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Zhu, Y.

Publications and source records attributed to Zhu, Y..

At least 307 records · Page 17Linked to original sources

The Whole Proteome, Phosphoproteome, and Glycoproteome Landscape of Pan-Cancer Cell Lines Profiled by Mass Spectrometry and Reverse Phase Protein Array

Mammalian cancer cell lines are essential model systems in biomedical research. We conducted multi-level proteomics analyses on 54 widely used cancer cell lines derived from various tissue-of-origins using two prominent proteomics technologies: mass spectrometry (MS) and reverse-phase protein array (RPPA). Our analysis identified 10,088 proteins, 33,609 phosphorylation sites across 7,289 phosphoproteins, and 56,350 site-specific glycans on 16,296 glycosylation sites from 5,966 glycoproteins, along with 305 drug-relevant protein and phosphoprotein targets. Our results reveal both consistent and distinct patterns in protein expression and modification between MS and RPPA, underscoring their complementary strengths as discovery tools. Additionally, we identified protein features that distinguish tissue origins across different cell line lineages. This dataset supports model system selection for drug target-related studies in vitro and provides valuable insights into key signaling pathways. Overall, this comprehensive resource enables new opportunities for exploration in cancer biology and offers significant value to research communities focused on biomarker profiling, drug target discovery, and understanding mechanisms across diverse cancer types.

cancer biology↗

Glycolysis inhibition functionally reprograms T follicular helper cells and reverses lupus

Systemic lupus erythematosus (SLE) is an autoimmune disease in which the production of pathogenic autoantibodies depends on T follicular helper (TFH) cells. This study was designed to investigate the mechanisms by which inhibition of glycolysis with 2-deoxy-d-glucose (2DG) reduces the expansion of TFH cells and the associated autoantibody production in lupus-prone mice. Integrated cellular, transcriptomic, epigenetic and metabolic analyses showed that 2DG reversed the enhanced cell expansion and effector functions, as well as mitochondrial and lysosomal defects in lupus TFH cells, which include an increased chaperone-mediated autophagy induced by TLR7 activation. Importantly, adoptive transfer of 2DG-reprogrammed TFH cells protected lupus-prone mice from disease progression. Orthologs of genes responsive to 2DG in murine lupus TFH cells were overexpressed in the TFH cells of SLE patients, suggesting a therapeutic potential of targeting glycolysis to eliminate aberrant TFH cells and curb the production of autoantibodies inducing tissue damage.

immunology↗

Pan-cistrome analysis of the leaf accessible chromatin regions of 214 maize inbred lines

Characterizing the noncoding regions of the genome, particularly the cis-regulatory elements (CREs) located in accessible chromatin regions (ACRs) in gene promoters, is crucial for understanding how gene expression is regulated and how genotype contributes to phenotypic diversity in plants.In this study, we used ATAC-seq to resequence and map the ACRs of 214 maize inbred lines. We identified 82,174 ACRs and reported that 39.55% of them exhibited significant variation across the population. Next, we used the accessibility of ACRs as a quantitative feature and performed a chromatin associability GWAS (caGWAS), resulting in 27,004 caQTLs. Among them, 2,463 were predicted to disrupt the cis-regulatory elements that TF binds in these ACRs, suggesting that TF binding affects chromatin accessibility. Specifically, we identified two caACRs that regulate the expression of fad7, which encodes a fatty acid desaturase and affects the linolenic acid content.Our findings highlight the dynamic nature of maize ACRs and demonstrate that chromatin accessibility information could be used for GWASs, offering key insights into the genetic and regulatory mechanisms of chromatin accessibility and its impact on complex traits in plants.

genomics↗

Tau load in select brainstem neurons predicts the severity and nature of balance deficits in the absence of cell death

Patients with tauopathies present with profoundly different clinical symptoms1, even within the same disorder2. A central hypothesis in the field, well-supported by biomarker studies3,4 and post-mortem pathology5-7, is that clinical heterogeneity reflects differential degeneration of vulnerable neuronal populations responsible for specific neurological functions. Recent work has revealed mechanisms underlying susceptibility of particular cell types8-10, but relating tau load to disrupted behavior -- es- pecially before cell death -- requires a targeted circuit-level approach. Here we studied two distinct balance behaviors in larval zebrafish11 expressing a human 0N/4R-tau allele12 in select populations of evolutionarily-conserved and well-characterized brainstem vestibular circuits13,14. We observed that human tau load predicted the severity of circuit-specific deficits in posture and navigation in the ab- sence of cell death. Targeting expression to either mid- or hindbrain balance neurons recapitulated these particular deficits in posture and navigation. By parametrically linking tau load in specific neu- rons to early behavioral deficits, our work moves beyond cell type to close the gap between pathological and neurological conceptions of tauopathy.

neuroscience↗

Arginine methylation coordinates with phosphorylation to regulate NADP+ synthesis

NADK is the sole cytosolic enzyme responsible for synthesizing NADP+ from NAD+ within cells. The homeostasis of NAD+/NADP+ is controlled by NADK, usually dysregulated in various cancers, yet the precise underlying regulatory mechanisms remain largely unknown. In this study, we discover that PRMT6 methylates NADK at R39, R41, and R45, resulting in the suppression of NADK kinase activity and NADP+ synthesis. Mutations of these sites promote cancer cell proliferation and tumor growth. PRMT6-mediated methylation of NADK coordinates with Akt-mediated phosphorylation to regulate NADK, which stimulates its activity to increase NADP+ production through relief of an autoinhibitory function inherent to its amino terminus. PRMT6 also inhibits NADK activity in a phosphorylation-independent manner. Furthermore, NADK methylation is upregulated by RB1/E2F pathway in high-fat diet mice. Downregulation of NADK methylation in HCC enhances NADP+ production to promote cancer development. Our findings illuminate the molecular regulatory mechanisms governing NAD+/NADP+ homeostasis, suggesting that the PRMT6-NADK axis emerges as a direct player in high energy state. Furthermore, our research suggests potential therapeutic targets through chemical and genetic interventions. SignificancePrevious studies revealed that phosphorylation of NADK activates its activity in response to nutrient or other signaling pathways. Here, we discovered that PRMT6 methylates NADK at residues R39, R41, and R45, leading to the suppression of NADK kinase activity and NADP+ synthesis. This PRMT6-mediated methylation works in conjunction with Akt-mediated phosphorylation to regulate NADK. Additionally, we found that NADK methylation is upregulated by the RB1/E2F pathway in mice on a high-fat diet. In hepatocellular carcinoma (HCC), the downregulation of NADK methylation enhances NADP+ production, thereby promoting cancer development. Our findings provide a significant breakthrough in understanding the regulation of NADK and its response to environmental factors.

cancer biology↗

Disruption of the Novel Nested Gene Aff3ir Mediates Disturbed Flow-Induced Atherosclerosis in Mice

Disturbed shear stress-induced endothelial atherogenic responses are pivotal in the initiation and progression of atherosclerosis, contributing to the uneven distribution of atherosclerotic lesions. This study investigates the role of Aff3ir-ORF2, a novel nested gene variant, in disturbed flow-induced endothelial cell activation and atherosclerosis. We demonstrate that disturbed shear stress significantly reduces Aff3ir-ORF2 expression in athero-prone regions. Using three distinct mouse models with manipulated AFF3ir-ORF2 expression, we demonstrate that AFF3ir-ORF2 exerts potent anti-inflammatory and anti-atherosclerotic effects in ApoE-/- mice. RNA sequencing revealed that interferon regulatory factor 5 (IRF5), a key regulator of inflammatory processes, mediates inflammatory responses associated with AFF3ir-ORF2 deficiency. AFF3ir-ORF2 interacts with IRF5, promoting its retention in the cytoplasm, thereby inhibiting the IRF5-dependent inflammatory pathways. Notably, IRF5 knockdown in AFF3ir-ORF2 deficient mice almost completely rescues the aggravated atherosclerotic phenotype. Moreover, endothelial-specific AFF3ir-ORF2 supplementation using the CRISPR/Cas9 system significantly ameliorated endothelial activation and atherosclerosis. These findings elucidate a novel role for AFF3ir-ORF2 in mitigating endothelial inflammation and atherosclerosis by acting as an inhibitor of IRF5, highlighting its potential as a valuable therapeutic approach for treating atherosclerosis.

cell biology↗

CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells

FOXP3-expressing regulatory T (Treg) cells play a pivotal role in maintaining immune homeostasis and tolerance, with their activation being crucial for preventing various inflammatory responses. However, the mechanisms governing the epigenetic program in Treg cells during their dynamic activation remain unclear. In this study, we demonstrate that CXXC finger protein 1 (CXXC1) interacts with the transcription factor FOXP3 and facilitates the regulation of target genes by modulating H3K4me3 deposition. Cxxc1 deletion in Treg cells leads to severe inflammatory disease and spontaneous T-cell activation, with impaired immunosuppressive function. As a transcriptional regulator, CXXC1 promotes the expression of key Treg functional markers under steady-state conditions, which are essential for the maintenance of Treg cell homeostasis and their suppressive functions. Epigenetically, CXXC1 binds to the genomic regulatory regions of Treg program genes in mouse Treg cells, overlapping with FOXP3 binding sites. Given its critical role in Treg cell homeostasis, CXXC1 presents itself as a promising therapeutic target for autoimmune diseases.

immunology↗

IL15/IL15Rα complex induces an anti-tumor immune response following radiation therapy only in the absence of Tregs and fails to induce expansion of progenitor TCF1+ CD8 T cells

BackgroundThis work seeks to understand whether IL15-incorporating treatments improve response to radiotherapy and uncover mechanistic rationale for overcoming resistance to IL15 agonism using novel therapeutic combinations. Experimental DesignOrthotopic tumor models of PDAC were used to determine response to treatment. IL15-/- and Rag1-/- mouse models were employed to determine dependence on IL15 and CTLs, respectively. Flow cytometry was used to assess immune cell frequency and activation state. Phospho-proteomic analyses were used to characterize intracellular signaling pathways. ResultsWe show that the combination of radiation therapy (RT) and an IL15/IL15Ra fusion complex (denoted IL15c) fails to confer anti-tumor efficacy; however, a CD8-driven anti-tumor immune response is elicited with the concurrent administration of an aCD25 Treg-depleting antibody. Using IL15-/- and Rag1-/- mice, we demonstrate that response to RT + IL15c + aCD25 is dependent on both IL15 and CTLs. Furthermore, despite an equivalent survival benefit following treatment with RT + IL15c + aCD25 and combination RT + PD1-IL2v, a novel immunocytokine with PD-1 and IL2R{beta}{gamma} binding domains, CTL immunophenotyping and phospho-proteomic analysis of intracellular metabolites showed significant upregulation of activation and functionality in CD8 T cells treated with RT + PD1-IL2v. Finally, we show the immunostimulatory response to RT + PD1-IL2v is significantly diminished with a concurrent lack of TCF+ CD8 T cell generation in the absence of functional IL15 signaling. ConclusionsOur results are illustrative of a mechanism wherein unimpeded effector T cell activation through IL2R{beta} signaling and Treg inhibition are necessary in mediating an anti-tumor immune response.

cancer biology↗

BTFBS: binding-prediction of bacterial transcription factors and binding sites based on deep learning

BackgroundThe binding of transcription factors (TFs) to TF-binding sites plays a vital role in the process of regulating gene expression and evolution. With the development of machine learning and deep learning, some successes have been achieved in predicting transcription factors and binding sites. Then a natural question arises: for a given transcription factor and a binding site, do they bind? This is the main motivation of this work. ResultsIn this paper, we develop a model BTFBS, which predicts whether the bacterial transcription factors and binding sites combine or not. The model takes both the amino acid sequences of bacterial transcription factors and the nucleotide sequences of binding sites as inputs, and extracts features through convolutional neural network and MultiheadAttention. For the model inputs, we use two negative sample sampling methods: RS and EE. On the test dataset of RS, the accuracy, sensitivity, specificity, F1-score and MCC of BTFBS are 0.91446, 0.89746, 0.93134, 0.91264 and 0.82946, respectively. And on the test dataset of EE, the accuracy, sensitivity, specificity, F1-score and MCC of BTFBS are 0.87868, 0.89354, 0.86394, 0.87996 and 0.75796, respectively. Meanwhile, our findings indicate that the optimal approach for obtaining negative samples in the context of bacterial research is to utilize the whole genome sequences of the corresponding bacteria, as opposed to the shuffling method. ConclusionsThe above results on the test dataset have shown that the proposed BTFBS model has a good performance in predicting the combination of bacterial transcription factors and their binding sites and provides an experimental guide. BTFBS is publicly available at https://github.com/Vceternal/BTFBS.

bioinformatics↗

Mutagenesis Sensitivity Mapping of HumanEnhancers In Vivo

Distant-acting enhancers are central to human development. However, our limited understanding of their functional sequence features prevents the interpretation of enhancer mutations in disease. Here, we determined the functional sensitivity to mutagenesis of human developmental enhancers in vivo. Focusing on seven enhancers active in the developing brain, heart, limb and face, we created over 1700 transgenic mice for over 260 mutagenized enhancer alleles. Systematic mutation of 12-basepair blocks collectively altered each sequence feature in each enhancer at least once. We show that 69% of all blocks are required for normal in vivo activity, with mutations more commonly resulting in loss (60%) than in gain (9%) of function. Using predictive modeling, we annotated critical nucleotides at base-pair resolution. The vast majority of motifs predicted by these machine learning models (88%) coincided with changes to in vivo function, and the models showed considerable sensitivity, identifying 59% of all functional blocks. Taken together, our results reveal that human enhancers contain a high density of sequence features required for their normal in vivo function and provide a rich resource for further exploration of human enhancer logic.

genomics↗

C7-substituted Quinolines as Potent Inhibitors of AdeG Efflux Pumps in Acinetobacter baumannii

Efflux, mediated by a series of multidrug efflux pumps, is a major contributor to antibiotic resistance in Gram-negative bacteria. Efflux pump inhibitors (EPIs), which can block efflux, have the potential to be used as adjuvant therapies to re-sensitize bacteria to existing antibiotics. In this study, 36 quinoline-based compounds were synthesized as potential EPIs targeting Resistance Nodulation Division (RND) family pumps in the multidrug-resistant pathogen Acinetobacter baumannii . In A. baumannii strains with overexpressed AdeFGH (chloramphenicol-adapted) and AdeABC (AYE, Ab5075-UW), these compounds enhanced Hoechst dye accumulation, indicating general efflux inhibition, and potentiated chloramphenicol which is an AdeG substrate. The research focused on two generations of quinoline compounds, with modifications at the C-7 position of first-generation compounds to improve hydrophobic interactions with the Phe loop in the AdeG efflux pump, to generate second-generation compounds. The modified quinolines showed strong pump inhibition and significant chloramphenicol potentiation, with MIC reductions of 4- to 64-fold. Notably, compounds 1.8 and 3.8 exhibited the highest inhibitory activity, while compounds 1.3 and 3.3 showed up to 64-fold potentiation, highlighting the importance of specific structural features at the C-7 position for efflux pump inhibition. The study also revealed selective inhibition of AdeFGH over AdeABC, with no potentiation observed for gentamicin, showing the specificity of these quinoline- based inhibitors. Importantly, the compounds showed no toxicity in a Galleria mellonella model at a 50 mg/kg dose level, highlighting their suitability as potential antibiotic adjuvants for combating bacterial resistance.

microbiology↗

Diversity and ecological roles of RNA viral communities in the cryosphere of the Tibetan Plateau

RNA viruses play crucial roles in modulating host communities, but their diversity and ecological roles in the cryosphere are poorly understood. We investigated the RNA virome from the cryosphere of the Tibetan Plateau (TPC), the largest area of the cryosphere in the mid-low latitude regions, which includes 79 metatranscriptomes from ecosystems including glaciers, proglacial lake sediments, permafrost wetland and upland soils. We obtained 8,799 RNA-dependent RNA polymerase encoding contigs, which clustered into 5,333 viral species, adding more than 4,900 new RNA viral species to the global RNA virome database. The recovered RNA viruses primarily infect prokaryotes, distinctively different from the dominance of eukaryotic RNA viruses in oceanic ecosystems. In addition to the known taxa such as Leviviricetes, we identified novel clades of putative prokaryotic RNA viruses, which greatly extended our understanding of their diversity. We further expanded the host of RNA virus by 20 additional prokaryotic phylum- or class-level taxonomic groups. Moreover, the TPC RNA viruses encoded dozens of auxiliary metabolic genes that could reprogram the metabolisms of diverse hosts, including photosynthesis in glacier eukaryotic algae and cyanobacteria, which may exert great impacts on glacier dynamics through modulating host adaptation. Furthermore, we identified potential pathogenic RNA viruses in various cryosphere environments, though their overall risks are low. This study provides the first comprehensive view of cryosphere RNA virome, highlighting their high diversity, vital ecological functions, and potential health impacts.

ecology↗

Autosomal dominant Retinitis Pigmentosa caused by the rhodopsin isoleucine 255 deletion features rapid neuroretinal degeneration, decreased synaptic connectivity, and neuroinflammation.

Retinitis Pigmentosa (RP) is a group of inherited retinal diseases that initially affects rod photoreceptors and causes progressive vision loss and blindness. Mutations in rhodopsin (RHO) can cause both autosomal recessive (ar) and dominant (ad) forms of RP, yet, the underlying degenerative mechanisms remain largely unknown, rendering the disease untreatable. Here, we focus on an in-frame, 3-base pair deletion, eliminating the isoleucine residue at codon 255 (i.e., RHO{Delta}I255) and resulting in adRP. We generated a novel knock-in mouse homologous to the human RHO{Delta}I255 mutation. This new mouse model displays a severe disruption of photoreceptor structure and function, as is seen in human patients. Our results indicate that this form of RP is a systems disease of the neuroretina that also impacts neuronal connectivity of bipolar- and horizontal cells, initiates neuroinflammation, and reduces the structural and functional integrity of the retina. Typical for adRP, Rho{Delta}I255 mice exhibit primary rod photoreceptor loss, followed by secondary cone degeneration, rhodopsin protein (RHO) mislocalization, progressive shortening of outer segments (OS), and disorganized OS structures. Subsequently, increasing gliosis, morphologic abnormalities of the inner retina, and impaired cone-driven visual function developed. In adRP, a single mutated allele is sufficient to cause the disease, as confirmed here in Rho{Delta}I255/+ heterozygous animals, where most photoreceptors were lost within two months after birth. Compared to this, homozygous Rho{Delta}I255/{Delta}I255 mutants exhibit an accelerated onset and even faster progression of retinal degeneration. The degeneration of Rho{Delta}I255-mutant photoreceptors was linked to the activation of both caspase- and calpain-type proteases, as well as poly(ADP-ribose) polymerase (PARP), indicating a parallel execution of both apoptotic and non-apoptotic processes. In conclusion, our data indicate that this form of RP affects the neuroretina beyond photoreceptor cell loss sharing features typical for other degenerative central nervous systems diseases, an insight, which may bear critical impact to understand and eventually develop treatment for these currently untreatable forms of blindness. Author summaryDominant mutations in the human rhodopsin gene are among the most common causes for the blinding disease retinitis pigmentosa (RP). To date, the underlying pathophysiological mechanisms are still largely unknown and dominant RP remains untreatable. Here, we introduce a new knock-in mouse model carrying the dominant human Rho{Delta}I255 mutation. As in humans, the Rho{Delta}I255 mouse suffers from a rapid degeneration of rod photoreceptors followed by subsequent cell death of cone photoreceptors and complete loss of visual function. The new mouse model displays sign of neuroinflammation and the concomitant activation of both apoptotic and non-apoptotic cell death mechanisms. These results will likely stimulate further studies into the degenerative processes governing dominant RP and may facilitate future therapy development for inherited retinal diseases that are still untreatable to this day.

pathology↗

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Camellia sinensis sp. Baihaozao

Baihaozao (Camellia sinensis sp. Baihaozao) is esteemed in the domain of tea plant cultivation for its early harvest period, profusion of bud trichomes, and exceptional suitability for tea processing. Nevertheless, the intricate phylogenetic relationships among species within this genus remain ambiguous, primarily due to the limited availability of genomic data. This study endeavors to comprehensively investigate the genomic resources of Baihaozao by sequencing, assembling, and annotating its entire chloroplast (cp) genome. The sequencing results indicated that the total length of the Baihaozao cp genome is 157,052 base pairs (bp), with an overall guanine-cytosine (GC) content of 37.30%. The genome exhibits a typical quadripartite structure, consisting of a large single-copy region (LSC) of 86,586 bp, a small single-copy region (SSC) of 18,227 bp, and a pair of inverted repeats (IRs) totaling 52,162 bp. A total of 133 genes were identified within this genome, including 8 ribosomal RNA (rRNA) genes, 37 transfer RNA (tRNA) genes, 87 protein-coding genes, and 1 pseudogene. Furthermore, the study identified 157 simple sequence repeats (SSRs) and 90 long repeat sequences. Analysis of codon usage bias indicated that codons encoding leucine (Leu) were the most frequently utilized, whereas those encoding cysteine (Cys) were the least utilized. Examination of nucleotide diversity within the Baihaozao cp genome revealed five highly variable regions with elevated Pi values (rps19, rpl32, ndhF, rpl22, matK), suggesting their potential utility as molecular markers. Phylogenetic analysis of 20 cp genomes of the Theaceae family indicated a close evolutionary relationship between Baihaozao and Camellia sinensis OL450428.1. This study not only provides valuable data support for elucidating the maternal origin of cultivated Camellia species but also holds significant scientific implications for further exploring the phylogenetic relationships and germplasm resource utilization of Camellia plants.

genomics↗

The KU70-SAP domain has an overlapping function with DNA-PKcs in limiting the lateral movement of KU along DNA

The non-homologous end-joining (NHEJ) pathway is critical for DNA double-strand break repair and is essential for lymphocyte development and maturation. The Ku70/Ku80 heterodimer (KU) binds to DNA ends, initiating NHEJ and recruiting additional factors, including DNA-dependent protein kinase catalytic subunit (DNA-PKcs) that caps the ends and pushes KU inward. The C-terminus of Ku70 in higher eukaryotes includes a flexible linker and a SAP domain, whose physiological role remains poorly understood. To investigate this, we generated a mouse model with knock-in deletion of the SAP domain (Ku70{Delta}SAP/{Delta}SAP). Ku70{Delta}SAP supports KU stability and its recruitment to DNA damage sites in vivo. In contrast to the growth retardation and immunodeficiency seen in Ku70-/- mice, Ku70{Delta}SAP/{Delta}SAP mice show no defects in lymphocyte development and maturation. Structural modeling of KU on long dsDNA, but not dsRNA suggests that the SAP domain can bind to an adjacent major groove, where it can limit KUs rotation and lateral movement along the dsDNA. Accordingly, in the absence of DNA-PKcs that caps the ends, Ku70{Delta}SAP fails to support stable DNA damage-induced KU foci. In DNA-PKcs-/- mice, Ku70{Delta}SAP abrogates the leaky T cell development and reduces both the qualitative and quantitative aspects of residual V(D)J recombination. In the absence of DNA-PKcs, purified Ku70{Delta}SAP has reduced affinity for DNA ends and dissociates more readily at lower concentration and accumulated as multimers at high concentration. These findings revealed a physiological role of the SAP domain in NHEJ by restricting KU rotation and lateral movement on DNA that is largely masked by DNA-PKcs. HighlightKu70 is a conserved non-homologous end-joining (NHEJ) factor. Using genetically engineered mouse models and biochemical analyses, our study uncovered a previously unappreciated role of the C-terminal SAP domain of Ku70 in limiting the lateral movement of KU on DNA ends and ensuring end protection. The presence of DNA-PKcs partially masks this role of the SAP domain.

genetics↗

Proteome structuring of crown-of-thorns starfish

This data report presents the proteome structuring of the crown-of-thorns starfish (COTS, Acanthaster planci) using the ColabFold system. The resulting dataset includes 31,743 predicted protein structures, covering 60.4% of residues with confident predictions and 35.5% with very high confidence. A preliminary structural bioinformatics analysis was conducted using post-AlphaFold methods, including fast structure clustering, ligand transplanting, and structure-based Gene Ontology (GO) annotation, which identified potential functions for previously uncharacterized proteins. These findings contribute to a deeper understanding of COTS biology and provide valuable data for developing biocontrol methods to mitigate the impact of COTS outbreaks on coral reefs.

bioinformatics↗

A single-molecule nanopore sequencing platform

Nanopore sequencing, a third-generation sequencing technology, has revolutionized the gene sequencing industry with its advantages of long reads, fast speed, real-time sequencing and analysis, and potential in detecting base modifications. This technology allows researchers to sequence longer DNA fragments in a single read, providing more comprehensive genomic information compared to previous methods. Nanopore sequencing operates on electrical signals generated by a nanopore embedded in a membrane separating two electrolyte-filled chambers. When single-stranded DNA (ssDNA) passes through the nanopore, it creates variations in the current that correspond to different DNA bases. By analyzing these current fluctuations with machine learning algorithms, the DNA sequence can be determined. In this study, we introduced several improvements to nanopore sequencing, including nanopore local chemistry sequencing, novel motor and pore proteins, chip design, and basecalling algorithms. Our new nanopore sequencing platform, CycloneSEQ, demonstrated long-duration sequencing (107 hours) on a single chip with high yield (>50 Gb). In human genomic DNA sequencing, CycloneSEQ was able to produce long reads with N50 33.6 kb and modal identity 97.0%. Preliminary findings on human whole-genome de novo assembly, variant calling, metagenomics sequencing, and single-cell RNA sequencing have further highlighted CycloneSEQs potential across different areas of genomics.

genomics↗

Influenza A virus within-host evolution and positive selection in a densely sampled household cohort over three seasons

While influenza A virus (IAV) antigenic drift has been documented globally, in experimental animal infections, and in immunocompromised hosts, positive selection has generally not been detected in acute infections. This is likely due to challenges in distinguishing selected rare mutations from sequencing error, a reliance on cross-sectional sampling, and/or the lack of formal tests of selection for individual sites. Here, we sequenced IAV populations from 346 serial, daily nasal swabs from 143 individuals collected over three influenza seasons in a household cohort. Viruses were sequenced in duplicate, and intrahost single nucleotide variants (iSNV) were identified at a 0.5% frequency threshold. Within-host populations were subject to purifying selection with >75% mutations present at <2% frequency. Children (0-5 years) had marginally higher within-host evolutionary rates than adolescents (6-18 years) and adults (>18 years, 4.4x10-6 vs. 9.42x10-7 and 3.45x10-6, p <0.001). Forty-five iSNV had evidence of parallel evolution, but were not overrepresented in HA and NA. Several increased from minority to consensus level, with strong linkage among iSNV across segments. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 23/256 loci (9%) in A(H3N2) specimens and 19/176 loci (11%) in A(H1N1)pdm09 specimens, and these were infrequently found in circulation. Overall, we found that within-host IAV populations were subject to purifying selection and genetic drift, with only subtle differences across seasons, subtypes, and age strata. Positive selection was rare and inconsistently detected.

microbiology↗