Search Results (40)

Neurodevelopmental disorders (NDDs), including autism spectrum disorder, intellectual disability, and attention-deficit/hyperactivity disorder, are genetically and phenotypically heterogeneous conditions affecting millions worldwide. High-throughput omics technologies—transcriptomics, proteomics, metabolomics, and epigenomics—offer a unique opportunity to link genetic variation to molecular and cellular mechanisms underlying these disorders. However, the high dimensionality, sparsity, batch effects, and complex covariance structures of omics data present significant statistical challenges, requiring robust normalization, batch correction, imputation, dimensionality reduction, and multivariate modeling approaches. This review provides a comprehensive overview of statistical frameworks for analyzing high-dimensional omics datasets in NDDs, including univariate and multivariate models, penalized regression, sparse canonical correlation analysis, partial least squares, and integrative multi-omics methods such as DIABLO, similarity network fusion, and MOFA. We illustrate how these approaches have revealed convergent molecular signatures—synaptic, mitochondrial, and immune dysregulation—across transcriptomic, proteomic, and metabolomic layers in human cohorts and experimental models. Finally, we discuss emerging strategies, including single-cell and spatially resolved omics, machine learning-driven integration, and longitudinal multi-modal analyses, highlighting their potential to translate complex molecular patterns into mechanistic insights, biomarkers, and therapeutic targets. Integrative multi-omics analyses, grounded in rigorous statistical methodology, are poised to advance mechanistic understanding and precision medicine in NDDs. Full article

Ochetobius elongatus, a critically endangered (CR) fish species of the Yangtze River Basin in China, has experienced a severe decline in its wild population. Understanding its mechanisms of phenotypic variation is essential for developing effective conservation and restoration strategies. Using geometric morphometrics based on 14 landmarks, we examined the phenotypic difference among five populations from the mainstem, the tributary, and the river-connected lakes of the middle Yangtze River. The results showed that significant phenotypic divergence was detected between river and lake populations. River individuals exhibited a more elongated body, smaller head, inferior mouth position, larger operculum, and narrower caudal peduncle, whereas lake individuals showed a deeper body, and anterior shift in the origin of pelvic fin. The first canonical variable effectively distinguished river and lake populations, with the accuracy of both original and cross-validation classification exceeding 90%, indicating that habitat heterogeneity was the primary driver of phenotypic differentiation. No significant correlation was found between morphological distance and geographical distance. Water temperature, flow velocity, water depth, and food abundance significantly influenced phenotypic variation, but their individual effects were limited, which suggested that environmental shaping of morphology depended more on synergistic effects. Our findings provide important insights into the adaptive evolution of this critically endangered species and offer a scientific basis for conservation efforts. Full article

Thymic epithelial tumors (TETs) display heterogeneous histology and often unpredictable clinical behavior. The Hippo signaling pathway has been implicated in tumorigenesis, but its role in TETs remains poorly characterized. We performed the first comprehensive immunohistochemical analysis of core and upstream Hippo pathway components—YAP1, active YAP (AYAP), TAZ, LATS1, MOB1A, MST1, SAV1, and TEAD4—in 77 TETs. Associations with clinicopathological parameters and survival were explored. We observed widespread expression of Hippo components in TETs with significant associations among molecules and differences in subcellular localization and expression in normal tissue. Early stage TETs showed higher nuclear YAP1 (p = 0.032) and AYAP (p = 0.007), while cytoplasmic MST1 (p = 0.002), LATS1 (p = 0.007), MOB1A (p = 0.033) and TEAD4 (p < 0.001) correlated with advanced stage. Cytoplasmic MST1 (p = 0.014), LATS1 (p < 0.001) and TEAD4 (p = 0.005) were associated with histological aggressiveness. Cytoplasmic TEAD4 overexpression was associated with poorer overall survival (log-rank, <70% versus ≥70%, p = 0.003). Our findings provide novel insights into the differential regulation and compartmentalization of Hippo components in TETs. While indolent tumors show features that are consistent with partial Hippo inactivation, more aggressive phenotypes exhibit reduced nuclear YAP/TAZ and altered TEAD4 compartmentalization, suggesting a context-dependent Hippo signaling state. Cytoplasmic TEAD4 emerges as a potential adverse prognosticator, indicating involvement in non-canonical or Hippo-independent mechanisms. Full article

Epipactis helleborine (L.) Crantz is considered a challenging and phenotypically difficult species to identify due to its wide range of morphological variability. This variability is mainly observed in the perianth parts but also extends to the gynostemium structure, which has so far been considered one of the most useful diagnostic characteristics. As a result, a simple graphic illustrating the structural pattern of gynostemium morphology has appeared in 10 different forms in available European taxonomic keys, which significantly complicates the identification of this species. A total of 122 flowers of E. helleborine were collected from four natural populations in the Lower Silesia region (Poland) between 2017 and 2019 and analysed for gynostemium morphological variation. Geometric morphometric analyses, including Procrustes ANOVA, PCA, and CVA, were used to examine gynostemium shape, with statistical tests assessing variation in size and stigma inclination angle among populations, individual plants (ramets), and years of research. Statistical analysis revealed significant positive correlations between gynostemium width and height, with significant variation in size and angle of stigma inclination, primarily driven by population, while ramet and year of research had a lesser impact. Geometric morphometric analyses indicated significant population-level variation in gynostemium shape, with principal component analysis identifying the ventral view as the most informative for discriminating these differences. The first two principal components explained the major shape variation, and canonical variate analysis confirmed that this view is most important for species identification. Full article

Background: Spinal muscular atrophy (SMA) is a severe neuromuscular disorder characterized by the degeneration of alpha motor neurons in the spinal cord, leading to progressive proximal muscle weakness and paralysis. SMA is clinically categorized into four phenotypes based on age of onset and motor function achieved. Patients with SMA type 3 (juvenile, Kugelberg-Welander disease) initially have the ability to walk unaided, but experience a gradual decline in motor abilities over time. However, their lifespan is not affected by the presence of the disease. Leptin, a cytokine-like hormone secreted by adipocytes, has receptors widely distributed in musculoskeletal tissues. Several studies suggest that adiponectin deficiency contributes to the development of insulin resistance, with lower adiponectin levels closely associated with greater insulin resistance and hyperinsulinemia. However, the role of adiponectin in different types of sarcopenia and its connection to insulin sensitivity remains controversial. The purpose of this study was to measure leptin and adiponectin levels in patients with SMA type 3 and explore their association with markers of insulin sensitivity. Methods: This cross-sectional study included 23 adult patients with SMA type 3 (SMA group) and 18 community-based healthy volunteers (control group), conducted from July 2020 to September 2024. Anthropometric parameters, body composition, body fat percentage, surrogate markers of insulin sensitivity (Homeostasis model assessment of insulin resistance index—HOMA-IR and ISI Matsuda), and circulating levels of leptin and adiponectin were measured in all participants. Results: Insulin resistance was present in 91.3% of patients with SMA type 3, as determined by HOMA-IR and ISI Matsuda insulin sensitivity markers. In the control group, 64.7% had insulin resistance (IR) according to HOMA-IR, while 44.4% met the ISI Matsuda criterion for IR, showing a significant difference in peripheral insulin sensitivity between groups. A significant difference in serum adiponectin levels was observed between patients with SMA type 3 and the control group, whereas there was no significant difference in serum leptin concentrations. High adiponectin levels were observed in 50% of patients with SMA type 3. In the healthy control group, adiponectin levels positively correlated with ISI Matsuda and negatively correlated with HOMA-IR, confirming the insulin-sensitizing role of adiponectin. However, this correlation was not observed in patients with SMA type 3. Conclusions: Our results suggest that in this specific type of hereditary neuromuscular disease, the interplay between sarcopenia and insulin leads to adiponectin resistance, challenging the canonical narrative between insulin sensitivity and adiponectin, and indicating a need for further research. Full article

Background: The epithelial-to-mesenchymal transition (EMT) is a common feature in early cancer invasion. Increased vimentin is a canonical marker of the EMT; however, the role of vimentin in EMT remains unknown. Methods: To clarify this, we induced EMT in lung cancer cells with TGF-β1, followed by treatment with the vimentin-targeting drug ALD-R491, live-cell imaging, and quantitative proteomics. Results: We identified 838 proteins in the intermediate filament fraction of cells. TGF-β1 treatment increased the proportion of vimentin in this fraction and the levels of 24 proteins. Variants of fibronectin showed the most pronounced increase (137-fold), followed by regulators of the cytoskeleton, cell motility, and division, such as the mRNA-splicing protein SON. TGF-β1 increased cell spreading and cell migration speed, and changed a positive correlation between cell migration speed and persistence to negative. ALD-R491 reversed these mesenchymal phenotypes to epithelial and the binding of RNA-binding proteins, including SON. Conclusions: These findings present many new interactors of intermediate filaments, describe how EMT and vimentin filament dynamics influence the intermediate filament interactome, and present ALD-R491 as a possible EMT-inhibitor. The observations support the hypothesis that the dynamic turnover of vimentin filaments and their interacting proteins govern mesenchymal cell migration, EMT, cell invasion, and cancer metastasis. Full article

Small Open Reading Frames (smORFs) of less than 100 codons remain mostly uncharacterised. About a thousand smORFs per genome encode peptides and microproteins about 70–80 aa long, often containing recognisable protein structures and markers of translation, and these are referred to as short Coding Sequences (sCDSs). The characterisation of individual sCDSs has provided examples of smORFs’ function and conservation, but we cannot infer the functionality of all other metazoan smORFs from these. sCDS function has been characterised at a genome-wide scale in yeast and bacteria, showing that hundreds can produce a phenotype, but attempts in metazoans have been less successful. Either most sCDSs are not functional, or classic experimental techniques do not work with smORFs due to their shortness. Here, we combine extensive proteomics with bioinformatics and genetics in order to detect and corroborate sCDS function in Drosophila. Our studies nearly double the number of sCDSs with detected peptides and microproteins and an experimentally corroborated function. Finally, we observe a correlation between proven sCDS protein function and bioinformatic markers such as conservation and GC content. Our results support that sCDSs peptides and microproteins act as membrane-related regulators of canonical proteins, regulators whose functions are best understood at the cellular level, and whose mutants produce little, if any, overt morphological phenotypes. Full article

Down syndrome (DS) is a multisystemic disorder that includes accelerated aging caused by trisomy 21. In particular, overexpression of cystathionine-β-synthase (CBS) is linked to excess intracellular hydrogen sulfide (H₂S), a mitochondrial toxin at higher concentrations, which impairs cellular viability. Concurrent overexpression of superoxide dismutase 1 (SOD1) may increase oxidative stress by generating excess hydrogen peroxide (H₂O₂) while also mitigating the toxic H₂S burden via a non-canonical sulfide-oxidizing mechanism. We investigated the phenotypic variability in basal H₂S levels in relation to DS B lymphocyte cell health and SOD1 in H₂S detoxification. The H₂S levels were negatively correlated with the DS B lymphocyte growth rates but not with CBS protein. Pharmacological inhibition of SOD1 using LCS-1 significantly increased the H₂S levels to a greater extent in DS cells while also decreasing the polysulfide products of H₂S oxidation. However, DS cells exhibited elevated H₂O₂ and lipid peroxidation, representing potential toxic consequences of SOD1 overexpression. Treatment of DS cells with a pleiotropic carbon nanozyme (pleozymes) decreased the total oxidative stress and reduced the levels of the H₂S-generating enzymes CBS and 3-mercaptopyruvate sulfurtransferase (MPST). Our results indicate that pleozymes may bridge the protective and deleterious effects of DS SOD1 overexpression on H₂S metabolism and oxidative stress, respectively, with cytoprotective benefits. Full article

The non-canonical PD-L1 pathway revealed that programmed-death ligand 1 (PD-L1) expression in immune cells also plays a crucial role in immune response. Moreover, immune cell distribution in a tumour microenvironment (TME) is pivotal for tumour genesis. However, the results remain controversial and further research is needed. Distribution of PD-L1-positive (PD-L1⁺) tumour-infiltrating lymphocytes in the context of TME was assessed in 72 archival I–III stage surgically resected NSCLC tumour specimens. Predominant PD-L1⁺ lymphocyte distribution in the tumour stroma, compared to islets, was found (p = 0.01). Higher PD-L1⁺ lymphocyte infiltration was detected in smokers due to their predominance in the stroma. High PD-L1⁺ lymphocyte infiltration in tumour stroma was more common in tumours with higher CD4⁺ T cell infiltration in islets and stroma, Foxp3⁺CD4⁺ T cell infiltration in islets and lover M1 macrophage infiltration in the stroma (p = 0.034, p = 0.034, p = 0.005 and p = 0.034 respectively). Meanwhile, high PD-L1⁺ lymphocyte infiltration in islets was predominantly found in tumours with high levels of IL-17A⁺CD4⁺ T cells in islets and Foxp3⁺CD4⁺ T cells in islets and stroma (p = 0.032, p = 0.009 and p = 0.034, respectively). Significant correlations between PD-L1⁺ lymphocytes and tumour-infiltrating CD4⁺, Foxp3⁺CD4⁺, IL-17A⁺CD4⁺ T cells and M2 macrophages were found. An analysis of the tumour-immune phenotype revealed a significant association between PD-L1 expression and IL17⁺CD4⁺ and Foxp3⁺CD4⁺ immune phenotypes. PD-L1⁺ lymphocytes are associated with the distribution of CD4⁺, Foxp3⁺CD4⁺, IL17A⁺CD4⁺ T cells, M1 and M2 macrophages in TME of resected NSCLC. Full article

Osteosarcoma is an aggressive bone malignancy, molecularly characterized by acquired genome complexity and frequent loss of TP53 and RB1. Obtaining a molecular understanding of the initiating mutations of osteosarcomagenesis has been challenged by the difficulty of parsing between passenger and driver mutations in genes. Here, a forward genetic screen in a genetic mouse model of osteosarcomagenesis initiated by Trp53 and Rb1 conditional loss in pre-osteoblasts identified that Arid1a loss contributes to OS progression. Arid1a is a member of the canonical BAF (SWI/SNF) complex and a known tumor suppressor gene in other cancers. We hypothesized that the loss of Arid1a increases the rate of tumor progression and metastasis. Phenotypic evaluation upon in vitro and in vivo deletion of Arid1a validated this hypothesis. Gene expression and pathway analysis revealed a correlation between Arid1a loss and genomic instability, and the subsequent dysregulation of genes involved in DNA DSB or SSB repair pathways. The most significant of these transcriptional changes was a concomitant decrease in DCLRE1C. Our findings suggest that Arid1a plays a role in genomic instability in aggressive osteosarcoma and a better understanding of this correlation can help with clinical prognoses and personalized patient care. Full article

The different susceptibility to HIV-1 infection in U937 cells—permissive (Plus) or nonpermissive (Minus)—is linked to the expression in Minus cells of interferon (IFN)-γ inducible antiviral factors such as tripartite motif-containing protein 22 (TRIM22) and class II transactivator (CIITA). CIITA interacts with Cyclin T1, a key component of the Positive-Transcription Elongation Factor b (P-TEFb) complex needed for the efficient transcription of HIV-1 upon interaction with the viral transactivator Tat. TRIM22 interacts with CIITA, recruiting it into nuclear bodies together with Cyclin T1. A 50 kDa Cyclin T1 was found only in Minus cells, alongside the canonical 80 kDa protein. The expression of this truncated form remained unaffected by proteasome inhibitors but was reduced by IFNγ treatment. Unlike the nuclear full-length protein, truncated Cyclin T1 was also present in the cytoplasm, and this subcellular localization correlated with its capacity to inhibit Tat-mediated HIV-1 transcription. The 50 kDa Cyclin T1 in Minus cells likely contributes to their non-permissive phenotype by acting as a dominant negative factor, disrupting P-TEFb complex formation and function. Its reduction upon IFNγ treatment suggests a regulatory loop by which its inhibitory role on HIV-1 replication is then exerted by the IFNγ-induced CIITA, which binds to the canonical Cyclin T1, displacing it from the P-TEFb complex. Full article

A genetic diagnosis of primary cardiomyopathies can be a long-unmet need in patients with complex phenotypes. We investigated a three-generation family with cardiomyopathy and various extracardiac abnormalities that had long sought a precise diagnosis. The 41-year-old proband had hypertrophic cardiomyopathy (HCM), left ventricular noncompaction, myocardial fibrosis, arrhythmias, and a short stature. His sister showed HCM, myocardial hypertrabeculation and fibrosis, sensorineural deafness, and congenital genitourinary malformations. Their father had left ventricular hypertrophy (LVH). The proband’s eldest daughter demonstrated developmental delay and seizures. We performed a clinical examination and whole-exome sequencing for all available family members. All patients with HCM/LVH shared a c.4411-2A>C variant in ALPK3, a recently known HCM-causative gene. Functional studies confirmed that this variant alters ALPK3 canonical splicing. Due to extracardiac symptoms in the female patients, we continued the search and found two additional single-gene disorders. The proband’s sister had a p.Trp329Gly missense in GATA3, linked to hypoparathyroidism, sensorineural deafness, and renal dysplasia; his daughter had a p.Ser251del in WDR45, associated with beta-propeller protein-associated neurodegeneration. This unique case of three monogenic disorders in one family shows how a comprehensive approach with thorough phenotyping and extensive genetic testing of all symptomatic individuals provides precise diagnoses and appropriate follow-up, embodying the concept of personalized medicine. We also present the first example of a splicing functional study for ALPK3 and describe the genotype–phenotype correlations in cardiomyopathy. Full article

The phenotypic evaluation of root traits in soybeans presents challenges in breeding due to its high cost and the requirement for experimental plot destruction. Establishing relationships between aerial and root traits is crucial, given the relative ease of phenotypic evaluations for aerial traits. Therefore, this study aims to utilize the canonical correlation technique to estimate latent variables, subsequently employing GBLUP for the genomic prediction of the root traits (length, volume, surface area, and dry mass) using phenotypic information from aerial part traits (hypocotyl diameter and dry mass). Our results demonstrate the effectiveness of the technique in predicting the root part, even when not directly evaluated. The agreement observed between the top 10% of individuals selected based on the canonical variable and each root trait individually was considered moderate or substantial. This enables the simultaneous selection of genotypes based on both trait groups, providing a valuable approach for soybean breeding programs. Full article

The NF-κB co-factor Bcl3 is a proto-oncogene that promotes breast cancer proliferation, metastasis and therapeutic resistance, yet its role in breast cancer cell survival is unclear. Here, we sought to determine the effect of Bcl3 suppression alone on breast cancer cell viability, with a view to informing future studies that aim to target Bcl3 therapeutically. Bcl3 was suppressed by siRNA in breast cancer cell lines before changes in viability, proliferation, apoptosis and senescence were examined. Bcl3 suppression significantly reduced viability and was shown to induce apoptosis in all cell lines tested, while an additional p53-dependent senescence and senescence-associated secretory phenotype was also observed in those cells with functional p53. The role of the Bcl3/NF-κB axis in this senescence response was confirmed via siRNA of the non-canonical NF-κB subunit NFKB2/p52, which resulted in increased cellular senescence and the canonical subunit NFKB1/p50, which induced the senescence-associated secretory phenotype. An analysis of clinical data showed a correlation between reduced relapse-free survival in patients that expressed high levels of Bcl3 and carried a p53 mutation. Together, these data demonstrate a dual role for Bcl3/NF-κB in the maintenance of breast cancer cell viability and suggests that targeting Bcl3 may be more beneficial to patients with tumours that lack functional p53. Full article

To characterize the hits from a phenotypic neurotoxicity screen, we obtained transcriptomics data for valinomycin, diethylstilbestrol, colchicine, rotenone, 1-methyl-4-phenylpyridinium (MPP), carbaryl and berberine (Ber). For all compounds, the concentration triggering neurite degeneration correlated with the onset of gene expression changes. The mechanistically diverse toxicants caused similar patterns of gene regulation: the responses were dominated by cell de-differentiation and a triggering of canonical stress response pathways driven by ATF4 and NRF2. To obtain more detailed and specific information on the modes-of-action, the effects on energy metabolism (respiration and glycolysis) were measured. Ber, rotenone and MPP inhibited the mitochondrial respiratory chain and they shared complex I as the target. This group of toxicants was further evaluated by metabolomics under experimental conditions that did not deplete ATP. Ber (204 changed metabolites) showed similar effects as MPP and rotenone. The overall metabolic situation was characterized by oxidative stress, an over-abundance of NADH (>1000% increase) and a re-routing of metabolism in order to dispose of the nitrogen resulting from increased amino acid turnover. This unique overall pattern led to the accumulation of metabolites known as biomarkers of neurodegeneration (saccharopine, aminoadipate and branched-chain ketoacids). These findings suggest that neurotoxicity of mitochondrial inhibitors may result from an ensemble of metabolic changes rather than from a simple ATP depletion. The combi-omics approach used here provided richer and more specific MoA data than the more common transcriptomics analysis alone. As Ber, a human drug and food supplement, mimicked closely the mode-of-action of known neurotoxicants, its potential hazard requires further investigation. Full article