Biology subjects

Xu, M.

Publications and source records attributed to Xu, M..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Primate-specific BTN3A2 protects against SARS-CoV-2 infection by interacting with and reducing ACE2

BackgroundCoronavirus disease 2019 (COVID-19) is an immune-related disorder caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The complete pathogenesis of the virus remains to be determined. Unraveling the molecular mechanisms governing SARS-CoV-2 interactions with host cells is crucial for the formulation of effective prophylactic measures and the advancement of COVID-19 therapeutics. MethodsWe analyzed human lung single-cell RNA sequencing dataset to discern the association of butyrophilin subfamily 3 member A2 (BTN3A2) expression with COVID-19. The BTN3A2 gene edited cell lines and transgenic mice were infected by live SARS-CoV-2 in a biosafety level 3 (BSL-3) laboratory. Immunoprecipitation, flow cytometry, biolayer interferometry and competition ELISA assays were performed in BTN3A2 gene edited cells. We performed quantitative real-time PCR, histological and/or immunohistochemical analyses for tissue samples from mice with or without SARS-CoV-2 infection. FindingsThe BTN3A2 mRNA level was correlated with COVID-19 severity. BTN3A2 expression was predominantly identified in epithelial cells, elevated in pathological epithelial cells from COVID-19 patients and co-occurred with ACE2 expression in the same lung cell subtypes. BTN3A2 targeted the early stage of the viral life cycle by inhibiting SARS-CoV-2 attachment through interactions with the receptor-binding domain (RBD) of the Spike protein and ACE2. BTN3A2 inhibited ACE2-mediated SARS-CoV-2 infection by reducing ACE2 in vitro and in vivo. InterpretationThese results reveal a key role of BTN3A2 in the fight against COVID-19. Identifying potential monoclonal antibodies which mimic BTN3A2 may facilitate disruption of SARS-CoV-2 infection, providing a therapeutic avenue for COVID-19. FundingThis study was supported by the National Natural Science Foundation of China (32070569, U1902215, and 32371017), the CAS "Light of West China" Program, and Yunnan Province (202305AH340006). Research in contextO_ST_ABSEvidence before this studyC_ST_ABSOur understanding of the pathogenesis of COVID-19, especially key molecular events in the early stage of viral infection, remains incompletely albeit we witnessed many progresses. This knowledge gap hinders the finding for effective and specific antiviral agents against SARS-CoV-2. The entry of SARS-CoV-2 is mediated by the entry receptor angiotensin-converting enzyme 2 (ACE2) and is affected by host antiviral defenses. Targeting these universal host factors required for virus replication is the most promising approach for effective prevention and treatment of COVID-19. Added value of this studyOur study revealed that BTN3A2, a primate-specific gene, acts as a potent inhibitor of SARS-CoV-2 infection in vitro and in vivo. The up-regulation of BTN3A2 upon SARS-CoV-2 infection competed with the ACE2 receptor for binding to the Spike protein, subsequently reducing ACE2 expression and ACE2-mediated SARS-CoV-2 entry. Implications of all the available evidenceThese data highlighted that BTN3A2 as a novel host factor with protective effects against SARS-CoV-2 infection. The BTN3A2 holds considerable potential as a therapeutic drug for mitigating the impact of SARS-CoV-2 and its variants of concern (VOCs).

cell biology↗

bioRxiv2024

The Nrf2/Id2 Axis in Vascular Smooth Muscle Cells: Novel Insights into the Interplay between Vascular Calcification and Aging

OBJECTIVEVascular calcification (VC) significantly contributes to cardiovascular morbidity and mortality and escalates with age. However, effective pharmaceutical interventions are lacking, and the molecular mechanisms linking aging to VC remain elusive. This study explores the role of nuclear factor erythroid 2-related factor 2 (NRF2) in VC, specifically focusing on the interplay between vascular senescence and oxidative stress (OS). APPROACH AND RESULTSUsing a chronological aging mouse model, we noted a significant decline in the expression and activity of Nrf2 in the aortas of aged mice, coinciding with increased medial VC. Administering NRF2 activators effectively reduced this calcification. In the vascular smooth muscle cell (VSMC)-specific Nrf2 knockout (Nrf2SMCKO) models, created using adenine and Vitamin D, there was an increase in calcium deposition within the aortic medial layer, alongside heightened VSMC senescence and OS. Furthermore, NRF2 knockout exacerbated VC in aortic rings and primary VSMCs in high-phosphate conditions, while Nrf2 overexpression in VSMCs inhibited calcium deposition by alleviating cell senescence and OS. RNAseq analysis of the aortas from Nrf2SMCKO and control mice highlighted a significant downstream regulator of Inhibitor of DNA Binding 2 (ID2). Our results show that reduced NRF2 levels lead to increased VSMC senescence, characterized by heightened p16 expression and diminished ID2 expression. Inhibiting ID2 negated NRF2s protective effects against VSMC senescence and VC. CONCLUSIONThis study emphasizes the critical role of NRF2 dysfunction in the nexus of vascular senescence, OS, and VC. It proposes the NRF2-ID2 axis in VSMCs as a promising therapeutic target for reducing VC and mitigating age-related cardiovascular diseases. HighlightsO_LIDecline in NRF2 activity is linked to increased vascular calcification (VC) and aging. C_LIO_LIVSMC-specific Nrf2 knockout causes a remarkable exacerbation of arterial calcification. C_LIO_LINRF2 alleviates VC by inhibiting oxidative stress and VSMC senescence. C_LIO_LIID2 contributes to the protective role of NRF2 in VSMC senescence and VC. C_LI

molecular biology↗

bioRxiv2023

Dispersal and evolution of the invasive snail Pomacea canaliculata, an intermediate host of Angiostrongylus cantonensis: A field study around its initial introduction site in China

Eosinophilic meningitis caused by Angiostrongylus cantonensis is an emerging infectious disease in mainland China. The invasive snail (Pomacea canaliculata) is one of the main intermediate host of the zoonotic nematode. To gain insights into the spatial distribution, phenotypic variation and dispersal pattern of the snail populations. A field survey was conducted using modified nested sampling and selecting ditches as the main habitats. Snail distribution and abundance were displayed with predictions based on an inverse distance-weighted model. Correlation and spatial autocorrelation were analyzed among the measured parameters. The findings of this study demonstrate the well-established and abundant presence of P. canaliculata in ditches. A total of 564 sampling sites were assessed, with measurements taken on 10,145 snails having shell heights greater than 1.5 cm. The average population density was determined to be 20.31 {+/-} 11.55 snails per square meter. Morphological analysis revealed an average snail body mass of 8.93 {+/-} 3.95 g, shell height of 3.38 {+/-} 0.66 cm, a sex ratio of 2.39 {+/-} 1.01 female to male, and a shell color ratio of 9.34 {+/-} 7.52 brown to yellow. Among these measurements, body mass was found to be significantly correlated with shell height (r = 0.88, p < 0.01) and shell color (r = 0.55, p < 0.05). Spatial-correlation analysis proved that shell height was the only factor significantly spatially autocorrelated (MI = 0.27, z = 2.20, p = 0.03), although weak autocorrelations appeared in body mass and shell color. The observed geographic variations of phenotypic traits indicated a human-mediated evolving process of the snail populations and a potential complexity of the parasite transmission system. These findings may enhance the assessment of the epidemiological health risk posed by angiostrongyliasis and inform strategies for controlling infectious snails.

ecology↗

bioRxiv2023

ST-GEARS: Advancing 3D Downstream Research through Accurate Spatial Information Recovery

Three-dimensional Spatial Transcriptomics has revolutionized our understanding of tissue regionalization, organogenesis, and development. However, to reconstruct single sections back to their in situ three-dimensional morphology, existing approaches either only adopt gene expression information to guide reconstruction or overlook shape correction against experiment-induced section distortions. This leads to significant discrepancies between reconstruction results and the actual in vivo locations of cells, imposing unreliable spatial profiles to downstream analysis. To address these challenges, we propose ST-GEARS (Spatial Transcriptomics GEospatial profile recovery system through AnchoRS), which solves optimized anchors between in situ closest spots utilizing expression and structural similarity across sections and recovers in vivo spatial information under the guidance of anchors. By employing innovative Distributive Constraints into the Optimization scheme, it retrieves anchors with higher precision compared to existing methods. Taking these anchors as reference points, ST-GEARS first rigidly aligns sections, then introduces and infers Elastic Fields to counteract distortions. ST-GEARS denoises the fields using context information by Gaussian Denoising. Utilizing the denoised fields, it eliminates distortions and eventually recovers original spatial profile through innovative and mathematically proved Bi-sectional Fields Application. Studying ST-GEARS on both bi-sectional registration and complete tissue reconstruction across sectional distances and sequencing platforms, we observed its outstanding performance in spatial information recovery across tissue, cell, and gene levels compared to current approaches. Through this recovery, ST-GEARS provides precise and well-explainable gears between in vivo situations and 3D in vitro analysis, powerfully fueling the potential of biological discoveries.

bioinformatics↗

bioRxiv2023

Spatially resolved molecular and cellular atlas of the mouse brain

A comprehensive atlas of genes, cell types, and their spatial distribution across a whole mammalian brain is fundamental for understanding function of the brain. Here, using snRNA-seq and Stereo-seq techniques, we generated a mouse brain atlas with spatial information for 308 cell clusters with single-cell resolution involving over 6 million cells as well as for 29,655 genes. We have identified new astrocyte clusters, and demonstrated that distinct cell clusters exhibit preference for cortical subregions. In addition, we identified 155 genes exhibiting regional specificity in the brainstem, and 513 long non-coding RNA exhibited regional specificity in the adult brain. Parcellation of brain regions based on spatial transcriptomic information showed large overlap with that by traditional method. Furthermore, we have uncovered 411 transcription factor regulons with spatiotemporal specificity during development. Thus, our study has discovered genes and regulon with spatiotemporal specificity, and provided a high-resolution spatial transcriptomic atlas of the mouse brain.

neuroscience↗

bioRxiv2023

Limitation of switching sensory information flow in flexible perceptual decision making

Humans can flexibly change rules to categorize sensory stimuli, but their performance degrades immediately after a task switch. This switch cost is believed to reflect a limitation in cognitive control, although the bottlenecks responsible for this remain controversial. Here, we show that humans exhibit a brief reduction in the efficiency of converting sensory inputs into decision evidence immediately after changing rules in perceptual tasks. Participants performed a flexible face categorization task in which they classified parametrically generated face stimuli based on one of two rules, switching every few trials. Although participants were always informed of a rule switch by a context cue, they showed a specific pattern of increase in reaction times, regardless of the time they were given to prepare for the switch. Psychophysical reverse correlation and computational modeling revealed a reduction in sensory weighting immediately after a rule switch, which recovered within a few hundred milliseconds after stimulus presentation. Furthermore, this cost depends on the sensory features being switched, suggesting a major bottleneck at the stage of adjusting the sensory information flow. We propose that decision-making circuits cannot fully adjust their sensory readout based on an abstract context cue alone, but rather require the presence of an actual stimulus to tune it, leading to a limitation in flexible perceptual decision making.

neuroscience↗

bioRxiv2023

Stereopy: modeling comparative and spatiotemporal cellular heterogeneity via multi-sample spatial transcriptomics

Tracing cellular dynamic changes across conditions, time, and space is crucial for understanding the molecular mechanisms underlying complex biological systems. However, integrating multi-sample data in a unified and flexible way to explore cellular heterogeneity remains a major challenge. Here, we present Stereopy, a flexible and versatile framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this flexible framework, we have developed three key components: a multi-sample tailored data container, a scope controller, and an analysis transformer. Furthermore, Stereopy showcases three transformative applications supported by pivotal algorithms. Firstly, the multi-sample cell community detection (CCD) algorithm introduces an innovative capability to detect specific cell communities and identify genes responsible for pathological changes in comparable datasets. Secondly, the spatially resolved temporal gene pattern inference (TGPI) algorithm represents a notable advancement in detecting important spatiotemporal gene patterns while concurrently considering spatial and temporal features, which enhances the identification of important genes, domains and regulatory factors closely associated with temporal datasets. Finally, the 3D niche-based regulation inference tool, named NicheReg3D, reconstructs the 3D cell niches to enable the inference of cell-gene interaction network within the spatial texture, thus bridging intercellular communications and intracellular regulations to unravel the intricate regulatory mechanisms that govern cellular behavior. Overall, Stereopy serves as both a bioinformatics toolbox and an extensible framework that provides researchers with enhanced data interpretation abilities and new perspectives for mining multi-sample spatial transcriptomics data.

bioinformatics↗

bioRxiv2023

Structural basis of anticancer drug recognition and amino acid transport by LAT1

LAT1 (SLC7A5) transports large neutral amino acids and their derivatives across the plasma membrane and plays pivotal roles in cancer cell proliferation, immune response and drug delivery across the blood-brain barrier. Despite recent advances in structural understanding of LAT1, how it discriminates substrates and inhibitors including the clinically relevant anticancer drugs remains elusive. Here we report six structures of LAT1, captured in three different conformations and bound with diverse bioactive ligands, elucidating its substrate transport and inhibitory mechanisms. JPH203, also known as nanvuranlat or KYT-0353 and currently in clinical trials as an anticancer drug, binds to the wide-open substrate-binding pocket of LAT1. It adopts a U-shaped conformer, with its amino-phenylbenzoxazol moiety pushing against transmembrane helix 3 (TM3), bending TM10 and arresting the transporter in the outward-facing conformation. In contrast, the physiological substrate L-Phe does not exhibit such inhibitory interactions, whereas melphalan, a slow substrate, poses steric hindrance in the pocket, explaining its inhibitory activity. Unexpectedly, the "classical" system L inhibitor BCH induces an occluded state, a key structural intermediate required for substrate transport. Trans stimulation assays show that BCH facilitates transporter turnover and is therefore a transportable substrate. These findings provide a structural framework for the intricate mechanisms of substrate recognition and inhibition of LAT1, paving the way for developing more specific and effective drugs against it.

biochemistry↗

bioRxiv2023

SpaGRN: investigating spatially informed regulatory paths for spatially resolved transcriptomics data

Cells expressing similar transcriptional regulatory circuits spatially aggregate into distinct cell types or states. However, most existing methods for inferring gene regulatory networks from spatially resolved transcriptomics are devoted to spatial co-expression modules or interactions between transcription factors and target genes, neglecting mediated effects from extracellular signals. Here we introduce SpaGRN, a statistical framework for predicting the comprehensive intracellular regulatory network underlying spatial patterns by integrating spatial expression profiles with prior knowledge on regulatory relationships and signaling paths. We validate and assess SpaGRN using simulated and real datasets, demonstrating its efficiency, performance, and robustness. When applied to 3D datasets of developing Drosophila embryos and larvae, SpaGRN identifies spatiotemporal variations in specific regulatory patterns, delineating the cascade of events from receptor stimulation to downstream transcription factors and targets, revealing synergetic regulation mechanism during organogenesis. Moreover, SpaGRN provides flexible visualization functions. We construct an online 3D regulatory network atlas database for interactive exploration and sharing.

bioinformatics↗

bioRxiv2023

Targeting CD74-positive macrophages improves neoadjuvant therapy in cervical cancer as revealed by single-cell transcriptomics analysis

Uterine cervical cancer (UCC) has the second-highest mortality rate among malignant tumors of the female reproductive system. Immune checkpoint inhibitors (ICIs) have emerged as a promising therapeutic strategy for cervical cancer. However, the efficacy of PD-1 (programmed cell death protein 1) blockade combined with neoadjuvant chemotherapy (NACT) and the ensuing alterations within the tumor microenvironment need further investigation. We conducted single-cell RNA sequencing using 46,950 cells from nine sequential human cervical cancer tissues representing different stages of NACT and PD-1 blockade combination therapy. We delineated the trajectory of cervical epithelial cells and unveiled crucial factors involved in the combination therapy. Cell communication analysis revealed the inferred interaction strength decreased between T cell-cancer cells, while the communication between macrophage-cancer cells intensified after NACT therapy. We verified that macrophages are necessary for PD-1 blockade combination to exert antitumor effects in vitro. Detailed analysis unraveled the CD74-positive macrophages frequently interacted with the immunoreactive Epi 3 subgroup during neoadjuvant combination therapy. CD74 upregulation limited phagocytosis and stimulated M2 polarization. The CD74 blockade enhanced macrophage phagocytosis, resulting in decreased viability of cervical cancer cells in vitro and in vivo. This study unveils the dynamic microenvironment of UCC influenced by NACT and PD-1 blockade combination therapy, and targeting CD74 was a potential strategy to augment the therapy efficacy.

cancer biology↗

bioRxiv2023

Hyperbolic graph embedding of MEG brain networks to study brain alterations in individuals with subjective cognitive decline

An expansive area of research focuses on discerning patterns of alterations in functional brain networks from the early stages of Alzheimers disease, even at the subjective cognitive decline (SCD) stage. Here, we developed a novel hyperbolic MEG brain network embedding framework for transforming high-dimensional complex MEG brain networks into lower-dimensional hyperbolic representations. Using this model, we computed hyperbolic embeddings of the MEG brain networks of two distinct participant groups: individuals with SCD and healthy controls. We demonstrated that these embeddings preserve both local and global geometric information, presenting reduced distortion compared to rival models, even when brain networks are mapped into low-dimensional spaces. In addition, our findings showed that the hyperbolic embeddings encompass unique SCD-related information that improves the discriminatory power above and beyond that of connectivity features alone. Notably, we introduced a unique metric--the radius of the node embeddings--which effectively proxies the hierarchical organization of the brain. Using this metric, we identified subtle hierarchy organizational differences between the two participant groups, suggesting increased hierarchy in the dorsal attention, frontoparietal, and ventral attention subnetworks among the SCD group. Last, we assessed the correlation between these hierarchical variations and cognitive assessment scores, revealing associations with diminished performance across multiple cognitive evaluations in the SCD group. Overall, this study presents the first evaluation of hyperbolic embeddings of MEG brain networks, offering novel insights into brain organization, cognitive decline, and potential diagnostic avenues of Alzheimers disease.

bioinformatics↗

bioRxiv2023

Constraints on Lanthanide Separation by Selective Biosorption

Rare Earth Elements (REE) are essential ingredients of sustainable energy technologies1-5, but separation of lanthanides is considered one of the hardest problems in chemistry today6. Biosorption, where molecules adsorb to the surface of biological materials, offers a sustainable alternative to environmentally harmful solvent extractions currently used for REE separations. The REE-biosorption capabilities of some microorganisms already allow for REE separations that under specialized conditions are competitive with solvent extractions7. Our recent work has discovered the genetic basis for REE biosorption selectivity8. However, it is unclear if the small changes to selectivity produced by changes to single genetic loci could allow biosorption to leapfrog existing REE separation technologies. In this article we present three models of lanthanide separation by biosorption and desorption. The first model shows that if a biosorbing microbe behaves as it if has a single type of binding site with small preference for one lanthanide, then the small changes in selectivity produced by changes to a single genetic locus could reduce the length of a separation process by {approx} 25%. Large multi-locus gene edits could reduce a separation process length by almost 90%. On the other hand, if the microbe contains multiple sites each with a distinct preference for an individual lanthanide, then separations become challenging and larger genetic edits would be needed to enable high purity. However, even if these large genetic edits are not possible, high purity separations could still be possible by combining multiple microbes, each with small increases in selectivity, with the first designed to enrich for the target lanthanide, while subsequent microbes are designed to remove contaminants.

synthetic biology↗

bioRxiv2023

Designing efficient randstrobes for sequence similarity analyses

Substrings of length k, commonly referred to as k-mers, play a vital role in sequence analysis, reducing the search space by providing anchors between queries and references. However, k-mers are limited to exact matches between sequences. This has led to alternative constructs, such as spaced k-mers, that can match across substitutions. We recently introduced a class of new constructs, strobemers, that can match across substitutions and smaller insertions and deletions. Randstrobes, the most sensitive strobemer proposed in [18], has been incorporated into several bioinformatics applications such as read classification, short read mapping, and read overlap detection. Randstrobes are constructed by linking together k-mers in a pseudo-random fashion and depend on a hash function, a link function, and a comparator for their construction. Recently, we showed that the more random this linking appears (measured in entropy), the more efficient the seeds for sequence similarity analysis. The level of pseudo-randomness will depend on the hashing, linking, and comparison operators. However, no study has investigated the efficacy of the underlying operators to produce randstrobes. In this study, we propose several new construction methods. One of our proposed methods is based on a Binary Search Tree (BST), which lowers the time complexity and practical runtime to other methods for some parametrizations. To our knowledge, we are also the first to describe and study the types of biases that occur during construction. We designed three metrics to measure the bias. Using these new evaluation metrics, we uncovered biases and limitations in previous methods and showed that our proposed methods have favorable speed and sampling uniformity to previously proposed methods. Lastly, guided by our results, we change the seed construction in strobealign, a short-read mapper, and find that the results change substantially. Also, we suggest combining the two versions to improve accuracy for the shortest reads in our evaluated datasets. Our evaluation highlights sampling biases that can occur and provides guidance on which operators to use when implementing randstrobes.

bioinformatics↗

bioRxiv2023

The Neural Basis of Drosophila Courtship Song

Many motor control systems generate multiple movements using a common set of muscles. How are premotor circuits able to flexibly generate diverse movement patterns? Here, we characterize the neuronal circuits that drive the distinct courtship songs of Drosophila melanogaster. Male flies vibrate their wings towards females to produce two different song modes - pulse and sine song - which signal species identity and male quality. Using cell-type specific genetic reagents and the connectome, we provide a cellular and synaptic map of the circuits in the male ventral nerve cord that generate these songs and examine how activating or inhibiting each cell type within these circuits affects the song. Our data reveal that the song circuit is organized into two nested feed-forward pathways, with extensive reciprocal and feed-back connections. The larger network produces pulse song, the more complex and ancestral song form. A subset of this network produces sine song, the simpler and more recent form. Such nested organization may be a common feature of motor control circuits in which evolution has layered increasing flexibility on to a basic movement pattern.

neuroscience↗

bioRxiv2023

CryoEM structures of the human CLC-2 voltage gated chloride channel reveal a ball and chain gating mechanism

CLC-2 is a voltage-gated chloride channel that contributes to electrical excitability and ion homeostasis in many different mammalian tissues and cell types. Among the nine mammalian CLC homologs, CLC-2 is uniquely activated by hyperpolarization, rather than depolarization, of the plasma membrane. The molecular basis for the divergence in polarity of voltage gating mechanisms among closely related CLC homologs has been a long-standing mystery, in part because few CLC channel structures are available, and those that exist exhibit high conformational similarity. Here, we report cryoEM structures of human CLC-2 at 2.46 - 2.76 [A], in the presence and absence of the potent and selective inhibitor AK-42. AK-42 binds within the extracellular entryway of the Cl--permeation pathway, occupying a pocket previously proposed through computational docking studies. In the apo structure, we observed two distinct apo conformations of CLC-2 involving rotation of one of the cytoplasmic C-terminal domains (CTDs). In the absence of CTD rotation, an intracellular N-terminal 15-residue hairpin peptide nestles against the TM domain to physically occlude the Cl--permeation pathway from the intracellular side. This peptide is highly conserved among species variants of CLC-2 but is not present in any other CLC homologs. Previous studies suggested that the N-terminal domain of CLC-2 influences channel properties via a "ball-and-chain" gating mechanism, but conflicting data cast doubt on such a mechanism, and thus the structure of the N-terminal domain and its interaction with the channel has been uncertain. Through electrophysiological studies of an N-terminal deletion mutant lacking the 15-residue hairpin peptide, we show that loss of this short sequence increases the magnitude and decreases the rectification of CLC-2 currents expressed in mammalian cells. Furthermore, we show that with repetitive hyperpolarization WT CLC-2 currents increase in resemblance to the hairpin-deleted CLC-2 currents. These functional results combined with our structural data support a model in which the N-terminal hairpin of CLC-2 stabilizes a closed state of the channel by blocking the cytoplasmic Cl--permeation pathway.

biophysics↗

bioRxiv2023

Long-read Transcriptome Landscapes of Primary and Metastatic Liver Cancers at Transcript Resolution

BackgroundThe liver is the sixth most common site of primary cancer in humans and is frequently colonized by metastases from cancers of other organs. Few studies have investigated the transcriptomic profiles of matched primary tumor and hepatic metastases of patients. Moreover, the read length of 100-200 bases in conventional short-read RNA sequencing is too short, which makes it difficult to directly infer the full-length transcript structure. To help develop effective treatments and improve survival, it is crucial to understand the complex and diverse molecular mechanisms of primary and metastatic liver cancers. MethodsNinety-five primary and secondary liver cancer patients who underwent hepatic resection were included with long-read sequencing isoform-sequencing and short-read RNA sequencing. We compared the transcriptome landscapes of primary and metastatic liver cancers and systematically investigated HCC, paired primary tumors and liver metastases, and matched non-tumor liver tissues. ResultsWe defined the full-length isoform-level transcriptome of human primary and metastatic liver cancers and identified isoform-level diversity in HCC and metastasis-associated transcriptome variations in metastatic liver cancers. Specific RNA transcripts and isoform switching events with clinical implications were profoundly discovered in liver cancer. Metastasis-specific transcripts that can predict the metastatic risk and identify the primary sites of cancers of unknown primary liver metastasis patients were defined. Additionally, we found that adjacent paracancerous liver tissues are abnormal and characterized the premetastatic immunological and metabolic alterations in the liver that favor the spread of cancer metastases. ConclusionsOur findings strongly highlight the powerfulness of full-length transcriptome profiling to yield novel biological insights into understanding the molecular basis of tumorigenesis and will further benefit the treatment of primary and metastatic liver cancers.

genomics↗

bioRxiv2023

MYCN driven oncogenesis involves cooperation with WDR5 to activate canonical MYC targets and G9a to repress differentiation genes

MYCN activates canonical MYC targets involved in ribosome biogenesis, protein synthesis and represses neuronal differentiation genes to drive oncogenesis in neuroblastoma (NB). How MYCN orchestrates global gene expression remains incompletely understood. Our study finds that MYCN binds promoters to up-regulate canonical MYC targets but binds to both enhancers and promoters to repress differentiation genes. MYCN-binding also increases H3K4me3 and H3K27ac on canonical MYC target promoters and decreases H3K27ac on neuronal differentiation gene enhancers and promoters. WDR5 is needed to facilitate MYCN promoter binding to activate canonical MYC target genes, whereas MYCN recruits G9a to enhancers to repress neuronal differentiation genes. Targeting both MYCNs active and repressive transcriptional activities using both WDR5 and G9a inhibitors synergistically suppresses NB growth. We demonstrate that MYCN cooperates with WDR5 and G9a to orchestrate global gene transcription. The targeting of both these cofactors is a novel therapeutic strategy to indirectly target the oncogenic activity of MYCN.

cancer biology↗

bioRxiv2023

Cell-type specific optogenetic fMRI on basal forebrain reveals functional network basis of behavioral preference

The basal forebrain (BF) is a complex structure that plays key roles in regulating various brain functions. However, it remains unclear how cholinergic and non-cholinergic BF neurons modulate large-scale functional networks and their relevance in intrinsic and extrinsic behaviors. With optimized awake mouse optogenetic fMRI approach, we revealed optogenetic stimulations of four BF neuron types evoked distinct cell-type specific whole-brain BOLD activations, which could attribute to BF-originated low dimensional structural networks. Additionally, optogenetic activation of VGLUT2, ChAT and PV neurons in BF modulated the preference of locomotion, exploration and grooming, respectively. Furthermore, we uncovered the functional network basis of the above BF-modulated behavioral preference, through a decoding model linking the BF-modulated BOLD activations, low dimensional structural networks, and behavioral preference. To summarize, we decoded functional network basis of differential behavioral preference with cell-type specific optogenetic fMRI on BF, and provided an avenue for investigating mouse behaviors from a whole-brain view.

neuroscience↗