BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

Microglia and CD8+ T cell activation precede neuronal loss in a murine model of spastic paraplegia 15

In central nervous system (CNS) diseases characterized by late-onset neurodegeneration, the interplay between innate and adaptive immune responses remains poorly understood. This knowledge gap is exacerbated by the prolonged protracted disease course as it complicates the delineation of brain-resident and infiltrating cells. Here, we conducted comprehensive profiling of innate and adaptive immune cells in a murine model of spastic paraplegia 15 (SPG15), a complicated form of hereditary spastic paraplegia. Using fate-mapping of bone marrow-derived cells, we identified microgliosis accompanied by infiltration and local expansion of T cells in the CNS of Spg15-/- mice. Single-cell analysis revealed an expansion of disease-associated microglia (DAM) and effector CD8+ T cells prior to neuronal loss. Analysis of potential cell-cell communication pathways suggested bidirectional interactions between DAM and effector CD8+ T cells, potentially contributing to disease progression in Spg15-/- mice. In summary, we identified a shift in microglial phenotypes associated with the recruitment and expansion of T cells as a new characteristic of Spg15-driven neuropathology.

Signs of Premature Kidney Aging in Mice With Error-Prone Protein Synthesis

Chronic kidney disease (CKD) is more prevalent with increasing age. The incidence of CKD is rising due to the widespread nature of its risk factors, hypertension and diabetes, and because aging causes a gradual decline in kidney function. This decline is a consequence of structural, molecular, and metabolic changes occurring in aging kidneys. Understanding the mechanisms that accelerate kidney aging may help manage CKD and promote healthy aging. Recently, it has been shown that protein translation errors accelerate aging in mammals. Mice heterozygous for the ribosomal ambiguity mutation Rps9D95N, which results in genome-wide error-prone translation, have reduced life span, increased macroscopic signs of aging, and exhibit a neuropathological phenotype resembling early signs of Alzheimer disease. Here, using deep phenotyping, we investigated the kidneys of Rps9D95N/+ mice and showed that genome-wide error-prone translation is also associated with signs of premature kidney aging. These mice have renal amyloidosis, an altered glomerular basement membrane, reduced autophagy in kidney tissue, and renal fibrosis compared to age-matched aged mice. These alterations in kidney tissue were accompanied by signs of kidney dysfunction such as albuminuria and elevated levels of Kim-1, a marker of kidney injury and kidney disease progression. In addition, lipid metabolism is altered, as shown by RNAseq and targeted metabolomic analysis, suggesting increased lipid deposition as lipid droplets in the Rps9D95N knock-in mice. Only mild changes in systemic phosphate metabolism were observed. Our findings provide insights into premature kidney aging, likely due to accelerated loss of proteostasis caused by genome-wide translation errors.

The transcription factor IID subunit Taf13 is dispensable for TATA binding protein promoter recruitment and RNA polymerase II transcription

The multiprotein complex TFIID, comprising the TATA binding protein (TBP) and 13 TBP-associated factors (TAFs), is an essential component of the RNA polymerase II (Pol II) preinitiation complex (PIC). Cryo-electron microscopy studies suggested a critical role of the TAF11-TAF13 heterodimer in TBP promoter deposition upstream of the transcription start site. To investigate this hypothesis, we inactivated the gene encoding Taf13 in mice and embryonic stem cells (ESCs). Taf13-null embryos implant and survive until E6.5, but fail to undergo gastrulation, while Taf13-null ESCs are viable, but fail to form embryoid bodies and differentiate. Taf13 loss had little effect on TFIID integrity and led to only a mild reduction of TBP promoter recruitment, but led to altered PIC formation and globally reduced Pol II recruitment. Thus, the Taf11-Taf13 heterodimer is not essential for TBP/TFIID recruitment, revealing plasticity in the pathways of PIC formation.

Uncovering hepatic transcriptomic and circulating proteomic signatures in MASH: A meta-analysis and machine learning-based biomarker discovery

BACKGROUND

Metabolic-associated steatohepatitis (MASH), the progressive form of metabolic-associated steatotic liver disease (MASLD), poses significant risks for liver fibrosis and cardiovascular complications. Despite extensive research, reliable biomarkers for MASH diagnosis and progression remain elusive. This study aimed to identify hepatic transcriptomic and circulating proteomic signatures specific to MASH, and to develop a machine learning-based biomarker discovery model.

METHODS

A systematic review of RNA-Seq and proteomic datasets was conducted, retrieving 7 hepatic transcriptomics and 3 circulating proteomics studies, encompassing 483 liver samples and 169 serum/plasma samples, respectively. Differential gene and protein expression analyses were performed, and pathways were enriched using gene set enrichment analysis. A machine learning (ML) model was developed to identify MASH-specific biomarkers, utilizing biologically significant protein ratios.

KEY FINDINGS

Hepatic transcriptomic analysis identified 5017 differentially expressed genes (DEGs), with significant enrichment of extracellular matrix (ECM) pathways. Serum proteomics revealed six differentially expressed proteins (DEPs), including complement-related proteins. Integration of transcriptomic and proteomic data highlighted the complement cascade as a key pathway in MASH, with discordant regulation between the liver and circulation. The ML-based biomarker discovery model, utilizing protein ratios, achieved an F1 scores of 0.83 and 0.64 in the training sets and 0.67 in an external validation set.

CONCLUSION

Our findings indicate ECM deregulation and complement system involvement in MASH progression. The novel ML model incorporating protein ratios offers a potential tool for MASH diagnosis. However, further refinement and validation across larger and more diverse cohorts is needed to generalize these results.

Exploratory analysis of differences at the transcriptional interface between the maternal and fetal compartments of the sheep placenta and potential influence of fetal sex

An understanding of the inner workings of the placenta is imperative to elucidate how the maternal and fetal compartments coordinate to mediate fetal development. The two compartments can be separated and studied before term in sheep, a feat not possible in humans, thus providing a valuable translational model. This study investigated differential expression of gene signaling networks in the maternal and fetal compartments of the placenta and explored the potential influence of fetal sex. On approximately gestational day 120 (term: 147 days), ewes were euthanized and fetuses removed and sexed. Placentomes [n = 5 male, n = 3 female] were collected, and caruncles (maternal) and cotyledons (fetal) were separated and sequenced to assess RNA expression. Analysis revealed 2627 differentially expressed genes (FDR<0.01, abslog2FC ≥ 2) contributing to key transcriptional differences between maternal and fetal compartments, which suggested that the maternal compartment drives extracellular signaling at the interface whereas the fetal compartment controls internal mechanisms crucial for fetal-placental development. X-chromosome inactivation equalized expression of a vast majority of X-linked genes in the fetal compartment. Additionally, the female placenta had more fine-tuned regulation of key pathways for fetal-placental development, such as DNA replication, mRNA surveillance, and RNA transport, compared to males, which had enrichment of metabolic pathways including TCA cycle and galactose metabolism. These findings, in addition to supporting differences in expression in the maternal and fetal placental compartments and the possible influence of fetal sex, offer a transcriptional platform to compare placental perturbations that occur at the maternal-fetal interface that contribute to adverse pregnancy outcomes.

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

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

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

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

The multi-level effect of chlorpyrifos during clownfish metamorphosis

Chemical pollution in coastal waters, particularly from agricultural runoff organophosphates, poses a significant threat to marine ecosystems, including coral reefs. Pollutants such as chlorpyrifos (CPF) are widely used in agriculture and have adverse effects on marine life and humans. In this paper, we investigate the impact of CPF on the metamorphosis of a coral reef fish model, the clownfish Amphiprion ocellaris, focusing on the disruption of thyroid hormone (TH) signalling pathways. Our findings reveal that by reducing TH levels, CPF exposure impairs the formation of characteristic white bands in clownfish larvae, indicative of metamorphosis progression. Interestingly, TH treatment can rescue these effects, establishing a direct causal link between CPF effect and TH disruption. The body shape changes occurring during metamorphosis are also impacted by CPF exposure, shape changes are less advanced in CPF-treated larvae than in control conditions. Moreover, transcriptomic analysis elucidates CPF's effects on all components of the TH signalling pathway. Additionally, CPF induces systemic effects on cholesterol and vitamin D metabolism, DNA repair, and immunity, highlighting its broader TH-independent impacts. Pollutants are often overlooked in marine ecosystems, particularly in coral reefs. Developing and enhancing coral reef fish models, such as Amphiprion ocellaris (Cuvier, 1830), offers a more comprehensive understanding of how chemical pollution affects these ecosystems. This approach provides new insights into the complex mechanisms underlying CPF toxicity during fish metamorphosis, shedding light on the broader impact of environmental pollutants on marine organisms.

Differential expression of sex regulatory genes in gonads of Astyanax mexicanus surface fish and cavefish

BACKGROUND

Astyanax mexicanus is a single species of fish that consists of river-dwelling (surface) and cave-dwelling morphotypes. Little is known about how sexual determination, differentiation or reproduction have evolved in the surface morphs or cavefish, though divergence in reproductive strategy is expected as the latter have adapted to the novel cave environment. Evolution of the gonad transcriptome may underlie the differences in gamete morphology, fertility, and fecundity previously reported between morphotypes.

RESULTS

We compared the ovary and testis transcriptome of surface fish and cavefish at juvenile and adult stages. We found that samples clustered by developmental stage, sex, and morphotype identity. Several key genes that are typically associated with the female gonad in other vertebrates showed a reversal in sexual dimorphism or were not differentially expressed between sexes in A. mexicanus. In contrast, gene expression typically associated with male gonads was largely conserved and consistent with vertebrate testicular expression profiles. Transcriptional and physiological differences between surface fish and cavefish morphotypes were observed in gonads from both sexes. Cavefish ovaries exhibited unique upregulation of neuron development and differentiation genes, and extensive innervation of the ovarian epithelium, while cavefish testes showed increased expression of angiogenesis regulating genes, and greater vasculature density compared to surface fish testes.

CONCLUSIONS

These results reveal significant gene expression differences between A. mexicanus surface fish and cavefish morphotypes that may have functional consequences in gonad morphogenesis and fertility. Our findings provide a foundation for investigating the evolution of sex regulatory pathways and reproductive strategies in animals adapting to new and challenging environments in which nutrient availability, temperature, and mate selection are suboptimal.

Evaluating regional heritability mapping methods for identifying QTLs in a wild population of Soay sheep

The study of complex traits and their genetic underpinnings is crucial for understanding the evolutionary processes and mechanisms that shape natural populations. Regional heritability mapping (RHM) is a method for estimating the heritability of genomic segments that may contain both common and rare variants affecting a complex trait. This research is important because it advances our ability to detect genetic loci that contribute to phenotypic variation, even those that might be missed by traditional methods such as genome-wide association studies (GWAS). Here, we compare three RHM methods: SNP-RHM, which uses genomic relationship matrices (GRMs) based on SNP genotypes; Hap-RHM, which utilizes GRMs based on haplotypes; and SNHap-RHM, which integrates both SNP-based and haplotype-based GRMs jointly. These methods were applied to data from a wild population of sheep, focusing on the analysis of eleven polygenic traits. The results were compared with findings from previous GWAS to assess how RHM performed at identifying both known and novel associated loci. We found that while the inclusion of the regional matrix did not account for significant variation in all regions associated with trait variation as identified by GWAS, it did uncover several regions that were not previously linked to trait variation. This suggests that RHM methods can provide additional insights into the genetic architecture of complex traits, highlighting regions of the genome that may be overlooked by GWAS alone. This study underscores the importance of using complementary approaches to fully understand the genetic basis of complex traits in natural populations.

Multi-omic integration with human dorsal root ganglia proteomics highlights TNFα signalling as a relevant sexually dimorphic pathway

ABSTRACT

The peripheral nervous system (PNS) plays a critical role in pathological conditions, including chronic pain disorders, that manifest differently in men and women. To investigate this sexual dimorphism at the molecular level, we integrated quantitative proteomic profiling of human dorsal root ganglia (hDRG) and peripheral nerve tissue into the expanding omics framework of the PNS. Using data-independent acquisition (DIA) mass spectrometry, we characterized a comprehensive proteomic profile, validating tissue-specific differences between the hDRG and peripheral nerve. Through multi-omic analyses and in vitro functional assays, we identified sex-specific molecular differences, with TNFα signalling emerging as a key sexually dimorphic pathway with higher prominence in men. Genetic evidence from genome-wide association studies further supports the functional relevance of TNFα signalling in the periphery, while clinical trial data and meta-analyses indicate a sex-dependent response to TNFα inhibitors. Collectively, these findings underscore a functionally sexual dimorphism in the PNS, with direct implications for sensory and pain-related clinical translation.

Serum RNA Profile Reflects Fluid Status and Atrophic Retinal Changes in Neovascular Age-Related Macular Degeneration

The increasing prevalence of age-related macular degeneration (AMD), a disease that can result in the loss of central vision, is an emerging problem worldwide due to aging societies. Growing patient numbers create a challenge for the healthcare system. Understanding the mechanisms of AMD pathogenesis will aid in early, personalized, and efficient intervention, helping to mitigate this issue. Current diagnostic methods rely on optical coherence tomography and angiography imaging, which identify existing damages, but do not provide information on the mechanisms behind them. In the present work, we demonstrate a difference in the serum RNA profile between neovascular AMD (nAMD) patients and controls. Moreover, the RNA profile of nAMD patients corresponded with anatomical changes in the retinal fluid compartments as well as atrophic changes of the retina. We followed two independent ways to control false positive leads, and when these approaches were combined, thioredoxin-related transmembrane protein 4 (TMX4) was observed to be differentially expressed by both approaches. This finding opens a new pathway in AMD studies, which are limited due to restricted access to live human target material and the limited value of animal models of human AMD.

A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs

BACKGROUND

Topologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries can lead to aberrant expression of neighboring genes. In our study, we analyzed high-throughput chromatin conformation capture (Hi-C) datasets from publicly available sources, integrating 71 datasets across five tissues in six pig breeds.

RESULTS

Our comprehensive analysis revealed 65,843 TADs in pigs, and we found that TAD boundaries are enriched for expression Quantitative Trait Loci (eQTL), splicing Quantitative Trait Loci (sQTL), Loss-of-Function variants (LoFs), and other regulatory variants. Genes within conserved TADs are associated with fundamental biological functions, while those in dynamic TADs may have tissue-specific roles. Specifically, we observed differential expression of the NCOA2 gene within dynamic TADs. This gene is highly expressed in adipose tissue, where it plays a crucial role in regulating lipid metabolism and maintaining energy homeostasis. Additionally, differential expression of the BMPER gene within dynamic TADs is associated with its role in modulating the activities of bone morphogenetic proteins (BMPs)-critical growth factors involved in bone and cartilage development.

CONCLUSION

Our investigations have shed light on the pivotal roles of TADs in governing gene expression and even influencing traits. Our study has unveiled a holistic interplay between chromatin interactions and gene regulation across various tissues and pig breeds. Furthermore, we anticipate that incorporating markers, such as structural variants (SVs), and phenotypes will enhance our understanding of their intricate interactions.

Explainable Machine Learning Identifies Factors for Dosage Compensation in Aneuploid Human Cancer Cells

Aneuploidy, a hallmark of cancer, leads to widespread changes in chromosome copy number, altering the abundance of hundreds or thousands of proteins. How-ever, evidence suggests that levels of proteins encoded on affected chromosomes are often buffered toward their abundances observed in diploid cells. Despite its preval-ence, the molecular mechanisms driving this protein dosage compensation remain largely unknown. It is unclear whether all proteins are buffered to a similar degree, what factors determine buffering, and whether dosage compensation varies across different cell lines or tumor types. Moreover, its potential adaptive advantage and therapeutic relevance remain unexplored. Here, we established a novel approach to quantify protein dosage buffering in a gene copy number-dependent manner, show-ing that dosage compensation is widespread but variable in cancer cell lines and in vivo tumor samples. By developing multifactorial machine learning models, we identify mean gene dependency, protein complex participation, haploinsufficiency, and mRNA decay as key predictors of buffering. We also show that dosage com-pensation can affect oncogenic potential and that higher buffering correlates with reduced proteotoxic stress and increased drug resistance. These findings highlight protein dosage compensation as a crucial regulatory mechanism and a potential therapeutic target in aneuploid cancers.

ASiDentify (ASiD): a machine learning model to predict new autism spectrum disorder risk genes

Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects nearly 3% of children and has a strong genetic component. While hundreds of ASD risk genes have been identified through sequencing studies, the genetic heterogeneity of ASD makes identifying additional risk genes using these methods challenging. To predict candidate ASD risk genes, we developed a simple machine learning model, ASiDentify (ASiD), using human genomic, RNA- and protein-based features. ASiD identified over 1,300 candidate ASD risk genes, over 300 of which have not been previously predicted. ASiD made accurate predictions of ASD risk genes using 6 features predictive of ASD risk gene status, including mutational constraint, synapse localization and gene expression in neurons, astrocytes and non-brain tissues. Particular functional groups of proteins found to be strongly implicated in ASD include RNA-binding proteins (RBPs) and chromatin regulators. We constructed additional logistic regression models to make predictions and assess informative features specific to RBPs, including mutational constraint, or chromatin regulators, for which both expression level in excitatory neurons and mutational constraint were informative. The fact that RBPs and chromatin regulators had informative features distinct from all protein-coding genes suggests that specific biological pathways connect risk genes with different molecular functions to ASD.

Characterizing the expression profile of 3R tau pathology in Pick's disease

Pick's disease (PiD) is a rare neurodegenerative disorder defined by dementia, frontotemporal lobe atrophy, and 3-repeat tau inclusions. To elucidate PiD pathobiology, we performed the first bulk transcriptomics study on PiD using short- and long-read sequencing on the parietal cortex of 28 PiD and 15 control samples. We identified several significantly differentially expressed genes, with CCL2 displaying the strongest association with 3-repeat tau pathology and increased burden in PiD compared to those in 4-repeat tau progressive supranuclear palsy (PSP) cases. Investigation of co-expressed genes and pathways suggested the involvement of mRNA processing, mitochondrial function, and immune processes in disease pathobiology. Long-read RNA sequencing on a subset of samples (eight PiD and four control) proposed novel, potentially disease-associated transcripts for AZGP1, CD44, HSD11B2, and WIF1, predicted to result in truncated proteins. In conclusion, we observed transcriptomic changes in the parietal cortex of patients with PiD that may inform into clinically relevant biomarkers and therapeutic strategies.

Genomic signatures associated with recurrent scale loss in cyprinid fish

Scale morphology represents a fundamental feature of fish and a key evolutionary trait underlying fish diversification. Despite frequent and recurrent scale loss throughout fish diversification, comprehensive genome-wide analyses of the genomic signatures associated with scale loss in divergent fish lineages remain scarce. In the current study, we investigated genome-wide signatures, specifically convergent protein-coding gene loss, amino acid substitutions, and cis-regulatory sequence changes, associated with recurrent scale loss in two divergent Cypriniformes lineages based on large-scale genomic, transcriptomic, and epigenetic data. Results demonstrated convergent changes in many genes related to scale formation in divergent scaleless fish lineages, including loss of P/Q-rich scpp genes (e.g. scpp6 and scpp7), accelerated evolution of non-coding elements adjacent to the fgf and fgfr genes, and convergent amino acid changes in genes (e.g. snap29) under relaxed selection. Collectively, these findings highlight the existence of a shared genetic architecture underlying recurrent scale loss in divergent fish lineages, suggesting that evolutionary outcomes may be genetically repeatable and predictable in the convergence of scale loss in fish.

Integrated proteome and lipidome analyses place OCIAD1 at the mitochondria-peroxisome intersection balancing lipid metabolism

Ovarian cancer immunoreactive antigen domain-containing 1 (OCIAD1) is a membrane protein largely localized to mitochondria; however, its function in health or disease is not well understood. To comprehensively characterize the molecular changes upon lack of OCIAD1, we used mass spectrometry to study the mitochondrial and cellular proteome and lipidome. We show that there is extensive lipidome rearrangement in OCIAD1 knockout (KO) cells, characterized by two main phenotypes of decreased levels of ether phospholipids and decreased levels of phospholipids with an odd number of carbons. The lipidomic changes suggest alterations in peroxisomal lipid metabolism. At the same time, proteins responsible for mitochondrial fatty acid β-oxidation are significantly increased. Together with a global loss in peroxisomal proteins, aberrant peroxisomal morphology, and a meta-analysis of proximity labeling data, this gives a function to the previously observed partial localization of OCIAD1 to peroxisomes. We suggest a role for OCIAD1 in balancing mitochondrial and peroxisomal lipid metabolism, and a direct impact on the key enzymes FAR1 and ABCD3.

Genetic architecture of thermotolerance traits in beef cattle: a novel integration of SNP and breed-of-origin effects

Background

Rising temperatures increasingly expose beef cattle to heat stress, reducing productivity and welfare, especially in tropical climates. Crossbreeding Bos t. taurus and Bos t. indicus has emerged as a critical strategy to balance the production efficiency of taurine breeds with the superior thermotolerance of indicine breeds. Understanding the genetic architecture of thermotolerance traits is essential for improving heat resilience in beef cattle populations.

Methods

Phenotypes for short hair length (SHL, undercoat) and long hair length (LHL, topcoat), sweat gland area (SGA), and thermal stress slope (TSS), a measure of body temperature fluctuations under heat stress, were collected from 3,962 crossbred Angus-Brahman heifers. Heifers were genotyped, and breed-of-origin (BOA) for each marker was determined using LAMP-LD. Genome-wide association studies were conducted using SNP-only, BOA-only, and integrated SNP + BOA models to identify quantitative trait loci (QTLs) associated with thermotolerance traits. Genes in QTL regions were used for functional enrichment analysis using Gene Ontology (GO) and KEGG pathways.

Results

Significant QTLs for SHL and LHL were identified on BTA20, overlapping the PRLR gene. A QTL on BTA19 for SHL and LHL was driven solely by BOA effects, with Brahman BOA associated with shorter hair lengths. For SGA, six suggestive QTLs were detected, predominantly linked to Angus-derived alleles associated with reduced sweat gland area. For TSS, a significant QTL on BTA1 exhibited a strong BOA effect, with Angus BOA associated with higher TSS values, indicative of reduced thermoregulatory efficiency. Integrated SNP + BOA models provided greater resolution and revealed novel QTLs compared to single-effect models. Functional enrichment using GO and KEGG identified MAPK and estrogen signaling pathways in both LHL and TSS, indicating potential overlap in the biological processes influencing hair length and thermoregulation.

Conclusion

This study demonstrates the value of integrating BOA with SNP-based models to uncover the genetic architecture of thermotolerance traits in beef cattle. By better capturing breed-specific contributions, these findings enhance our understanding of thermoregulation and provide actionable insights for improving heat resilience in cattle.

Non-recurrent mutations and copy number changes predominate pituitary adenoma genomes

OBJECTIVE

Pituitary adenomas (PAs) are common neoplasms. Our current understanding of the molecular basis of PA formation is incomplete. Routine implementation of targeted genomics has enabled the discovery of rare, potentially clinically actionable events.

METHODS

We used a cancer-focused gene panel to sequence a cohort of 171 PAs from patients who underwent surgery at Brigham and Women's Hospital from 2012 to 2020.

RESULTS

We identified known genetic variants enriched in specific PA subtypes: GNAS (somatotroph) and USP8 (Cushing's disease). Total mutational burden did not vary across adenoma subtypes; most adenomas possessed a few non-recurrent mutations in various established oncogenes and tumor suppressors. In contrast, the burden of copy number alterations varied widely across adenoma subtypes and was associated with higher MIB1 labeling index. We identified frequent deletions spanning MEN1 in prolactinomas and silent corticotroph adenomas, and subtype-specific copy number changes including 16p, 16q alterations in somatotroph adenomas without GNAS mutations. Within the corticotroph lineage, adenomas leading to Cushing's disease had few copy number alterations while silent corticotroph adenomas had numerous.

CONCLUSIONS

This study highlights a role for individualized genetic events in PA formation and suggests that divergent patterns of genomic instability may facilitate tumorigenesis even within the same lineage. Taken together, we demonstrate how gene panels may illuminate novel biology in endocrine tumors.

DNA methylation associated with the serum alanine aminotransferase concentration: evidence from Chinese monozygotic twins

BACKGROUND

To identify nongenetic factors influences on DNA methylation (DNAm) variations associated with blood Alanine Aminotransferase (ALT) concentration, this study conducted an epigenome-wide association study (EWAS) on Chinese monozygotic twins.

METHODS

A total of 61 pairs of Chinese monozygotic twins involved in this study. Whole blood samples were analyzed for DNAm profiling using the Reduced Representation Bisulfite Sequencing (RRBS) technique. We examined the relationship between DNAm levels at each CpG site and serum ALT using a linear mixed-effects model. Enrichment analysis and causal inference analysis was conducted, and differentially methylated regions (DMRs) were further identified. Candidate CpGs were validated in a community sample. Genome-wide significance were calculated by Bonferroni correction (p < 2.14 × 10-7).

RESULTS

We identified 85 CpGs reaching genome-wide significance (p < 2.14 × 10-7), located in 16 genes including FLT4, ADARB2, MRPS31P2, and RELB. Causal inference suggested that DNAm at 61 out of 85 significant CpGs within 14 genes influenced ALT level. 52 DMRs and 1765 pathways such as low voltage-gated calcium channel activity and focal adhesion were identified having influences on ALT levels. Further validation using community population found four CpGs mapped to FLT4 and three to RELB showing hypomethylation and hypermethylation in cases with abnormal ALT (ALT > 40 U/L), respectively.

CONCLUSION

This study identified several differentially methylated CpG sites associated with serum ALT in the Chinese population, particularly within FLT4 and RELB. These findings provide new insights into the epigenetic modifications underlying liver function.

Srsf3-Dependent APA Drives Macrophage Maturation and Limits Atherosclerosis

BACKGROUND

Circulating monocytes largely contribute to macrophage buildup in atheromata, which is crucial for clearing subendothelial LDLs (low-density lipoproteins) and dead cells; however, the transitional trajectory from monocytes to macrophages in atherosclerotic plaques and the underlying regulatory mechanism remain unclear. Moreover, the role of alternative polyadenylation, a posttranscriptional regulator of cell fate, in monocyte/macrophage fate decisions during atherogenesis is not entirely understood.

METHODS

To identify monocyte/macrophage subtypes in atherosclerotic lesions and the effect of alternative polyadenylation on these subtypes and atherogenesis, single-cell RNA sequencing, 3'-end sequencing, flow cytometric, and histopathologic analyses were performed on plaques obtained from Apoe-/- mouse arteries with or without myeloid deletion of Srsf3 (serine/arginine-rich splicing factor 3). Cell fractionation, polysome profiling, L-azidohomoalanine metabolic labeling assay, and metabolomic profiling were conducted to disclose the underlying mechanisms. Reprogramming of widespread alternative polyadenylation patterns was estimated in human plaques via bulk RNA sequencing.

RESULTS

We identified a subset of lesional cells in a monocyte-to-macrophage transitional state, which exhibited high expression of chemokines in mice. Srsf3 deletion caused a maturation delay of these transitional cells and phagocytic impairment of lesional macrophages, aggravating atherosclerosis. Mechanistically, Srsf3 deficiency shortened 3' untranslated regions of mitochondria-associated Aars2 (alanyl-tRNA synthetase 2), disrupting its translation. The resultant impairment of protein synthesis in mitochondria led to mitochondrial dysfunction with declined NAD+ (nicotinamide adenine dinucleotide, oxidized form) levels, activation of the integrated stress response, and metabolic reprogramming in macrophages. Administering an NAD+ precursor nicotinamide mononucleotide or the integrated stress response inhibitor partially restored Srsf3-deficient macrophage maturation, and nicotinamide mononucleotide treatment mitigated the proatherosclerotic effects of Srsf3 deficiency. Consistently, Srsf3 downregulation, global 3' untranslated region shortening, and accumulation of these transitional macrophages were associated with atherosclerosis progression in humans.

CONCLUSIONS

Our study reveals that Srsf3-dependent generation of long 3' untranslated region is required for efficient mitochondrial translation, which promotes mature phagocytic macrophage formation, thereby playing a protective role in atherosclerosis.

Transcriptomic profiling in canine B-cell lymphoma supports a synergistic effect of BTK and PI3K inhibitors

Introduction

B-cell receptor (BCR) signaling has revealed itself as a critical pathway in the pathogenesis of B-cell lymphoma. Within this pathway, the inhibition of Bruton's tyrosine kinase (BTK) or Phosphoinositide 3-kinases (PI3Ks) alone presents encouraging efficacy in the treatment of certain both canine and human hematological malignancies.

Methods

Here we characterized the effects of the BTK inhibitor Ibrutinib and the PI3K inhibitor AS-605240 as single and combined agents in the canine pre-clinical diffuse large B cell lymphoma (DLBCL) model CLBL-1 by assaying cell proliferation and metabolic activity, and performing RNA-seq to measure gene expression changes.

Results

We found 2,336 differentially expressed genes (DEGs) across all treatment types and time points relative to the control. The largest number of DEGs were induced by the combination of Ibrutinib and AS-605240. These genes were involved in adaptive immune response, leukotriene D4 metabolic and terms related to regulation of GTP and GTPase mediated signal transduction. Weighted gene co-expression network analysis (WGCNA) detected nine gene modules, five of which were associated with treatment response. Eighteen-percent of genes within these modules were also differentially expressed. Notably, we observed one module that was exclusively associated with the combined treatment whose gene members were related to cellular metabolism, homeostasis signaling, and protein synthesis and regulation.

Conclusion

Narrowing in on highly connected genes of modules associated with treatment response with large fold changes across treatments which play roles in the main targeted pathways identified PAG1, PRKAR2A, ACACA, FOS, and PRKCA as potential primary candidates of the synergistic treatment effect.

Social context prevents heat hormetic effects against mutagens during fish development

Since stress can be transmitted to congeners via social metabolites, it is paramount to understand how the social context of abiotic stress influences aquatic organisms' responses to global changes. Here, we integrated the transcriptomic and phenotypic responses of zebrafish embryos to a UV damage/repair assay following scenarios of heat stress, its social context and their combination. Heat stress preceding UV exposure had a hormetic effect through the cellular stress response and DNA repair, rescuing and/or protecting embryos from UV damage. However, experiencing heat stress within a social context negated this molecular hormetic effect and lowered larval fitness. We discuss the molecular basis of interindividual chemical transmission within animal groups as another layer of complexity to organisms' responses to environmental stressors.

Freeze-Dependent Physiological and Transcriptional Changes in Olea europaea L. Cultivars with Different Cold Resistances

Understanding the transcriptional responses of plants under cold stress conditions is critical for olive cultivation, particularly in regions prone to extreme weather fluctuations and especially with increasing threats from climate change. In controlled experiments, we subjected leaves of three cold-tolerant and three cold-susceptible cultivars to moderate (-7 °C) and severe (-12 °C) freezing stress, followed by recovery at baseline temperatures. The study measured photosynthetic efficiency and enzymatic activity and showed physiological and gene expression changes using different methods. Distinct transcriptomic adaptations were revealed. Cultivars displayed enhanced differential expression associated with photosynthetic recovery and gene regulation in metabolic pathways. Two overlapping DEGs with increased expression were found in all cultivars during initial freezing.

Spinal Cord Organoids from Human Amniotic Fluid iPSC Recapitulate the Diversity of Cell Phenotypes During Fetal Neural Tube Morphogenesis

Myelomeningocele (MMC) is a severe form of spina bifida associated with substantial neurologic morbidity. In vitro modeling systems of human spinal cord development may help to elucidate the underlying pathophysiology of the MMC spinal cord. To that end, we developed spinal cord organoids (SCO), defined as self-organized, three-dimensional clusters of spinal tissue, that were derived from human amniotic fluid-induced pluripotent stem cells. Here, we used a variety of analyses, including immunofluorescent and single-cell transcriptomic approaches, to characterize SCOs from healthy and MMC fetuses. Organoids contained a diverse range of neural and mesodermal phenotypes when cultured for up to 130 days in vitro. Multielectrode arrays revealed functional activity with evidence of emerging neuronal networks. Fetal spina bifida environment modeling was successfully established by culturing SCOs in second- and third-trimester amniotic fluid for 3 weeks. Taken together, we show that functional SCOs can recapitulate the cellular identity of the fetal spinal cord and represent a novel research platform to study the interplay between cellular, biochemical, and mechanical cues during human MMC neural tube morphogenesis.

Transcriptome-wide Mendelian randomisation exploring dynamic CD4+ T cell gene expression in colorectal cancer development

Background

Recent research has identified a potential protective effect of higher numbers of circulating lymphocytes on colorectal cancer (CRC) development. However, the importance of different lymphocyte subtypes and activation states in CRC development and the biological pathways driving this relationship remain poorly understood and warrant further investigation. Specifically, CD4+ T cells - a highly dynamic lymphocyte subtype - undergo remodelling upon activation to induce the expression of genes critical for their effector function. Previous studies investigating their role in CRC risk have used bulk tissue, limiting our current understanding of the role of these cells to static, non-dynamic relationships only.

Methods

Here, we combined two genetic epidemiological methods - Mendelian randomisation (MR) and genetic colocalisation - to evaluate evidence for causal relationships of gene expression on CRC risk across multiple CD4+ T cell subtypes and activation stage. Genetic proxies were obtained from single-cell transcriptomic data, allowing us to investigate the causal effect of expression of 1,805 genes across five CD4+ T cell activation states on CRC risk (78,473 cases; 107,143 controls). We repeated analyses stratified by CRC anatomical subsites and sex, and performed a sensitivity analysis to evaluate whether the observed effect estimates were likely to be CD4+ T cell-specific.

Results

We identified six genes with evidence (FDR-P<0.05 in MR analyses and H4>0.8 in genetic colocalisation analyses) for a causal role of CD4+ T cell expression in CRC development - FADS2, FHL3, HLA-DRB1, HLA-DRB5, RPL28, and TMEM258. We observed differences in causal estimates of gene expression on CRC risk across different CD4+ T cell subtypes and activation timepoints, as well as CRC anatomical subsites and sex. However, our sensitivity analysis revealed that the genetic proxies used to instrument gene expression in CD4+ T cells also act as eQTLs in other tissues, highlighting the challenges of using genetic proxies to instrument tissue-specific expression changes.

Conclusions

Our study demonstrates the importance of capturing the dynamic nature of CD4+ T cells in understanding disease risk, and prioritises genes for further investigation in cancer prevention research.

Local patterns of genetic sharing between neuropsychiatric and insulin resistance-related conditions

The co-occurrence of insulin resistance (IR)-related metabolic conditions with neuropsychiatric disorders is a major public health challenge. Evidence of the genetic links between these phenotypes is emerging, but little is currently known about the genomic regions and biological functions that are involved. To address this, we performed Local Analysis of [co]Variant Association (LAVA) using large-scale (N = 9,725-933,970) genome-wide association studies (GWASs) results for three IR-related conditions (type 2 diabetes mellitus, obesity, and metabolic syndrome) and nine neuropsychiatric disorders. Subsequently, positional and expression quantitative trait locus (eQTL)-based gene mapping and downstream functional genomic analyses were performed on the significant loci. Patterns of negative and positive local genetic correlations (|rg| = 0.21-1, pFDR < 0.05) were identified at 109 unique genomic regions across all phenotype pairs. Local correlations emerged even in the absence of global genetic correlations between IR-related conditions and Alzheimer's disease, bipolar disorder, and Tourette's syndrome. Genes mapped to the correlated regions showed enrichment in biological pathways integral to immune-inflammatory function, vesicle trafficking, insulin signalling, oxygen transport, and lipid metabolism. Colocalisation analyses further prioritised 10 genetically correlated regions for likely harbouring shared causal variants, displaying high deleterious or regulatory potential. These variants were found within or in close proximity to genes, such as SLC39A8 and HLA-DRB1, that can be targeted by supplements and already known drugs, including omega-3/6 fatty acids, immunomodulatory, antihypertensive, and cholesterol-lowering drugs. Overall, our findings highlight the complex genetic architecture of IR-neuropsychiatric multimorbidity, advocating for an integrated disease model and offering novel insights for research and treatment strategies in this domain.

Flux Sampling Suggests Metabolic Signatures of High Antibody-Producing CHO Cells

Chinese hamster ovary (CHO) cells remain the industry standard for producing numerous therapeutic proteins, particularly monoclonal antibodies (mAbs). However, achieving higher recombinant protein titers remains an ongoing challenge and a fundamental understanding of the cellular mechanism driving improved bioprocess performance remains elusive. To directly address these challenges and achieve substantial improvements, a more in-depth understanding of cellular function within a bioprocess environment may be required. Over the past decade, significant advancements have been made in the building of genome-scale metabolic models (GEMs) for CHO cells, bridging the gap between high information content 'omics data and the ability to perform in silico phenotypic predictions. Here, time-course transcriptomics has been employed to constrain culture phase-specific GEMs, representing the early exponential, late exponential, and stationary/death phases of CHO cell fed-batch bioreactor culture. Temporal bioprocess data, including metabolite uptake and secretion rates, as well as growth and productivity, has been used to validate flux sampling results. Additionally, high mAb-producing solutions have been identified and the metabolic signatures associated with improved mAb production have been hypothesized. Finally, constraint-based modeling has been utilized to infer specific amino acids, cysteine, histidine, leucine, isoleucine, asparagine, and serine, which could drive increased mAb production and guide optimal media and feed formulations.

Transcriptomic characterization of human pancreatic CD206- and CD206 + macrophages

Macrophages reside in all organs and participate in homeostatic- and immune regulative processes. Little is known about pancreatic macrophage gene expression. In the present study, global gene expression was characterized in human pancreatic macrophage subpopulations. CD206- and CD206 + macrophages were sorted separately from pancreatic islets and exocrine tissue to high purity using flow cytometry, followed by RNA-seq analysis. Comparing CD206- with CD206 + macrophages, CD206- showed enrichment in histones, proliferation and cell cycle regulation, glycolysis and SPP1-associated immunosuppressive polarization while CD206 + showed enrichment in complement and coagulation-, IL-10 and IL-2RA immune regulation, as well as scavenging-related gene sets. Comparing islet CD206- with exocrine CD206-, enrichments in islet samples included two sets involved in immune regulation, while enrichments in exocrine samples included sets related to extracellular matrix and immune activation. Fewer differences were found between CD206 + macrophages, with enrichments in islet samples including two IL2-RA related gene sets, while enrichments in exocrine samples included sets related to extracellular matrix and immune activation. Comparing macrophages between individuals with normoglycemia, elevated HbA1c or type 2 diabetes, only a few diverse differentially expressed genes were identified. This work characterizes global gene expression and identifies differences between CD206- and CD206 + macrophage populations within the human pancreas.

Feature selection methods affect the performance of scRNA-seq data integration and querying

The availability of single-cell transcriptomics has allowed the construction of reference cell atlases, but their usefulness depends on the quality of dataset integration and the ability to map new samples. Previous benchmarks have compared integration methods and suggest that feature selection improves performance but have not explored how best to select features. Here, we benchmark feature selection methods for single-cell RNA sequencing integration using metrics beyond batch correction and preservation of biological variation to assess query mapping, label transfer and the detection of unseen populations. We reinforce common practice by showing that highly variable feature selection is effective for producing high-quality integrations and provide further guidance on the effect of the number of features selected, batch-aware feature selection, lineage-specific feature selection and integration and the interaction between feature selection and integration models. These results are informative for analysts working on large-scale tissue atlases, using atlases or integrating their own data to tackle specific biological questions.

Probing the limits of cis-acting gene regulation using a model of allelic imbalance quantitative trait loci

Imbalance in gene expression between alleles is a hallmark of cis-acting expression quantitative trait loci (eQTLs) and several methods have been developed to exploit allelic imbalance to support the identification of eQTLs. Allelic imbalance is also of scientific and, potentially, clinical interest as it can erode the degree to which the effects of deleterious variants are buffered in a diploid organism and has been reported to be associated with the penetrance of pathological genomic variants. Here, we develop and apply a statistical model that is designed to evaluate whether the genotype of a locus is associated with the degree of allelic imbalance of a gene and refer to such loci as allelic imbalance quantitative trait loci (aiQTLs). An advantage of our approach is that it does not depend on linkage disequilibrium between the aiQTL and the associated gene and is, therefore, suited to the identification of eQTLs that act in cis over very large distances. We applied our model to data from the GTEx consortium and examined the relationship between the distance of an eQTL from the TSS of the associated gene and the evidence that the eQTL acts in cis. Previous studies have used a distance of 1Mb from the target gene as an indication that an eQTL acts in cis; however, our results suggest that the majority of eQTLs at distances more than 500 kb from the TSS of the target gene are likely to act in trans (and thus to affect both gene copies). The model used here is also well suited to comparing the overall extent of allelic imbalance between samples. We show that in some tissues allelic imbalance is correlated with age; however, this correlation may be due to changes in the abundance of immune cell populations with age, as we found strong correlations between sample-level allelic imbalance and the inferred abundance of multiple immune cell types across whole blood samples.

False positive NUP98 fluorescence in situ hybridization rearrangements in B-acute lymphoblastic leukemia

Gene fusions involving NUP98 have been reported in several hematologic malignancies yet have been very rarely reported in B-acute lymphoblastic leukemia (B-ALL). Two cases of B-ALL for which chromosome banding analysis (CBA) and fluorescence in situ hybridization (FISH) suggested apparent NUP98 rearrangements were further investigated with next-generation sequencing-based methodologies to verify the findings obtained with traditional cytogenetic methodologies. In the first case, CBA revealed a hyperdiploid karyotype with multiple structural abnormalities including additional material of unknown origin at 11p15; subsequent break-apart probe (BAP) FISH for NUP98 demonstrated 2 intact fusion signals and a single separate 5'NUP98 signal. However, whole-genome sequencing found no evidence of a NUP98 gene fusion. The results obtained with conventional cytogenetic methodologies were in fact attributable to structural variants (SV) with breakpoints not within NUP98 but within the 5'NUP98 BAP probe-binding sequence. In the second case, CBA revealed several structural and numeric abnormalities including a complex translocation between chromosomes 11 (at 11p15.4) and 19 (at 19p13.3) and an insertion of unknown material at 11p15.4. BAP FISH demonstrated a typical FISH signal pattern consistent with an apparent NUP98 rearrangement. However, no evidence of a NUP98 fusion was found on RNA sequencing. In conclusion, the two cases thus presented with clinical false positive NUP98 rearrangements by FISH. In the clinical laboratory, SVs in the vicinity of genes involved in recurrent rearrangements in hematologic malignancies may result in misleading results with conventional chromosome methodologies. This may preclude an accurate definition of the genetic attributes of malignancies with ensuing impacts on risk stratification and management. Higher-resolution testing methodologies such as whole-genome sequencing and RNA sequencing may be helpful in resolving unexpected results with conventional chromosome methodologies and enhancing the accuracy of genetic characterization of hematological malignancies in the clinical laboratory.

Dynamics in zebrafish development define transcriptomic specificity after angiogenesis inhibitor exposure

Testing for developmental toxicity is an integral part of chemical regulations. The applied tests are laborious and costly and require a large number of vertebrate test animals. To reduce animal numbers and associated costs, the zebrafish embryo was proposed as an alternative model. In this study, we investigated the potential of transcriptome analysis in the zebrafish embryo model to support the identification of potential biomarkers for key events in developmental toxicity, using the inhibition of angiogenesis as a proof of principle. Therefore, the effects on the zebrafish transcriptome after exposure to the tyrosine kinase inhibitors, sorafenib (1.3 µM and 2.4 µM) and SU4312 (1 µM, 2 µM, and 5 µM), and the putative vascular disruptor compound rotenone (25 nM and 50 nM) were analyzed. An early (2 hpf-hours post fertilization) and a late (24 hpf) exposure start with a time resolved transcriptome analysis was performed to compare the specificity and sensitivity of the responses with respect to anti-angiogenesis. We also showed that toxicodynamic responses were related to the course of the internal concentrations. To identify differentially expressed genes (DEGs) the time series data were compared by applying generalized additive models (GAMs). We observed mainly unspecific developmental toxicity in the early exposure scenario, while a specific repression of vascular related genes was only partially observed. In contrast, differential expression of vascular-related genes could be identified clearly in the late exposure scenario. Rotenone did not show angiogenesis-specific response on a transcriptomic level, indicating that the observed mild phenotype of angiogenesis inhibition may represent a secondary effect.

Strong nuclear expression of HOXB13 is a reliable surrogate marker for DNA methylome profiling to distinguish myxopapillary ependymoma from spinal ependymoma

Spinal ependymoma and myxopapillary ependymoma are the two most common spinal ependymal tumor types that feature distinct histological characteristics, genetic alterations and DNA methylation profiles. Their histological distinction may be difficult in individual cases and molecular diagnostic assessment, in particular DNA methylome profiling, may then be required to assign the correct diagnosis. Expression of the homeobox gene HOXB13 at the mRNA and protein levels has been reported as a frequent finding in myxopapillary ependymoma that may serve as a diagnostic marker for these tumors. Here, we evaluated the diagnostic role of HOXB13 immunostaining in 143 spinal neoplasms, comprising 54 histologically classified myxopapillary ependymomas, 46 histologically classified spinal ependymomas, and various other tumor types. Immunohistochemical results for HOXB13 protein were compared to molecular findings obtained by bead array-based DNA methylation and DNA copy number profiling, as well as next generation gene panel sequencing-based mutational analysis. Our findings indicate strong nuclear HOXB13 expression as a reliable diagnostic marker for molecularly confirmed myxopapillary ependymoma. Moreover, we provide evidence that differential HOXB13 protein expression is related to differential HOXB13-associated CpG site methylation in myxopapillary vs. spinal ependymomas, which can be assessed by targeted DNA methylation analysis. Taken together, immunohistochemistry for HOXB13 protein expression and targeted DNA methylation analysis of HOXB13 represent useful surrogate approaches that may substitute for DNA methylome profiling in routine diagnostics and facilitate precise classification of spinal ependymal tumors. In particular, strong nuclear HOXB13 immunoreactivity may serve as a novel diagnostic criterion for the classification of myxopapillary ependymoma.

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.

Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions

BACKGROUND

Copy number variations (CNVs) represent a common and highly specific type of variation in the genome, potentially influencing genetic diversity and mammalian phenotypic development. Structural variants, such as deletions, duplications, and insertions, have frequently been highlighted as key factors influencing traits in high-production pigs. However, comprehensive CNV analyses in miniature pig breeds are limited despite their value in biomedical research.

RESULTS

This study performed whole-genome sequencing in 36 miniature pigs from nine breeds from America, Asia and Oceania, and Europe. By employing a multi-tool approach (CNVpytor, Delly, GATK gCNV, Smoove), the accuracy of CNV identification was improved. In total, 34 homozygous CNVs overlapped with exonic regions in all samples, suggesting a role in expressing specific phenotypes such as uniform growth patterns, fertility, or metabolic function. In addition, 386 copy number variation regions (CNVRs) shared by all breeds were detected, covering 33.6 Mb (1.48% of the autosomal genome). Further, 132 exclusive CNVRs were identified for American breeds, 47 for Asian and Oceanian breeds, and 114 for European breeds. Functional enrichment analysis revealed genes within the common CNVRs involved in body height determination and other growth-related parameters. Exclusive CNVRs were located in the region of genes enriched for lipid metabolism in American minipigs, reproductive traits in Asian and Oceanian breeds, and cardiovascular features and body height in European breeds. In the selected groups, quantitative trait loci associated with body size, meat quality, reproduction, and disease susceptibility were highlighted.

CONCLUSION

This investigation of the CNV landscape of minipigs underlines the impact of selective breeding on structural variants and its role in the development of specific breed phenotypes across geographical areas. The multi-tool approach provides a valuable resource for future studies on the effects of artificial selection on livestock genomes.

Geometric deep learning and multiple-instance learning for 3D cell-shape profiling

The three-dimensional (3D) morphology of cells emerges from complex cellular and environmental interactions, serving as an indicator of cell state and function. In this study, we used deep learning to discover morphology representations and understand cell states. This study introduced MorphoMIL, a computational pipeline combining geometric deep learning and attention-based multiple-instance learning to profile 3D cell and nuclear shapes. We used 3D point-cloud input and captured morphological signatures at single-cell and population levels, accounting for phenotypic heterogeneity. We applied these methods to over 95,000 melanoma cells treated with clinically relevant and cytoskeleton-modulating chemical and genetic perturbations. The pipeline accurately predicted drug perturbations and cell states. Our framework revealed subtle morphological changes associated with perturbations, key shapes correlating with signaling activity, and interpretable insights into cell-state heterogeneity. MorphoMIL demonstrated superior performance and generalized across diverse datasets, paving the way for scalable, high-throughput morphological profiling in drug discovery. A record of this paper's transparent peer review process is included in the supplemental information.

Methionine intervention induces PD-L1 expression to enhance the immune checkpoint therapy response in MTAP-deleted osteosarcoma

Osteosarcoma (OS), a malignant bone tumor with limited treatment options, exhibits low sensitivity to immune checkpoint therapy (ICT). Through genomics and transcriptomics analyses, we identify a subgroup of OS with methylthioadenosine phosphorylase (MTAP) deletion, which contributes to ICT resistance, leading to a "cold" tumor microenvironment. MTAP-deleted OS relies on methionine metabolism and is sensitive to methionine intervention, achieved through either dietary restriction or inhibition of methionine adenosyltransferase 2a (MAT2A), a key enzyme in methionine metabolism. We further demonstrate that methionine intervention triggers programmed death-ligand 1 (PD-L1) transcription factor IKAROS family zinc finger 1 (IKZF1) and enhances PD-L1 expression in MTAP-deleted OS cells. Methionine intervention also activates the immune-related signaling pathways in MTAP-deleted OS cells and attracts CD8+ T cells, thereby enhancing the efficacy of ICT. Combining methionine intervention with ICT provides a significant survival benefit in MTAP-deleted OS murine models, suggesting a rationale for combination regimens in OS ICT.

Multi-omic integration with human DRG proteomics highlights TNFα signalling as a relevant sexually dimorphic pathway

The peripheral nervous system (PNS) plays a critical role in pathological conditions, including chronic pain disorders, that manifest differently in men and women. To investigate this sexual dimorphism at the molecular level, we integrated quantitative proteomic profiling of human dorsal root ganglia (hDRG) and peripheral nerve tissue into the expanding omics framework of the PNS. Using data-independent acquisition (DIA) mass spectrometry, we characterized a comprehensive proteomic profile, validating tissue-specific differences between the hDRG and peripheral nerve. Through multi-omic analyses and in vitro functional assays, we identified sex-specific molecular differences, with TNFα signalling emerging as a key sexually dimorphic pathway with higher prominence in males. Genetic evidence from genome-wide association studies (GWAS) further supports the functional relevance of TNFα signalling in the periphery, while clinical trial data and meta-analyses indicate a sex-dependent response to TNFα inhibitors. Collectively, these findings underscore a functionally sexual dimorphism in the PNS, with direct implications for sensory and pain-related clinical translation.

Activation of Neutrophil Extracellular Trap Formation in Patients with Heart Failure and a Preserved Ejection Fraction

INTRODUCTION

Pathophysiological differences between heart failure (HF) with preserved ejection fraction (HFpEF) and HF with reduced ejection fraction (HFrEF) remain poorly understood. Therefore, we performed pathway analyses from whole-blood transcriptomics to distinguish HFpEF from HFrEF.

METHODS AND RESULTS

Lexogen's QuantSeq was used to carry out whole-blood transcriptomics in 500 patients with HF (HFpEF n = 250, HFrEF n = 250). Differential gene expression analysis was performed on all protein-coding genes that met a predefined minimum expression level. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology over-representation analysis was utilized to identify upregulated and downregulated biological pathways. The findings were validated in an independent cohort of 727 patients with HF. Out of 7672 protein-coding transcripts, 217 were upregulated and 110 were downregulated in patients with HFpEF compared with HFrEF. The 3 most significantly upregulated genes were neutrophil-expressed elastase, defensin alpha 4, and pro-platelet basic protein. The 3 most significantly downregulated genes were lymphotoxin beta, bridging integrator 1, and V-set pre-B cell surrogate light chain 3. Translation of differentially expressed genes into biological pathways demonstrated that the most significantly activated KEGG pathway in HFpEF was neutrophil extracellular trap formation.

DISCUSSION

Transcriptomics analyses suggest activation of neutrophil extracellular trap formation pathways in patients with HFpEF. This pathway is associated with endothelial and coronary microvascular dysfunction and might be a target for future drug development in patients with HFpEF.

Searching for Sulfotyrosines (sY) in a HA(pY)STACK

Protein sulfation can be crucial in regulating protein-protein interactions but remains largely underexplored. Sulfation is nearly isobaric to phosphorylation, making it particularly challenging to investigate using mass spectrometry. The degree to which tyrosine sulfation (sY) is misidentified as phosphorylation (pY) is, thus, an unresolved concern. This study explores the extent of sY misidentification within the human phosphoproteome by distinguishing between sulfation and phosphorylation based on their mass difference. Using Gaussian mixture models (GMMs), we screened ∼45 M peptide-spectrum matches (PSMs) from the PeptideAtlas human phosphoproteome build for peptidoforms with mass error shifts indicative of sulfation. This analysis pinpointed 104 candidate sulfated peptidoforms, backed up by Gene Ontology (GO) terms and custom terms linked to sulfation. False positive filtering by manual annotation resulted in 31 convincing peptidoforms spanning 7 known and 7 novel sY sites. Y47 in calumenin was particularly intriguing since mass error shifts, acidic motif conservation, and MS2 neutral loss patterns characteristic of sulfation provided strong evidence that this site is sulfated rather than phosphorylated. Overall, although misidentification of sulfation in phosphoproteomics data sets derived from cell and tissue intracellular extracts can occur, it appears relatively rare and should not be considered a substantive confounding factor in high-quality phosphoproteomics data sets.

Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders

A meta-genome-wide association study across eight psychiatric disorders has highlighted the genetic architecture of pleiotropy in major psychiatric disorders. However, mechanisms underlying pleiotropic effects of the associated variants remain to be explored. We conducted a massively parallel reporter assay to decode the regulatory logic of variants with pleiotropic and disorder-specific effects. Pleiotropic variants differ from disorder-specific variants by exhibiting chromatin accessibility that extends across diverse cell types in the neuronal lineage and by altering motifs for transcription factors with higher connectivity in protein-protein interaction networks. We mapped pleiotropic and disorder-specific variants to putative target genes using functional genomics approaches and CRISPR perturbation. In vivo CRISPR perturbation of a pleiotropic and a disorder-specific gene suggests that pleiotropy may involve the regulation of genes expressed broadly across neuronal cell types and with higher network connectivity.

Restoration of excitation/inhibition balance enhances neuronal signal-to-noise ratio and rescues social deficits in autism-associated Scn2a-deficiency

Social behavior is critical for survival and adaptation, which is profoundly disrupted in autism spectrum disorders (ASD). Social withdrawal due to information overload was often described in ASD, and it was suspected that increased basal noise, i.e., excessive background neuronal activities in the brain could be a disease mechanism. However, experimental test of this hypothesis is limited. Loss-of-function mutations (deficiency) in SCN2A, which encodes the voltage-gated sodium channel NaV1.2, have been revealed as a leading monogenic cause of profound ASD. Here, we revealed that Scn2a deficiency results in robust and multifaceted social impairments in mice. Scn2a-deficient neurons displayed an increased excitation-inhibition (E/I) ratio, contributing to elevated basal neuronal noise and diminished signal-to-noise ratio (SNR) during social interactions. Notably, the restoration of Scn2a expression in adulthood is able to rescue both SNR and social deficits. By balancing the E/I ratio and reducing basal neuronal firing, an FDA-approved GABAA receptor-positive allosteric modulator improves sociability in Scn2a-deficient mice and normalizes neuronal activities in translationally relevant human brain organoids carrying autism-associated SCN2A nonsense mutation. Collectively, our findings revealed a critical role of the NaV1.2 channel in the regulation of social behaviors, and identified molecular, cellular, and circuitry mechanisms underlying SCN2A-associated disorders.

Evolutionary divergence between homologous X-Y chromosome genes shapes sex-biased biology

Sex chromosomes are a fundamental aspect of sex-biased biology, but the extent to which homologous X-Y gene pairs ('the gametologs') contribute to sex-biased phenotypes remains hotly debated. Although these genes tend to exhibit large sex differences in expression throughout the body (XX females can express both X members, and XY males can express one X and one Y member), there is conflicting evidence regarding the degree of functional divergence between the X and Y members. Here we develop and apply co-expression fingerprint analysis to characterize functional divergence between the X and Y members of 17 gametolog gene pairs across >40 human tissues. Gametolog pairs exhibit functional divergence between the sexes that is driven by divergence between the X versus Y members (assayed in males), and this within-pair divergence is greatest among pairs with evolutionarily distant X and Y members. These patterns reflect that X versus Y gametologs show coordinated patterns of asymmetric coupling with large sets of autosomal genes, which are enriched for functional pathways and gene sets implicated in sex-biased biology and disease. Our findings suggest that the X versus Y gametologs have diverged in function and prioritize specific gametolog pairs for future targeted experimental studies.

Alternative splicing landscape in mouse skeletal muscle and adipose tissue: Effects of intermittent fasting and exercise

Alternative splicing contributes to diversify the cellular protein landscape, but aberrant splicing is implicated in many diseases. To which extent mis-splicing contributes to insulin resistance as the causal defect of type 2 diabetes and whether this can be reversed by lifestyle interventions is largely unknown. Therefore, RNA sequencing data from skeletal muscle and adipose tissue of diabetes-susceptible NZO mice treated with or without intermittent fasting and of healthy C57BL/6J mice subjected to exercise were analyzed for alternative splicing differences using Whippet and rMATS. Diet and exercise interventions triggered comparable levels of splicing changes, although the splicing profile of skeletal muscle appeared to be more flexible than that of adipose tissue, with 72-114 differential splicing events in muscle and less than 25 in adipose tissue. Splicing changes induced by time-restricted feeding, alternate-day fasting and exercise were generally mild, with a maximal percent spliced in (PSI) difference of 67%, indicating that alternative splicing plays a rather minor role in lifestyle-induced adaptations of muscle and adipose tissue in mice. However, intron retention contributed to the regulation of gene expression, influencing genes whose expression was directly linked to phenotypic parameters (e.g. Eno2 and Pan2). Alternate-day fasting promoted skipping of exon 7 in Mlxipl (coding for ChREBP), thereby affecting the glucose sensing module of this carbohydrate-responsive transcription factor. Both intermittent fasting and exercise training led to alternative splicing of known diabetes-related GWAS genes (e.g. Abcc8, Ifnar2, Smarcad1), highlighting the potential metabolic relevance of these changes.

Comparative transcriptome and mutation analyses of the pancreatic islets of a rat model of obese type 2 diabetes identifies a frequently distributed nonsense mutation in the lipocalin 2 gene

Type 2 diabetes (T2D) is a multifactorial disease caused by insulin resistance and impaired insulin secretion from pancreatic β-cells, but the precise mechanisms remain to be elucidated. To identify primary genetic factors of T2D in a rat model, we performed comparative transcriptome and mutation analyses of the pancreatic islets between the obese Zucker fatty rat and the Zucker fatty rat-derived T2D model Zucker fatty diabetes mellitus (ZFDM) rat. Among differentially expressed genes irrespective of obesity and glucose intolerance states, we identified a nonsense mutation, c.409C > T (p.Gln137X), in the lipocalin 2 (Lcn2) gene which encodes a secreted protein called neutrophil gelatinase-associated lipocalin, a well-known biomarker for inflammation. We examined the relevance of the Lcn2 mutation with T2D in the ZFDM rat by using genome editing and genetic linkage analysis and confirmed that the Lcn2 mutation exhibits no significant association with the onset of T2D. Interestingly, we found that the Lcn2 mutation is distributed widely in rat species, such as commonly used DA and F344 strains. Our data indicate that several rat strains would serve as Lcn2 deficient models, contributing to elucidate the pathophysiological roles of Lcn2 in a wide variety of phenotypes.

Oronasal mucosal melanoma is defined by two transcriptional subtypes in humans and dogs with implications for diagnosis and therapy

Mucosal melanoma is a rare melanoma subtype associated with a poor prognosis and limited existing therapeutic interventions, in part due to a lack of actionable targets and translational animal models for preclinical trials. Comprehensive data on this tumour type are scarce, and existing data often overlooks the importance of the anatomical site of origin. We evaluated human and canine oronasal mucosal melanoma (OMM) to determine whether the common canine disease could inform the rare human equivalent. Using a human and canine primary OMM cohort of treatment-naive archival tissue, alongside clinicopathological data, we obtained transcriptomic, immunohistochemical, and microbiome data from both species. We defined the transcriptomic landscape in both species and linked our findings to immunohistochemical, microbiome, and clinical data. Human and dog OMM stratified into two distinctive transcriptional groups, which we defined using a species-independent 41-gene signature. These two subgroups are termed CTLA4-high and MET-high and indicate actionable targets for OMM patients. To guide clinical decision-making, we developed immunohistochemical diagnostic tools that distinguish between transcriptomic subgroups. We found that OMM had conserved transcriptomic subtypes and biological similarity between human and canine OMM, with significant implications for patient classification, treatment, and clinical trial design. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

An Attention-Based Deep Neural Network Model to Detect Cis-Regulatory Elements at the Single-Cell Level From Multi-Omics Data

Cis-regulatory elements (cREs) play a crucial role in regulating gene expression and determining cell differentiation and state transitions. To capture the heterogeneous transitions of cell states associated with these processes, detecting cRE activity at the single-cell level is essential. However, current analytical methods can only capture the average behavior of cREs in cell populations, thereby obscuring cell-specific variations. To address this limitation, we proposed an attention-based deep neural network framework that integrates DNA sequences, genomic distances, and single-cell multi-omics data to detect cREs and their activities in individual cells. Our model shows higher accuracy in identifying cREs within single-cell multi-omics data from healthy human peripheral blood mononuclear cells than other existing methods. Furthermore, it clusters cells more precisely based on predicted cRE activities, enabling a finer differentiation of cell states. When applied to publicly available single-cell data from patients with glioma, the model successfully identified tumor-specific SOX2 activity. Additionally, it revealed the heterogeneous activation of the ZEB1 transcription factor, a regulator of epithelial-to-mesenchymal transition-related genes, which conventional methods struggle to detect. Overall, our model is a powerful tool for detecting cRE regulation at the single-cell level, which may contribute to revealing drug resistance mechanisms in cell sub-populations.

Human-correlated genetic models identify precision therapy for liver cancer

Hepatocellular carcinoma (HCC), the most common form of primary liver cancer, is a leading cause of cancer-related mortality worldwide1,2. HCC occurs typically from a background of chronic liver disease, caused by a spectrum of predisposing conditions. Tumour development is driven by the expansion of clones that accumulate progressive driver mutations3, with hepatocytes the most likely cell of origin2. However, the landscape of driver mutations in HCC is broadly independent of the underlying aetiologies4. Despite an increasing range of systemic treatment options for advanced HCC, outcomes remain heterogeneous and typically poor. Emerging data suggest that drug efficacies depend on disease aetiology and genetic alterations5,6. Exploring subtypes in preclinical models with human relevance will therefore be essential to advance precision medicine in HCC7. Here we generated a suite of genetically driven immunocompetent in vivo and matched in vitro HCC models. Our models represent multiple features of human HCC, including clonal origin, histopathological appearance and metastasis. We integrated transcriptomic data from the mouse models with human HCC data and identified four common human-mouse subtype clusters. The subtype clusters had distinct transcriptomic characteristics that aligned with the human histopathology. In a proof-of-principle analysis, we verified response to standard-of-care treatment and used a linked in vitro-in vivo pipeline to identify a promising therapeutic candidate, cladribine, that has not previously been linked to HCC treatment. Cladribine acts in a highly effective subtype-specific manner in combination with standard-of-care therapy.