Theoretical framework for the difference of two negative binomial distributions and its application in comparative analysis of sequencing data.

High-throughput sequencing (HTS) technologies have been instrumental in investigating biological questions at the bulk and single-cell levels. Comparative analysis of two HTS data sets often relies on testing the statistical significance for the difference of two negative binomial distributions (DOTNB). Although negative binomial distributions are well studied, the theoretical results for DOTNB remain largely unexplored. Here, we derive basic analytical results for DOTNB and examine its asymptotic properties. As a state-of-the-art application of DOTNB, we introduce DEGage, a computational method for detecting differentially expressed genes (DEGs) in scRNA-seq data. DEGage calculates the mean of the sample-wise differences of gene expression levels as the test statistic and determines significant differential expression by computing the P-value with DOTNB. Extensive validation using simulated and real scRNA-seq data sets demonstrates that DEGage outperforms five popular DEG analysis tools: DEGseq2, DEsingle, edgeR, Monocle3, and scDD. DEGage is robust against high dropout levels and exhibits superior sensitivity when applied to balanced and imbalanced data sets, even with small sample sizes. We utilize DEGage to analyze prostate cancer scRNA-seq data sets and identify marker genes for 17 cell types. Furthermore, we apply DEGage to scRNA-seq data sets of mouse neurons with and without fear memory and reveal eight potential memory-related genes overlooked in previous analyses. The theoretical results and supporting software for DOTNB can be widely applied to comparative analyses of dispersed count data in HTS and broad research questions.

Structural Basis of Dot1L Stimulation by Histone H2B Lysine 120 Ubiquitination.

The essential histone H3 lysine 79 methyltransferase Dot1L regulates transcription and genomic stability and is deregulated in leukemia. The activity of Dot1L is stimulated by mono-ubiquitination of histone H2B on lysine 120 (H2BK120Ub); however, the detailed mechanism is not understood. We report cryo-EM structures of human Dot1L bound to (1) H2BK120Ub and (2) unmodified nucleosome substrates at 3.5 Å and 4.9 Å, respectively. Comparison of both structures, complemented with biochemical experiments, provides critical insights into the mechanism of Dot1L stimulation by H2BK120Ub. Both structures show Dot1L binding to the same extended surface of the histone octamer. In yeast, this surface is used by silencing proteins involved in heterochromatin formation, explaining the mechanism of their competition with Dot1. These results provide a strong foundation for understanding conserved crosstalk between histone modifications found at actively transcribed genes and offer a general model of how ubiquitin might regulate the activity of chromatin enzymes.

Boosting the toolbox for live imaging of translation.

Live imaging of translation based on tag recognition by a single-chain antibody is a powerful technique to assess translation regulation in living cells. However, this approach is challenging and requires optimization in terms of expression level and detection sensitivity of the system, especially in a multicellular organism. Here, we improved existing fluorescent tools and developed new ones to image and quantify nascent translation in the living Drosophila embryo and in mammalian cells. We tested and characterized five different green fluorescent protein variants fused to the single-chain fragment variable (scFv) and uncovered photobleaching, aggregation, and intensity disparities. Using different strengths of germline and somatic drivers, we determined that the availability of the scFv is critical in order to detect translation throughout development. We introduced a new translation imaging method based on a nanobody/tag system named ALFA-array, allowing the sensitive and simultaneous detection of the translation of several distinct mRNA species. Finally, we developed a largely improved RNA imaging system based on an MCP-tdStaygold fusion.

Self-supervised deep clustering of single-cell RNA-seq data to hierarchically detect rare cell populations.

Single-cell RNA sequencing (scRNA-seq) is a widely used technique for characterizing individual cells and studying gene expression at the single-cell level. Clustering plays a vital role in grouping similar cells together for various downstream analyses. However, the high sparsity and dimensionality of large scRNA-seq data pose challenges to clustering performance. Although several deep learning-based clustering algorithms have been proposed, most existing clustering methods have limitations in capturing the precise distribution types of the data or fully utilizing the relationships between cells, leaving a considerable scope for improving the clustering performance, particularly in detecting rare cell populations from large scRNA-seq data. We introduce DeepScena, a novel single-cell hierarchical clustering tool that fully incorporates nonlinear dimension reduction, negative binomial-based convolutional autoencoder for data fitting, and a self-supervision model for cell similarity enhancement. In comprehensive evaluation using multiple large-scale scRNA-seq datasets, DeepScena consistently outperformed seven popular clustering tools in terms of accuracy. Notably, DeepScena exhibits high proficiency in identifying rare cell populations within large datasets that contain large numbers of clusters. When applied to scRNA-seq data of multiple myeloma cells, DeepScena successfully identified not only previously labeled large cell types but also subpopulations in CD14 monocytes, T cells and natural killer cells, respectively.

EGR1-mediated metabolic reprogramming to oxidative phosphorylation contributes to ibrutinib resistance in B-cell lymphoma.

The use of Bruton tyrosine kinase inhibitors, such as ibrutinib, to block B-cell receptor signaling has achieved a remarkable clinical response in several B-cell malignancies, including mantle cell lymphoma (MCL) and diffuse large B-cell lymphoma (DLBCL). Acquired drug resistance, however, is significant and affects the long-term survival of these patients. Here, we demonstrate that the transcription factor early growth response gene 1 (EGR1) is involved in ibrutinib resistance. We found that EGR1 expression is elevated in ibrutinib-resistant activated B-cell-like subtype DLBCL and MCL cells and can be further upregulated upon ibrutinib treatment. Genetic and pharmacological analyses revealed that overexpressed EGR1 mediates ibrutinib resistance. Mechanistically, TCF4 and EGR1 self-regulation induce EGR1 overexpression that mediates metabolic reprogramming to oxidative phosphorylation (OXPHOS) through the transcriptional activation of PDP1, a phosphatase that dephosphorylates and activates the E1 component of the large pyruvate dehydrogenase complex. Therefore, EGR1-mediated PDP1 activation increases intracellular adenosine triphosphate production, leading to sufficient energy to enhance the proliferation and survival of ibrutinib-resistant lymphoma cells. Finally, we demonstrate that targeting OXPHOS with metformin or IM156, a newly developed OXPHOS inhibitor, inhibits the growth of ibrutinib-resistant lymphoma cells both in vitro and in a patient-derived xenograft mouse model. These findings suggest that targeting EGR1-mediated metabolic reprogramming to OXPHOS with metformin or IM156 provides a potential therapeutic strategy to overcome ibrutinib resistance in relapsed/refractory DLBCL or MCL.

A Non-Flammable and Flexible Aluminum Derived Lithium-Ion Storage Device with a Wide Temperature Range of Operation.

With the rapid development and increasing popularity of electric vehicles and wearables, battery safety has become a leading focus in the field of energy storage research. Specifically, aluminum-ion batteries are gaining increasing attention as low-cost energy-storage systems with high safety levels and theoretical energy density. However, the dense alumina passivation layer on the aluminum anode surface and slow kinetic performance of commonly used ionic liquid electrolytes still render poor performance. This report presents a new type of aluminum-derived lithium-ion battery (ALIB) that maintains a certain discharge performance under damaging conditions, including continuous bending, high- and low-temperature environments, and shearing. This new ALIB effectively meets the current demand for flexible and wearable batteries. The prepared ALIB achieves a stable cycle of 130 mAh g-1 specific capacity and ≈260 Wh kg-1 theoretical energy density at a wide voltage platform of 2 V and a test temperature of 25 °C without undergoing combustion. Additionally, the study analyzes the reaction mechanism of this ALIB based on density functional theory and conducts ex situ XRD and XPS analyses to elucidate the underlying storage mechanism.

Novel NASICON-Type Na-V-Mn-Ni-Containing Cathodes for High-Rate and Long-Life SIBs.

Partial substitution of V by other transition metals in Na3 V2 (PO4 )3 (NVP) can improve the electrochemical performance of NVP as a cathode for sodium-ion batteries (SIBs). Herein, phosphate Na-V-Mn-Ni-containing composites based on NASICON (Natrium Super Ionic Conductor)-type structure have been fabricated by sol-gel method. The synchrotron-based X-ray study, X-ray diffraction (XRD), and X-ray photoelectron spectroscopy (XPS) studies show that manganese/nickel combinations successfully substitute the vanadium in its site within certain limits. Among the received samples, composite based on Na3.83 V1.17 Mn0.58 Ni0.25 (PO4 )3 (VMN-0.5, 108.1 mAh g-1 at 0.2 C) shows the highest electrochemical ability. The cyclic voltammetry, galvanostatic intermittent titration technique, in situ XRD, ex situ XPS, and bond valence site energy calculations exhibit the kinetic properties and the sodium storage mechanism of VMN-0.5. Moreover, VMN-0.5 electrode also exhibits excellent electrochemical performance in quasi-solid-state sodium metal batteries with PVDF-HFP quasi-solid electrolyte membranes. The presented work analyzes the advantages of VMN-0.5 and the nature of the substituted metal in relation to the electrochemical properties of the NASICON-type structure, which will facilitate further commercialization of SIBs.

Mechanistic Insight into the Synthesis and Morphological Evolution of Superhydrophobic Silica Nanotubes.

Silica nanotubes have significant applications in various fields, including thermal insulation, self-cleaning, and catalysis. Currently, the synthesis methods of silica nanotubes are mostly limited to the template method. In this work, a template-free strategy and vapor-phase approach were used to prepare silica nanotubes. Poly(methylhydrosiloxane) (PMHS) was hydrolyzed and condensed in a high-temperature closed reactor by using ammonia as a catalyst. The resulting product was then subjected to template-free self-assembly to synthesize silica nanotubes incorporating methyl groups. The silica nanotubes were synthesized under varying conditions, resulting in lengths ranging from 50 nm to several micrometers, exterior diameters between 40 and 120 nm, and wall thicknesses varying from 7 to 30 nm. The synthesized products underwent morphology analysis using TEM and FESEM for morphology analysis, elemental composition analysis using XPS, and chemical structure identification using FTIR, and the possible formation mechanism of silica nanotubes formation was also speculated. Furthermore, the coatings formed by silica nanotubes exhibited remarkable superhydrophobic self-cleaning properties with a water contact angle of 162° and a rolling angle of less than 1°.

Fat-associated lymphoid clusters as expandable niches for ectopic liver development.

BACKGROUND AND AIMS: Hepatocyte transplantation holds great promise as an alternative approach to whole-organ transplantation. Intraportal and intrasplenic cell infusions are primary hepatocyte transplantation delivery routes for this procedure. However, patients with severe liver diseases often have disrupted liver and spleen architectures, which introduce risks in the engraftment process. We previously demonstrated i.p. injection of hepatocytes as an alternative route of delivery that could benefit this subpopulation of patients, particularly if less invasive and low-risk procedures are required; and we have established that lymph nodes may serve as extrahepatic sites for hepatocyte engraftment. However, whether other niches in the abdominal cavity support the survival and proliferation of the transplanted hepatocytes remains unclear. APPROACH AND RESULTS: Here, we showed that hepatocytes transplanted by i.p. injection engraft and generate ectopic liver tissues in fat-associated lymphoid clusters (FALCs), which are adipose tissue-embedded, tertiary lymphoid structures localized throughout the peritoneal cavity. The FALC-engrafted hepatocytes formed functional ectopic livers that rescued tyrosinemic mice from liver failure. Consistently, analyses of ectopic and native liver transcriptomes revealed a selective ectopic compensatory gene expression of hepatic function-controlling genes in ectopic livers, implying a regulated functional integration between the two livers. The lack of FALCs in the abdominal cavity of immunodeficient tyrosinemic mice hindered ectopic liver development, whereas the restoration of FALC formation through bone marrow transplantation restored ectopic liver development in these mice. Accordingly, induced abdominal inflammation increased FALC numbers, which improved hepatocyte engraftment and accelerated the recovery of tyrosinemic mice from liver failure. CONCLUSIONS: Abdominal FALCs are essential extrahepatic sites for hepatocyte engraftment after i.p. transplantation and, as such, represent an easy-to-access and expandable niche for ectopic liver regeneration when adequate growth stimulus is present.

Deep-learning-based 3D blood flow reconstruction in transmissive laser speckle imaging.

Transmissive laser speckle imaging (LSI) is useful for monitoring large field-of-view (FOV) blood flow in thick tissues. However, after longer transmissions, the contrast of the transmitted speckle images is more likely to be blurred by multiple scattering, resulting in decreased accuracy and spatial resolution of deep vessels. This study proposes a deep-learning-based strategy for high spatiotemporal resolution three-dimensional (3D) reconstruction from a single transilluminated laser speckle contrast image, providing more structural and functional details without multifocus two-dimensional (2D) imaging or 3D optical imaging with point/line scanning. Based on the correlation transfer equation, a large training dataset is generated by convolving vessel masks with depth-dependent point spread functions (PSF). The UNet and ResNet are used for deblurring and depth estimation. The blood flow in the reconstructed 3D vessels is estimated by a depth-dependent contrast model. The proposed method is evaluated with simulated data and phantom experiments, achieving high-fidelity structural reconstruction with a depth-independent estimation of blood flow. This fast 3D blood flow imaging technique is suitable for real-time monitoring of thick tissue and the diagnosis of vascular diseases.

NEIL3 promotes hepatoma epithelial-mesenchymal transition by activating the BRAF/MEK/ERK/TWIST signaling pathway.

Hepatocellular carcinoma (HCC) is among the most prevalent visceral neoplasms. So far, reliable biomarkers for predicting HCC recurrence in patients undergoing surgery are far from adequate. In the aim of searching for genetic biomarkers involved in HCC development, we performed analyses of cDNA microarrays and found that the DNA repair gene NEIL3 was remarkably overexpressed in tumors. NEIL3 belongs to the Fpg/Nei protein superfamily, which contains DNA glycosylase activity required for the base excision repair for DNA lesions. Notably, the other Fpg/Nei family proteins NEIL1 and NEIL2, which have the same glycosylase activity as NEIL3, were not elevated in HCC; NEIL3 was specifically induced to participate in HCC development independently of its glycosylase activity. Using RNA-seq and invasion/migration assays, we found that NEIL3 elevated the expression of epithelial-mesenchymal transition (EMT) factors, including the E/N-cadherin switch and the transcription of MMP genes, and promoted the invasion, migration, and stemness phenotypes of HCC cells. Moreover, NEIL3 directly interacted with the key EMT player TWIST1 to enhance invasion and migration activities. In mouse orthotopic HCC studies, NEIL3 overexpression also caused a prominent E-cadherin decrease, tumor volume increase, and lung metastasis, indicating that NEIL3 led to EMT and tumor metastasis in mice. We further found that NEIL3 induced the transcription of MDR1 (ABCB1) and BRAF genes through the canonical E-box (CANNTG) promoter region, which the TWIST1 transcription factor recognizes and binds to, leading to the BRAF/MEK/ERK pathway-mediated cell proliferation as well as anti-cancer drug resistance, respectively. In the HCC cohort, the tumor NEIL3 level demonstrated a high positive correlation with disease-free and overall survival after surgery. In conclusion, NEIL3 activated the BRAF/MEK/ERK/TWIST pathway-mediated EMT and therapeutic resistances, leading to HCC progression. Targeted inhibition of NEIL3 in HCC individuals with NEIL3 induction is a promising therapeutic approach. © 2022 The Pathological Society of Great Britain and Ireland.

Comparing the Ability of Secretory Signal Peptides for Heterologous Expression of Anti-Lipopolysaccharide Factor 3 in Chlamydomonas reinhardtii.

Anti-lipopolysaccharide factor 3 (ALFPm3) possesses a wide antimicrobial spectrum and high antibacterial and viral activities for broad application prospects in the aquaculture industry. However, the application of ALFPm3 is limited by its low production in nature, as well as its low activity when expressed in Escherichia coli and yeast. Although it has been proven that its secretory expression can be used to produce antimicrobial peptides with strong antimicrobial activity, there is no study on the high-efficiency secretory expression of ALFPm3 in Chlamydomonas reinhardtii. In this study, signal peptides ARS1 and CAH1 were fused with ALFPm3 and inserted into the pESVH vector to construct pH-aALF and pH-cALF plasmids, respectively, that were transformed to C. reinhardtii JUV using the glass bead method. Subsequently, through antibiotic screening, DNA-PCR, and RT-PCR, transformants expressing ALFPm3 were confirmed and named T-JaA and T-JcA, respectively. The peptide ALFPm3 could be detected in algal cells and culture medium by immunoblot, meaning that ALFPm3 was successfully expressed in C. reinhardtii and secreted into the extracellular environment. Moreover, ALFPm3 extracts from the culture media of T-JaA and T-JcA showed significant inhibitory effects on the growth of V. harveyi, V. alginolyticus, V. anguillarum, and V. parahaemolyticus within 24 h. Interestingly, the inhibitory rate of c-ALFPm3 from T-JcA against four Vibrio was 2.77 to 6.23 times greater than that of a-ALFPm3 from T-JaA, indicating that the CAH1 signal peptide was more helpful in enhancing the secreted expression of the ALFPm3 peptide. Our results provided a new strategy for the secretory production of ALFPm3 with high antibacterial activity in C. reinhardtii, which could improve the application potentiality of ALFPm3 in the aquaculture industry.

Fusion dsRNA in targeting salivary protein genes enhance the RNAi-based aphid control.

RNA interference (RNAi) is a promising tool for pest control and relies on sequence-specific gene silencing. Salivary proteins are cooperatively secreted into plants to guarantee the feeding of aphids; thus they have potential to develop as selective targets for RNAi-based pest control strategy. For this purpose, we firstly analyzed 18 salivary proteomes of various aphid species, and these salivary proteins can be mainly categorized into seven functional groups. Secondly, we created a work-flow for fusion dsRNA design that can target multiple genes but were selectively safe to beneficial insects. Based on this approach, seven fusion dsRNAs were designed to feed the green peach aphid, which induced a significant reduction in aphid fitness. Among them, ingestion of dsperoxidase induced the highest mortality in aphids, which was also significantly higher than that of traditional dsRNAs in targeting three peroxidases separately. In addition, dsperoxidase-fed green peach aphids triggered the highest H2O2 content of host plants as well as the attraction to natural enemies (ladybeetle and parasitic wasp) but repellent to other control aphids. Our results indicate that the fusion dsRNA design approach can improve aphid control capacity, and the fusion dsRNA targeting salivary protein-encoding genes can enhance the direct and indirect defenses of host plants, thus providing a new strategy for RNAi-based aphid control.

Gate-Tunable Transport in Quasi-One-Dimensional α-Bi4I4 Field Effect Transistors.

Bi4I4 belongs to a novel family of quasi-one-dimensional (1D) topological insulators (TIs). While its ß phase was demonstrated to be a prototypical weak TI, the α phase, long thought to be a trivial insulator, was recently predicted to be a rare higher order TI. Here, we report the first gate tunable transport together with evidence for unconventional band topology in exfoliated α-Bi4I4 field effect transistors. We observe a Dirac-like longitudinal resistance peak and a sign change in the Hall resistance; their temperature dependences suggest competing transport mechanisms: a hole-doped insulating bulk and one or more gate-tunable ambipolar boundary channels. Our combined transport, photoemission, and theoretical results indicate that the gate-tunable channels likely arise from novel gapped side surface states, two-dimensional (2D) TI in the bottommost layer, and/or helical hinge states of the upper layers. Markedly, a gate-tunable supercurrent is observed in an α-Bi4I4 Josephson junction, underscoring the potential of these boundary channels to mediate topological superconductivity.

Jobs-housing relationships before and amid COVID-19: An excess-commuting approach.

The outbreak of COVID-19 and subsequent pandemic containment measures have significantly affected our daily life, which has been extensively examined in the existing scholarship. However, the existing scholarship has done little on the jobs/housing relationship impacts of COVID-19. We attempted to fill this gap by using an excess-commuting approach. The approach allows us to analyse a series of jobs-housing matrices based on the location-based service big data of around fifty million individuals in the Pearl River Delta (PRD), China before and amid COVID-19. In the PRD, a zero-COVID policy was implemented, which presents a distinct and interesting context for our study. We found that after the COVID-19 outbreak: (1) residences and employment became more centrally located in downtowns, which is opposite to the suburbanization trend elsewhere; (2) in the whole PRD, the minimum and maximum commutes became smaller while the actual commute became larger, indicating the simultaneous presences of some paradoxical phenomena: a better spatial juxtaposition of jobs and housing, more compressed distribution of jobs and housing, and longer average actual commutes; (3) inter-city commutes between large cities were significantly refrained and decreased, while new inter-city commuters between smaller cities emerged; (4) it was more likely for the less-educated and female workers to see smaller minimum commutes amid COVID-19. This paper illustrates the potential of big data in the longitudinal study on jobs-housing relationships and excess commuting. It also produces new insights into such relationships in a unique context where stringent anti-COVID-19 policies have been continuously in place.

The promising novel therapies for familial hypercholesterolemia.

BACKGROUND: The incidence of premature atherosclerotic cardiovascular disease in familial hypercholesterolemia (FH) is high. In recent years, novel therapeutic modalities have shown significant lipid-lowering ability. In this paper, we summarize the recent developments in novel therapies for FH via the treatment of different targets and discuss the characteristics of each targeted therapy. Based on the process of protein synthesis, we attempt to summarize the direct-effect targets including protein, RNA, and DNA. METHODS: For this systematic review, relevant studies are assessed by searching in several databases including PubMed, Web of Science, Scopus, and Google Scholar. The publications of original researches are considered for screening. RESULTS: Most drugs are protein-targeted such as molecule-based and monoclonal antibodies, including statins, ezetimibe, alirocumab, evolocumab, and evinacumab. Both antisense oligonucleotide (ASO) and small interfering RNA (siRNA) approaches, such as mipomersen, vupanorsen, inclisiran, and ARO-ANG3, are designed to reduce the number of mRNA transcripts and then degrade proteins. DNA-targeted therapies such as adeno-associated virus or CRISPR-Cas9 modification could be used to deliver or edit genes to address a genetic deficiency and improve the related phenotype. CONCLUSION: While the therapies based on different targets including protein, RNA, and DNA are on different stages of development, the mechanisms of these novel therapies may provide new ideas for precision medicine.

[Discrimination of quality markers of Shujin Huoxue Capsules based on five principles coupled with cobweb model].

The quality markers(Q-markers) of Shujin Huoxue Capsules were comprehensively discriminated based on the five principles of transfer and traceability, specificity, compatibility, effectiveness and measurability. The compounds that could be transferred from the original medicinal materials to the preparation were selected with the principle of transfer and traceability. The specific components in the prescription were screened by reviewing literature with the principle of specificity. According to the principle of compatibility, the attributes of compounds were evaluated by the sovereign, minister, assistant and guide combination rules of the original medicinal materials in the prescription. According to the principle of measurability, the measurable components were summarized by reference to the pharmacopoeia and literature combined with the content. The mechanism of Shujin Huoxue Capsules in the treatment of osteoporosis was studied through network pharmacology based on the principle of effectiveness, which was the evaluation index of effectiveness. The chemical components screened out above were regarded as candidate Q-markers, and the cobweb model was plotted to obtain the comprehensive score of Q-markers. Hydroxysafflor yellow A, trachelosid, eleutheroside B, α-cyperone, protocatechuic acid, protocatechualdehyde and 4-methoxy salicylaldehyde were discriminated as the Q-markers of Shujin Huoxue Capsules based on the five principles combined with cobweb model.

Epstein-Barr virus latent membrane protein-1 upregulates autophagy and promotes viability in Hodgkin lymphoma: Implications for targeted therapy.

Hodgkin lymphoma (HL) is composed of neoplastic Hodgkin and Reed-Sternberg cells in an inflammatory background. The neoplastic cells are derived from germinal center B cells that, in most cases, are infected by Epstein-Barr virus (EBV), which may play a role in tumorigenesis. Given that EBV-latent membrane protein 1 (LMP1) regulates autophagy in B cells, we explored the role of autophagy mediated by EBV or LMP1 in HL. We found that EBV-LMP1 transfection in HL cells induced a modest increase in autophagy signals, attenuated starvation-induced autophagic stress, and alleviated autophagy inhibition- or doxorubicin-induced cell death. LMP1 knockdown leads to decreased autophagy LC3 signals. A xenograft mouse model further showed that EBV infection significantly increased expression of the autophagy marker LC3 in HL cells. Clinically, LC3 was expressed in 15% (19/127) of HL samples, but was absent in all cases of nodular lymphocyte-predominant and lymphocyte-rich classic HL cases. Although expression of LC3 was not correlated with EBV status or clinical outcome, autophagic blockade effectively eradicated LMP1-positive HL xenografts with better efficacy than LMP1-negative HL xenografts. Collectively, these results suggest that EBV-LMP1 enhances autophagy and promotes the viability of HL cells. Autophagic inhibition may be a potential therapeutic strategy for treating patients with HL, especially EBV-positive cases.

The LDLR c.501C>A is a disease-causing variant in familial hypercholesterolemia.

BACKGROUND: As an autosomal dominant disorder, familial hypercholesterolemia (FH) is mainly attributed to disease-causing variants in the low-density lipoprotein receptor (LDLR) gene. The aim of this study was to explore the molecular mechanism of LDLR c.501C>A variant in FH and assess the efficacy of proprotein convertase subtilisin kexin type 9 (PCSK9) inhibitor treatment for FH patients. METHODS: The whole-exome sequencing was performed on two families to identify disease-causing variants, which were verified by Sanger sequencing. The function of LDLR variant was further explored in HEK293 cells by Western Blot and confocal microscopy. Besides, the therapeutic effects of PCSK9 inhibitor treatment for two probands were assessed for 3 months. RESULTS: All members of the two families with the LDLR c.501C>A variant showed high levels of LDLC. The relationship between the clinical phenotype and LDLR variants was confirmed in the current study. Both in silico and in vitro analyses showed that LDLR c.501C>A variant decreased LDLR expression and LDL uptake. PCSK9 inhibitor treatment lowered the lipid level in proband 1 by 24.91%. However, the treatment was ineffective for proband 2. A follow-up study revealed that the PCSK9 inhibitor treatment had low ability of lipid-lowering effect in the patients. CONCLUSIONS: LDLR c.501C>A variant might be pathogenic for FH. The PCSK9 inhibitor therapy is not a highly effective option for treatment of FH patients with LDLR c.501C>A variant.

Crystal structure of the yeast heterodimeric ADAT2/3 deaminase.

BACKGROUND: The adenosine-to-inosine (A-to-I) editing in anticodons of tRNAs is critical for wobble base-pairing during translation. This modification is produced via deamination on A34 and catalyzed by the adenosine deaminase acting on tRNA (ADAT) enzyme. Eukaryotic ADATs are heterodimers composed of the catalytic subunit ADAT2 and the structural subunit ADAT3, but their molecular assemblies and catalytic mechanisms are largely unclear. RESULTS: Here, we report a 2.8-Å crystal structure of Saccharomyces cerevisiae ADAT2/3 (ScADAT2/3), revealing its heterodimeric assembly and substrate recognition mechanism. While each subunit clearly contains a domain resembling their prokaryotic homolog TadA, suggesting an evolutionary gene duplication event, they also display accessory domains for additional structural or functional purposes. The N-lobe of ScADAT3 exhibits a positively charged region with a potential role in the recognition and binding of tRNA, supported by our biochemical analysis. Interestingly, ScADAT3 employs its C-terminus to block tRNA's entry into its pseudo-active site and thus inactivates itself for deamination despite the preservation of a zinc-binding site, a mechanism possibly shared only among yeasts. CONCLUSIONS: Combining the structural with biochemical, bioinformatic, and in vivo functional studies, we propose a stepwise model for the pathway of deamination by ADAT2/3. Our work provides insight into the molecular mechanism of the A-to-I editing by the eukaryotic ADAT heterodimer, especially the role of ADAT3 in catalysis.