Biology subjects

Feng, S.

Publications and source records attributed to Feng, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Identification and Characterization of a Small Molecule Ligand for the Huntingtin-HAP40 Complex

Huntingtons disease (HD) is caused by a CAG repeat expansion mutation, giving rise to a polyglutamine expansion in the huntingtin (HTT). However, the explicit molecular functions of HTT and opportunities for direct pharmacological modulation remain incompletely understood. Here, we report the discovery of a small molecule ligand for the full-length HTT protein in complex with its partner, HAP40. Using affinity selection mass spectrometry (AS-MS), we identified a stereoselective binder, whose binding was characterized by surface plasmon resonance, hydrogen-deuterium exchange mass spectrometry, and cryo-electron microscopy at 2.3 [A] resolution. The ligand binds HTT-HAP40 in vitro with single-digit micromolar affinity and one-to-one stoichiometry at a druggable interface previously predicted computationally. In silico studies predicted and experimental analyses confirmed the (R)-enantiomer as the eutomer and initial structure activity relationship was established experimentally. This work details a structurally-validated chemical scaffold and highlights a ligandable pocket which could enable development of chemical probes for probing HTT biology, as well as therapeutics such as degraders and imaging agents for HD.

pharmacology and toxicology↗

bioRxiv2025

CDH3 as a Novel Therapeutic Target in Basal-like Double-Negative Prostate Cancer

PurposeBasal-like (also known as double-negative) prostate cancers are aggressive tumors that lack effective targeted therapies. We aimed to delineate the role of CDH3 (P-cadherin) in basal-like prostate cancer and evaluate CDH3-directed therapeutic strategies. MethodsWe integrated genetically engineered mouse models (GEMMs) of prostate cancer, bulk and single-cell transcriptomic analyses, and a suite of in vitro and in vivo experiments. CDH3 expression and associated signaling pathways were examined in Pten/Apc double-knockout mouse prostates and human datasets. Functional studies included antibody-drug conjugate (ADC) cytotoxicity assays and the development of chimeric antigen receptor (CAR) T cells targeting CDH3, tested in prostate cancer cell lines and xenograft models. ResultsPten/Apc double deletion in prostate GEMMs led to highly aggressive tumors with markedly elevated CDH3 expression and enrichment of non-canonical WNT signaling components. Transcriptomic analyses of patient-derived prostate tumors confirmed that CDH3 is significantly upregulated in basal-like prostate cancer subtypes relative to luminal subtypes. Single-cell RNA sequencing revealed CDH3 expression predominantly in basal epithelial cells. Mechanistically, we found that active YAP1 signaling and a WNT5A-ROR2 non-canonical WNT axis drive CDH3 expression. Targeting CDH3 with a CDH3-specific ADC induced potent, antigen-dependent killing of CDH3 prostate cancer cells in vitro and significantly suppressed tumor growth in in vivo metastatic prostate cancer models. Likewise, CDH3-targeted CAR T cells specifically recognized and lysed CDH3-expressing prostate tumor cells while sparing CDH3-negative cells, leading to tumor regression and improved survival in mouse models, especially when combined with PD-1 checkpoint blockade. ConclusionsCDH3 is a key marker and functional driver of basal-like prostate cancer. Therapeutic strategies leveraging CDH3, including ADCs and CAR T cells, demonstrate strong preclinical efficacy, supporting the development of CDH3-targeted treatments to overcome resistance in aggressive prostate cancer.

cancer biology↗

bioRxiv2025

Virus induced transgene- and tissue-culture free heritable genome editing in tomato

Genome editing has emerged as a powerful tool for genome manipulation and trait improvement in crops. However, most commonly used approaches rely on tissue culture and transgenic materials, which are time-consuming, labor-intensive, and often strongly genotype-dependent. Here, we developed a tobacco rattle virus (TRV)-based system to deliver the compact ISYmu1 TnpB endonuclease, coupled with in planta shoot regeneration, to achieve somatic and heritable genome editing across different tomato cultivars without tissue culture. By targeting SlPDS, we successfully generated virus-free homozygous mutant progeny in a single generation. Furthermore, we extended this system to the functional analysis of the previously uncharacterized SlDA1 locus, revealing its involvement in organ size regulation, and recovered transgene-free SlDA1 mutants displaying enlarged fruits. Given the wide host range of TRV, our system should be broadly applicable for rapid, non-transgenic and less genotype-dependent heritable genome editing, thereby advancing both functional genomics and crop improvement. SignificanceEfficient genome editing without the need for transgenesis or tissue culture remains a major challenge in crop breeding. Here, we establish a simple single-step system for transgene- and tissue culture-free genome editing in tomato based on Tobacco Rattle Virus-mediated delivery of the compact RNA-guided TnpB enzyme ISYmuI and its guide RNA. This strategy enabled somatic editing of de novo shoots and heritable transmission of targeted mutations to the next generation. Notably, editing an agronomically relevant gene produced tomato plants with larger fruits, highlighting the potential of this system for crop improvement.

plant biology↗

bioRxiv2025

A 5'-end based Molecular Marker Enables Identification and Deployment of a Functional Rpi-vnt1.1 Allele for Durable Late Blight Resistance in Potato

Potato (Solanum tuberosum) is a globally important food crop, yet its production is severely threatened by late blight, caused by Phytophthora infestans. Deploying resistance (R) genes in breeding programs offers a sustainable approach for disease management. Rpi-vnt1.1 is a broad-spectrum R gene cloned from wild Solanum species Solanum venturii. Here, we developed a PCR marker targeting the 5'-end extension of Rpi-vnt1.1, which enables efficient and specific detection of the resistant alleles. Screening of advanced breeding lines from the International Potato Center (CIP) identified line C1848, which carries a functional Rpi-vnt1.1 allele. Inoculation assays confirmed C1848 confers strong resistance to P. infestans. Subsequent functional assays, including RNAi-mediated silencing in C1848 and heterologous expression in Nicotiana benthamiana, demonstrated that this resistance is specifically mediated by the Rpi-vnt1.1 allele. This specific marker provides a rapid, low-cost tool for marker-assisted breeding, facilitating the deployment of potato cultivars carrying Rpi-vnt1.1.

plant biology↗

bioRxiv2025

CDCA7 facilitates MET1-mediated CG DNA methylation maintenance in centromeric heterochromatin via histone H1

DNA methylation is a conserved epigenetic modification essential for maintaining genome stability. However, how methyltransferases maintain CG methylation within compact chromatin, including centromeres, remains unclear. In humans, CDCA7 is necessary for the inheritance of DNA methylation at juxta-centromeres. Mutations that impair its ability to bind chromatin result in Immunodeficiency, Centromeric Instability, and Facial Anomalies (ICF) syndrome, characterized by centromeric instability. To investigate whether CDCA7 function is conserved, we identified two Arabidopsis thaliana orthologs, CDCA7A and CDCA7B. The loss of both copies results in CG hypomethylation at pericentromeric regions and centromeric satellite repeat arrays. Machine learning analysis suggested that heterochromatic nucleosomes, with enrichment of H1, H2A.W, and H3K9me2 levels, depend heavily on CDCA7 proteins for CG methylation maintenance of the associated DNA. Loss of H1 restores heterochromatic DNA methylation in cdca7a cdca7b mutants, indicating that CDCA7A and CDCA7B mainly remodel H1-containing nucleosomes for methyltransferases to access DNA. Notably, in h1.1 h1.2 mutants, CG methylation shows a significant increase in centromeres, which reveals a new inhibitory role of H1 in DNA methylation maintenance within satellite repeat arrays. Centromeric DNA hypermethylation is lost in h1.1 h1.2 cdca7a cdca7b quadruple mutants, demonstrating that CDCA7A and CDCA7B can act independently of H1 to enhance MET1 activity. Overall, these findings establish CDCA7A and CDCA7B as conserved regulators of DNA methylation within heterochromatin and centromeric satellite repeat arrays.

molecular biology↗

bioRxiv2025

CryoDataBot: a pipeline to curate cryoEM datasets for AI-driven structural biology

Cryogenic electron microscopy (cryoEM) has revolutionized structural biology by enabling atomic-resolution visualization of biomacromolecules. To automate atomic model building from cryoEM maps, artificial intelligence (AI) methods have emerged as powerful tools. Although high-quality, task-specific datasets play a critical role in AI-based modeling, assembling such resources often requires considerable effort and domain expertise. We present CryoDataBot, an automated pipeline that addresses this gap. It streamlines data retrieval, preprocessing, and labeling, with fine-grained quality control and flexible customization, enabling efficient generation of robust datasets. CryoDataBots effectiveness is demonstrated through improved training efficiency in U-Net models and rapid, effective retraining of CryoREAD, a widely used RNA modeling tool. By simplifying the workflow and offering customizable quality control, CryoDataBot enables researchers to easily tailor dataset construction to the specific objectives of their models, while ensuring high data quality and reducing manual workload. This flexibility supports a wide range of applications in AI-driven structural biology.

molecular biology↗

bioRxiv2025

Diploid genomes of the booklouse reveal evolutionary consequences ofasexuality

The "Meselson Effect"--a cornerstone of evolutionary theory predicting that asexual organisms accumulate mutations independently across haplotypes due to the absence of recombination--has long eluded robust empirical validation. Here, we address this gap using three high-quality diploid genome assemblies of the obligately parthenogenetic booklouse Liposcelis bostrychophila, a species characterized by apomictic meiosis and striking intraspecific variation. Combining Illumina, PacBio, and Hi-C sequencing, we generated three diploid genomes of three populations (Lb_1, Lb_2, Lb_3), revealing exceptionally high heterozygosity rates (1.67-3.92%) and minimal recombination--hallmarks of prolonged asexuality. Critically, in population Lb_2, intra-individual SNP divergence surpassed inter-population levels, directly demonstrating the Meselson Effect. Phylogenetic analyses of 7,029 genes revealed that while haplotypes within populations clustered as expected under sexual reproduction, nearly 15% of gene trees exhibited topologies consistent with asexual divergence--a signature of incipient Meselson-driven evolution. Comparative genomic analyses further uncovered a twofold expansion of repetitive elements in asexual lineages relative to their sexual relatives (L. brunnea) and widespread relaxation of purifying selection, particularly affecting transcription factor activities. We propose that relaxed selection on transcriptional regulators may act as a compensatory mechanism, buffering the functional consequences of escalating heterozygosity in non-recombining genomes. By integrating population genomics, phylogenomics, and selection analyses, this work not only provides the clearest evidence to date of the Meselson Effect but also establishes L. bostrychophila as a pivotal model for unraveling the genomic paradox of parthenogenesis. Significance StatementThe Meselson Effect, a theoretical prediction that asexual organisms should accumulate mutations independently in their two haplotypes, has been difficult to confirm empirically due to limited genomic data and contradictory findings in prior studies. Here, we provide strong evidence for the Meselson Effect in the parthenogenetic booklouse Liposcelis bostrychophila, using high-quality diploid genomes from three populations. We show that one population exhibits higher genetic divergence within individuals than between populations, a key signature of the Meselson Effect. Additionally, we found a possible novel compensatory mechanism for maintaining genomic stability in the face of increased heterozygosity. These findings advance our understanding of the genomic impacts under asexuality and establish L. bostrychophila as a model for studying the evolutionary consequences of parthenogenesis.

evolutionary biology↗

bioRxiv2025

SPT5 regulates Pol II pausing and elongation in different ways at early versus late embryonic stages

Transcription involves a cycle of initiation, pausing, elongation, and termination. SPT5 regulates both promoter proximal pausing and elongation, but how it orchestrates both steps during dynamic changes in gene expression remains unclear. Here, using Drosophila embryogenesis, we show that pausing both precedes and follows gene expression, while active transcription is accompanied by pause release. Optogenetic rapid depletion of SPT5 from the nucleus uncovered different sensitivities at different developmental stages. In early embryogenesis, SPT5 depletion caused a downstream shift in Pol II pausing to the +1 nucleosome, resulting in defective elongation and early termination. In late embryogenesis, it led to both up- and downregulation of expression, depending on the genes transcriptional and pausing state - upregulation is caused by pause release while downregulation is due to defective elongation. These changes are intensified when genes are increasing or decreasing their transcriptional state, indicating that SPT5 contributes to fine-tuning dynamic changes in gene expression.

genomics↗

bioRxiv2025

Sequence-Specific Installation of Aryl Groups in RNA via DNA-Catalyst Conjugates

Installing functional groups at specific sites in existing RNA molecules remains a challenge for modification, labeling, and therapeutic strategies. Here we describe the use of DNA oligonucleotides carrying a catalytic amine group to effect the aqueous SNAr arylation of 2'-OH groups at sequence-complementary sites in RNAs. Chloro-pyrimidine electrophiles are shown to react with amino-DNA conjugates, resulting in a proposed transient ammonium aryl intermediate that can react with RNA near the DNA binding site, delivering the heterocycle to the RNA in high yields. In a test of utility, we construct an aryl electrophile carrying an azide group, and apply this strategy to fluorescently label messenger RNAs locally at the polyA tail. We also employ the approach to direct in vitro arylation in the coding region of a messenger RNA, knocking down protein expression selectively in the presence of another coding RNA. This sequence-directed catalytic strategy enables multiple applications in RNA labeling and modification.

biochemistry↗

bioRxiv2025

Active learning-guided optimization of cell-free biosensors for lead testing in drinking water

Point-of-use diagnostics based on allosteric transcription factors (aTFs) are promising tools for environmental monitoring and human health. However, biosensors relying on natural aTFs rarely exhibit the sensitivity and selectivity needed for real-world applications, and traditional directed evolution struggles to optimize multiple biosensor properties at once. To overcome these challenges, we develop a multi-objective, machine learning (ML)-guided cell-free gene expression workflow for engineering aTF-based biosensors. Our approach rapidly generates high-quality sequence-to-function data, which we transform into an augmented paired dataset to train an ML model using directional labels that capture how aTF mutations alter performance. We apply our workflow to engineer the aTF PbrR as a point-of-use diagnostic for lead contamination in water. We tune the sensitivity of PbrR to sense at the U.S. Environmental Protection Agency (EPA) action level for lead and modify the selectivity away from zinc, a common metal found in water supplies. Finally, we show that the engineered PbrR functions in freeze-dried cell-free reactions, enabling a diagnostic capable of detecting lead in drinking water down to [~]5.7 ppb. Our ML-driven, multi-objective framework--powered by directional tokens-- can generalize to other biosensors and proteins, accelerating the development of synthetic biology tools for biotechnology applications.

synthetic biology↗

bioRxiv2025

HSV-1 infection induces brain cofilin hyperphosphorylation in the 5xFAD Alzheimer's Disease mouse model

Alzheimers disease (AD) is a degenerative neurological disease characterized by various biological signatures, including synaptic dysfunction, {beta}-amyloid plaques, hyperphosphorylated Tau, cofilin-actin rods, and Hirano bodies, all of which are linked to the actin cytoskeleton and its regulators. Additionally, the presence of herpes simplex virus type 1 (HSV-1) in the brains of AD patients has long been suggested as a contributing factor for AD. However, mechanisms by which HSV-1 accelerates AD pathogenesis remain poorly understood. Here we report that HSV-1 infection induces hyperphosphorylation of cofilin in the brains of 5xFAD mice. Cofilin is an actin depolymerizing factor, and its S3 phosphorylation inactivates cofilins activity to depolymerize actin filaments. These findings facilitate the understanding of impacts of HSV-1 infection on the development of Alzheimers disease and have implications in AD therapeutics.

microbiology↗

bioRxiv2025

ProteoMeter: A pipeline for integrating multi-PTM and limited proteolysis data to reveal modification-structure coupling at the residue level

Systemic perturbations trigger extensive changes across the proteome-altering protein abundance, post-translational modifications (PTMs), conformational states, and complex assembly. Interpreting these effects demands computational pipelines capable of integrating diverse proteomics modalities, such as multi-PTM profiling, limited proteolysis mass spectrometry (LiP-MS), and cross-linking mass spectrometry (XL-MS), within a unified and interoperable framework. Because instrument data are quantified at the peptide level, mapping these measurements to individual residue or modification site is essential for biologically meaningful interpretation. We introduce ProteoMeter, an open-source Python library designed to integrate multi-modal proteomics datasets and map them to single-residue resolution using a standardized coordinate framework. We showcase its capabilities in a combined multi-PTM and LiP-MS analysis profiling the proteomic response to human coronavirus 229e (HCoV-229E) infection.ProteoMeteris actively maintained and is freely available-including all source code and figure-generation scripts-at the following repository: https://github.com/PNNL-Predictive-Phenomics/ProteoMeter.

systems biology↗

bioRxiv2025

SORLA upregulation suppresses global pathological effects in aged tauopathy mouse brain

A role for the trafficking receptor SORLA in reducing A{beta} levels has been well-established, however, relatively little is known with respect to whether and how SORLA can potentially affect tau pathology in vivo. Here, we show that transgenic SORLA upregulation (SORLA TG) can reverse pathological effects in aged PS19 (P301S tau) mouse brain, including tau phosphorylation and seeding, ventricle dilation, synapse loss, LTP impairment and glial hyperactivation. Proteomic analysis indicates reversion of PS19 profiles in PS19/SORLA TG hippocampus, including pathological changes in synapse-related proteins as well as key drivers of synaptic dysfunction such as Apoe and C1q. snRNA-seq analysis reveals suppression of PS19- signatures with SORLA upregulation, including proinflammatory induction of Plxnb1/Plxnb2 in glia. Tau seeding and aggregation, neuroinflammation, as well as PlxnB1/B2 induction are exacerbated in PS19 hippocampus with SORLA deletion. These results implicate a global role for SORLA in neuroprotection from tau toxicity in PS19 mouse brain.

neuroscience↗

bioRxiv2025

Genome-wide CRISPR screens identify PTGES3 as a novel AR modulator

The androgen receptor (AR) is a critical driver of prostate cancer (PCa). To study regulators of AR protein levels and oncogenic activity, we created the first live cell quantitative endogenous AR fluorescent reporters. Leveraging this novel AR reporter, we performed genome-scale CRISPRi flow cytometry sorting screens to systematically identify genes that modulate AR protein levels. We identified and validated known AR protein regulators including HOXB13 and GATA2 and also unexpected top hits including PTGES3, a poorly characterized gene in PCa. PTGES3 repression resulted in loss of AR protein, cell cycle arrest, and cell death in AR-driven PCa models. PTGES3 is not a commonly essential gene, and our data nominate it as a prime PCa therapeutic target. Clinically, analysis of PCa data demonstrate that PTGES3 expression is associated with AR-directed therapy resistance. Mechanistically, we show PTGES3 binds directly to AR, forms a protein complex with AR in the nucleus, regulates AR protein stability in vitro and in vivo and modulates AR function in the nucleus at AR target genes. PTGES3 represents a novel therapeutic target for overcoming known mechanisms of resistance to existing AR-directed therapies in PCa.

cancer biology↗

bioRxiv2025

Bona fide hematopoietic stem cells in zebrafish originate from the supra-intestinal artery

Hematopoietic stem cells (HSCs) in vertebrates are widely believed to originate from hemogenic endothelial cells (HECs) in the dorsal aorta (DA) through endothelial-to-hematopoietic transition. However, conclusive in vivo DA-specific lineage-tracing studies to confirm this origin are lacking. Here, leveraging infrared light-mediated temporospatial-resolution lineage-tracing technology, we demonstrate that in zebrafish, HSCs do not originate from the DA. Instead, following the DA hematopoiesis, which produces hematopoietic precursors with limited renewal potential, lifelong renewable HSCs emerge from the supra-intestinal artery (SIA). Remarkably, while the DA produces hematopoietic cells from unipotent HECs, the SIA generates hematopoietic cells from both unipotent HECs and bipotent vessel-resident hemangioblasts (VRHs). These VRHs undergo multiple rounds of division and budding, generating both hematopoietic cells and SIA-resident endothelial cells. The distinct characteristics of DA and SIA cells are further reinforced by single-cell transcriptomic profiling. Our findings challenge the current paradigm of HSC development, underscoring the complexity of vertebrate hematopoiesis.

developmental biology↗

bioRxiv2025

SoftAlign: End-to-end protein structures alignment

With the recent breakthrough of highly accurate structure prediction methods, there has been a rapid growth of available protein structures. Efficient methods are needed to infer structural similarity within these datasets. We present an end-to-end alignment method, called SoftAlign, which takes as input the 3D coordinates of a protein pair and outputs a structural alignment. In addition to the traditional Smith-Waterman alignment method, we introduce a modified softmax alignment that shows very promising results for structure similarity detection. We demonstrate that the SoftAlign model is able to recapitulate TM-align alignments while running faster, and it is more accurate than Foldseek on alignment and classification tasks. Although SoftAlign is not the fastest method available, it is highly precise and can be used effectively with other prefilters. In addition to developing an end-to-end structural aligner, our main contribution is the introduction and analysis of a pseudo-alignment method based on softmax, which can be used with other architectures, even those not based on structural information. The code for SoftAlign is available at https://github.com/jtrinquier/SoftAlign.

bioinformatics↗

bioRxiv2025

BABA: Naturalistic fMRI and MEG recordings during viewing of a reality TV show

Prior neuroimaging datasets using naturalistic listening paradigms have predominantly focused on single-talker scenarios. While these studies have been invaluable for advancing our understanding of speech and language processing in the brain, they do not capture the complexities of real-world multi-talker environments. Here, we introduce the "Le Petit Prince (LPP) Multi-talker Dataset", a high-quality, naturalistic neuroimaging dataset featuring 40 minutes of electroencephalogram (EEG) and 7T functional magnetic resonance imaging (fMRI) recordings from 26 native Mandarin Chinese speakers as they listened to both single-talker and multi-talker speech streams. Validation analyses conducted on both EEG and fMRI data demonstrate the datasets high quality and robustness. Additionally, the dataset includes detailed transcriptions and prosodic and linguistic annotations of the speech stimuli, enabling fine-grained analyses of neural responses to specific linguistic and acoustic features. The LPP Multi-talker Dataset is well-suited for addressing a wide range of research questions in cognitive neuroscience, including selective attention, auditory stream segregation, and working memory processes in naturalistic listening contexts.

neuroscience↗

bioRxiv2025

Effects of amendments on remediation of heavy metal contaminated soil and accumulation of Cd and Pb in potato

With the development of agriculture and industry, a large amount of heavy metals are loaded into the soil, posing a high ecological and public health risk. Many methods have been proposed to repair heavy metal contaminated soil, such as electroremediation, chemical washing, phytoremediation and in situ fixation. In the above methods, the application of passivators to in-situ immobilization of heavy metals is an environmentally friendly and cost-effective choice. The effects of different amendments on the improvement of heavy metal contaminated soil and the accumulation of Cd and Pb in potato plants were investigated by using attapulgite, diatomite and humic acid as materials.The results showed that soil pH, organic matter content and cation exchange capacity increased after the application of amendments. Under the treatment of attapulgite+humic acid, the soil pH, organic matter content and cation exchange capacity were increased by 0.57units, 10.0 mg/kg and 7.28cmol/kg, respectively, compared with the control. The content of soil hydrolyzable nitrogen increased, and the content of available phosphorus decreased. The application of amendments increased soil enzyme activity; effectively reduce the bioavailability of Cd and Pb in soil ; under the treatment of attapulgite+humic acid, the contents of Cd and Pb in potato plants decreased by 85.50%and 55.54%respectively, and the contents of Cd and Pb in potato tubers decreased to 0.08 mg/kg and 1.41 mg/kg respectively. The application of amendments affected the accumulation and transport of heavy metals Cd and Pb in potato plants to a certain extent and promoted the transformation of Cd and Pb from acid-soluble and reduced states to oxidized and residual states.

ecology↗