Global Gene Expression Patterns Research Articles

Time-dependent changes in genome-wide gene expression and post-transcriptional regulation across the post death process in silkworm.

Despite death marking the end of life, several gene expression and miRNA-mediated post-transcriptional regulation events may persist or be initiated. The silkworm (Bombyx mori) is a valuable model for exploring life processes, including death. In this study, we combined transcriptomics and miRNAomics analyses of young, old, and postmortem silkworms across the entire process after death to unravel the dynamics of gene expression and miRNA-mediated post-transcriptional regulation. In total, 171 genes exhibited sustained differential expression in postmortem silkworms compared to the pre-death state, which are primarily involved in nerve signaling, transport, and immune response. Postmortem time-specific genes were associated with cell cycle regulation, thermogenesis, immunity, and zinc ion homeostasis. We found that the down-regulated expression of 36 genes related to transcription, epigenetic modification, and homeostasis resulted in a significant shift in global gene expression patterns at 2h post-death. We also identified five mRNA-miRNA pairs (i.e., bmo-miR-2795-mhca, 2784-achi, 2762-oa1, 277-5p-creb, and 1000-tcb1) associated with stress hormone regulation, transcription activity, and signal transduction. The roles of these pairs were validated through in vivo experiments using miRNA mimics in silkworms. The findings provide valuable insights into the intricate mechanisms underlying the transcriptional and miRNA-mediated post-transcriptional regulation events in animals after death.

Abstract PR-14: Meta-analysis of spatial transcriptomics data from pancreatic cancer precursors proposes a common molecular framework for PanIN and IPMN

Abstract INTRODUCTION Pancreatic ductal adenocarcinoma (PDAC) arises from either pancreatic intraepithelial neoplasia (PanIN) or intraductal papillary mucinous neoplasm (IPMN). Transcriptomic studies of PanIN and IPMN conducted in isolation both aim to improve early detection, risk stratification, and therapeutic target selection. Here, we curated existing and new whole transcriptome digital spatial profiles (DSP-RNA) from normal to malignant pancreatic epithelium to map the molecular landscape of PDAC progenitors. METHODS New NanoString GeoMx DSP-RNA datasets were generated from 1) surgical IPMN specimens resected at Duke University and 2) deceased donor pancreas specimens collected by the Gift of Life Michigan Donor Care Center that could not be used for transplantation and thus allocated to the University of Michigan for approved research. Published studies were downloaded from GEO (GSE229752, GSE226829, GSE199102) and the NanoString Spatial Organ Atlas. Epithelial areas of interest (AOIs) were processed and analyzed with stgeomx (https://github.com/mkiyer/stgeomx) and R/Bioconductor packages. Quality control (QC) procedures removed low quality AOIs. Batch effects were mitigated by defining highly variable genes within each dataset and merging them into a common set for downstream analysis. Molecular subtype gene signatures were obtained from the pdacR package and quantified using Gene Set Variation Analysis. RESULTS We assembled a pancreatic epithelial DSP-RNA cohort consisting of 768 AOIs from 62 patients. AOIs were annotated as normal duct (n=193), acini (n=53), acinar-ductal metaplasia (ADM) (n=57), PanIN (n=108), IPMN (n=92), and PDAC (n=265). Principal component analysis (PCA) revealed compelling associations between DSP-RNA profiles and the established classical, basal-like, and exocrine molecular subtypes of PDAC. The first principal component (PC1) stratified the exocrine and basal-like PDAC subtypes on opposite ends of its axis (PC1 vs exocrine Pearson r=0.929, p < 0.001, PC1 vs basal-like Pearson r=-0.775, padj < 0.001). PC2 further distinguished classical from basal-like AOIs, and PC3 separated normal (CRISP3+) from neoplastic (MUC5AC+) ductal epithelium. Unsupervised clustering of AOIs proposed four epithelial subtypes: “acinar/ADM” (cAcinar), “normal duct” (cDuct), “low-risk neoplasm” (cLR), and “high-risk/malignant” (cHR). PanIN and IPMN lesions exhibited remarkably similar global gene expression patterns, suggesting that they arise from a common lineage. CONCLUSIONS Meta-analysis of pancreatic epithelial DSP-RNA datasets provided a unifying molecular context for PanIN, IPMN, and PDAC. The established classical, basal-like, and exocrine PDAC subtypes explained global patterns of gene expression variation. Intriguingly, PanIN and IPMN transcriptomes appeared similar, suggesting that early detection and therapeutic selection strategies may be broadly applicable to PDAC precursors. Citation Format: Matthew K Iyer, Ashley Fletcher, Elishama Kanu, Chanjuan Shi, Rosina Carr, Ahmed M. Elhossiny, Daniel P. Nussbaum, Eileen S. Carpenter, Marina Pasca di Magliano, Arul M. Chinnaiyan, Peter J. Allen, Timothy L. Frankel. Meta-analysis of spatial transcriptomics data from pancreatic cancer precursors proposes a common molecular framework for PanIN and IPMN [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr PR-14.

Eicosatetraynoic Acid Regulates Pro-Fibrotic Pathways in an Induced Pluripotent Stem Cell Derived Macrophage:Human Intestinal Organoid Model of Crohn's Disease.

We previously identified small molecules predicted to reverse an ileal gene signature for future Crohn's Disease (CD) strictures. Here we used a new human intestinal organoid (HIO) model system containing macrophages to test a lead candidate, eicosatetraynoic acid (ETYA). Induced pluripotent stem cell lines (iPSC) were derived from CD patients and differentiated into macrophages and HIOs. Macrophages and macrophage:HIO co-cultures were exposed to lipopolysaccharide (LPS) with and without ETYA pre-treatment. Cytospin and flow cytometry characterized macrophage morphology and activation markers, and RNA sequencing defined the global pattern of macrophage gene expression. TaqMan Low Density Array, Luminex multiplex assay, immunohistologic staining, and sirius red polarized light microscopy were performed to measure macrophage cytokine production and HIO pro-fibrotic gene expression and collagen content. iPSC-derived macrophages exhibited morphology similar to primary macrophages and expressed inflammatory macrophage cell surface markers including CD64 and CD68. LPS-stimulated macrophages expressed a global pattern of gene expression enriched in CD ileal inflammatory macrophages and matrisome secreted products, and produced cytokines and chemokines including CCL2, IL1B, and OSM implicated in refractory disease. ETYA suppressed CD64 abundance and pro-fibrotic gene expression pathways in LPS stimulated macrophages. Co-culture of LPS-primed macrophages with HIO led to up-regulation of fibroblast activation genes including ACTA2 and COL1A1, and an increase in HIO collagen content. ETYA pre-treatment prevented pro-fibrotic effects of LPS-primed macrophages. ETYA inhibits pro-fibrotic effects of LPS-primed macrophages upon co-cultured HIO. This model may be used in future untargeted screens for small molecules to treat refractory CD.

SymNOM-GED: Symmetric neighbor outlier mining in gene expression datasets

The accurate detection of outliers in gene expression datasets plays a crucial role in the unraveling of intricate biological processes. This research introduces "SymNOM-GED," an innovative algorithm for outlier mining in gene expression datasets, with a focus on Esophageal Squamous Cell Carcinoma (ESCC). SymNOM-GED leverages symmetric neighbor to effectively identify outliers by considering local and global gene expression patterns. Extensive experiments demonstrate that SymNOM-GED outperforms existing algorithms in terms of accuracy, robustness, and scalability. The algorithm's performance is validated using clustering coefficient, graph density, and modularity, confirming its superiority. SymNOM-GED's precise and reliable outlier detection capabilities contribute significantly to bioinformatics research, offering insights into gene expression patterns in diverse biological contexts.

Structure and transcription of integrated HPV DNA in vulvar carcinomas

HPV infections are associated with a fraction of vulvar cancers. Through hybridization capture and DNA sequencing, HPV DNA was detected in five of thirteen vulvar cancers. HPV16 DNA was integrated into human DNA in three of the five. The insertions were in introns of human NCKAP1, C5orf67, and LRP1B. Integrations in NCKAP1 and C5orf67 were flanked by short direct repeats in the human DNA, consistent with HPV DNA insertions at sites of abortive, staggered, endonucleolytic incisions. The insertion in C5orf67 was present as a 36 kbp, human-HPV-hetero-catemeric DNA as either an extrachromosomal circle or a tandem repeat within the human genome. The human circularization/repeat junction was defined at single nucleotide resolution. The integrated viral DNA segments all retained an intact upstream regulatory region and the adjacent viral E6 and E7 oncogenes. RNA sequencing revealed that the only HPV genes consistently transcribed from the integrated viral DNAs were E7 and E6*I. The other two HPV DNA+ tumors had coinfections, but no evidence for integration. HPV-positive and HPV-negative vulvar cancers exhibited contrasting human, global gene expression patterns partially overlapping with previously observed differences between HPV-positive and HPV-negative cervical and oropharyngeal cancers. A substantial fraction of the differentially expressed genes involved immune system function. Thus, transcription and HPV DNA integration in vulvar cancers resemble those in other HPV-positive cancers. This study emphasizes the power of hybridization capture coupled with DNA and RNA sequencing to identify a broad spectrum of HPV types, determine human genome integration status of viral DNAs, and elucidate their structures.

Pan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast

Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at the species level. Here we generated and analyzed the pan-transcriptome of ~1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of transcriptome divergence. Global gene expression patterns combined with population structure showed that variation in heritable expression mainly lies within subpopulation-specific signatures, for which accessory genes are overrepresented. Genome-wide association analyses consistently highlighted that accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.

Gene Expression and Ultrastructural Evidence for Metabolic Derangement in the Primary Mitral Regurgitation Heart

Abstract Aims Chronic neurohormonal activation and hemodynamic load cause derangement in myocardial substrate utilization. We test the hypothesis that the primary mitral regurgitation heart (PMR) heart shows altered metabolic gene profile and cardiac ultrastructure consistent with decreased fatty acid and glucose metabolism despite LVEF > 60%. Methods and Results Metabolic gene expression in right atrial (RA), left atrial (LA), and left ventricular (LV) biopsies from donor hearts (n = 10) and from patients with moderate to severe PMR (n = 11) at surgery showed decreased mRNA glucose transporter type 4 (GLUT-4), GLUT-1 and insulin receptor substrate 2 and increased mRNA hexokinase 2, O-linked N-acetylglucosamine transferase and O-GlcNAcase, rate-limiting steps in the hexosamine biosynthetic pathway. Pericardial fluid levels of Neuropeptide Y were 4-fold higher than simultaneous plasma indicative of increased sympathetic drive. Quantitative TEM shows glycogen accumulation, glycophagy, increased lipid droplets, and mitochondrial cristae lysis. These findings are associated with increased mRNA for glycogen synthase kinase 3β, decreased carnitine palmitoyl transferase 2, and fatty acid synthase in PMR vs. normals. Cardiac magnetic resonance/positron emission tomography for 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) uptake showed decreased LV [18F]FDG uptake and increased plasma HbA1c, free fatty acids, mtDAMPs in a separate cohort of stable moderate PMR patients with LVEF > 60% (n = 8) vs. normal controls (n = 8). Conclusions The PMR heart has a global ultrastructural and metabolic gene expression pattern of decreased glucose uptake along with increased glycogen and lipid droplets. Further studies must determine whether this presentation is an adaptation or maladaptation in the PMR heart in the clinical evaluation of PMR.

Transcriptomics and starch biosynthesis analysis in leaves and developing seeds of mung bean provide a basis for genetic engineering of starch composition and seed quality.

Mung bean starch is distinguished by its exceptional high amylose content and regulation of starch biosynthesis in leaves and storage tissues, such as seeds, share considerable similarities. Genetic engineering of starch composition and content, requires detailed knowledge of starch biosynthetic gene expression and enzymatic regulation. In this study we applied detailed transcriptomic analyses to unravel the global differential gene expression patterns in mung bean leaves and in seeds during various stages of development. The objective was to identify candidate genes and regulatory mechanisms that may enable generation of desirable seed qualities through the use of genetic engineering. Notable differences in gene expression, in particular low expression of the Protein Targeting to Starch (PTST), starch synthase (SS) 3, and starch branching enzyme1 (SBE1) encoding genes in developing seeds as compared to leaves were evident. These differences were related to starch molecular structures and granule morphologies. Specifically, the starch molecular size distribution at different stages of seed development correlated with the starch biosynthesis gene expression of the SBE1, SS1, granule-bound starch synthases (GBSS) and isoamylase 1 (ISA1) encoding genes. Furthermore, putative hormonal and redox controlled regulation were observed, which may be explained by abscisic acid (ABA) and indole-3-acetic acid (IAA) induced signal transduction, and redox regulation of ferredoxins and thioredoxins, respectively. The morphology of starch granules in leaves and developing seeds were clearly distinguishable and could be correlated to differential expression of SS1. Here, we present a first comprehensive transcriptomic dataset of developing mung bean seeds, and combined these findings may enable generation of genetic engineering strategies of for example starch biosynthetic genes for increasing starch levels in seeds and constitute a valuable toolkit for improving mung bean seed quality.

Gene Expression Profiling Reveals Fundamental Sex-Specific Differences in SIRT3-Mediated Redox and Metabolic Signaling in Mouse Embryonic Fibroblasts.

Sirt-3 is an important regulator of mitochondrial function and cellular energy homeostasis, whose function is associated with aging and various pathologies such as Alzheimer's disease, Parkinson's disease, cardiovascular diseases, and cancers. Many of these conditions show differences in incidence, onset, and progression between the sexes. In search of hormone-independent, sex-specific roles of Sirt-3, we performed mRNA sequencing in male and female Sirt-3 WT and KO mouse embryonic fibroblasts (MEFs). The aim of this study was to investigate the sex-specific cellular responses to the loss of Sirt-3. By comparing WT and KO MEF of both sexes, the differences in global gene expression patterns as well as in metabolic and stress responses associated with the loss of Sirt-3 have been elucidated. Significant differences in the activities of basal metabolic pathways were found both between genotypes and between sexes. In-depth pathway analysis of metabolic pathways revealed several important sex-specific phenomena. Male cells mount an adaptive Hif-1a response, shifting their metabolism toward glycolysis and energy production from fatty acids. Furthermore, the loss of Sirt-3 in male MEFs leads to mitochondrial and endoplasmic reticulum stress. Since Sirt-3 knock-out is permanent, male cells are forced to function in a state of persistent oxidative and metabolic stress. Female MEFs are able to at least partially compensate for the loss of Sirt-3 by a higher expression of antioxidant enzymes. The activation of neither Hif-1a, mitochondrial stress response, nor oxidative stress response was observed in female cells lacking Sirt-3. These findings emphasize the sex-specific role of Sirt-3, which should be considered in future research.

Abstract 5641: Transcriptional regulation by nuclear deformation

Abstract Establishment and maintenance of cell identities requires transcriptional rewiring and modulation of three-dimensional genome organization. The nucleus is subject to constant mechanical forces, both intrinsic from the cytoskeleton and extrinsic, such as compression, confinement, and stretch. Recently, work from us and others implicate mechanical force, through activating biochemical signaling pathways as well as direct nuclear deformation, in remodeling nuclear architecture, chromatin state and global gene expression patterns. Thus, we hypothesize that mechanical force plays an important role in coordinating and thresholding transcriptional responses. Here, we challenge this hypothesis by quantifying the effect of nuclear deformation on transcription in real time at single cell resolution quasi genome wide. Further, recent work elucidated that the MYC oncogene exerts global effects on transcriptional output by altering the binding dynamics of transcription factors involved in the activation and productive elongation of RNA Polymerase II. This contrasts with mechanical stress which reduces global levels of RNA Polymerase II. Here we interrogate how transcriptional output is tuned for specific genetic programs/loci by mechanical force using MYC as a paradigm. Citation Format: Andrew Cook, Rebecca Stephens, Nadezda Fursova, Carson C. Chow, Dan Larson, Yekaterina Miroshnikova. Transcriptional regulation by nuclear deformation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 5641.

Viral afterlife: SARS-CoV-2 as a reservoir of immunomimetic peptides that reassemble into proinflammatory supramolecular complexes

It is unclear how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection leads to the strong but ineffective inflammatory response that characterizes severe Coronavirus disease 2019 (COVID-19), with amplified immune activation in diverse cell types, including cells without angiotensin-converting enzyme 2 receptors necessary for infection. Proteolytic degradation of SARS-CoV-2 virions is a milestone in host viral clearance, but the impact of remnant viral peptide fragments from high viral loads is not known. Here, we examine the inflammatory capacity of fragmented viral components from the perspective of supramolecular self-organization in the infected host environment. Interestingly, a machine learning analysis to SARS-CoV-2 proteome reveals sequence motifs that mimic host antimicrobial peptides (xenoAMPs), especially highly cationic human cathelicidin LL-37 capable of augmenting inflammation. Such xenoAMPs are strongly enriched in SARS-CoV-2 relative to low-pathogenicity coronaviruses. Moreover, xenoAMPs from SARS-CoV-2 but not low-pathogenicity homologs assemble double-stranded RNA (dsRNA) into nanocrystalline complexes with lattice constants commensurate with the steric size of Toll-like receptor (TLR)-3 and therefore capable of multivalent binding. Such complexes amplify cytokine secretion in diverse uninfected cell types in culture (epithelial cells, endothelial cells, keratinocytes, monocytes, and macrophages), similar to cathelicidin's role in rheumatoid arthritis and lupus. The induced transcriptome matches well with the global gene expression pattern in COVID-19, despite using <0.3% of the viral proteome. Delivery of these complexes to uninfected mice boosts plasma interleukin-6 and CXCL1 levels as observed in COVID-19 patients.

Low-flow in aortic valve stenosis patients with reduced ejection fraction does not depend on left ventricular function.

Patients with severe aortic stenosis (AS) and reduced left ventricular ejection fraction (LVEF) can be distinguished into high- (HG) and low-gradient (LG) subgroups. However, less is known about their characteristics and underlying (pathophysiological) hemodynamic mechanisms. 98 AS patients with reduced LVEF were included. Subgroup characteristics were analyzed by a multimodal approach using clinical and histological data, next-generation sequencing (NGS) and applying echocardiography as well as cardiovascular magnetic resonance (CMR) imaging. Biopsy samples were analyzed with respect to fibrosis and mRNA expression profiles. 40 patients were classified as HG-AS and 58 patients as LG-AS. Severity of AS was comparable between the subgroups. Comparison of both subgroups revealed no differences in LVEF (p = 0.1), LV mass (p = 0.6) or end-diastolic LV diameter (p = 0.12). Neither histological (HG: 23.2% vs. LG: 25.6%, p = 0.73) and circulating biomarker-based assessment (HG: 2.6 ± 2.2% vs. LG: 3.2 ± 3.1%; p = 0.46) of myocardial fibrosis nor global gene expression patterns differed between subgroups. Mitral regurgitation (MR), atrial fibrillation (AF) and impaired right ventricular function (MR: HG: 8% vs. LG: 24%; p < 0.001; AF: HG: 30% vs. LG: 51.7%; p = 0.03; RVSVi: HG 36.7 vs. LG 31.1ml/m2, p = 0.045; TAPSE: HG 20.2 vs. LG 17.3mm, p = 0.002) were more frequent in LG-AS patients compared to HG-AS. These pathologies could explain the higher mortality of LG vs. HG-AS patients. In patients with low-flow severe aortic stenosis, low transaortic gradient and cardiac output are not primarily due to LV dysfunction or global changes in gene expression, but may be attributed to other additional cardiac pathologies like mitral regurgitation, atrial fibrillation or right ventricular dysfunction. These factors should also be considered during planning of aortic valve replacement.

The mammosphere-derived epithelial cell secretome modulates neutrophil functions in the bovine model.

Innovative therapies against bacterial infections are needed. One approach is to focus on host-directed immunotherapy (HDT), with treatments that exploit natural processes of the host immune system. The goals of this type of therapy are to stimulate protective immunity while minimizing inflammation-induced tissue damage. We use non-traditional large animal models to explore the potential of the mammosphere-derived epithelial cell (MDEC) secretome, consisting of all bioactive factors released by the cells, to modulate host immune functions. MDEC cultures are enriched for mammary stem and progenitor cells and can be generated from virtually any mammal. We previously demonstrated that the bovine MDEC secretome, collected and delivered as conditioned medium (CM), inhibits the growth of bacteria in vitro and stimulates functions related to tissue repair in cultured endothelial and epithelial cells. The immunomodulatory effects of the bovine MDEC secretome on bovine neutrophils, an innate immune cell type critical for resolving bacterial infections, were determined in vitro using functional assays. The effects of MDEC CM on neutrophil molecular pathways were explored by evaluating the production of specific cytokines by neutrophils and examining global gene expression patterns in MDEC CM-treated neutrophils. Enzyme linked immunosorbent assays were used to determine the concentrations of select proteins in MDEC CM and siRNAs were used to reduce the expression of specific MDEC-secreted proteins, allowing for the identification of bioactive factors modulating neutrophil functions. Neutrophils exposed to MDEC secretome exhibited increased chemotaxis and phagocytosis and decreased intracellular reactive oxygen species and extracellular trap formation, when compared to neutrophils exposed to control medium. C-X-C motif chemokine 6, superoxide dismutase, peroxiredoxin-2, and catalase, each present in the bovine MDEC secretome, were found to modulate neutrophil functions. The MDEC secretome administered to treat bacterial infections may increase neutrophil recruitment to the site of infection, stimulate pathogen phagocytosis by neutrophils, and reduce neutrophil-produced ROS accumulation. As a result, pathogen clearance might be improved and local inflammation and tissue damage reduced.

Uncovering a unique pathogenic mechanism of SARS-CoV-2 omicron variant: selective induction of cellular senescence.

SARS-CoV-2 variants are constantly emerging with a variety of changes in the conformation of the spike protein, resulting in alterations of virus entry mechanisms. Solely omicron variants use the endosomal clathrin-mediated entry. Here, we investigate the influence of defined altered spike formations to study their impact on premature cellular senescence. In our study, in vitro infections of SARS-CoV-2 variants delta (B.1.617.2) and omicron (B.1.1.529) were analyzed by using human primary small alveolar epithelial cells and human ex vivo lung slices. We confirmed cellular senescence in human lungs of COVID-19 patients. Hence, global gene expression patterns of infected human primary alveolar epithelial cells were identified via mRNA sequencing. Solely omicron variants of SARS-CoV-2 influenced the expression of cell cycle genes, highlighted by an increased p21 expression in human primary lung cells and human ex vivo lungs. Additionally, an upregulated senescence-associated secretory phenotype (SASP) was detected. Transcriptomic data indicate an increased gene expression of p16, and p38 in omicron-infected lung cells. Significant changes due to different SARS-CoV-2 infections in human primary alveolar epithelial cells with an overall impact on premature aging could be identified. A substantially different cellular response with an upregulation of cell cycle, inflammation- and integrin-associated pathways in omicron infected cells indicates premature cellular senescence.

A CircRNA-miRNA-mRNA Network for Exploring Doxorubicin- and Myocet-Induced Cardiotoxicity in a Translational Porcine Model.

Despite the widespread use of doxorubicin (DOX) as a chemotherapeutic agent, its severe cumulative cardiotoxicity represents a significant limitation. While the liposomal encapsulation of doxorubicin (Myocet, MYO) reduces cardiotoxicity, it is crucial to understand the molecular background of doxorubicin-induced cardiotoxicity. Here, we examined circular RNA expression in a translational model of pigs treated with either DOX or MYO and its potential impact on the global gene expression pattern in the myocardium. This study furthers our knowledge about the regulatory network of circRNA/miRNA/mRNA and its interaction with chemotherapeutics. Domestic pigs were treated with three cycles of anthracycline drugs (DOX, n = 5; MYO, n = 5) to induce cardiotoxicity. Untreated animals served as controls (control, n = 3). We applied a bulk mRNA-seq approach and the CIRIquant algorithm to identify circRNAs. The most differentially regulated circRNAs were validated under cell culture conditions, following forecasting of the circRNA-miRNA-mRNA network. We identified eight novel significantly regulated circRNAs from exonic and mitochondrial regions in the porcine myocardium. The forecasted circRNA-miRNA-mRNA network suggested candidate circRNAs that sponge miR-17, miR-15b, miR-130b, the let-7 family, and miR125, together with their mRNA targets. The identified circRNA-miRNA-mRNA network provides an updated, coherent view of the mechanisms involved in anthracycline-induced cardiotoxicity.

An engineered Escherichia coli Nissle strain prevents lethal liver injury in a mouse model of tyrosinemia type 1

Hereditary tyrosinemia type 1 (HT1) results from the loss of fumarylacetoacetate hydrolase (FAH) activity and can lead to lethal liver injury. Therapeutic options for HT1 remain limited. In this study, we aimed to construct an engineered bacterium capable of reprogramming host metabolism and thereby provide a potential alternative approach for the treatment of HT1. Escherichia coli Nissle 1917 (EcN) was engineered to express genes involved in tyrosine metabolism in the anoxic conditions that are characteristic of the intestine (EcN-HT). Bodyweight, survival rate, plasma (tyrosine/liver function), H&E staining and RNA sequencing were used to assess its ability to degrade tyrosine and protect against lethal liver injury in Fah-knockout (KO) mice, a well-accepted model of HT1. EcN-HT consumed tyrosine and produced L-DOPA (levodopa) in an invitro system. Importantly, in Fah-KO mice, the oral administration of EcN-HT enhanced tyrosine degradation, reduced the accumulation of toxic metabolites, and protected against lethal liver injury. RNA sequencing analysis revealed that EcN-HT rescued the global gene expression pattern in the livers of Fah-KO mice, particularly of genes involved in metabolic signaling and liver homeostasis. Moreover, EcN-HT treatment was found to be safe and well-tolerated in the mouse intestine. This is the first report of an engineered live bacterium that can degrade tyrosine and alleviate lethal liver injury in mice with HT1. EcN-HT represents a novel engineered probiotic with the potential to treat this condition. Patients with hereditary tyrosinemia type 1 (HT1) are characterized by an inability to metabolize tyrosine normally and suffer from liver failure, renal dysfunction, neurological impairments, and cancer. Given the overlap and complementarity between the host and microbial metabolic pathways, the gut microbiome provides a potential chance to regulate host metabolism through degradation of tyrosine and reduction of byproducts that might be toxic. Herein, we demonstrated that an engineered live bacterium, EcN-HT, could enhance tyrosine breakdown, reduce the accumulation of toxic tyrosine byproducts, and protect against lethal liver injury in Fah-knockout mice. These findings suggested that engineered live biotherapeutics that can degrade tyrosine in the gut may represent a viable and safe strategy for the prevention of lethal liver injury in HT1 as well as the mitigation of its associated pathologies.

Deciphering the Clinical Benefit of Pola-R-CHP versus R-CHOP in Different Genetic Subtypes Beyond Cell of Origin in the POLARIX Study

Introduction: In the POLARIX study, polatuzumab vedotin in combination with rituximab plus cyclophosphamide, doxorubicin, and prednisone (Pola-R-CHP) demonstrated prolonged progression-free survival (PFS) vs rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) in patients (pts) with previously untreated diffuse large B-cell lymphoma (DLBCL; NCT03274492; Tilly et al. N Engl J Med 2022); the PFS benefit was sustained with longer follow-up (Herrera et al. Blood 2022). Exploratory analyses demonstrated a trend towards greater PFS improvement in activated B cell-like (ABC) DLBCL with Pola-R-CHP vs R-CHOP (Tilly et al. N Engl J Med 2022). Although not yet available for daily practice, more granular molecular subtypes of DLBCL beyond cell of origin (COO) classification have demonstrated poor prognosis with R-CHOP, including EZH2 mutations/ BCL2 translocations (EZB), MYD88/ CD79B-mutated (MCD; as defined by LymphGen; Wright et al. Cancer Cell 2020), and dark zone gene expression signature (DZsig; Alduaij et al. Blood 2023). Here, in a post hoc exploratory analysis, we investigate the prevalence and clinical outcomes of molecularly defined subtypes of DLBCL in pts treated with Pola-R-CHP vs R-CHOP in POLARIX. Methods: All genetic analyses were performed on baseline tumor biopsies. Using mutations derived from whole exome sequencing (WES), pts were allocated to different genetic subtypes, as defined by the LymphGen classifier. DZsig status was determined from global gene expression patterns (GEP) as measured by RNAseq, as previously described (Ennishi et al. J Clin Oncol 2019). COO was determined by NanoString. Hazard ratios (HR) were adjusted for International Prognostic Index score (2 vs 3-5) and age (≤60 vs &amp;gt;60 years). Due to the exploratory nature of the subtype analyses, all statistics are descriptive. Results: WES data were available for 594 pts (Pola-R-CHP, n=292; R-CHOP, n=302), and baseline clinical characteristics were balanced between treatment arms. The observed 2-year PFS rates with EZB and MCD subtypes were numerically higher but not statistically significant in the Pola-R-CHP vs R-CHOP arm ( Table): EZB, 83% (95% confidence interval [CI]: 76-92) vs 75% (95% CI: 65-86), HR 0.61, 95% CI: 0.33-1.13; MCD, 85% (95% CI: 73-98) vs 73% (95% CI: 63-90), HR 0.64, 95% CI: 0.24-1.70. Lower 2-year PFS rates were observed in pts with the BCL6 fusions and NOTCH2 mutations (BN2) subtype treated with Pola-R-CHP vs R-CHOP (HR 1.82, 95% CI: 0.46-7.18; Table). In the subgroup of pts with an undetermined genetic subtype, 2-year PFS estimates were numerically higher with Pola-R-CHP vs R-CHOP (74% vs 62%, respectively; HR 0.70, 95% CI: 0.46-1.07). GEP data were available for 665 pts (Pola-R-CHP, n=331; R-CHOP, n=334); 108 (16.2%) were DZsig+ (Pola-R-CHP, n=52; R-CHOP, n=56). Of those who were DZsig+, 103 (95.4%) had germinal center B cell-like (GCB) DLBCL, 3 (2.8%) had ABC DLBCL, and 2 (1.9%) had an unknown COO. In pts who were DZsig+ and had FISH results, 54/86 (62.8%) had BCL2 translocations, 41/92 (44.6%) had MYC translocations, and 6/40 (15%) had BCL6 translocations (BCL6 FISH was only done in pts with a MYC translocation), resulting in 23/90 (25.6%) pts with double/triple-hit DLBCL. Pts who were DZsig+ were predominantly within the EZB genetic subtype (60.3%). In the R-CHOP arm, pts who were DZsig+ had shorter PFS vs pts who were DZsig− (2-yr PFS: 62% [95% CI: 51-77] vs 73% [95% CI: 68-79], respectively; HR 1.61, 95% CI: 1.02-2.56; Figure). In the Pola-R-CHP arm, no significant difference in PFS was observed between pts who were DZsig+ vs DZsig− (2-yr PFS: 77% [95% CI: 66-89] vs 79% [95% CI: 74-84]; HR 0.97, 95% CI: 0.54-1.75). Improved PFS was demonstrated in pts who were DZsig+ and treated with Pola-R-CHP vs R-CHOP (HR 0.47, 95% CI: 0.24-0.95). Conclusions: In this exploratory biomarker analysis, we recapitulated that pts with molecularly defined DLBCL subtypes, including EZB and MCD by LymphGen and DZsig+ by RNAseq, have poor outcomes with R-CHOP therapy. In pts with the EZB and MCD subtypes, Pola-R-CHP appeared to improve 2-year PFS compared with R-CHOP. Pts with GCB DLBCL who were DZsig+ significantly benefited from Pola-R-CHP vs R-CHOP. In summary, our data indicate that molecular analysis beyond COO leads to identification of distinct molecular subsets of DLBCL that may respond favorably to Pola-R-CHP; future prospective validation is required.

3D Genome Organization and Single-Cell Characterization of Pediatric Intrachromosomal Amplification of Chromosome 21 (iAMP21) B-Cell Acute Lymphoblastic Leukemia

B-cell Acute Lymphoblastic Leukemia (B-ALL) is the most frequent childhood cancer, and around 2% of these cases are associated with intrachromosomal amplification of chromosome 21 (iAMP21). The iAMP21 cases represent one of the high-risk but least understood sub-group of B-ALL. The sub-group also has a significantly low survival rate and a higher risk of relapse than non-iAMP21 cases. Recent studies suggest that structural variations in iAMP21 are linked to complex rearrangements such as a chromothripsis event on chromosome 21. The consequences of chromothripsis by which it drives the tumorigenesis are still unclear. Given the limited knowledge of chromothripsis and its impact on the epigenetic landscape in pediatric iAMP21 cases, we aim to systematically provide a critical understanding of the causes and consequences of such complex genomic rearrangements. We conducted an in-depth analysis of 9 iAMP21 and 10 non-iAMP21 pediatric patient samples associated with B-ALL using different sequencing techniques. These included whole genome sequencing (WGS), long-read sequencing, RNA-sequencing, and 3D genome organization. The WGS analysis revealed that iAMP21 cases had more genomic rearrangements compared to the non-iAMP21 group. Interestingly, iAMP21 subtypes displayed a unique feature - the presence or absence of the chromothripsis signature on chromosome 21. However, all patients shared a common characteristic - amplified and frequently deleted regions on chromosome 21, suggesting these genetic changes are a key aspect of the iAMP21 subtype, regardless of chromothripsis. Genomic rearrangements, a crucial element in oncogenesis, also modify the 3D structure of the human genome, and iAMP21 is no exception. Our Hi-C data analysis showed the devastating effect of chromothripsis on the 3D organization of chromosomes in iAMP21 patients. We observed a significant reconfiguration of the genomic compartments, along with changes in cis- and trans-acting regulatory elements such as enhancers and promoters. These changes disrupt the delicate balance of gene expression profile. To better understand the impact of these genomic rearrangements on the transcriptional landscape, we examined global gene expression patterns in iAMP21 subtypes, identifying distinct upregulated and downregulated genes. Our comparison between iAMP21 and non-iAMP21 groups identified a unique set of 186 upregulated and 174 downregulated genes in iAMP21 patients. Further, tumor diversity can greatly influence cancer diagnosis and treatment responses. Therefore, analyzing gene expression at the single-cell level is essential to uncover this diversity and identify unique cellular characteristics. Our analysis provided clear evidence of iAMP21 subclones within individual patient samples, resulting from differences in genomic rearrangements in each cancer cell. The iAMP21 cases with complex chromosomal rearrangement make it a high-risk and poorly characterized subtype of pediatric ALL. We hypothesize that even though related to worse outcomes, investigating the chromosomal rearrangement and the epigenetic landscape in iAMP21 may expose specific vulnerabilities of cancer cells in these patients allowing for targeted therapies and devising new therapeutic strategies. While our findings so far are preliminary, they offer valuable insights that can guide the formulation of hypotheses for further detailed experiments and data analysis. The project has already amassed a wealth of genomic data and a consistent approach to data analysis, addressing the challenging task of identifying relevant prognostic and predictive molecular factors in patients battling aggressive forms of cancer.

Divergent responses in desiccation experiments in two ecophysiologically different Zygnematophyceae.

Water scarcity can be considered a major stressor on land, with desiccation being its most extreme form. Land plants have found two different solutions to this challenge: avoidance and tolerance. The closest algal relatives to land plants, the Zygnematophyceae, use the latter, and how this is realized is of great interest for our understanding of the conquest of land. Here, we worked with two representatives of the Zygnematophyceae, Zygnema circumcarinatum SAG 698-1b and Mesotaenium endlicherianum SAG 12.97, who differ in habitats and drought resilience. We challenged both algal species with severe desiccation in a laboratory setup until photosynthesis ceased, followed by a recovery period. We assessed their morphological, photophysiological, and transcriptomic responses. Our data pinpoint global differential gene expression patterns that speak of conserved responses, from calcium-mediated signaling to the adjustment of plastid biology, cell envelopes, and amino acid pathways, between Zygnematophyceae and land plants despite their strong ecophysiological divergence. The main difference between the two species appears to rest in a readjustment of the photobiology of Zygnema, while Mesotaenium experiences stress beyond a tipping point.

Enrichment of Deleterious Mutated Genes Involved in Ciliary Function and Histone Modification in Brain Cancer Patient-Derived Xenograft Models.

Patient-derived xenograft (PDX) models, which can retain the characteristics of original tumors in an in vivo-mimicking environment, have been developed to identify better treatment options. However, although original tumors and xenograft tissues mostly share oncogenic mutations and global gene expression patterns, their detailed mutation profiles occasionally do not overlap, indicating that selection occurs in the xenograft environment. To understand this mutational alteration in xenografts, we established 13 PDX models derived from 11 brain tumor patients and confirmed their histopathological similarity. Surprisingly, only a limited number of somatic mutations were shared between the original tumor and xenograft tissue. By analyzing deleteriously mutated genes in tumors and xenografts, we found that previously reported brain tumor-related genes were enriched in PDX samples, demonstrating that xenografts are a valuable platform for studying brain tumors. Furthermore, mutated genes involved in cilium movement, microtubule depolymerization, and histone methylation were enriched in PDX samples compared with the original tumors. Even with the limitations of the heterogeneity of clinical lesions with a heterotropic model, our study demonstrates that PDX models can provide more information in genetic analysis using samples with high heterogeneity, such as brain tumors.