STAR: ultrafast universal RNA-seq aligner

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.

CREBBP inactivation sensitizes B cell acute lymphoblastic leukemia to ferroptotic cell death upon BCL2 inhibition

B-cell acute lymphoblastic leukemia (B-ALL) is a leading cause of death in childhood and outcomes in adults remain dismal. There is therefore an urgent clinical need for therapies that target the highest risk cases. Mutations in the histone acetyltransferase CREBBP confer high-risk and increased chemoresistance in ALL. Performing a targeted drug-screen in isogenic human cell lines, we identify a number of small molecules that specifically target CREBBP-mutated B-ALL, the most potent being the BCL2-inhibitor Venetoclax. Of note, this acts through a non-canonical mechanism resulting in ferroptotic rather than apoptotic cell death. CREBBP-mutated cell lines show differences in cell-cycle, metabolism, lipid composition and response to oxidative stress, predisposing them to ferroptosis, which are further dysregulated upon acquisition of Venetoclax resistance. Lastly, small-molecule inhibition of CREBBP pharmacocopies CREBBP-mutation, sensitizing B-ALL cells, regardless of genotype, to Venetoclax-induced ferroptosis in-vitro and in-vivo, providing a promising drug combination for broader clinical translation in B-ALL.

Morphotype-Specific Antifungal Defense in Cacopsylla chinensis Arises from Metabolic and Immune Network Restructuring

Pear psylla (Cacopsylla chinensis), a major pear tree pest widely distributed in China, is increasingly affecting the productivity of orchards. This species exhibits seasonal polyphenism with two distinct forms, namely, a summer form and a winter form. Through topically applying Beauveria bassiana conidial suspensions to the abdominal cuticle of C. chinensis, we demonstrated that the entomopathogenic fungus B. bassiana exhibits significant yet phenotypically divergent virulence against these two forms. Using PacBio SMRT sequencing and Illumina RNA-seq, we analyzed transcriptomic changes post-infection, revealing form-specific immune responses, with 18,232 and 5027 differentially expressed genes identified in summer- and winter-form pear psylla, respectively, and a total of 3715 DEGs shared between the two seasonal phenotypes. In summer-form individuals, B. bassiana infection disrupted oxidative phosphorylation and downregulated immune recognition genes, cellular immune-related genes, and signaling genes, along with the upregulation of the immune inhibitor serpin, indicating immunosuppression. Conversely, in winter-form individuals, immune-related genes and glycolytic rate-limiting enzymes were upregulated after infection, suggesting that the winter-form immune system normally responds to B. bassiana infection and supports efficient defense through metabolic reprogramming to fuel energy-demanding defenses. These findings advance our understanding of C. chinensis/B. bassiana interactions, providing a basis for elucidating immune regulation in seasonally polymorphic insects. The results also inform strategies to optimize B. bassiana-based biocontrol, contributing to sustainable pear psylla management.

Tumor immune microenvironment delineates progression trajectories of distinct nasopharyngeal carcinoma phenotypes

We investigate the molecular landscape of locally advanced nasopharyngeal carcinoma (LA-NPC) subtypes: limited (L), ascending (A), descending (D), and ascending-descending (AD). Using a cohort of 994 patients, we perform germline and somatic whole-exome sequencing (WES), transcriptomic profiling, multiplex immunohistochemistry (mIHC), and spatial histopathological analyses of tumor whole-slide images (WSIs). Germline WES reveals the most variants in AD subtypes, but somatic WES shows no subtype-specific mutations. Transcriptomics reveals higher extracellular matrix (ECM) gene expression in A and AD subtypes and higher immune gene expression in D and AD subtypes, agreeing with deconvolution and mIHC. Tumor immune microenvironment (TIME) of node-negative (N0) and node-positive (N+) L subtypes, considered early nasopharyngeal carcinoma (NPC), resembles A and D subtypes, respectively, suggesting distinct evolutionary trajectories. Spatial WSI analyses identify the most immune-dense tumors among D subtypes and association of TIME with disease-free survival in AD subtypes. These findings highlight the TIME's role in LA-NPC progression and its potential impact on treatment strategies.

SMIM20 promotes complex IV biogenesis and Ca2+ signaling in mice heart

Mitochondria are key to cellular energetics, metabolism, and signaling. Their dysfunction is linked to devastating diseases, including mitochondrial disorders, diabetes, neurodegenerative diseases, cardiac disorders, and cancer. Here, we present a knockout mouse model lacking the complex IV assembly factor SMIM20/MITRAC7. SMIM20-/- mice display cardiac pathology with reduced heart weight and cardiac output. Heart mitochondria present with reduced levels of complex IV associated with increased complex I activity, have altered fatty acid oxidation, and display elevated levels of ROS production. Interestingly, mutant mouse ventricular myocytes show unphysiological Ca2+ handling, which can be attributed to the increase in mitochondrial ROS production. Our study presents an example of a tissue-specific phenotype in the context of OXPHOS dysfunction. Moreover, our data suggest a link between complex IV dysfunction and Ca2+ handling at the endoplasmic reticulum through ROS signaling.

Targeting epigenetic regulators to overcome drug resistance in the emerging human fungal pathogen Candida auris

The rise of drug-resistant fungal species, such as Candida auris, poses a serious threat to global health, with mortality rates exceeding 40% and resistance rates surpassing 90%. The limited arsenal of effective antifungal agents underscores the urgent need for novel strategies. Here, we systematically evaluate the role of histone H3 post-translational modifications in C. auris drug resistance, focusing on acetylation mediated by Gcn5 and Rtt109, and methylation mediated by Set1, Set2, and Dot1. Mutants deficient in these enzymes exhibit varying degrees of antifungal drug sensitivity. Notably, we discover that GCN5 depletion and the subsequent loss of histone H3 acetylation downregulates key genes involved in ergosterol biosynthesis and drug efflux, resulting in increased susceptibility to azoles and polyenes. Additionally, Gcn5 regulates cell wall integrity and echinocandin resistance through the calcineurin signaling pathway and transcription factor Cas5. In infection models using Galleria mellonella and immunocompromised mice, GCN5 deletion significantly reduces the virulence of C. auris. Furthermore, the Gcn5 inhibitor CPTH2 synergizes with caspofungin in vitro and in vivo without notable toxicity. These findings highlight the critical role of Gcn5 in the resistance and pathogenicity of C. auris, positioning it as a promising therapeutic target for combating invasive fungal infections.

In depth transcriptomic profiling defines a landscape of dysfunctional immune responses in patients with VEXAS syndrome

VEXAS (Vacuoles, E1 enzyme, X-linked, Autoinflammatory, Somatic) syndrome is caused by inactivating somatic mutations in the UBA1 gene. Here, we characterize the immunological landscape of VEXAS syndrome by performing multi-omics single-cell RNA analysis, cytokine multiplex assays, and in vitro functional assays on patients' peripheral blood. Our data reveals a broad immune system activation with upregulation of multiple inflammatory response pathways and proinflammatory cytokines. Unexpectedly, we find that monocytes have dysfunctional features irrespective of UBA1 mutation status, exhibiting impaired efferocytosis and blunted cytokine production in vitro. In contrast, UBA1-mutated NK cells show an upregulation of the inflammation pathways and enhanced cytotoxicity. Within the lymphocyte subsets, predominantly UBA1 wild-type, we identify clonal expansion of effector memory CD8+ T cells and skewed B cell differentiation with loss of transitional B cells and expansion of plasmablasts. Thus, our analysis indicates that VEXAS syndrome is characterized by profound alterations in both adaptive and innate immune systems, accounting for the complex pathophysiology of the disease, and provides a basis to understand the marked clinical heterogeneity and variable disease course.

Gα13 Promotes Clonogenic Growth by Increasing Tolerance to Oxidative Metabolic Stress in Prostate Cancer Cells

The oncogenic role of the G12 family in many human solid cancers has been extensively studied, primarily through the effects of constitutively active mutants of these proteins on cell migration and invasion. However, these mutations are not seen in cancers, and the biological role of Gα13 in prostate cancer tumorigenesis is largely unexplored. Here, we report that Gα13 promotes anchorage-independent colony formation, spheroid formation, and xenograft tumor growth in human prostate cancer cell lines. Transcriptome analyses suggest that Gα13 modulates genes in the mitochondria and are involved in the oxidative stress response. Silencing of GNA13 increased mitochondrial superoxide levels when prostate cancer cells were cultured in galactose medium and increased the sensitivity to oxidative metabolic stress when the cells were cultured in media containing non-glycolytic metabolites. Furthermore, Gα13 levels impacts the abundance of superoxide dismutase 2 (SOD2) in the mitochondria, as well as SOD2 promoter activity and mRNA expression. Importantly, expression of SOD2 could rescue the effect of Gα13 loss on suppression of anchorage-independent growth. Likewise, stable knockdown of SOD2 decreased anchorage-independent cell growth, which was enhanced by overexpression of Gα13. These results outline a novel biological function of Gα13 mediated via SOD2 in prostate cancer tumorigenesis and highlight it as a potential treatment target.

Whole genome sequencing improves tissue-of-origin diagnosis and treatment options for cancer of unknown primary

Genomics can inform both tissue-of-origin (TOO) and precision treatments for patients with cancer of unknown primary (CUP). Here, we use whole genome and transcriptome sequencing (WGTS) for 72 patients and show diagnostic superiority of WGTS over panel testing (386-523 genes) in 71 paired cases. WGTS detects all reportable DNA features found by panel as well as additional mutations of diagnostic or therapeutic relevance in 76% of cases. Curated WGTS features and a CUP prediction algorithm (CUPPA) trained on WGTS data of known cancer types informs TOO in 71% of cases otherwise undiagnosed by clinicopathology review. WGTS informs treatments for 79% of patients, compared to 59% by panel testing. Finally, WGS of cell-free DNA (cfDNA) from patients with a high cfDNA tumour fraction (>7%), enables high-likelihood CUPPA predictions in 41% of cases. WGTS is therefore superior to panel testing, broadens treatment options, and is feasible using routine pathology samples and cfDNA.

Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant

The gut microbiota influences systemic immunity and the function of distal tissues, including the brain, liver, skin, lung, and muscle. However, the role of the gut microbiota in the foreign body response and fibrosis is largely unexplored. To investigate this connection, we perturbed the homeostasis of the murine gut microbiota via infection with the pathogenic bacterial species enterotoxigenic Bacteroides fragilis (ETBF) and implanted particulate material (mean particle size <600 μm) of the synthetic polymer polycaprolactone (PCL) into a distal muscle injury. ETBF infection in mice led to increased neutrophil and γδ T cell infiltration into the PCL implant site. ETBF infection alone promoted systemic inflammation, increased levels of neutrophils in lymphoid tissues, and altered skeletal muscle gene expression. At the PCL implant site, we found significant changes in the transcriptome of sorted stromal cells between infected and control mice, including differences related to ECM components such as proteoglycans and glycosaminoglycans. However, we did not observe ETBF-induced differences in fibrosis levels. These results demonstrate the ability of the gut microbiota to mediate long-distance effects such as immune and stromal responses to a distal biomaterial implant.

Genomic and transcriptomic determinants of clinical outcomes in patients with AML and DNMT3A mutations

Acute myeloid leukemia (AML) and DNMT3A mutations (DNMT3Amut) are considered to carry intermediate risk under the 2022 European LeukemiaNet (ELN-2022) classification in the absence of other co-mutations or cytogenetic abnormalities. However, this group is highly heterogeneous. In this study, the genomic and transcriptomic features influencing outcomes in DNMT3A-mutated AML were examined in a cohort of 884 patients with AML receiving standard chemotherapy. Stratification by NPM1 and FLT3-ITD status revealed worse survival among patients with NPM1 mutations and wild-type FLT3-ITD (NPM1mut/FLT3-ITDwt) than patients in the ELN-2022 favorable risk group. The other three subgroups (NPM1mut/FLT3-ITDmut, NPM1wt/FLT3-ITDmut, and NPM1wt/FLT3-ITDwt) exhibited worse prognoses than patients in the ELN-2022 intermediate risk group. Additionally, the presence of TET2mut in patients with AML and DNMT3Amut/NPM1mut/FLT3-ITDwt led to reclassification from favorable risk to intermediate risk in the ELN-2022. RNA-sequencing analysis revealed a distinct transcriptomic profile in patients with TET2mut, highlighting the enrichment of leukemic stem cell signatures and dendritic cell migration, with MMP14, CD200, and CT45A5 identified as key differentially expressed genes. In conclusion, co-mutation patterns strongly affected AML outcomes in patients with DNMT3Amut. Patients with TET2mut constituted a unique subgroup within the ELN-2022 favorable DNMT3Amut/NPM1mut/FLT3-ITDwt group, characterized by distinct transcriptomic features and an unfavorable prognosis.

Sequential activation of transcription factors promotes liver regeneration through specific and developmental enhancers

The mammalian liver exhibits remarkable regenerative capabilities after injury or resection. Central to this process is the precise modulation of gene expression, driven by changes in chromatin structure and the temporal activation of distal regulatory elements. In this study, we integrated chromatin accessibility and transcriptomic data after partial hepatectomy in mice. We show that the expression of crucial regeneration genes is orchestrated by a diverse array of cis-regulatory elements, including regeneration-specific enhancers and enhancers repurposed from various developmental stages. These enhancers collaborate to activate the transcriptional programs required for hepatocyte priming and proliferation, with their activity initially regulated by the activator protein-1 (AP-1) complex and ATF3, and subsequently by nuclear factor erythroid 2 (NFE2)-related factor 2 (NRF2) during proliferation. Our results also indicate that hepatic regeneration involves the repression of enhancers regulating liver-specific metabolic functions, particularly those involved in lipid metabolism. This study provides a genome-wide atlas of enhancer-gene interactions, offering new insights into the regulatory mechanisms underlying liver regeneration.

Constitutive Differences in Immune Gene Expression Are Correlated With Wood Frog Populations From Contrasting Winter Environments

Many terrestrial ectotherms have gone to great evolutionary lengths to adapt to long cold winters; some have even evolved the ability to tolerate the freezing of most of the extracellular fluid in the body. Now, however, high-elevation and high-latitude winters are experiencing an accelerated period of warming. Specialised winter adaptations that promoted fitness in a seasonally frozen environment may soon be superfluous or even maladaptive. We ask whether winter adaptations include changes in immune functions, and whether changing winter conditions could exert disparate effects on populations of a wide-ranging terrestrial ectotherm, the wood frog (Lithobates sylvaticus). By rearing wood frogs from ancestral winter environments that vary in length and temperature in a common garden, and reciprocally exposing post-metamorphic frogs to unfrozen and frozen artificial winter conditions in the lab, we were able to decompose transcriptomic differences in ventral skin gene expression into those that were environmentally induced (responsive to temperature) and genetically determined and those that varied as an interaction between the genotype and environment. We found that frogs from harsh ancestral winter environments constitutively upregulated immune processes, including cellular immunity, inflammatory processes and adaptive immune processes, as compared to frogs from mild ancestral winter environments. Further, we saw that the expression of several genes varied in an interaction between the genotype and artificial winter. We suggest that just as winter climates likely served as the selective force resulting in remarkable winter adaptations such as freeze tolerance, they may have also induced constitutive changes in immune gene expression.

Single-cell RNA-sequencing reveals early mitochondrial dysfunction unique to motor neurons shared across FUS- and TARDBP-ALS

Mutations in FUS and TARDBP cause amyotrophic lateral sclerosis (ALS), but the precise mechanisms of selective motor neuron degeneration remain unresolved. To address if pathomechanisms are shared across mutations and related to either gain- or loss-of-function, we performed single-cell RNA sequencing across isogenic induced pluripotent stem cell-derived neuron types, harbouring FUS P525L, FUS R495X, TARDBP M337V mutations or FUS knockout. Transcriptional changes were far more pronounced in motor neurons than interneurons. About 20% of uniquely dysregulated motor neuron transcripts were shared across FUS mutations, half from gain-of-function. Most indicated mitochondrial impairments, with attenuated pathways shared with mutant TARDBP M337V as well as C9orf72-ALS patient motor neurons. Mitochondrial motility was impaired in ALS motor axons, even with nuclear localized FUS mutants, demonstrating shared toxic gain-of-function mechanisms across FUS- and TARDBP-ALS, uncoupled from protein mislocalization. These early mitochondrial dysfunctions unique to motor neurons may affect survival and represent therapeutic targets in ALS.

Spatiotemporal single-cell analysis elucidates the cellular and molecular dynamics of human cornea aging

BACKGROUND

The human cornea is a transparent and uniquely ordered optical-biological system. Precise coordination of its cellular mechanisms is essential to maintain its transparency and functionality. However, the spatial, cellular and molecular architecture of the human cornea and its intercellular interactions during aging have not been elucidated.

METHODS

We performed single-cell RNA sequencing (scRNA-seq) and single-cell SpaTial Enhanced REsolution Omics-sequencing (scStereo-seq) analysis in corneal tissue from eight eyes of donors aged 33-88 years to elucidate the spatiotemporal cellular and molecular dynamics of human cornea aging. Immunofluorescence staining and Western blotting were performed to validate the findings.

RESULTS

Spatiotemporal single-cell analysis revealed the complex cellular landscape, spatial organization and intercellular communication within the human cornea. The subpopulations of major cell types of the cornea were elucidated with precise spatial positions. In particular, we identified novel subpopulations, mapped the spatial positioning of limbal stem cells within the limbal niche, and delineated the interactions between major cell types. We observed that three basal cell subsets migrate centripetally from the peripheral to the central cornea with age, suggesting the "spatiotemporal centripetal pattern" as a novel paradigm for the age-related migration of corneal epithelial cells. Furthermore, we elucidated the age-related, region-specific molecular and functional characteristics of the corneal endothelium, demonstrating differential metabolic capacities and functional properties between the peripheral and central regions.

CONCLUSIONS

As the first comprehensive spatiotemporal atlas, our work provides a valuable resource for understanding tissue homeostasis in the human cornea and advances research on corneal pathology, transplantation, senescence and regenerative medicine in the context of corneal aging.

Whole-Blood RNA Sequencing Profiling of Patients With Rheumatoid Arthritis Treated With Tofacitinib

OBJECTIVE

Patients with rheumatoid arthritis (RA) often fail to respond to therapies, including JAK inhibitors (JAKi), and treatment allocation is made via a trial-and-error strategy. A comprehensive analysis of responses to JAKi, including tofacitinib, by RNA sequencing (RNAseq) would allow the discovery of transcriptomic markers with a two-fold meaning: (1) an improved knowledge about the mechanisms of response to treatment (inference modeling) and (2) the definition of features that may be useful in treatment optimization and assignment (predictive modeling).

METHODS

Thirty-three patients with active RA were treated with a tofacitinib dose of 5 mg twice a day for 24 weeks and evaluated for EULAR Disease Activity Score in 28 joints using the C-reactive protein level response. Whole-blood RNA was collected before and after treatment to perform RNAseq transcriptome analysis. Linear models were used to determine differentially expressed genes (DEGs) (1) at baseline according to clinical responses and (2) in the pre-post comparison after tofacitinib treatment and in relation to EULAR responses. The capability of DEGs to predict a successful treatment was tested via machine learning modeling after extensive internal validation.

RESULTS

Of 26 patients who completed the study (per-protocol analysis), 15 (57.7%) achieved good responses, and 7 (26.9%) and 4 (15.3%) had moderate and no responses, respectively. Overall, 273 baseline genes were significantly associated with the attainment of good responses, contributing to several pathways linked to the immune system or RA pathogenesis (eg, citrullination processes and the negative regulation of natural killer function). The expression of several molecules was reverted by tofacitinib when good responses were reached, including AKT3, GK5, KLF12, FCRL3, BIRC3, TSPOAP1, and P2RY10. Finally, we isolated 14 markers that singularly were capable of predicting the attainment of good responses, including, NKG2D, CD226, CLEC2D, and CD52.

CONCLUSION

Whole-blood transcriptome analysis of patients with RA treated with tofacitinib identified genes whose expression may be relevant in prognostication and understanding the mechanisms of responses to therapy.

A CRISPR/Cas9-based enhancement of high-throughput single-cell transcriptomics

Single-cell RNA-seq (scRNAseq) struggles to capture the cellular heterogeneity of transcripts within individual cells due to the prevalence of highly abundant and ubiquitous transcripts, which can obscure the detection of biologically distinct transcripts expressed up to several orders of magnitude lower levels. To address this challenge, here we introduce single-cell CRISPRclean (scCLEAN), a molecular method that globally recomposes scRNAseq libraries, providing a benefit that cannot be recapitulated with deeper sequencing. scCLEAN utilizes the programmability of CRISPR/Cas9 to target and remove less than 1% of the transcriptome while redistributing approximately half of reads, shifting the focus toward less abundant transcripts. We experimentally apply scCLEAN to both heterogeneous immune cells and homogenous vascular smooth muscle cells to demonstrate its ability to uncover biological signatures in different biological contexts. We further emphasize scCLEAN's versatility by applying it to a third-generation sequencing method, single-cell MAS-Seq, to increase transcript-level detection and discovery. Here we show the possible utility of scCLEAN across a wide array of human tissues and cell types, indicating which contexts this technology proves beneficial and those in which its application is not advisable.

Cathepsin X is a conserved cell death protein involved in algal response to environmental stress

Phytoplankton are responsible for half of the global photosynthesis and form vast blooms in aquatic ecosystems. Bloom demise fuels marine microbial life and is suggested to be mediated by programmed cell death (PCD) induced by diverse environmental stressors. Despite its importance, the molecular basis for algal PCD remains elusive. Here, we reveal novel PCD genes conserved across distant algal lineages using cell-to-cell heterogeneity in the response of the diatom Phaeodactylum tricornutum to oxidative stress. Comparative transcriptomics of sorted sensitive and resilient subpopulations following oxidative stress revealed genes directly linked to their contrasting fates of cell death and survival. Comparing these genes with those found in a large-scale mutant screen in the green alga Chlamydomonas reinhardtii identified functionally relevant conserved PCD gene candidates, including the cysteine protease cathepsin X/Z (CPX). CPX mutants in P. tricornutum CPX1 and C. reinhardtii CYSTEINE ENDOPEPTIDASE 12 (CEP12) exhibited resilience to oxidative stress and infochemicals that induce PCD, supporting a conserved function of these genes in algal PCD. Phylogenetic and predictive structural analyses show that CPX is highly conserved in eukaryotes, and algae exhibit strong structural similarity to human Cathepsin X/Z (CTSZ), a protein linked to various diseases. CPX is expressed by diverse algae across the oceans and correlates with upcoming demise events during toxic Pseudo-nitzschia blooms, providing support for its ecological significance. Elucidating PCD components in algae sheds light on the evolutionary origin of PCD in unicellular organisms and on the cellular strategies employed by the population to cope with stressful conditions.

Wnt/β-catenin activation by mutually exclusive FBXW11 and CTNNB1 hotspot mutations drives salivary basal cell adenoma

Basal cell adenoma (BCA) and basal cell adenocarcinoma (BCAC) of the salivary gland are rare tumours that can be difficult to distinguish from each other and other salivary gland tumour subtypes. Using next-generation sequencing, we identify a recurrent FBXW11 missense mutation (p.F517S) in BCA that is mutually exclusive with the previously reported CTNNB1 p.I35T gain-of-function (GoF) mutation with these mutations collectively accounting for 94% of BCAs. In vitro, mutant FBXW11 is characterised by defective binding to β-catenin and higher protein levels within the nucleus. This is consistent with the increased nuclear expression of β-catenin and activation of the Wnt/β-catenin pathway. The genomic profiles of BCAC are distinct from BCA, with hotspot DICER1 and HRAS mutations and putative driver mutations affecting PI3K/AKT and NF-κB signalling pathway genes. These findings have important implications for the diagnosis and treatment of BCA and BCAC, which, despite histopathologic overlap, may be unrelated entities.

High-resolution sequencing reveals that the Paf1 complex may be a conserved transcription elongation factor for eukaryotic RNA polymerase I

In eukaryotes, at least three Pols (I, II, and III) are responsible for synthesizing unique RNA products. Many trans-acting factors affect the efficiency of transcription by the three Pols. Some of these factors influence more than one of the nuclear Pols. One such factor is polymerase-associated factor 1 complex (Paf1C). Paf1C, composed of five subunits in Saccharomyces cerevisiae (yeast), has been shown to promote transcription by Pols I and II and is conserved across eukaryotes. Although several studies have demonstrated that Paf1C associates with Pol I machinery, its roles in ribosomal RNA synthesis are not well-defined. In this study, we used native elongating transcript sequencing (NET-seq), to investigate the effect of the loss of two of the five Paf1C subunits (Paf1 and Cdc73) on Pol I occupancy at single-nucleotide resolution in yeast. We found that in both paf1Δ and cdc73Δ mutants, there was a significant reduction in Pol I occupancy at the 5' end of the DNA template as compared to WT yeast, accompanied by other occupancy pattern changes throughout the gene. To complement these results, we also analyzed a PRO-seq dataset that was generated with DLD1 mammalian cells. Interestingly, we found that when Paf1C was knocked-down, there was also a reduction in the occupancy of Pol I at the 5' end of the gene, consistent with our NET-seq analysis. Overall, our results support the conclusion that Paf1C is an important transcription elongation factor for Pol I and may play a conserved role across species.

Transcriptional and epigenetic rewiring by the NUP98::KDM5A fusion oncoprotein directly activates CDK12

Nucleoporin 98 (NUP98) fusion oncoproteins are strong drivers of pediatric acute myeloid leukemia (AML) with poor prognosis. Here we show that NUP98 fusion-expressing AML harbors an epigenetic signature that is characterized by increased accessibility of hematopoietic stem cell genes and enrichment of activating histone marks. We employ an AML model for ligand-induced degradation of the NUP98::KDM5A fusion oncoprotein to identify epigenetic programs and transcriptional targets that are directly regulated by NUP98::KDM5A through CUT&Tag and nascent RNA-seq. Orthogonal genome-wide CRISPR/Cas9 screening identifies 12 direct NUP98::KDM5A target genes, which are essential for AML cell growth. Among these, we validate cyclin-dependent kinase 12 (CDK12) as a druggable vulnerability in NUP98::KDM5A-expressing AML. In line with its role in the transcription of DNA damage repair genes, small-molecule-mediated CDK12 inactivation causes increased DNA damage, leading to AML cell death. Altogether, we show that NUP98::KDM5A directly regulates a core set of essential target genes and reveal CDK12 as an actionable vulnerability in AML with oncogenic NUP98 fusions.

Integrative analysis of epigenetic and transcriptional interrelations identifies histotype-specific biomarkers in early-stage ovarian carcinoma

BACKGROUND

Epithelial ovarian cancer (EOC) is a deadly and heterogenous disease comprising five major histotypes: clear cell carcinoma (CCC), endometrioid carcinoma (EC), low- and high-grade serous carcinoma (LGSC, HGSC), and mucinous carcinoma (MC). Despite this heterogeneity, EOC is often treated as a homogenous disease, and reliable screening tests are lacking. Although progress has been made, there is a pressing need for biomarkers to refine patient stratification, guide treatment, and improve outcomes. Here, we elucidated the relationship between DNA methylation and gene expression patterns in EOC to identify histotype-specific biomarkers.

METHODS

Differential DNA methylation and gene expression analyses were performed for 86 early-stage EOC samples after histopathological reclassification stratified by histotype. The correlation between DNA methylation and gene expression was examined, and histotype-specific biomarkers were identified. Hierarchical clustering and predictive machine learning modeling were employed to assess the performance of the histotype-specific biomarkers using four external cohorts.

RESULTS

EOC histotypes exhibited distinct epigenetic, transcriptional, and functional profiles, with candidate histotype-specific biomarkers such as CTSE and VCAN effectively distinguishing CCC, HGSC, and MC on the transcriptional level. Gene expression for the candidate biomarkers was found to be reproducible across external cohorts, with histotype-specific differences remaining homogenous.

CONCLUSIONS

This study identified promising histotype-specific biomarkers for EOC using integrative transcriptomic and epigenomic analysis. Furthermore, these findings indicate that additional stratification or potential reclassification of the EC histotype is warranted in future studies.

Dynamic deployment of H2A.Z positive nucleosome mediated transcriptomic plasticity within vascular smooth muscle cell

BACKGROUND

To maintain homeostasis in the mature human body, certain differentiated cells adopted high plasticity to refine their cellular functions. However, mechanisms that supported cellular plasticity still remained elusive. Here, through comprehensive transcriptomic and epigenetic studies of highly plastic vascular smooth muscle cells (SMCs), we aimed to decipher the chromatin basis that could mediate cellular plasticity.

RESULTS

In vascular smooth muscle cells, actively transcribed and highly adjustable genes tended to be associated with a continuously accessible region downstream of transcription start site (CAR-downTSS). This CAR-downTSS was located beyond the classic RNA polymerase II paused region, accessible at mono-nucleosome level and incorporated with histone variant H2A.Z. Depletion of H2A.Z reduced active histone modifications within CAR-downTSS, impaired RNA polymerase II transpassing when cells were stimulated, and consequently inhibited the ability of CAR-downTSS-associated genes to adjust their expression. Further in vitro and in vivo studies verified that this CAR-downTSS could be dynamically re-deployed onto different genes in vascular SMCs, whereas it was deployed in smaller quantities and remained quantitatively stable on genome within the quiescent cardiomyocytes.

CONCLUSIONS

Vascular SMCs dynamically deployed H2A.Z-positive nucleosomes extending continuously downstream transcription start sites on different genes to support their transcriptional adjustability, which served as an important mechanism mediating cellular plasticity.

Synovial Gene expression after Hemarthrosis differs between FVIII-deficient mice treated with recombinant FVIII or FVIII-Fc Fusion Protein

To investigate if FVIII-Fc Fusion protein (FcFVIII) may modulate inflammation and immune stimulation in hemophilic synovium via the Fc-portion of immunoglobulin used for half-life extension we performed gene expression profiling in FVIII-deficient mice. Hemarthrosis was induced by sub-patellar puncture in FVIII-KO mice, + /- periprocedural recombinant human (rh)FVIII,murine (m)FcFVIII, or mIgG2a. Synovium was harvested at baseline and on days (D) 3 and 14, followed by RNA extraction and sequencing, and histological analysis. RNASeq data were processed using standard protocols followed by differential gene expression (DGE) analysis. Functional enrichment analysis generated molecular pathways (KEGG and Reactome). To distinguish between on-target and off-target (related and unrelated to injury/bleed) effects the following groups were compared: i) Baseline vs. injured-saline, ii) injured-saline vs. injured-rhFVIII, iii) injured-saline vs. injured-mFcFVIII. Knee injury in FVIII-KO mice resulted in hemarthrosis, which was prevented by peri-procedural rhFVIII and mFcFVIII treatments. Only a small proportion of genes was affected by FVIII treatment, exhibiting overlap but also distinct differences between both FVIII-preparations. Acutely (D3), mFcFVIII had unique on-target effects related to immune and inflammatory regulation, whereas rhFVIII mostly affected mRNA and protein processing. On day 14, macrophage profiling indicated a transition from M1 to M2, and only mFcFVIII uniquely influenced pathways and genes associated with tissue remodeling and repair. Some mFcFVIII DGE patterns resembled mIgG2a patterns. Synovial vascular remodeling and cartilage health were better with mFcFVIII than rhFVIII. Interestingly, both FVIII-preparations exerted off-target effects on immune system pathways, albeit with temporal differences. These observations provide proof-of-principle that the type of FVIII preparation can influence synovial processes beyond acute hemostasis control, deserving exploration in the setting of joint bleed control in hemophilia.

hiPSC-neurons recapitulate the subtype-specific cell intrinsic nature of susceptibility to neurodegenerative disease-relevant aggregation

Alzheimer's disease (AD) is characterized by the accumulation and spread of Tau intraneuronal inclusions throughout most of the telencephalon, leaving hindbrain regions like the cerebellum and spinal cord largely spared. These neuropathological observations, along with the identification of specific vulnerable sub-populations from AD brain-derived single nuclei transcriptomics, suggest that a subset of brain regions and neuronal subtypes possess a selective vulnerability to Tau pathology. Given the inability to culture neurons from patient brains, a disease-relevant in vitro model which recapitulates these features would serve as a critical tool to validate modulators of vulnerability and resilience. Using our recently established platform for inducing endogenous Tau aggregation in human induced pluripotent stem cell (hiPSC)-derived cortical excitatory neurons via application of AD brain-derived exogenous Tau aggregates, we explored whether Tau aggregates preferentially induce aggregation in specific neuronal subtypes. We compared Tau seeding in hiPSC-derived neuron subtypes representing regional identities across the forebrain, midbrain, and hindbrain. Higher susceptibility (i.e. more Tau aggregation) was consistently observed among cortical neuron subtypes, with CTIP2-positive, somatostatin (SST)-positive cortical inhibitory neurons showing the greatest aggregation levels across hiPSC lines from multiple donors. hiPSC-neurons also delineated between the disease-specific vulnerabilities of different protein aggregates, as α-synuclein preformed fibrils showed an increased propensity to induce aggregates in midbrain dopaminergic (mDA)-like neurons, mimicking Parkinson's disease (PD)-specific susceptibility. Aggregate uptake and degradation rates were insufficient to explain differential susceptibility. The absence of a consistent transcriptional response following aggregate seeding further indicated that intrinsic neuronal subtype-specific properties could drive susceptibility. The present data provides evidence that hiPSC-neurons exhibit features of selective neuronal vulnerability which manifest in a cell autonomous manner, suggesting that mining intrinsic (or basal) transcriptomic signatures of more vulnerable compared to more resilient hiPSC-neurons could uncover the molecular underpinnings of differential susceptibility to protein aggregation found in a variety of neurodegenerative diseases.

The comprehensive transcriptomic atlas of porcine immune tissues and the peripheral blood mononuclear cell (PBMC) immune dynamics reveal core immune genes

BACKGROUND

Viral diseases have profoundly influenced the sustainable development of the swine farming industry. With the development of genomics technology, the combination of transcriptome, genetic variation, immune response, and QTL mapping data to illustrate the interactions between pathogen and host immune system, will be an effective tool for identification of disease resistance genes in pigs. The immune system of an organism is the source of disease resistance in livestock, consisting of various immune tissues, as well as the immune cells and cytokines they produced. However, comprehensive systematic studies on transcriptome of porcine immune tissues are still rare. Poly(I:C), as a viral mimic, is commonly used to study immune responses of the body during viral infections, and serves as a valuable tool for investigating immune mechanisms in swine.

RESULTS

WGCNA analysis identified core immune genes across six immune tissues (bone marrow, jejunum, lymph node, PBMC, spleen, thymus) in Landrace pigs, which are also crucial for the development of PBMCs. The examination of the changes in the proportion of immune cells during three developmental stages (1-month-old, 4-month-old, 7-month-old) shows a shift from innate immunity to humoral immunity. By integrating different epigenetic genomics datasets, we identified several core immune genes and their causal variants, including IFI44, IFIT5, EIF2AK2 and others, which are closely related to immune development and response. Functional validation studies reveal that the IFI44 gene acts as a negative regulator of the antiviral response; its inhibition effect significantly reduced Poly(I:C)-induced cell necrosis, while enhancing apoptosis to combat viral infections.

CONCLUSION

Our study elucidated the fundamental transcriptional program in porcine immune tissues and the immunodynamics underlying development of PBMCs, identifying many core immune genes, including IFI44, which plays a critical negative regulator role in the antiviral response, providing valuable insights for breeding programs aimed at enhancing pig disease resistance.

Deciphering the role of histone modifications in memory and exhausted CD8 T cells

Exhausted CD8 T cells (TEX) arising during chronic infections and cancer have reduced functional capacity and limited fate flexibility that prevents optimal disease control and response to immunotherapies. Compared to memory (TMEM) cells, TEX have a unique open chromatin landscape underlying a distinct gene expression program. How TEX transcriptional and epigenetic landscapes are regulated through histone post-translational modifications (hPTMs) remains unclear. Here, we profiled key activating (H3K27ac and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in naive CD8 T cells (TN), TMEM and TEX. We identified H3K27ac-associated super-enhancers that distinguish TN, TMEM and TEX, along with key transcription factor networks predicted to regulate these different transcriptional landscapes. Promoters of some key genes were poised in TN, but activated in TMEM or TEX whereas other genes poised in TN were repressed in TMEM or TEX, indicating that both repression and activation of poised genes may enforce these distinct cell states. Moreover, narrow peaks of repressive H3K9me3 were associated with increased gene expression in TEX, suggesting an atypical role for this modification. These data indicate that beyond chromatin accessibility, hPTMs differentially regulate specific gene expression programs of TEX compared to TMEM through both activating and repressive pathways.

Transcriptomic profiling of immune modulation induced by vitamin D3 in the VitDPAS and VitDHiD cohort studies

The VitDPAS study (NCT06104111) was designed as a medical experiment to assess the in vivo effects of vitamin D on immune responses. This study enrolled 45 healthy individuals from Olsztyn, Poland, who received a body weight-adjusted bolus dose of vitamin D3 (1,000 IU/kg). Transcriptome-wide differential gene expression analysis of peripheral blood mononuclear cells, collected before and 24 h after supplementation, identified 758 significantly responsive genes (p < 0.05). By correlating individual gene expression changes with alterations in vitamin D status, participants were categorized into three response groups: 17 high responders, 19 mid responders, and 9 low responders. A comparative analysis with the VitDHiD study (NCT03537027), conducted on a Finnish cohort of 25 healthy participants, revealed 232 overlapping target genes, enabling an integrated assessment of vitamin D responsiveness across all 70 individuals. Applying a more stringent statistical threshold (false discovery rate < 0.05) highlighted 26 shared target genes, demonstrating a consistent in vivo response to vitamin D3 across both cohorts. The modulation of inflammatory processes, mediated primarily via tumor necrosis factor and nuclear factor κB signaling pathways, emerged as a shared effect, highlightening the immunomodulatory potential of vitamin D as a key function of the vitamin in healthy individuals.

A cell type-specific expression atlas of small and total RNA in the heart after myocardial infarction

Acute myocardial infarction (AMI) is a leading cause of mortality worldwide. MicroRNAs (miRNAs), among other small non-coding RNAs, shape the transcriptome and control cellular functions. Although single-cell technologies are now available to study myocardial ischemia response, the study of small RNA regulation is limited by depth of expression, capture efficiency and lack of full coverage of transcripts. In addition, the kinetic expression of miRNAs is unknown. Using paired small and total RNA sequencing, we built an expression atlas to study the temporal dynamics of miRNAs and genes in four major heart cell types after AMI. Expression dynamics reveal enriched functions highlighting cell type-specific AMI stress responses. Many deregulated mouse genes after AMI overlap with known human cardiovascular disease genes. The dataset is highly valuable for additional research on small and long non-coding RNAs, such as regulation of RNA variants by splicing or alternative ORFs. All in all, the RNA expression atlas provides a useful resource to study different roles of RNAs in major cell types of the heart after AMI.

The gene regulatory mechanisms shaping the heterogeneity of venom production in the Cape coral snake

BACKGROUND

Venoms and their associated glands and delivery structures have evolved numerous times among animals. Within these venom systems, the molecular, cellular, and morphological components interact and co-evolve to generate distinct, venom phenotypes that are increasingly recognized as models for studying adaptive evolution. However, toxins are often unevenly distributed across venom-producing tissues in patterns that are not necessarily adaptive but instead likely result from constraints associated with protein secretion.

RESULTS

We generate a high-quality draft genome of the Cape coral snake (Aspidelaps lubricus) and combine analyses of venom gland single-cell RNA-seq data with spatial venom gland in situ toxin distributions. Our results reveal that while different toxin families are produced by distinct populations of cells, toxin expression is fine-tuned by regulatory modules that result in further specialization of toxin production within each cell population. We also find that the evolution of regulatory elements closely mirrors the evolution of their associated toxin genes, resulting in spatial association of closely related and functionally similar toxins in the venom gland. While this compartmentalization is non-adaptive, the modularity of the underlying regulatory network likely facilitated the repeated evolution of defensive venom in spitting cobras.

CONCLUSIONS

Our results provide new insight into the variability of toxin regulation across snakes, reveal the molecular mechanisms underlying the heterogeneous toxin production in snake venom glands, and provide an example of how constraints can result in non-adaptive character states that appear to be adaptive, which may nevertheless facilitate evolutionary innovation and novelty.

Chemoproteomic Approach for Identifying Nuclear Arsenite-Binding Proteins

Trivalent arsenic, i.e., As(III), is the main form of arsenic species in the environment. Prolonged exposure to arsenicals through ingesting contaminated food and water has been implicated in the development of cancer and diabetes as well as cardiovascular and neurodegenerative diseases. A number of studies have been conducted to examine the mechanisms underlying the toxic effects of arsenite exposure, where As(III) was shown to displace Zn(II) and impair the functions of zinc-binding proteins. Considering that many zinc-binding proteins can bind to nucleic acids, we reason that systematic identification of arsenite-binding proteins in the nucleus may provide additional insights into the molecular targets of arsenite, thereby improving our understanding of the mechanisms of arsenic toxicity. Here, we conducted a quantitative proteomics experiment relying on affinity pull-down from nuclear protein lysate with a biotin-As(III) probe to identify nuclear arsenite-binding proteins. We uncovered a number of candidate As(III)-binding proteins that are involved in mRNA splicing, DNA repair, and replication. We also found that As(III) could bind to splicing factor 1 (SF1) and that this binding perturbs mRNA splicing in human cells. Together, our work provided insights into the mechanisms of As(III) toxicity by revealing new nuclear protein targets of As(III).

Expanding the clinical phenotype and understanding the biochemical consequences of Muscle Glycogen Synthase Deficiency (GSD0B)

AIMS

Glycogen storage disease type 0b (GSD 0b) is an exceptionally rare metabolic disorder caused by biallelic pathogenic variants in the GYS1 gene, leading to deficient glycogen synthase (GS) activity. In 2022, two cases were reported for the first time with a phenotype presenting as adult-onset myopathy.

METHODS

A 56-year-old woman with a history of progressive limb-girdle and axial weakness was evaluated. Clinical assessments, muscle biopsy, genetic analyses, RNA sequencing from muscle tissue, and western blot analyses were performed. Muscle glycogen levels were quantified using spectrophotometry.

RESULTS

The patient was found to have a biallelic pathogenic variant (c.678 + 1G > A) in the GYS1 gene. Skeletal muscle MRI showed a distinctive pattern with potential diagnostic value. Transcriptome sequencing indicated that the variant caused skipping of exon 4 in half of the transcripts and retention of intron 4 in the remainder. Muscle biopsy revealed marked glycogen depletion. In our study, we have also observed the molecular and biochemical consequences resulting from the presence of pathogenic variants in the GYS1 gene. Glycogen quantification confirmed a significant reduction in muscle glycogen content. Our findings elucidate the molecular consequences of GYS1 deficiency, showing severely reduced GS protein levels, leading to compensatory decreases in glycogen degradation (PHKA1, PHKB, PHKG1 and AGL) and glycolytic (PFKM, PKM1 and the phosphorylated form of pPDHE) enzymes. Additionally, the absence of GS affects STBD1 and prompts a shift towards oxidative metabolism due to reduced glycogen levels.

CONCLUSION

This case of GSD 0b, caused by a novel GYS1 variant, highlights the disease's clinical and molecular heterogeneity. Understanding the molecular consequences of GS deficiency can aid in developing management strategies for GSD 0b.

Knockout of SIN3B modulates transcriptional programs and cell survival in cutaneous melanoma

SIN3 is a critical component of the histone deacetylase complex. Utilizing whole transcriptome data from melanoma patient samples we reveal that elevated levels of SIN3B are associated with poor survival outcomes with in vitro studies showing increased SIN3B expression in BRAF-mutant metastatic melanoma cell lines. The generation of isogenic SIN3B knockout cell lines indicated that SIN3B disruption led to a decrease in pathways associated with tumor invasion, migration, and cell-cell interactions. Moreover, pooled genome-wide CRISPR/Cas9 screens highlighted POLE4 and STK11 as crucial for the fitness and survival of SIN3B-knockout melanoma cells suggesting a role for these genes in epistasis with SIN3B. In summary, our findings suggest that SIN3B plays a pivotal role in modulating the behavior of melanoma cells, with implications for tumor growth and response to therapy.

Chromosome-level genome assembly of the parasitoid wasp Aenasius arizonensis

Aenasius arizonensis is an important solitary endoparasitoid successfully used for biocontrol of cotton mealybug. However, lacking genomic resources has limited molecular-level investigations. Our exploration produced a superior genomic assembly of A. arizonensis from the chromosome level by combining MGISEQ short reads, Hi-C scaffolding, and PacBio Revio sequencing techniques. The genome measured 398.69 Mb, including a contig N50 of 4.73 Mb, a BUSCO completeness level of 97.07%, and a scaffold N50 of 35.96 Mb. Hi-C data were further utilized cluster and anchor 98.66% of the genome sequences into 11 chromosomes. Approximately, 165.90 Mb, representing about 41.61% of the genome, was identified as repeat elements. Non-coding sequence annotation identified 171 rRNAs, 117 small RNAs, 331 regulatory RNAs, and 872 tRNAs. Genome annotation reveals 11,727 protein-coding genes, with 10,842 (92.45%) genes functionally annotated. In summary, our chromosome-level genome assembly serves as a significant resource for advancing research on Encyrtidae parasitoids.

Alternative mRNA splicing in anthracycline-induced cardiomyopathy - a COG-ALTE03N1 report

BACKGROUND

Anthracycline-induced cardiomyopathy is a well-established adverse consequence in childhood cancer survivors. Altered mRNA expression in the peripheral blood has been found at the level of genes and pathways among anthracycline-exposed childhood cancer survivors with and without cardiomyopathy. However, the role of aberrant alternative splicing in anthracycline-induced cardiomyopathy remains unexplored. The present study examined if transcript-specific events, due to alternative splicing occur in anthracycline-exposed childhood cancer survivors with and without cardiomyopathy.

METHODS

Participants were anthracycline-exposed childhood cancer survivors with cardiomyopathy (cases) matched with anthracycline-exposed childhood cancer survivors without cardiomyopathy (controls; matched on primary cancer diagnosis, year of diagnosis, and race/ethnicity). mRNA sequencing was performed on total RNA from peripheral blood in 32 cases and 32 matched controls. Event-level splicing tool, rMATS (replicate Multivariate Analysis of Transcript Splicing) was used for quantitative profiling of alternative splicing events.

RESULTS

A total of 45 alternative splicing events in 36 genes were identified. Using a prioritization strategy to filter the alternative splicing events, intron retention in RPS24 and skipped exon of PFND5 showed differential expression of altered transcripts.

CONCLUSIONS

We identified specific alternative splicing events in anthracycline-exposed childhood cancer survivors with and without cardiomyopathy. Our findings suggest that differential alternative splicing events can provide additional insight into the peripheral blood transcriptomic landscape of anthracycline-induced cardiomyopathy.

New insights into tumor microenvironment and HPV integrations in cervical cancer pathogenesis revealed by single-cell transcriptome data

HPV infection is common among women and can result in serious illnesses. This research utilizes single-cell RNA-sequencing (scRNA-seq) to study the connection between cellular heterogeneity and HPV integrations in cervical histopathology. scRNA-seq was used to examine heterogeneity among normal patients and those in three disease stages: high-grade squamous intraepithelial lesions (HSIL), microinvasive carcinoma (MIC), and cervical squamous epithelium carcinoma cancer (CSCC) tissues. A method was developed to identify HPV integration events from scRNA-seq data. Our results indicated an increase in squamous epithelial cells and a decrease in columnar epithelial cells as the disease progressed from normal to CSCC. We discovered HPV genes that were differentially expressed across normal patients and those in the three disease stages. Notably, HPV integration events were more common in squamous epithelial cells at the single-cell level. The ratio of HPV-integrated cells increased as the disease progressed from normal tissue to CSCC, eventually stabilizing. Several genes, such as EGR1, S100A11, S100A8, KRT5, RPL34, ATP1B1, RPS4X and EEF2, were frequently integrated by HPV across patients. In contrast, genes like PAN3, BABAM2, SPEN, TCIM-SIRLNT, TEX41-PABPC1P2 and KCNV1-LINC01608 showed frequent integration events across cells. KRT5, ATP1B1, RPS4X, PAN3 and SPEN were novel recurrent HPV-integrated genes we observed at the patient or cell level in this study. Additionally, we found that HPV genes from various HPV types exhibited integration preferences in various samples and disease stages. This provides a valuable insight into the mechanism of HPV-induced cervical cancer from a single-cell standpoint, highlighting its clinical relevance.

The nucleolar granular component mediates genome-nucleolus interactions and establishes their repressive chromatin states

Repressive chromatin domains often localize to the nuclear lamina or nucleolus. Although nucleolar-associated domains (NADs) have recently been mapped, their mechanisms of nucleolar association and functional significance remain unclear. Here, we show that nucleophosmin (NPM1), a factor located in the granular component of the nucleolus, mediates NAD association in mouse embryonic stem cells. NPM1 binds NADs, interacts with the histone methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of a DNA-binding-deficient mutant disrupts NAD-nucleolus association and reduces H3K9me2 specifically at NADs. G9a is dispensable for NAD-nucleolus contacts, indicating that H3K9me2 is acquired after NADs associate with NPM1 at nucleoli. These findings reveal mechanistic insights into how genomic domains associate with nucleoli and form repressive chromatin and indicate that the nucleolus not only serves as a scaffold for positioning repressive domains but also plays a direct role in establishing their repressive chromatin states.

Spatiotemporal 3D chromatin organization across multiple brain regions during human fetal development

Elucidating the regulatory mechanisms underlying the development of different brain regions in humans is essential for understanding advanced cognition and neuropsychiatric disorders. However, the spatiotemporal organization of three-dimensional (3D) chromatin structure and its regulatory functions across different brain regions remain poorly understood. Here, we generated an atlas of high-resolution 3D chromatin structure across six developing human brain regions, including the prefrontal cortex (PFC), primary visual cortex (V1), cerebellum (CB), subcortical corpus striatum (CS), thalamus (TL), and hippocampus (HP), spanning gestational weeks 11-26. We found that the spatial and temporal dynamics of 3D chromatin organization play a key role in regulating brain region development. We also identified H3K27ac-marked super-enhancers as key contributors to shaping brain region-specific 3D chromatin structures and gene expression patterns. Finally, we uncovered hundreds of neuropsychiatric GWAS SNP-linked genes, shedding light on critical molecules in various neuropsychiatric disorders. In summary, our findings provide important insights into the 3D chromatin regulatory mechanisms governing brain region-specific development and can serve as a valuable resource for advancing our understanding of neuropsychiatric disorders.

MCSP+ metastasis founder cells activate immunosuppression early in human melanoma metastatic colonization

To investigate the early, poorly understood events driving metastatic progression, we searched for the earliest detectable disseminated cancer cells (DCCs), also often referred to as disseminated tumor cells (DTCs), in sentinel lymph node (SLN) biopsies of 492 patients with stage I-III melanoma. Using micromanipulator-assisted isolation of rare DCCs, single-cell mRNA and DNA sequencing, codetection by indexing immunofluorescence imaging and survival analysis, we identified melanoma-associated chondroitin sulfate proteoglycan (MCSP)+ melanoma cells as metastasis founder cells (MFCs). We found that DCCs entering SLNs predominantly exhibited a transitory phenotype that, upon interferon-γ exposure triggered by CD8 T cells, dedifferentiated into a neural-crest-like phenotype. This was accompanied by increased production of small extracellular vesicles (sEVs) carrying the immunomodulatory proteins CD155 and CD276 but rarely programmed cell death protein 1 ligand 1. The sEVs suppressed CD8 T cell proliferation and function, facilitating colony formation. Targeting MCSP+ MFCs or their immune escape mechanisms could be key to curing melanoma early by preventing manifestation of metastasis.

Changes in Gene Expression Patterns in Young and Senescent Fibroblasts in Glycated Three-Dimensional Collagen Matrices

Glycation, or non-enzymatic glycosylation, has recently attracted increasing interest in the context of its impact on aging. Advanced glycation end products (AGEs) contribute to various age-related pathological conditions such as inflammation, fibrosis, and vascular calcification. However, the molecular mechanisms underlying glycation-induced disruption of cell-matrix interactions during cellular senescence are not fully understood. The aim of this study was to investigate transcriptomic changes in young and senescent dermal fibroblasts (HdFbs) cultured in 3D post-glycated collagen type I matrices after 10 and 17 days. Our findings indicate that D-ribose-mediated glycation increases the accumulation of fluorescent AGEs and the stiffness of matrices in a dose-dependent manner. The transcriptome alterations in cells encompassed the modulation of age-related genes and signaling pathways, including activation of genes related to senescence-associated secretory phenotype (SASP). Notably, the alterations in the transcriptome profiles due to glycation were more pronounced (in terms of both the number of genes and their fold changes) after 10 days of culture compared to day 17 in both passages. These findings suggest that cellular responses to glycation and resulting stiffness depend on both the concentration of reducing sugar and the time spent under those conditions.

Salvianolic acid B ameliorates Aβ42 toxicity in Aβ42-expressing Drosophila model: behavioral and transcriptomic profiling

Alzheimer's disease (AD) is one of the most common neurodegenerative diseases worldwide. It is characterized by the accumulation of amyloid-beta (Aβ) plaques in which Aβ42 is the most toxic and aggressive species. This work investigates the possibility of salvianolic acid B (SalB), a natural compound with established neuroprotective activity, to counteract the Aβ42-induced toxicity in a Drosophila melanogaster model of AD. SalB's effect was assessed in the Aβ42-expressing Drosophila model by measuring three major AD-related behavioural symptoms: eye morphology (cytotoxicity), lifespan, and locomotor activity. The eye assay, longevity, and locomotion assays were employed, followed by RNA sequencing (RNA-seq) to identify molecular alterations following SalB treatment. Aβ42 expression in the Aβ42-expressing Drosophila model resulted in deformed eye morphology, reduced lifespan, and motor impairment. Treatment with SalB restored part of eye morphology, extended lifespan, and improved locomotion. RNA-seq revealed differential gene expression in oxidative phosphorylation, glutathione metabolism, and detoxification processes, suggesting the involvement of antioxidant defence in SalB-mediated neuroprotection. These findings indicate that SalB could be therapeutic for AD and other neurodegenerative disorders, possibly through the modulation of oxidative stress against Aβ42 toxicity. Further research is warranted to address its mechanisms and other uses in neurodegenerative therapy.