STAR: ultrafast universal RNA-seq aligner

Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis

The establishment of germ layers during early development is crucial for body formation. The Drosophila zygote serves as a model for investigating these transitions in relation to the chromatin landscape. However, the cellular heterogeneity of the blastoderm embryo poses a challenge for gaining mechanistic insights. Using 10× Multiome, we simultaneously analyzed the in vivo epigenomic and transcriptomic states of wild-type, E(z)-, and CBP-depleted embryos during zygotic genome activation at single-cell resolution. We found that pre-zygotic H3K27me3 safeguards tissue-specific gene expression by modulating cis-regulatory elements. Furthermore, we demonstrate that CBP is essential for cell fate specification functioning as a transcriptional activator by stabilizing transcriptional factors binding at key developmental genes. Surprisingly, while CBP depletion leads to transcriptional arrest, chromatin accessibility continues to progress independently through the retention of stalled RNA Polymerase II. Our study reveals fundamental principles of chromatin-mediated gene regulation essential for establishing and maintaining cellular identities during early embryogenesis.

Praja2 controls P-body assembly and translation in glioblastoma by non-proteolytic ubiquitylation of DDX6

Glioblastoma multiforme (GBM) is the most lethal form of malignant brain tumor in adults. Dysregulation of protein synthesis contributes to cancer cell plasticity, driving GBM cell heterogeneity, metastatic behavior, and drug resistance. Understanding the complex network and signaling pathways governing protein translation, is therefore an important goal for GBM treatment. Here we identify a novel signaling network centered on the E3 ubiquitin ligase praja2 that controls protein translation in GBM. Praja2 forms a multimeric complex with the RNA helicase DDX6, which inhibits translation of target RNAs within processing bodies (P-bodies). Stimulation of cAMP signaling through activation of G-protein-coupled receptors induces P-body assembly through praja2-mediated non-proteolytic polyubiquitylation of DDX6. Genetic inactivation of praja2 reshapes DDX6/mRNA complexes and translating polysomes and promotes cellular senescence and GBM growth arrest. Expression of an ubiquitylation-defective DDX6 mutant suppresses the assembly of P-bodies and sustains GBM growth. Taken together, our findings identify a cAMP-driven network that controls translation in P-bodies and GBM growth.

A mouse model of cardiac immunoglobulin light chain amyloidosis reveals insights into tissue accumulation and toxicity of amyloid fibrils

Immunoglobulin light chain (LC) amyloidosis (AL) is one of the most common types of systemic amyloidosis but there is no reliable in vivo model for better understanding this disease. Here, we develop a transgenic mouse model producing a human AL LC. We show that the soluble full length LC is not toxic but a single injection of pre-formed amyloid fibrils or an unstable fragment of the LC leads to systemic amyloid deposits associated with early cardiac dysfunction. AL fibrils in mice are highly similar to that of human, arguing for a conserved mechanism of amyloid fibrils formation. Overall, this transgenic mice closely reproduces human cardiac AL amyloidosis and shows that a partial degradation of the LC is likely to initiate the formation of amyloid fibrils in vivo, which in turn leads to cardiac dysfunction. This is a valuable model for research on AL amyloidosis and preclinical evaluation of new therapies.

A personalized metabolic modelling approach through integrated analysis of RNA-Seq-based genomic variants and gene expression levels in Alzheimer's disease

Generating condition-specific metabolic models by mapping gene expression data to genome-scale metabolic models (GEMs) is a routine approach to elucidate disease mechanisms from a metabolic perspective. On the other hand, integrating variants that perturb enzyme functionality from the same RNA-seq data may enhance GEM accuracy, offering insights into genome-wide metabolic pathology. Our study pioneers the extraction of both transcriptomic and genomic data from the same RNA-seq data to reconstruct personalized metabolic models. We map genes with significantly higher load of pathogenic variants in Alzheimer's disease (AD) onto a human GEM together with the gene expression data. Comparative analysis of the resulting personalized patient metabolic models with the control models shows enhanced accuracy in detecting AD-associated metabolic pathways compared to the case where only expression data is mapped on the GEM. Besides, several otherwise would-be missed pathways are annotated in AD by considering the effect of genomic variants.

Spatial transcriptomic imaging of an intact organism using volumetric DNA microscopy

Lymphatic, nervous and tumor tissues exhibit complex physiology arising from three-dimensional interactions within genetically unique microenvironments. Here we develop a technology capable of volumetrically imaging transcriptomes, genotypes and morphologies in a single measurement, without relying on prior knowledge of spatial organization or genetic sequences. Our method extends DNA microscopy into three dimensions at scales involving 107 molecules by forming a distributed intermolecular network of proximal unique DNA barcodes tagging complementary DNA molecules inside the specimen. After sequencing the DNA-encoded network, an image of molecular positions is inferred using geodesic spectral embeddings, a dimensionality reduction approach that we show to be especially suitable for this data-inverse problem. Applying whole-transcriptome volumetric DNA microscopy to intact zebrafish embryos, we demonstrate that three-dimensional image inference recapitulates zebrafish morphology and known gene expression patterns, capturing the spatial organization of gene sequences. Our extension of spatial genetic measurements to three dimensions, independent of prior templates, opens the door to detailed joint resolution of genomics and morphology in biological tissues.

Impact of BRCA mutations, age, surgical indication, and hormone status on the molecular phenotype of the human Fallopian tube

The human Fallopian tube (FT) is an important organ in the female reproductive system and has been implicated as a site of origin for pelvic serous cancers, including high-grade serous tubo-ovarian carcinoma (HGSC). We have generated comprehensive whole-genome bisulfite sequencing, RNA-seq, and proteomic data of over 100 human FTs, with detailed clinical covariate annotations. Our results challenge existing paradigms that extensive epigenetic, transcriptomic and proteomic alterations exist in the FTs from women carrying heterozygous germline BRCA1/2 pathogenic variants. We find minimal differences between BRCA1/2 carriers and non-carriers prior to loss of heterozygosity. Covariates such as age and surgical indication can confound BRCA1/2-related differences reported in the literature, mainly through their impact on cell composition. We systematically document and highlight the degree of variations across normal human FT, defining five groups capturing major cellular and molecular changes across various reproductive stages, pregnancy, and aging. We are able to associate gene, protein, and epigenetic changes with these and other clinical covariates, but not heterozygous BRCA1/2 mutation status. This sheds new light into prevention and early detection of tumorigenesis in populations at high-risk for ovarian cancer.

Regulatory and disruptive variants in the CLCN2 gene are associated with modified skin color pattern phenotypes in the corn snake

BACKGROUND

Snakes exhibit a broad variety of adaptive colors and color patterns, generated by the spatial arrangement of chromatophores, but little is known of the mechanisms responsible for these spectacular traits. Here, we investigate a mono-locus trait with two recessive alleles, motley and stripe, that both cause pattern aberrations in the corn snake.

RESULTS

We use mapping-by-sequencing to identify the genomic interval where the causal mutations reside. With our differential gene expression analyses, we find that CLCN2 (Chloride Voltage-Gated Channel 2), a gene within the genomic interval, is significantly downregulated in Motley embryonic skin. Furthermore, we identify the stripe allele as the insertion of an LTR-retrotransposon in CLCN2, resulting in a disruptive mutation of the protein. We confirm the involvement of CLCN2 in color pattern formation by producing knock-out snakes that present a phenotype similar to Stripe. In humans and mice, disruption of CLCN2 results in leukoencephalopathy, as well as retinal and testes degeneration. Our single-cell transcriptomic analyses in snakes reveal that CLCN2 is indeed expressed in chromatophores during embryogenesis and in the adult brain, but the behavior and fertility of Motley and Stripe corn snakes are not impacted.

CONCLUSIONS

Our genomic, transcriptomic, and functional analyses identify a plasma membrane anion channel to be involved in color pattern development in snakes and show that an active LTR-retrotransposon might be a key driver of trait diversification in corn snakes.

Leveraging Vitamin C to Augment Nanoenabled Photothermal Immunotherapy

Photothermal immunotherapy (PTI) is valuable for precise tumor targeting and immune activation. However, its efficacy is hindered by insufficient immune response, elevated antioxidant levels within tumor, and intrinsic tumor resistance mechanisms. This study introduces Vitamin C (VC), a widely available dietary nutrient, as an effective enhancer for PTI. High-dose VC induces oxidative imbalance in tumor cells, making them more susceptible to nanoenabled near-infrared-II photothermal therapy (NIR-II PTT) with the photosensitizer IR1080. The combination of VC and NIR-II PTT significantly amplifies antitumor immunity by upregulating CXCL16 expression and promoting CXCR6+ T cell infiltration. Clinical data reveal that higher CXCL16 and CXCR6 levels in human tumors correlate with improved survival and T cell infiltration, underscoring the translational potential of this approach. This study positions VC as a safe, accessible, and cost-effective dietary enhancer for PTI, reshaping the role of dietary nutrients in cancer therapy and offering a strategy for overcoming treatment resistance.

irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA

RNA-binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport and translation1-3. Dysfunctional RNA-RBP interactions contribute to the pathogenesis of human disease1,4,5; however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. Here, to address this, non-isotopic ligation-based ultraviolet-light-induced cross-linking and immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest. irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, revealing patterns of RBP-RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodelling in response to epidermal growth factor (EGF), revealing that EGF-induced recruitment of UPF1 adjacent to HNRNPC promotes splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships observed in irCLIP-RNP and identified HNRNPC and UPF1 RBP co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.

Stem cell culture conditions affect in vitro differentiation potential and mouse gastruloid formation

Aggregating low numbers of mouse embryonic stem cells (mESCs) and inducing Wnt signalling generates 'gastruloids', self-organising complex structures that display an anteroposterior organisation of cell types derived from all three germ layers. Current gastruloid protocols display considerable heterogeneity between experiments in terms of morphology, elongation efficiency, and cell type composition. We therefore investigated whether altering the mESC pluripotency state would provide more consistent results. By growing three mESC lines from two different genetic backgrounds in different intervals of ESLIF and 2i medium the pluripotency state of cells was modulated, and mESC culture as well as the resulting gastruloids were analysed. Microscopic analysis showed a pre-culture-specific effect on gastruloid formation, in terms of aspect ratio and reproducibility. RNA-seq analysis of the mESC start population confirmed that short-term pulses of 2i and ESLIF modulate the pluripotency state, and result in different cellular states. Since multiple epigenetic regulators were detected among the top differentially expressed genes, we further analysed genome-wide DNA methylation and H3K27me3 distributions. We observed epigenetic differences between conditions, most dominantly in the promoter regions of developmental regulators. Lastly, when we investigated the cell type composition of gastruloids grown from these different pre-cultures, we observed that mESCs subjected to 2i-ESLIF preceding aggregation generated gastruloids more consistently, including more complex mesodermal contributions as compared to the ESLIF-only control. These results indicate that optimisation of the mESCs pluripotency state allows the modulation of cell differentiation during gastruloid formation.

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.

High-quality genome assembly of the azooxanthellate coral Tubastraea coccinea (Lesson, 1829)

Coral reefs are among the most biodiverse and economically significant ecosystems globally, yet they are increasingly degrading due to global climate change and local human activities. The sun coral Tubastraea coccinea (T. coccinea) an obligate heterotroph lacking symbiotic zooxanthellae, exhibits remarkable tolerance to conditions that cause bleaching and mortality in zooxanthellate species. With its extensive low-latitude distribution across multiple oceans, T. coccinea has become a highly invasive species, adversely impacting native species, degrading local ecosystems, and causing significant socio-economic challenges that demand effective management. Despite substantial research efforts, the molecular biology of T. coccinea remains insufficiently characterized. To address this gap, we generated a draft genome assembly for T. coccinea using PacBio Hi-Fi long-read sequencing. The assembly spans 875.9 Mb with a scaffold N50 of 694.3 kb and demonstrates high completeness, with a BUSCO score of 97.4%. A total of 37,307 protein-coding sequences were identified, 95.2% of which were functionally annotated through comparisons with established protein databases. This reference genome provides a valuable resource for understanding the genetic structure of T. coccinea, advancing research into its adaptive mechanism to environmental changes, and informing conservation and management strategies to mitigate its invasive impact.

Oncogenic properties of wild-type DNA repair gene FANCA in breast cancer

FANCA is one of the 23 genes whose deficiencies lead to defective DNA interstrand crosslink repair and cancer-prone Fanconi anemia disease. Beyond its functions in DNA repair and tumor suppression, we report that high FANCA expression is strongly associated with breast cancer development. Overexpression of WT-FANCA significantly promotes breast cancer cell proliferation and tumor growth both in vitro and in vivo, while FANCA deficiency severely compromises the proliferation of breast cancer cells, but not non-tumorigenic breast epithelial cells. Heterozygous knockout of FANCA in breast cancer mouse models is sufficient to cause significant reduction of breast tumor growth in vivo. Furthermore, we have shown that high FANCA expression in breast cancer correlates with promoter hypomethylation in a TET-dependent manner, and TET inhibition recapitulates the proliferation defects caused by FANCA deficiency. Our study identifies the oncogenic properties of WT-FANCA and shows that FANCA is a promising target for breast cancer intervention.

Survey of gene, lncRNA and transposon transcription patterns in four mouse organs highlights shared and organ-specific sex-biased regulation

BACKGROUND

Sex-biased gene regulation is the basis of sexual dimorphism in phenotypes and has been studied across different cell types and different developmental stages. However, sex-biased expression of transposable elements (TEs), which represent nearly half of the mammalian genome and have the potential of influencing genome integrity and regulation, remains underexplored.

RESULTS

We report a survey of gene, lncRNA, and TE expression in four organs from mice with different combinations of gonadal and genetic sex. The data show remarkable variability among organs with respect to the impact of gonadal sex on transcription with the strongest effects observed in the liver. In contrast, the X-chromosome dosage alone had a modest influence on sex-biased transcription across organs, albeit interaction between X-dosage and gonadal sex cannot be ruled out. The presence of the Y-chromosome influences TE, but not gene or lncRNA, expression in the liver. Notably, 90% of sex-biased TEs (sDETEs) reside in clusters. Moreover, 54% of these clusters overlap or reside less than 100 kb from sex-biased genes or lncRNAs, share the same sex bias, and also have higher expression levels than sDETE clusters that do not co-localize with other types of sex-biased transcripts. We test the heterochromatic sink hypothesis that predicts higher expression of TEs in XX individuals finding no evidence to support it.

CONCLUSIONS

Our data show that sex-biased expression of TEs varies among organs with the highest numbers of sDETEs found in the liver following trends observed for genes and lncRNAs. It is enhanced by proximity to other types of sex-biased transcripts.

Natural genetic variation in wild-derived mice controls host survival and transcriptional responses during endotoxic shock

Innate immune cells sense microbial danger signals, resulting in dynamic transcriptional reprogramming and rapid inflammatory responses. If not properly regulated, such responses can be detrimental to the host, as is seen in septic shock. A better understanding of the genetic regulation of responses during endotoxemia could provide potential therapeutic insights. However, the majority of animal model studies have been performed using classic inbred laboratory strains of mice, capturing limited genetic diversity. Here, we compared classic inbred C57BL/6 (B6) mice with wild-derived and genetically divergent PWD/PhJ (PWD) mice using in vivo and in vitro models of endotoxemia. Compared with B6 mice, PWD mice were markedly resistant to bacterial lipopolysaccharide (LPS)-induced endotoxic shock. Using LPS stimulation of bone marrow derived dendritic cells (BMDC) and RNA sequencing, we demonstrate that B6 and PWD BMDCs exhibit partially overlapping yet highly divergent transcriptional responses, with B6 skewed toward stereotypical proinflammatory pathway activation, and PWD engaging regulatory or developmental pathways. To dissect genetic regulation of inflammatory responses by allelic variants, we used BMDCs from a sub-consomic strain carrying a ∼50 Mb PWD-derived portion of chromosome 11 on the B6 background. This identified a subset of cis-regulated and a large number of trans-regulated genes. Bioinformatic analyses identified candidate trans regulators encoded in the chromosome 11 locus as transcription factors Irf1, Ncor1, and Srebf1. Our results demonstrate that natural genetic variation controls host survival and transcriptional reprogramming during endotoxemia, suggesting possibilities for prediction of sepsis risk and/or personalized therapeutic interventions.

Mechanistic Insights into Hybridization-Based Off-Target Activity of GalNAc-siRNA Conjugates

Nonclinical safety screening of small interfering RNAs (siRNAs) conjugated to a trivalent N-acetylgalactosamine (GalNAc) ligand is typically carried out in rats at exaggerated exposures in a repeat-dose regimen. We have previously shown that at these suprapharmacological doses, hepatotoxicity observed with a subset of GalNAc-siRNAs is largely driven by undesired RNA-induced silencing complex (RISC)-mediated antisense strand seed-based off-target activity, similar to microRNA-like regulation. However, the RISC component requirements for off-target activity of siRNAs have not been evaluated. Here, we evaluate the roles of major RISC components, AGO and TNRC6 (or GW182) proteins, in driving on- and off-target activity of GalNAc-siRNAs in hepatocytes, in vitro and in vivo. We demonstrate that knocking down AGO2, but not AGO1 or AGO4, is protective against GalNAc-siRNA-driven off-target activity and hepatotoxicity. As expected, knocking down AGO2, but not AGO1 or AGO4, reduces the on-target activity of GalNAc-siRNA. Similarly, knocking down TNRC6 paralogs, TNRC6A or TNRC6B, but not TNRC6C, is protective against off-target activity and hepatotoxicity while having minimal impact on the on-target activity of GalNAc-siRNA. These data indicate that while AGO2 is the only RISC component required for the on-target activity of GalNAc-siRNAs, the undesired off-target activity and hepatotoxicity of a subset of GalNAc-siRNAs are mediated via the RISC composed predominantly of AGO2 and TNRC6 paralogs TNRC6A and/or TNRC6B.

CREB3 gain of function variants protect against ALS

Amyotrophic lateral sclerosis (ALS) is a fatal and rapidly evolving neurodegenerative disease arising from the loss of glutamatergic corticospinal neurons (CSN) and cholinergic motoneurons (MN). Here, we performed comparative cross-species transcriptomics of CSN using published snRNA-seq data from the motor cortex of ALS and control postmortem tissues, and performed longitudinal RNA-seq on CSN purified from male Sod1G86R mice. We report that CSN undergo ER stress and altered mRNA translation, and identify the transcription factor CREB3 and its regulatory network as a resilience marker of ALS, not only amongst vulnerable neuronal populations, but across all neuronal populations as well as other cell types. Using genetic and epidemiologic analyses we further identify the rare variant CREB3R119G (rs11538707) as a positive disease modifier in ALS. Through gain of function, CREB3R119G decreases the risk of developing ALS and the motor progression rate of ALS patients.

Callus organoids reveal distinct cartilage to bone transition mechanisms across donors and a role for biological sex

Clinical translation of tissue-engineered advanced therapeutic medicinal products is hindered by a lack of patient-dependent and independent in-process biological quality controls that are reflective of in vivo outcomes. Recent insights into the mechanism of native bone repair highlight a robust path dependence. Organoid-based bottom-up developmental engineering mimics this path-dependence to design personalized living implants scaffold-free, with in-build outcome predictability. Yet, adequate (noninvasive) quality metrics of engineered tissues are lacking. Moreover, insufficient insight into the role of donor variability and biological sex as influencing factors for the mechanism toward bone repair hinders the implementation of such protocols for personalized bone implants. Here, male and female bone-forming organoids were compared to non-bone-forming organoids regarding their extracellular matrix composition, transcriptome, and secreted proteome signatures to directly link in vivo outcomes to quality metrics. As a result, donor variability in bone-forming callus organoids pointed towards two distinct pathways to bone, through either a hypertrophic cartilage or a fibrocartilaginous template. The followed pathway was determined early, as a biological sex-dependent activation of distinct progenitor populations. Independent of donor or biological sex, a cartilage-to-bone transition was driven by a common panel of secreted factors that played a role in extracellular matrix remodeling, mineralization, and attraction of vasculature. Hence, the secreted proteome is a source of noninvasive biomarkers that report on biological potency and could be the missing link toward data-driven decision-making in organoid-based bone tissue engineering.

Implication of bone marrow adipose tissue in bone homeostasis during osteoarthritis

OBJECTIVE

To explore the role of bone marrow adipocytes (BMAds) in osteoarthritis (OA).

METHODS

Male and female C57BL/6 mice (n=4/group) underwent meniscectomy (MNX) or SHAM surgery. OA was determined using OARSI score and the number of perilipin+ adipocytes was quantified. Mesenchymal Stromal Cells (MSCs) from MNX and SHAM mice were differentiated into osteoblasts and adipocytes. Human adipocytes and MSCs (n=8) were enzymatically isolated from epiphyseal and metaphyseal marrow, and from subcutaneous adipose tissue (SCAT) of hip OA patients. Human OA MSCs were differentiated into osteoblasts and adipocytes (OA-Diff-hAdipo). Gene expression patterns of epiphyseal and metaphyseal BMAds, SCAT adipocytes and OA-Diff-hAdipo were evaluated by RNAseq (n=4). The effect conditioned media from OA epiphyseal bone (n=5) on the alkaline phosphatase (ALP) activity and mineralization kinetics was assessed in vitro.

RESULTS

Increase in BMAd density was positively correlated with cartilage degradation in MNX mice. OA modified the differentiation capacity of MSCs, accelerating adipocyte differentiation and failing to produce osteoblasts in both human and mice. Human epiphyseal, metaphyseal and SCAT adipocytes from the same OA patients each displayed a specific transcriptome, suggesting different functions. Enrichment analysis defined metaphyseal OA-BMAds as cells implicated in hematopoietic stem cell differentiation. On the other hand, epiphyseal OA-BMAds were considered as osteogenic cells showing an up-regulation of genes related to bone mineralization and remodeling. Specifically, OA epiphysis-secreted molecules decreased ALP activity and altered in vitro the mineralization process.

CONCLUSION

All these results support the emergence of BMAds as new cell partners in OA, opening new venues for therapeutic approaches.

Chromosome-level genome assembly of an endoparasitoid Cotesia ruficrus

Cotesia ruficrus is a gregarious larval endoparasitoid of many important agricultural pest moths, such as the fall armyworm, northern armyworm and rice leaffolder. While eight of Cotesia genomes had been reported, high-quality genomic data of C. ruficrus has yet to be performed. This study presents a chromosome-scale genome assembly of C. ruficrus, utilizing both PacBio HiFi-reads and Hi-C reads. The genome size is about 185.3 Mb harboring 10 chromosomes, and 209 unanchored scaffolds with a scaffold N50 length of 15.81 Mb. The anchored rate of sequences to chromosomes is 95.55%. A total of 14,001 genes have been annotated. This work delivers a first high-quality, chromosome-scale genome for C. ruficrus, enriching the datasets for comparative evolutionary studies within the Cotesia genus. Additionally, it offers a valuable genomic resource for future biological and genetic research, as well as for enhancing pest management strategies, such as biological control.

Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer

Extrachromosomal circular DNA (ecDNA) has been found in most types of human cancers, and ecDNA incorporating viral genomes has recently been described, specifically in human papillomavirus (HPV)-mediated oropharyngeal cancer (OPC). However, the molecular mechanisms of human-viral hybrid ecDNA (hybrid ecDNA) for carcinogenesis remains elusive. We characterize the epigenetic status of hybrid ecDNA using HPVOPC cell lines and patient-derived tumor xenografts, identifying HPV oncogenes E6/E7 in hybrid ecDNA are flanked by previously unrecognized somatic DNA enhancers and HPV L1 enhancers, with strong cis-interactions. Targeting of these enhancers by clustered regularly interspaced short palindromic repeats interference or hybrid ecDNA by bromodomain and extra-terminal inhibitor reduces E6/E7 expression, and significantly inhibites in vitro and/or in vivo growth only in ecDNA(+) models. HPV DNA in hybrid ecDNA structures are associated with previously unrecognized somatic and HPV enhancers in hybrid ecDNA that drive HPV ongogene expression and carcinogenesis, and can be targeted with ecDNA disrupting therapeutics.

LocusMasterTE: integrating long-read RNA sequencing improves locus-specific quantification of transposable element expression

Transposable elements (TEs) can influence human diseases by disrupting genome integrity, yet their quantification has been challenging due to the repetitive nature of these sequences across the genome. We develop LocusMasterTE, a method that integrates long-read with short-read RNA-seq to increase the accuracy of TE expression quantification. By incorporating fractional transcript per million values from long-read sequencing data into an expectation-maximization algorithm, LocusMasterTE reassigns multi-mapped reads, enhancing accuracy in short-read-based TE quantification. We validate the method with simulated and human datasets. LocusMasterTE may give new insights into TE functions through precise quantification.

Single-cell transcriptomic analysis identifies tissue-specific fibroblasts as the main modulators of myeloid cells in peritoneal metastasis of different origin

Colorectal cancer (CRC) peritoneal metastasis (CPM) is related to limited therapy options and poor prognosis. Although stromal cells heavily infiltrate most CPMs, interactions between different cell types in their microenvironment remain unclear. Here, we investigated tumor and distant normal tissue from CPM and CRC patients using single-cell RNA sequencing. Investigating the incoming and outgoing signals between cells revealed that fibroblasts dominate the CPM signaling landscape with myeloid cells as their strongest interaction partner. Using immunohistochemistry, we confirmed that fibroblasts co-localize with macrophages in the CPM microenvironment. A fibroblast sub-population detected only in CPM and normal peritoneum demonstrated immunoregulatory properties in co-culture experiments, and was further detected in additional peritoneal malignancies derived from ovarian and gastric origin. This novel fibroblast type and its communication with macrophages could be attractive targets for therapeutic interventions in CPM and potentially peritoneal surface malignancies in general.

Human long noncoding RNA VILMIR is induced by major respiratory viral infections and modulates the host interferon response

Long noncoding RNAs (lncRNAs) are a newer class of noncoding transcripts identified as key regulators of biological processes. Here, we aimed to identify novel lncRNA targets that play critical roles in major human respiratory viral infections by systematically mining large-scale transcriptomic data sets. Using bulk RNA-sequencing (RNA-seq) analysis, we identified a previously uncharacterized lncRNA, named virus-inducible lncRNA modulator of interferon response (VILMIR), that was consistently upregulated after in vitro influenza infection across multiple human epithelial cell lines and influenza A virus subtypes. VILMIR was also upregulated after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and respiratory syncytial virus (RSV) infections in vitro. We experimentally confirmed the response of VILMIR to influenza infection and interferon-beta (IFN-β) treatment in the A549 human epithelial cell line and found the expression of VILMIR was robustly induced by IFN-β treatment in a dose- and time-specific manner. Single-cell RNA-seq analysis of bronchoalveolar lavage fluid samples from coronavirus disease 2019 (COVID-19) patients uncovered that VILMIR was upregulated across various cell types, including at least five immune cells. The upregulation of VILMIR in immune cells was further confirmed in the human T cell and monocyte cell lines, SUP-T1 and THP-1, after IFN-β treatment. Finally, we found that knockdown of VILMIR expression reduced the magnitude of host transcriptional responses to both IFN-β treatment and influenza A virus infection in A549 cells. Together, our results show that VILMIR is a novel interferon-stimulated gene (ISG) that regulates the host interferon response and may be a potential therapeutic target for human respiratory viral infections upon further mechanistic investigation.IMPORTANCEIdentifying host factors that regulate the immune response to human respiratory viral infection is critical to developing new therapeutics. Human long noncoding RNAs (lncRNAs) have been found to play key regulatory roles during biological processes; however, the majority of lncRNA functions within the host antiviral response remain unknown. In this study, we identified that a previously uncharacterized lncRNA, virus-inducible lncRNA modulator of interferon response (VILMIR), is upregulated after major respiratory viral infections including influenza, severe acute respiratory syndrome coronavirus 2, and respiratory syncytial virus. We demonstrated that VILMIR is an interferon-stimulated gene that is upregulated after interferon-beta (IFN-β) in several human cell types. We also found that knockdown of VILMIR reduced the magnitude of host transcriptional responses to IFN-β treatment and influenza A infection in human epithelial cells. Our results reveal that VILMIR regulates the host interferon response and may present a new therapeutic target during human respiratory viral infections.

N-acetyltransferase 10 catalyzes RNA N4-acetylcytidine to regulate photosynthesis in rice

N4-acetylcytidine (ac4C) is a novel mRNA modification that enhances RNA stability and translation in mammals and plants. We previously identified ac4C in Arabidopsis, introduced by two homologs of human N-acetyltransferase 10 (NAT10). While ac4C influences leaf development in Arabidopsis, its role in rice is unclear. In this study, we identify OsNAT10 as the ac4C writer in rice. osnat10 mutants show developmental defects, including shorter roots, fewer tillers, and lower yield. Compared with wild type, ac4C-modified genes are less abundant in osnat10, particularly those related to photosynthesis. Additionally, osnat10 exhibits decreased photosynthetic capacity and reduced RNA stability and translation efficiency of ac4C target genes, like LIGHT-INDUCED RICE 1 (LIR1). Overexpressing OsLIR1 partially rescues osnat10 defects, underscoring OsNAT10's role in photosynthesis regulation. Our findings highlight ac4C's crucial function in photosynthesis and plant development, offering insights into epitranscriptomic modifications for crop improvement.

Transcriptomic profiling of blood platelets identifies a diagnostic signature for pancreatic cancer

BACKGROUND

Pancreatic cancer (PaCa) is a deadly malignancy that is often diagnosed at an advanced stage, limiting treatment and reducing survival. There is an urgent need for convenient and accurate diagnostic markers for the early detection of PaCa.

METHODS

In this multicenter case-control study, we performed transcriptome analysis of 673 platelet samples from different in-house and public cohorts. RNA sequencing and RT-qPCR were used to discover and validate potential platelet biomarkers. A multi-gene signature was developed using binomial generalized linear model and independently validated in multicenter cohorts.

RESULTS

Two platelet RNAs, SCN1B and MAGOHB, consistently showed robust altered expression patterns between PaCa and healthy controls across cohorts, as confirmed by both RNA sequencing and RT-qPCR. The diagnostic two-RNA signature, PLA2Sig, demonstrated remarkable performance in detecting PaCa, with area under the receiver operating characteristic curve (AUC) values of 0.808, 0.900, 0.783, and 0.830 across multicenter cohorts. Furthermore, PLA2Sig effectively identified resectable stage I&II PaCa cases with an AUC of 0.812. Notably, PLA2Sig outperformed the traditional serum markers carcinoembryonic antigen and carbohydrate antigen 19-9 in distinguishing PaCa from healthy controls, and is complementary to established blood-based screening biomarkers.

CONCLUSION

These findings provide preliminary but promising evidence for the potential utility of platelet RNAs as an alternative non-invasive liquid biopsy tool for the early detection of PaCa.

Transcriptomic characterisation of acute myeloid leukemia cell lines bearing the same t(9;11) driver mutation reveals different molecular signatures

BACKGROUND

Acute myeloid leukemia (AML) is the most common type of acute leukemia, accounting for 20% of cases in children and adolescents. Genome-wide studies have identified genes that are commonly mutated in AML, including many epigenetic regulators involved in either DNA methylation (DNMT3A, TET2, IDH1/2) or histone post-translational modifications (ASXL1, EZH2, MLL1). Several cell lines derived from AML patients are widely used in cancer research. Whether important differences in these cell lines exist remains poorly characterised.

RESULTS

Here, we used RNA sequencing (RNA-Seq) to contrast the transcriptome of four commonly used AML-derived cell lines: THP-1, NOMO-1, MOLM-13 bearing the common initiating t(9;11) translocation, and MV4.11 bearing the t(4;11) translocation. Gene set enrichment analyses and comparison of key transcription and epigenetic regulator genes revealed important differences in the transcriptome, distinguishing these AML models. Among these, we found striking differences in the expression of clusters of genes located on chromosome 19 encoding Zinc Finger (ZNF) transcriptional repressors. Low expression of many ZNF genes within these clusters is associated with poor survival in AML patients.

CONCLUSION

The present study offers a valuable resource by providing a detailed comparative characterisation of the transcriptome of cell lines within the same AML subtype used as models for leukemia research.

Integrative multi-omics analysis of metabolic dysregulation induced by occupational benzene exposure in mice

Type 2 Diabetes Mellitus (T2DM) is a significant public health burden. Emerging evidence links volatile organic compounds (VOCs), such as benzene to endocrine disruption and metabolic dysfunction. However, the effects of chronic environmentally relevant VOC exposures on metabolic health are still emerging. Building on our previous findings that benzene exposure at smoking levels (50 ppm) induces metabolic impairments in male mice, we investigated the effects of benzene exposure below OSHA's Occupational Exposure Limit (OEL) on metabolic health. Adult male C57BL/6 mice were exposed to 0.9 ppm benzene 8 h a day for 9 weeks. We assessed measures of metabolic homeostasis and conducted RNA and proteome sequencing on insulin-sensitive organs (liver, skeletal muscle, adipose tissue). At this dose, exposure caused significant metabolic disruptions, including hyperglycemia, hyperinsulinemia, and insulin resistance. Transcriptomic analysis of liver, muscle, and adipose tissue identified key changes in metabolic and immune pathways especially in liver. Proteomic analysis of the liver revealed mitochondrial dysfunction as a shared feature, with disruptions in oxidative phosphorylation, mitophagy, and immune activation. Comparative analysis with high-dose (50 ppm) exposure showed conserved and dose-specific transcriptomic changes in liver, particularly in metabolic and immune responses. Our study is the first to comprehensively assess the impacts of occupational benzene exposure on metabolic health, highlighting mitochondrial dysfunction as a central mechanism and the dose-dependent molecular pathways in insulin-sensitive organs driving benzene-induced metabolic imbalance. Our data indicate that the current OSHA OEL for benzene is insufficient and needs to be lowered, as they could result in adverse metabolic health in exposed workers, particularly men, following chronic exposure.

Placental transcriptome analysis in opioid-exposed versus non-opioid exposed pregnancies

INTRODUCTION

Opioid exposure during pregnancy may significantly alter gene expression in the placenta, potentially disrupting its function and influencing fetal brain development. These alterations may contribute to adverse outcomes such as neonatal opioid withdrawal syndrome (NOWS). In this study, we aim to systematically investigate the changes in placental gene expression associated with maternal opioid exposure to better understand the underlying molecular mechanisms and their implications for fetal health.

METHODS

Fresh placental tissue samples were collected from 18 opioid-exposed pregnancies and 26 non-opioid-exposed control pregnancies. Transcriptomic changes related to opioid exposure were assessed using RNA sequencing (RNA-seq).

RESULTS

Among the 16,172 genes detected, 55 showed differential expression (Padjusted < 0.25 or Punadjusted < 0.001) in opioid-exposed placentas. Gene Set Enrichment Analysis (GSEA) revealed that the differentially expressed genes were primarily associated with immune responses, neuronal development and function, as well as cell replication and division. Computational deconvolution using the PlacentaCellEnrich program identified significant enrichment of upregulated genes in decidual NK cells. Furthermore, integrative analysis of DNA methylation and gene expression showed an enrichment of differentially methylated genes among downregulated genes in opioid-exposed placentas.

DISCUSSION

Our findings suggest that opioid exposure during pregnancy may disrupt critical placental pathways, particularly those involved in immune responses. Future studies focusing on transcriptomic changes in specific placental cell types will be essential for fully understanding the structural and functional alterations in the placenta due to opioid exposure during pregnancy.

The balance between IFN-γ and ERK/MAPK signaling activities ensures lifelong maintenance of intestinal stem cells

While the intestinal epithelium has the highest cellular turnover rates in the mammalian body, it is also considered one of the tissues most resilient to aging-related disorders. Here, we reveal an innate protective mechanism that safeguards intestinal stem cells (ISCs) from environmental conditions in the aged intestine. Using in vivo phenotypic analysis, transcriptomics, and in vitro intestinal organoid studies, we show that age-dependent activation of interferon-γ (IFN-γ) signaling and inactivation of extracellular signal-regulated kinase/mitogen-activated protein kinase (ERK/MAPK) signaling are responsible for establishing an equilibrium of Lgr5+ ISCs-between active and quiescent states-to preserve the ISC pool during aging. Furthermore, we show that differentiated cells have different sensitivities to each of the two signaling pathways, which may induce aging-related, functional, and metabolic changes in the body. Thus, our findings reveal an exquisitely balanced, age-dependent signaling mechanism that preserves stem cells at the expense of differentiated cells.

Maternal progesterone and adipose mPRε in pregnancy regulate the embryonic nutritional state

Sex steroid hormones such as progesterone play a pivotal role in reproductive functions and maintaining pregnancy; however, the impact of progesterone on the interaction between mother and embryo is unclear. Here, we demonstrate that the relationship between maternal progesterone and membrane progesterone receptor epsilon (mPRε) in adipose tissue regulates embryonic nutritional environment and growth after birth in mice. The activation of adipose mPRε by increased progesterone during pregnancy enhances maternal insulin resistance via prostaglandin production, efficiently providing glucose to embryos. Correspondingly, the offspring of mPRε-deficient mothers exhibited metabolic dysfunction, whereas mPRε-deficient mothers with high-fat diet-induced obesity exhibited improved insulin sensitivity. These findings establish the importance of progesterone as a nutritional regulator between mother and embryo. Additionally, mPRε may represent a modulator for treating pregnant glycemic control disorders such as gestational diabetes mellitus, as well as metabolic syndrome in offspring.

Functional inhibition of core spliceosomal machinery activates intronic premature cleavage and polyadenylation of pre-mRNAs

The catalytic role of U6 snRNP in pre-mRNA splicing has been well established. In this study, we utilize an antisense morpholino oligonucleotide (AMO) specifically targeting catalytic sites of U6 snRNA to achieve functional knockdown of U6 snRNP in HeLa cells. The data show a significant increase in global intronic premature cleavage and polyadenylation (PCPA) events, similar to those observed with U1 AMO treatment, as demonstrated by mRNA 3'-seq analysis. Mechanistically, we provide evidence that U6 AMO-mediated splicing inhibition might be the driving force for PCPA as application of another specific AMO targeting U2 snRNP results in similar global PCPA effects. Together with our recently published findings that demonstrate the global inhibitory effect of U4 snRNP on intronic PCPA, our data highlight the critical role of splicing in suppressing intronic PCPA and support a model in which splicing and polyadenylation may compete with each other within introns during co-transcriptional mRNA processing.

The role of osteopontin in modulating macrophage phagocytosis of calcium oxalate crystals

In inflammation, osteopontin (OPN) acts as both a stone matrix component for calcium oxalate (CaOx) crystal formation and an inflammatory mediator. While previous studies have demonstrated the individual roles of OPN and macrophages (Mφ) in renal CaOx stone formation during inflammation, their interaction remains poorly understood. This study aimed to elucidate the role of OPN in modulating Mφ function during crystal formation, using an ex vivo model. Bone marrow-derived macrophages (BMDM) were isolated from eight-week-old male C57BL/6J wild-type and OPN knockout mice. BMDMs from OPN-positive (BMDMOPN+) and OPN-negative (BMDMOPN-) mice were co-cultured with fluorescently labeled CaOx monohydrate (COM) crystals for phagocytosis assays and analyzed using the IN Cell Analyzer 6000. We further performed real-time quantitative reverse transcription PCR and RNA sequencing to identify gene expression profiles and clarify the role of OPN in Mφ function. The assay analysis demonstrated that phagocytosis rates were significantly higher in BMDMOPN- than in BMDMOPN+. Inflammatory markers, such as IL-6, TNF, CD44, were upregulated following COM exposure, and IL-6 expression was significantly lower in BMDMOPN- than in BMDMOPN+. RNA sequencing revealed that BMDMOPN- exhibited a less pro-inflammatory and more anti-inflammatory phenotype (Csf2low, Irf5low, Itgaxlow, Csf1high, Cd163high), resembling M2-like Mφs. Further functional analysis indicated that OPN knockdown in Mφs increased the S100 family and CREB signaling, which enhanced the M2-like phenotype shift and phagosome formation. In conclusion, OPN plays a critical role in enhancing pro-inflammatory Mφ function, potentially limiting COM phagocytosis. Modulating OPN expression in circulating Mφs may represent a therapeutic approach for kidney stone disease.

Segregated basal ganglia output pathways correspond to genetically divergent neuronal subclasses

The basal ganglia control multiple sensorimotor behaviors through anatomically segregated and topographically organized subcircuits with outputs to specific downstream circuits. However, it is unclear how the anatomical organization of basal ganglia output circuits relates to the molecular diversity of cell types. Here, we demonstrate that the major output nucleus of the basal ganglia, the substantia nigra pars reticulata (SNr), is comprised of transcriptomically distinct subclasses that reflect its distinct progenitor lineages. We show that these subclasses are topographically organized within the SNr, project to distinct targets in the midbrain and hindbrain, and receive inputs from different striatal subregions. Finally, we show that these mouse subclasses are also identifiable in human SNr neurons, suggesting that the genetic organization of the SNr is evolutionarily conserved. These findings provide a unifying logic for how the developmental specification of diverse SNr neurons relates to the anatomical organization of basal ganglia circuits controlling specialized downstream brain regions.

Lung IL-13 gene signatures are associated with raised tissue eosinophils in COPD

BACKGROUND

The role of eosinophils in COPD and their utility as biomarkers for cytokine targeting monoclonal therapies remains unclear. We investigated the distribution of eosinophils across different tissue compartments in COPD and analysed gene expression to understand the possible mechanistic drivers of eosinophilic inflammation in COPD.

METHODS

Blood and BAL from ex-smoking volunteers with mild/moderate COPD (n = 31) and healthy ex-smoking controls (n = 20), and bronchial biopsy tissue in a subcohort (n = 19 and n = 8, respectively) was analysed. Differentially-expressed genes (DEGs) were characterised using RNASeq. Proteomic analysis of BAL was conducted using mass-spectrometry.

RESULTS

COPD subjects had more eosinophils in blood and lung tissue compared to controls, with increased eosinophil protein CLC/Galectin-10 in BAL. However, peripheral blood eosinophil counts related poorly to numbers in lung tissue (rho = -0.09192, p = 0.3541) or proportions in BAL (rho = 0.01762, p = 0.4632). Tissue IL-5Rα expression was higher in frequent exacerbators and related to tissue eosinophils, but not peripheral blood eosinophils. Higher blood eosinophils were associated with DEGs that differed with compartment. Higher tissue eosinophil levels were associated with IL-13-induced DEGs including POSTN in bronchial brushes and CCL26 in bronchial biopsies. Gene-set enrichment analysis on data from brushings revealed significant enrichment of IL-4/IL-13, but not IL-5, pathways associated with eosinophil presence.

CONCLUSION

Eosinophilic lung inflammation is related to exacerbation frequency, but lung eosinophils are not predicted by blood eosinophil counts in COPD. Our data suggest IL-13-mediated pathways may be responsible for the presence of tissue eosinophils in COPD. Further work to establish more predictive biomarkers of lung eosinophil biology are required to unlock this axis to optimised treatment.

XBP1s-EDEM2 Prevents the Onset and Development of HFpEF by Ameliorating Cardiac Lipotoxicity

BACKGROUND

Morbidity and mortality of heart failure with preserved ejection fraction (HFpEF) is increased in metabolic disorders. However, options for preventing and treating these prevalent outcomes are limited. Intramyocardial lipotoxicity contributes to cardiac dysfunction. Here, we investigate the mechanisms underlying endoplasmic reticulum degradation enhancing EDEM2 (endoplasmic reticulum degradation-enhancing alpha-mannosidase-like protein 2) regulation of cardiac lipid homeostasis and assess strategies that inhibit the incidence and progression of HFpEF.

METHODS

Metabolic stress was induced in C57BL/6 male mice using a high-fat diet and Nω-nitro-l-arginine methyl ester. The recombinant adeno-associated virus 9 delivery system was used for loss- and gain-of-function studies. Palmitic acid and oleic acid stimulation of rat cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes imitated a condition of high lipids in vitro. Molecular mechanisms were investigated via RNA sequencing, mass spectrometry proteomics, lipidomic analyses, transmission electron microscopy, histology, and luciferase reporter assays.

RESULTS

In the human heart, we first detected lipid overload accompanied by a reduction of XBP1 (X-box binding protein 1) under metabolic stress. Thereafter, a decrease in EDEM2 was confirmed in human and mouse HFpEF hearts. Given that the spliced form of XBP1 (XBP1s) is a transcription factor, EDEM2 was identified as its new target in cardiomyocytes. EDEM2 knockdown mice manifested lipid droplet accumulation and higher levels of triglycerides and diglycerides in the myocardium, aggravating oxidative stress, hypertrophy, and the onset and progression of HFpEF under metabolic stress. XBP1s ablation mice displayed a similar myocardial lipid disturbance and cardiac phenotypes, which were reversed by EDEM2 overexpression. Mechanistically, the findings obtained from rat cardiomyocytes and human induced pluripotent stem cell-derived cardiomyocytes demonstrated that, in the presence of EDEM2, SEC23A mediated intracellular translocation of ATGL (adipose triglyceride lipase) under fatty acid stimulation, inhibiting ATGL degradation and excessive intracellular lipid droplets. Furthermore, the functional studies supported that EDEM2 prevention of lipid overload occurred in an ATGL-dependent manner. Therapeutically, cardiac XBP1s or EDEM2 restoration mitigated lipid deposition and preserved lipid profiles in the myocardium, thus preventing the development of HFpEF.

CONCLUSIONS

We demonstrate a cardioprotective mechanism regulating myocardial lipid homeostasis. The findings provide a promising therapeutic target to prevent and treat HfpEF, a condition with limited treatment options.

Neural stem cell relay from B1 to B2 cells in the adult mouse ventricular-subventricular zone

Neurogenesis and gliogenesis continue in the ventricular-subventricular zone (V-SVZ) of the adult rodent brain. V-SVZ astroglial cells with apical contact with the ventricle (B1 cells) function as neural stem cells (NSCs). B1 cells sharply decline during early postnatal life; in contrast, neurogenesis decreases at a slower rate. Here, we show that a second population of astroglia (B2 cells) that do not contact the ventricle also function as NSCs in the adult mouse brain. B2 cell numbers increase postnatally, are sustained in adults, and decrease with aging. We reveal the transcriptomic profile of B1 and B2 cells and show that, like B1 cells, B2 cells can be quiescent or activated. Transplantation and lineage tracing of B2 cells demonstrate their function as primary progenitors for adult neurogenesis. This study reveals that NSC function is progressively relayed from B1 to B2 progenitors helping explain how neurogenesis is maintained into adult life.

BATF2 is a regulator of interferon-γ signaling in astrocytes during neuroinflammation

Astrocytic interferon (IFN)γ signaling is associated with reduced neuroinflammation; however, downstream effectors responsible for regulating this protection are unknown. Here, we identify an IFN-specific transcription factor, basic leucine zipper ATF-like transcription factor (BATF)2, that plays a key role in modulating the consequences of IFNγ signaling in astrocytes. Chromatin immunoprecipitation sequencing revealed that BATF2 binds and prevents the overexpression of IFN regulatory factor (IRF)1 and IRF1 targets such as caspase-1. We also show that Batf2-/- mice exhibit exacerbated clinical disease severity in a murine model of central nervous system autoimmunity and express increased astrocyte-specific IRF1 and caspase-1, suggesting an amplified IFN response in vivo. Additionally, we demonstrate that BATF2 is expressed primarily in astrocytes within multiple sclerosis lesions and that this expression is colocalized with IRF1. Collectively, our results further support evidence of protective functions for IFNγ and implicate BATF2 as a key suppressor of overactive immune signaling in astrocytes during neuroinflammation.

Comparative analysis of transcriptomic profiles of mesenchymal stem cells at the onset of senescence and after exposure to acute exogenous oxidative stress

Cellular senescence can be triggered by a wide range of stress-inducing factors, including environmental and internal damaging events, such as oxidative stress. Moreover, stressed and senescent cells exhibit modifications in their transcriptional expression profile, but little is known regarding the common genes and pathways regulating these processes. Here, we analyzed the effects of long-term culture as well as exogenous acute oxidative stress on the transcriptional program of Wharton's jelly mesenchymal stem cells (WJ-MSCs). We demonstrate that, exposure to H2O2 compromised genomic stability and mitochondrial function in early passage WJ-MSCs, potentially initiating senescence to prevent cellular transformation. On the other hand, prolonged in vitro expansion of WJ-MSCs activated processes linked to integrins and extracellular matrix organization, possibly indicating the unfavorable consequences that senescence has on tissue integrity. Additionally, cells entering senescence and oxidative stressed young WJ-MSCs over-activated transcription factors related to permanent proliferative arrest and suppressed anti-senescence factors. Common differentially expressed genes in the late passage and H2O2-treated WJ-MSCs were implicated in DNA damage response and cell cycle arrest, which are known to trigger a senescent phenotype. Notably, the TP53INP1 gene emerged as a significantly upregulated gene in both late passage and H2O2-treated young WJ-MSCs, marking it as a potent senescence indicator. Silencing TP53INP1 mitigated the senescent phenotype, a role that appeared to be facilitated by autophagy regulation. Taken together, our results shed light on how transcriptomic changes govern MSCs' senescence program and identify key molecular drivers that could prove crucial for WJ-MSCs-based clinical applications.

ALS molecular subtypes are a combination of cellular and pathological features learned by deep multiomics classifiers

Amyotrophic lateral sclerosis (ALS) is a complex syndrome with multiple genetic causes and wide variation in disease presentation. Despite this heterogeneity, large-scale genomics studies revealed that ALS postmortem samples can be grouped into a small number of subtypes, defined by transcriptomic signatures of mitochondrial dysfunction and oxidative stress (ALS-Ox), microglial activation and neuroinflammation (ALS-Glia), or TDP-43 pathology and associated transposable elements (ALS-TE). In this study, we present a deep ALS neural net classifier (DANCer) for ALS molecular subtypes. Applying DANCer to an expanded cohort from the NYGC ALS Consortium highlights two subtypes that strongly correlate with disease duration: ALS-TE in cortex and ALS-Glia in spinal cord. Finally, single-nucleus transcriptomes demonstrate that ALS subtypes are recapitulated in neurons and glia, with both ALS-wide and subtype-specific alterations in all cell types. In summary, ALS molecular subtypes represent a combination of cellular and pathological features that correlate with clinical features of ALS.

Genome-scale CRISPR/Cas9 screening reveals the role of PSMD4 in colibactin-mediated cell cycle arrest

Colibactin is a genotoxic secondary metabolite produced by certain Enterobacteriaceae strains that populate the intestine and produces a specific mutational signature in human colonocytes. However, the host pathways involved in colibactin response remain unclear. To address this gap, we performed genome-wide CRISPR/Cas9 knockout screens and RNA sequencing utilizing live pks+ bacteria and a synthetic colibactin analog. We identified 20 enriched genes with a MAGeCK score of >2.0 in both screens, including proteasomal subunits (e.g., PSMG4 and PSMD4), RNA processing factors (e.g., SF1 and PRPF8), and RNA polymerase III (e.g., CRCP), and validated the role of PSMD4 in colibactin sensitization. PSMD4 knockout in HEK293T and HT-29 cells promoted cell viability and ameliorated G2-M cell cycle arrest but did not affect the amount of phosphorylated H2AX foci after exposure to synthetic colibactin 742. Consistent with these observations, PSMD4-/- cells had a significantly higher colony formation rate and bigger colony size than control cells after 742 exposure. These findings suggest that PSMD4 regulates cell cycle arrest following colibactin-induced DNA damage and that cells with PSMD4 deficiency may continue to replicate despite DNA damage, potentially increasing the risk of malignant transformation.

IMPORTANCE

Colibactin has been implicated as a causative agent of colorectal cancer. However, colibactin-producing bacteria are also present in many healthy individuals, leading to the hypothesis that some aspects of colibactin regulation or host response dictate the molecule's carcinogenic potential. Elucidating the host-response pathways involved in dictating cell fate after colibactin intoxication has been difficult, partially due to an inability to isolate the molecule. This study provides the first high-throughput CRISPR/Cas9 screening to identify genes conferring colibactin sensitivity. Here, we utilize both bacterial infection and a synthetic colibactin analog to identify genes directly involved in colibactin response. These findings provide insight into how differences in gene expression may render certain individuals more vulnerable to colibactin-initiated tumor formation after DNA damage.

Multiple mechanisms of termination modulate the dynamics of RNAPI transcription

Transcription elongation is stochastic, driven by a Brownian ratchet, making it subject to changes in velocity. On the rDNA, multiple polymerases are linked by "torsional entrainment" generated by DNA rotation. We report that release of entrainment by co-transcriptional 3' end cleavage, is permissive for relative movement between polymerases, promoting pausing and backtracking. Subsequent termination (polymerase release) is facilitated by the 5' exonuclease Rat1 (Xrn2) and backtracked transcript cleavage by the RNA polymerase I (RNAPI) subunit Rpa12. These activities are reproduced in vitro. Short nascent transcripts close to the transcriptional start site, combined with nascent transcript folding energy, similarly facilitate RNAPI pausing. Nascent, backtracked transcripts at pause sites are terminated by forward and reverse "torpedoes": Rat1 and the exosome cofactor Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP), respectively. Topoisomerase 2 localizes adjacent to RNAPI pause sites, potentially allowing continued elongation by downstream polymerases. Mathematical modeling supported substantial premature termination. These basic insights into transcription in vivo will be relevant to many systems.

A bHLH interaction code controls bipotential differentiation and self-renewal in the Drosophila gut

Multipotent adult stem cells balance self-renewal with differentiation into various cell types. How this balance is regulated at the transcriptional level is poorly understood. Here, we show that a network of basic helix-loop-helix (bHLH) transcription factors controls both stemness and bipotential differentiation in the Drosophila adult intestine. We find that homodimers of Daughterless (Da), a homolog of mammalian E proteins, maintain self-renewal of intestinal stem cells (ISCs), antagonizing the enteroendocrine fate promoted by heterodimers of Da and Scute (Sc; homolog of ASCL). The HLH factor Extramacrochaetae (Emc; homologous to Id proteins) promotes absorptive differentiation by titrating Da and Sc. Emc prevents the committed absorptive progenitor from dedifferentiating, underscoring the plasticity of these cells. Switching physical interaction partners in this way enables the active maintenance of stemness while priming stem cells for differentiation along two alternative fates. Such regulatory logic is likely operative in other bipotent stem cell systems.

JA and ABA signaling pathways converge to protect plant regeneration in stress conditions

In cuttings, detached leaves or stems are exposed to many stresses during the root regeneration process. Here, we show that the detached Arabidopsis thaliana leaf can tolerate mild osmotic stress and still regenerate roots. Under stress conditions, wounding and stress upregulate the jasmonate (JA) signaling pathway transcription factor gene MYC2 and the abscisic acid (ABA) signaling pathway transcription factor gene ABA INSENSITIVE5 (ABI5). The MYC2-ABI5 complex upregulates the expression of β-GLUCOSIDASE18 (BGLU18), which releases ABA from ABA glucose ester, resulting in ABA accumulation in the detached leaf. Mutations in MYC2, ABI5, and BGLU18 lead to the loss of stress tolerance and defects in root regeneration under osmotic stress. The successive application of JA and ABA can enhance the root regeneration ability in Arabidopsis and poplar cuttings. Overall, the JA-mediated wound signaling pathway and the ABA-mediated stress signaling pathway collaboratively amplify ABA signals to protect root regeneration under stress conditions.

Antagonistic roles for MITF and TFE3 in melanoma plasticity

Melanoma cells can switch from a melanocytic and proliferative state to a mesenchymal and invasive state and back again. This plasticity drives intratumoral heterogeneity, progression, and therapeutic resistance. Microphthalmia-associated transcription factor (MITF) promotes the melanocytic/proliferative phenotype, but factors that drive the mesenchymal/invasive phenotype and the mechanisms that effect the switch between cell states are unclear. Here, we identify the MITF paralog, TFE3, and the non-canonical mTORC1 pathway as regulators of the mesenchymal state. We show that TFE3 expression drives the metastatic phenotype in melanoma cell lines and tumors. Deletion of TFE3 in MITF-low melanoma cell lines suppresses their ability to migrate and metastasize. Further, MITF suppresses the mesenchymal phenotype by directly or indirectly activating expression of FNIP1, FNIP2, and FLCN, which encode components of the non-canonical mTORC1 pathway, thereby promoting cytoplasmic retention and lysosome-mediated degradation of TFE3. These findings highlight a molecular pathway controlling melanoma plasticity and invasiveness.

Intermittent fasting boosts sexual behavior by limiting the central availability of tryptophan and serotonin

Aging affects reproductive capabilities in males through physiological and behavioral alterations, including endocrine changes and decreased libido. In this study, we investigated the influence of intermittent fasting (IF) on these aging-related declines, using male C57BL/6J mice. Our findings revealed that IF significantly preserved reproductive success in aged mice, not by improving traditional reproductive metrics such as sperm quality or endocrine functions but by enhancing mating behavior. This behavioral improvement was attributed to IF's ability to counter age-dependent increases in serotonergic inhibition, primarily through the decreased supply of the serotonin precursor tryptophan from the periphery to the brain. Our research underscores the potential of dietary interventions like IF in mitigating age-associated declines in male reproductive health and suggests a novel approach to managing conditions related to reduced sexual desire, highlighting the complex interplay between diet, metabolism, and reproductive behavior.

Adhesion strength of tumor cells predicts metastatic disease in vivo

Although only a fraction of tumor cells contribute to metastatic disease, no prognostic biomarkers currently exist to identify these cells. We show that a physical marker-adhesion strength-predicts metastatic potential in a mouse breast cancer model and that it may stratify human disease. Cells disseminating from murine mammary tumors are weakly adherent, and, when pre-sorted by adhesion, primary tumors created from strongly adherent cells exhibit fewer lung metastases than weakly adherent cells do. We demonstrate that admixed cancer lines can be separated by label-free adhesive signatures. When applied to murine metastatic tumors, adhesion retrospectively predicts metastatic disease with 100% specificity, 85% sensitivity, and area under the curve (AUC) of 0.94. Cells from human reduction mammoplasties have a higher adhesion strength versus resected human tumors, which may also be stratified between invasive and more indolent cancers. Thus, highly metastatic cells may have a distinct physical phenotype that may be a predictive marker of clinical outcomes.

Immunoglobulin A controls intestinal virus colonization to preserve immune homeostasis

Immunoglobulin A (IgA) is the predominant immunoglobulin isotype in mammals, primarily secreted at type I mucosal surfaces. Despite its abundance, the precise role of secretory IgA in the intestinal lumen, where it coats a diverse array of commensal microbiota, has remained elusive. Our study reveals that germinal center IgA responses are essential for preventing chronic colonization of the gut by specific viruses. In the absence of IgA, chronic viral colonization triggers an antigen-driven expansion of CD8αβ+ intraepithelial lymphocytes (IELs). Although these IELs are unable to clear the virus, they contribute to maintaining homeostasis by regulating its load and type I interferon responses. Consequently, IgA deficiency increases susceptibility to colitis in genetically susceptible hosts or following chemical induction but only in the presence of viral pathobionts requiring IgA for their clearance. These findings underscore the potential vulnerability of IgA-deficient individuals to immunopathology when exposed to selective viral pathobionts.

A Csde1-Strap complex regulates plasma cell differentiation by coupling mRNA translation and decay

Upon encountering antigens, B cells may undergo multiple differentiation paths, including becoming plasma cells and memory B cells. Although it is well-known that transcription factors govern gene expression programs underpinning these fate decisions in transcriptional level, the role of post-transcriptional regulators, with a focus on RNA-binding proteins, in the fate determination are lesser known. Here we find by RNA interactome capture-coupled CRISPR/Cas9 functional screening that the Csde1-Strap complex plays an important role in plasma cell differentiation. Mechanistically, the Csde1-Strap complex establishes the expression kinetics of Bach2, a key regulator of plasma cell differentiation. Bach2 expression is rapidly induced to promote B cell expansion and then decreased to initiate plasma cell differentiation. The Csde1-Strap interaction is critical for their binding to Bach2 mRNA to couple its decay with translation to restrain the magnitude and duration of Bach2 protein expression. In the absence of Csde1 or Strap, Bach2 translation is de-coupled from mRNA decay, leading to elevated and prolonged expression of Bach2 protein and impaired plasma cell differentiation. This study thus establishes the functional RBP landscape in B cells and illustrates the fundamental importance of controlling protein expression kinetics in cell fate determination.

Restoration of retinal regenerative potential of Müller glia by disrupting intercellular Prox1 transfer

Individuals with retinal degenerative diseases struggle to restore vision due to the inability to regenerate retinal cells. Unlike cold-blooded vertebrates, mammals lack Müller glia (MG)-mediated retinal regeneration, indicating the limited regenerative capacity of mammalian MG. Here, we identify prospero-related homeobox 1 (Prox1) as a key factor restricting this process. Prox1 accumulates in MG of degenerating human and mouse retinas but not in regenerating zebrafish. In mice, Prox1 in MG originates from neighboring retinal neurons via intercellular transfer. Blocking this transfer enables MG reprogramming into retinal progenitor cells in injured mouse retinas. Moreover, adeno-associated viral delivery of an anti-Prox1 antibody, which sequesters extracellular Prox1, promotes retinal neuron regeneration and delays vision loss in a retinitis pigmentosa model. These findings establish Prox1 as a barrier to MG-mediated regeneration and highlight anti-Prox1 therapy as a promising strategy for restoring retinal regeneration in mammals.