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Zhang, M.

Publications and source records attributed to Zhang, M..

At least 289 records · Page 16Linked to original sources

Cryo-EM structural insights into Vγ9Vδ2 TCR activation via multiple butyrophilins

Human V{gamma}9V{delta}2 T cells detect cancerous and pathogen-infected cells through an "inside-out" mechanism wherein intracellular domains of butyrophilin (BTN) proteins recognize phosphoantigens (pAgs) to prime BTN ectodomains to engage with the T cell receptor (TCR) to activate V{gamma}9V{delta}2 T cells. Here, we present cryo-electron microscopy (cryo-EM) structures, including the full-length BTN3A1-BTN3A2-BTN2A1 complex stabilized by the pAg HMBPP and an HMBPP-primed BTN multimer complex engaged with the V{gamma}9V{delta}2 TCR. The HMBPP-primed BTN3A1-BTN3A2-BTN2A1 complex confirms that this pAg bridges the intracellular B30.2 domains of BTN3A1 and BTN2A1, while also revealing an association of the ectodomains of BTN3A2 and BTN2A1. Upon TCR engagement, the TCR undergoes a substantial conformational change and BTN3A2-BTN2A1 ectodomain interaction dissociates, allowing BTN2A1 to bind to the lateral surface of the V{gamma}9 chain, while BTN3A2 binds to the apical surface of the V{delta}2 chain. Beyond demonstrating that BTN3A2 as a bona fide TCR ligand, this dissociation/binding sequence suggests a "pliers-like gripping" mechanism for TCR activation. We also obtained cryo-EM structures of BTN proteins in complex with functional antibodies, further elucidating the overall V{gamma}9V{delta}2 T cell activation process. Thus, our structural insights into how BTN proteins sense antigens and drive TCR activation lay the groundwork for developing targeted {gamma}{delta} T cell immunotherapies.

immunology↗

SIRT4 enhances the cytotoxicity of NK cells toward hepatic stellate cells and reverses liver fibrosis via AMPKα/P-p53/NKG2DL pathway

Natural killer (NK) cells exhibit antifibrotic properties in liver fibrosis (LF) by suppressing activated hepatic stellate cells (HSCs). SIRT4, a mitochondrial regulatory protein, plays a crucial role as a link between energy metabolism and cell viability. However, the role of SIRT4 in the cytotoxicity of NK cells toward HSCs remains unexplored. In this study, we found that SIRT4 was markedly downregulated in both mouse models and patients with LF. The loss of SIRT4 reduced the cytotoxicity of NK cells against activated HSCs, while its overexpression enhanced this cytotoxicity. Mechanistically, SIRT4 activates AMPK to promote p53 phosphorylation and facilitates its nuclear translocation, which induces the transcription of ULBP1 and ULBP2, members of the NK group 2D Legend (NKG2DL) family of molecules. Finally, overexpression of SIRT4 activated mouse hepatic NK cells and reversed LF by constructing adeno-associated viruses (AAV) that specifically target HSCs. Thus, SIRT4 is essential for the cytotoxicity of NK cells toward HSCs, and AAV8-pGAFP-SIRT4 may serve as a therapeutic approach for managing LF. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/615768v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1e6e987org.highwire.dtl.DTLVardef@edcc2dorg.highwire.dtl.DTLVardef@1f7c2bcorg.highwire.dtl.DTLVardef@111d81d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

Multi-omics analysis reveals the mechanism of BnC07MYB3a is involved in seed coat color in Brassica napus L.

In rapeseed (Brassica napus), yellow-seeded varieties accumulate less flavonoid pigments (anthocyanins/proanthocyanidins) in their seed coats compared with black-seeded varieties. The yellow-seeded trait is associated with greatly improved seed oil yield, quality, and commercial value. Many R2R3 MYB activators have been characterized in rapeseed, but how MYB-type repressors affect pigment biosynthesis is not yet fully understood. In this study, we performed transcriptome sequencing and metabolomic analysis of B. napus varieties with extreme differences in seed coat color, combined with weighted gene co-expression network analysis. This analysis identified an R2R3-MYB-type transcription factor, BnC07MYB3a (BnaC07G0178800ZS), as a candidate regulator of the yellow-seeded trait in B. napus. Overexpressing BnC07MYB3a in Arabidopsis thaliana and B. napus downregulated the expression of flavonoid biosynthetic genes, resulting in significantly lower anthocyanin and proanthocyanidin accumulation than in the wild-type and a lighter seed coat color in transgenic plants. BnC07MYB3a directly binds to the promoter of the TRANSPARENT TESTA (TT) gene BnTT6 and represses its expression. BnC07MYB3a also physically interacts with BnA06bHLH92a and the WD40 transcription factor TRANSPARENT TESTA GLABRA1 (BnTTG1), suggesting that they might form a previously unidentified MYB-bHLH-WD40 transcription factor complex. Our results reveal the molecular mechanism and regulatory network of BnC07MYB3a in determining seed coat color in B. napus and provide a genetic resource for breeding yellow-seeded cultivars of B. napus.

molecular biology↗

The dynamics of wild Vitis species in response to climate change facilitate the breeding of grapevine and its rootstocks with climate resilience

Climate change poses significant challenges to agricultural suitability and food security due to the limited adaptability of domesticated crops, however, our understanding of their climate adaptability is still limited. In this study, we compare the potential distributional dynamics in response to future climate change between grapevine and its wild relatives (Vitis L.) based on ecological niche models (ENMs). We reveal that the annual mean temperature is the primary factor influencing the potential distribution of cultivated grapes (V. vinifera L.). By 2080, under RCP 8.5, suitable areas for wine and table grapes from V. vinifera are predicted to reduced by 15.04x105 km{superscript 2} and 13.26x105 km{superscript 2}, respectively. The results suggest that grape cultivation, particularly for table grapes, will face serious threats from future climate change. In contrast, seventy percent of wild grapes are well able to withstand future climate conditions. For example, under RCP 8.5, North American wild grapes like V. rotundifolia and V. labrusca, as well as East Asian wild grapes such as V. heyneana and V. davidii, are projected to demonstrate significant adaptability. These wild grapes have the potential to provide rootstocks that could enhance the adaptability of cultivated grapes and serve as invaluable resources for breeding programs aimed at developing new cultivars better suited to withstand the environmental pressures of climate change. Our results not only predict potential suitable distribution areas of wild grapes in the future, but also emphasize the essential impact of these wild genetic resources on grape breeding for promoting adaptation to future climate change.

plant biology↗

Deep learning facilitates precise identification of disease-resistance genes in plants

The identification of plant disease-resistance genes is essential for understanding the plant immune system and accelerating crop breeding with disease resistance. Therefore, there is a pressing need for a method capable of accurately and comprehensively annotating resistance genes at a genome-wide scale. In this study, we propose Evolutionary Scale Modeling for LRR (ESM-LRR), a novel approach based on the deep protein language model to accurately identify LRR domains which are substantially variable structures in disease-resistance proteins. ESM-LRR achieved its highest F1 score of 0.80 on a test set using the 90% identity as the matching threshold. Building upon ESM-LRR, we developed the Plant Disease-Resistance Gene Predictor (R-Predictor), a framework designed to simultaneously annotate 15 diverse domain topologies, extensively covering recently characterised resistance genes across the entire genome. R-Predictor integrates four modules, each employing superior methods that outperform existing methods (F1 score of 0.89 for RLKs and 0.88 for NLRs), demonstrating its high accuracy and practicality in annotating disease-resistance genes (R genes). R-Predictor were also applied to identify R genes in rice, tomato, and grapevine. Furthermore, AlphaFold3 was employed to screen interactions between 1,116 protein pairs involving three NLRs identified exclusively by R-Predictor and 372 literature-reported plant-pathogen effectors, resulting in the identification of 15 putative NLR-effector complexes. Overall, this study presents a novel approach for advancing our understanding of plant immune mechanisms.

bioinformatics↗

Identification of novel components of the Ced and Ups systems in Saccharolobus islandicus REY15A

In the cells of Sulfolobales, the Ced (Crenarchaeal system for exchange of DNA) and Ups (UV-inducible pili of Sulfolobus) systems are highly induced by DNA damages and function in chromosomal DNA exchange by mediating DNA import and cell aggregation, respectively. The Ced system is composed of CedA, CedA1, CedA2, and CedB. The Ups is composed of UpsA, UpsB, UpsE and UpsF. However, how the DNA is transported by these systems is far from clear. Here, we report two novel components of the Ced system, CedD (SiRe_1715) and CedE (SiRe_2100), which are paralogs of CedB and CedA, respectively, and one new component of the Ups system, UpsC (SiRe_1957), which is a paralog of UpsA and UpsB, in Saccharolobus islandicus REY15A. DNA exchange assay revealed that cedD, cedE, and upsC are essential for DNA import while cedE and upsC are also important for DNA export. Further microscopy analysis revealed that upsC is involved in cell aggregation like other Ups genes. Besides, we found that cedB and cedD co-occur in the genomes of crenarchaea which lack virB4 and the presence of cedB and cedD, and virB4 is complementary. Both proteins show homology to different parts of the N-terminal domain of VirB4 in a complementary manner and form stable homo-oligomers in vitro. Collectively, our results indicate that CedD and CedE, and UpsC are essential components of the Ced and Ups systems, respectively.

microbiology↗

YTHDF1 Facilitates Lung Adenocarcinoma Progression via Promotion of EEF1G Translation in a m6A-Dependent Manner

Lung adenocarcinoma (LUAD) is a malignant tumor with high morbidity and mortality worldwide, and overall survival rates for LUAD patients remain unimproved. RNA modification is a key process in post-transcriptional gene regulation in epigenetics, with N6-methyladenosine (m6A) being a common RNA modification. The molecular mechanisms of LUAD are unclear, but evidence suggests that m6A RNA methylation plays a significant role. This study aimed to clarify the role of YTHDF1 in LUAD development and pathogenesis. These findings confirmed that YTHDF1, a m6A reader protein, is highly expressed in LUAD tissues and is correlated with tumor differentiation and TNM stage. The results of functional loss experiments in LUAD cell lines revealed that downregulating YTHDF1 inhibits proliferation, migration, and invasion and induces apoptosis, with opposite effects observed upon YTHDF1 upregulation. In vivo, YTHDF1 knockout suppressed LUAD xenograft growth. RNA-seq, MeRIP-seq, RIP-seq, and bioinformatics analyses identified EEF1G as a downstream target of YTHDF1 in LUAD, and high expression of EEF1G was confirmed. The interaction between YTHDF1 and EEF1G was validated through RIP-qPCR, Co-IP and Co-IF assays. The overexpression of EEF1G in LUAD cells partially counteracts the tumor suppression induced by YTHDF1 silencing, and the knockdown of EEF1G has the opposite effect, further confirming the regulatory relationship. In summary, this study describes a novel YTHDF1/EEF1G regulatory pathway in which YTHDF1 promotes LUAD progression by recognizing and binding to the m6A-modified mRNA of EEF1G, accelerating its translation, suggesting that YTHDF1 may be a potential biomarker and therapeutic target.

cancer biology↗

Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in Xingjiang

AbstractsMunage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is recognized for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate specific mutations and associated genes in Munake and the genes associated with fruit color traits. Selective analysis between Munage clones and Eurasian grapes suggested that adaptive selection exists in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. The study examined the mutations within Munage grapes and found that the genes PMAT2 on chromosome 12 and MYB123 on chromosome 13 are likely responsible for color variation in RM. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine.

genomics↗

Controlled retrieval relies on directed interactions between semantic control regions and visual cortex: MEG evidence from oscillatory dynamics

To navigate the world, we store knowledge about relationships between concepts and retrieve this information flexibly to suit our goals. The semantic control network, comprising left inferior frontal gyrus (IFG) and posterior middle temporal gyrus (pMTG), is thought to orchestrate this flexible retrieval by modulating sensory inputs. However, interactions between semantic control and input regions are not sufficiently understood. Moreover, pMTGs well-formed structural connections to IFG and visual cortex suggest it as a candidate region to integrate control and input processes. We used magnetoencephalography to investigate oscillatory dynamics during semantic decisions to pairs of words, when participants (both sexes) did or did not know the type of semantic relation between them. IFG showed increases and decreases in oscillatory activity to prior task knowledge, while pMTG only showed positive task knowledge effects. Furthermore, IFG provided sustained feedback to pMTG when task goals were known, while in the absence of goals this feedback was delayed until receiving bottom-up input from the second word. This goal-dependent feedback coincided with an earlier onset of feedforward signalling from visual cortex to pMTG, indicating rapid retrieval of task-relevant features. This pattern supports a model of semantic cognition in which pMTG integrates top-down control from IFG with bottom-up input from visual cortex to activate task-relevant semantic representations. Our findings elucidate the separate roles of anterior and posterior components of the semantic control network and reveal the spectro-temporal cascade of interactions between semantic and visual regions that underlie our ability to flexibly adapt cognition to the current goals. Significance StatementUsing magnetoencephalography, we characterize the spectro-temporal dynamics that underlie our ability to flexibly adapt semantic cognition to the current context and goals. We find that semantic goals increase oscillatory activity in IFG and pMTG, and ultimately facilitate visual processing. Effective connectivity analyses reveal more sustained feedback from IFG to pMTG, and more rapid feedforward signalling from visual cortex to pMTG, resulting in rapid retrieval when semantic goals are known. Crucially, our findings suggest differential roles for the two semantic control regions: while IFG controls goal-dependent retrieval, pMTG integrates top-down information from IFG with bottom-up visual input.

neuroscience↗

Test-retest reliability of resting-state EEG intrinsic neural timescales

Intrinsic neural timescales (INTs), which reflect the duration of neural information storage within local brain regions and capacity for information integration, are typically measured using autocorrelation windows (ACWs). Extraction of INTs from resting-state brain activity has been extensively applied in psychiatric disease research. Given the potential of INTs as a neural marker for psychiatric disorders, investigating their reliability is crucial. This study, using an open-source database, aimed to evaluate the test-retest reliability of ACW-0 and ACW-50 under both eyes-open and eyes-closed conditions across three sessions. The intraclass correlation coefficients (ICCs) were employed to quantify the reliability of the INTs. Our results showed that INTs exhibited good reliability (ICC > 0.6) at the whole-brain level across different index types and eye states. Spatially, except for the right temporal region in the eyes-open condition, all other regions showed moderate-to-high ICCs. Over 60% of the electrodes demonstrated moderate-to-high INT ICCs under both eyes-open and eyes-closed conditions, with ACW-0 being more stable than ACW-50. This present study comprehensively assessed the reliability of INT under various conditions, providing robust evidence for their stability in neuroscience and psychiatry.

neuroscience↗

Cardiac Fibroblasts regulate myocardium and coronary vasculature development via the collagen signaling pathway

The fibroblast (FB), cardiomyocyte (CM), and vascular endothelial cell (Vas_EC) are the three major cell types in the heart, yet their relationships during development are largely unexplored. To address this gap, we employed RNA staining of the FB marker gene Col1a1 together with the CM marker gene Actn2 and the Vas_EC marker gene Cdh5 at different stages. This approach enabled us to discern the anatomical pattern of cardiac FBs and identify approximately one EC and four CMs directly interacting with each FB. Molecularly, through the analysis of single-cell mRNA sequencing (scRNA-seq) data, we unveiled collagen as the top signaling molecule derived from FBs influencing CM and Vas_EC development. Subsequently, we used a Pdgfra-CreER controlled diphtheria toxin A (DTA) system to ablate the FBs at different stages. We found that the ablation of FBs disrupted myocardium and vasculature development and led to embryonic heart defects. Using scRNA-seq, we further profiled the ablated hearts and identified molecular defects in their ventricular CMs and Vas_ECs compared to control hearts. Moreover, we identified a reduction of collagen in the ablated hearts and predicted collagen as the major signaling pathway regulating the differentially expressed genes in the ablated ventricular CMs. Finally, we performed both short-term and long-term fibroblast ablation at the neonatal stage. We found that short-term ablation caused a reduction in collagen and Vas_EC density, while long-term ablation may induce compensatory collagen expression without causing heart function reduction. In summary, our study has identified the function of fibroblasts in regulating myocardium and vasculature development and implicated an important role for the collagen pathway in this process.

developmental biology↗

Spatial and Single Cell Mapping of Castleman Disease Reveals Key Stromal Cell Types and Cytokine Pathways

Castleman disease (CD) is inflammatory lymphoproliferative disorder of unclear etiology. To determine the cellular and molecular basis of CD, we analyzed the spatial proteome of 4,485,009 single cells, transcriptome of 50,117 single nuclei, immune repertoire of 8187 single nuclei, and pathogenic mutations in Unicentric CD, idiopathic Multicentric CD, HHV8-associated MCD, and reactive lymph nodes. CD was characterized by increased non-lymphoid and stromal cells that formed unique microenvironments where they interacted with lymphoid cells. Interaction of activated follicular dendritic cell (FDC) cytoplasmic meshworks with mantle zone B cells was associated with B cell activation and differentiation. VEGF, IL-6, MAPK, and extracellular matrix pathways were elevated in stromal cells of CD. CXCL13+ FDCs, PDGFRA+ T-zone reticular cells (TRC), and ACTA2-positive perivascular reticular cells (PRC) were identified as the predominant source of increased VEGF expression and IL-6 signaling in CD. VEGF expression by FDCs was associated with peri-follicular neovascularization. FDC, TRC and PRC of CD activated JAK-STAT, TGF{beta}, and MAPK pathways via ligand-receptor interactions involving collagen, integrins, complement components, and VEGF receptors. T, B and plasma cells were polyclonal but showed class-switched and somatically hypermutated IgG1+ plasma cells consistent with stromal cell-driven germinal center activation. In conclusion, our findings show that stromal cell activation and associated B-cell activation and differentiation, neovascularization and stromal remodeling underlie CD and suggest new targets for treatment. Key pointsO_LICastleman Disease is characterized by activation and proliferation of CXCL13+ FDCs, PDGFRA+ reticular cells, and ACTA2-positive PRCs. C_LIO_LIVEGF and IL-6 from lymph node stromal cells are associated with B-cell activation and differentiation, endothelial proliferation, and inflammation in CD C_LI

pathology↗

Vibrio alginolyticus is the pathogen of 'Baotou disease causing serious damage to Gracilariopsis lemaneiformis cultivation in China

Gracilariopsis lemaneiformis and Saccharina japonica, the two very important cultivated economic seaweeds, are often co-cultured in China due to their growth periods overlapped for about 3 months. These two seaweeds are often plagued with bleaching diseases during their high-density commercial cultivation. In recent years, a disease called Baotou has been causing large-scale yield reductions of G. lemaneiformis in China. Interestingly, Vibrio alginolyticus once reported to be beneficial to S. japonica by reducing the bleaching disease risk, was strongly proved to be the pathogen causing Baotou disease in this study. Analysis of 16S rRNA gene profiling revealed that V. alginolyticus was the most abundant and dominant bacterium on the algal thalli suffering from Baotou disease, whereas its presence was scarcely detected on healthy thalli. Scanning electron microscope (SEM) analysis revealed that a large number of V. alginolyticus cells were found to be attached to the algal thalli with Baotou disease and the rotten thalli acquired by the lab infection treatment. V. alginolyticus could cause the rotten symptoms which were consistent with those of Baotou disease. According to Kochs postulates, V. alginolyticus was identified as the pathogen causing Baotou disease. IMPORTANCEA highly contagious disease known as Baotou disease has persistently triggered significant yield reductions in G. lemaneiformis throughout China. The pathogen of Baotou disease was isolated and identified as V. alginolyticus which was once reported to be beneficial to S. japonica by reducing the bleaching disease risk. The study indicates that V. alginolyticus is closely involved in the competition or co-existence between G. lemaneiformis and S. japonica co-cultured in China, and provides a novel perspective and evidence that bacteria are closely involved in the competition or co-existence among different species of seaweeds that grow together.

microbiology↗

Evolution of the Spatial transcriptomic landscape during the progression of high-grade pancreatic intraductal papillary mucinous neoplasms to invasive cancer

Intraductal papillary mucinous neoplasms (IPMN) is one of the known precancerous lesions. Patients prognosis is aggravated as IPMN transforms into invasive Pancreatic Ductal Adenocarcinoma (PDAC). The molecular mechanisms underlying this progression lack effective experimental models and urgently need to be elaborated. We performed spatial transcriptomics (ST) on fresh tissue samples from the same patient including normal pancreas, high-grade IPMN, and invasive PDAC, and described the step-by-step development of transcriptional landscape including clone evolution and adjacent TME feature variation. Our findings identified the master transcript factors and critical signaling pathways promoting IPMN progression to invasive PDAC. Additionally, both IPMN and PDAC harbored the ELF3, MYC, and KLF4 amplification. The Spatial CNV profile demonstrated significant heterogeneity among PDAC in their spatial distribution compared to IPMN, with seven distinct subclones showing diverse functions, such as hypoxia, oxidative phosphorylation, and epithelial-mesenchymal Transition. We observed a marked shift in the immune landscape, with the depletion of CD4+ T-cells and dendritic cells and an increase in immune-suppressive M2 macrophages in invasive PDAC, indicating a transition to an immune-evasive microenvironment. Additionally, cancer-associated fibroblasts (CAFs), particularly myofibroblastic CAFs, were enriched adjacent to invasive PDAC, suggesting their active role in tumor progression. By leveraging spatial transcriptomic analysis, our study provides comprehensive insights into the intricate molecular landscape that underlies the progression of IPMNs to invasive PDAC. These findings not only enhance our understanding of this complex process but also offer valuable knowledge for early diagnosis and intervention. HighlightsO_LISpatial CNV analysis reveals clonal evolution and distinct subclones in PDAC. C_LIO_LIKey drivers like ELF3, MYC, and KLF4 are amplified in both IPMN and invasive PDAC. C_LIO_LIImmune landscape shifts from pro-inflammatory in IPMN to immune-evasive in PDAC. C_LIO_LIEnrichment of myofibroblastic CAFs suggests their role in tumor progression C_LI

cancer biology↗

Remodelling of the glycome of B-cell precursor acute lymphoblastic leukemia cells developing drug-tolerance

Reduced responsiveness of precursor B-acute lymphoblastic leukemia (BCP-ALL) to chemotherapy can be first detected in the form of minimal residual disease leukemia cells that persist after 28 days of initial treatment. The ability of these cells to resist chemotherapy is partly due to the microenvironment of the bone marrow, which promotes leukemia cell growth and provides protection, particularly under these conditions of stress. It is unknown if and how the glycocalyx of such cells is remodelled during the development of tolerance to drug treatment, even though glycosylation is the most abundant cell surface post-translational modification present on the plasma membrane. To investigate this, we performed omics analysis of BCP-ALL cells that survived a 30-day vincristine chemotherapy treatment while in co-culture with bone marrow stromal cells. Proteomics showed decreased levels of some metabolic enzymes. Overall glycocalyx changes included a shift from Core-2 to less complex Core-1 O-glycans, and reduced overall sialylation, with a shift from 2-6 to 2-3 linked Neu5Ac. Interestingly, there was a clear increase in bisecting complex N-glycans with a concomitant increased mRNA expression of MGAT3, the only enzyme known to form bisecting N-glycans. These small but reproducible quantitative differences suggest that individual glycoproteins become differentially glycosylated. Glycoproteomics confirmed glycosite-specific modulation of cell surface and lysosomal proteins in drug-tolerant BCP-ALL cells, including HLA-DRA, CD38, LAMP1 and PPT1. We conclude that drug-tolerant persister leukemia cells that grow under continuous chemotherapy stress have characteristic glycotraits that correlate with and perhaps contribute to their ability to survive and could be tested as neoantigens in drug-resistant leukemia.

cancer biology↗

A molecular brain atlas reveals cellular shifts during the repair phase of stroke

Ischemic stroke triggers a cascade of pathological events that affect multiple cell types and often lead to incomplete functional recovery. Despite advances in single-cell technologies, the molecular and cellular responses that contribute to long-term post-stroke impairment remain poorly understood. To gain better insight into the underlying mechanisms, we generated a single-cell transcriptomic atlas from distinct brain regions using a mouse model of permanent focal ischemia at one month post-injury. Our findings reveal cell- and region-specific changes within the stroke-injured and peri-infarct brain tissue. For instance, GABAergic and glutamatergic neurons exhibited upregulated genes in signaling pathways involved in axon guidance and synaptic plasticity, and downregulated pathways associated with aerobic metabolism. Using cell-cell communication analysis, we identified increased strength in predicted interactions within stroke tissue among both neural and non-neural cells via signaling pathways such as those involving collagen, protein tyrosine phosphatase receptor, neuronal growth regulator, laminin, and several cell adhesion molecules. Furthermore, we found a strong correlation between mouse transcriptome responses after stroke and those observed in human nonfatal brain stroke lesions. Common molecular features were linked to inflammatory responses, extracellular matrix organization, and angiogenesis. Our findings provide a detailed resource for advancing our molecular understanding of stroke pathology and for discovering therapeutic targets in the repair phase of stroke recovery.

neuroscience↗

An in vivo screen identifies NAT10 as a master regulator of brain metastasis

Metastasis is the major cause of cancer-related deaths. Emerging evidence has shown that epigenetic regulation plays a fundamental role in cancer metastasis. To better understand the epigenetic regulation of metastasis, we conducted an in vivo shRNA screen for vulnerabilities of brain metastasis and identified N-acetyltransferase 10 (NAT10) as a driver of brain metastasis. Knockdown of NAT10 significantly restrains cancer cell proliferation and migration in vitro, and tumor growth and brain metastasis in vivo. Structure-function analysis of NAT10 showed that its poorly characterized RNA helicase domain is critical for breast cancer cell growth in vitro, while its N-acetyltransferase domain is essential for primary tumor growth and brain metastasis in vivo. Integrative transcriptomic and proteomic analyses revealed key downstream effectors of NAT10, including PHGDH and PSAT1, two catalyzing enzymes for serine biosynthesis implicated in brain metastasis, and HSPA5, known to promote metastasis. We found that distant metastases of breast cancer, especially brain metastases express higher levels of NAT10, PHGDH, PSAT1, and HSPA5. Silencing PHGDH/PSAT1 or HSPA5 in metastatic breast cancer cells inhibits their ability to grow in the serine/glycine-limited condition or migrate, respectively, phenocopying the effects of NAT10 depletion. Moreover, NAT10 promotes the expression of PHGDH, PSAT1, and HSPA5 in its RNA helicase-dependent manner. These findings establish NAT10 as a master regulator of brain metastasis and shed light on the biological functions of its RNA helicase domain, nominating NAT10 as a target for treating metastatic diseases.

cancer biology↗

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↗