midbrain, striatum, and primary somatosensory cortex. Altogether, this characterization revealed cell-type-specific changes in the primary somatosensory cortex that are consistent with both decreased tactile acuity and hyperalgesia in Parkinson's disease patients. This suggests that the loss of dopamine neurons, potentially including those that innervate primary somatosensory cortex, contributes to somatosensory impairments associated with Parkinson's disease.

neuroscience↗

bioRxiv2025

Lymphotoxin-driven cancer cell eradication by tumoricidal CD8+ tumor-infiltrating lymphocytes

Tumor-infiltrating lymphocyte (TIL) therapy is FDA-approved for patients with treatment-resistant advanced melanoma, but the TIL subpopulations critical for tumor eradication remains incompletely understood. Using patient-derived TIL-melanoma co-cultures, we identified and characterized a novel subset of CD8+ TIL, capable of class I HLA-independent cancer cell lysis. The lymphotoxin {beta} receptor (LT{beta}R) and interferon (IFN) sensing pathways were nominated as key determinants of TIL-mediated cancer cell killing from a whole-genome, loss-of-function CRISPR screen. Validation studies confirmed that dual LT{beta}R and IFN sensing is necessary and sufficient for cancer cell lysis, and that expanded CD8+ TIL express high lymphotoxin {beta} (LTB) and upregulate lymphotoxin (LTA) upon coculture with cancer cells. Leveraging paired scRNA-seq and scTCR-seq data, we confirmed that enrichment of LTB+CD8+ T cells is associated with clinical response to TIL, and that LTB+CD8+ TIL are expanded from putative neoantigen-reactive, LTBlo CD8+ T cells in resected tumors. SignificanceWe have uncovered a previously unrecognized mechanism of TIL-mediated tumor eradication, providing mechanistic insights into the role of LTBR/IFN signaling in TIL-mediated cancer cell killing, and potentially offering insights into novel strategies to isolate, enrich, and expand tumoricidal TIL or augment specific TIL functions to enhance tumor control.

cancer biology↗

bioRxiv2025

Segmented poly(A) tails with microRNA target sites confer tissue-specific regulation for mRNA therapeutics

Targeted delivery and controlled expression of mRNA-LNPs are critical for the development of safe and effective mRNA medicines. However, efficient post-delivery regulation of mRNA-LNP expression remains challenging. In this study, we engineered segmented poly(A) tail variants that function as gene-specific regulatory elements for synthetic mRNAs. Specifically, we inserted microRNA target sites (MTS) for miR-122 or miR-142 at various positions of the poly(A) tail of synthesized luciferase reporter mRNA. These modifications significantly reduced luciferase expression in non-target tissues in vitro and in vivo, demonstrating position-dependent selective expression control. Furthermore, by incorporating triple-MTS sequences for miR-142, miR-126, and miR-148a in all possible combinations at the 5 end of the poly(A) tail, we identified triple-MTS arrangements that simultaneously decrease luciferase activities in three non-target hepatic cell types, while preserving robust expression in hepatocytes. The results highlighted the importance of MTS insertion order for optimal mRNA silencing. These triple-MTS modules significantly expanded the utility of single miRNA-responsive elements, enabling cell-type selective regulation for mRNA therapeutics. By complementing tissue-tropic delivery LNPs, our mRNA cargo regulatory elements have the potential to improve tissue and cell type selectivity as a novel platform for post-delivery regulation of mRNA-LNP.

bioengineering↗

bioRxiv2025

Combining Selenocystine Based Fluorescence Assay with Structural Prediction for Enhanced Detection and Analysis of Cystine Stone Pathology

BackgroundCystine stones, a rare but recurrent type of kidney stones, primarily result from cystinuria, an inherited disorder caused by mutations in the genes SLC3A1 and SLC7A9, which encode renal cystine transporters. These mutations impair cystine reabsorption, resulting in elevated urinary cystine concentrations and stone formation. Current diagnostic methods are limited, particularly for detecting molecular-level dysfunctions. We aimed to develop a nonradioactive method for functional assessment of cystine transporters and mutation-specific pathologies. MethodsWe designed an innovative diagnostic approach combining a selenocystine-based fluorescence assay with structural predictions using AlphaFold to rapidly and accurately assess cystine transporter function and the molecular impacts of genetic mutations. ResultsOur assay demonstrated comparable transport efficiencies of cystine and selenocystine by the SLC3A1/SLC7A9 complex, and effectively differentiated mild, moderate, and severe functional impairments associated with known clinical mutations, including A354T and P482L. Structural modeling further provided mechanistic insights into mutation-induced dysfunctions. ConclusionThis integrated approach--combining a sensitive selenocystine fluorescence assay with AI-powered structural analysis--enables rapid, precise diagnosis of cystinuria variants and delivers mechanistic insights for personalized therapeutic strategies.

genetics↗

bioRxiv2024

Cell types associated with human brain functional connectomes and their implications in psychiatric diseases

Cell types are fundamental to the functional organization of the human brain, yet the specific cell clusters contributing to functional connectomes remain unclear. Using human whole-brain single-cell RNA sequencing data, we investigated the relationship between cortical cell cluster distribution and functional connectomes. Our analysis identified dozens of cell clusters significantly associated with resting-state network connectivity, with excitatory neurons predominantly driving positive correlations and inhibitory neurons driving negative correlations. Many of these cell clusters are also conserved in macaques. Notably, functional network connectivity is predicted by cellular communication among these clusters. We further identified cell clusters linked to various neuropsychiatric disorders, with several clusters implicated in multiple conditions. Comparative analysis of schizophrenia and autism spectrum disorder revealed distinct expression patterns, highlighting disease-specific cellular mechanisms. These findings underscore the critical role of specific cell clusters in shaping functional connectomes and their implications for neuropsychiatric diseases.

neuroscience↗

bioRxiv2022

G2019S selective LRRK2 kinase inhibitor abrogates mitochondrial DNA damage

Pathogenic mutations in LRRK2 cause Parkinsons disease (PD). The G2019S variant is the most common, which results in abnormally high kinase activity. Compounds that target LRRK2 kinase activity are currently being developed and tested in clinical trials. We recently found that G2019S LRRK2 causes mitochondrial DNA (mtDNA) damage and treatment with multiple classes of LRRK2 kinase inhibitors at concentrations associated with dephosphorylation of LRRK2 reversed mtDNA damage to healthy control levels. Because maintaining the normal function of LRRK2 in heterozygous G2019S LRRK2 carriers while specifically targeting the G2019S LRRK2 activity could have an advantageous safety profile, we explored the efficacy of a G2019S mutant selective LRRK2 inhibitor to reverse mtDNA damage in G2019S LRRK2 models and patient cells relative to non-selective LRRK2 inhibitors. Potency of LRRK2 kinase inhibition by EB-42168, a G2019S mutant LRRK2 kinase inhibitor, and MLi-2, a nonselective inhibitor, was determined by measuring phosphorylation of LRRK2 at Ser935 and/or Ser1292 using quantitative western immunoblot analysis. The Mito DNADX assay, a novel system that allows for the accurate real-time quantification of mtDNA damage in a 96-well platform, was performed in parallel. We confirmed that EB-42168 selectively inhibits LRRK2 phosphorylation on G2019S LRRK2 relative to wild-type LRRK2. On the other hand, MLi-2 was equipotent for wild-type and G2019S LRRK2. Acute treatment with EB-42168 inhibited LRRK2 phosphorylation and also restored mtDNA damage to healthy control levels. Precision medicine is a common approach in modern day cancer research that is not yet routinely applied to neurodegenerative diseases. Abrogation of mtDNA damage with mutant selective tool inhibitor EB-42168 demonstrates the promise of a precision medicine approach for LRRK2 G2019S PD. Levels of mtDNA damage may serve as a potential pharmacodynamic biomarker of altered kinase activity that could be useful for small molecule development and clinical trials.

neuroscience↗

bioRxiv2022

Multi-dimensional protein solubility optimization with an ultra-high-throughput microfluidic platform

Protein-based biologics are highly suitable for drug development, as they exhibit low toxicity and high specificity for their targets. However, for therapeutic applications, biologics must often be formulated to very high concentrations, making insufficient solubility a critical bottleneck in drug development pipelines. Here, we report an ultra-high-throughput microfluidic platform for protein solubility screening. In comparison with previous methods, this microfluidic platform can make, incubate, and measure samples in a few minutes, uses just 20 micrograms of protein (> 10-fold improvement) and yields 10,000 data points (1000-fold improvement). This allows quantitative comparison of formulation additives, such as salt, polysorbate, histidine, arginine and sucrose. Additionally, we can measure how solubility is affected by different concentrations of multiple additives, find a suitable pH for the formulation, and measure the impact of single mutations on solubility, thus enabling the screening of large libraries. By reducing material and time costs, this approach makes detailed multi-dimensional solubility optimization experiments possible, streamlining drug development and increasing our understanding of biotherapeutic solubility and the effects of excipients.

biophysics↗

bioRxiv2022

Intranasal delivery of NS1-deleted influenza virus vectored COVID-19 vaccine restrains the SARS-CoV-2 inflammatory response

The emergence of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) variants and "anatomical escape" characteristics threaten the effectiveness of current coronavirus disease (COVID-19) vaccines. There is an urgent need to understand the immunological mechanism of broad-spectrum respiratory tract protection to guide broader vaccines development. In this study, we investigated immune responses induced by an NS1-deleted influenza virus vectored intranasal COVID-19 vaccine (dNS1-RBD) which provides broad-spectrum protection against SARS-CoV-2 variants. Intranasal delivery of dNS1-RBD induced innate immunity, trained immunity and tissue-resident memory T cells covering the upper and lower respiratory tract. It restrained the inflammatory response by suppressing early phase viral load post SARS-CoV-2 challenge and attenuating pro-inflammatory cytokine (IL-6, IL-1B, and IFN-{gamma}) levels, thereby reducing excess immune-induced tissue injury compared with the control group. By inducing local cellular immunity and trained immunity, intranasal delivery of NS1-deleted influenza virus vectored vaccine represents a broad-spectrum COVID-19 vaccine strategy to reduce disease burden.

immunology↗

bioRxiv2022

FOXP2 confers oncogenic effects in prostate cancer through activating MET signalling

Identification oncogenes is fundamental to revealing the molecular basis of cancer. Here, we found that FOXP2 is overexpressed in human prostate cancer cells and prostate tumors, but its expression is absent in normal prostate epithelial cells and low in benign prostatic hyperplasia. To date, little is known regarding the link of FOXP2 to prostate cancer. We observed that high FOXP2 expression and frequent amplification are significantly associated with high Gleason score. Ectopic expression of FOXP2 induces malignant transformation of mouse NIH3T3 fibroblasts and human prostate epithelial cell RWPE-1. Conversely, FOXP2 knockdown suppresses the proliferation of prostate cancer cells. Transgenic overexpression of FOXP2 in the mouse prostate causes prostatic intraepithelial neoplasia. Overexpression of FOXP2 aberrantly activates oncogenic MET signalling and inhibitors targeting MET signalling effectively reverts the FOXP2-induced oncogenic phenotype. Additionally, the novel recurrent FOXP2-CPED1 fusion identified in prostate tumors results in high expression of truncated FOXP2, which exhibit a similar capacity for malignant transformation. Together, our data demonstrate for the first time that FOXP2 is an oncogene involved in tumorigenicity of prostate.

cancer biology↗

bioRxiv2022

A mitochondrial blood-based patient stratification candidate biomarker for Parkinson's disease

Parkinsons disease (PD) is the most common neurodegenerative movement disorder and neuroprotective interventions remain elusive. High throughput biomarkers aimed to stratify patients based on shared etiology is one critical path to the success of disease-modifying therapies in clinical trials. Mitochondrial dysfunction plays a prominent role in the pathogenesis of PD. Previously, we found brain region-specific mitochondrial DNA (mtDNA) damage accumulation in neuronal and in vivo PD models, as well as human PD postmortem brain tissue. In this study, to investigate mtDNA damage as a potential blood biomarker for PD, we describe a novel Mito DNADX assay that allows for the accurate real-time quantification of mtDNA damage in a 96-well platform, compatible with assessing large cohorts of patient samples. We found that levels of mtDNA damage were increased in blood derived from early-stage idiopathic PD patients or those harboring the pathogenic LRRK2 G2019S mutation compared to age-matched healthy controls. Given that increased mtDNA damage was also found in non-manifesting LRRK2 mutation carriers, mtDNA damage may begin to accumulate prior to a clinical PD diagnosis. LRRK2 kinase inhibition mitigated mtDNA damage in idiopathic PD models and patient-derived cells. The latter observations further substantiate a mechanistic role for wild-type LRRK2 kinase activity in idiopathic PD and support mtDNA damage reversal as a suitable approach to slow PD-related pathology. In light of recent advances in the field of precision medicine, the analysis of mtDNA damage as a blood-based patient stratification biomarker should be included in future clinical trials. One Sentence SummaryBlood test identifies Parkinsons patients most likely to respond to mitochondria-targeted therapeutics facilitating a precision medicine approach.

neuroscience↗

bioRxiv2021

A live attenuated influenza virus-vectored intranasal COVID-19 vaccine provides rapid, prolonged, and broad protection against SARS-CoV-2 infection

Remarkable progress has been made in developing intramuscular vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, they are limited with respect to eliciting local immunity in the respiratory tract, which is the primary infection site for SARS-CoV-2. To overcome the limitations of intramuscular vaccines, we constructed a nasal vaccine candidate based on an influenza vector by inserting a gene encoding the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2, named CA4-dNS1-nCoV-RBD (dNS1-RBD). A preclinical study showed that in hamsters challenged 1 day and 7 days after single-dose vaccination or 6 months after booster vaccination, dNS1-RBD largely mitigated lung pathology, with no loss of body weight, caused by either the prototype-like strain or beta variant of SARS-CoV-2. Lasted data showed that the animals could be well protected against beta variant challenge 9 months after vaccination. Notably, the weight loss and lung pathological changes of hamsters could still be significantly reduced when the hamster was vaccinated 24 h after challenge. Moreover, such cellular immunity is relatively unimpaired for the most concerning SARS-CoV-2 variants. The protective immune mechanism of dNS1-RBD could be attributed to the innate immune response in the nasal epithelium, local RBD-specific T cell response in the lung, and RBD-specific IgA and IgG response. Thus, this study demonstrates that the intranasally delivered dNS1-RBD vaccine candidate may offer an important addition to fight against the ongoing COVID-19 pandemic, compensating limitations of current intramuscular vaccines, particularly at the start of an outbreak.

pathology↗

bioRxiv2021

The chromatin regulator HMGA1a undergoes phase separation in the nucleus

The protein high mobility group A1 (HMGA1) is an important regulator of chromatin organization and function. However, the mechanisms by which it exerts its biological function are not fully understood. Here, we report that the HMGA isoform, HMGA1a, nucleates into foci that display liquid-like properties in the nucleus, and that the protein readily undergoes phase separation to form liquid condensates in vitro. By bringing together machine-leaning modelling, cellular and biophysical experiments and multiscale simulations, we demonstrate that phase separation of HMGA1a is critically promoted by protein-DNA interactions, and has the potential to be modulated by post-transcriptional effects such as phosphorylation. We further show that the intrinsically disordered C-terminal tail of HMGA1a significantly contributes to its phase separation through cation-{pi} and electrostatic interactions. Our work sheds light on HMGA1 phase separation as an emergent biophysical factor in regulating chromatin structure.

biophysics↗

bioRxiv2021

Deep Transfer Learning of Drug Sensitivity by Integrating Bulk and Single-cell RNA-seq data

Massively bulk RNA sequencing databases incorporating drug screening have opened up an avenue to inform the optimal clinical application of cancer drugs. Meanwhile, the growing single-cell RNA sequencing (scRNA-seq) data contributes to improving therapeutic effectiveness by studying the heterogeneity of drug responses for cancer cell subpopulations. There is a clear significance in developing computational biology approaches to predict and interpret cancer drug response in single cell data from clinical samples. Here, we introduce scDEAL, a deep transfer learning framework for cancer drug response prediction at single-cell level by integrating large-scale bulk cell line data. The true innovation of scDEAL is to translate cancer cell line drug responses into predicting clinical drug responses via learning relations of gene expressions and drug responses at bulk-level and transfer to predict drug responses in scRNA-seq. Another innovation is the integrated gradient feature interpretation to infer a comprehensive set of signature genes to reveal potential drug resistance mechanisms. We benchmarked scDEAL on six scRNA-seq datasets and indicate its model interpretability through these case studies. We believe that this work may help study cell reprogramming, drug selection, and repurposing for improving therapeutic efficacy.

bioinformatics↗

bioRxiv2021

Structure of the Infective Getah Virus at 2.8 A-resolution Determined by Cryo-electron Microscopy

Getah virus (GETV), a member of genus alphavirus, is a mosquito-borne pathogen that can cause pyrexia and reproductive losses in animals. Although antibodies to GETV have been found in over 10% of healthy people, there are no reports of clinical symptom associated with GETV. The biological and pathological properties of GETV are largely unknown. Here, we present the structure of infective GETV at a resolution of 2.8 [A] with the capsid protein and the envelope glycoproteins E1 and E2. We have identified numerous glycosylation and S-acylation sites in E1 and E2. The surface-exposed glycans revealed their impact on the viral immune evasion and host cell invasion. The S-acylation sites involve in stabilizing the transmembrane assembly. In addition, a cholesterol and a phospholipid molecule are observed in a transmembrane hydrophobic pocket, together with two more cholesterols surrounding the pocket. The structural information will assist structure-based antiviral and vaccine design.

biophysics↗

bioRxiv2021

Selective Corticofugal Modulation on Sound Processing in Auditory Thalamus of Awake Marmosets

Cortical feedback has long been considered crucial for modulation of sensory processing. In the mammalian auditory system, studies have suggested that corticofugal feedback can have excitatory, inhibitory, or both effects on the response of subcortical neurons, leading to controversies regarding the role of corticothalamic influence. This has been further complicated by studies conducted under different brain states. In the current study, we used cryo-inactivation in the primary auditory cortex (A1) to examine the role of corticothalamic feedback on medial geniculate body (MGB) neurons in awake marmosets. The primary effects of A1 inactivation were a frequency-specific decrease in the auditory response of MGB neurons coupled with an increased spontaneous firing rate, which together resulted in a decrease in the signal-to-noise ratio. In addition, we report for the first-time that A1 robustly modulated the long-lasting sustained response of MGB neurons which changed the frequency tuning after A1 inactivation, e.g., neurons with sharp tuning increased tuning bandwidth whereas those with broad tuning decreased tuning bandwidth. Taken together, our results demonstrate that corticothalamic modulation in awake marmosets serves to enhance sensory processing in a way similar to center-surround models proposed in visual and somatosensory systems, a finding which supports common principles of corticothalamic processing across sensory systems.

neuroscience↗

bioRxiv2020

Rotavirus Replication Factories Are Complex Ribonucleoprotein Condensates

RNA viruses induce formation of subcellular organelles that provide microenvironments conducive to their replication. Here we show that replication factories of rotaviruses represent protein-RNA condensates that are formed via liquid-liquid phase separation. We demonstrate that rotavirus proteins NSP5 and NSP2 undergo phase separation in vitro and form RNA-rich condensates in vivo that can be reversibly dissolved by aliphatic diols. During infection, these RNA-protein condensates became less dynamic and impervious to aliphatic diols, indicating a transition from a liquid to solid state. Some aspects of assembly of rotavirus replication factories mirror the formation of cytoplasmic ribonucleoprotein granules, while the selective enrichment of viral transcripts appears to be a unique feature of these condensates. Such complex RNA-protein condensates that underlie replication of RNA viruses represent an attractive target for developing novel therapeutic approaches.

biophysics↗

bioRxiv2020

Sterilizing immunity against SARS-CoV-2 in hamsters conferred by a novel recombinant subunit vaccine

A safe and effective SARS-CoV-2 vaccine is essential to avert the on-going COVID-19 pandemic. Here, we developed a subunit vaccine, which is comprised of CHO-expressed spike ectodomain protein (StriFK) and nitrogen bisphosphonates-modified zinc-aluminum hybrid adjuvant (FH002C). This vaccine candidate rapidly elicited the robust humoral response, Th1/Th2 balanced helper CD4 T cell and CD8 T cell immune response in animal models. In mice, hamsters, and non-human primates, 2-shot and 3-shot immunization of StriFK-FH002C generated 28- to 38-fold and 47- to 269-fold higher neutralizing antibody titers than the human COVID-19 convalescent plasmas, respectively. More importantly, the StriFK-FH002C immunization conferred sterilizing immunity to prevent SARS-CoV-2 infection and transmission, which also protected animals from virus-induced weight loss, COVID-19-like symptoms, and pneumonia in hamsters. Vaccine-induced neutralizing and cell-based receptor-blocking antibody titers correlated well with protective efficacy in hamsters, suggesting vaccine-elicited protection is immune-associated. The StriFK-FH002C provided a promising SARS-CoV-2 vaccine candidate for further clinical evaluation.

microbiology↗