Biology subjects

Ruan, L.

Publications and source records attributed to Ruan, L..

18 recordsLinked to original sources

bioRxiv2026

Parental Genome Assemblies of Suyunuo1 Reveal Structural Variation Underlying Edible Waxy Maize Evolution, Superior Hybrid Performance and Yield - Flavor Balance

Edible waxy maize is a unique domesticated cereal valued for its superior sensory and nutritional properties, yet high quality gap free genomes remain lacking, hindering the exploration of structural variations (SVs) and domestication related divergence. Here, we assembled two chromosome level, gap free genomes of the elite waxy maize inbred lines Tongxi 5 and Hengbai 522, the parents of the widely cultivated hybrid Suyunuo 1. Comparative genomic analysis revealed substantial genome size variation, prominent megabase scale SVs, and extensive knob repeat expansion in Tongxi 5. We identified widespread gene presence absence variation and hyperdivergent regions enriched in transposable elements, which largely underpin genomic differentiation between waxy and field maize. Population genomic analyses further demonstrated asymmetric introgression from field maize into the two parents, whereas the conserved waxy haplotype supports a shared ancestral origin. Integrative GWAS based on SNPs, InDels and SVs revealed that SVs substantially contribute to phenotypic diversity and mediate the co-regulation of yield traits and flavor-related metabolites. Our results uncover key genomic events underlying post-domestication divergence and highlight the essential roles of SVs in heterosis and flavor-yield balance, providing valuable genomic resources for waxy maize improvement.

plant biology↗

bioRxiv2026

Nanoscale rheological heterogeneity revealed by Single Particle orientation Tracking (SPoT) of ultrashort carbon nanotubes in brain tissue

Transport in complex biological tissues is governed by local rheological heterogeneity at the nanoscale, yet probing such environments deep inside living systems remains challenging. Here, we introduce an orientation-sensitive single-particle tracking (SPoT) approach that simultaneously resolves translational and rotational dynamics of individual carbon nanotubes deep within biological tissue. By exploiting the intrinsic dipole-like emission and short-wave infrared luminescence of carbon nanotubes enhanced through the incorporation of quantum color-centers our method enables long-duration tracking with high signal-to-noise ratio in optically dense environments. Crucially, the length of these nanotubes can be precisely shortened down to a few tens of nanometers to adapt to diffusion environmental dimensions, further optimizing the tracking applicability. SPoT of single carbon nanotubes provides access to relative changes in local viscosity, steric constraints, and environmental anisotropy. When applied to the brain extracellular space, SPoT demonstrates that local variations in the translational and rotational diffusion of tracers are heterogeneous and not systematically correlated. By combining trajectory-based signatures of confinement with rotational dynamics, this analysis allows the local contributions of effective viscosity and spatial tortuosity to be disentangled. By enabling combined translational and rotational tracking of nano-emitters over unprecedented depths and timescales, this work establishes a new framework for probing nanoscale transport and rheological heterogeneity in intact biological tissues and more generally in complex diffusive environments.

biophysics↗

bioRxiv2026

GPNMB overexpression- a marker of resistance to CDK4/6 inhibitors

Resistance to cyclin-dependent kinase 4/6 inhibitors remains a major clinical challenge in treating estrogen receptor-positive breast cancer, with no reliable predictive biomarkers currently available for patient selection. To investigate resistance mechanisms, we generated drug-tolerant persisters (DTPs) to abemaciclib and palbociclib in a panel of estrogen receptor-positive breast cancer cell lines. Functional analyses revealed that DTPs showed resistance to CDK4/6 inhibition, maintained G1 arrest, and exhibited increased senescence phenotype. To identify clinically relevant markers of resistance, we compared transcriptomic profiles from DTPs with publicly available gene-expression data from the phase III PEARL trial. Glycoprotein non-metastatic B (GPNMB) emerged as one of the most strongly upregulated transcripts in DTPs, and also was amongst the genes associated with resistance in the PEARL dataset. We further verified that GPNMB overexpression (GPNMB-OE) in sensitive cells conferred resistance to CDK4/6 inhibition, and enhanced migratory capacity. Overexpression of GPNMB drove substantially faster tumor progression and eliminated the growth-inhibitory effect of abemaciclib, which remained highly effective in control tumors. Across all treatment arms, GPNMB-OE tumors failed to respond to CDK4/6 blockade, highlighting a strong resistance phenotype. These results identify GPNMB as a potent promoter of tumor progression and a key mediator of resistance to abemaciclib. Our findings position GPNMB as a potential biomarker and therapeutic target that may help identify patients unlikely to benefit from CDK4/6 inhibition.

cancer biology↗

bioRxiv2025

ATF4 alleviates doxorubicin-induced cardiomyopathy through H2S-mediated antioxidation

BackgroundDoxorubicin (DOX) remains a cornerstone in the treatment of various cancers. However, its clinical utilization is significantly hampered by dose-dependent cardiotoxicity. The generation of reactive oxygen species (ROS) constitutes the central component of the pathogenesis of DOX-induced cardiotoxicity. Activating transcription factor 4 (ATF4) has been demonstrated to exert a cardioprotective effect and augment cardiac antioxidative capacity in settings of heart failure. However, the role of ATF4 in DOX-induced cardiomyopathy (DIC) remains unknown. MethodsTo explore the role of ATF4 in DOX-induced cardiomyopathy, cardiac-specific ATF4 conditional heterozygous mice and AAV9 mediated ATF4 overexpression mouse models were utilized. Cardiac function was assessed by echocardiography. The upstream regulator and downstream mediator of ATF4 were evaluated using RNA-seq analysis and further verified using ChIP assay and luciferase reporter assay. ResultsWe found a substantial decrease in ATF4 expression levels in the heart of DIC mice. ATF4+/- mice exhibited a higher degree of susceptibility to DOX-induced cardiotoxicity in comparison with ATF4flox/flox mice, as evidenced by the manifestation of more severe cardiac dysfunction and a significantly earlier mortality rate. In contrast, cardiacc-specific overexpression ATF4 by AAV9 confers robust cardioprotection against DOX-induced cardiomyopathy. Mechanistically, we identified the upstream regulator of ATF4 as KLF16, which was significantly suppressed during DOX treatment. Further, the decrease of ATF4 led to a reduction in cystathionine {gamma}-lyase (CSE) transcription and hydrogen sulfide (H2S) production in the context of DOX-induced cardiotoxicity. ChIP and luciferase reporter assays revealed that ATF4 functioned as the transcription factor of the CSE gene, which is a key enzyme in the synthesis of H2S to counteract oxidative stress. Consistently, ROS scavengers or H2S donors was shown to mitigate the consequences of ATF4 deficiency. In contrast, the ectopic expression of ATF4 mitigated oxidative stress and apoptosis in DOX-induced cardiotoxicity, both in vivo and in vitro. ConclusionsOur study revealed a novel function of ATF4 in counteracting oxidative stress in DOX cardiotoxicity by promoting the transcription of CSE. ATF4 may represent a promising therapeutic target for the treatment of DOX-induced cardiomyopathy.

pathology↗

bioRxiv2025

Effects of Exercise and Konjac on Lipid Metabolism and Mechanism in Obese Rats

ObjectiveTo study the effects of exercise and konjac on body weight and lipid metabolism in obese rats, and the possible mechanism of exercise combined with konjac on body weight and lipid metabolism. MethodsFifty male Sprague Dawley rats were randomly divided into 5 groups. After six weeks of intervention, blood lipid, body weight, liver weight, inflammatory factors, oxidative stress markers and proteins were measured. ResultsWeight and liver weight in HFD group were significantly higher (P<0.05, P<0.01) than those in CON group. Compared with HFD group, blood lipid index in intervention group were significantly decreased; The levels of MDA (P<0.01, P<0.05, P<0.05) and SOD (P<0.05) in intervention group were significantly decreased; the GSH levels in HAE group and HKE group were significantly increased(P<0.01, P<0.05); the levels of IL-6, TNF-, and leptin in HAE group (P<0.05, P<0.05, P<0.01) and HKE group (P<0.01, P<0.01, P<0.05) were significantly decreased; ApoA5 in intervention group was significantly increased (P<0.01), SREBP-1c and LXR was significantly decreased (P<0.01). ConclusionKonjac or exercise alone can improve the lipid metabolism, and the comprehensive effect is better. The mechanism of regulating lipid metabolism may be related to the expression of LXR, SREBP-1c and ApoA5.

biochemistry↗

bioRxiv2025

A Novel COE-D8-Fosfomycin Conjugate Effectively Against First-line Antibiotic Resistant Uropathogenic Escherichia coli

Recurrent urinary tract infections (UTIs) are increasingly associated with antibiotic resistance, posing significant clinical challenges. This study evaluates the antimicrobial efficacy of the membrane-intercalating conjugated oligoelectrolyte COE-D8 against uropathogenic Escherichia coli (UPEC). Among 93 clinical UPEC isolates, over 50% demonstrated resistance to first-line antibiotics, with compound sulfamethoxazole showing the highest resistance (75% at a minimum inhibitory concentration (MIC) >512 g/mL). COE-D8 significantly reduced resistance rates, achieving less than 50% at 32 g/mL and below 5% at 512 g/mL, while demonstrating at least fourfold faster bacterial elimination than standard antibiotics. Mechanistic studies revealed that COE-D8 disrupts bacterial membranes, inducing rapid lysis. However, its cytotoxicity in mammalian cells at 2 g/mL limits clinical application. To address this, a combination therapy with fosfomycin was explored, significantly reducing COE-D8 toxicity by at least fourfold in vitro. In mouse models, fosfomycin co-administration mitigated COE-D8-induced toxicity and prevented mortality at higher doses without compromising antimicrobial efficacy. These findings highlight the potential of COE-D8, particularly in combination with fosfomycin, as a promising strategy to combat antibiotic-resistant UPEC while addressing toxicity challenges.

microbiology↗

bioRxiv2024

Divergent and Convergent TMEM106B Pathology in Murine Models of Neurodegeneration and Human Disease

TMEM106B is a lysosomal/late endosome protein that is a potent genetic modifier of multiple neurodegenerative diseases as well as general aging. Recently, TMEM106B was shown to form insoluble aggregates in postmortem human brain tissue, drawing attention to TMEM106B pathology and the potential role of TMEM106B aggregation in disease. In the context of neurodegenerative diseases, TMEM106B has been studied in vivo using animal models of neurodegeneration, but these studies rely on overexpression or knockdown approaches. To date, endogenous TMEM106B pathology and its relationship to known canonical pathology in animal models has not been reported. Here, we analyze histological patterns of TMEM106B in murine models of C9ORF72-related amyotrophic lateral sclerosis and frontotemporal dementia (C9-ALS/FTD), SOD1-related ALS, and tauopathy and compare these to postmortem human tissue from patients with C9-ALS/FTD, Alzheimers disease (AD), and AD with limbic-predominant age-related TDP-43 encephalopathy (AD/LATE). We show that there are significant differences between TMEM106B pathology in mouse models and human patient tissue. Importantly, we also identified convergent evidence from both murine models and human patients that links TMEM106B pathology to TDP-43 nuclear clearance specifically in C9-ALS. Similarly, we find a relationship at the cellular level between TMEM106B pathology and phosphorylated Tau burden in Alzheimers disease. By characterizing endogenous TMEM106B pathology in both mice and human postmortem tissue, our work reveals considerations that must be taken into account when analyzing data from in vivo mouse studies and elucidates new insights supporting the involvement of TMEM106B in the pathogenesis and progression of multiple neurodegenerative diseases.

neuroscience↗

bioRxiv2024

Intra-genomic genes-to-genes correlation enables genome representaion

The bacterial pan-genome consists of core genes shared by all members of a taxonomy and accessory genes found in only a subset. The correlation among genes within the pan-genome could advance our understanding of evolution and tackle medical challenges. Here, we discovered a strong intra-genomic correlation among bacterial pan-genes within each of Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, and Campylobacter jejuni. With a convolutional neural network assisted core genome knock-out simulation, we found that different combinations of fewer than 20 highly variable core genes could recover the sub-species type classified by complete core genome with accuracy >95%. This observation led us to test the genes-to-genes predictability: with more than 52,000 assemblies from each species, combinations of highly variable core genes could predict the sequence variants of other core genes (average accuracy >94%) within the same genome and could also predict sequence variants (average accuracy >91%) as well as the presence (average AUROC >0.91) of some accessory genes. Furthermore, combinations of highly variable core genes could also predict multiple antibiotic resistances (AUROC >0.80) in large published datasets of E. coli, S. aureus, and Mycobacterium tuberculosis. Collectively, we propose that genes within the same genome can strongly correlate with each other. Therefore, the strain phylogeny and the status of other genes could be uniformly represented by combinations of highly variable core genes, which could further represent certain phenotypes including in vitro resistance.

bioinformatics↗

bioRxiv2023

Trojan horse virus delivering CRISPR-AsCas12f1 controls plant bacterial wilt caused by Ralstonia solanacearum

Plant bacterial wilt caused by the Ralstonia solanacearum species complex results in huge food and economic losses. Accordingly, the development of an effective control method for this disease is urgently required. Traditional lytic phage biocontrol methods have inherent limitations. However, filamentous phages, which do not lyse host bacteria and exert minimal burden, offer a potential solution. A filamentous phage RSCq that infects R. solanacearum was isolated in this study through genome mining. We constructed engineered filamentous phages based on RSCq by employing our proposed approach with a wide applicability to non-model phages, enabling the infection of R. solanacearum in medium and soil and delivering exogenous genes into bacterial cells. Similar to the Greek soldiers hidden within the Trojan horse, CRISPR-AsCas12f1 gene editing system that targets the key virulence regulator gene hrpB was implanted into the engineered phage, generating the engineered phage RSCqCRISPR-Cas. Our findings demonstrated that RSCqCRISPR-Cas could disarm the key "weapon", hrpB, of R. solanacearum, in medium and in plants. Remarkably, pretreatment with RSCqCRISPR-Cas significantly controlled tobacco bacterial wilt, highlighting the potential of engineered filamentous phages as promising biocontrol agents against plant bacterial wilt and other bacterial diseases.

microbiology↗

bioRxiv2023

Disruption of Epithelium Integrity by Inflammation-Associated Fibroblasts through Prostaglandin Signaling

Inflammation-associated fibroblasts (IAFs) are associated with the progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial function and architecture is unknown. In this study, we developed an in vitro model whereby human colon fibroblasts are induced to become IAFs by specific cytokines and recapitulate key features of IAFs in vivo. When co-cultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid swelling and barrier disruption due to swelling and rupture of individual epithelial cells. Epithelial cells co-cultured with IAFs also exhibit increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated through a paracrine pathway involving prostaglandin E2 (PGE2) and the PGE2 receptor EP4, leading to PKA-dependent activation of the CFTR chloride channel. Importantly, EP4-specific chemical inhibitors effectively prevented colonoid swelling and restored normal proliferation and genome stability of IAF-exposed epithelial cells. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a potential treatment to mitigate inflammation-associated epithelial injury. TeaserInflammation-associated fibroblasts compromise colon epithelial barrier integrity and genome stability via PGE2-EP4 signaling.

cell biology↗

bioRxiv2023

GPI-anchored Gas1 protein regulates cytosolic proteostasis in yeast

Decline in protein homeostasis (proteostasis) is a hallmark of cellular aging and aging-related diseases. Maintaining a balanced proteostasis requires a complex network of molecular machineries that govern protein synthesis, folding, localization, and degradation. Under proteotoxic stress, misfolded proteins that accumulate in cytosol can be imported into mitochondria for degradation via mitochondrial as guardian in cytosol (MAGIC) pathway. Here we report an unexpected role of yeast Gas1, a cell wall-bound glycosylphosphatidylinositol (GPI)-anchored {beta}-1,3-glucanosyltransferase, in differentially regulating MAGIC and ubiquitin-proteasome system (UPS). Deletion of Gas1 inhibits MAGIC but elevates polyubiquitination and UPS-mediated protein degradation. Interestingly, we found that Gas1 exhibits mitochondrial localization attributed to its C-terminal GPI anchor signal. But this mitochondria-associated GPI anchor signal is not required for mitochondrial import and degradation of misfolded proteins via MAGIC. By contrast, catalytic inactivation of Gas1 via the gas1E161Qmutation inhibits MAGIC but not its mitochondrial localization. These data suggest that the glucanosyltransferase activity of Gas1 is important for regulating cytosolic proteostasis.

cell biology↗

bioRxiv2023

Metabolic regulation of misfolded protein import into mitochondria

Mitochondria are the cellular energy hub and central target of metabolic regulation. Mitochondria also facilitate proteostasis through pathways such as the mitochondria as guardian in cytosol (MAGIC) whereby cytosolic misfolded proteins (MPs) are imported into and degraded inside mitochondria. In this study, a genome-wide screen in yeast uncovered that Snf1, the yeast AMP-activated protein kinase (AMPK), inhibits the import of MPs into mitochondria while promoting mitochondrial biogenesis under glucose starvation. We show that this inhibition requires a downstream transcription factor regulating mitochondrial gene expression and is likely to be conferred through substrate competition and mitochondrial import channel selectivity. We further show that Snf1/AMPK activation protects mitochondrial fitness in yeast and human cells under stress induced by MPs such as those associated with neurodegenerative diseases.

cell biology↗

bioRxiv2022

The genome of a vestimentiferan tubeworm (Ridgeia piscesae) provides insights into its adaptation to a deep-sea environment

Vestimentifera (Polychaeta, Siboglinidae) is a taxon of deep-sea worm-like animals living in the deep-sea hydrothermal vent and cold seep areas. The morphology and lifespan of Ridgeia piscesae, which is the only vestimentiferan tubeworm species found in the hydrothermal vents on the Juan de Fuca Ridge, vary greatly according to the endemic environments. Recent analyses have revealed the genomic basis of adaptation in three vent- and seep-dwelling vestimentiferan tubeworms. However, the evolutionary history and mechanism of adaptation in R. piscesae, a unique species in the family Siboglinidae, is remained to be investigated. Here we report a high-quality genome of R. piscesae collected at Cathedral vent of the Juan de Fuca Ridge. Comparative genomic analysis revealed that that the high growth rates of vent-dwelling tubeworms might derive from small genome size. The small genome sizes of these tubeworms are attributed to the repeat content but not the number of genes and intron sizes. Additionally, four genes involved in cell proliferation were subject to positive selection in the genome of R. piscesae, suggesting that, besides apoptosis, cell proliferation is important for regulating growth rate in this species.

genomics↗

bioRxiv2021

A novel multifunctional role for Hsp70 in binding post-translational modifications on clients

Hsp70 interactions are critical for cellular viability and the response to stress. Previous attempts to characterize Hsp70 interactions have been limited by their transient nature and inability of current technologies to distinguish direct vs bridged interactions. We report the novel use of cross-linking mass spectrometry (XL-MS) to comprehensively characterize the budding yeast Hsp70 protein interactome. Using this approach, we have gained fundamental new insights into Hsp70 function, including definitive evidence of Hsp70 self-association as well as multi-point interaction with its client proteins. In addition to identifying a novel set of direct Hsp70 interactors which can be used to probe chaperone function in cells, we have also identified a suite of PTM-associated Hsp70 interactions. The majority of these PTMs have not been previously reported and appear to be critical in the regulation of client protein function. These data indicate that one of the mechanisms by which PTMs contribute to protein function is by facilitating interaction with chaperones. Taken together, we propose that XL-MS analysis of chaperone complexes may be used as a unique way to identify biologically-important PTMs on client proteins. O_LIIn vivo confirmation of Hsp70 dimerization C_LIO_LIComprehensive direct interactome of Hsp70 C_LIO_LIMulti-domain interactions between Hsp70 and client proteins C_LIO_LIIdentification of novel biologically-important client protein PTMs C_LI

molecular biology↗

bioRxiv2019

Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice

Xanthomonas oryzae pv. oryzae (Xoo) causes bacterial blight disease, which reduces crop yield by up to 50% in rice production. Despite its substantial threat on food production worldwide, knowledge about its population structure, virulence diversity and the relationship between them is limited. We used whole-genome sequencing to explore the diversity and evolution of Xoo during the past 30 years in the main rice-planting areas of China. Six separate lineages were revealed by phylogenomic analysis, with CX-5 and CX-6 predominating in the population for decades. The recent sporadic outbreaks were respectively caused by Xoo derived from these lineages especially the two major ones. The lineage and sub-lineage distribution of isolates strongly correlated to their geographical origin, which was found to be mainly determined by the planting of the two major rice subspecies, indica and japonica. Large-scale virulence testing was conducted to evaluate the diversity of pathogenicity for Xoo. We found rapid virulence dynamics against rice, and its determinant factors including genetic background of Xoo, rice resistance genes and the planting environment of rice. Genetic background was investigated deeply by comparative genomics, which indicates that transposition events contributing the most to evolution of the Xoo genome and the rapid diversification of virulence. This study provided a good model to understand the evolution and dynamics of plant pathogens in the context of interaction with their hosts which are influenced by both geographical conditions and farming practices.

genomics↗

bioRxiv2018

The effect of varied exercise intensity on antioxidant function, and aortic endothelial cell function and serum lipids in a non-alcoholic fatty liver disease rats.

Exercise and diet may improve cardio-metabolic health in non-alcoholic fatty liver disease, but the optimal exercise prescription remains unclear. We aimed to compare the effects of diet and exercise at different intensities on antioxidant function, and aortic endothelial cell function and serum lipids in a non-alcoholic fatty liver disease rats. Fifty Sprague Dawley rats (180-220g) were randomly divided into two experimental groups and fed either standard rodent chow diet or a high-fat diet. After16 weeks, these animals that received the HFD were randomly separated into a high fat control group or three exercise training groups: HF and low intensity exercise, HF and moderate intensity exercise, HF and incremental intensity exercise, these experimental rats keep sedentary or training for the next 6 weeks. Markers of Aortic Oxidative stress were detected using assay kit. Immunohistochemical analysis was performed to determine the expression level of eNOS and ET-1. Lipid metabolism parameters were detected with an automatic analyzer. Exercise at different intensities improved lipid metabolism, enhanced anti-oxidation function, reduced MDA, increased NO, and improved the expression of eNOS and ET-1 protein levels. Decreased blood lipids were exhibited in all exercise groups. Notably, moderate intensity exercise demonstrated more effect on increasing GSH contents, and decreased the expression of ET-1 protein levels.

physiology↗

bioRxiv2018

Rules for PP2A-controlled phosphosignalling and drug responses

Systemic understanding of protein phosphatase 2A (PP2A)-regulated cellular processes is still at infancy. Here, we present mass-spectrometry analysis of phospho-targets (dephosphorylome) regulated by PP2A modulation. In addition to PP2A-regulated processes and targets, the data reveal important general concepts and rules related to PP2A-mediated phosphoregulation. These include the unidirectionality paradigm of regulation of phosphorylation, and differential spatial distribution of kinase-and phosphatase-dominated phosphotargets. Data also present first systemic analysis of targets of PP2A-modulating oncoproteins, CIP2A, PME-1, and SET; including targets via which PP2A may coordinately regulate activities of cancer drivers and tumor suppressors such as MYC or TP53. To validate functional utility of this dataset, PP2A dephosphorylome activity was correlated with cancer cell responses to over 300 drugs. Notably, we find that cancer therapy responses can be broadly classified based on PP2A dephosphorylome activity, both in quantitative and qualitative manner. In summary, our data characterize rules by which PP2A coordinate cancer cell phosphosignaling and drug responses. The results also may also direct the use of emerging pharmacological approaches for PP2A activity modulation in human diseases.

systems biology↗

bioRxiv2017

Candidate cancer driver mutations in super-enhancers and long-range chromatin interaction networks

A comprehensive catalogue of the mutations that drive tumorigenesis and progression is essential to understanding tumor biology and developing therapies. Protein-coding driver mutations have been well-characterized by large exome-sequencing studies, however many tumors have no mutations in protein-coding driver genes. Non-coding mutations are thought to explain many of these cases, however few non-coding drivers besides TERT promoter are known. To fill this gap, we analyzed 150,000 cis-regulatory regions in 1,844 whole cancer genomes from the ICGC-TCGA PCAWG project. Using our new method, ActiveDriverWGS, we found 41 frequently mutated regulatory elements (FMREs) enriched in non-coding SNVs and indels (FDR<0.05) characterized by aging-associated mutation signatures and frequent structural variants. Most FMREs are distal from genes, reported here for the first time and also recovered by additional driver discovery methods. FMREs were enriched in super-enhancers, H3K27ac enhancer marks of primary tumors and long-range chromatin interactions, suggesting that the mutations drive cancer by distally controlling gene expression through threedimensional genome organization. In support of this hypothesis, the chromatin interaction network of FMREs and target genes revealed associations of mutations and differential gene expression of known and novel cancer genes (e.g., CNNB1IP1, RCC1), activation of immune response pathways and altered enhancer marks. Thus distal genomic regions may include additional, infrequently mutated drivers that act on target genes via chromatin loops. Our study is an important step towards finding such regulatory regions and deciphering the somatic mutation landscape of the non-coding genome.

cancer biology↗