Biology subjects

Hilal, N.

Publications and source records attributed to Hilal, N..

3 recordsLinked to original sources

bioRxiv2025

Benchmarking of duplex sequencing approaches to reveal somatic mutation landscapes

Detecting somatic mutations in normal tissues is challenging due to sequencing errors and the low allele fractions of post-zygotic variants. Duplex sequencing greatly reduces errors and can detect mutations at any allele fraction, but systematic, cross-platform comparisons are lacking. We present a comprehensive benchmarking of six duplex sequencing technologies used by the SMaHT Network: CODEC, CompDuplex-seq, HiDEF-seq, NanoSeq, ppmSeq, and VISTA-seq. We evaluated their performance using cord blood DNA, a tumor-normal cell line mixture, and homogenates from six human tissues. Each method shows distinct profiles in genomic footprint, sensitivity, and cost. Despite differences in library construction and sequencing platforms, estimates of mutation rates and mutational signatures are highly concordant. Integration with ultra-deep whole-genome sequencing shows that duplex approaches sensitively capture mutations and signatures beyond embryonic or clonally expanded variants. These results provide a foundation for selecting duplex methods and interpreting their data, enabling scalable single-molecule analyses of somatic mutation landscapes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/692823v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@123b221org.highwire.dtl.DTLVardef@83ba0aorg.highwire.dtl.DTLVardef@2b0ab0org.highwire.dtl.DTLVardef@1cae35e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2023

High-Quality Nuclei Isolation from Postmortem Human Heart Muscle Tissues for Single-Cell Studies

Single-cell approaches have become an increasingly popular way of understanding the genetic factors behind disease. Isolation of DNA and RNA from human tissues is necessary to analyze multi-omic data sets, providing information on the single-cell genome, transcriptome, and epigenome. Here, we isolated high-quality single-nuclei from postmortem human heart tissues for DNA and RNA analysis. Postmortem human tissues were obtained from 106 individuals, 33 with a history of myocardial disease, diabetes, or smoking, and 73 controls without heart disease. We demonstrated that the Qiagen EZ1 instrument and kit consistently isolated genomic DNA of high yield, which can be used for checking DNA quality before conducting single-cell experiments. Here, we provide a method for single-nuclei isolation from cardiac tissue, otherwise known as the SoNIC method, which allows for the isolation of single cardiomyocyte nuclei from postmortem tissue by nuclear ploidy status. We also provide a detailed quality control measure for single-nuclei whole genome amplification and a pre-amplification method for confirming genomic integrity.

genetics↗

bioRxiv2021

sMEK1 promotes crosstalk between IRE1 and Akt signaling pathway: Evidence for a novel IRE1/sMEK1/Akt complex

The Unfolded Protein Response (UPR) is a dynamic cellular pathway that helps maintain proteostasis during endoplasmic reticulum (ER) stress. One of the key UPR sensors is IRE1, which plays a central role in managing ER stress and interacts with other cellular pathways to regulate cell homeostasis. The Akt signalling pathway, on the other hand, is a crucial survival pathway involved in diverse cellular functions like growth, proliferation, glucose metabolism, and survival. This study explores the interplay between these two important cell signalling pathways. Specifically, our study revealed that IRE1 negatively regulates Akt through the protein phosphatase sMEK1. We identified sMEK1 and Akt as novel interacting partners of IRE1, which together form a ternary complex that helps coordinate the IRE1 and Akt signalling networks. The IRE1/sMEK1/Akt ternary complex results in the dephosphorylation of Akt by sMEK1 in the presence of activated IRE1. Together, this study sheds light on the molecular mechanism underlying the UPR/Akt link and provides valuable insights into the overall impact of their interaction.

cell biology↗