Regulatory de novo mutations underlying intellectual disability

Correlation of peripheral olfactomedin 1 with Alzheimer's disease and cognitive functions

Olfactomedin 1 (OLFM1) is thought to be involved in neuronal development, synaptic structure and function. However, the expression level of peripheral OLFM1 in Alzheimer's disease (AD) and its role in AD are unclear. The present study was conducted to assess the relationship of serum OLFM1 with AD and cognitive function. This study comprised 120 patients with AD and 118 healthy controls (HC). Serum OLFM1 levels, cognitive functions, and brain region volumes were evaluated in all participants. The results demonstrated a significant reduction in serum OLFM1 levels in AD patients (749.8 ± 42.3 pg/mL) compared to HC (804.4 ± 45.7 pg/mL). Among participants carrying the APOE ε4 allele, a significant positive correlation was observed between OLFM1 levels and cognitive assessments, including Mini-Mental State Examination (MMSE), Montreal Cognitive Assessment (MoCA), and Memory and Executive Screening (MES). Furthermore, reduced OLFM1 levels were significantly associated with hippocampus (β = 0.005, 95% CI = 0.001-0.011, p = 0.042) and angular gyrus (β = 0.012, 95% CI = 0.001-0.022, p = 0.025) atrophy. The integration of serum OLFM1 with basic clinical characteristics exhibited robust discriminatory power in differentiating AD patients from HC, evidenced by an area under the curve of 0.881 (95% CI = 0.834-0.926). In summary, serum OLFM1 is a potential peripheral biomarker for AD, that correlates with cognitive function and specific brain volumes. In addition, APOE ε4 may modulate the influence of OLFM1 on cognitive function.

Evolutionary Innovations in Conserved Regulatory Elements Associate With Developmental Genes in Mammals

Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Genetic variation within enhancer sequences is an important contributor to phenotypic variation including evolutionary adaptations and human disease. Certain genes and pathways may be more prone to regulatory evolution than others, with different patterns across diverse organisms, but whether such patterns exist has not been investigated at a sufficient scale. To address this question, we identified signatures of accelerated sequence evolution in conserved enhancer elements throughout the mammalian phylogeny at an unprecedented scale. While different genes and pathways were enriched for regulatory evolution in different parts of the tree, we found a striking overall pattern of pleiotropic genes involved in gene regulatory and developmental processes being enriched for accelerated enhancer evolution. These genes were connected to more enhancers than other genes, which was the basis for having an increased amount of sequence acceleration over all their enhancers combined. We provide evidence that sequence acceleration is associated with turnover of regulatory function. Detailed study of one acceleration event in an enhancer of HES1 revealed that sequence evolution led to a new activity domain in the developing limb that emerged concurrently with the evolution of digit reduction in hoofed mammals. Our results provide evidence that enhancer evolution has been a frequent contributor to regulatory innovation at conserved developmental signaling genes in mammals.

The Role of KDM2A and H3K36me2 Demethylation in Modulating MAPK Signaling During Neurodevelopment

Intellectual disability (ID) is a condition characterized by cognitive impairment and difficulties in adaptive functioning. In our research, we identified two de novo mutations (c.955C>T and c.732C>A) at the KDM2A locus in individuals with varying degrees of ID. In addition, by using the Gene4Denovo database, we discovered five additional cases of de novo mutations in KDM2A. The mutations we identified significantly decreased the expression of the KDM2A protein. To investigate the role of KDM2A in neural development, we used both 2D neural stem cell models and 3D cerebral organoids. Our findings demonstrated that the reduced expression of KDM2A impairs the proliferation of neural progenitor cells (NPCs), increases apoptosis, induces premature neuronal differentiation, and affects synapse maturation. Through ChIP-Seq analysis, we found that KDM2A exhibited binding to the transcription start site regions of genes involved in neurogenesis. In addition, the knockdown of KDM2A hindered H3K36me2 binding to the downstream regulatory elements of genes. By integrating ChIP-Seq and RNA-Seq data, we made a significant discovery of the core genes' remarkable enrichment in the MAPK signaling pathway. Importantly, this enrichment was specifically linked to the p38 MAPK pathway. Furthermore, disease enrichment analysis linked the differentially-expressed genes identified from RNA-Seq of NPCs and cerebral organoids to neurodevelopmental disorders such as ID, autism spectrum disorder, and schizophrenia. Overall, our findings suggest that KDM2A plays a crucial role in regulating the H3K36me2 modification of downstream genes, thereby modulating the MAPK signaling pathway and potentially impacting early brain development.

Evolutionary innovation in conserved regulatory elements across the mammalian tree of life

Transcriptional enhancers orchestrate cell type- and time point-specific gene expression programs. Evolution of enhancer sequences can alter target gene expression without causing detrimental misexpression in other contexts. It has long been thought that this modularity allows evolutionary changes in enhancers to escape pleiotropic constraints, which is especially important for evolutionary constrained developmental patterning genes. However, there is still little data supporting this hypothesis. Here we identified signatures of accelerated evolution in conserved enhancer elements across the mammalian phylogeny. We found that pleiotropic genes involved in gene regulatory and developmental processes were enriched for accelerated sequence evolution within their enhancer elements. These genes were associated with an excess number of enhancers compared to other genes, and due to this they exhibit a substantial degree of sequence acceleration over all their enhancers combined. We provide evidence that sequence acceleration is associated with turnover of regulatory function. We studied one acceleration event in depth and found that its sequence evolution led to the emergence of a new enhancer activity domain that may be involved in the evolution of digit reduction in hoofed mammals. Our results provide tangible evidence that enhancer evolution has been a frequent contributor to modifications involving constrained developmental signaling genes in mammals.