STAR: ultrafast universal RNA-seq aligner

Tape-strip profiling identifies unique immune and lipid dysregulation in patients with seborrheic dermatitis

BACKGROUND

Seborrheic dermatitis (SD) is a common, chronic inflammatory skin disease with limited understanding of its pathophysiology. Molecular profiling has been limited by invasiveness of sampling methods.

OBJECTIVE

To analyze the molecular skin profile of adult patients with SD using tape strips.

METHODS

Tape-strips obtained from facial lesions of 26 adult SD patients and 18 demographically matched healthy controls were evaluated with RNA sequencing.

RESULTS

SD molecular skin fingerprint was characterized by strong and significant upregulation of interleukin (IL)23/T-helper (Th)17 and Th22 (i.e. IL23A, IL22, PI3, LL37, S100A8, S100A12), some Th1 skewing (OASL, STAT1, CXCL9), and limited Th2 modulation. A parallel downregulation of barrier markers (CLDN1/8, FA2H, ELOVL3) was also observed.

LIMITATIONS

Limited representation of mild and severe SD patients.

CONCLUSION

These data deepen our understanding of SD suggesting that it has robust Th17/Th22, some Th1 skewing, and minimal Th2 activation, and associated skin barrier alterations. This provides rationale for novel immunomodulatory treatment approaches for SD patients targeting IL23/Th17 and/or Th22 pathways.

Diverse effects of Bacillus sp. NYG5-emitted volatile organic compounds on plant growth, rhizosphere microbiome, and soil chemistry

Bacterial strains in the rhizosphere secrete volatile organic compounds (VOCs) that play critical roles in inter- and intra-kingdom signaling, influencing both microbe-microbe and microbe-plant interactions. In this study we evaluated the plant growth-promoting effects of VOCs emitted by Bacillus sp. NYG5 on Arabidopsis thaliana, Nicotiana tabacum, and Cucumis sativus, focusing on VOC-induced alterations in plant metabolic pathways, rhizosphere microbial communities, and soil chemical properties. NYG5 VOCs enhanced plant biomass across all tested species and induced significant shifts in rhizosphere microbial community composition, specifically increasing relative abundance of Gammaproteobacteria and reducing Deltaproteobacteria (Linear discriminant analysis Effect Size, p < 0.05). Soil analysis revealed a considerable reduction in humic substance concentrations following VOCs exposure, as detected by fluorescent spectral analysis. Using SPME-GC-MS, several novel VOCs were identified, some of which directly promoted plant growth. Transcriptomic analysis of N. tabacum exposed to NYG5 VOCs demonstrated activation of pathways related to phenylpropanoid biosynthesis, sugar metabolism, and hormone signal transduction. Within the phenylpropanoid biosynthesis pathway, a significant upregulation (p adj = 1.16e-14) of caffeic acid 3-O-methyltransferase was observed, a key enzyme leading to lignin and suberin monomer biosynthesis. These results highlight the complex mechanisms through which bacterial VOCs influence plant growth, including metabolic modulation, rhizosphere microbiome restructuring, and soil chemical changes. Collectively, this study highlights the pivotal role of bacterial VOCs in shaping plant-microbe-soil interactions.

Krüppel-like factor 5 remodels lipid metabolism in exercised skeletal muscle

Regular physical activity induces a variety of health benefits, preventing and counteracting diseases caused by a sedentary lifestyle. However, the molecular underpinnings of skeletal muscle plasticity in exercise remain poorly understood. We identified a role of the Krüppel-Like Factor 5 (Klf5) in this process, in particular in the regulation of lipid homeostasis. Surprisingly, gain- and loss-of-function studies in muscle in vivo revealed seemingly opposite functions of Klf5 in the response to an acute exercise bout and chronic training, modulating lipid oxidation and synthesis, respectively. Thus, even though only transiently induced, the function of Klf5 is complex and fundamental for a normal long-term training response. These findings highlight the importance of this mediator of external stress response to adaptive remodeling of skeletal muscle tissue.

Noncoding RNAs evolutionarily extend animal lifespan

The mechanisms underlying the evolution of lifespan across organisms remain mysterious. This study computes multiple large datasets and reveals that noncoding RNAs (ncRNAs), rather than proteins, drive animal lifespan evolution. Species in the animal kingdom evolutionarily increase their ncRNA length in their genomes, coinciding with trimming of the mitochondrial genome length. This leads to a low energy consumption and longevity. Notably, as species evolve and extend their lifespans, they tend to acquire long-lived ncRNA motifs while simultaneously losing short-lived ones, in contrast to the conservative patterns observed in protein evolution. These longevity-associated ncRNA motifs, such as GGTGCG, are particularly active in crucial tissues including the endometrium, ovaries, testes, and cerebral cortex. The ovary and endometrium carry more activating ncRNAs than the testis, offering insight into why women generally outlive men. Taken together, ncRNAs drive the evolution of the two most important traits of organisms: longevity and reproduction, and they execute many more fundamental functions than those conventionally thought. This discovery provides the foundation for combating longevity and aging.

HKDC1 promotes liver cancer stemness under hypoxia through stabilizing β-catenin

BACKGROUND AND AIMS

Hexokinases (HKs), a group of enzymes catalyzing the first step of glycolysis, have been shown to play important roles in liver metabolism and tumorigenesis. Our recent studies identified hexokinase domain containing 1 (HKDC1) as a top candidate associated with liver cancer metastasis. We aimed to compare its cell-type specificity with other HKs upregulated in liver cancer and investigate the molecular mechanisms underlying its involvement in liver cancer metastasis.

APPROACH AND RESULTS

We found that, compared to HK1 and HK2, the other 2 commonly upregulated HKs in liver cancer, HKDC1 was most strongly associated with the metastasis potential of tumors and organoids derived from 2 liver cancer mouse models we previously established. RNA in situ hybridization and single-cell RNA-seq analysis revealed that HKDC1 was specifically upregulated in malignant cells in HCC and cholangiocarcinoma patient tumors, whereas HK1 and HK2 were widespread across various tumor microenvironment lineages. An unbiased metabolomic profiling demonstrated that HKDC1 overexpression in HCC cells led to metabolic alterations distinct from those from HK1 and HK2 overexpression, with HKDC1 particularly impacting the tricarboxylic acid cycle. HKDC1 was prometastatic in HCC orthotopic and tail vein injection mouse models. Molecularly, HKDC1 was induced by hypoxia and bound to glycogen synthase kinase 3β to stabilize β-catenin, leading to enhanced stemness of HCC cells.

CONCLUSIONS

Overall, our findings underscore HKDC1 as a prometastatic HK specifically expressed in the malignant compartment of primary liver tumors, thereby providing a mechanistic basis for targeting this enzyme in advanced liver cancer.

Tracing the dynamic changes in the lncRNA-mediated competing endogenous RNA network during bovine preimplantation embryo development

Long noncoding RNAs (lncRNAs) can regulate gene expression by "sponging" microRNAs (miRNAs), reducing their inhibitory effects on mRNAs. However, this mechanism has been minimally investigated in preimplantation embryo development. In this study, we revisited existing RNA sequencing and small RNA sequencing data to investigate the role of lncRNAs in in vitro-produced bovine preimplantation embryos. Our findings revealed that although lncRNAs exhibit expression patterns similar to mRNAs, maternal lncRNAs degrade earlier than mRNAs during embryonic genome activation (EGA). Weighted gene co-expression network analysis identified 27 modules of mRNA and lncRNA, with enrichment analysis showing a significant negative correlation between the polycomb repressive complex pathway and blastocyst formation (R2 = -0.98). Additionally, bioinformatics analysis was used to predict and construct lncRNA-miRNA-mRNA networks, highlighting that lncRNAs bind more to miRNAs compared with mRNAs. Moreover, lncRNA-induced lncRNA-miRNA-mRNA axes participated in mRNA degradation and biogenesis around the EGA stage. These interactions became stronger after EGA, especially after the 16-cell stage. Overall, our study provides new insights into lncRNA-mediated regulatory networks during bovine preimplantation development.

Activation of steroid hormone receptors by metabolism-disrupting chemicals

Exposure to metabolism-disrupting chemicals (MDCs), compounds largely belonging to the group of endocrine-disrupting chemicals (EDCs), is associated with metabolic dysfunctions such as dyslipidemia, insulin resistance and hepatic steatosis. Steroid hormone receptors (SHRs) are known targets for MDCs but their regulatory environment in the presence of environmental chemicals remains elusive. Here, we studied the activation and molecular interactions of SHRs exposed to 17 suspected MDCs including pesticides, plasticizers, pharmaceuticals, flame retardants, industrial chemicals and their metabolites by combining in vitro and in silico approaches. We first established and pre-validated reporter gene assays in HepG2 hepatoma cells to assess the activation of estrogen (ER), androgen (AR), glucocorticoid (GR) and progesterone (PR) receptors. Next, using RNA-seq and publicly available protein interaction data, we identified relevant SHR-interacting coregulators expressed in hepatic cells and measured their MDC-dependent interactions with SHRs using the Microarray Assay for Real-time Coregulator-Nuclear receptor Interaction (MARCoNI) technology. Finally, we examined MDC binding to ER and GR using molecular dynamics simulations. These combined approaches lead to identification of MDCs capable of SHR activation at picomolar-to-low micromolar concentrations and paralleled with their ability to induce recruitment of multiple coregulators. MDCs induced distinct SHR-coregulator binding patterns involving multiple coactivators, corepressors and other modulatory proteins. Our results have broadened the test battery to detect MDCs and indicate that the activation of SHRs by MDCs is driven by diverse molecular interactions.

Modeling a mesenchymal cell state by bioprinting for the molecular analysis of dormancy in melanoma

Malignant melanoma is a highly aggressive tumor originating from the pigment producing cells, the melanocytes. It accounts for the majority of skin cancer related deaths worldwide. This is often due to the development of therapy resistance or tumor dormancy, eventually resulting in tumor relapse by yet undefined mechanisms. Tumor dormancy is thought to be mediated by the cellular microenvironment and models taking this factor into account are urgently needed. We 3D bioprinted melanoma cells in the hydrogels Cellink Bioink (CIB) or Matrigel (MG), each as a substitute of the extracellular matrix, and, thereby, induced a quiescent or a proliferative phenotype of the melanoma cell lines, respectively. RNA-Seq with subsequent comprehensive bioinformatical and molecular analyses assigned CIB-cultured cells to a predominantly mesenchymal and Matrigel-cultured cells to a more mitotic phenotype, emphasizing the CIB model as a suitable platform for the investigation of dormancy under consideration of the microenvironment. Melanoma cells in CIB 3D culture reflect a quiescent and migratory active cell state e.g. by revealing significant downregulation of genes associated with replication and cell cycle progression in this setting. Using this model system, we identified the mechanosensory gene FHL2 as one early sensor of changes in the ECM and suggest a FHL2-p21/AP-1 axis contributing to the dormant phenotype of melanoma cells in CIB.

Transcriptomics of HERVs reveals clinico-biological characterization of LTR5_Hs and HERVS71 loci in gastric cancer

Human endogenous retroviruses (HERVs), a type of endogenous transposable elements (ETE), have emerged as potential biomarkers and therapeutic targets for cancers. However, the transcriptional relevance of HERV elements in gastric cancer (GC) remains largely unexplored. This study aims to elucidate the interactions between locus-specific HERVs expression and clinical dynamics in GC patients. We compared HERVs locus-specific expression profiles from RNA sequencing of tumor and adjacent tissues, validated using the GEO database and RT-PCR. Analysis of dysregulated ETEs revealed 113 upregulated and 46 downregulated ETEs in tumor tissues compared to adjacent non-tumor tissues. Significant differences were found in HERVs clades such as HERVK, HERVS71, and HERVH. Four clinically relevant HERV elements-LTR5_Hs_1q22 and HERVS71_19q13.22 (int, rve, RNase_H)-were validated in serum samples via RT-PCR. Higher HERVs expression (HERVshigh) correlated with larger tumor size, higher grade, increased lymph node metastasis, and higher Odds ratio compared to lower expression (HERVslow) groups. The diagnostic performance of the four HERV elements surpassed that of conventional biomarkers and improved with combined biomarker analysis. Differential and functional analysis indicated that these HERV elements significantly impacted the cell cycle, with their upregulation linked to tumor growth both in vitro and in vivo. Our exploration demonstrates the clinical significance of HERVs in tumor progression, highlighting their functional role and providing a valuable resource for developing new biomarkers and therapeutic targets in GC.

Molecular correlates of glycine receptor activity in human β cells

OBJECTIVES

Glycine acts in an autocrine positive feedback loop in human β cells through its ionotropic receptors (GlyRs). In type 2 diabetes (T2D), islet GlyR activity is impaired by unknown mechanisms. We sought to investigate if the GlyR dysfunction in T2D is replicated by hyperglycemia per se, and to further characterize its action in β cells and islets.

METHODS

GlyR-mediated currents were measured using whole-cell patch-clamp in human β cells from donors with or without T2D, or after high glucose (15 mM) culture. We also correlated glycine-induced current amplitude with transcript expression levels through patch-seq. The expression of the GlyR α1, α3, and β subunit mRNA splice variants was compared between islets from donors with and without T2D, and after high glucose culture. Insulin secretion from human islets was measured in the presence or absence of the GlyR antagonist strychnine.

RESULTS

Although gene expression of GlyRs was decreased in T2D islets, and β cell GlyR-mediated currents were smaller, we found no evidence for a shift in GlyR subunit splicing. Glycine-induced currents are also reduced after 48 h culture of islets from donors without diabetes in high glucose, where we also find the reduction of the α1 subunit expression, but an increase in the α3 subunit. We discovered that glycine-evoked currents are highly heterogeneous amongst β cells, inversely correlate with donor HbA1c, and are significantly correlated to the expression of 92 different transcripts and gene regulatory networks (GRNs) that include CREB3(+), RREB1(+) and ZNF697(+). Finally, glucose-stimulated insulin secretion is decreased in the presence of the GlyR antagonist strychnine.

CONCLUSIONS

We demonstrate that glucose can modulate GlyR expression, and that the current decrease in T2D is likely due to the receptor gene expression downregulation, and not a change in transcript splicing. Moreover, we define a previously unknown set of genes and regulons that are correlated to GlyR-mediated currents and could be involved in GlyR downregulation in T2D. Among those we validate the negative impact of EIF4EBP1 expression on GlyR activity.

Remodeling Process of the Tendon Graft After Anterior Cruciate Ligament Reconstruction: Comprehensive Analysis With RNA Sequencing in a Murine Model

The tendon graft is known to undergo a remodeling process after anterior cruciate ligament (ACL) reconstruction. However, little is known about the transcriptional profile of this process. The aim of the present study is to identify differentially expressed genes inside the remodeling ACL graft in the early phase after ACL reconstruction in our murine model using RNA sequencing (RNAseq). Fifty four male C57BL/6 mice were used in this study. The mice were euthanized at 1, 2, and 4 weeks after surgery and used for histological evaluations and RNAseq of the tendon graft. Histologically, there was a progressive decrease in the tendon-bone interface gap space and increased tissue continuity between the grafted tendon and the bone tunnel over time. At 1 and 2 weeks after surgery, cell increase and loss of collagen fiber organization inside the tendon graft were observed. RNAseq showed that genes related to inflammation, matrix metalloproteinases, bone metabolism, chemokines and signaling pathways were upregulated at 1 and 2 weeks after surgery compared to the control group (p < 0.0001). Our transcriptional profiling data suggests that expression of inflammatory mediators and bone remodeling genes may play an important role in the early events in graft-to-bone healing. Further validation at the protein level is necessary to draw firm conclusions about the role of these mediators in graft remodeling and healing. Understanding the remodeling process of the grafted tendons may lead to the identification of new approaches to improve clinical outcomes after ACL reconstruction.

Breast implant silicone exposure induces immunogenic response and autoimmune markers in human periprosthetic tissue

Silicone-based breast implants are commonly used, but there are concerns about their long-term safety. While implantation results in the formation of a periprosthetic tissue that isolates the implant from the rest of the host body, silicone can leak and reach surrounding tissues. We combined histological analysis and gene expression profiling (RNA sequencing) of samples from human patients with silicone breast implants with different fillers (silicone or serum), surface topographies and/or shell rupture, and performed systematic cross-comparisons. Our study shows that exposure to silicone gel filler, even in clinically asymptomatic cases, induces an immune response. This response includes the expression of markers associated with various autoimmune diseases. This study provides the first biological evidence of an association between silicone implants and autoimmune markers, highlighting the need for further research and stricter implant safety regulations. We suggest that implant design factors, such as filler type and surface texture, may influence the inflammatory response. Re-evaluation of existing clinical trials is warranted to investigate the association between implant characteristics and potential health risks.

Sex- and age-dependent neurovascular abnormalities linked to neuroinflammation lead to exacerbated post-ischemic brain injury in Marfan syndrome mice

Fibrillin 1 gene (Fbn1) mutations cause Marfan syndrome (MFS), triggering life-threatening aortic complications and multi-organ effects. MFS is increasingly linked to neurovascular complications, amplified by aortic surgery risks. However, the impact of MFS on the brain remains unclear, including the roles of sex, aging, and their contribution to cerebral injury. This study examines brain alterations and their role in cerebral ischemic injury in an MFS mouse model. RNA-seq analysis of young (3-month-old) and aged (13-month-old) male and female wild-type and MFS (Fbn1C1041G/+) mice revealed disruptions in TGF-β and extracellular matrix (ECM) pathways in MFS brains, most pronounced in young males and aged females with reduced estrogen levels. Inflammatory pathways were upregulated across all MFS mice. Consequently, changes in TGF-β signaling, ECM turnover, redox stress and inflammatory pathways were assessed through RT-qPCR, immunostaining, Western blot, lucigenin chemiluminescence, spectrophotometry, HPLC, and synchrotron radiation-based microspectroscopy, while cerebrovascular properties were assessed by pressure myography and confocal microscopy in the basilar artery. Aged MFS mice showed decreased brain TGF-β1 levels, while dysregulated collagen turnover was only observed in female MFS mice. Despite increased NADPH oxidase activity and redox damage in the corpus callosum of male MFS mice, brain redox stress levels remain largely unchanged. Young female MFS mice exhibited hypertrophic remodeling of the basilar artery. Remarkably, neuroinflammation driven by reactive gliosis increased in MFS mice, regardless of sex and age. To determine the impact on ischemic vulnerability, young mice underwent bilateral common carotid artery occlusion (5 min)/reperfusion (3 days). MFS mice showed greater post-ischemic brain damage, evidenced by worsened behavioral impairments, hippocampal neurodegeneration, and neuroinflammation. This study identifies sex- and age-dependent disruptions in TGF-β1, ECM, and cerebrovascular integrity in MFS mice. Persistent neuroinflammation and increased vulnerability to post-ischemic brain injury suggests that MFS patients, alongside well-documented aortic complications, have an intrinsic predisposition to cerebral damage.

SIRT3 deficiency reduces PFKFB3-driven T-cell glycolysis and promotes arthritic inflammation

Cell metabolism is an indispensable biochemical process that provides the basic energy and materials necessary for normal cell function. Accumulating evidence implicates abnormal metabolism of T cells as playing a critical role in the pathogenesis of rheumatoid arthritis (RA). The deacetylase SIRT3 has been shown to directly regulate energy metabolism in nonimmune cells. However, the role of SIRT3 in T cells and whether it participates in RA process remain unclear. In this study, we demonstrated that T-cell glycolysis was inhibited after SIRT3 deficiency. Compared to wild-type mice, SIRT3 knockout mice exhibited more severe arthritis, cartilage erosion, and inflammation after immunization with antigen-induced arthritis (AIA). It is interesting to note that SIRT3 deficiency reduced the expression of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3 (PFKFB3), a regulatory and rate-limiting enzyme in glycolysis. Overexpression of PFKFB3 was shown to restore the impaired ATP production caused by SIRT3 deficiency in T cells, and protects T cells from apoptosis. In summary, SIRT3 plays an important role in the regulation of T-cell metabolism in the pathogenesis of RA. SIRT3 deficiency decreases glycolysis, reduces ATP production, induces apoptosis in CD4+ T cells, and further promotes AIA in mice.

Fast analysis of Spatial Transcriptomics (FaST): an ultra lightweight and fast pipeline for the analysis of high resolution spatial transcriptomics

Recently, several protocols repurposing the Illumina flow cells or DNA nanoballs as an RNA capture device for spatial transcriptomics have been reported. These protocols yield high volumes of sequencing data which are usually analyzed through the use of high-performance computing clusters. I report Fast analysis of Spatial Transcriptomic (FaST), a novel pipeline for the analysis of subcellular resolution spatial transcriptomics datasets based on barcoding. FaST is compatible with OpenST, seq-scope, Stereo-seq, and potentially other protocols. It allows full reconstruction of the spatially resolved transcriptome, including cell segmentation, of datasets consisting of >500 M million reads in as little as 1 h on a standard multi core workstation with 32 Gb of RAM. The FaST pipeline returns RNA segmented Spatial Transcriptomics datasets suitable for subsequent analysis through commonly used packages (e.g scanpy or seurat). Notably, the pipeline I present relies on the spateo-release package for RNA segmentation and does not require hematoxylin/eosin or any other imaging procedure to guide cell segmentation. Nevertheless, integration with other software for imaging-guided cell segmentation is still possible. FaST is publicly available on github (https://github.com/flcvlr/FaST).

Viral integration and fusion transcript characteristics of possibly high-risk HPV in cervical cancer

HPV34, HPV66, HPV73, and HPV82 are classified by the International Agency for Research on Cancer as possibly high-risk HPV (pHR-HPV) types. Despite their relatively lower pathogenicity, some cervical cancer (CC) patients have been found to be infected with pHR-HPV, though the underlying pathogenic characteristics remain unclear. Using viral integration detection and RNA sequencing in 8 pHR-HPV+ CC samples, we identified that the integration of pHR-HPV into the human genome and the formation of pHR-HPV-human fusion transcripts are critical events in cervical carcinogenesis. These events disrupt normal gene expression and favor the stable expression of oncogenes. Additionally, we discovered that pHR-HPV undergoes alternative splicing from the AGGTA motif. Despite their lower pathogenicity, pHR-HPV integration may represent a significant risk factor for CC development. Our findings underscore the importance of considering pHR-HPV infections in future HPV screening strategies and clinical management of cervical lesions, especially those associated with HPV integration.

Regulation of detoxifying enzymes expression and restriction of picorna-like virus infection by natural polysaccharide extracts in Drosophila cells

The world is currently witnessing a rise in viral infections, while the availability of antiviral drugs remains limited. Traditional Chinese medicine (TCM) has historically served as a valuable source of novel compounds for disease treatment. In this study, we assessed the antiviral potential of various TCM compounds using Drosophila melanogaster as a model organism. Our findings reveal that natural polysaccharide extracts, prepared from 10 commonly used medicinal herbs or fungi, exhibit antiviral activity against two picorna-like viruses. Importantly, the antiviral effect is not directly attributable to the compound itself but is instead mediated by cellular responses induced by treatment with the extract. We observed that the polysaccharide extract triggers a broad transcriptional response, which partially overlaps with NF-κB pathway activation in Drosophila. However, the antiviral activity of the extract was independent of classical innate immune pathways, such as RNA interference or NF-κB signaling. Instead, the extract appears to uniquely stimulate detoxification pathways, including upregulation of cytochrome P450 and glutathione S-transferase genes, which correlates with its antiviral effects.

Genomic and transcriptomic insights into legume-rhizobia symbiosis in the nitrogen-fixing tree Robinia pseudoacacia

Robinia pseudoacacia L. (black locust) is a nitrogen (N)-fixing legume tree with significant ecological and agricultural importance. Unlike well-studied herbaceous legumes, R. pseudoacacia is a perennial woody species, representing an understudied group of legume trees that establish symbiosis with Mesorhizobium. Understanding its genomic and transcriptional responses to nodulation provides key insights into N fixation in long-lived plants and their role in ecosystem N cycling. We assembled a high-quality 699.6-Mb reference genome and performed transcriptomic analyses comparing inoculated and noninoculated plants. Differential expression and co-expression network analyses revealed organ-specific regulatory pathways, identifying key genes associated with symbiosis, nutrient transport, and stress adaptation. Unlike Medicago truncatula, which predominantly responds to nodulation in roots, R. pseudoacacia exhibited stem-centered transcriptional reprogramming, with the majority of differentially expressed genes located in stems rather than in roots. Co-expression network analysis identified gene modules associated with "leghemoglobins", metal detoxification, and systemic nutrient allocation, highlighting a coordinated long-distance response to N fixation. This study establishes R. pseudoacacia as a genomic model for nodulating trees, providing essential resources for evolutionary, ecological, and applied research. These findings have significant implications for reforestation, phytoremediation, forestry, and sustainable N management, particularly in depleted, degraded, and contaminated soil ecosystems.

Fine mapping of PmL270, a new powdery mildew resistance gene on chromosome 7AL in wheat

Wheat (Triticum aestivum) is one of the most important cereal crops, providing essential food and nutrition for humans. Wheat powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici (Bgt), seriously threatens wheat production by reducing yield and quality. Utilizing effective powdery mildew resistance (Pm) genes to develop resistant cultivars is a powerful means for controlling this disease. In this study, we identified a new resistance gene, PmL270, from the wheat line L270. By means of bulked segregant RNA‑Seq (BSR‑Seq) and molecular marker analysis, we fine-mapped PmL270 to a 0.1-cM interval on chromosome 7AL, flanked by the markers X7AL07 and X7AL09. This interval corresponds to a 630-kb region in the reference genome of Chinese Spring. Comparative analysis showed that PmL270 is distinct from other Pm genes previously reported on the same chromosome arm. A co-dominant marker, X7AL08, developed from a candidate NLR gene, co-segregated with PmL270 in the mapping population and showed high specificity for this gene. The mapping and development of co-segregation marker will facilitate the cloning of PmL270 and contribute to its rapid utilization in wheat resistance breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01574-0.

Proximal tubule pannexin 1 contributes to mitochondrial dysfunction and cell death during acute kidney injury

Pannexin 1 (Panx1) is a membrane-associated channel that, when activated, facilitates the release of small metabolites into the extracellular environment. These metabolites signal as damage-associated molecular patterns (DAMP) and initiate inflammation. Upregulation and activation of Panx1 is one of the early events during inflammatory injury. Animal models show that a lack of Panx1 is protective against acute kidney injury (AKI). How Panx1 modulates AKI is poorly understood. We utilized both in vivo and in vitro models of PANX1 overexpression to study mitochondrial function, cell death, and inflammation to evaluate how Panx1 contributes to AKI. We used two models of AKI, ischemia-reperfusion injury (IRI) and cisplatin-induced AKI (cis-AKI), in animals that overexpress PANX1 globally or specifically in the proximal tubule or in the endothelium. Cisplatin-induced injury was investigated in vitro in PANX1-overexpressing proximal tubule cells in culture. Both global and proximal tubule-specific overexpression of PANX1 exacerbated AKI, whereas endothelium-specific overexpression had no effect. Panx1-dependent metabolite release and alterations in the intracellular compartment in proximal tubules independently contributed to cell death in vitro. PANX1 overexpression impaired mitochondrial function and increased mitochondrial reactive oxygen species (ROS) production. PANX1 overexpression resulted in increased inflammation in the kidneys during cis-AKI. We showed that PANX1 overexpression resulted in overt renal injury during AKI that is in part mediated by reduced mitochondrial function, increased cell death, and inflammation. Selective strategies to inhibit Panx1 could help prevent or treat AKI.NEW & NOTEWORTHY Despite the huge medical, economical, and quality of life burden that AKI poses to patients, there are no Food and Drug Administration (FDA)-approved therapeutic or pharmaceutical interventions for AKI. Pannexin 1 (Panx1), which is upregulated in patients with AKI as well as in animals that develop experimental AKI, plays a crucial role in mediating both inflammation and cell death during AKI. Our findings suggest clinical interventions with molecules that inhibit Panx1 channel activity could improve outcomes in AKI patients.

A biofilm-targeting lipo-peptoid to treat Pseudomonas aeruginosa and Staphylococcus aureus co-infections

Antibiotic-resistant bacterial infections are a significant clinical challenge, especially when involving multiple species. Antimicrobial peptides and their synthetic analogues, peptoids, which target bacterial cell membranes as well as intracellular components, offer potential solutions. We evaluated the biological activities of novel peptoids TM11-TM20, which include an additional charged NLys residue, against multidrug-resistant Pseudomonas aeruginosa and Staphylococcus aureus, both in vitro and in vivo. Building on insights from previously reported compounds TM1-TM10, the lipo-peptoid TM18, which forms self-assembled ellipsoidal micelles, demonstrated potent antimicrobial, anti-biofilm, and anti-abscess activity. Transcriptome sequencing (RNA-seq) revealed that TM18 disrupted gene expression pathways linked to antibiotic resistance and tolerance, and biofilm formation in both pathogens. Under dual-species conditions, TM18 induced overlapping but attenuated transcriptional changes, suggesting a priming effect that enhances bacterial tolerance. In a murine skin infection model, TM18 significantly reduced dermonecrosis and bacterial burden in mono-species infections. When combined with the antibiotic meropenem, they synergistically nearly cleared co-infections. Our findings highlight that TM18 has potential as a novel therapeutic for combating antibiotic-resistant pathogens and associated biofilm-driven tolerance.

Integrated transcriptomic and proteomic profiling reveals the anti-inflammatory mechanism of dihydroartemisinin in the treatment of acute liver injury by targeting CYBA and CYBB

Acute liver injury (ALI) is a prevalent inflammatory disease with no currently available effective targeted therapies that characterized by high mortality and morbidity. Dihydroartemisinin (DHA), a derivative of the renowned antimalarial compound artemisinin, has garnered attention for its anti-inflammatory property. However, the precise anti-inflammatory mechanisms underlying its efficacy in treating ALI remain unclear. Notably, the excessive inflammatory cytokines secreted by macrophages represents a critical factor of liver damage. In our comprehensive study, transcriptome and proteomic analysis of M1 macrophages after DHA treatment was performed to unearth the potential anti-inflammatory targets for ALI treatment. Transcriptomics analysis indicated that DHA significantly mitigated inflammation, primarily by downregulating the expressions of CCL1, CCL2, CCL7, CCL13, and CXCL13. Concurrently, proteomics analysis identified six proteins, such as CYBA and CYBB, that were consistently downregulated in the DHA intervention groups compared to the M1 group. Intriguingly, a protein-protein interaction network analysis highlighted the close association of CYBA and CYBB with the aforementioned chemokine genes. Through meticulous screening, DHA curtailed the production of reactive oxygen species (ROS) by targeting CYBA and CYBB, subsequently suppressing the secretion of several chemokines and dampening the inflammatory response in M1 macrophages. More importantly, DHA not only reduced ROS and chemokine levels but also restored liver function by downregulating CYBA and CYBB to inhibit NF-κB pathway in ALI mice, demonstrating strong anti-inflammatory effects. In conclusion, our findings throw novel light into the underlying anti-inflammatory mechanism of DHA in ALI management, offering valuable insights for future clinical research and therapeutic strategies for inflammatory diseases.

Genome-Wide Association Study on Muscle Stiffness Identified Novel Locus for Predisposition to Muscle Strain Injury

PURPOSE

We aimed to screen the entire genome for genetic variants associated with passive muscle stiffness, which has been suggested as a risk factor for muscle strain injury.

METHODS

This genome-wide association study (GWAS) on passive muscle stiffness included 350 physically active young Japanese individuals. Three hamstring constituents were measured using ultrasound shear wave elastography. Skeletal muscle transcriptomes were compared across the genotypes of GWAS-identified variants in 48 healthy Japanese individuals. Association between GWAS-identified variants and history of muscle strain injury was examined in 1428 Japanese athletes.

RESULTS

Two loci on chromosome 11 demonstrated a genome-wide significant association with passive muscle stiffness of the biceps femoris long head (rs12807854 T/C: P = 5.19 × 10 -10 , rs78405694 T/C: P = 2.09 × 10 -8 ; linear regression analysis adjusted for sex, age, and stretching exercise habits). Skeletal muscle RNA sequencing revealed significantly elevated expression of extracellular matrix-related genes in muscles carrying stiffness-increasing alleles of these variants. Among athletes, rs12807854 T/C was significantly associated with a history of muscle strain injury ( P = 0.0254; logistic regression analysis adjusted for age, sex, competitive level, and main sport). Carriers of the C allele, associated with increased muscle stiffness, exhibited a heightened risk of muscle strain injury (odds ratio = 1.62; 95% confidence interval = 1.06-2.47 per C allele increase). By contrast, rs78405694 did not show a significant association with muscle strain injury in this population.

CONCLUSIONS

A novel locus associated with passive muscle stiffness and muscle strain injury was identified. Elucidating the detailed mechanisms linking the identified locus to passive muscle stiffness may lead to the development of new strategies to prevent muscle strain injuries.

Ref-1 redox activity modulates canonical Wnt signaling in endothelial cells

Ischemic retinopathies, including proliferative diabetic retinopathy (PDR) and retinopathy of prematurity (ROP), are characterized by abnormal retinal neovascularization and can lead to blindness in children and adults. Current treatments, such as intravitreal anti-VEGF injections, face limitations due to high treatment burden and variable efficacy, as multiple signaling pathways, beyond VEGF, contribute to retinal neovascularization. Previous studies demonstrate that targeting the redox-mediated transcriptional regulatory function of APE1/Ref-1 reduces pathological neovascularization. We aimed to identify novel signaling pathways regulated by Ref-1 redox activity utilizing RNA sequencing of human retinal endothelial cells (HRECs) treated with a Ref-1 redox inhibitor. We found that Wnt/β-catenin signaling was significantly downregulated after Ref-1 inhibition. Given the role of Wnt signaling in vascular pathologies, we investigated how Ref-1 regulates Wnt/β-catenin signaling. Ref-1 inhibition downregulated Wnt co-receptors LRP5/6 at both the mRNA and protein levels in endothelial cells, suggesting transcriptional regulation. Ref-1 redox inhibitors APX3330 and APX2009 reduced Wnt3a-induced nuclear β-catenin levels, decreased Wnt transcriptional activity by TOPFlash luciferase assay, and blocked hypoxia-induced Wnt/β-catenin activation in HRECs. In the oxygen-induced retinopathy mouse model of retinal neovascularization, Ref-1 specific inhibitor APX2009 reduced the expression of Wnt-related genes at sites of neovascularization. These findings reveal a novel role for Ref-1 redox activity in modulating Wnt/β-catenin signaling in endothelial cells and highlight the potential of Ref-1 redox activity targeted inhibitors as a novel therapeutic approach for retinal neovascular diseases by modulating multiple disease-relevant pathways.

Mitochondrial tRNA fragment, mt-tRF-Tyr-GTA-001 (tRF-21-X3OJI8EWB), in breast cancer and its potential clinical implications

BACKGROUND

Transfer RNA (tRNA) fragments (tRFs) are a group of small non-coding RNAs with biological functions. The involvement of tRNAs in cancer has also been recognized, but most studies focused on nuclear tRFs, very few on mitochondrial tRFs.

METHODS

We analyzed the TCGA microRNAseq data to identify differentially expressed mitochondrial tRFs (mt-tRFs) in breast tumors and evaluated their associations with the disease outcome. Cox proportional hazards regression was used to determine the associations between mt-tRFs and patient survival while adjusting for clinicopathological variables. Quantitative RT-PCR was developed to measure a specific tRF expression in a validation study.

RESULTS

Our analysis of 1,060 tumor samples from TCGA revealed that mt-tRF-Tyr-GTA-001 (tRF-21-X3OJI8EWB or t00018104) expression, a tRF from mitochondrial tRNA with tyrosine anticodon GTA (mt-tRNA-Tyr-GTA), was significantly lower in breast tumors than the adjacent tissues (p< 0.0001). Patients with low expression had significantly higher risk of death (HR = 1.69, p = 0.0018) regardless of their age at diagnosis, disease stage, tumor grade, and hormone receptor status. This survival association was replicated in an independent study where mt-tRF-Tyr-GTA-001 expression was measured with qRT-PCR. Further analysis suggested that the mt-tRF expression was correlated with ribonuclease ANG and RNase 4 known to cleave tRNAs and upregulated under hypoxia. IPA interrogation of the mt-tRF-Tyr-GTA-001 expression signature indicated the inhibitory effects of mt-tRF-Tyr-GTA-001 on malignant transformation, tumor growth, and cell invasion. In silico analysis showed that the binding targets of mt-tRF-Tyr-GTA-001 included several oncogenic transcription factors (E2Fs, CCNE1, FOXM1). We also found the mt-tRF correlated with the abundances of M0 macrophages and resting mast cells, two of the immune cells known for innate immunity.

CONCLUSIONS

In summary, our study suggests that mt-tRF-Tyr-GTA-001, a mitochondrial tRF, may suppress breast cancer progression through its involvement in regulation of cell phenotype and tumor immunity.

Identification of molecular signatures for azole fungicide toxicity in zebrafish embryos by integrating transcriptomics and gene network analysis

Azoles control fungal growth by inhibiting sterol biosynthesis in fungi according to the fungicide resistance action committee. Furthermore, previous studies have highlighted several effects of azole fungicides in fish including endocrine disruption. In this study, we analysed the transcriptome responses of zebrafish embryos exposed to azole fungicides to identify gene expression fingerprints indicating toxic effects such as endocrine disruption induced by sterol biosynthesis inhibition. Firstly, a modified zebrafish embryo toxicity test was conducted following the OECD 236 guideline, exposing embryos to difenoconazole, epoxiconazole, and tebuconazole. After 96 h, RNA was extracted for transcriptome analysis, which revealed concentration-dependent responses for each fungicide. Additionally, overrepresentation analysis of significantly differentially expressed genes revealed biological functions related to sterol biosynthesis and endocrine disruption. A gene set with specific expression patterns was was identified as molecular signature for indicating adverse effects induced by sterol biosynthesis inhibitors in zebrafish embryos. After further validation, the gene expression fingerprints and biomarkers identified in this study may be used in the future to identify endocrine activity of substances under development in a pre-regulatory screening using the zebrafish embryo model.

Genetic variation in a tandemly duplicated TPS gene cluster contributes to the diversity of aroma in lychee fruit

Fruits undergo a similar ripening process, yet they exhibit a range of differences in color, taste, and shape, both across different species and within the same species. How does this diversity arise? We uncovered a conserved fruit ripening process in lychee fruit in which a NAC transcription factor, LcNAC1, acts as a master regulator. LcNAC1 regulates the expression of two terpene synthase genes, LcTPSa1 and LcTPSa2, which belong to a gene cluster consisting of four TPS genes. LcTPSa1-LcTPSa3 are responsible for catalyzing the production of farnesol, which in turn dictates the aromatic diversity in fruit of different lychee varieties. Through comparative, transcriptomic, and genomic analyses across various lychee varieties, we found these four TPS genes exhibit distinct expression levels due to natural genetic variation. These include copy number variations, presence/absence variations, insertions and deletions, and single nucleotide polymorphisms, many of which affect the binding affinity of LcNAC1. A single nucleotide mutation in LcTPSa1 caused a premature translational termination, resulting in a truncated version of the TPS protein, which surprisingly remains functional. All these genomic changes in the LcNAC1-regulated TPS genes are likely to contribute to the great aromatic diversity observed in lychee fruit. This diversification of fruit aroma in lychee varieties offers a compelling example of how species- or variety-specific traits evolve - the phenotypic diversity is primarily derived from natural genetic variation accumulated in downstream structural genes within an evolutionarily conserved regulatory circuit.

Exploring the dynamic pathogenesis of Parkinson's disease by case-control and longitudinal blood transcriptome analyses

The pathogenesis of Parkinson's disease (PD) was recently hypothesized to change along with the disease course. Given the fact that transcriptional changes in blood can provide insightful clues for PD pathogenesis, we performed case-control and longitudinal whole blood transcriptome analyses to identify the signature genes underlying the hypothesized dynamic pathogenesis of PD. In the case-control study, we compared the gene expression patterns in healthy control (N = 189), prodromal (N = 58) and de novo idiopathic PD subjects (N = 390). The results showed that the prodromal subjects were at the tipping-point stage, which is characterized by the abnormal expression patterns of 414 genes associated with oxygen transport and reactive oxygen species metabolic process. We next performed a longitudinal transcriptome analysis on 255 PD patients from the baseline to the third year, and identified 203 genes related to immune and inflammatory responses during disease progression. These findings not just offer deeper insights into the dynamic pathogenesis of PD, but also help to find potential drugs to prevent the early neurodegeneration process.

CD200-based cell sorting results in homogeneous transplantable striatal neuroblasts for human cell therapy for Huntington's disease

Neurodegenerative diseases are characterized by selective loss of neurons. Cell replacement therapies are the most promising therapeutic strategies to restore the neuronal functions lost during these neurodegenerative processes. However, cell replacement-based clinical trials for Huntington's (HD) and Parkinson's diseases (PD) failed due to the large heterogeneity of the samples. Here, we identify CD200 as a cell surface marker for human striatal neuroblasts (NBs) using massively parallel single-cell RNA sequencing. Next, we set up a CD200-based immunomagnetic sorting pipeline that allows high-yield enrichment of human striatal NBs from in vitro differentiation of human pluripotent stem cells (hPSCs). We also show that sorted CD200-positive cells are striatal projection neuron (SPN)-committed NBs which survive upon intra-striatal transplantation in adult mice with no evidence of graft overgrowth in vivo. In conclusion, we implemented a new CD200 cell selection strategy that reduces the heterogeneity and batch-to-batch variation and potentially decreases the teratogenic risk of hPSC-based cell therapy for neurodegenerative diseases.

Comprehensive sequencing profile and functional analysis of IsomiRs in human pancreatic islets and beta cells

AIMS/HYPOTHESIS

MiRNAs regulate gene expression, influencing beta cell function and pathways. Isoforms of miRNA (isomiRs), sequence variants of miRNAs with post-transcriptional modifications, exhibit cell-type-specific expression and functions. Despite their biological significance, a comprehensive isomiR profile in human pancreatic islets and beta cells remains unexplored. This study aims to profile isomiR expression in four beta cell sources: (1) laser capture microdissected human islets (LCM-HI); (2) collagenase-isolated human islets (CI-HI); (3) sorted beta cells; and (4) the EndoC-βH1 beta cell line, and to investigate their potential role in beta cell function.

METHODS

Small RNA-seq and/or small RNA dataset analysis was conducted on human pancreatic islets and beta cells. Data were processed using the sRNAbench bioinformatics pipeline to classify isomiRs based on sequence variations. A beta cell-specific isomiR signature was identified via cross-validation across datasets. Correlations between LCM-HI isomiR expression and in vivo clinical parameters were analysed using regression models. Functional validation of isomiR-411-5p-Ext5p(+1) was performed via overexpression in EndoC-βH1 cells and CI-HI, followed by glucose-stimulated insulin secretion (GSIS) assays and/or transcriptomic analysis.

RESULTS

IsomiRs constituted 59.2 ± 1.9% (LCM-HI), 59.6 ± 2.4% (CI-HI), 42.3 ± 7.2% (sorted beta cells) and 43.8 ± 1.2% (EndoC-βH1) of total miRNA reads (data represented as mean ± SD), with 3' end trimming (Trim3p) being the predominant modification. A beta cell-specific isomiR signature of 30 sequences was identified, with isomiR-411-5p-Ext5p(+1) showing a significant inverse correlation with basal insulin secretion (p=0.0009, partial R2=0.68) and total insulin secretion (p=0.005, partial R2=0.54). Overexpression of isomiR-411-5p-Ext5p(+1), but not of its canonical counterpart, importantly reduced GSIS by 51% ( ± 15.2%; mean ± SD) (p=0.01) in EndoC-βH1 cells. Transcriptomic analysis performed in EndoC-βH1 cells and CI-HI identified 47 genes significantly downregulated by isomiR-411-5p-Ext5p(+1) (false discovery rate [FDR]<0.05) but not by the canonical miRNA, with enriched pathways related to Golgi vesicle biogenesis (FDR=0.017) and trans-Golgi vesicle budding (FDR=0.018). TargetScan analysis confirmed seed sequence-dependent target specificity for 81 genes uniquely regulated by the isomiR (p=1.1 × 10⁻⁹).

CONCLUSIONS/INTERPRETATION

This study provides the first comprehensive isomiR profiling in human islets and beta cells, revealing their substantial contribution to miRNA regulation. IsomiR-411-5p-Ext5p(+1) emerges as a distinct key modulator of insulin secretion and granule dynamics in beta cells. These findings highlight isomiRs as potential biomarkers and therapeutic targets for diabetes, warranting further exploration of their roles in beta cell biology.

RIG-I-driven CDKN1A stabilization reinforces cellular senescence

The innate immune signaling network follows a canonical format for signal transmission. The innate immune pathway is crucial for defense against pathogens, yet its mechanistic crosstalk with aging processes remains largely unexplored. Retinoic acid-inducible gene-I (RIG-I), a key mediator of antiviral immunity within this pathway, has an enigmatic role in stem cell senescence. Our study reveals that RIG-I levels increase in human genetic and physiological cellular aging models, and its accumulation drives cellular senescence. Conversely, CRISPR/Cas9-mediated RIG-I deletion or pharmacological inhibition in human mesenchymal stem cells (hMSCs) confers resistance to senescence. Mechanistically, RIG-I binds to endogenous mRNAs, with CDKN1A mRNA being a prominent target. Specifically, RIG-I stabilizes CDKN1A mRNA, resulting in elevated CDKN1A transcript levels and increased p21Cip1 protein expression, which precipitates senescence. Collectively, our findings establish RIG-I as a post-transcriptional regulator of senescence and suggest potential targets for the mitigation of aging-related diseases.

Spaceflight alters protein levels and gene expression associated with stress response and metabolic characteristics in human cardiac spheroids

Cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs) possess tremendous advantage for cardiac regeneration. However, cell survival is challenging upon cell transplantation. Since microgravity can profoundly affect cellular properties, we investigated the effect of spaceflight on hiPSC-CMs. Cardiac spheroids derived from hiPSCs were transported to the International Space Station (ISS) via the SpaceX Crew-8 mission and cultured under space microgravity for 8 days. Beating cardiac spheroids were observed on the ISS and upon successful experimentation by the astronauts in space, the live cultures were returned to Earth. These cells had normal displacement (an indicator of contraction) and Ca2+ transient parameters in 3D live cell imaging. Proteomic analysis revealed that spaceflight upregulated many proteins involved in metabolism (n = 90), cellular component of mitochondrion (n = 62) and regulation of proliferation (n = 10). Specific metabolic pathways enriched by spaceflight included glutathione metabolism, biosynthesis of amino acids, and pyruvate metabolism. In addition, the top upregulated proteins in spaceflight samples included those involved in cellular stress response, cell survival, and metabolism. Transcriptomic profiles indicated that spaceflight upregulated genes associated with cardiomyocyte development, and cellular components of cardiac structure and mitochondrion. Furthermore, spaceflight upregulated genes in metabolic pathways associated with cell survival such as glycerophospholipid metabolism and glycerolipid metabolism. These findings indicate that short-term exposure of 3D hiPSC-CMs to the space environment led to significant changes in protein levels and gene expression involved in cell survival and metabolism.

A Case-Driven Multi-Omics Analysis for Longitudinal Ibrutinib Response Evaluation of Patients With Chronic Lymphocytic Leukemia

Patients with chronic lymphocytic leukemia (CLL) undergoing ibrutinib treatment often experience incomplete response, yet the molecular level underlying clonal inertia remains to be explored. We investigated the molecular and clinical dynamics of CLL during 16 months of ibrutinib monotherapy by analyzing blood samples from two patients who continued having CLL cells in the peripheral blood during treatment. At diagnosis, the clonal burden within the B cell compartment was found to be 55% (pt1) and 86% (pt2) for the dominant clones. At 16 months following treatment these clones still constituted 66% and 89%, respectively. Utilizing multi-omic methodologies at the DNA and RNA levels, including single-cell transcriptomics, we aimed to establish a comprehensive framework for multi-omics analysis for longitudinal ibrutinib response evaluation. The presented study revealed genomically stable disease during ibrutinib treatment, but with intensified expression of genes involved in pathways related to apoptosis, cellular stress response, and canonical NF-κB signaling from diagnosis to 16 months of treatment.

Differential gene expression in uterine endometrioid cancer cells and adjusted normal tissue

Endometrial cancer is a significant public health concern with rising incidence rates globally. Understanding the molecular mechanisms underlying this disease is crucial for developing effective therapeutic strategies. Our study aimed to characterize transcriptional changes in endometrial cancer tissues compared to adjusted healthy tissue. Using RNA sequencing, we identified 2483 differentially expressed genes (DEGs), including protein-coding genes, long non-coding RNAs (lncRNAs), and microRNAs (miRNAs). Notably, several known cancer-related genes were differentially expressed, such as MYC, AKT3, CCND1, and CDKN2A. Pathway analysis revealed significant alterations in cell cycle regulation, several signaling pathways, and metabolic processes. These findings provide valuable insights into the molecular pathways dysregulated in endometrial cancer. Our results may contribute to the development of novel therapeutic targets and biomarkers for this disease.

Differential gene expression study in whole blood identifies candidate genes for psychosis in African American individuals

Genome-wide association has identified regions of the genome that mediate risk for psychosis. It is possible that variants in these regions confer risk by altering gene expression. This work has predominantly been conducted in individuals of European descent and has focused narrowly on schizophrenia rather than psychosis as a syndrome. In the present study we investigated alterations in gene expression in African American individuals with a range of psychotic diagnoses to increase understanding of the etiology in an underserved population. We performed RNA-seq in whole bloody to survey the transcriptome in 126 patients with a psychosis-spectrum disorder and 217 healthy controls and applied differential gene expression analyses across the genome while controlling for age, sex, population stratification and batch. We found 18 differentially expressed genes (DEGs), some of the locations of the corresponding genes overlap with previously implicated regions for psychosis, but many of which were novel associations. Enrichment analysis of nominally significant genes (p < 0.05) revealed overrepresentation of biological processes relating to platelet, immune and cellular function, and sensory perception. Weighted gene co-expression network analysis, applied to identify modules of co-expressed genes associated with psychosis, revealed 10 modules, one of which was significantly associated with psychosis. This module was significantly enriched for DEGs, and for platelet function. These results support the potential role of immune function in the etiology of psychosis, identify novel candidate gene expression phenotypes that correspond to both established and new genomic regions, in individuals of African American ancestry.

Carposphere microbiota alters grape volatiles and shapes the wine grape typicality

While specific environments are known to shape plant metabolomes and the makeup of their associated microbiome, it is as yet unclear whether carposphere microbiota contribute to the characteristics of grape fruit flavor of a particular wine region. Here, carposphere microbiomes and berry transcriptomes and metabolomes of three grape cultivars growing at six geographic sites were analyzed. The composition of the carposphere microbiome was determined mainly by environmental conditions, rather than grape genotype. Bacterial microbiota likely contributed to grape volatile profiles. Particularly, candidate operational taxonomic units (OTUs) in genus Sphingomonas were highly correlated with grape C6 aldehyde volatiles (also called green leaf volatiles, GLVs), which contribute to a fresh taste. Furthermore, a core set of expressed genes was enriched in lipid metabolism, which is responsible for bacterial colonization and C6 aldehyde volatile synthesis activation. Finally, a similar grape volatile profile was observed after inoculating the berry skin of two grape cultivars with Sphingomonas sp., thus providing evidence for the hypothetical microbe-metabolite relationship. These results provide novel insight into how the environment-microbiome-plant quality (E × Mi × Q) interaction may shape berry flavor and thereby typicality, serving as a foundation for decision-making in vineyard microbial management.

Identification of the CYPome associated with acetamiprid resistance based on the chromosome-level genome of Megalurothrips usitatus (Bagnall) (Thysanoptera: Thripidae)

BACKGROUND

The bean flower thrips, Megalurothrips usitatus, poses a great threat to cowpea and other legume cultivars. Chemical insecticides have been applied to control M. usitatus, but have resulted in little profit because of the rapid evolution of insecticide resistance. To characterize the potential insecticide resistance mechanisms in M. usitatus, we sequenced and assembled a chromosome-level genome of M. usitatus by combining PacBio sequencing and Hi-C technology using a susceptible population.

RESULTS

The genome size was 248.60 Mb and contained 14 128 protein-coding genes. The expansion genes of M. usitatus were enriched in the functional categories of heme binding and monooxygenase activity. We further identified 103 cytochrome P450 genes from the M. usitatus genome, 33 of which belonged to the CYP6 family. Ten CYP6 genes were significantly overexpressed in an acetamiprid-resistant population of M. usitatus. An RNA interference bioassay showed that knockdown of CYP6FW1, CYP6GM5, CYP6GM6, and CYP6GM7 significantly reduced acetamiprid resistance in the resistant population. In addition, the expression of all four genes could be induced by acetamiprid exposure. AlphaFold2-based homology modeling and molecular docking analysis showed that the proteins with relevance to acetamiprid resistance had relatively lower binding free energy with the acetamiprid molecule.

CONCLUSION

This study provides a reference genome and gene resources for future studies on the evolution of M. usitatus and related pest species, and highlights the importance of cytochrome P450s in insecticide resistance in this pest insect. © 2025 Society of Chemical Industry.

High-resolution transcriptome analysis on a mouse model of neonatal hypoxic-ischemic encephalopathy using single-nucleus RNA-seq

Neonatal hypoxic-ischemic encephalopathy (HIE) encompasses brain injuries resulting from dysregulated oxygen or blood flow to the brain before, during, or immediately after birth. During the acute phase, neuronal damage is driven by excitotoxicity, with permanent injury manifesting over the subsequent hours. Treatment options have limited efficacy, requiring deeper insights into HIE pathogenesis. Recent advances in single-cell RNA sequencing have enabled molecular investigations of diverse diseases. However, the large size of certain cells, such as neurons, has posed challenges in studying conditions where neuronal damage is central. Thus, we employed single-nucleus RNA sequencing to evaluate damages in a mouse model of HIE and found pronounced changes in the hippocampus with significantly reduced neuronal populations. We observed the characteristic activation of hippocampal microglia, confirmed by immunostaining in the HIE model. These alterations were specific to combined hypoxic-ischemic conditions and were not observed with hypoxia or ischemia alone. These findings provide insights into the molecular and anatomical impact of HIE and highlight the hippocampus as a critical focus for understanding disease mechanisms and therapeutic development.

IRnet: Immunotherapy response prediction using pathway knowledge-informed graph neural network

INTRODUCTION

Immune checkpoint inhibitors (ICIs) are potent and precise therapies for various cancer types, significantly improving survival rates in patients who respond positively to them. However, only a minority of patients benefit from ICI treatments.

OBJECTIVES

Identifying ICI responders before treatment could greatly conserve medical resources, minimize potential drug side effects, and expedite the search for alternative therapies. Our goal is to introduce a novel deep-learning method to predict ICI treatment responses in cancer patients.

METHODS

The proposed deep-learning framework leverages graph neural network and biological pathway knowledge. We trained and tested our method using ICI-treated patients' data from several clinical trials covering melanoma, gastric cancer, and bladder cancer.

RESULTS

Our results demonstrate that this predictive model outperforms current state-of-the-art methods and tumor microenvironment-based predictors. Additionally, the model quantifies the importance of pathways, pathway interactions, and genes in its predictions. A web server for IRnet has been developed and deployed, providing broad accessibility to users at https://irnet.missouri.edu.

CONCLUSION

IRnet is a competitive tool for predicting patient responses to immunotherapy, specifically ICIs. Its interpretability also offers valuable insights into the mechanisms underlying ICI treatments.

Intrinsically Disordered Regions Define Unique Protein Interaction Networks in CHD Family Remodelers

Chromodomain helicase DNA-binding (CHD) enzymes play a pivotal role in genome regulation. They possess highly conserved ATPase domains flanked by poorly characterized and intrinsically disordered N- and C-termini. Using mass spectrometry, we identify dozens of novel protein-protein interactions (PPIs) within the N- and C-termini of human CHD family members. We also define a highly conserved aggregation-prone region (APR) within the C-terminus of CHD4 which is critical for its interaction with the nucleosome remodeling and deacetylase (NuRD), as well as ChAHP (CHD4, activity-dependent neuroprotective protein (ADNP), and HP1γ) complexes. Further analysis reveals a regulatory role for the CHD4 APR in gene transcription during erythrocyte formation. Our results highlight that the N- and C-termini of CHD chromatin remodelers shape protein interaction networks that drive unique transcriptional programs.

IFITM1/OVOL1 Axis Is a Novel Regulator of the Expansion of the Limbal Epithelial Stem/Early Transient Amplifying Cell Population

Limbal epithelial stem cells (LESCs), located in the basal layer of the limbal epithelium, rarely proliferate under normal conditions. Upon proliferation, LESCs give rise to early transient amplifying (eTA) cells, which are thought to be morphologically and phenotypically indistinguishable from LESCs. Following corneal epithelial wounding, LESCs are activated to repair the corneal epithelium via expansion of eTA cells, a process crucial for maintaining corneal epithelial homeostasis and tissue transparency as well as essential for clear vision. To understand how this process is regulated, we conducted a single cell RNA sequencing assay of mouse corneal rims with and without injury and observed an expansion of the stem/eTA cell cluster after corneal injury. Interestingly, we found that Interferon Induced Transmembrane Protein 1 (IFITM1) was predominantly expressed in stem/eTA cells and was positively associated with such stem/eTA cell expansion after corneal wounding. In vivo knockdown of IFITM1 using an AAV (adeno-associated virus) vector significantly attenuated stem/eTA cell expansion and activation of stem/eTA cells to proliferate after mouse corneal wounding. In human limbal epithelial cell cultures, IFITM1 positively impacted the proliferation of stem/eTA cell-enriched limbal epithelial cells, contributing to expansion of the stem/eTA cell population. Such expansion was due, in part, to inhibition of OVOL1 (Ovo like zinc finger 1), a negative regulator of epithelial cell proliferation. These results provide key molecular insights into how stem cell activation and eTA cell expansion are regulated. Elucidating the IFITM1/OVOL1 pathway that governs stem/eTA cell proliferation not only deepens our knowledge of tissue homeostasis but also opens avenues for developing novel regenerative therapies.

Antibiofilm properties of 4-hydroxy-3-methyl-2-alkenylquinoline, a novel Burkholderia-derived alkaloid

Biofilms are an important colonization mechanism employed by several microbial species to better establish themselves and monopolize the acquisition of resources across different environs. Some bacteria have evolved specialized metabolites that, when secreted, disrupt the formation and stability of biofilms generated by competing heterospecies, providing the producing organism with an ecological advantage. Soil-derived species are probable candidates for the identification of such compounds, given the intense level of competition that occurs within the terrestrial ecosystem. The MS14 strain of Burkholderia contaminans isolated from soil in Mississippi has previously been shown to produce antimicrobial compounds like occidiofungin and ornibactin. In this report, we demonstrate that this strain also produces 4-hydroxy-3-methyl-2-alkenylquinoline (HMAQ-7), an alkaloid-based metabolite structurally similar to others produced by Burkholderia. HMAQ-7 was isolated and purified in sufficient quantities to enable the elucidation of its covalent structure and the evaluation of its biological effects. The compound was found to possess a unique ability to inhibit biofilm biosynthesis in several species, including opportunistic pathogens like Staphylococcus haemolyticus and within saliva-derived multispecies biofilms. HMAQ-7 also demonstrated an ability to modulate additional cellular behaviors in Bacillus subtilis, including motility and sporulation, suggesting that this molecule is important to the interspecies dynamics present across many diverse microenvironments.IMPORTANCEThe present study furthers our understanding of the structural complexity and the biological functions of the 2-alkyl-4(1H)-quinolone metabolites produced by Burkholderia spp. Low micromolar concentrations of HMAQ-7' induced observable bacterial growth morphology differences. The antibiofilm properties of the HMAQ-7' characterized in this study will promote future investigations into possible biological and applied roles. The ability to alter biofilm formation using HMAQ-7' may facilitate Burkholderia spp. colonization in a multitude of environments, that is, aquatic, soil, and possibly during infection. HMAQ may subvert competition by potential competitor species in natural environments of Burkholderia spp. and possibly lung infections of cystic fibrosis patients.

Whole-blood transcriptomic analysis reveals preoperative complement inhibitor deficiencies linked to postoperative delirium

Postoperative delirium is a type of acute cognitive dysfunction characterized by inattention, disorganized thinking, and altered levels of consciousness that commonly develops after major surgery. Efforts to reduce the incidence of delirium have focused primarily on optimizing perioperative care, however the development of prophylactic interventions have been hindered by a limited understanding of the underlying mechanisms involved in delirium. In this secondary analysis of the Minimizing ICU Neurological Dysfunction with Dexmedetomidine-induced Sleep (MINDDS) trial, a nested case-control study (n = 51) was conducted using total RNA-sequencing analysis of whole-blood to investigate genes associated with delirium risk and development. Transcriptomic analysis revealed significantly lower expression of a key complement pathway inhibitor, C4BPA, in participants who experienced postoperative delirium. This finding was confirmed by quantitative PCR in the MINDDS cohort (n = 319) in adjusted logistic models. Furthermore, complement inhibitor CD55 was also found to be under-expressed in participants who developed delirium. Dexmedetomidine treatment modified associations between C4BPA and CD55 expression and the incidence of postoperative delirium by decreasing incidence in participants with low C4BPA and CD55 expression. This study revealed key complement regulators as risk biomarkers of postoperative delirium. Importantly, our findings suggest postoperative delirium risk is modifiable. Unlike previous research that has mainly focused on proteomics, this study underscores the effectiveness of whole-blood transcriptomics in identifying biomarkers and underlying biological mechanisms of postoperative delirium.

Differentiating Peromyscus leucopus bone marrow-derived macrophages for characterization of responses to Borrelia burgdorferi and lipopolysaccharide

Currently, most tools utilized in host-pathogen interaction studies depend on the use of human or mouse (Mus musculus) cells and tissues. While these species have led to countless breakthroughs in our understanding of infectious disease, there are undoubtedly important biological processes that are missed by limiting studies to these two vertebrate species. For instance, it is well-established that a common deermouse in North America, Peromyscus leucopus, has unique interactions with microbes, which likely shape its ability to serve as a critical reservoir for numerous zoonotic pathogens, including a Lyme disease spirochete, Borrelia burgdorferi. In this work, we expand the immunological toolkit to study P. leucopus biology by performing the first differentiation of deermouse bone marrow to macrophages using P. leucopus M-CSF producing HEK293T cells. We find that P. leucopus BMDMs generated through this method behave broadly very similarly to C57BL/6J macrophages generated with the L-929 supernatant, although RNA sequencing revealed modest differences in transcriptomic responses to B. burgdorferi and lipopolysaccharide. In particular, differences in Il-10 induction and caspase expression were observed between the species.

An antisense oligonucleotide-based strategy to ameliorate cognitive dysfunction in the 22q11.2 Deletion Syndrome

Adults and children with the 22q11.2 Deletion Syndrome demonstrate cognitive, social, and emotional impairments and high risk for schizophrenia. Work in mouse model of the 22q11.2 deletion provided compelling evidence for abnormal expression and processing of microRNAs. A major transcriptional effect of the microRNA dysregulation is upregulation of Emc10, a component of the ER membrane complex, which promotes membrane insertion of a subset of polytopic and tail-anchored membrane proteins. We previously uncovered a key contribution of EMC10 in mediating the behavioral phenotypes observed in 22q11.2 deletion mouse models. Here, we show that expression and processing of miRNAs is abnormal and EMC10 expression is elevated in neurons derived from 22q11.2 deletion carriers. Reduction of EMC10 levels restores defects in neurite outgrowth and calcium signaling in patient neurons. Furthermore, antisense oligonucleotide administration and normalization of Emc10 in the adult mouse brain not only alleviates cognitive deficits in social and spatial memory but remarkably sustains these improvements for over 2 months post-injection, indicating its therapeutic potential. Broadly, our study integrates findings from both animal models and human neurons to elucidate the translational potential of modulating EMC10 levels and downstream targets as a specific venue to ameliorate disease progression in 22q11.2 Deletion Syndrome.

The APOE isoforms differentially shape the transcriptomic and epigenomic landscapes of human microglia xenografted into a mouse model of Alzheimer's disease

Microglia play a key role in the response to amyloid beta in Alzheimer's disease (AD). In this context, the major transcriptional response of microglia is the upregulation of APOE, the strongest late-onset AD risk gene. Of its three isoforms, APOE2 is thought to be protective, while APOE4 increases AD risk. We hypothesised that the isoforms change gene regulatory patterns that link back to biological function by shaping microglial transcriptomic and chromatin landscapes. We use RNA- and ATAC-sequencing to profile gene expression and chromatin accessibility of human microglia xenotransplantated into the brains of male APPNL-G-F mice. We identify widespread transcriptomic and epigenomic differences which are dependent on APOE genotype and are corroborated across the profiling assays. Our results indicate that impaired microglial proliferation, migration and immune responses may contribute to the increased risk for late-onset AD in APOE4 carriers, while increased phagocytic capabilities and DNA-binding of the vitamin D receptor in APOE2 microglia may contribute to the isoform's protective role.

Genotype-Specific Responses of Common Bean to Meloidogyne incognita

The root-knot nematode Meloidogyne incognita causes large galls on roots, interfering with the flow of water and nutrients to the plant. In the common bean, no major resistance (R) genes have been described. Instead, resistance is controlled by multiple genes, which have not proved effective so far. An RNA sequencing approach was used to identify genes involved in common bean response to M. incognita at the stages of nematode invasion and root galling. When comparing infected and uninfected treatments of a moderately resistant (MR) and a susceptible (S) genotype, several genes were identified as differentially expressed. Their functional annotation indicated that both genotypes underwent complex transcriptional reprogramming from early to later periods of the interaction, but defense-related genes were mostly upregulated in the MR genotype. At the early stage, a large set of genes was activated in both genotypes, including those involved in cell wall organization, signaling, hormonal pathways, transcription factors, oxidative stress, and putative resistance gene analogs. Later, most of the previously activated defense mechanisms were no longer expressed in the S genotype. There was an increased expression of genes encoding proteins involved in hormonal signaling pathways (salicylic acid and gibberellin-related), protein kinases, transcription factors, and oxidative stress in the MR genotype. However, a decreased expression of genes involved in signaling mediated by calcium and oxidative stress occurred in the S genotype, indicating susceptibility. The repertoire of genes identified herein will facilitate research in plant-nematode interactions, with possible applications for the improvement of the common bean.

FOXA2 promotes metastatic competence in small cell lung cancer

Small cell lung cancer (SCLC) is known for its high metastatic potential, with most patients demonstrating clinically evident metastases in multiple organs at diagnosis. The factors contributing to this exceptional metastatic capacity have not been defined. To bridge this gap, we compare gene expression in SCLC patient samples who never experienced metastasis or relapse throughout their clinical course, versus primary SCLC patient samples from more typical patients who had metastatic disease at diagnosis. This analysis identifies FOXA2 as a transcription factor strongly associated with SCLC metastasis. Subsequent analyses in experimental models demonstrates that FOXA2 induces a fetal neuroendocrine gene expression program and promotes multi-site metastasis. Moreover, we identify ASCL1, a transcription factor known for its initiating role in SCLC tumorigenesis, as a direct binder of the FOXA2 promoter and regulator of FOXA2 expression. Taken together, these data define the ASCL1-FOXA2 axis as a critical driver of multiorgan SCLC metastasis.

Cellular hierarchies of embryonal tumors with multilayered rosettes are shaped by oncogenic microRNAs and receptor-ligand interactions

Embryonal tumor with multilayered rosettes (ETMR) is a pediatric brain tumor with dismal prognosis. Characteristic alterations of the chromosome 19 microRNA cluster (C19MC) are observed in most ETMR; however, the ramifications of C19MC activation and the complex cellular architecture of ETMR remain understudied. Here we analyze 11 ETMR samples from patients using single-cell transcriptomics and multiplexed spatial imaging. We reveal a spatially distinct cellular hierarchy that spans highly proliferative neural stem-like cells and more differentiated neuron-like cells. C19MC is predominantly expressed in stem-like cells and controls a transcriptional network governing stemness and lineage commitment, as resolved by genome-wide analysis of microRNA-mRNA binding. Systematic analysis of receptor-ligand interactions between malignant cell types reveals fibroblast growth factor receptor and Notch signaling as oncogenic pathways that can be successfully targeted in preclinical models and in one patient with ETMR. Our study provides fundamental insights into ETMR pathobiology and a powerful rationale for more effective targeted therapies.

Induced variation in BRASSINOSTEROID INSENSITIVE 1 (BRI1) confers a compact wheat architecture

BACKGROUND

The brassinosteroid (BR) plant hormones regulate numerous developmental processes, including those determining stem height, leaf angle, and grain size that have agronomic relevance in cereals. Indeed, barley (Hordeum vulgare) varieties containing uzu alleles that impair BR perception through mutations in the BR receptor BRASSINOSTEROID INSENSITIVE 1 (BRI1) exhibit a semi-dwarf growth habit and more upright leaves suitable for high-density planting. We used forward and reverse genetic approaches to develop novel BRI1 alleles in wheat (Triticum aestivum L.) and investigated their potential for crop productivity improvement.

RESULTS

The combination of ethyl methanesulfonate-induced mutations introducing premature stop codons in all three homoeologous TaBRI1 genes resulted in severe dwarfism, malformed leaves and sterility as observed in bri1 mutants in other species. Double mutants had reduced flag-leaf angles (FLAs) conferring a more upright canopy but exhibited no differences in height or grain weight. In a targeted forward genetics screen using a double mutant, we identified two BR-insensitive lines with reduced height and FLA that contained amino acid substitutions in conserved regions of BRI-A1. The less severe mutant had a 56% reduction in FLA and was 35% shorter than the wild type, although seed set, seed area and grain weights were also reduced. The most severe mutants contained elevated levels of bioactive BRs and increased expression of BR-biosynthesis genes consistent with reduced feedback suppression of biosynthesis.

CONCLUSION

Our study gives a better understanding of BRI1 function in wheat and provides mutants that could potentially be explored for improving grain yields when sown at high density.