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Biology subjects

Pang, B.

Publications and source records attributed to Pang, B..

14 recordsLinked to original sources

Prevention of Unc13a cryptic splicing is sufficient to preserve memory

TDP-43 dysfunction is thought to underlie frontotemporal dementia and limbic-predominant age-related TDP-43 encephalopathy, neurodegenerative dementias currently without effective therapy. Therapeutic strategies are designed to correct individual cryptic targets of TDP-43, such as UNC13A, whereby its cryptic splicing compromises synaptic function, yet the sufficiency of such an approach to prevent memory deficits is unclear. Using a forebrain neuron-specific TDP-43 knockout mouse model that recapitulates TDP-43 dysfunction occurring during early stages of human disorders, we found here that prevention of cryptic splicing to include that of Unc13a attenuated memory deficits. We show that genetic ablation of Unc13a cryptic exon solely in such TDP-43 knockout mice is sufficient to preserve cognition, supporting the clinical value of targeting UNC13A to mitigate memory deficits. Prevention of cryptic splicing of multiple targets of TDP-43 additionally attenuate neuron loss. For optimal outcomes in TDP-43 related dementias, these findings thus strongly support strategies designed to repress cryptic splicing of multiple targets of TDP-43, including UNC13A.

pathology↗

Designing Fidelity of CRISPR-Cas Endonucleases by Kinetic Insights

Finding high-fidelity CRISPR-Cas variants is critical for both the precision of in vitro DNA detection and the safety of in vivo gene-editing therapeutics. However, the large size of the Cas enzyme and the distinct selection criteria between its natural evolution and clinical practice lead to extensive experimental trials and limited success rate for de novo design, directed evolution, protein language model (PLM)-based filtering. Here, we present a PLM-assisted physics-driven approach that utilizes atomistic molecular dynamics simulations and automated path searching to efficiently obtain the complete kinetic insights, including the transition state structures, for the conformational changes of Cas before DNA cleavage. We show that these kinetic insights can pinpoint a few fidelity-diminishing protein residues during the early stage of target recognition, and have led to SpyCas9 and FnCas12a variants with ultra-high fidelity surpassing previously reported counterparts at minimal cost of a few wet-lab trials.

biophysics↗

Adaptive gene transcription in Escherichia coli under environmental stress

Escherichia coli is highly sensitive to acid and osmotic stress but adapts by modulating the expression of stress responsive genes. Nucleoid-associated proteins (NAPs) play key roles in DNA organization and sensing environmental changes. The histone-like nucleoid structuring protein H-NS is an NAP acting as a global regulator of stress genes. H-NS may alter local chromatin structure to modulate the expression of such genes in response to environmental stress. The H-NS homolog StpA co-regulates several target genes, but its precise role is poorly defined. To investigate the regulatory interplay between these two proteins, we examined transcription, DNA binding and chromatin structure at two regulated operons, hdeAB and proVWX, in E. coli following exposure to acid and salt shock. Our results show that H-NS senses pH and osmotic cues to remodel chromatin and relieve repression, while StpA compensates for H-NS loss, particularly at proVWX, highlighting a coordinated regulatory network.

microbiology↗

Delivery of collagen-encoding mRNA to the skin for cosmetic applications

Collagens, the predominant structural proteins in mammalian, maintain tissue integrity through its unique triple-helical conformation. Traditionally, cosmetic collagens have been administered as hydrolyzed peptides derived from animal sources, which exhibit poor bioavailability and functional efficacy due to limited skin penetration and disrupted tertiary/quaternary structures. To overcome these limitations, we developed a novel system for in vivo collagen expression. This system utilizes the topical application of in vitro synthesized, AI-designed mRNAs encoding types I, III, and XVII collagens to improve human skin condition. Significant upregulation of target collagen expression was observed in dermal fibroblasts, leading to improved skin condition through in situ assembly of collagens in natural conformation.

bioengineering↗

Broad brain biodistribution conferred by an AAV to restore TDP-43 function mitigates Frontotemporal Demenia-like deficits

TDP-43 dysfunction is an early pathogenic determinant of frontotemporal lobar degeneration with TDP-43 pathology (FTLD-TDP), a devastating disorder currently without effective therapy. Here, we exploit a blood-brain-barrier (BBB)-permeable AAV (AAV-PHP.eB) that confers broad brain biodistribution to restore TDP-43 function in a TDP-43 deficient model (CamKIIa-CreER;Tardbp mice) that mimics the early stage of TDP-43 dysfunction occurring in FTLD-TDP. Intracerebroventricular delivery by AAV-PHP.eB of CTR, our previously characterized splicing repressor, revealed its accumulation in [~]40% of adult hippocampal neurons. Remarkably, treatment of adult CamKIIa-CreER;Tardbpf/fmice with AAV-PHP.eB-CTR restored TDP-43 function, attenuated neuronal aberrant activity and memory deficits, and rescued neuron loss. Importantly, we showed that TDP-43s autoregulatory element restricts CTR expression to a physiological range. No overt phenotype was observed after long-term exposure to AAV-PHP.eB-CTR in aged mice, highlighting a favorable safety profile for this gene therapy. These results validate that BBB-crossing AAVs can deliver CTR with a biodistribution in the adult brain that is broad enough to rescue FTD-like phenotypes, supporting clinical testing of this gene therapy for FTLD-TDP.

neuroscience↗

A Multi-Disciplinary Framework for Decoding S1PR1-Selective Agonism

Sphingosine-1-phosphate (S1P), a key metabolite of sphingolipids, plays crucial roles in a wide range of physiological and pathological processes. S1P primarily exerts its functions by binding to G protein-coupled sphingosine-1-phosphate receptors (S1PRs), which include five subtypes (S1PR1-5), thereby activating these receptors and their downstream signaling pathways. Understanding the molecular determinants that govern agonist selectivity among different S1PR subtypes is vital for the rational and precise development of targeted therapeutic agents. Here, four cryo-electron microscopy structures of agonist-bound S1PR1-Gi complexes are reported. Through an integrated approach combining structural analysis, molecular dynamics simulations, and pharmacological assays, the molecular basis for the selectivity of CYM5442, HY-X-1011, Ponesimod, and SAR247799 toward S1PR1 over S1PR3 and S1PR5 is uncovered. Specifically, the selectivity arises from a combination of non-conserved residues within the ligand-binding pocket and at the Gi-protein interface, distinct curved agonist-binding modes oriented toward transmembrane helices 5-7 that cause steric clashes with S1PR3, and the presence of branched moieties at the lower part of three agonists. These features collectively enhance agonist potency and efficacy for S1PR1 while reducing activity at S1PR3 and S1PR5. These findings establish a structural framework for the rational design of next-generation S1PR1 highly selective agonists with improved therapeutic potential.

biochemistry↗

Genetic variants within silencer elements contribute to human blood cell traits

Genome-wide association studies (GWAS) have identified numerous non-coding loci associated with human complex traits and diseases. However, assigning the functional impacts to the underlying variants remains challenging. In this study, we performed high-throughput ReSE screening to characterize the effects of 14,720 fine-mapped causal non-coding SNPs associated with 15 diverse blood traits on the potential silencer activity. By prioritizing non-coding variants that confer allelic imbalances in silencer activity, we identified epigenomic signatures of silencer-related variants and assessed their heritability contributions to specific blood traits. We conducted mechanistic studies on individual silencer variants and characterized the transcriptional factors (TF) that may recognize the silencer elements harboring the blood traits-related GWAS variants. We showed the silencer activity of GWAS variants rs4808806 which is related to red blood cell distribution width (RDW) and rs10758656 which is associate with mean corpuscular hemoglobin (MCH) and mean corpuscular volume (MCV) traits. Our study underscores the importance of investigating the silencer-activity-related variants in post-GWAS functional studies.

genetics↗

PROTAC molecule-mediated SpCas9 protein degradation for precise genome editing

CRISPR (clustered regularly interspaced short palindromic repeats) technology has revolutionized both fundamental research and genomic medicine. The need for precise control of SpCas9-based CRISPR genome editing has led to the development of various strategies to regulate Cas9 activity, aiming to minimize off-target effects. Proteolysis-targeting chimeras (PROTACs) use the ubiquitin-proteasome system to selectively degrade target proteins. Here, we developed CASPROTAC 6, a reversible and cell-permeable PROTAC degrader that directly targets SpCas9 proteins for degradation. The CASPROTAC 6 molecule was derived by linking a known SpCas9 binder BRD7087 with an S-substituted Lenalidomide cereblon (CRBN) ligand via a six-carbon alkyl linker. Our data show that CASPROTAC 6 is a broad-spectrum degrader of SpCas9 and variants such as dCas9 and Cas9 nickases. CASPROTAC 6 degrades SpCas9 and the SpCas9-guide RNA complex via the proteasome system by approximately 50%. As a result, CASPROTAC 6 effectively enhanced the precision of CRISPR/Cas9-mediated genome editing by increasing target specificity. CASPROTAC 6 may serve as modulators of CRISPR/SpCas9-associated nucleases, enabling precise genome editing while reducing off-target effects and enhancing biosafety.

biochemistry↗

Targeting the 3D genome by anthracyclines for chemotherapeutic effects

The chromatin is folded into three-dimensional (3D) structures, and aberrant 3D chromatin folding has been implicated in cancer. We performed ATAC-seq and TOP2A ChIP-seq to assess the potential effects of various anthracycline drugs on the chromatin architecture. We found that specific anthracycline variants selectively disrupt chromatin looping anchors by interfering with CTCF binding, suggesting an additional therapeutic mechanism of anthracycline drugs targeting the 3D genome. Hi-C experiments in K562 cells treated with anthracycline drugs revealed widespread disruption of 3D chromatin organization, including altered long-range regulation at the Myc locus. Furthermore, AML patients treated with anthracycline drugs exhibited changes in chromatin structures near possible looping anchors, which were associated with distinct clinical outcomes. Together, our findings indicate that anthracycline drugs function as potent and selective epigenomic modulators, with the capacity to further target the 3D genome to exert anticancer effects, highlighting their potential for personalized therapy in tumors with aberrant 3D chromatin architecture. SignificanceChromatin structure plays a crucial role in regulating gene expression and maintaining cellular function. Aberrant chromatin 3D organization is a common feature in cancer. In this study, we investigate how anthracycline chemotherapy affects chromatin architecture using state-of-the-art genomic profiling techniques, including ATAC-seq, TOP2A ChIP-seq, CTCF ChIP-seq, and Hi-C. We show that certain anthracycline variants disrupt chromatin looping by interfering with CTCF binding, thereby altering the spatial genome organization. This disruption leads to changes in the regulation of associated genes, as exemplified by the Myc locus, and is associated with distinct clinical outcomes in AML patients. These findings highlight the potential of anthracycline drugs as therapeutics that target both the epigenome and 3D chromatin architecture, a promising strategy in personalized therapy.

cancer biology↗

The structural basis of itch receptor MRGPRX1 activation

Mas-related G-protein-coupled receptors X1-X4 (MRGPRX1-X4) are four primate-specific receptors that are recently reported to be responsible for many biological processes, including itch sensation, pain transmission, and inflammatory reactions. MRGPRX1 is the first identified human MRGPR, and its expression is restricted to primary sensory neurons. Due to its dual roles in itch and pain signaling pathways, MRGPRX1 has been regarded as a promising target for itch remission and pain inhibition. Here, we reported a cryo-electron microscopy (cryo-EM) structure of Gq-coupled MRGPRX1 in complex with a synthetic agonist compound 16 in an active conformation at an overall resolution of 3.0 angstrom via a NanoBiT tethering strategy. Compound 16 is a new pain-relieving compound with high potency and selectivity to MRGPRX1 over opioid receptor. According to the structure analysis, we revealed that MRGPRX1 shares common features of the Gq-mediated receptor activation mechanism of MRGPRX family members. However, the variable residues in orthosteric pocket of MRGPRX1 exhibits the unique agonist recognition pattern, which may facilitate to design MRGPRX1-specific modulators. Together with receptor activation and itch behavior evaluation assays, our study provides a structural snapshot to modify therapeutic molecules for itch relieving and analgesia targeting MRGPRX1.

biochemistry↗

Transcriptome analysis of SARS-CoV-2 naive and recovered individuals vaccinated with inactivated vaccine

The urgent approval of the use of the inactivated COVID-19 vaccine is essential to reduce the threat and burden of the epidemic on global public health, however, our current understanding of the host immune response to inactivated vaccine remains limited. Herein, we performed serum IgG antibody detection and transcriptomics analysis on 20 SARS-CoV-2 naive individuals who received multiple doses of inactivated vaccine and 5 SARS-CoV-2 recovered individuals who received single dose of inactivated vaccine. Our research revealed the important role of many innate immune pathways after vaccination, identified a significant correlation with the third dose of booster vaccine and proteasome-related genes, and found that SARS-CoV-2 recovered individuals can produces a strong immune response to a single dose of inactivated vaccine. These results help us understand the reaction mechanism of the hosts molecular immune system to the inactivated vaccine, and provide a basis for the choice of vaccination strategy.

microbiology↗

Crystal structure of steroid reductase SRD5A reveals conserved steroid reduction mechanism

Steroid hormones are essential in stress response, immune system regulation, and reproduction in mammals. Steroids with 3-oxo-{Delta}4 structure, such as testosterone, androstenedione and progesterone, could be catalyzed by steroid 5-reductases (SRD5As) to generate their corresponding 3-oxo-5 steroids, which are essential for multiple physiological and pathological processes. Abnormal activities of SRD5As will lead to benign prostatic hyperplasia, alopecia, prostatic cancer or infertility due to the poor quality of sperms. However, the detailed reduction mechanisms of SRD5As remain elusive. Here we report the crystal structure of PbSRD5A, which shares 60.6% and 51.5% sequence similarities with human SRD5A1 and -2 respectively, from Proteobacteria bacterium in complex with the cofactor NADPH at 2.0 [A] resolution. PbSRD5A exists as a monomer comprised of seven transmembrane segments (TMs). The TM1-4 enclose a hydrophobic cavity for steroids substrates binding, whereas TM5-7 coordinate with cofactor NADPH through extensive hydrogen bonds network. Homology-based structural models of HsSRD5A1 and -2, together with extensive biochemical characterizations, for the first time unveiled the substrate recognition of SRD5As and provide an important framework for further understanding of the mechanism of NADPH mediated steroids 3-oxo-{Delta}4 reduction. Based on these analyses, the design of therapeutic molecules targeting SRD5As with improved specificity and therapeutic efficacy would be possible. One Sentence SummaryStructural and biochemical characterizations decipher the evolutionarily conserved mechanism in steroid 5-reductases catalyzing NADPH mediated steroids reduction.

biochemistry↗

Evolution-guided engineering of small-molecule biosensors

Allosteric transcription factors (aTFs) have proven widely applicable for biotechnology and synthetic biology as ligand-specific biosensors enabling real-time monitoring, selection and regulation of cellular metabolism. However, both the biosensor specificity and the correlation between ligand concentration and biosensor output signal, also known as the transfer function, often needs to be optimized before meeting application needs. Here, we present a versatile and high-throughput method to evolve and functionalize prokaryotic aTF specificity and transfer functions in a eukaryote chassis, namely bakers yeast Saccharomyces cerevisiae. From a single round of directed evolution of the effector-binding domain (EBD) coupled with various toggled selection regimes, we robustly select aTF variants of the cis, cis-muconic acid-inducible transcription factor BenM evolved for change in ligand specificity, increased dynamic output range, shifts in operational range, and a complete inversion of function from activation to repression. Importantly, by targeting only the EBD, the evolved biosensors display DNA-binding affinities similar to BenM, and are functional when ported back into a non-native prokaryote chassis. The developed platform technology thus leverages aTF evolvability for the development of new host-agnostic biosensors with user-defined small-molecule specificities and transfer functions.

synthetic biology↗

ASCOT identifies key regulators of neuronal subtype-specific splicing

Public archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here we present ASCOT, a resource that allows researchers to summarize, visualize, and query alternative splicing patterns in public RNA-Seq data. ASCOT enables rapid identification of splice-variants across tens of thousands of bulk and single-cell RNA-Seq datasets in human and mouse. To demonstrate the utility of ASCOT, we first focused on the nervous system and identified many alternative exons used only by a single neuronal subtype. We then leveraged datasets from the ENCODE and GTEx consortiums to study the unique splicing patterns of rod photoreceptors and found that PTBP1 knockdown combined with overexpression of MSI1 and PCBP2 activates rod-specific exons in HepG2 liver cancer cells. Furthermore, we observed that MSI1 targets intronic UAG motifs proximal to the 5 splice site and interacts synergistically with PTBP1 downregulation. Finally, we show that knockdown of MSI1 in the retina abolishes rod-specific splicing. This work demonstrates how large-scale analysis of public RNA-Seq datasets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events. ASCOT splicing and gene expression data tables, software, and interactive browser are available at http://ascot.cs.jhu.edu.

neuroscience↗