STAR: ultrafast universal RNA-seq aligner

Heat stress response in the cave nectar bat Eonycteris spelaea differs from that of Mus musculus

Bats as the only flying mammals incur a high metabolic cost during extended powered flight, which results in febrile-like temperatures without injury. Herein, we investigate the in vivo heat shock response (HSR) in the cave nectar bat Eonycteris spelaea. We demonstrate that E. spelaea exhibits enhanced physiological heat resistance, marked by reduced lethality, tissue damage and serum corticosterone levels in comparison to mice upon heat challenge. Additionally, E. spelaea did not exhibit an acute transcriptional response observed in heat stressed mice. Instead, bats displayed a delayed and non-canonical HSR that did not involve the activation of classical heat shock related genes and pathways. This altered response in E. spelaea is attributed to the elevated basal expression of heat shock proteins, which we demonstrate to be a common characteristic exhibited by bats from diverse sub-orders, families and diets. Taken together, we demonstrate a distinct HSR in E. spelaea relative to the conventional model organism, mouse, which may provide insights to understand novel regulatory targets and effector proteins that underlie the mammalian heat shock response.

Pathogen-induced root glutamine concentration is a determinant of the outcome of the Medicago truncatula-Aphanomyces euteiches interaction

MAIN CONCLUSION

Our work highlights that glutamine plays a central role in contributing to the outcome of disease in the Medicago truncatula-Aphanomyces euteiches interaction when modulating plant N supply. Nitrogen (N) is essential for the growth of plants and microorganisms. The quantity and quality of N supply can impact plant development but also its interaction with pathogens. Our previous work showed that N modulated Medicago truncatula (Mt) susceptibility to the oomycete pathogen Aphanomyces euteiches (Ae) when plants were grown in vitro and glutamine (Gln) was proposed to mediate this effect of N on plant disease. Using more than 30 lines representative of Mt diversity, we show here that pathogen-induced root Gln concentrations are correlated with higher susceptibility to Ae. N modulation of the response to Ae of the partially resistant Mt A17 genotype was associated with changes in the expression of MtGS1 genes encoding cytosolic glutamine synthetases (GSs). This raises the question of the importance of Gln during Mt/Ae interaction and a possible role of cytosolic GS in mediating Mt susceptibility to Ae. Interestingly, exogenous Gln induced a higher susceptibility of the A17 line to Ae and induced a metabolic profile of inoculated A17 roots similar to that of a susceptible genotype. RNAseq experiments highlighted a higher expression of numerous plant defense genes in non-inoculated roots on Gln. On the pathogen side, a higher expression of genes encoding proteases and a lower expression of genes encoding elicitins as well as a better growth of Ae on Gln could explain the higher susceptibility of Mt on Gln. Altogether our results highlight the delicate balance between plant immunity, pathogen growth and virulence in contributing to the outcome of disease when modulating N supply and that Gln plays a central role in this process.

Blood RNA-seq in rare disease diagnostics: a comparative study of cases with and without candidate variants

BACKGROUND

Approximately 60% of rare disease cases remain unsolved after exome and genome sequencing (ES/GS). Blood RNA sequencing (RNA-seq) complements DNA-level diagnosis by revealing the functional impact of variants on gene expression and splicing, but to what extent RNA-driven approaches offer diagnostic benefits across different scenarios-with and without pre-existing candidate variants-remains uncertain.

METHODS

128 unrelated probands with suspected Mendelian disorders who had previously undergone ES/GS were recruited. A validation cohort (n = 7, with variants expected to alter RNA) and a test cohort (n = 121, including 10 with variants of uncertain significance (VUS) and 111 with no previously identified candidate variants) were analyzed. Blood RNA-seq was performed, and aberrant splicing (AS) and aberrant expression (AE) were detected using the DROP pipeline. SpliceAI predictions were compared with RNA-seq results for splicing-related VUS variants, and pathogenicity was re-evaluated. AS/AE outliers were evaluated for diagnostic potential in cases without candidate variants. The feasibility of an RNA-driven approach was assessed by ranking causal variant-associated aberrant events.

RESULTS

The pipeline correctly identified all expected AS/AE events in the validation cohort. In the test cohort with candidate VUS, RNA-seq provided a 60% (6/10) diagnostic uplift. Notably, SpliceAI predictions matched RNA-seq observations perfectly only in 40% of these VUS. A 2.7% (3/111) diagnostic uplift was achieved in the test cohort with no prior candidates. Overall, target AS and AE events ranked among the top eight in 14 of the 16 diagnosed cases using a purely RNA-driven approach; however, two cases would have been missed without prior candidate identification from DNA sequencing.

CONCLUSION

Blood RNA-seq is highly effective in refining the interpretation of splicing VUS, frequently leading to reclassification and diagnosis. Meanwhile, RNA-driven identification of causal variants shows a more modest yield in cases without prior candidates. This study supports an RNA-complementary approach as the preferred strategy for clinical utility.

Skeletal muscle endothelial dysfunction through the activin A-PGC1α axis drives progression of cancer cachexia

Cachexia is the wasting of skeletal muscle in cancer and is a major complication that impacts a person's quality of life. We hypothesized that cachexia is mediated by dysfunction of the vascular system, which is essential for maintaining perfusion and tempering inappropriate immune responses. Using transparent tissue topography, we discovered that loss of muscle vascular density precedes muscle wasting in multiple complementary tumor models, including pancreatic adenocarcinoma, colon carcinoma, lung adenocarcinoma and melanoma models. We also observed that persons suffering from cancer cachexia exhibit substantial loss of muscle vascular density. As tumors progress, increased circulating activin A remotely suppresses the expression of peroxisome proliferator-activated receptor-γ coactivator 1α (PGC1α) in the muscle endothelium, thus inducing vascular leakage. Restoring endothelial PGC1α activity preserved vascular density and muscle mass in tumor-bearing mice. Our study suggests that restoring muscle endothelial function could be a valuable therapeutic approach for cancer cachexia.

Translating Muscle RNAseq Into the Clinic for the Diagnosis of Muscle Diseases

OBJECTIVE

Approximately half of patients with hereditary myopathies remain without a definitive genetic diagnosis after DNA next-generation sequencing (NGS). Here, we implemented transcriptome analysis of muscle biopsies as a complementary diagnostic tool for patients with muscle disease but no definitive genetic diagnosis after exome sequencing.

METHODS

In total, 70 undiagnosed cases with suspected genetic muscular dystrophies or congenital myopathies were included in the study. Muscle RNAseq comprised the analysis of aberrant splicing, aberrant expression, and monoallelic expression. In addition, existing NGS data or variant calling from RNAseq were reanalyzed, and genome sequencing was performed in selected cases. Four aberrant splicing open-source tools were compared and assessed.

RESULTS

RNAseq established a diagnosis in 10/70 patients (14.3%) by identifying aberrant transcripts produced by single nucleotide variants (7/10) or copy number variants (3/10). Reanalysis of NGS data allowed the diagnosis in 9/70 individuals (12.9%). Based on this cohort, FRASER was the tool that reported more splicing outlier events per sample while showing the highest accuracy (81.26%).

CONCLUSIONS

We demonstrate the utility of RNAseq in identifying causative variants in muscle diseases. Evaluation of four aberrant splicing tools allowed efficient identification of most pathogenic splicing events, obtaining a manageable number of candidate events for manual inspection, demonstrating feasibility for translation into a clinical setting. We also show how the integration of omic technologies reduces the turnaround time to identify causative variants.

Developing a disease-specific accessible transcriptional signature as a biomarker for ataxia with oculomotor apraxia type 2

BACKGROUND

Genetic ataxias are clinically heterogenous neurodegenerative conditions often involving rare or private mutations and it is often difficult to assign pathogenicity to rare gene variants solely based on DNA sequencing. An effective functional assay from an easy-to-obtain biospecimen would aid this assessment and be of high clinical value. SETX encodes a ubiquitous DNA/RNA helicase crucial for resolving R-loops and maintaining genome stability. Loss-of-function mutations cause a recessive disorder, Ataxia with Oculomotor Apraxia Type 2 (AOA2).

METHODS

Here we utilize Weighted Gene Co-expression Network Analysis (WGCNA) from patient blood to construct an AOA2-specific transcriptomic signature as a biomarker to evaluate SETX variants in patients clinically suspected of having AOA2.

RESULTS

WGCNA from peripheral blood RNA of 11 AOA2 patients from 7 families initially identified a single gene module that was modestly effective in distinguishing individuals with AOA2 from controls (sensitivity 73%, specificity 97%) and was able to robustly differentiate AOA2 patients from those with genetically distinct, yet phenotypically similar, neurological disorders (sensitivity 100%, specificity 100%). An independent derivation of the transcriptional biomarker identified a dual module model that was able to better distinguish individuals with AOA2 from controls (sensitivity 100%, specificity 97%). As validation, we examined a second cohort of 21 patients from 13 families and demonstrate that this dual module transcriptional biomarker could discriminate patients clinically suspected of AOA2 from controls (57%, 95%CI: 34%-78%). Overall, the transcriptional biomarker was able to separate AOA2 subjects (n = 32) from controls (n = 35) with 72% sensitivity and 97% specificity. Notably, this transcriptomic biomarker enabled verification of the first pathogenic SETX mutation found in a non-canonical transcript, expanding the spectrum of mutations that contribute to AOA2.

CONCLUSIONS

Our study identified a transcriptional biomarker that was able to differentiate AOA2 from controls and from other related neurological disorders, consequently expanding the spectrum of known pathogenic mutations. This proof-of-concept study illustrates that transcriptional biomarkers may be used to validate variants of uncertain significance in known genetic diseases.

Spatio-Temporal Regulation of Gibberellin Biosynthesis Contributes to Optimal Rhizome Bud Development

The perennial life cycle involves the reiterative development of sexual and asexual organs. Asexual structures such as rhizomes are found in various plant species, fostering extensive growth and competitive advantages. In the African wild rice Oryza longistaminata, we investigated the formation of rhizomes from axillary buds, which notably bend diagonally downward of the main stem, as the factors determining whether axillary buds become rhizomes or tillers are unclear. Our study revealed that rhizome buds initiate between the third and fifth nodes of seedlings beyond the 6-leaf stage, while the buds above the sixth node develop into tillers. We propose that precise regulation of gibberellin (GA) biosynthesis plays a pivotal role in optimal rhizome bud development, as demonstrated by a comparative transcriptome analysis between tiller buds and rhizome buds and quantification of phytohormones. Furthermore, GA4 treatment upregulated the expression of genes associated with flowering repression and cell wall modification. These findings highlight the integration of GA biosynthesis and flowering repression genes as crucial in asexual organ development, shedding new light on the molecular mechanisms governing rhizome bud development in O. longistaminata and deepening our understanding of asexual reproduction regulation in perennial plants.

Comprehensive curation and validation of genomic datasets for chestnut

The Chinese chestnut (Castanea mollissima) stands out as a plant with significant ecological and economic value, excellent nutritional quality and natural resistance to pests and diseases. Recent strides in high-throughput techniques have enabled the continuous accumulation of genomic data on chestnuts, presenting a promising future for genetic research and advancing traits in this species. To facilitate the accessibility and utility of this data, we have curated and analyzed a collection of genomic datasets for eight Castanea species, including functional annotations, 213 RNA-Seq samples, and 330 resequencing samples. These datasets are publicly available on Figshare and are also available through other platforms such as GEO and EVA, providing a valuable resource for researchers studying Castanea genetics, functional genomics, and evolutionary biology. Furthermore, the datasets are integrated into the Castanea Genome Database (CGD, http://castaneadb.net ), which serves as a complementary platform, offering advanced data mining and analysis tools, including BLAST, Batch Query, GO/KEGG Enrichment Analysis, and Synteny Viewer, to enhance the usability of the curated datasets.

Transcriptional dynamics and functions of WUSCHEL-related homeobox (WOX) genes from Ginkgo biloba in tissue culture

BACKGROUND

In vitro regeneration presents significant challenges for the propagation and genetic improvement of most woody plants, particularly gymnosperms. The WUSCHEL-related homeobox (WOX) genes are known to play vital roles as growth regulators in tissue culture regeneration in several plant species. However, the specific functions of WOX genes in the regeneration processes of gymnosperms had not been previously elucidated. This study aims to systematically identify and analyze the WOX gene family in Ginkgo biloba to understand its potential role in tissue culture regeneration.

RESULTS

Thirteen WOX genes from Ginkgo biloba, designated as GbWUS and GbWOXs, were systematically identified. Phylogenetic analysis revealed the presence of nine genes in the WUSCHEL (WUS) clade, one in the intermediate clade, and three in the ancient clade. Transcriptome analysis indicated tissue-specific expression of seven GbWOXs, with two gymnosperm-specific GbWOXs characterized by extra-long introns exhibiting constitutive expression. Further investigation through Ginkgo tissue culture indicated that GbWOX2 was specifically expressed in embryos and facilitated callus induction, while GbWOX3A showed preferential expression during the early stages of embryo and callus development. Co-expression and Gene Ontology (GO) enrichment analyses suggested interactions and functional roles among GbWOXs. Three genes (GbWOX1, GbWOX2, and GbWOX3A) were then cloned and transformed into poplar and/or tobacco. Overexpression of GbWOX2 resulted in larger and denser callus formation, whereas GbWOX3A effectively enhanced shoot regeneration and noticeably increased the rate of adventitious shoot induction.

CONCLUSIONS

This study provides the first comprehensive analysis of the WOX gene family in Ginkgo biloba and highlights its significant role in tissue culture regeneration. The findings suggest that specific GbWOXs are critical for embryo development and callus regeneration, which provides the foundation for the establishment of effective tissue culture systems in Ginkgo. Moreover, this research contributes valuable insights that could be beneficial for improving propagation techniques and genetic studies in other forest trees, especially within the gymnosperm group.

Angiopoietin-TIE2 feedforward circuit promotes PIK3CA-driven venous malformations

Venous malformations (VMs) are vascular anomalies lacking curative treatments, often caused by somatic PIK3CA mutations that hyperactivate the PI3Kα-AKT-mTOR signaling pathway. Here, we identify a venous-specific signaling circuit driving disease progression, where excessive PI3Kα activity amplifies upstream TIE2 receptor signaling through autocrine and paracrine mechanisms. In Pik3caH1047R-driven VM mouse models, single-cell transcriptomics and lineage tracking revealed clonal expansion of mutant endothelial cells with a post-capillary venous phenotype, characterized by suppression of the AKT-inhibited FOXO1 and its target genes, including the TIE2 antagonist ANGPT2. An imbalance in TIE2 ligands, likely exacerbated by aberrant recruitment of smooth muscle cells producing the agonist ANGPT1, increased TIE2 activity in both mouse and human VMs. While mTOR blockade had limited effects on advanced VMs in mice, inhibiting TIE2 or ANGPT effectively suppressed their growth. These findings uncover a PI3K-FOXO1-ANGPT-TIE2 circuit as a core driver of PIK3CA-related VMs and highlight TIE2 as a promising therapeutic target.

Small intestinal neuroendocrine tumors lack early genomic drivers, acquire DNA repair defects and harbor hallmarks of low REST expression

The tumorigenesis of small intestinal neuroendocrine tumors (siNETs) is not understood and comprehensive genomic and transcriptomic data sets are limited. Therefore, we performed whole genome and transcriptome analysis of 39 well differentiated siNET samples. Our genomic data revealed a lack of recurrent driver mutations and demonstrated that multifocal siNETs from individual patients can arise genetically independently. We detected germline mutations in Fanconi anemia DNA repair pathway (FANC) genes, involved in homologous recombination (HR) DNA repair, in 9% of patients and found mutational signatures of defective HR DNA repair in late-stage tumor evolution. Furthermore, transcriptomic analysis revealed low expression of the transcriptional repressor REST. Summarizing, we identify a novel common transcriptomic signature of siNETs and demonstrate that genomic alterations alone do not explain initial tumor formation, while impaired DNA repair likely contributes to tumor evolution and represents a potential pharmaceutical target in a subset of patients.

Spatiotemporal transcriptomic maps of mouse intracerebral hemorrhage at single-cell resolution

Intracerebral hemorrhage (ICH) is a prevalent disease with high mortality. Despite advances in clinical care, the prognosis of ICH remains poor due to an incomplete understanding of the complex pathological processes. To address this challenge, we generated single-cell-resolution spatiotemporal transcriptomic maps of the mouse brain following ICH. This dataset is the most extensive resource available, providing detailed information about the temporal expression of genes along with a high-resolution cellular profile and preserved cellular organization. We identified 100 distinct cell subclasses, 17 of which were found to play significant roles in the pathophysiology of ICH. We also report similarities and differences between two experimental ICH models and human postmortem ICH brain tissue. This study advances the understanding of the local and global responses of brain cells to ICH. It provides a valuable resource that can facilitate future research and aid the development of novel therapies for this devastating condition.

Increased maize chromosome number by engineered chromosome fission

Activation of synthetic centromeres on chromosome 4 in maize leads to its breakage and formation of trisomic fragments called neochromosomes. A limitation of neochromosomes is their low and unpredictable transmission rates due to trisomy. Here, we report that selecting for dicentric recombinants through male crosses uncovers stabilized chromosome 4 fission events, which split it into 4a-4b complementary chromosome pairs, where 4a carries a native centromere and 4b carries a synthetic one. The cells rapidly stabilized chromosome ends by de novo telomere formation, and the new centromeres spread among genes without altering their expression. When both 4a and 4b chromosomes were made homozygous, they segregated through meiosis indistinguishably from wild type and gave rise to healthy plants with normal seed set, indicating that the synthetic centromere was fully functional. This work leverages synthetic centromeres to engineer chromosome fission, raising the diploid chromosome number of maize from 20 to 22.

Resistance to BRAF inhibitors drives melanoma sensitivity to Chk1 inhibition

BRAF inhibitor-resistant melanomas (BRAFiR) acquire (epi)genetic and functional alterations that enable them to evade alternative treatments. Identifying these alterations is critical to advancing treatment strategies. Here, we explored the effect of Chk1 inhibition (Chk1i) on BRAFiR cells, revealing higher sensitivity compared to treatment-naïve cells both in vitro and in vivo. Using FUCCI-labeling and time-lapse microscopy, we show that S phase progression is required for Chk1i-induced cytotoxicity in BRAFiR cells, but not in treatment-naïve cells. Replication stress markers, including reduced BrdU incorporation and increased phospho-RPA and γH2AX, were observed mostly in BRAFiR cells with increased sensitivity to Chk1i. Untreated BRAFiR cells exhibited upregulated DNA replication genes, reduced progressing forks and increased origin firing, suggesting intrinsic replication changes. MAPK pathway reactivation in treatment-naïve cells mimicked BRAFiR traits, increasing sensitivity to Chk1i. These findings indicate that Chk1i exploits elevated replication stress specifically in BRAFiR cells, highlighting its therapeutic potential in overcoming MAPK inhibitor resistance in BRAF600-mutant melanoma.

Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq

Transcriptomes provide highly informative molecular phenotypes that, combined with gene perturbation, can connect genotype to phenotype. An ultimate goal is to perturb every gene and measure transcriptome changes, however, this is challenging, especially in whole animals. Here, we present 'Worm Perturb-Seq (WPS)', a method that provides high-resolution RNA-sequencing profiles for hundreds of replicate perturbations at a time in living animals. WPS introduces multiple experimental advances combining strengths of Caenhorhabditis elegans genetics and multiplexed RNA-sequencing with a novel analytical framework, EmpirDE. EmpirDE leverages the unique power of large transcriptomic datasets and improves statistical rigor by using gene-specific empirical null distributions to identify DEGs. We apply WPS to 103 nuclear hormone receptors (NHRs) and find a striking 'pairwise modularity' in which pairs of NHRs regulate shared target genes. We envision the advances of WPS to be useful not only for C. elegans, but broadly for other models, including human cells.

Beta 2 adrenergic receptor gene methylation activates innate lymphoid cells to drive hypertension in lymphocyte deficient hosts

AIMS

T cells contribute to hypertension; however, hypertension occurs in settings of T cell deficiency.

METHODS AND RESULTS

We studied two colonies of T/B cell-deficient RAG-1-/- mice with disparate responses to angiotensin II, being one protected from blood pressure increase and the other one responsive. This difference depends on the capability of hypertensive RAG-1-/- mice to expand natural killer and innate lymphoid cells (NK/ILCs) that produce pro-hypertensive cytokines. This process is regulated by the DNA methylation status of the β2 adrenergic receptor (β2-AdR). Angiotensin II caused blood pressure elevation in T and NK/ILCs-deficient mice only when either T or NK/ILCs cells were adoptively reconstituted. Additional studies showed NK cell expansion in humans that underwent B cell depletion, and this was augmented in those with hypertension.

CONCLUSIONS

These findings illustrate that the modulation of NK/ILCs activation by adrenergic signalling governs an escape mechanism in lymphocyte-deficient host, enabling the development of hypertension.

Inhibition of Talin2 dedifferentiates myofibroblasts and reverses lung and kidney fibrosis

Fibrosis is involved in 45% of deaths in the United States, and no treatment exists to reverse progression of the disease. To find novel targets for fibrosis therapeutics, we developed a model for the differentiation of monocytes to myofibroblasts that allowed us to screen for proteins involved in myofibroblast differentiation. Inhibition of a novel protein target generated by our model, talin2, reduces myofibroblast-specific morphology, α-smooth muscle actin content, and collagen I content and lowers the pro-fibrotic secretome of myofibroblasts. We find that knockdown of talin2 de-differentiates myofibroblasts and reverses bleomycin-induced lung fibrosis in mice, and further that Tln2-/- mice are resistant to bleomycin-induced lung fibrosis and resistant to unilateral ureteral obstruction-induced kidney fibrosis. Talin2 inhibition is thus a potential treatment for reversing lung and kidney fibroses.

Cross-species transcriptome-wide meta-analysis of anterior cruciate ligament rupture

BACKGROUND

The Anterior Cruciate Ligament (ACL) plays a critical role in maintaining the musculoskeletal stability of the knee. Its injury has been linked to an increased risk of developing osteoarthritis. This study aims to identify cross-species responses to ACL rupture providing insights on its molecular basis. We analyzed five publicly available transcriptomic datasets from Homo sapiens, Mus musculus, Canis lupus familiaris, and Oryctolagus cuniculus. Differential gene expression analysis was performed for each dataset, producing a genome-wide transcriptional signature of fold-change significance for individual genes. Stouffer's method was used to integrate the results, identifying genes significantly deregulated across all species. Additionally, gene-set enrichment analysis revealed pathways that were consistently upregulated or downregulated.

RESULTS

A positive correlation in expression was observed between human and the other three species (r2 = 0.177-0.305, p-value ≤ 2.7 × 10- 113), identifying 210 genes as the most consistently up- and down-regulated in response to ACL rupture (p-adjusted ≤ 1.27 × 10- 23). These genes are primarily involved in cellular mitosis, collagen pathways, and cartilage development. Furthermore, 60 pathways were found to be significantly up- or down-regulated across all species (p-adjusted ≤ 4.57 × 10- 4). Among these, the upregulation of inhibition of bone mineralization (p-adjusted ≤ 2.99 × 10- 6) aligns with previous findings on the reduction of subchondral bone mineral density following ACL rupture.

CONCLUSIONS

This study highlights that distinct species exhibit common molecular responses to ACL rupture, underscoring the value of mice, dogs, and rabbits as potential translational model organisms for ACL rupture research. Furthermore, the identified genes and pathways highlight the molecular mechanisms underlying ACL rupture.

Large-scale purifications reveal yeast and human stress granule cores are heterogeneous particles with complex transcriptomes and proteomes

Stress granules are a conserved response of eukaryotic cells to environmental insults. These cytoplasmic ribonucleoprotein condensates have hitherto been primarily studied by microscopy, which showed previously that they comprise dense ∼200 nm cores embedded in a diffuse shell. We have developed large-scale purifications of budding yeast and mammalian (HEK293T cell) stress granule cores that do not rely on immunoprecipitation of candidate protein constituents. These unbiased preparations reveal that stress granule cores are discrete particles with variable size (average, 135 and 225 nm for yeast and human, respectively) and shape. Proteomics and transcriptomics demonstrate complex composition. The results of hybridization chain reaction fluorescence in situ hybridization (FISH) analyses in HEK293T cells are consistent with stress granule cores having heterogeneous composition, i.e., each stress granule core particle contains only a limited number of mRNA species. Biochemical purification now opens the way to mechanistic analysis of the heterogeneity and complexity of stress granules.

Multiomic analysis of human kidney disease identifies a tractable inflammatory and pro-fibrotic tubular cell phenotype

Maladaptive proximal tubular (PT) epithelial cells have been implicated in progression of chronic kidney disease (CKD), however the complexity of epithelial cell states within the fibrotic niche remains incompletely understood. Hence, we integrated snRNA and ATAC-seq with high-plex single-cell molecular imaging to generate a spatially-revolved multiomic atlas of human kidney disease. We demonstrate that in injured kidneys, a subset of HAVCR1+VCAM1+ PT cells acquired an inflammatory phenotype, upregulating genes encoding chemokines, pro-fibrotic and senescence-associated proteins and adhesion molecules including ICAM1. Spatial transcriptomic and multiplex-immunofluorescence determined that specifically these VCAM1+ICAM1+ inflammatory PT cells localised to the fibrotic niche. Ligand-receptor analysis highlighted paracrine signaling from inflammatory PT cells mediating leucocyte recruitment and myofibroblast activation. Loss of HNF4α and activation of NF-κβ and AP-1 transcription factors epigenetically imprinted the inflammatory phenotype. Targeting inflammatory tubular cells by administering an AP-1 inhibitor or senolytic agent ameliorated inflammation and fibrosis in murine models of kidney injury, hence these cells may be a tractable target in CKD.

MePCE promotes homologous recombination through coordinating R-loop resolution at DNA double-stranded breaks

MePCE is a multifunctional protein that regulates the positive transcription elongation factor b (P-TEFb) partitioning between the nucleosol and chromatin. MePCE's role in sequestering P-TEFb in the nucleosol via the 7SK ribonuclear protein complex (RNPc) is clear, but its functions on chromatin remain obscure. We report that chromatin-associated MePCE interacts with R-loop processing and DNA repair factors. MePCE is recruited to DNA double-stranded breaks (DSBs), and MePCE depletion impairs DSB repair by homologous recombination (HR), decreases RAD51 loading, and enhances R-loop levels at AsiSI-induced DSBs at specific genomic locations. Besides decreasing specific R-loop processing factors and chromatin remodelers, MePCE depletion increases the interaction with R-loops of the other constitutive member of the 7SK RNPc, LARP7, which is degraded by BRCA1/BARD1 upon DSB. Overall, our results uncover dynamic regulation of the 7SK RNPc at DSBs during the DSB repair process and explain the recently observed synthetic lethality of MePCE and BRCA1 deficiency.

Identification of human pathways acting on nuclear non-coding RNAs using the Mirror forward genetic approach

Despite critical roles in diseases, human pathways acting on strictly nuclear non-coding RNAs have been refractory to forward genetics. To enable their forward genetic discovery, we developed a single-cell approach that "Mirrors" activities of nuclear pathways with cytoplasmic fluorescence. Application of Mirror to two nuclear pathways targeting MALAT1's 3' end, the pathway of its maturation and the other, the degradation pathway blocked by the triple-helical Element for Nuclear Expression (ENE), identified nearly all components of three complexes: Ribonuclease P and the RNA Exosome, including nuclear DIS3, EXOSC10, and C1D, as well as the Nuclear Exosome Targeting (NEXT) complex. Additionally, Mirror identified DEAD-box helicase DDX59 associated with the genetic disorder Oral-Facial-Digital syndrome (OFD), yet lacking known substrates or roles in nuclear RNA degradation. Knockout of DDX59 exhibits stabilization of the full-length MALAT1 with a stability-compromised ENE and increases levels of 3'-extended forms of small nuclear RNAs. It also exhibits extensive retention of minor introns, including in OFD-associated genes, suggesting a mechanism for DDX59 association with OFD. Mirror efficiently identifies pathways acting on strictly nuclear non-coding RNAs, including essential and indirectly-acting components, and as a result can uncover unexpected links to human disease.

Single cell analysis of diverse immune cell in pneumococcal meningitis

Streptococcus pneumoniae, a Gram-positive, human-specific commensal infectious pathogen, poses a significant global health threat, especially in children under five, often resulting in fatalities. The intricacies of the immune response in pneumococcal meningitis (PM) remain elusive, necessitating a meticulous examination of immune cell subsets at the single-cell resolution. In this study, we performed single-cell RNA sequencing of peripheral blood mononuclear cells from PM patients and healthy individuals. We found significant relative changes in the compositions of immune cell subset, with significant relative increases in platelets, neutrophils, and their precursors, alongside relative decreases in natural killer (NK) cells, T cell subtypes, and plasmacytoid dendritic cells in PM patients. Functional enrichment analyses revealed an up-regulation of neutrophils-related immune genes across multiple immune cell types, including platelets, myeloid cells and B cells, suggesting excessive neutrophil activation. However, a down-regulation of genes involved in antigen processing and presentation in myeloid cells and B cells in the PM group indicated a relative dampening of the adaptive immune response in the PM patients. This was further corroborated by the reduced proportions of plasmacytoid dendritic cells and T cells. Furthermore, genes involved in cytotoxity were down-regulated in both NK cells and T cells, alongside impaired T cell activation. Notably, distinct B cell subtypes, including unique naïve B cell clusters, demonstrated differentially expressed genes associated with both innate and adaptive immune responses. In conclusion, our study provides a comprehensive single-cell transcriptomic landscape of immune responses in PM. The identified cellular and molecular signatures offer potential targets for therapeutic intervention and provide a foundation for further investigation into the immunopathogenesis of pneumococcal meningitis.

Kaposi's sarcoma-associated herpesvirus induces mitochondrial fission to evade host immune responses and promote viral production

Mitochondrial dynamics are pivotal for host immune responses upon infection, yet how viruses manipulate these processes to impair host defence and enhance viral fitness remains unclear. Here we show that Kaposi's sarcoma-associated herpesvirus (KSHV), an oncogenic virus also known as human herpesvirus 8, encodes Bcl-2 (vBcl-2), which reprogrammes mitochondrial architecture. It binds with NM23-H2, a host nucleoside diphosphate (NDP) kinase, to stimulate GTP loading of the dynamin-related protein (DRP1) GTPase, which triggers mitochondrial fission, inhibits mitochondrial antiviral signalling protein (MAVS) aggregation and impairs interferon responses in cell lines. An NM23-H2-binding-defective vBcl-2 mutant fails to evoke fission, leading to defective virion assembly due to activated MAVS-IFN signalling. Notably, we identify two key interferon-stimulated genes restricting vBcl-2-dependent virion morphogenesis. Using a high-throughput drug screening, we discover an inhibitor targeting vBcl-2-NM23-H2 interaction that blocks virion production in vitro. Our study identifies a mechanism in which KSHV manipulates mitochondrial dynamics to allow for virus assembly and shows that targeting the virus-mitochondria interface represents a potential therapeutic strategy.

METTL14 promotes intimal hyperplasia through m6A-mediated control of vascular smooth muscle dedifferentiation genes

Vascular smooth muscle cells (VSMCs) possess significant phenotypic plasticity, shifting between a contractile phenotype and a synthetic state for vascular repair/remodeling. Dysregulated VSMC transformation, marked by excessive proliferation and migration, primarily drives intimal hyperplasia. N6-methyladenosine (m6A), the most prevalent RNA modification in eukaryotes, plays a critical role in gene expression regulation; however, its impact on VSMC plasticity is not fully understood. We investigated the changes in m6A modification and its regulatory factors during VSMC phenotypic shifts and their influence on intimal hyperplasia. We demonstrate that METTL14, crucial for m6A deposition, significantly promoted VSMC dedifferentiation. METTL14 expression, initially negligible, was elevated in synthetic VSMC cultures, postinjury neointimal VSMCs, and human restenotic arteries. Reducing Mettl14 levels in mouse primary VSMCs decreased prosynthetic genes, suppressing their proliferation and migration. m6A-RIP-seq profiling showed key VSMC gene networks undergo altered m6A regulation in Mettl14-deficient cells. Mettl14 enhanced Klf4 and Serpine1 expression through increased m6A deposition. Local Mettl14 knockdown significantly curbed neointimal formation after arterial injury, and reducing Mettl14 in hyperplastic arteries halted further neointimal development. We show that Mettl14 is a pivotal regulator of VSMC dedifferentiation, influencing Klf4- and Serpine1-mediated phenotypic conversion. Inhibiting METTL14 is a viable strategy for preventing restenosis and halting restenotic occlusions.

Dose-dependent CHCHD10 dysregulation dictates motor neuron disease severity and alters creatine metabolism

Dominant defects in CHCHD10, a mitochondrial intermembrane space protein, lead to a range of neurological and muscle disease phenotypes including amyotrophic lateral sclerosis. Many patients present with spinal muscular atrophy Jokela type (SMAJ), which is caused by heterozygous p.G66V variant. While most disease variants lead to aggregation of CHCHD10 and activation of proteotoxic stress responses, the pathogenic mechanisms of the p.G66V variant are less clear. Here we report the first homozygous CHCHD10 patient, and show that the variant dosage dictates the severity of the motor neuron disease in SMAJ. We demonstrate that the amount of the mutant CHCHD10 is reduced, but the disease mechanism of p.G66V is not full haploinsufficiency as residual mutant CHCHD10 protein is present even in a homozygous state. Novel knock-in mouse model recapitulates the dose-dependent reduction of mutant CHCHD10 protein and the slow disease progression of SMAJ. With metabolome analysis of patients' primary fibroblasts and patient-specific motor neurons, we show that CHCHD10 p.G66V dysregulates energy metabolism, leading to altered redox balance and energy buffering by creatine metabolism.

Characterization of RNA editing gene APOBEC3C as a candidate tumor suppressor in prostate cancer

The human genome encodes 19 adenosine and cytidine deaminase genes, classified as A-to-I versus C-to-U editors. A-to-I editors have been widely identified as a promising therapeutic target in various cancers. Conversely, the investigation into C-to-U editors is relatively limited. This study evaluated RNA-editing genes in prostate cancer (PCa). Notably, the APOBEC3 genes are clustered in terms of their chromosomal locations, and their transcriptional changes exhibit significant positive correlations in both primary PCa and castration-resistant prostate cancer (CRPC). One member of this family, APOBEC3C, is demonstrated here as an androgen receptor (AR)-repressed gene. Consistently, APOBEC3 loci are epigenetically inhibited in PCa progression, with APOBEC3C level lower in PSA-high patients. APOBEC3C-low PCa cohorts exhibit increased resistance to Abiraterone and Enzalutamide. Clinicopathological profiling further confirmed APOBEC3C downregulation along PCa progression to advanced phases (grade IV/V, stage III-IV, and pathological stage T3-4), underscoring its prognostic value. Additionally, APOBEC3C expression inversely correlates with PCa relapse and mortality, and low APOBEC3C levels are linked to unfavorable survival. Notably, integrated analyses identified APOBEC3C as the sole RNA-editing gene with significance in both differential expression and PCa prognosis, and APOBEC3C had the best diagnostic performance among 19 genes. Our efforts provide a foundation for further RNA editors research in PCa diagnosis and therapy, and grant APOBEC3C as a candidate tumor suppressor.

Improving genetic diagnostic yield in familial and sporadic cerebral cavernous malformations: detection of copy number and deep Intronic variants

Cerebral cavernous malformations (CCMs) are intracranial vascular lesions associated with risk of haemorrhages and seizures. While the majority are sporadic and often associated with somatic variants in PIK3CA and MAP3K3, around 20% are familial with germline variants in one of three CCM genes-KRIT1/CCM1, CCM2 and PDCD10/CCM3. We performed comprehensive phenotyping and genetic analysis of nine multiplex families and ten sporadic individuals with CCM. In the familial cases, initial standard analyses had a low yield, we therefore searched for small copy number changes and deep intronic variants. Subsequently, pathogenic germline variants in KRIT1/CCM1 or CCM2 were identified in all 9 multiplex families. Single or multiple exon deletions or splice site variants in KRIT1/CCM1 were found in 3/9 families. Where cavernous malformation tissue was available, second hit somatic PIK3CA variants were identified in 4/7 individuals. These 4 individuals were from separate families with germline KRIT1/CCM1 variants. In 8/10 sporadic cases, we detected recurrent pathogenic somatic PIK3CA, MAP3K3 or CCM2 variants. All familial cases had multiple CCMs, whereas the sporadic cases had a single lesion only, which was in the temporal lobe in 9/10 individuals. Our comprehensive approach interrogating deep intronic variants combined with detection of small copy number variants warrants implementation in standard clinical genetic testing pipelines to increase diagnostic yield. We also build on the established second hit germline and somatic variant mechanism in some CCM lesions. Genetic diagnosis has clinical implications such as reproductive counselling and provides potential eligibility for precision medicine therapies to treat rapidly growing CCMs.

The patient-specific mouse model with Foxg1 frameshift mutation provides insights into the pathophysiology of FOXG1 syndrome

Single allelic mutations in the FOXG1 gene lead to FOXG1 syndrome (FS). To understand the pathophysiology of FS, which vary depending on FOXG1 mutation types, patient-specific animal models are critical. Here, we report a patient-specific Q84Pfs heterozygous (Q84Pfs-Het) mouse model, which recapitulates various FS phenotypes across cellular, brain structural, and behavioral levels. Q84Pfs-Het cortex shows dysregulations of genes controlling cell proliferation, neuronal projection and migration, synaptic assembly, and synaptic vesicle transport. The Q84Pfs allele produces the N-terminal fragment of FOXG1 (Q84Pfs protein) in Q84Pfs-Het mouse brains, which forms intracellular speckles, interacts with FOXG1 full-length protein, and triggers the sequestration of FOXG1 to distinct subcellular domains. Q84Pfs protein promotes the radial glial cell identity and suppresses neuronal migration in the cortex. Our study uncovers the role of the FOXG1 fragment from FS-causing FOXG1 variants and identifies the genes involved in FS-like cellular and behavioral phenotypes, providing insights into the pathophysiology of FS.

Type 2 cytokines act on enteric sensory neurons to regulate neuropeptide-driven host defense

Enteric nervous system (ENS)-derived neuropeptides modulate immune cell function, yet our understanding of how inflammatory cues directly influence enteric neuron responses during infection is considerably lacking. Here, we characterized a primary enteric sensory neuron (PSN) subset producing the neuropeptides neuromedin U (NMU) and calcitonin gene-related peptide β (CGRPβ) and coexpressing receptors for the type 2 cytokines interleukin-4 (IL-4) and IL-13. Type 2 cytokines amplified NMU and CGRPβ expression in PSNs, in vitro and in vivo, which was abrogated by PSN-specific Il13ra1 deletion. Deletion of Il13ra1 in PSNs impaired host defense to the gastrointestinal helminth Heligmosomoides polygyrus and blunted muscularis immune responses. Co-administration of NMU23 and CGRPβ rescued helminth clearance deficits and restored anti-helminth immunity, highlighting the essential bi-directional neuro-immune crosstalk regulating intestinal type 2 inflammation.

Nuclear m6A modification regulates satellite transcription and chromosome segregation

The precise location and functions of N6-methyladenosine (m6A) modification on mammalian nuclear noncoding RNA remain largely unknown. Here we developed nuclear-m6A-label-seq to directly map human and mouse cell nuclear RNA m6A methylome at single-base resolution. Specifically, m6A modifications have been identified on abundant human γ satellite DNA II (GSATII) RNA transcripts, a type of repeat RNA, transcribed from SST1-TAR1-GSATII satellite arrays in the pericentromeric region of chromosome 9. GSATII RNA m6A positively regulates the transcription of GSATII-located satellite arrays as well as trans-associated peri/centromeric satellites, typically chromosome 3 centromeric higher-order repeat α satellite. Dysregulation of this circuit renders a phenotype of abnormal chromosome segregation. Mechanistic study reveals that YTHDC1 reads GSATII RNA m6A marks and recruits bromodomain protein 4 (BRD4) to promote transcriptions of the associated satellites via an m6A-YTHDC1-BRD4-H3K27ac axis. These results uncover a mechanism governing the transcription of cis- and trans-associated pericentromeric and centromeric satellites via cross-talk between epitranscriptomic and epigenomic marks.

Single microorganism RNA sequencing of microbiomes using smRandom-Seq

Bacteria colonize nearly every part of the human body and various environments, displaying remarkable diversity. Traditional population-level transcriptomics measurements provide only average population behaviors, often overlooking the heterogeneity within bacterial communities. To address this limitation, we have developed a droplet-based, high-throughput single-microorganism RNA sequencing method (smRandom-seq) that offers highly species specific and sensitive gene detection. Here we detail procedures for microbial sample preprocessing, in situ preindexed cDNA synthesis, in situ poly(dA) tailing, droplet barcoding, ribosomal RNA depletion and library preparation. The main smRandom-seq workflow, including sample processing, in situ reactions and library construction, takes ~2 days. This method features enhanced RNA coverage, reduced doublet rates and minimized ribosomal RNA contamination, thus enabling in-depth analysis of microbial heterogeneity. smRandom-seq is compatible with microorganisms from both laboratory cultures and complex microbial community samples, making it well suited for constructing single-microorganism transcriptomic atlases of bacterial strains and diverse microbial communities. This Protocol requires experience in molecular biology and RNA sequencing techniques, and it holds promising potential for researchers investigating bacterial resistance, microbiome heterogeneity and host-microorganism interactions.

Protocol for high-quality RNA sequencing, cell surface protein analysis, and genotyping in single cells using TARGET-seq

Studying the consequences of somatic mutations in pre-malignant and cancerous tissues is challenging due to noise in single-cell transcriptome data and difficulty in identifying the clonal identity of single cells. We optimized TARGET-seq to develop TARGET-seq+, which combines RNA sequencing (RNA-seq), the analysis of cell surface protein expression, and genotyping in single cells with improved sensitivity. We describe the steps for cell isolation, the preparation of single-cell RNA-seq (scRNA-seq) and genotyping libraries, and sequencing. We also provide guidance on the analysis of single-cell genotyping, transcriptome pre-processing, and data integration. For complete details on the use and execution of this protocol, please refer to Jakobsen et al.1.

GLP-1R/GCGR dual agonism dissipates hepatic steatosis to restore insulin sensitivity and rescue pancreatic β-cell function in obese male mice

An early driver of Type 2 diabetes mellitus (T2D) is ectopic fat accumulation, especially in the liver, that impairs insulin sensitivity. In T2D, GLP-1R/GCGR dual-agonists reduce glycaemia, body weight and hepatic steatosis. Here, we utilize cotadutide, a well characterized GLP-1R/GCGR dual-agonist, and demonstrate improvement of insulin sensitivity during hyperinsulinemic euglycemic clamp following sub-chronic dosing in male, diet-induced obese (DIO) mice. Phosphoproteomic analyses of insulin stimulated liver from cotadutide-treated mice identifies previously unknown and known phosphorylation sites on key insulin signaling proteins associated with improved insulin sensitivity. Cotadutide or GCGR mono-agonist treatment also increases brown adipose tissue (BAT) insulin-stimulated glucose uptake, while GLP-1R mono-agonist shows a weak effect. BAT from cotadutide-treated mice have induction of UCP-1 protein, increased mitochondrial area and a transcriptomic profile of increased fat oxidation and mitochondrial activity. Finally, the cotadutide-induced improvement in insulin sensitivity is associated with reduction of insulin secretion from isolated pancreatic islets indicating reduced insulin secretory demand. Here we show, GLP-1R/GCGR dual agonism provides multimodal efficacy to decrease hepatic steatosis and consequently improve insulin sensitivity, in concert with recovery of endogenous β-cell function and reduced insulin demand. This substantiates GLP-1R/GCGR dual-agonism as a potentially effective T2D treatment.

Gonadotrophs have a dual origin, with most derived from early postnatal pituitary stem cells

Gonadotrophs are the essential pituitary endocrine cells for reproduction. They produce both luteinizing (LH) and follicle-stimulating (FSH) hormones that act on the gonads to promote germ cell maturation and steroidogenesis. Their secretion is controlled by the hypothalamic gonadotrophin-releasing hormone (GnRH), and gonadal steroid feedback. Gonadotrophs first appear in the embryonic pituitary, along with other endocrine cell types, and all expand after birth. While gonadotrophs may display heterogeneity in their response to GnRH, they appear, at least transcriptionally, as a homogenous population. The pituitary also contains a population of stem cells (SCs), whose contribution to postnatal growth is unclear, in part because endocrine cells maintain the ability to proliferate. Here we show an unsuspected dual origin of the murine adult gonadotroph population, with most gonadotrophs originating from postnatal pituitary stem cells starting early postnatally and up to puberty, while embryonic gonadotrophs are maintained. We further demonstrate that postnatal gonadotroph differentiation happens independently of gonadal signals and is not affected by impairment of GnRH signalling. The division of gonadotrophs based on separate origins has implications for our understanding of the establishment and regulation of reproductive functions, both in health and in disease.

Seeded aggregation of TDP-43 induces its loss of function and reveals early pathological signatures

Neurodegeneration in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) results from both gain of toxicity and loss of normal function of the RNA-binding protein TDP-43, but their mechanistic connection remains unclear. Increasing evidence suggests that TDP-43 aggregates act as self-templating seeds, propagating pathology through the central nervous system via a prion-like cascade. We developed a robust TDP-43-seeding platform for quantitative assessment of TDP-43 aggregate uptake, cell-to-cell spreading, and loss of function within living cells, while they progress toward pathology. We show that both patient-derived and recombinant TDP-43 pathological aggregates were abundantly internalized by human neuron-like cells, efficiently recruited endogenous TDP-43, and formed cytoplasmic inclusions reminiscent of ALS/FTD pathology. Combining a fluorescent reporter of TDP-43 function with RNA sequencing and proteomics, we demonstrated aberrant cryptic splicing and a loss-of-function profile resulting from TDP-43-templated aggregation. Our data highlight known and novel pathological signatures in the context of seed-induced TDP-43 loss of function.

MicroRNA mechanisms instructing Purkinje cell specification

MicroRNAs (miRNAs) are critical for brain development; however, if, when, and how miRNAs drive neuronal subtype specification remains poorly understood. To address this, we engineered technologies with vastly improved spatiotemporal resolution that allow the dissection of cell-type-specific miRNA-target networks. Fast and reversible miRNA loss of function showed that miRNAs are necessary for Purkinje cell (PC) differentiation, which previously appeared to be miRNA independent, and identified distinct critical miRNA windows for dendritogenesis and climbing fiber synaptogenesis, structural features defining PC identity. Using new mouse models that enable miRNA-target network mapping in rare cell types, we uncovered PC-specific post-transcriptional programs. Manipulation of these programs revealed that the PC-enriched miR-206 and targets Shank3, Prag1, En2, and Vash1, which are uniquely repressed in PCs, are critical regulators of PC-specific dendritogenesis and synaptogenesis, with miR-206 knockdown and target overexpression partially phenocopying miRNA loss of function. Our results suggest that gene expression regulation by miRNAs, beyond transcription, is critical for neuronal subtype specification.

Joint analysis of chromatin accessibility and gene expression in the same single cells reveals cancer-specific regulatory programs

Biological analyses conducted at the single-cell scale have revealed profound impacts of heterogeneity and plasticity of chromatin states and gene expression on physiology and cancer. Here, we developed Parallel-seq, a technology for simultaneously measuring chromatin accessibility and gene expression in the same single cells. By combining combinatorial cell indexing and droplet overloading, Parallel-seq generates high-quality data in an ultra-high-throughput fashion and at a cost two orders of magnitude lower than alternative technologies (10× Multiome and ISSAAC-seq). We applied Parallel-seq to 40 lung tumor and tumor-adjacent clinical samples and obtained over 200,000 high-quality joint scATAC-and-scRNA profiles. Leveraging this large dataset, we characterized copy-number variations (CNVs) and extrachromosomal circular DNA (eccDNA) heterogeneity in tumor cells, predicted hundreds of thousands of cell-type-specific regulatory events, and identified enhancer mutations affecting tumor progression. Our analyses highlight Parallel-seq's power in investigating epigenetic and genetic factors driving cancer development at the cell-type-specific level and its utility for revealing vulnerable therapeutic targets.

Multi-omics analysis of SFTS virus infection in Rhipicephalus microplus cells reveals antiviral tick factors

The increasing prevalence of tick-borne arboviral infections worldwide necessitates advanced control strategies, particularly those targeting vectors, to mitigate the disease burden. However, the cellular interactions between arboviruses and ticks, especially for negative-strand RNA viruses, remain largely unexplored. Here, we employ a proteomics informed by transcriptomics approach to elucidate the cellular response of the Rhipicephalus microplus-derived BME/CTVM6 cell line to severe fever with thrombocytopenia syndrome virus (SFTSV) infection. We generate the de novo transcriptomes and proteomes of SFTSV- and mock-infected tick cells, identifying key host responses and regulatory pathways. Additionally, interactome analysis of the viral nucleoprotein (N) integrated host responses with viral replication and dsRNA-mediated gene silencing screen reveals two anti-SFTSV effectors: the N interacting RNA helicases DHX9 and UPF1. Collectively, our results provide insights into the antiviral responses of R. microplus vector cells and highlight critical SFTSV restriction factors, while enriching transcriptomic and proteomic resources for future research.

A homozygous single-nucleotide variant in TNNT1 causes abnormal troponin T isoform expression in a patient with severe nemaline myopathy: A case report

BACKGROUND

Slow skeletal troponin T (ssTnT, TNNT1) is the tropomyosin-binding subunit of the troponin complex in the slow-twitch fibers of skeletal muscle. Exon 5 of TNNT1 is alternatively spliced, and retention of the 3' region of intron 11 (exon 12') has also been described. Variants in TNNT1 are known to cause nemaline myopathy (NM).

OBJECTIVE

To identify and further investigate the disease-causing variant in a patient with lethal NM.

METHODS

The genetic analyses included a gene panel, Sanger sequencing, whole-exome sequencing, and targeted array-CGH. Muscle biopsy was analyzed using routine histopathological methods. The alternative splicing of TNNT1 exon 12 in patient muscle was quantified from RNA sequencing data, and the protein expression was confirmed by western blot. Expression of ssTnT in patient muscle was studied by immunohistology.

RESULTS

The patient presented with arthrogryposis, stiffness, respiratory insufficiency, and minimal spontaneous movements. Histopathology showed hypotrophy and predominance of type II fibers, perimysial connective tissue accumulation, and nemaline bodies. The patient was homozygous for the TNNT1 missense variant (NM_003283.6:c.653C > G, p.(Pro218Arg), NM_ 001126132.3:c.612-7C > G), predicted to disrupt splicing. RNA-seq revealed inclusion of exon 12' in 49.85% of transcripts, whereas in controls exon 12' was not expressed. Exon 12' expression on the protein level was confirmed by western blot. Immunohistology showed strong ssTnT expression in remaining type I fibers, and low expression in type IIA fibers.

CONCLUSIONS

The c.653C > G variant was shown to alter TNNT1 splicing. The results suggest a novel pathogenetic mechanism involving abnormal expression of a troponin T isoform.

APOBEC affects tumor evolution and age at onset of lung cancer in smokers

Most solid tumors harbor somatic mutations attributed to off-target activities of APOBEC3A (A3A) and/or APOBEC3B (A3B). However, how APOBEC3A/B enzymes affect tumor evolution in the presence of exogenous mutagenic processes is largely unknown. Here, multi-omics profiling of 309 lung cancers from smokers identifies two subtypes defined by low (LAS) and high (HAS) APOBEC mutagenesis. LAS are enriched for A3B-like mutagenesis and KRAS mutations; HAS for A3A-like mutagenesis and TP53 mutations. Compared to LAS, HAS have older age at onset and high proportions of newly generated progenitor-like cells likely due to the combined tobacco smoking- and APOBEC3A-associated DNA damage and apoptosis. Consistently, HAS exhibit high expression of pulmonary healing signaling pathway, stemness markers, distal cell-of-origin, more neoantigens, slower clonal expansion, but no smoking-associated genomic/epigenomic changes. With validation in 184 lung tumor samples, these findings show how heterogeneity in mutational burden across co-occurring mutational processes and cell types contributes to tumor development.

Exploring effector candidates in Rhynchosporium commune: insights into their expression dynamics during barley infection

Rhynchosporium commune is a fungal pathogen responsible for causing scald disease in barley, leading to significant yield losses and reduced grain quality in susceptible cultivars. Effector proteins secreted by R. commune play crucial roles in manipulating host defenses and facilitating infection. Hence, this study aimed to identify and characterize effector candidates (ECs) in R. commune using a comprehensive bioinformatics approach combined with experimental validation. Initially, a dataset of 12,211 genes from the R. commune strain UK7 genome was analyzed to identify potential ECs, resulting in the selection of 48 candidate proteins. These candidates were further validated using RNA-Seq analysis, which confirmed significant expression of 27 ECs during infection. Our analysis re-identified key effectors, including CZT06923 and CZT13833, with 100% identity to NIP3 and NIP2, respectively, in R. commune. Novel ECs, such as CZT07600, CZT13755, and CZT13375, were identified with lower identity to NIP2, suggesting potential variants. Additionally, structural analysis revealed that CZT07873 EC indicates significant structural similarity to known fungal effector. qRT-PCR validation confirmed the differential expression of CZS93219 and CZT13755, with peak expression at 9 and 12 dpi, respectively. This comprehensive approach enhances our understanding of R. commune's pathogenic mechanisms and provides insights into potential targets for developing disease management strategies in barley cultivation.

Role of LEAFLESS, an AP2/ERF family transcription factor, in the regulation of trichome specialized metabolism

Acylsugars, specialized metabolites produced by trichomes of many solanaceous species, provide protection against biotic and abiotic stresses. Many acylsugar metabolic enzymes have been identified; however, regulatory factors remain unknown. Our multidisciplinary approaches identified LEAFLESS (APETALA 2/ ETHYLENE RESPONSE FACTOR (AP2/ERF) family member) as a positive regulator of acylsugar biosynthesis. Virus-induced gene silencing (VIGS) of LEAFLESS in Solanum pennellii (SpLFS/Sopen05g008450) revealed its distinct roles in two related but separate processes: acylsugar biosynthesis and trichome development. Most acylsugar (and several flavonoid) metabolic genes were downregulated in SpLFS-silenced plants and showed strong co-expression with SpLFS. Phylogenetic and additional data analyses indicated trichome-enriched expression of SpLFS orthologs in other acylsugar-producing solanaceous species, and VIGS of SpLFS orthologs in Nicotiana benthamiana reduced acylsugar production. Transcriptional reporter showed expression of SpLFS in type I/IV trichome tip cells, the site of acylsugar biosynthesis. Electrophoretic mobility shift assays indicated that SpLFS directly binds to promoters of several acylsugar (and flavonoid) metabolic genes. Additionally, data mining suggested remarkable spatiotemporal functional diversity: from coordinating leaf initiation at incipient primordia (previously reported for the S. lycopersicum ortholog SlLFS/Solyc05g013540) to regulating trichome specialized metabolism (acylsugar and flavonoid). Our work highlights a critical role of LEAFLESS in trichome specialized metabolism, paving the way to disentangle the acylsugar regulatory network.

PUS10-induced tRNA fragmentation impacts retrotransposon-driven inflammation

Pseudouridine synthases (PUSs) catalyze the isomerization of uridine (U)-to-pseudouridine (Ψ) and have emerging roles in development and disease. How PUSs adapt gene expression under stress remains mostly unexplored. We identify an unconventional role for the Ψ "writer" PUS10 impacting intracellular innate immunity. Using Pus10 knockout mice, we uncover cell-intrinsic upregulation of interferon (IFN) signaling, conferring resistance to inflammation in vivo. Pus10 loss alters tRNA-derived small RNAs (tdRs) abundance, perturbing translation and endogenous retroelements expression. These alterations promote proinflammatory RNA-DNA hybrids accumulation, potentially activating cyclic GMP-AMP synthase (cGAS)-stimulator of interferon gene (STING). Supplementation with selected tdR pools partly rescues these effects through interactions with RNA processing factors that modulate immune responses, revealing a regulatory circuit that counteracts cell-intrinsic inflammation. By extension, we define a PUS10-specific molecular fingerprint linking its dysregulation to human autoimmune disorders, including inflammatory bowel diseases. Collectively, these findings establish PUS10 as a viral mimicry modulator, with broad implications for innate immune homeostasis and autoimmunity.

A multi-kingdom genetic barcoding system for precise clone isolation

Cell-tagging strategies with DNA barcodes have enabled the analysis of clone size dynamics and clone-restricted transcriptomic landscapes in heterogeneous populations. However, isolating a target clone that displays a specific phenotype from a complex population remains challenging. Here we present a multi-kingdom genetic barcoding system, CloneSelect, which enables a target cell clone to be triggered to express a reporter gene for isolation through barcode-specific CRISPR base editing. In CloneSelect, cells are first stably tagged with DNA barcodes and propagated so that their subpopulation can be subjected to a given experiment. A clone that shows a phenotype or genotype of interest at a given time can then be isolated from the initial or subsequent cell pools stored during the experiment using CRISPR base editing. CloneSelect is scalable and compatible with single-cell RNA sequencing. We demonstrate the versatility of CloneSelect in human embryonic kidney 293T cells, mouse embryonic stem cells, human pluripotent stem cells, yeast cells and bacterial cells.

Identification of a Reduced Rate Combination of a Plant Growth Inhibitor with a Plant Defense Inducer for the Management of the Shoot Blight Phase of Fire Blight

The secondary shoot blight phase of fire blight is a critical component of disease epidemics in apples, pears, and other Rosaceae family plants with infection occurring at the tips of vigorously growing branches. Shoot blight infections are exacerbated in modern high-density apple plantings, where growers emphasize maximizing tree growth to recapture planting costs and increase yields of high-quality fruit. The overarching goal of this study was to develop new strategies for shoot blight management that do not impact the growth and yield of young apple trees. 'Gala' apple trees of various ages were inoculated with the fire blight pathogen Erwinia amylovora. Being treated with a combination of reduced rate mixtures of prohexadione calcium (ProCa; 6-12× rate reduction) with acibenzolar-S-methyl (ASM; 2× reduction) resulted in a significant decrease in shoot blight incidence and severity without significant impacts on branch growth. The systemic spread of E. amylovora was significantly reduced in trees sprayed with these lower-rate mixtures. Comparable rates of either treatment alone were not as effective in reducing lesion length. A transcriptomic analysis revealed a synergistic effect in which the expression of marker genes associated with systemic acquired resistance was higher in apple trees sprayed with the low-rate mixture of ProCa + ASM than with either compound alone. We conclude that the combination of ProCa + ASM at reduced rates is an effective treatment for the shoot blight phase of fire blight without impacting horticultural practices associated with high-density apple production.

BCG Vaccination Reprograms the Function of M-MDSCs and Aggravates Necrotizing Enterocolitis in Neonates

Bacillus Calmette-Guérin (BCG), a live-attenuated vaccine primarily used against tuberculosis (TB), also provides protection against a broad array of antigens or heterologous antigens through the induction of trained immunity (TI). While BCG is generally safe for full-term infants, its application in preterm infants is contentious due to their immature immune systems and heightened susceptibility to adverse effects. Preterm infants, particularly those with low birth weight, are at an elevated risk of severe complications, such as necrotizing enterocolitis (NEC), a life-threatening inflammatory condition of the intestines. NEC is characterised by dysregulated immune responses to microbial colonisation, with myeloid-derived suppressor cells (MDSCs) playing a crucial role in maintaining immune tolerance during early life. This study reveals that BCG vaccination significantly exacerbates NEC severity (p = 0.0048) by enhancing glycolysis and upregulating mTOR-HIF1α signalling in neonatal monocytic MDSCs (M-MDSCs), thereby impairing their immunosuppressive function. Pharmacological or genetic inhibition of mTOR-HIF1α signalling or glycolysis pathways restored M-MDSC function and mitigated NEC severity. These findings complement our previous work on BCG's effects on polymorphonuclear (PMN)-MDSCs and highlight the dual role of BCG: while it provides protective benefits in certain contexts, it may also increase NEC risk in preterm infants by disrupting MDSC-mediated immune tolerance. This study offers critical insights into the mechanisms underlying BCG's off-target effects and underscores the necessity of tailored vaccination strategies for preterm infants to minimise potential risks.

Identification of differentially expressed genes and pathways in the post-ovulatory ampulla of cyclic pigs through a transcriptomics approach

BACKGROUND

Information on global transcriptomic changes in the porcine ampulla after ovulation is crucial for understanding of oviductal physiology at the molecular level. The objective of the present study was to investigate the differentially expressed genes (DEGs) and signalling pathways regulating the functionality of ampulla in pigs post-ovulation.

METHODS AND RESULTS

The RNA-sequencing of the post-ovulatory ampulla (POA) and early luteal ampulla (ELA) tissues was conducted using Illumina NextSeq2000. The R package NOISeq was used to obtain significantly differentially expressed genes (DEGs) with the probability of differential expression (1-FDR) value ≥ 0.95 and log2 fold change (log2FC) ≥ 1, which revealed 817 DEGs (657 up- and 160 down-regulated) in the POA vs. ELA group comparison. These DEGs were functionally annotated with various gene ontology terms like sterol biosynthetic process, growth, cell migration, and Reactome pathways like signal transduction, metabolism, and cell cycle, indicating key role of these molecular events in POA. The WNT, TNFR2 non-canonical NF-kB, and hedgehog signalling pathways along with the activation of the immune system process, were enriched in the POA vs. ELA group, which indicates their role in cell-cell interactions and cell fate determination in remodelling the oviductal microenvironment during transition from estrogen to progesterone domination. The highly connected upregulated hub genes ESR1, RAD51, YARS1, TYMS and CDK2 can be regarded as key regulatory factors in synchronizing the changes in POA at the molecular level in the oviduct.

CONCLUSION

The present study revealed several DEGs, signalling pathways and novel modulatory factors associated with the ampullary physiology during early embryonic development in the POA, which may influence fertility and litter size in pigs.

Tracking the genome-wide occupancy of Arabidopsis LEAFY COTYLEDON1 in endosperm development

Endosperm development is crucial for embryo growth and seed maturation. LEAFY COTYLEDON1 (LEC1), expressed in both endosperm and embryo, serves as a key regulator of seed development, orchestrating processes such as embryogenesis and seed maturation. LEC1 expression in the endosperm is detectable within a day after fertilization, yet its specific regulatory networks and developmental functions in this tissue remain unclear. To address this, we employed a modified INTACT system to isolate endosperm nuclei and performed ChIP-seq to map the genome-wide binding profile of LEC1 in developing endosperm. Integrating ChIP-seq with transcriptomic analyses, we uncover a critical role for LEC1 in regulating diverse biological pathways. Differential gene expression analysis in the endosperms of lec1 mutant and wild type shows substantial changes, particularly in genes involved in secondary cell wall biogenesis, photosynthesis, and lipid metabolism. Notably, LEC1's regulatory networks in the endosperm shift significantly after cellularization, with distinct genes being activated in the cellular and degeneration stages. The absence of LEC1 causes significant alterations in endosperm metabolism, particularly affecting storage lipid fatty acid composition. These findings provide insights into the essential role of LEC1 in endosperm development and its broader impact on seed formation.

Molecular Evidence Supporting MEK Inhibitor Therapy in NF1 Pseudarthrosis

BACKGROUND

Neurofibromatosis type 1 (NF1) is a genetic condition predisposing children to fracture pseudarthroses. MEK inhibitors are U.S. Food and Drug Administration-approved or are under study for the treatment of malignant pathologies associated with NF1. However, their potential to treat pseudarthrosis is largely unknown.

METHODS

Primary cells cultured from control bone or fracture pseudarthroses from children with NF1 were treated with vehicle or with the MEK inhibitors trametinib or selumetinib. Gene expression was evaluated with use of transcriptome sequencing (RNAseq), and the activation of the downstream signaling pathway was evaluated with use of western blotting. Results were replicated in an independent cohort of patient fracture pseudarthrosis-derived primary cells.

RESULTS

Pseudarthrosis samples were reproducibly associated with the reduced expression of gene signatures implicated in osteoblast differentiation, skeletal development, and the formation of the extracellular matrix. The expression of these gene signatures was significantly rescued following treatment with MEK inhibitors and concomitant reduced MEK/ERK (MAPK) pathway activation.

CONCLUSIONS

Our study identified molecular signatures associated with fracture pseudarthrosis that were rescued with MEK inhibitor treatment.

CLINICAL RELEVANCE

MEK inhibitors may promote the healing of fracture pseudarthroses in children with NF1.