Biology subjects

Kaikkonen, M. U.

Publications and source records attributed to Kaikkonen, M. U..

At least 19 recordsLinked to original sources

bioRxiv2026

An in vitro System for Studying Osteochondrogenic Differentiation of Smooth Muscle Cells and Modeling Intimal Vascular Calcification

Objective: Smooth muscle cells (SMCs) undergo phenotypic transitions during atherosclerosis, including towards a chondromyocyte (CMC) state associated with intimal calcification. Although standard in vitro calcification assays robustly reproduce mineral deposition, it remains unclear how well they recapitulate these disease-associated SMC states. We sought to define the CMC transcriptional phenotype in atherosclerosis and develop an in vitro system that faithfully reproduces it. Approach and Results: We firstly identified a CMC transcriptional signature in murine and human atherosclerotic plaque through single-cell RNA-sequencing, and spatial transcriptomics. CMCs showed a conserved osteochondrogenic program which localized within plaques and adjacent to calcified regions. We then developed an osteochondrogenic differentiation (OCD) assay by combining well-established calcification components with a high-density SMC micromass culture and TGF-{beta}1 supplementation and benchmarked it against a standard calcification (SC) assay using calcium quantification and bulk RNA-sequencing. Despite comparable calcification, OCD and SC resulted in distinct transcriptional states, with OCD showing preferential upregulation of osteochondrogenic programs, and a higher CMC signature score. Additionally, OCD upregulated genes with a stronger enrichment near coronary artery disease (CAD)-associated loci. These responses were reproducible across several primary human SMC lines. Timecourse analysis also showed that chondrogenic programs preceded calcification and showed directional concordance with the inferred in vivo SMC-to-CMC trajectory. To interrogate regulatory pathways controlling this process, we overexpressed the chondrogenic regulator SOX9, which enhanced cartilage and extracellular matrix programs while repressing inflammatory pathways. Finally, we examined 552 CAD-associated genes nominated across five genome-wide association studies. Of these, 240 were differentially expressed by day 12, and included established SMC regulators as well as a number of candidates not previously characterized in osteochondrogenic SMC transition. Conclusions: The OCD assay results in a strong calcification phenotype together with a disease-associated CMC-like transcriptional state, providing a reliable in vitro model for mechanistic investigation of SMC phenotypic transition and prioritization of candidate regulators.

cell biology↗

bioRxiv2026

Cross-Cohort Optimal Transport Maps Macrophage Plasticity and Competing Routes to Inflammation and Fibrosis in Human Atherosclerotic Plaques

Single-cell transcriptomics has revealed extensive macrophage heterogeneity in atherosclerotic plaques, but how macrophages move between states, and whether transition mechanisms depend on cellular origin, remain unclear. Here we develop a computational framework that reconstructs directed cell-state transition networks from cross-sectional single-cell RNA-sequencing data by combining optimal transport with RNA velocity and systematic cross-cohort validation. Applying this approach to seven human atherosclerotic plaque cohorts, we generate an integrated atlas of 81,633 monocytes and macrophages and identify 15 statistically significant pairwise transitions, of which 11 directed transitions organize into three biological axes: monocyte fate diversification, inflammatory reactivation, and fibrotic remodeling. The strongest transition links scavenging macrophages to inflammatory macrophages, suggesting that plaque inflammation is driven predominantly by reactivation of tissue-adapted macrophages rather than by direct differentiation of newly recruited monocytes. By tracking gene expression changes along the OT target-association gradient, we find that macrophage plasticity follows an origin-dependent spectrum. Tissue-resident macrophages, in particular scavenging macrophages, acquire inflammatory programs while preserving and reinforcing their resident scavenging identity, a mechanism we term transcriptional layering, whereas monocyte-derived transitions proceed through selective loss of source-identity modules. Despite these distinct routes, transitions converging on the same fate activate shared destination-specific regulatory circuits, with inflammatory and fibrotic programs governed by mutually antagonistic transcription factor networks. These findings identify inflammatory reactivation of scavenging macrophages as a dominant transition axis in human atherosclerosis and suggest that macrophage origin constrains how disease-associated programs are acquired. More broadly, this framework provides a general strategy for quantifying cell-state transitions and dissecting plasticity mechanisms in chronic inflammatory disease.

bioinformatics↗

bioRxiv2025

Investigating the Intracellular Compartmental Dynamics of miRNAs in Response to Hypoxia

MicroRNAs (miRNAs) are a class of small non-coding RNAs (ncRNAs) with established functions in cytoplasmic gene regulation, where they interact with mRNA transcripts, impeding their translation--a process known as post-transcriptional gene silencing (PTGS). Recent studies have found that miRNAs and other components involved in PTGS are abundantly present in the nucleus of the cells, where they also play important roles in gene regulation. However, the understanding of their function in the nucleus is not well characterized, particularly in response to cellular stress. We conducted nuclear-cytoplasmic fractionation of primary human endothelial cells (ECs) to assess the distribution of miRNAs during hypoxia. The onset of hypoxia led to changes in miRNA expression in both nuclear and cytoplasmic compartments. Notably, a larger proportion of deregulated miRNAs were identified in the nucleus than in the cytoplasm upon hypoxia exposure. We focused on these nuclear-enriched, differentially expressed miRNAs to investigate their cellular functions and their effects on target mRNAs in different compartments. The data indicated a more pronounced alteration in nuclear mRNA expression compared to cytoplasmic expression, pointing towards a nuclear-specific role for these miRNAs. Several miRNAs influenced target mRNAs associated with pathways of cell proliferation and inflammation. Functional assays under hypoxia showed that miR-5091 and miR-7974 reduced EC cell proliferation, while miR-1246 increased it. Additionally, miR-3662 was found to regulate the secretion levels of specific cytokines, impacting the inflammatory response. Overall, our findings highlight the significant role of miRNAs in the nuclear compartment of ECs in modulating the hypoxic response and provide insights into their multifaceted functions.

molecular biology↗

bioRxiv2025

Nuclear Speckles are Regulatory Hubs for Viral and Host mRNA Expression During HSV-1 Infection

Herpes simplex virus type 1 (HSV-1) infection remodels the host nucleus, marginalizing chromatin and forming viral replication compartments (VRCs). Nuclear speckles, nuclear bodies enriched in RNA-processing factors, reposition around VRCs and undergo structural changes. While viral mRNAs are transcribed in VRCs and host transcription is largely suppressed, the nuclear routes used by viral and upregulated host transcripts and their relationship with nuclear bodies, remain unclear. We show that immediate-early (IE) viral transcripts uniquely accumulate in nuclear speckles prior to export, unlike early or late transcripts, revealing a selective nuclear speckle-dependent pathway. Similarly, host mRNAs upregulated during infection traffic into nuclear speckles after transcription. Moreover, nuclear speckles are structurally remodeled, marked by lncRNA MALAT1 removal and increased dynamics of the nuclear speckle core protein SRRM2. Lastly, we found that blocking mRNA export causes IE transcripts to accumulate in nuclear speckles, and that nuclear speckle disassembly severely impairs IE mRNA export, preventing downstream viral gene expression. These findings establish nuclear speckles as dynamic regulatory hubs that selectively facilitate the processing and export of IE viral mRNAs during HSV-1 infection. Significance statementThis study reveals how herpes simplex virus type 1 (HSV-1) manipulates structures in the nucleus termed nuclear speckles, which are essential for processing of mRNA. We discovered that early viral messages specifically pass through these nuclear speckles before exporting out of the nucleus. We find that disassembling nuclear speckles severely limits viral RNA export. Moreover, certain host cell messages also rely on nuclear speckles during infection, suggesting a shared nuclear pathway for host and viral mRNAs during infection.

cell biology↗

bioRxiv2025

Adipose tissue-derived fibroblasts engage in immune-stromal crosstalk during obesity-aggravated atherosclerosis in mice

Atherosclerosis involves changes in the vascular wall and surrounding perivascular adipose tissue, yet the cellular contributors to disease progression remain incompletely understood. Obesity exacerbates atherogenesis, but the cell types driving this aggravation are unclear. We aimed to define the key cell populations across tissues in a highly atherogenic mouse model under obese and normal-weight conditions and to identify obesity-associated cellular changes. We employed 5 single-cell RNA sequencing combined with antibody staining in Ldlr-/-Apob100/100 male mice fed either a high-fat or control diet. Aorta, perivascular and epididymal adipose tissues, and spleen were analyzed, with CD45 enrichment of aortic samples and CITE-seq using a 138-antibody panel. Key findings were validated in mice by immunohistochemistry and multiplexed immunofluorescence and explored in human aorta and carotid arteries using spatial transcriptomics. Analysis of [~]46,000 cells enabled characterization of cell states, gene enrichment, regulon activity, and inferred interactions. Adipose-derived fibroblast subsets displayed immune-associated transcriptional programs in obesity. Pi16 progenitor fibroblasts were reduced alongside marked PVAT remodeling, and the top mouse differentially expressed genes exhibited clear spatial patterning in human arteries.

genomics↗

bioRxiv2025

Integrated ambient modeling and genetic demultiplexing of single-cell RNA+ATAC multiome experiments with Ambimux

Single cell technologies have advanced at a rapid pace, providing assays for various molecular phenotypes. Droplet-based single cell technologies, particularly those based on nuclei isolation, such as simultaneous RNA+ATAC single-cell multiome, are susceptible to exogenous ambient molecule contamination, which can increase noise in cell type-level associations. We reasoned that genotype-based sample multiplexing can provide an opportunity to infer this ambient contamination by leveraging DNA variation in sequenced reads. Thus, we developed ambimux, a likelihood-based method to estimate ambient fractions and demultiplex single-cell multiome experiments using genotype-level data. Ambimux models the ambient or nuclear probability at the read level and thus can classify empty droplets and estimate droplet-specific ambient molecule fractions in each modality. We first evaluated our method using simulated data sets across a range of parameters. We found that ambimux closely estimated the ground truth droplet contamination fractions in the RNA (MAE=0.048) and ATAC (MAE=0.042) modalities. As a result, ambimux maintained high specificity (>95%) and was able to correctly assign singlets at considerably high ambient fractions (up to 60%) for both RNA and ATAC modalities. In comparison with models that do not consider ambient contamination, these only maintained similar sensitivity levels at considerably lower ambient fractions (up to 25%). We then generated a real data set of seven visceral adipose tissue biopsies run on a single 10x Multiome channel. We ran ambimux and detected 4,986 singlets, capturing similar numbers as other methods. Then, we sought to evaluate the fidelity of the ambient fraction estimates from ambimux. We split singlets into ambient-enriched (>5% contamination in both modalities) or nuclear-enriched (<5% in both) droplets and performed gene-peak linkage analysis. Low ambient droplets resulted in more significant hits with gene-peak links enriched at the transcription start site relative to high ambient droplets, suggesting that the ambient droplets identified by ambimux hamper the identification of biologically meaningful signals. In summary, we developed a joint single-cell multiome demultiplexing method, ambimux, that accurately models and estimates ambient molecule contamination in each modality.

bioinformatics↗

bioRxiv2025

Nucleus softens during herpesvirus infection

Nuclear mechanics is remodeled not only by extracellular forces but also by internal modifications, such as those induced by viral infections. During herpes simplex virus type 1 infection, the nuclear structures undergo drastic reorganization, but little is known about how nuclear mechanobiology changes as a result. We show that the nucleus softens dramatically during the infection. To understand the phenomenon, we used advanced microscopy and computational modeling. We discovered that the enlarged viral replication compartment had a low biomolecular density, partially explaining the observed nuclear softening. The mobility of the nuclear lamina decreased, which suggests increased rigidity and an inability to induce softening. However, computational modeling supported by experimental data showed that reduced outward forces, such as cytoskeletal pull and intranuclear osmotic pressure acting both on and within the nucleus, can explain the decreased nuclear stiffness. Our findings reveal that during infection, the nucleus is subject to changes in multiple mechanical forces, leading to decreased nuclear stiffness. Author SummaryDNA viruses take over the host cell nucleus, inducing dramatic structural modifications. There is currently very little knowledge of how the progression of viral infection modifies the mechanical properties of the nucleus, which are essential for various cellular processes, including gene expression and cell migration. Here, we show that the nucleus softens when herpesvirus infection progresses. We discovered that the viral replication compartment established in the central parts of the nucleus had a low biomolecular density, which may contribute to the nuclear softening. The shape and motion of the nuclear lamina suggested that it became more rigid, indicating that another mechanism was involved in the decreased elasticity. Our mechanical simulations and experiments showed that a reduction in outward forces, such as actin cytoskeleton pull or osmotic pressure, is the most likely factor in the nuclear softening. Our study provides new insights into the effects of DNA viruses on the mechanics of host cell nuclei, significantly expanding the knowledge of viral infection mechanobiology.

cell biology↗

bioRxiv2024

The critical role of isomiRs in accurate differential expression analysis of miRNA-seq data

MicroRNAs (miRNAs) are crucial for the regulation of gene expression and are promising biomarkers and therapeutic targets. miRNA isoforms (isomiRs) differ in their start/end offsets, which can impact the target gene selection and non-canonical function of the miRNA species. In addition, isomiRs frequently differ in their expression patterns from their parent miRNAs, yet their roles and tissue-specific responses are currently understudied, leading to their typical omission in miRNA research. Here, we evaluate the expression differences of isomiRs across conditions and their impact on standard miRNA-seq quantification results. We analyze 28 public miRNA-seq datasets, showing significant expression pattern differences between the isomiRs and their corresponding reference miRNAs, leading to misinterpretation of differential expression signals for both. As a case study, we generate a new dataset assessing isomiR abundance under hypoxia in human endothelial cells between the nuclear and cytosolic compartments. The results suggest that isomiRs are dramatically altered in their nuclear localization in response to hypoxia, indicating a potential non-canonical effect of the species, which would be missed without isomiR-aware analysis. Our results call for a comprehensive re-evaluation of the miRNA-seq analysis practices.

bioinformatics↗

bioRxiv2023

Progression of herpesvirus infection remodels mitochondrial organization and metabolism

Viruses target mitochondria to promote their replication, and infection-induced stress during the progression of infection leads to the regulation of antiviral defenses and mitochondrial metabolism which are opposed by counteracting viral factors. The precise structural and functional changes that underlie how mitochondria react to the infection remain largely unclear. Here we show extensive transcriptional remodeling of protein-encoding host genes involved in the respiratory chain, apoptosis, and structural organization of mitochondria as herpes simplex virus type 1 lytic infection proceeds from early to late stages of infection. High-resolution microscopy and interaction analyses unveiled infection-induced emergence of rough, thin, and elongated mitochondria relocalized at the perinuclear area, a significant increase in the number and clustering of ER-mitochondria contact sites, and thickening and shortening of mitochondrial cristae. Finally, metabolic analyses demonstrated that reactivation of ATP production is accompanied by increased mitochondrial Ca2+ content and proton leakage as the infection proceeds. Overall, the significant structural and functional changes in the mitochondria triggered by the viral invasion are tightly connected to the progression of the virus infection.

microbiology↗

bioRxiv2023

Oncogenic KEAP1 mutations activate TRAF2-NFκB signaling to prevent apoptosis in lung cancer cells

The Kelch-like ECH-associated protein 1 (KEAP1) - Nuclear factor erythroid 2-related factor 2 (NRF2) pathway is the major transcriptional stress response system in cells against oxidative and electrophilic stress. NRF2 is frequently constitutively active in many cancers, rendering the cells resistant to chemo- and radiotherapy. Loss-of-function (LOF) mutations in the repressor protein KEAP1 are common in non-small cell lung cancer, particularly adenocarcinoma. While the mutations can occur throughout the gene, they are enriched in certain areas, indicating that these may have unique functional importance. In this study, we show that in the GSEA analysis of TCGA lung adenocarcinoma RNA-seq data, the KEAP1 mutations in R320 and R470 were associated with enhanced Tumor Necrosis Factor alpha (TNF) - Nuclear Factor kappa subunit B (NF{kappa}B) signaling as well as MYC and MTORC1 pathways. To address the functional role of these hotspot mutations, affinity purification and mass spectrometry (AP-MS) analysis of wild type (wt) KEAP1 and the mutants was employed to interrogate differences in the protein interactome. We identified TNF receptor associated factor 2 (TRAF2) as a putative protein interaction partner. Both mutant KEAP1 forms showed increased interaction with TRAF2 and other anti-apoptotic proteins, suggesting that apoptosis signalling could be affected by the protein interactions. A549 lung adenocarcinoma cells overexpressing mutant KEAP1 showed high TRAF2-mediated NF{kappa}B activity and increased protection against apoptosis, XIAP being one of the key proteins involved in anti-apoptotic signalling. To conclude, KEAP1 R320Q and R470C and its interaction with TRAF2 leads to activation of NF{kappa}B pathway, thereby protecting against apoptosis.

cancer biology↗

bioRxiv2023

Cell-type-specific characterization of miRNA gene dynamics in immune cell subpopulations during aging and atherosclerosis disease development at single-cell resolution

MicroRNAs (miRNAs) are a class of regulatory non-coding RNAs that finetune cellular functions by modulating the stability and abundance of their target mRNAs, thereby contributing to regulation of tissue homeostasis. MiRNA genes are transcribed similarly to protein-coding genes and recent studies have enabled their annotation and quantification genome-wide from bulk nascent transcriptomes. Here, we developed an approach to quantify and integrate miRNA gene signatures into single-cell studies. To characterize miRNA gene expression dynamics, we first compared the suitability of droplet and plate-based single-cell RNA-sequencing (scRNA-seq) platforms using the matched datasets provided by the Tabula Muris Senis and Tabula Sapiens consortiums. We found high concordance between the platforms and with cell type-specific bulk expression data. Based on the comprehensive aging profiles, our analysis comparing spleen immune cells between young and old mice revealed a concordant regulation of miRNAs involved in senescence and inflammatory pathways in multiple immune cell types, including up-regulation of mmu-mir-146a, mmu-mir-101a and mmu-mir-30 family genes. To study the aberrant regulation of immune cell homeostasis and tissue inflammation that pre-dispose to aging-related disease development, we collected transcriptome profiles from atherosclerosis development in LDLR-/-ApoB100/100 mice. We found an elevated myeloid cell proportion in the adipose tissue and further characterized the cell subtypes based on reproducible transcriptome clusters. We then compared miRNA gene expression in early versus late disease and upon inflammatory challenge to monitor different stages during disease progression. At atherosclerotic stage, pro-inflammatory mmu-mir-511 expression increased in several macrophage subtypes, while immunosuppressive mmu-mir-23b[~]mir-24-2[~]mir-27b up-regulation was specific to Trem2+ lipid-associated macrophages. The infiltrating monocytes up-regulated mmu-mir-1938 and mmu-mir-22 expression and in classical monocytes maturation further increased mmu-mir-221[~]222, mmu-mir-511 and mmu-mir-155 expression. To validate that these changes detected from single cell profiles represent miRNA gene transcriptional regulation, we used nascent transcriptomics data from ex vivo macrophage cultures with pro-inflammatory stimulation, confirming both rapid and long-lasting transcriptional activation of the miRNA loci studied. Collectively, our work enables integrating miRNA gene analysis to current single cell genomics pipelines and facilitates characterization of miRNA regulatory networks during aging and disease development.

molecular biology↗

bioRxiv2023

Colchicine promotes atherosclerotic plaque stability independently of inflammation

Atherosclerosis is a chronic inflammatory disease which is driven in part by the aberrant trans-differentiation of vascular smooth muscle cells (SMCs). No therapeutic drug has been shown to reverse detrimental SMC-derived cell phenotypes into protective phenotypes, a hypothesized enabler of plaque regression and improved patient outcome. Herein, we describe a novel function of colchicine in the beneficial modulation of SMC-derived cell phenotype, independent of its conventional anti-inflammatory effects. Using SMC fate mapping in an advanced atherosclerotic lesion model, colchicine induced plaque regression by converting pathogenic SMC-derived macrophage-like and osteoblast-like cells into protective myofibroblast-like cells which thickened, and thereby stabilized, the fibrous cap. This was dependent on Notch3 signaling in SMC-derived plaque cells. These findings may help explain the success of colchicine in clinical trials relative to other anti-inflammatory drugs. Thus, we demonstrate the potential of regulating SMC phenotype in advanced plaque regression through Notch3 signaling, in addition to the canonical anti-inflammatory actions of drugs to treat atherosclerosis.

cell biology↗

bioRxiv2023

Coronary Artery Disease risk variant dampens the expression of CALCRL by reducing HSF binding to shear stress responsive enhancer in endothelial cells

Coronary artery disease (CAD) is one of the major causes of mortality worldwide. Recent genome-wide association studies have started to unravel the genetic architecture of the disease. Such efforts have identified Calcitonin receptor-like (CALCRL), an important mediator of the endothelial fluid shear stress response, associated with CAD risk variants. In this study we functionally characterized the non-coding regulatory elements carrying CAD risks SNPs and studied their role in the regulation of CALCRL expression in endothelial cells. We demonstrate that rs880890-harboring regulatory element exhibits high enhancer activity and significant allelic bias with A allele showing 40% more activity than G allele. We also observed that the A allele of rs880890 is favored over the G allele under shear stress. CRISPR deletion of rs880890-enhancer resulted in downregulation of CALCRL expression. EMSA further showed that heat shock factors are binding to the enhancer with a preference for A allele over the G allele. In line with this, HSF1 knockdown resulted in a significant decrease in CALCRL expression. CALCRL knockdown as well as variant perturbation experiments confirmed the role of CALCRL in the regulation of eNOS, apelin, angiopoietin, prostaglandins and endothelin-1 signaling pathways while demonstrating a significant decrease in cell proliferation and tube formation. Overall, our results demonstrate the existence of an endothelial-specific heat shock factor regulated transcriptional enhancer carrying a CAD risk SNP rs880890 that regulates CALCRL expression. Better understanding of CALCRL gene regulation and the role of SNPs in modulation of CALCRL expression could provide important steps towards understanding genetic regulation of shear stress signaling responses.

genetics↗

bioRxiv2022

ErbB Signalling is a Potential Therapeutic Target for Vascular Lesions with Fibrous Component

BackgroundSporadic venous malformation (VM) and angiomatosis of soft tissue (AST) are benign, congenital vascular anomalies affecting venous vasculature. Depending on the size and location of the lesion, symptoms vary from motility disturbances to pain and disfigurement. Due to high recurrence of the lesions more effective therapies are needed. MethodsAs targeting stromal cells has been an emerging concept in anti-angiogenic therapies, here, by using VM/AST patient samples, RNA-sequencing, cell culture techniques and a xenograft mouse model, we investigated the crosstalk of endothelial cells (EC) and fibroblasts and its effect on vascular lesion growth. ResultsWe report, for the first time, expression and secretion of transforming growth factor A (TGFA) in ECs or intervascular stromal cells in AST and VM lesions. TGFA induced secretion of VEGF-A paracrinally, and regulated EC proliferation. Oncogenic PIK3CA variant in p.H1047R, a common somatic mutation found in these lesions, increased TGFA expression, enrichment of hallmark hypoxia, and in a mouse xenograft model, lesion size and vascularization. Treatment with afatinib, a pan-ErbB tyrosine-kinase inhibitor, decreased vascularization and lesion size in mouse xenograft model with ECs expressing oncogenic PIK3CA p.H1047R variant and fibroblasts. ConclusionsBased on the data, we suggest that targeting of both intervascular stromal cells and ECs is a potential treatment strategy for vascular lesions having a fibrous component. FundingAcademy of Finland, Ella and Georg Ehnrooth foundation, the ERC grants, Sigrid Juselius Foundation, Finnish Foundation for Cardiovascular Research, Jane and Aatos Erkko Foundation, and Department of Musculosceletal and Plastic Surgery, Helsinki University Hospital. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/509204v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@14ec94aorg.highwire.dtl.DTLVardef@1812747org.highwire.dtl.DTLVardef@39d01eorg.highwire.dtl.DTLVardef@18e9e35_HPS_FORMAT_FIGEXP M_FIG Graphical abstract. Proposed model for the paracrine signaling of TGFA/VEGF-A in vascular lesion Schematic illustration showing the general structure of venous malformation or angiomatosis of soft tissue. Pathological vasculature in the lesion (dark blue) is surrounded by disorganized extracellular matrix (ECM) and intervascular stromal cells (SCs, orange). High magnification from the area close to vessel wall demonstrates the proposed model for crosstalk between endothelial cells (ECs) and SCs. A mutation in phosphatidylinositol-4,5-biphosphate 3-kinase catalytic subunit alpha (PIK3CA) gene (1) or other processes promote ECs to express high level of transforming growth factor A (TGFA) (2). TGFA binds to epithelial growth factor receptor (EGFR) on the surface of adjacent SCs (3). Activated EGFR-downstream signaling (4) promotes elevated expression of vascular endothelial growth factor (VEGF)-A in SCs and increases the expression of TGFA (5). VEGF-A secreted from SCs (6) binds to VEGF-recetor-2 (VEGFR2) on surface of ECs (7) and together with TGFA activates angiogenic EC phenotype. TGFA secreted from the SCs (8), can further activate EGFR and its downstream signaling. C_FIG

cell biology↗

bioRxiv2022

Pan-cancer scale screening reveals NRF2 associated immunoevasive characteristics in non-small cell lung cancer and squamous malignancies

The NRF2 pathway is frequently activated in various cancer types, yet a comprehensive analysis of its effects across different malignancies is currently lacking. We developed a robust NRF2 activity metric and utilized it to conduct a pan-cancer wide analysis of oncogenic NRF2 signaling. We identified a distinct immunoevasive phenotype where high NRF2 activity is associated with low interferon-gamma (IFN{gamma}), HLA-I expression and T-cell infiltration spanning non-small cell lung cancer (NSCLC) and squamous malignancies of head and neck area, cervix and esophagus. In squamous cell cancers, NRF2 overactive tumors comprise a molecular phenotype with SOX2/TP63 amplification, TP53 mutation and CDKN2A loss. These immune-cold NRF2 hyperactive diseases are associated with upregulation of immunomodulatory NAMPT, WNT5A, SPP1, SLC7A11 and SLC2A1 that represent candidate NRF2 target genes, suggesting direct modulation of the tumor immune milieu. Based on single-cell mRNA data, coupled with a priori information on intercellular ligand-receptor interactions, cancer cells of this subtype exhibit decreased expression of IFN{gamma} responsive ligands, and increased expression of immunosuppressive ligands NAMPT, SPP1 and WNT5A that mediate signaling in intercellular crosstalk. As we observed differential cytokine mRNA expression with IFN{gamma} treatment in NSCLC adenocarcinoma subtype, we explored the cytokine secretome in vitro. We found that secreted neutrophil chemoattractants interleukin-8 (CXCL8) and ENA-78 (CXCL5) are elevated in NRF2 overactive cells, suggesting contribution of immunosuppressive neutrophils in NRF2 driven immune escape. Importantly, as overactive NRF2 is associated with immune-cold characteristics, our results highlight the utility of NRF2 pathway activation as a putative biomarker for stratifying immune-checkpoint blockade responders and non-responders across NSCLC and squamous cancers. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=166 SRC="FIGDIR/small/489654v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1f45782org.highwire.dtl.DTLVardef@9d40d0org.highwire.dtl.DTLVardef@a31a5org.highwire.dtl.DTLVardef@1418220_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2022

Genetic regulation of human aortic smooth muscle cell gene expression and splicing predict causal coronary artery disease genes

Coronary artery disease (CAD) is the leading cause of death worldwide. Recent meta-analyses of genome-wide association studies (GWAS) have identified over 175 loci associated with CAD. The majority of these loci are in non-coding regions and are predicted to regulate gene expression. Given that vascular smooth muscle cells (SMCs) play critical roles in the development and progression of CAD, we hypothesized that a subset of the CAD GWAS risk loci are associated with the regulation of transcription in distinct SMC phenotypes. Here, we measured gene expression in SMCs isolated from the ascending aortas of 151 ethnically diverse heart transplant donors in quiescent or proliferative conditions and calculated the association of their expression and splicing with [~]6.3 million imputed single nucleotide polymorphism (SNP) markers across the genome. We identified 4,910 expression and 4,412 splice quantitative trait loci (sQTL) that represent regions of the genome associated with transcript abundance and splicing. 3,660 of the eQTLs had not been observed in the publicly available Genotype-Tissue Expression dataset. Further, 29 and 880 of the eQTLs were SMC- and sex-specific, respectively. To identify the effector transcript(s) regulated by CAD GWAS loci, we used four distinct colocalization approaches and identified 84 eQTL and 164 sQTLs that colocalized with CAD loci, highlighting the importance of genetic regulation of mRNA splicing as a molecular mechanism for CAD genetic risk. Notably, 20% and 35% of the eQTLs were unique to quiescent or proliferative SMCs, respectively. Two CAD loci colocalized with a SMC sex-specific eQTL (AL160313.1 and TERF2IP) and another locus colocalized with SMC-specific eQTL (ALKBH8). Also, 27% and 37% of the sQTLs were unique to quiescent or proliferative SMCs, respectively. The most significantly associated CAD locus, 9p21, was an sQTL for the long non-coding RNA CDKN2B-AS1, also known as ANRIL, in proliferative SMCs. Collectively, these results provide evidence for the molecular mechanisms of genetic susceptibility to CAD in distinct SMC phenotypes.

genetics↗

bioRxiv2021

isomiRs-specific differential expression is the rule, not the exception: Are we missing hundreds of species in microRNA analysis?

MicroRNAs (miRNAs) are small RNA molecules that act as regulators of gene expression through targeted mRNA degradation. They are involved in many biological and pathophysiological processes and are widely studied as potential biomarkers and therapeutics agents for human diseases, including cardiovascular disorders. Recently discovered isoforms of miRNAs (isomiRs) exist in high quantities and are very diverse. Despite having few differences with their corresponding reference miRNAs, they display specific functions and expression profiles, across tissues and conditions. However, they are still overlooked and understudied, as we lack a comprehensive view on their condition-specific regulation and impact on differential expression analysis. Here, we show that isomiRs can have major effects on differential expression analysis results, as their expression is independent of their host miRNA genes or reference sequences. We present two miRNA-seq datasets from human umbilical vein endothelial cells, and assess isomiR expression in response to senescence and compartment-specificity (nuclear/cytosolic) under hypoxia. We compare three different methods for miRNA analysis, including isomiR-specific analysis, and show that ignoring isomiRs induces major biases in differential expression. Moreover, isomiR analysis permits higher resolution of complex signal dissection, such as the impact of hypoxia on compartment localization, and differential isomiR type enrichments between compartments. Finally, we show important distribution differences across conditions, independently of global miRNA expression signals. Our results raise concerns over the quasi exclusive use of miRNA reference sequences in miRNA-seq processing and experimental assays. We hope that our work will guide future isomiR expression studies, which will correct some biases introduced by golden standard analysis, improving the resolution of such assays and the biological significance of their downstream studies.

bioinformatics↗

bioRxiv2021

Functional non-coding SNPs in human endothelial cells fine-map vascular trait associations

Functional consequences of genetic variation in the non-coding human genome are difficult to ascertain despite demonstrated associations to common, complex disease traits. To elucidate properties of functional non-coding SNPs with effects in human endothelial cells (EC), we utilized molecular Quantitative Trait Locus (molQTL) analysis for transcription factor binding, chromatin accessibility, and H3K27 acetylation to nominate a set of likely functional non-coding SNPs. Together with information from genome-wide association studies for vascular disease traits, we tested the ability of 34,344 variants to perturb enhancer function in ECs using the highly multiplexed STARR-seq assay. Of these, 5,592 variants validated, whose enriched attributes included: 1) mutations to TF binding motifs for ETS or AP1 that are regulators of EC state, 2) location in accessible and H3K27ac-marked EC chromatin, and 3) molQTLs associations whereby alleles associate with differences in chromatin accessibility and TF binding across genetically diverse ECs. Next, using pro-inflammatory IL1B as an activator of cell state, we observed robust evidence (>50%) of context-specific SNP effects, underscoring the prevalence of non-coding gene-by-environment (GxE) effects. Lastly, using these cumulative data, we fine-mapped vascular disease loci and highlight evidence suggesting mechanisms by which non-coding SNPs at two loci affect risk for Pulse Pressure/Large Artery Stroke, and Abdominal Aortic Aneurysm through respective effects on transcriptional regulation of POU4F1 and LDAH. Together, we highlight the attributes and context dependence of functional non-coding SNPs, and provide new mechanisms underlying vascular disease risk.

genetics↗