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Dong, H.

Publications and source records attributed to Dong, H..

At least 55 records · Page 3Linked to original sources

Molecular insights into early malignant transition of hepatocellular carcinoma

The molecular continuum of premalignant-to-malignant transition remains elusive in carcinogenesis, primarily due to the difficulty in sampling transitional lesions. Here, we present comprehensive genomic and immunological profiling of 21 very early hepatocellular carcinomas (veHCCs) arising within 17 cancer-prone DNs. Surprisingly, 82% of cancer-prone DNs harbored TERT alterations, suggesting a predisposing rather than causative role in malignancy transition. A substantial increase in CNA burden, rather than SNV, was noted, indicating a role of chromosome instability in malignancy transition. Additionally, veHCC-originating DNs showed immune inactivity, not falling into the prevailing paradigm that HCCs develop in a context of chronic inflammation. 43% of veHCCs showed an inflamed phenotype with relatively mild CNA burden but already exhibited immune evasion features. Two major evolutionary scenarios were thus proposed: 1) CNA-dominant progression and 2) early immune evasion of those with mild CNA burden. Collectively, our findings illustrate previously unexplored molecular paradigms in HCC initiation, highlighting the therapeutic potential of immunotherapy for early intervention.

cancer biology↗

Reshaping epistatic network modules enhances wheat yield potential

Increasing wheat yield is a key approach to ensuring global food security and an enduring focus in crop breeding. Here, we assembled a panel of 3,030 wheat lines to dissect the genetic mechanisms of yield improvement. We conducted large-scale field trials across five ecological environments over two consecutive years to evaluate yield performance and constructed a haplotype atlas using the Wheat 660K genotype array. 234 quantitative trait loci (QTLs) and 522 haplotype blocks (HBs) were identified for 14 traits through genome-wide association studies (GWAS), including 10 QTLs and 35 HBs associated with grain yield. Genomic analysis revealed that wheat yield improvement is primarily driven by changes in the epistatic network rather than the introduction of new haplotype segments. SNPs or HBs explain 53.3%-62.9% of the phenotypic variation in yield, whereas epistasis explains 70.4%, highlighting the role of epistasis in yield improvement. Moreover, yield improvement is significantly correlated with the accumulation of favorable epistatic modules. Pedigree-based analysis revealed that the modules remained relatively stable under the pressure of breeding selection, while new favorable modules were also created during hybrid breeding, highlighting that crop design breeding should be based on genetic modules. This study provides insights into genetic mechanism of wheat yield improvement and guidance for designing future wheat in the era of artificial intelligence.

genetics↗

Genome-wide analysis reveals the genetic basis of key agronomic traits and modern wheat breeding in Henan Province

Despite the continuous improvement of wheat cultivars in Henan Province, the largest Chinese wheat-producing area, there have been no reports of studies on their breeding advances in the past decades. This study aims to elucidate their genetic basis and breeding advances. A total of 351 landraces and 265 cultivars in Henan Province were employed in selective sweep studies and genome-wide association studies. All the wheat accessions were planted in five locations in Henan Province in 2016-2017, 2017-2018 and 2018-2019. Candidate genes were identified through differential expression, GO annotation, gene homology, and haplotype analyses. Breeding advances were summarized based on four breeding periods (1950s, 1960s-1970s, 1980s-1990s, and post-2000s) of all 265 cultivars. The results demonstrated that 263 known genes with selection signals were found to be associated with important traits. Around the detected quantitative trait loci, 51 genes had been previously reported, while 252 genes were identified as candidate genes. Of the 303 genes and loci identified, 80 genes and 50 loci contributed to the improvement of 12 traits like plant height, and 12 key candidate genes was verified by qRT-PCR, while superior haplotypes of 24 genes explained cultivar climate adaptation. The superior haplotypes of 164 genes are available for future breeding. Transmission of superior haplotypes in four varietal pedigrees revealed pyramiding of superior haplotypes in elite cultivars. The analysis of post-2000 cultivars suggests a broader range of germplasm resources should be considered in parental selection than only recent accessions. This study provides a genetic basis and guide for wheat improvement.

genetics↗

Epigenetic Control of TERRA by FTSJ3 is Critical for Telomerase-Driven Cancers

Telomerase reverse transcriptase (hTERT) overexpression, a hallmark of most cancers, drives tumorigenesis by enabling limitless replicative potential. Direct targeting of hTERT is challenging, necessitating alternative strategies. Through genome-wide synthetic dosage lethality (SDL) screening in cancer models, including patient-derived organoids, we identify FTSJ3, an RNA 2-O-methyltransferase, as a critical vulnerability in hTERT-overexpressing cells. FTSJ3 methylates telomeric repeat-containing RNA (TERRA), a modification essential for recruiting SUV39H1 to telomeric ends to mediate H3K9 trimethylation and establish stable heterochromatin. Loss of FTSJ3 disrupts this cascade, impairing H3K9 trimethylation, HP1-alpha recruitment, and telomeric heterochromatin maintenance. Notably, this reveals an unexpected dependency on TERRA methylation for telomeric heterochromatin stability in hTERT-driven cancers. Non-malignant cells, lacking telomerase activity and de novo telomere repeat synthesis, are unaffected by FTSJ3 suppression. Our findings establish the FTSJ3/TERRA/SUV39H1 axis as a critical mechanism supporting telomeric heterochromatin stability in hTERT-driven cancers. This telomere-directed epigenetic strategy provides a robust framework for translational therapeutic innovation.

cancer biology↗

PD-1 prelimits both the cytotoxic and exhaustion potential in thymic CD8+ T cells and impacts the maintenance of peripheral tumor immunity

Durable T cell immunity against cancer depends on the continual replenishment of effector CD8+ T cells. Thymic output has been correlated with favorable prognosis in cancer patients across a range of ages, suggesting that the thymus is an important source for replenishing T cells capable of controlling cancer progression. However, the effector potential of thymic mature CD8+ T cells and their regulation have not been clearly defined. In this study, we identified the ability of thymic single positive CD8+ T cells to gain effector potential after thymic selection, but they are subject to the regulation of PD-1. We found a previously undisclosed role of PD-1 in limiting both the cytotoxic and exhaustion potential of thymic and peripheral CD8+ T cells. Our results show that although PD-1 inhibition facilitates the expansion of effector CD8+ T cells, effector CD8+ cells gradually lose their antitumor activity within tumor tissues due to advanced exhaustion in the absence of PD-1. Thus, although the preset effector potential in thymic mature CD8+ T cells allows them to rapidly respond to malignant cells in the periphery, PD-1, as a checkpoint, is embedded in the thymic mature CD8+ T cells after positive selection to balance their effector function from exaggeration and exhaustion. Therefore, we propose that a strategy capable of upholding the cytotoxic capacity and avoiding exhaustion of CD8+ T cells during the early stages of PD-1 inhibition therapy is needed to achieve durable antitumor immunity.

immunology↗

In vivo multiplex imaging of dynamic neurochemical networks with designed far-red dopamine sensors

Neurochemical signals like dopamine (DA) play a crucial role in a variety of brain functions through intricate interactions with other neuromodulators and intracellular signaling pathways. However, studying these complex networks has been hindered by the challenge of detecting multiple neurochemicals in vivo simultaneously. To overcome this limitation, we developed a single-protein chemigenetic DA sensor, HaloDA1.0, which combines a cpHaloTag-chemical dye approach with the G protein-coupled receptor activation-based (GRAB) strategy, providing high sensitivity for DA, sub-second response kinetics, and an extensive spectral range from far-red to near-infrared. When used together with existing green and red fluorescent neuromodulator sensors, Ca2+ indicators, cAMP sensors, and optogenetic tools, HaloDA1.0 provides high versatility for multiplex imaging in cultured neurons, brain slices, and behaving animals, facilitating in-depth studies of dynamic neurochemical networks.

neuroscience↗

Single CAR-Dual target: Intracranial Delivery of Anti-PD-L1 CAR T Cells Effectively Eradicates Glioma and Immunosuppressive Cells in the Tumor Microenvironment.

With the goal to overcome the limited treatment options and poor prognosis of glioblastoma (GBM), we have developed a PD-L1-targeting CAR T cell therapy, MC9999. In vitro experiments with MC9999 CAR T cells derived from GBM patients exhibited potent, antigen-specific cytotoxicity against autologous tumor cells and immunosuppressive cells within the tumor microenvironment (TME). In an orthotopic GBM model using patient-derived brain tumor-initiating cells, the intracranial delivery of MC9999 CAR T cells eradicated established tumors and improved survival. Single-cell RNA sequencing indicated that MC9999 CAR T cells activate interferon pathways, leading to GBM cell apoptosis. Multi-immunohistochemistry confirmed localized PD-L1 expression on tumor cells and TME-residing macrophages, but not in neurons or glia in patient tissue. The local delivery of MC9999 CAR T cells may be a safe, effective approach for simultaneously targeting PD-L1-positive GBM and its immunosuppressive TME and a strategy to overcome immune evasion and enhance the therapeutic potency of CAR T cell therapy against GBM.

cancer biology↗

Investigate c-Fos changes in genetically identified amygdala neurons after mild footshock stress

The amygdala is a key brain region that processes stress-related inputs to reshape future behaviors. The lateral amygdala (LA), basolateral amygdala (BLA), and central amygdala (CeA) are important subregions that mediate different aspects of stress experiences from receiving sensory input to memory formation and behavioral responding. The principal neurons in these regions are glutamatergic pyramidal neurons, which are genetically separable into two subpopulations, protein phosphatase 1 regulatory subunit 1B-positive (Ppp1r1b, also known as DARPP-32) parvocellular neurons and R-spondin2-positive (Rspo2) magnocellular neurons. Recent studies show that these two subpopulations of amygdala neurons differentially regulate appetitive versus aversive behaviors. The research goal of this study is to explore whether amygdala Ppp1r1b and Rspo2 neurons are transcriptionally activated by moderate stress experience, such that persistent cellular changes are made to influence future functional output of these two subtypes of neurons. To test transcriptional activation, we focused on c-Fos, one of the early genes that are transiently expressed in response to cellular stimulations to regulate downstream gene transcription. Moderate stress was introduced through brief footshocks, with mice without footshock as controls. Between shocked and control mice, we observed similar numbers of Ppp1r1b or Rspo2 neurons per unit area that expressed c-Fos, which was consistent across LA-BLA and CeA. Moreover, in LA-BLA, Ppp1r1b/c-Fos cells consistently outnumber Rspo2/c-Fos cells across treatment conditions, and the reverse is true in CeA. These results suggest that moderate stress experience is not sufficient to induce robust transcriptional alterations in the two key subpopulations of amygdala neurons, and Ppp1r1b versus Rspo2 neuron activities, as measured by c-Fos expression levels, show differential dominance in amygdala subregions.

neuroscience↗

Intranasal hemagglutinin protein boosters induce robust mucosal immunity and cross-protection against influenza A viral challenge

Licensed parenteral influenza vaccines induce systemic antibody responses and alleviate disease severity but do not efficiently prevent viral entry and transmission due to the lack of local mucosal immune responses. Here, we describe intranasal booster strategy with unadjuvanted recombinant hemagglutinin (HA) following initial mRNA-LNP vaccination, Prime and HA. This regimen establishes highly protective HA-specific mucosal immune memory responses in the respiratory tract. Intranasal HA boosters provided significantly reduced viral replication compared to parenteral mRNA-LNP boosters in both young and old mice. Correlation analysis revealed that slightly increased levels of nasal IgA are significantly associated with a reduced viral burden in the upper respiratory tract. Intranasal boosting with an antigenically distinct H1 HA conferred sterilizing immunity against heterologous H1N1 virus challenge. Additionally, a heterosubtypic intranasal H5 HA booster elicited cross-reactive mucosal humoral responses. Our work illustrates the potential of a nasal HA protein booster as a needle- and adjuvant-free strategy to prevent infection and disease from influenza A viruses. One Sentence SummaryAdjuvant-free nasal booster induces protective immunity against influenza infection.

immunology↗

Spatial Single-Cell Mapping of Transcriptional Differences Across Genetic Backgrounds in Mouse Brains

Genetic variation can alter organ structure and, in turn, function. Comparative statistical analysis of organs across genetic backgrounds requires spatial, single-cell, atlas-scale data in replicates, which current technologies do not provide at scale. We introduce Atlas-scale Transcriptome Localization using Aggregate Signatures (ATLAS), a scalable tissue mapping method. ATLAS learns transcriptional signatures from scRNAseq data, encodes them in situ with tens of thousands of oligonucleotide probes, and decodes them to infer cell types and imputed transcriptomes. We validated ATLAS in the mouse brain by comparing its cell type inferences with direct MERFISH measurements of marker genes and quantitative comparisons to four other technologies. Using ATLAS, we mapped the central brains of five male and five female C57BL/6J (B6) mice and five male BTBR T+ tf/J (BTBR) mice, an idiopathic model of autism, collectively profiling over 40 million cells across over 400 coronal sections. Our analysis revealed over 40 significant differences in cell type distributions and identified 16 regional composition changes across male-female and B6-BTBR comparisons. ATLAS thus enables systematic comparative studies, facilitating organ-level structure-function analysis of disease models.

genomics↗

D-lactate derived from intestinal bacteria drives lysine D-lactylation to modulate transcription in liver cells

Emerging evidence indicates that the accumulated D-lactate (D-la) from intestinal bacteria induces diverse effects in human intestinal injury diseases. However, its regulatory mechanism and functional consequence remain unclear. Here, we show that the secreted D-la induces lysine D-lactylation (K-Dla) to modulate transcription in host cells. We uncover K-Dla in HepG2 cells stimulated by D-la from E. coli secretions. Then, we confirm the occurrence of D-la-driven K-Dla by four orthogonal approaches. We further validate that the existence of K-Dla in organisms by detecting the mouse liver and human intestinal tissue. Besides, we demonstrate a SCOT1-catalyzed biosynthetic pathway of D-lactyl-CoA, serving as a key donor for K-Dla. Next, we identify the K-Dla landscape with 2895 sites and further suggest the regulation of histone K-Dla in transcription by MNase ChIP-seq and RNA-seq assays. Finally, we show the potential effect of K-Dla on inhibiting the hepatocellular carcinoma cell proliferation. In summary, we report that the secreted D-la can induce K-Dla to regulate transcription, providing a new insight into the function of D-la secreted by gut microbiota and the effect of protein chemical modifications induced by bacterial secretions.

molecular biology↗

Computational Analysis of Zn2+ Mediated Non-Competitive Inhibition to Caspase-3

Caspase-3, a critical mediator of apoptosis, is implicated in neurodegenerative diseases and cancer, making it an attractive therapeutic target. Here, we elucidated the molecular mechanisms of caspase-3 inhibition through computational methods. We first investigated the binding of the canonical substrate DEVD and novel peptidomimetic inhibitors, characterizing their competitive inhibition mechanisms. Using AlphaFold3 and molecular dynamics simulations, we then identify Zn2+-binding sites and characterize conformational changes induced by Zn2+ chelation, revealing a mechanism for non-competitive inhibition. Our results provide atomic-level insights into both competitive and Zn2+-mediated non-competitive inhibition of caspase-3, enhancing our understanding of apoptotic pathways. These findings could help guide the development of targeted therapies for apoptosis-related disorders, encompassing both competitive inhibitors and non-competitive modulators.

biophysics↗

Photochemical processes drive thermal responses of dissolved organic matter in the dark ocean

How dissolved organic matter (DOM) responds to climate warming is critical for understanding its role in future ocean carbon cycling. Here, we use a highly resolved dataset of over 800 DOM samples covering the surface waters to the deep Atlantic, Southern, and Pacific oceans to examine the changes in DOM molecular composition in response to warming water temperatures, referred to as DOM thermal responses. Towards the deep waters, the strength (i.e., overall magnitude) and diversity (i.e., variation among molecules) of these thermal responses both decline. However, these responses show opposite trends with the concentration of more recalcitrant molecules, decreasing and increasing, respectively. These contrasting trends concur with the observation that, compared to the strength of thermal responses, their diversity is more strongly explained by photochemical processes of DOM. By projecting global ocean thermal responses from 1950 to 2020 using environmental temperature, salinity and radiation, we predict that increases in the diversity of thermal responses are unexpectedly largest at deeper depths (> 1,000 m). Such increases could elevate the recalcitrant deep-ocean carbon sink by approximately 10 Tg C yr-1, which accounts for > 5% of the carbon flux reaching and persisting in the deep ocean. Our findings highlight the role of photochemical processes in imprinting DOM thermal responses, offering new insights into the future capacity of the oceanic carbon sink under global climate change.

ecology↗

eProbe: a capture probe design toolkit for genetic diversity reconstructions from ancient environmental DNA

Ancient environmental DNA (aeDNA) is now commonly used in paleoecology and evolutionary ecology, yet due to difficulties in gaining sufficient genome coverage on individual species from metagenome data, its genetic perspectives remain largely uninvestigated. Hybridization capture has proven as an effective approach for enriching the DNA of target species, thus increasing the genome coverage of sequencing data and enabling population and evolutionary genetics analysis. However, to date there is no tool available for designing capture probe sets tailored for aeDNA based population genetics. Here we present eProbe, an efficient, flexible and easy-to-use program toolkit that provides a complete workflow for capture probe design, assessment and validation. By benchmarking a probe set for foxtail millet, an annual grass, made by the eProbe workflow, we demonstrate a remarkable increase of capturing efficiency, with the target taxa recovery rate improved by 577-fold, and the genome coverage achieved by soil capture-sequencing data even higher than data directly shotgun sequenced from the plant tissues. Probes that underwent our filtering panels show notably higher efficiency. The capture sequencing data enabled accurate population and evolutionary genetic analysis, by effectively inferring the fine-scale genetic structures and patterns, as well as the genotypes on functional genes.

bioinformatics↗

Effect of fumarate and live yeast on methane emissions, rumen fermentation, blood metabolites, and lactation performance in dairy goats

The objective of this study was to evaluate the effects and combined effects of fumarate (32 g/d) and active dry yeast (ADY) (1.5 g/d) on methane emissions, rumen fermentation, microbial community and function, apparent total tract digestibility, blood metabolites, and lactation performance in 28 lactating goats using a randomized complete block design with a 2 x 2 factorial arrangement. Fumarate supplementation inhibited methane emission rates for 3 h post-feeding, while ADY increased the methane emission rates for 2 h pre-feeding, without combined effects between them. Fumarate increased the rumen pH and reduced total VFA concentration without changing the VFA profiles before feeding. Based on two custom dataset of 4,674 metagenome-assembled genomes and 7,758,615 nonredundant genes, neither fumarate nor live yeast influenced the rumen microbial community and function. The addition of fumarate reduced the concentrations of glucose, serum malondialdehyde (MDA), and ammonia in the serum, as well as the activity of insulin, while increasing the activity of serum malate dehydrogenase (MDH) and the levels of urea in both serum and milk. The addition of live yeast reduced serum glucose levels and increased serum MDA concentrations and MUN levels. There was a negative interaction between fumaric acid and live yeast on the levels of urea nitrogen in serum and milk. ConclusionsThe methane inhibition effect of fumaric acid persists for 3 h post-feeding, reflecting its retention or metabolism time in the rumen. Fumaric acid enhances the TCA cycle and the urea cycle in dairy goats, thereby improving energy utilization efficiency and reducing the risk of ammonia toxicity.

microbiology↗

A novel role for Neurog2 in MYCN driven neuroendocrine plasticity of prostate cancer

Neuroendocrine prostate cancer (NEPC) presents a formidable clinical challenge owing to its aggressive progression and resistance to conventional therapies. A key driver of NEPC is the overexpression of MYCN, a well-established oncogene associated with neuroendocrine tumors. However, efforts to directly inhibit the N-Myc protein encoded by this gene have resulted in limited success, thereby hindering therapeutic advancements. To overcome this obstacle, we conducted unbiased genome-wide screening using isogenic prostate cancer cell lines to identify the synthetic vulnerabilities of MYCN. Among the identified candidates, NEUROG2 emerged as a significant candidate. Neurog2 is a proneural transcription factor (PTF) known for its role in developmental processes and trans-differentiation of adult cells. Our findings demonstrate that Neurog2 depletion does not affect non-malignant cells, but significantly suppresses the growth of MYCN-overexpressing cells and tumors in orthotopic NEPC models. Furthermore, our observations indicate that the Neurog2-mediated regulation of PTFs can facilitate NEPC development. Thus, targeting Neurog2 holds promise as an effective therapeutic strategy for MYCN-overexpressing NEPC.

cancer biology↗

TBK1 and IKKϵ protect target cells from IFNγ-mediated T cell killing via an inflammatory apoptotic mechanism

Cytotoxic T cells produce interferon gamma (IFN{gamma}), which plays a critical role in anti-microbial and anti-tumor responses. However, it is not clear whether T cell-derived IFN{gamma} directly kills infected and tumor target cells, and how this may be regulated. Here, we report that target cell expression of the kinases TBK1 and IKK{varepsilon} regulate IFN{gamma} cytotoxicity by suppressing the ability of T cell-derived IFN{gamma} to kill target cells. In tumor targets lacking TBK1 and IKK{varepsilon}, IFN{gamma} induces expression of TNFR1 and the Z-nucleic acid sensor, ZBP1, to trigger RIPK1-dependent apoptosis, largely in a target cell-autonomous manner. Unexpectedly, IFN{gamma}, which is not known to signal to NF{kappa}B, induces hyperactivation of NF{kappa}B in TBK1 and IKK{varepsilon} double-deficient cells. TBK1 and IKK{varepsilon} suppress IKK/{beta} activity and in their absence, IFN{gamma} induces elevated NF{kappa}B-dependent expression of inflammatory chemokines and cytokines. Apoptosis is thought to be non-inflammatory, but our observations demonstrate that IFN{gamma} can induce an inflammatory form of apoptosis, and this is suppressed by TBK1 and IKK{varepsilon}. The two kinases provide a critical connection between innate and adaptive immunological responses by regulating three key responses: (1) phosphorylation of IRF3/7 to induce type I IFN; (2) inhibition of RIPK1-dependent death; and (3) inhibition of NF{kappa}B-dependent inflammation. We propose that these kinases evolved these functions such that their inhibition by pathogens attempting to block type I IFN expression would enable IFN{gamma} to trigger apoptosis accompanied by an alternative inflammatory response. Our findings show that loss of TBK1 and IKK{varepsilon} in target cells sensitizes them to inflammatory apoptosis induced by T cell-derived IFN{gamma}. Short SummaryIn the absence of TBK1 and IKK{varepsilon}, target cells are killed by T cells in an IFN{gamma}-dependent manner. In TBK1 and IKK{varepsilon}-deficient cells, IFN{gamma} induces RIPK1-dependent death, as well as hyper-induction of NF{kappa}B-dependent inflammatory genes. This suggests that any inhibition of TBK1/IKK{varepsilon} to block type I IFN expression will result in the demise of the cell accompanied by an alternate inflammatory program. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/606693v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@1606b75org.highwire.dtl.DTLVardef@12eebc0org.highwire.dtl.DTLVardef@177c033org.highwire.dtl.DTLVardef@eb5819_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Identification of targetable vulnerabilities of PLK1-overexpressing cancers by synthetic dosage lethality

Tumor heterogeneity poses a significant challenge in combating treatment resistance. Despite Polo-like kinase 1 (PLK1) being universally overexpressed in cancers and contributing to chromosomal instability (CIN), direct PLK1 inhibition hasnt yielded clinical progress. To address this, we utilized the synthetic dosage lethality (SDL) approach, targeting PLK1s genetic interactions for selective killing of overexpressed tumor cells while mitigating heterogeneity-associated challenges. Employing computational methods, we conducted a genome-wide shRNA screen, identifying 105 SDL candidates. Further in vivo CRISPR screening in a breast cancer xenograft model and in vitro CRISPR analysis validated these candidates. Employing Perturb-seq revealed IGF2BP2/IMP2 as a key SDL hit eliminating PLK1-overexpressing cells. Suppression of IGF2BP2, genetically or pharmacologically, downregulated PLK1 and limited tumor growth. Our findings strongly propose targeting PLK1s genetic interactions as a promising therapeutic approach, holding broad implications across multiple cancers where PLK1 is overexpressed.

cancer biology↗