Biology subjects

Si, Y.

Publications and source records attributed to Si, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Recurrent mitotic error and purifying selection shape chromosomal mosaicism across human tissues

Mosaic chromosomal alterations (mCAs) have been extensively studied in cancer and clonal hematopoiesis but less so in healthy solid tissues. Here, we characterized mCAs in 19 tissues across 25 donors (aged 42-89+ years) by analyzing >200x whole-genome sequencing data generated by the Somatic Mosaicism across Human Tissues (SMaHT) Network. Across 722 tissue samples, we identified 1,008 autosomal mCAs >1 Mb in length and ubiquitous losses of sex chromosomes. Surprisingly, the highest levels of Y chromosome loss in males (5-10% cell fraction in elderly donors) were observed in the lung, adrenal gland, and heart. These tissues also tended to experience more X loss in females, revealing a gradient of mitotic error burden across human tissues. Autosomal aneuploidies displayed distinct tissue-specific patterns indicative of negative selection against most events, except in the adrenal gland, in which low-level aneuploidy was pervasive. In contrast to the adrenal gland, testis rarely harbored aneuploidies but frequently experienced low-level copy-neutral loss of heterozygosity (CN-LOH), suggesting increased mitotic recombination in spermatogonial stem cells. Recurrent X chromosome losses within tissues of female donors exhibited allelic skews explained by a combination of genetic and epigenetic effects. Together, these results show that the chromosomal landscape of aging human tissues is shaped by genetics and recurrent mutations, most but not all of which are held in check by purifying selection.

genomics↗

bioRxiv2026

Molecule-resolved inference reveals the spatial organization of transcriptional programs

Transcriptional programs encode cellular identity and physiological activity, linking gene regulation to cellular phenotypes. Although spatial transcriptomics measures individual RNA molecules across intact tissues, most analyses aggregate them into cells or pixels, obscuring molecular level functional dynamics. We introduce FICTURE2, a statistical model that infers the transcriptional program from which each individual molecule is generated, using gene identity and spatial context alone without segmentation or binning. FICTURE2 learns programs with distinct spatial distributions, ranging from millimeter-scale continuous transition to micron-scale subcellular localization, the coexisting patterns of which then reveal both cellular identity and physiological activity with unified interpretations. FICTURE2 supports both unsupervised and reference-guided inference and is orders of magnitude more efficient than alternative approaches, enabling systematic analysis of large-scale spatial datasets as we demonstrate in data across diverse tissue types profiled by various spatial technologies.

genomics↗

bioRxiv2026

Disrupted RGS coupling underlies a clinically distinct subset of GNAO1-related disorder

Heterotrimeric G proteins are transducers for a wide variety of neurotransmitter receptors. Mutations in the G protein o subunit are implicated in an early-onset neurological condition, GNAO1-related disorder, that manifests as movement disorders, developmental delays, and/or epileptic seizures. In a screen of disease-linked mutations in Go, we identified a subset that had no obvious biochemical defects, warranting further investigation. By structural modeling, protein-protein binding experiments in vitro and in cells, as well as measures of downstream ion channel electrophysiology, we identified a subset that impairs interactions with regulator of G protein signaling (RGS) proteins. RGS proteins accelerate G protein GTPase activity and are therefore critical for proper neurotransmitter signaling. Further, synthesis of current clinical data revealed that patients harboring these variants have comparatively mild symptoms. Our study demonstrates the importance of RGS regulation in G protein function, cell signaling, and human neurobiology.

biochemistry↗

bioRxiv2026

Creation of a High-Resolution, Continually Evolvable Lineage Tracer

Cellular diversity is required for the proper function of many tissues, including the retina, with its ~130 cell types.1-3 Previous lineage studies suggested that retinal progenitor cells (RPCs) generate cell diversity through biased cell divisions.4-9 However, the extent to which each progenitor cell contributes to diversity, and the overarching rules governing the lineages of the collection of progenitor cells, are unknown. While classic lineage tracing approaches including retroviral labeling4,6,10, dye injection11,12, and time-lapse microscopy13,14 were used to make the foundational insights regarding retinal lineages, they cannot be used to interrogate multigenerational lineages at scale. Here we describe the creation of an evolvable lineage tracing tool, "SCRIBBLE" for Sequential Combinatorial Recorder for Iterative Barcode-Based Lineage Evolution. SCRIBBLE uses prime editor to iteratively edit a barcode sequence while preserving the order of genesis of clonally related progeny. Through a series of rationally designed high-throughput screens and design optimizations, we identified novel sequences that support a high level of barcode editing and information content. Evaluation of SCRIBBLE in embryonic mouse retina recapitulated known lineages in retinal development, demonstrating that SCRIBBLE is capable of high-resolution lineage tracing in a complex tissue.

developmental biology↗

bioRxiv2026

Chronic Polystyrene Nanoplastics Exposure Reprograms Gene Expression, Alternative Splicing, and Disrupts Host Microbiome Metabolic Networks to Promote Atherosclerosis in LDLr- Knockout Mice

Although micro- and nanoplastics have been detected in human atherosclerotic plaques, their mechanistic contribution to disease pathogenesis remains poorly defined. Most experimental studies have used microplastics (particles > 1 m) in non-atherosclerotic animal models or the ApoE-/- mouse, relying on short-term exposure or single-pathway analyses, whereas the chronic cardiovascular effects of nanoplastics (< 100 nm) remain exceedingly scarce--despite their higher biological reactivity and greater tissue penetrance. To address this gap, this study employs a multi-omics approach to investigate the chronic (12-week) oral exposure to 80 nm polystyrene nanoplastics in LDLr-/- mice. We uniquely integrate aortic plaque quantification, hepatic transcriptomics with global alternative splicing profiling, gut microbiome 16S sequencing, and liver untargeted metabolomics to construct a unified host-microbiome-metabolite network. Nanoplastic exposure significantly exacerbates aortic lipid deposition, suppresses hepatic detoxification and anti-atherogenic lipid pathways primarily through transcriptional and post-transcriptional level changes driven by alternative splicing events (e.g., intron retention and isoform switching), and induces gut dysbiosis marked by a reduction in SCFA-producing commensals and enrichment of pro-atherogenic pathobionts--perturbations that correlate with specific hepatic functional modules. Metabolomic changes, including decreased levels of the glutathione precursor {gamma}-glutamylcysteine and the choline-derived metabolite neurine, implicate oxidative stress and TMAO-related pathways. Cross-species validation using human atherosclerotic transcriptomic and metagenomic datasets supports the clinical translatability. By integrating multi-level biological responses, this work establishes nanoplastics as an environmental cardiovascular risk factor and uncovers novel regulatory mechanisms involving splicing-associated transcriptional reprogramming and gut-liver crosstalk, offering potential early-warning biomarkers and therapeutic targets for nanoplastic-associated cardiovascular disease. HighlightsO_LIExposure to polystyrene nanoplastics (80 nm) increases aortic lipid burden in LDLr-/- mice. C_LIO_LIAlternative splicing and isoform switching were identified as novel hepatic responses. C_LIO_LISCFA-producing gut commensals are depleted, and pathobionts are enriched in response to nanoplastics. C_LIO_LIA gut-liver network links suppressed detoxification to gut microbial dysbiosis. C_LIO_LIMouse transcriptomics and metagenomics overlap with human atherosclerosis omics datasets. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/736446v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@196ad0eorg.highwire.dtl.DTLVardef@13b95d3org.highwire.dtl.DTLVardef@e963c4org.highwire.dtl.DTLVardef@94f60c_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

molecular biology↗

bioRxiv2026

Cognitive function depends upon Satb2 gene dosage in cortical projection neurons

SATB2-associated syndrome (SAS) is a severe neurodevelopmental disorder caused by de novo heterozygous SATB2 mutations, yet how haploinsufficiency disrupts brain development remains poorly understood. While homozygous Satb2 loss causes profound embryonic cell-fate defects, we demonstrate using a heterozygous mouse model that SAS phenotypes emerge primarily during postnatal circuit maturation. Integrating chromatin profiling, transcriptomics, electrophysiology, and behavior, we show that SATB2 acts as a dose-sensitive chromatin regulator that binds conserved enhancer-promoter landscapes to orchestrate networks linked to human intelligence. Although excitatory neuron subtype specification is preserved, Satb2 heterozygotes adopt an intermediate epigenetic state that drives cell-type-specific dysregulation of genes enriched for intellectual disability risk variants. Consequently, mutant neurons exhibit simplified dendritic arborization, reduced intrinsic excitability, and weakened layer 2/3-to-layer 5 intracortical connectivity. These circuit deficits culminate in the disorganization of the somatosensory barrel cortex and severe impairments in whisker-dependent texture discrimination. Finally, by restricting Satb2 heterozygosity to the cortex, we decouple these cortical sensory deficits from subcortical vocalization phenotypes. Together, our work links SATB2 dosage to chromatin architecture and postnatal circuit maturation, revealing a critical, post-mitotic therapeutic window for intervention in SAS.

neuroscience↗

bioRxiv2026

Designing urban green-space heterogeneity across urbanisation gradients to maintain avian richness

Urban expansion drives land cover change and habitat simplification, contributing to biodiversity loss. Urban green spaces can mitigate these impacts, but their effectiveness depends on its configuration and implementation. Here, we examine how three complementary dimensions of environmental heterogeneity--plant species richness, habitat heterogeneity, and foliage-layer richness--shape bird richness along an urbanisation gradient in the Netherlands. Using bird and plant occurrence data, LiDAR-derived vegetation structure, and land-use data, we fitted generalized additive models at three spatial scales (100, 200, and 300 m) to assess how these relationships vary across the urbanisation gradient. Plant species richness showed the strongest and consistent positive effect on bird richness, disregarding urbanization intensities. Habitat heterogeneity showed most pronounced positive effects at intermediate levels of urbanisation. In contrast, foliage-layer richness had weak associations with bird richness across urbanization intensities. Together, these results demonstrate that sustaining urban bird diversity requires urbanisation-intensity-dependent design of green-space heterogeneity. Increasing plant richness is generally recommended across urbanization intensities. Increasing habitat heterogeneity is more effective at intermediate levels of urbanisation and appears less suitable in highly urbanised contexts. Beyond simply expanding green space area or their spatial complexity alone, urban planning should focus on the thoughtful design of different types of environmental heterogeneity. This includes city-wide species-rich planting and structurally diverse habitat mosaics in mid-density areas to sustain urban bird diversity.

ecology↗

bioRxiv2026

Integration of in situ hybridization and scRNA-seq data provides a 2D topographical map of the developing retina across species

Precise regional patterning is fundamental to tissue organization, yet the spatial logic that governs it remains poorly defined for many tissues. In the vertebrate retina, molecular domains along the dorsoventral and nasotemporal axes provide positional cues for regional specializations such as the high-acuity area (HAA). We combined multiplexed in situ hybridization data with single-cell transcriptomic data to create quantitative two-dimensional maps of developing retinal cells. In the developing chicken retina, this approach resolved sharp expression boundaries of genes involved in patterning, and revealed novel candidates enriched in the anlagen of the HAA. Comparative analysis of chicken, mouse, and human data demonstrated conserved axis-based programs, but distinct fine-scale organization consistent with presence/absence of an HAA. Here, we show that spatial reconstruction from scRNA-seq data, anchored by experimental benchmarks, enables comparative 2D topographic mapping of gene expression across species and provides a generalizable strategy to investigate the spatial logic of molecular organization in developing tissues. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/697548v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@e9b84aorg.highwire.dtl.DTLVardef@4207deorg.highwire.dtl.DTLVardef@112bc79org.highwire.dtl.DTLVardef@113e1d3_HPS_FORMAT_FIGEXP M_FIG C_FIG HIGHLIGHTSO_LIQuantification of multiplexed RNA-FISH signals generated reproducible spatial expression maps in the developing chicken retina. C_LIO_LIResolution of relative boundaries for early patterning genes revealed nested expression domains marking the boundaries of the developing HAA. C_LIO_LIRNA-FISH experimental data using genes with axis-specific expression allowed the generation of DV and NT scores which enabled the localization of each cell in a scRNA-seq dataset onto a 2D topographical map of the developing retina. C_LIO_LI2D topographic maps derived from scRNA-seq data revealed novel HAA-enriched genes in the developing chicken retina. C_LIO_LICross-species comparisons showed conserved DV/NT programs but divergent fine-scale organization in retinal development. C_LIO_LICyp26c1 expression pattern was validated in human retina correlating with the location of the future HAA. C_LI

developmental biology↗

bioRxiv2025

Non-redundant roles for paralogous proteins in the yeast glucose-sensing pathway

Paralogs engage in biological processes through both redundant and non-redundant functions. In the yeast Saccharomyces cerevisiae, approximately one-fifth of the genome consists of paralogs, with their encoded proteins involved in multiple pathways. However, the unique contributions of individual paralogs have remained poorly defined. Here, we undertook a systematic examination of eight paralog pairs in the glucose-sensing pathways, deleting each component and measuring the resulting changes in gene expression. To that end we established a new transcription reporter system to monitor the response to glucose as well as to non-preferred sugars in single cells. Focusing on the PKA catalytic subunits, comprised of the paralogs Tpk1 and Tpk3 as well as the isomorphic kinase Tpk2, we employed mass spectrometry to identify their contribution to cellular metabolism, used a GFP-based sensor to follow changes in cytosolic pH, and used BioID to identify unique and shared binding partners. Our data reveal that paralogs in the glucose-sensing pathway contribute in multiple and unique ways to signal transduction, and establish potential mechanisms driving the preservation of these and other duplicated genes throughout long periods of evolution.

genetics↗

bioRxiv2025

Nitrate availability modulates the temperature effect on N2O and N2 production from denitrification

Nitrous oxide (N2O) can be both produced and subsequently reduced to dinitrogen gas (N2) via canonical denitrification, making the balance between these steps a key control on the net flux of this potent climate gas. Through a meta-analysis, we showed that net N2O and N2 production from denitrification respond differently to temperature, exhibiting distinct temperature sensitivities. In addition, nitrate availability plays a critical role in regulating this balance, yet only few studies have examined the combined effects of temperature and nitrate availability in natural sediments. Using 15N-isotope labelling and anoxic sediment incubations, we found that temperature effects on N2O and N2 production from denitrification were evident only under high nitrate levels (100 {micro}M), while no significant temperature response occurred under low nitrate concentration (10 {micro}M). At high nitrate availability, N2 production increased at higher temperatures, whereas net N2O production declined, leading to a lower production ratio of N2O to N2 at warmer temperatures. These findings suggest that in nitrogen-limited ecosystems, substrate availability plays a stronger role than temperature in regulating denitrification. More broadly, they provide insights into how nutrient loading and climate warming interact to shape nitrogen cycling and greenhouse gas emissions in aquatic ecosystems.

biochemistry↗

bioRxiv2025

ZNF638 represses the transcription of HBV closed circular DNA involving HUSH complex-mediated histone modifications of epigenetic silencing

Hepatitis B virus (HBV) infection poses a critical threat to public health burden worldwide. As the major template of viral transcription, the covalently closed circular DNAs (cccDNAs) of HBV was known to form microchromosomes and interact with various host proteins. In the present study, ZNF638 was found to significantly reduce the transcription of HBV into pgRNAs, and subsequently reduce cccDNA formation and viral propagation. We discovered that ZNF638 was able to bind the preS and S gene regions of HBV, repressing the transcription of cccDNA upon increased modification of H3K9me3 mediated by SETDB1. This epigenetic silencing of cccDNA transcription was further demonstrated to involve the activity of HUSH, a multi-protein complex to mediate epigenetic modifications of histone into suppressed nucleosomes. In in vivo models, we evaluated the effects of ZNF638 deficiency on HBV-targeting siRNA therapy. A significant reduction of the efficacy was observed in animals with reduced ZNF638 expression. In summary, we report that ZNF638 is a potent host factor to repress the transcription of HBV DNAs and to attenuate HBV infection. The role of ZNF638 on HBV repression involves its binding to cccDNA at specific regions for recruiting HUSH complex to write H3K9me3 histone marks for epigenetic silencing. ZNF638 serves as a critical host factor to associate HBV infection and disease progression. Additionally, ZNF638 serves as a potential indicator to predict the outcome of HBV-targeting siRNA therapy.

biochemistry↗

bioRxiv2025

INHBA promotes the progression of gastric cancer by activating MAPK signaling pathway via targeting ITGA6

Gastric cancer (GC) is one of the most common malignancies, ranking as the fifth most common cancer and the fourth leading cause among cancer related deaths worldwide. Upregulated INHBA expression in gastric cancer tissues compared to adjacent non-cancerous tissues was confirmed by immunohistochemistry and qRT-PCR analysis. This increased expression of INHBA was found to be significantly associated with the incidence of tumor lesion, lymph node metastasis and the progression to more advanced TNM stages in patients. Functional experiments showed that INHBA could promote the proliferation of GC cells, enhance migration and invasion in vitro, while simultaneously facilitating the inhibition of apoptosis. To test whether INHBA regulated the tumor growth in vivo, the animal studies were performed. The indicated that INHBA over-expression promoted the tumor growth, including weight and volume. Moreover, this study demonstrated through a series of experiments including RNA-seq, Co-IP, Co-IF, Western blot, and Rescue studies that INHBA promotes the progression of GC by targeting ITGA6 to regulate the MAPK signaling pathway. In summary, understanding the role of INHBA/ITGA6/MAPK in tumourigenesis could provide new insights into gastric cancer therapy and targeted inhibition of INHBA might be a potential therapeutic approach for GC treatment.

cancer biology↗

bioRxiv2025

Population-scale gene expression analysis reveals the contribution of expression diversity to the modern wheat improvement

Changes in gene expression are crucial for crop breeding, yet population genomics has primarily focused on sequence polymorphisms rather than gene expression diversity. The strategy of using single genome reference for RNA-seq analysis could not handle introgression bias, especially for hexaploidy wheat. Here, we conducted RNA-seq for 328 wheat lines, including representative diverse landraces and elite cultivars from China and the United States, to investigate the role of gene expression variation in shaping agronomic traits. Using pan-genome resources, we identified 20,615 more transcripts than using the Chinese Spring reference genome alone. We constructed a pan-gene atlas regulatory map through eQTL analysis, demonstrating that genes introgressed from wild relatives were under tight genetic control. Genes responding to environmental stress show higher activity after introgressed into the wheat genome, demonstrating how long-term breeding selection impacted the gene expression regulation of targeted introgression. Multi-omics modeling identified 231 high-confidence candidate genes for 34 field agronomic traits and the seedling resistance phenotypes of 8 powdery mildew isolates. More than one fifth of those candidates have no homolog in Chinese Spring reference genome. By utilizing the indexed KN9204 EMS library, 80% candidates showed significant trait difference between wild type and mutant lines. Furthermore, directional shifts in genes of which expression were changed by breeding improvement demonstrated distinct adaptations to local environments. Our study constructed a pan-gene atlas to correct the reference bias of reads mapping in RNA-seq studies and revealed the expression patterns of introgressed genes within the wheat genome and their regulatory mechanisms, which highlighted the impact of breeding selection on gene expression of the worlds most important crop.

plant biology↗

bioRxiv2025

Seq-Scope-eXpanded: Spatial Omics Beyond Optical Resolution

Sequencing-based spatial transcriptomics (sST) enables transcriptome-wide gene expression mapping but falls short of reaching the optical resolution (200-300 nm) of imaging-based methods. Here, we present Seq-Scope-X (Seq-Scope-eXpanded), which empowers submicrometer-resolution Seq-Scope with tissue expansion to surpass this limitation. By physically enlarging tissues, Seq-Scope-X minimizes transcript diffusion effects and increases spatial feature density by an additional order of magnitude. In liver tissue, this approach resolves nuclear and cytoplasmic compartments in nearly every single cell, uncovering widespread differences between nuclear and cytoplasmic transcriptome patterns. Independently confirmed by imaging-based methods, these results suggest that individual hepatocytes can dynamically switch their metabolic roles. Seq-Scope-X is also applicable to non-hepatic tissues such as brain and colon, and can be modified to perform spatial proteomic analysis, simultaneously profiling hundreds of barcode-tagged antibody stains at microscopic resolutions in mouse spleens and human tonsils. These findings establish Seq-Scope-X as a transformative tool for ultra-high-resolution whole-transcriptome and proteome profiling, offering unparalleled spatial precision and advancing our understanding of cellular architecture, function, and disease mechanisms.

genomics↗

bioRxiv2025

YTHDF3 promotes the progression of gastric cancer by activating Wnt/β-catenin signaling pathway via targeting NEK7

Gastric cancer (GC) is a widespread and deadly malignancy among global digestive tract tumors, alarmingly ranked the fifth most common cancer in terms of incidence and mortality. This study used immunohistochemistry and RT-qPCR to reveal a significant upregulation of YTHDF3 expression in GC tissues compared with that of adjacent normal tissues. This increased expression of YTHDF3 was closely associated with the incidence of lymph node metastasis and the progression to more advanced TNM stages. In vitro experiments demonstrated that YTHDF3 was crucial in promoting the aggressive characteristics of GC cells by enhancing their ability to proliferate, migrate, and invade, while simultaneously inhibiting apoptosis. The role of YTHDF3 in the progression of GC was further confirmed using the BALB/c nude mice subcutaneous tumor model, which showed a slowed tumor growth after YTHDF3 knockdown. This study further confirmed through Co-IF RIP-qPCR, western blotting, and rescue studies that YTHDF3 promotes GC progression by targeting NEK7 to regulate the Wnt/{beta}-catenin signaling pathway. In conclusion, our pivotal findings highlight the YTHDF3/NEK7/Wnt/{beta}-catenin axis as a promising and accessible therapeutic target for the development of new treatments aimed at improving clinical outcome of patients with GC.

cancer biology↗

bioRxiv2025

Characterization of auditory responsive neurons in the mouse superior colliculus to naturalistic sounds

Locating the source of a specific sound in a complex environment and determining its saliency is critical for survival. The superior colliculus (SC), a sensorimotor midbrain structure, plays an important role in sound localization and has been shown to have a topographic map of the auditory space in a range of species. In mice, previous studies using broadband white noise stimuli found that neurons use high-frequency monaural spectral cues and interaural level differences (ILDs) to compute spatially restricted receptive fields (RFs), and that these RFs are organized topographically along the azimuth. However, in a naturalistic environment, the auditory stimuli that an animal encounters may have rich spectral components; however, these sound sources can still be localized efficiently. It remains unknown whether and how the SC neurons respond to naturalistic sounds and, in turn, compute a spatially restricted RF. Here, we show results from large-scale in vivo physiological recordings of SC neurons in response to white noise, naturalistic ultrasonic pup calls and chirps. We find that mouse SC auditory neurons respond to pup calls with distinct temporal patterns and a spatial preference predominantly at [~]60 degrees in contralateral azimuth. In addition, we categorized auditory SC neurons based on their spectrotemporal receptive field patterns and demonstrated that there are at least 4 distinct subtypes of auditory responsive SC neurons. Significance StatementThe superior colliculus (SC) receives visual and auditory information that is used to localize objects. While the organization and composition of visually responsive SC neurons is well described, much less is known about the types and response properties of auditory SC neurons. Here, we presented white noise, ultrasonic mouse pup calls, and chirp stimuli to mice while recording from SC neurons. Analysis of neuronal responses defines 4 distinct classes of auditory neurons. We also show that while auditory neurons respond to naturalistic stimuli, these responses mainly occur when presented from the side but not the front of the animal. These results lead to the hypothesis that mice use different strategies to localize sound depending on the spectral composition of the source.

neuroscience↗

bioRxiv2024

ITGB4 promotes the progression of colorectal cancer by activating Wnt/β-catenin signaling pathway via targeting EZR

ObjectivesColorectal cancer (CRC) is a major cause of cancer-related mortality worldwide. Integrin beta 4 (ITGB4) has been previously identified as being overexpressed in CRC; however, its precise oncogenic mechanism remains unclear. The present study aimed to elucidate the functional role of ITGB4 in CRC progression and identify its downstream molecular effectors to provide new insights for targeted therapy. MethodsThe biological functions of ITGB4 were investigated in CRC cell lines (SW480 and HCT116) using a series of in vitro assays, including CCK-8, colony formation, Transwell migration and invasion, and flow cytometry for apoptosis following ITGB4 knockdown. An in vivo xenograft mouse model was used to evaluate the effect of ITGB4 on tumor growth. Downstream targets were screened using RNA sequencing (RNA-seq) and validated by co-immunoprecipitation and co-immunofluorescence. The underlying signaling pathway was investigated by Western blotting and functional rescue experiments. ResultsKnockdown of ITGB4 significantly suppressed CRC cell proliferation, migration, and invasion, while promoting apoptosis in vitro. Similarly, silencing ITGB4 markedly inhibited tumor growth in the in vivo xenograft model. RNA-seq analysis identified Ezrin (EZR) as a key downstream target of ITGB4, and a direct protein-protein interaction was confirmed between them. Mechanistically, ITGB4 knockdown decreased the expression of EZR at both the mRNA and protein levels. ITGB4 was demonstrated to exert its pro-tumorigenic effects through the regulation of EZR, which subsequently activated the Wnt/{beta}-catenin signaling pathway. Interestingly, EZR overexpression partially restored ITGB4 levels, suggesting a potential positive feedback loop via Wnt/{beta}-catenin signaling that further amplifies this oncogenic axis. Notably, the malignant phenotypes suppressed by ITGB4 silencing were significantly rescued by the overexpression of EZR. ConclusionThe present study identified a novel ITGB4/EZR/Wnt/{beta}-catenin signaling axis in colorectal cancer. ITGB4 promotes CRC progression by modulating EZR expression and subsequently activating the Wnt/{beta}-catenin pathway. These findings highlight ITGB4 as a potential prognostic biomarker and a promising therapeutic target for CRC.

molecular biology↗

bioRxiv2024

CNV-Profile Regression: A New Approach for Copy Number Variant Association Analysis in Whole Genome Sequencing Data

Copy number variants (CNVs) are DNA gains or losses involving >50 base pairs. Assessing CNV effects on disease risk requires consideration of several factors. First, there are no natural definitions for CNV loci. Second, CNV effects can depend on dosage and length. Third, CNV effects can be more accurately estimated when all CNV events in a genomic region are analyzed together to assess their joint effects. We propose a new framework for association analysis that directly models an individuals entire CNV profile within a genomic region. This framework represents an individuals CNVs using a CNV profile curve to capture variations in CNV length and dosage and to bypass the need to predefine CNV loci. CNV effects are estimated at each genome position, making the results comparable across different studies. To jointly estimate the effects of all CNVs, we use a Lasso penalty to select CNVs associated with the trait and integrate a weighted L2-fusion penalty to encourage similar effects of adjacent CNVs when supported by the data. Simulations show that the proposed model can more effectively identify causal CNVs while maintaining false positive rates comparable to baseline methods and yield more precise effect-size estimates across different settings. When applied to CNV derived from whole genome sequencing data of the Alzheimers Disease Sequencing Project, the proposed methods identify additional CNVs associated with Alzheimers Disease (AD). These identified CNVs overlap with several known AD-risk genes and are significantly enriched by biological processes related to neuron structures and functions crucial in AD development.

bioinformatics↗