Biology subjects

Lin, S. J.

Publications and source records attributed to Lin, S. J..

6 recordsLinked to original sources

bioRxiv2025

Identification of novel protective loci for executive function using the trail making test part B in the Long Life Family Study

The Trail Making Test (TMT) Part B (TMT-B), a well-established assessment of cognitive function, is a frequent component of diagnostic assessments for Mild Cognitive Impairment and dementia in older adults. Identifying the genetic variants associated with the TMT-B will not only gain insights of genetic determinants of cognitive function, but also the molecular mechanisms for dementia. Published GWAS to date for TMT-B suffer from relatively low power due to the use of population level data and imputation methods. To address these deficits, we used a family-based study design to identify the genetic variants associated with the TMT-B incorporating both genome-wide linkage analysis (GWLS) and whole genome sequencing (WGS). As such, we examined the sequenced genetic determinants of TMT-B using GWLS in over 2000 participants from Long Life Family Study (LLFS). In GWLS, the estimated heritability of TMT-B was 0.29. We detected one significant linkage peak at 15q25 (LOD>3.0). Statistical fine-mapping nominated five variants including three SNPs (NTRK3-rs74031103, protective CEMIP-rs2271159, and protective AGBL1-rs4134376) and two INDELs (protective KLHL25-15:85882445:IND, and protective CEMIP-15:80893381:IND) contributing to the linkage peak. Four out of these five variants are protective for TMT-B. The rs2271159 SNP influences CEMIP expression in cerebellum and hippocampus, while the 15:80893381:IND modulates CEMIP expression in blood. Additionally, the variant rs4134376 is a basal ganglia-specific eQTL for AGBL1. In conclusion, we utilized GWLS, leveraged multi-omics data (whole genome sequence genomic data, transcriptomic data, and lipidomic data), and identified novel protective variants and genes for TMT-B performance.

genomics↗

bioRxiv2024

A Paradigm For Calling Sequence In Families: The Long Life Family Study

Over Several years, we have developed a system for assuring the quality of whole genome sequence (WGS) data in the LLFS families. We have focused on providing data to identify germline genetic variants with the aim of releasing as many variants on as many individuals as possible. We aim to assure the quality of the individual calls. The availability of family data has enabled us to use and validate some filters not commonly used in population-based studies. We developed slightly different procedures for the autosomal, X, Y, and Mitochondrial (MT) chromosomes. Some of these filters are specific to family data, but some can be used with any WGS data set. We also describe the procedure we use to construct linkage markers from the SNP sequence data and how we compute IBD values for use in linkage analysis.

genetics↗

bioRxiv2024

A Novel Gene ARHGAP44 for Longitudinal Changes in Glycated Hemoglobin (HbA1c) in Subjects without Type 2 Diabetes: Evidence from the Long Life Family Study (LLFS) and the Framingham Offspring Study (FOS)

Glycated hemoglobin (HbA1c) indicates average glucose levels over three months and is associated with insulin resistance and type 2 diabetes (T2D). Longitudinal changes in HbA1c ({Delta}HbA1c) are also associated with aging processes, cognitive performance, and mortality. We analyzed {Delta}HbA1c in 1,886 non-diabetic Europeans from the Long Life Family Study to uncover gene variants influencing {Delta}HbA1c. Using growth curve modeling adjusted for multiple covariates, we derived {Delta}HbA1c and conducted linkage-guided sequence analysis. Our genome-wide linkage scan identified a significant locus on 17p12. In-depth analysis of this locus revealed a variant rs56340929 (explaining 27% of the linkage peak) in the ARHGAP44 gene that was significantly associated with {Delta}HbA1c. RNA transcription of ARHGAP44 was associated with {Delta}HbA1c. The Framingham Offspring Study data further supported these findings on the gene level. Together, we found a novel gene ARHGAP44 for {Delta}HbA1c in family members without T2D. Follow-up studies using longitudinal omics data in large independent cohorts are warranted.

genetics↗

bioRxiv2023

H2A.X mutants exhibit enhanced DNA demethylation in Arabidopsis thaliana

H2A.X is an H2A variant histone in eukaryotes, unique for its ability to respond to DNA damage, initiating the DNA repair pathway. H2A.X replacement within the histone octamer is mediated by the FAcilitates Chromatin Transactions (FACT) complex, a key chromatin remodeler. FACT is required for DEMETER (DME)-mediated DNA demethylation at certain loci in Arabidopsis thaliana female gametophytes during reproduction, though it is not known how FACT targets DME sites. Here, we investigated whether H2AX is involved in DME- and FACT-mediated DNA demethylation during Arabidopsis reproduction. We show that h2a.x mutants are more sensitive to genotoxic stress, consistent with previous reports. H2A.X fused to the Green Fluorescent Protein (GFP) gene under the H2A.X promoter was highly expressed in newly developing Arabidopsis tissues, including in male and female gametophytes. We examined DNA methylation in h2a.x developing seeds using whole genome bisulfite sequencing, and found that CG DNA methylation in the developing endosperm, but not the embryo, is decreased genome-wide in h2a.x mutants, predominately in transposons and intergenic DNA. Hypomethylated sites overlapped 62 % with canonical DME loci. These data indicate that H2A.X is not required for DME function, but is important for DNA methylation homeostasis in the unique chromatin environment of Arabidopsis endosperm.

plant biology↗

bioRxiv2022

Manipulating the 3D organization of the largest synthetic yeast chromosome

Whether synthetic genomes can power life has attracted broad interest in the synthetic biology field, especially when the synthetic genomes are extensively modified with thousands of designer features. Here we report de novo synthesis of the largest eukaryotic chromosome thus far, synIV, a 1,454,621-bp Saccharomyces cerevisiae chromosome resulting from extensive genome streamlining and modification. During the construction of synIV, we developed megachunk assembly combined with a hierarchical integration strategy, which significantly increased the accuracy and flexibility of synthetic chromosome construction and facilitated chromosome debugging. In addition to the drastic sequence changes made to synIV by rewriting it, we further manipulated the three-dimensional structure of synIV in the yeast nucleus to explore spatial gene regulation within the nuclear space. Surprisingly, we found few gene expression changes, suggesting that positioning inside the yeast nucleoplasm plays a minor role in gene regulation. Lastly, we tethered synIV to the inner nuclear membrane via its hundreds of loxPsym sites and observed transcriptional repression of the entire chromosome, demonstrating chromosome-wide transcription manipulation without changing the DNA sequences. Our manipulation of the spatial structure of the largest synthetic yeast chromosome shed light on higher-order architectural design of the synthetic genomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/487066v2_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@18bf586org.highwire.dtl.DTLVardef@1a471d5org.highwire.dtl.DTLVardef@12d7690org.highwire.dtl.DTLVardef@1c32510_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDe novo synthesis of the largest eukaryotic chromosome, synIV C_LIO_LISynIV shows similar 3D structure to wild-type IV, despite thousands of changes made to it C_LIO_LI"Inside-out" repositioning of synIV in nucleus shows minor transcriptional changes C_LIO_LIMultipoint tethering synIV to inner nuclear membrane represses transcription of whole chromosome C_LI

synthetic biology↗

bioRxiv2021

A single cell atlas of human and mouse white adipose tissue

White adipose tissue (WAT), once regarded as morphologically and functionally bland, is now recognized to be dynamic, plastic, heterogenous, and involved in a wide array of biological processes including energy homeostasis, glucose and lipid handling, blood pressure control, and host defense1. High fat feeding and other metabolic stressors cause dramatic changes in adipose morphology, physiology, and cellular composition1, and alterations in adiposity are associated with insulin resistance, dyslipidemia, and type 2 diabetes (T2D)2. Here, we provide detailed cellular atlases of human and murine subcutaneous and visceral white fat at single cell resolution across a range of body weight. We identify subpopulations of adipocytes, adipose stem and progenitor cells (ASPCs), vascular, and immune cells and demonstrate commonalities and differences across species and dietary conditions. We link specific cell types to increased risk of metabolic disease, and we provide an initial blueprint for a comprehensive set of interactions between individual cell types in the adipose niche in leanness and obesity. These data comprise an extensive resource for the exploration of genes, traits, and cell types in the function of WAT across species, depots, and nutritional conditions.

physiology↗