HGG Advances最新文献

To advance understanding of cellular heterogeneity in disease from single-cell sequencing data, we introduce residual principal-component analysis (ResidPCA), a robust method for identifying cell states that explicitly models cell-type heterogeneity. In simulations, ResidPCA achieved more than 4-fold higher accuracy than conventional PCA and over 3-fold higher accuracy than non-negative matrix factorization (NMF)-based methods in detecting states expressed across multiple cell types. Applied to single-cell RNA sequencing of light-stimulated mouse visual cortex cells, ResidPCA captured stimulus-driven variability with an accuracy more than 5-fold higher than NMF-based approaches. In single-nucleus datasets from an Alzheimer disease cohort, ResidPCA identified 44 chromatin accessibility-based states from single-nucleus ATAC-seq (snATAC-seq) and 42 transcriptional states from single-nucleus RNA-seq. Thirty snATAC-seq states were significantly enriched for Alzheimer disease heritability, often more so than established cell types such as microglia. The snATAC-seq state most significantly enriched for heritability further elucidates a recently implicated neuron-oligodendrocyte-microglial mechanistic axis, linking early amyloid production in neurons and oligodendrocytes with later microglial activation and immune response. These results highlight the ability of ResidPCA to uncover previously hidden biological variation in single-cell data and reveal disease-relevant cell states.

Stillbirth is a devastating adverse pregnancy outcome affecting 2 million pregnancies worldwide. Although an etiology may be found in some stillbirths, one-third remain unexplained. Stillbirth clusters in families and few underlying inherited genes associated with stillbirth are known. Well-characterized family-based studies may aid in identifying genetic contributors to unexplained stillbirth. Using the Utah Population Database, we defined pedigrees with high familial risk of stillbirth. Comprehensive phenotyping with review of primary medical records was conducted to identify stillbirth cases without identifiable causes. We generated whole-genome sequencing in seven stillborn placentas from three pedigrees. We performed shared genomic segments analysis to identify evidence for segregating haplotypes shared by the stillbirths to provide evidence for inherited risk. A region at 15q26.3 was identified in two independent pedigrees with genome-wide significance in both (a 1.2 Mb segment shared by two stillbirths in pedigree A, and a 1.8 Mb segment shared by two stillbirths in pedigree B). Four other regions reached genome-wide significance in single pedigrees at 16p13.13-p13.12, 9p13.3-p13.1, and 6p22.2-p22.1 (shared by the same two stillbirths in pedigree B), and a 0.8 Mb segment at 14q.32.2 shared by three stillbirths in pedigree C. The identified regions are implicated in in utero and postnatal development, pregnancy loss, and infertility. We identified evidence for inherited risk loci in stillbirth placental genes that are implicated in in utero and postnatal development, pregnancy loss, and infertility. Identification of inherited genes in stillbirth risk may provide therapeutic targets for prevention and treatment to improve pregnancy outcomes.

In studies of individuals of primarily European genetic ancestry, common and low-frequency variants and rare coding variants have been found to be associated with the risk of bipolar disorder (BD) and schizophrenia (SZ). However, less is known for individuals of other genetic ancestries or the role of rare non-coding variants in BD and SZ risk. We performed whole-genome sequencing (∼27X) of African American individuals: 1,598 with BD, 3,295 with SZ, and 2,651 unaffected controls (InPSYght study). We increased power by incorporating 14,812 jointly called psychiatrically unscreened ancestry-matched controls from the Trans-Omics for Precision Medicine (TOPMed) Program for a total of 17,463 controls (∼37X). To identify variants and sets of variants associated with BD and/or SZ, we performed single-variant tests, gene-based tests for singleton protein truncating variants, and rare and low-frequency variant annotation-based tests with conservation and universal chromatin states and sliding windows. We found suggestive evidence of the association of BD with single variants on chromosome 18 and of lower BD risk associated with rare and low-frequency variants on chromosome 11 in a region with multiple BD genome-wide association study loci, using a sliding window approach. We also found that chromatin and conservation state tests can be used to detect differential calling of variants in controls sequenced at different centers and to assess the effectiveness of sequencing metric covariate adjustments. Our findings reinforce the need for continued whole-genome sequencing in additional samples of African American individuals and more comprehensive functional annotation of non-coding variants.

The primary cilium is a small organelle that plays key roles in cellular signaling. Defects in primary cilia formation, morphology, and function cause a heterogeneous group of developmental syndromes termed ciliopathies. The inturned planar cell polarity protein (INTU) gene acts in the CPLANE complex to facilitate ciliogenesis and support cilia signaling. Bi-allelic genetic variants in INTU have previously been reported in seven patients with pleiotropic disorders, but a core set of phenotypes from these patients has not been codified and functional studies into these variants have failed to fully demonstrate mechanistic perturbations caused by INTU dysfunction. Here, we report on a person with cardiac abnormalities, distinctive craniofacial features, developmental delays, tongue hamartomas, bilateral clinodactyly, and polydactyly of the left great toe. Trio whole-exome sequencing identified compound heterozygous variants in the INTU gene. Functional studies provide evidence that these INTU variants confer human disease through altered ciliogenesis and/or cilia signaling. Furthermore, we suggest that this study along with previous reports sufficiently establishes an association between a pleiotropic disorder and variants in the INTU gene to enhance clinical interpretation of INTU variants in future studies.

Acute lymphoblastic leukemia (ALL) is the most common childhood cancer, with Hispanic/Latino children having a higher incidence of ALL than other racial/ethnic groups. Among the genetic variants previously implicated in ALL risk, a number of them were found to be enriched in Indigenous American (IA)-like ancestries and inherited by many Hispanic/Latino individuals. However, due to potential confounding from environmental factors, the association between IA-like ancestry and risk for ALL has remained unclear. In this study, we characterized the impact of IA-like ancestry on overall ALL risk and on the frequency and effect size of known risk alleles, while accounting for non-genetic correlates of ancestry. Contrary to previous findings, we found that global IA-like ancestry was not significantly associated with ALL risk after adjusting for socioeconomic indicators. However, locally at known ALL risk regions, we uncovered that increasing copies of the IA-like haplotype were positively and significantly associated with ALL risk (e.g., the IA-like haplotype had ∼1.33 times the odds of harboring the risk allele compared to non-IA-like haplotypes), but we found no evidence of interaction between genotype and ancestry in relation to ALL. Admixture mapping identified replicable association signals at chr7p12.2 and chr10q21.2, consistent with the benefit of leveraging genetic ancestry in identifying genetic risk loci. Our results suggest that increased risk of ALL in Hispanic/Latino children may be conferred by the higher frequency of risk alleles within IA-like ancestry and that local ancestry-based analyses are robust strategies to elucidate genetic etiology of disease.

Polygenic scores (PGSs) are appealing for detecting gene-environment interactions due to the aggregation of genetic effects and reduced multiple testing burden compared to single-variant genome-wide interaction studies (GWISs). However, standard PGSs reflect many different biological mechanisms, limiting interpretation and potentially diluting pathway-specific interaction signals. Previous work has uncovered a significant genome-wide PGS×Adiposity signal impacting liver function, but there is an opportunity for additional and more interpretable discoveries. Here, we leveraged pathway-specific polygenic scores (pPGSs) to discover mechanism-specific gene-adiposity interactions. We tested for body mass index (BMI) interactions impacting three liver-related biomarkers (ALT, AST, and GGT) using (1) a standard, genome-wide PGS, (2) an array of pPGSs containing variant subsets derived from KEGG pathways, and (3) a GWIS. For ALT, we identified 49 significant pPGS×BMI interactions at a Bonferroni corrected p < 2.7 × 10^-4, 80% of which were not explained by genes close to the 8 loci found in the associated GWIS. Across all biomarkers, we found interactions with 83 unique pPGSs. We tested alternate pathway collections (hallmark, KEGG Medicus), finding that the choice of pathway collection strongly impacts discovery. Our findings reinforced known biology (e.g., glycerolipid metabolism and hepatic lipid export affecting ALT release) and captured additional phenomena (e.g., actin cytoskeleton remodeling-associated variants alter the liver's robustness to lipid mechanical stress and thus GGT release). These results support the use of pPGSs for well powered and interpretable discovery of pPGS×E interactions with adiposity-related exposures for liver biomarkers and motivate future studies using a broader collection of exposures and outcomes.

The hexanucleotide (G₄C₂) repeat expansion in the promoter region of C9orf72 is the most frequent genetic cause of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS). In this study, we conducted a genome-wide DNA methylation (DNAm) analysis using EPIC version 2 (EPICv2) arrays on an FTD cohort comprising 27 carriers and 250 non-carriers of the pathogenic C9orf72 repeat expansion from the Amsterdam Dementia Cohort. We identified differentially methylated CpGs probes associated with the pathogenic C9orf72 expansion and used these findings to create a DNAm least absolute shrinkage and selection operator (LASSO) predictor to identify repeat expansion carriers. Eight CpG sites at the C9orf72 locus were significantly differentially hypermethylated in repeat expansion carriers compared to non-carriers. The LASSO model predicted repeat expansion status with an average accuracy of 98.6%. The LASSO predictor was further validated in a separate, independent validation cohort containing 1,589 subjects with bipolar disorder, 580 first-degree relatives, and 289 independent control subjects with available EPICv2 data, identifying four C9orf72 repeat expansion carriers, subsequently confirmed by repeat-primed PCR. This result highlights the accuracy and generalizability of the DNAm predictor of C9orf72 repeat expansion carriers. The identification of a highly accurate DNAm biomarker for a repeat expansion locus associated with neurodegenerative disorders may provide great value for studying this locus. The approach holds significant promise for investigating this and other repeat expansion loci, particularly given the growing interest in epigenetic epidemiological studies involving large cohorts with available DNAm data.

Clinical interest in polygenic (PRS) and integrated (PRS plus clinical factors) risk scores (IRS) is growing, yet little data exist on how healthcare providers navigate returning these results to patients. The eMERGE IV study implemented a genome-informed risk assessment for 11 common complex conditions, incorporating PRS, IRS, and monogenic findings, offering an opportunity to examine providers' experiences disclosing these results. We used a cross-sectional survey with closed- and open-ended questions to assess result disclosure experiences. All study providers involved in disclosing high-risk results were invited to participate. Of 21 respondents, 86% were female and the mean age was 35 years. Most were genetic counselors (76%), followed by pharmacists (10%), research coordinators (10%), and a nurse/nurse practitioner (5%). Confidence in disclosing high-risk results was highest for monogenic (92% extremely/very confident), followed by PRS (78%) and IRS (69%). Most rated disclosures as slightly/moderately complex (77% monogenic, 89% PRS, 69% IRS). Breast cancer (69%) and obesity (39%) were rated as the most challenging conditions to disclose. Key considerations when delivering PRS/IRS included clarifying clinical meaning, clear communication of risk, and acknowledging limitations. Challenges involved ensuring patient understanding, confusion over care recommendations, and PRS complexity. Concerns reflected both personal and perceived patient views, including PRS validity, interpretation of relative risk, and healthcare impact. Study findings provide early insights into result disclosure practices for different types of genomic risk and conditions, which can inform training, resources, and clinical integration of these emerging genomic tools.

Exceptional responders to targeted cancer therapies offer a unique opportunity to uncover molecular determinants of drug sensitivity. In this study, we aimed to identify genomic alterations associated with exceptional response to cyclin-dependent kinase inhibitors (CDKi) combined with endocrine therapy in individuals with estrogen receptor (ER)-positive, human epidermal growth factor receptor 2 (HER2)-negative advanced breast cancer. Sixteen people who achieved prolonged complete or partial responses were retrospectively analyzed using whole-exome sequencing. Among these, six individuals provided high-quality tumor and matched normal blood samples suitable for downstream variant analysis. This cohort exhibited a diverse landscape of germline, somatic, and loss of heterozygosity variants, several of which occurred in genes linked to hormone signaling, cell-cycle regulation, and transcriptional regulation. One shared alteration was a common germline single-nucleotide polymorphism (SNP), rs771205, in the gene MINDY1, a deubiquitylase regulating estrogen receptor alpha (ERα) stability. To explore the functional consequences of this variant, we used CRISPR genome editing to introduce the MINDY1 SNP into breast cancer cell lines. While the variant had no measurable effect on MINDY1 transcript or protein levels, comparative transcriptomic and proteomic profiling associated the variant with alterations in key signaling pathways relevant to palbociclib response. These findings demonstrate how infrequent germline variants can modulate therapeutic response through protein function rather than expression levels. Our work emphasizes the importance of personalized genomic analysis in revealing mechanisms underlying exceptional response, and it highlights MINDY1 as a potential biomarker or co-target in CDK4/6i-treated ER⁺ breast cancers.

Human development is a complex process that requires precise control of gene expression through regulatory proteins. Recently, heterozygous variants in PRR12, encoding a proline-rich regulatory protein, were found to cause a variable phenotype involving developmental delay/cognitive impairment, neuropsychiatric diagnoses, structural eye anomalies, congenital heart and kidney defects, and poor growth. QSER1, encoding glutamine- and serine-rich protein 1, represents a paralog of PRR12 that shares 28% overall identity at the protein level and stronger conservation (43%) in the C-terminal region. QSER1 deficiency in human embryonic stem cells causes hypermethylation of many key transcription factor genes, implicating it in the development of multiple organs. Here, we present three unrelated individuals with neurodevelopmental phenotypes, variable other multisystem anomalies, and heterozygous variants in QSER1. This includes two novel de novo frameshift alleles (p.(Lys1565Argfs∗36) and p.(Phe896fs∗28)) and one ultra-rare canonical splice site variant resulting in a combination of abnormal transcripts, frameshift (p.(Glu1393Glyfs∗26)), and in-frame deletion of a conserved amino acid (p.(Glu1393del)), supported by in silico predictions and minigene assays. In situ hybridization revealed dynamic and broad expression of qser1 in zebrafish embryos, including a strong presence in the developing brain. These data suggest a possible role for QSER1/qser1 in vertebrate development and human disease.