A multi-omic analysis of human naïve CD4+ T cells

Background: Cellular function and diversity are orchestrated by complex interactions of fundamental biomolecules including DNA, RNA and proteins. Technological advances in genomics, epigenomics, transcriptomics and proteomics have enabled massively parallel and unbiased measurements. Such high-throughput technologies have been extensively used to carry out broad, unbiased studies, particularly in the context of human diseases. Nevertheless, a unified analysis of the genome, epigenome, transcriptome and proteome of a single human cell type to obtain a coherent view of the complex interplay between various biomolecules has not yet been undertaken. Here, we report the first multi-omic analysis of human primary naïve CD4+ T cells isolated from a single individual. Results: Integrating multi-omics datasets allowed us to investigate genome-wide methylation and its effect on mRNA/protein expression patterns, extent of RNA editing under normal physiological conditions and allele specific expression in naïve CD4+ T cells. In addition, we carried out a multi-omic comparative analysis of naïve with primary resting memory CD4+ T cells to identify molecular changes underlying T cell differentiation. This analysis provided mechanistic insights into how several molecules involved in T cell receptor signaling are regulated at the DNA, RNA and protein levels. Phosphoproteomics revealed downstream signaling events that regulate these two cellular states. Availability of multi-omics data from an identical genetic background also allowed us to employ novel proteogenomics approaches to identify individual-specific variants and putative novel protein coding regions in the human genome. Conclusions: We utilized multiple high-throughput technologies to derive a comprehensive profile of two primary human cell types, naïve CD4+ T cells and memory CD4+ T cells, from a single donor. Through vertical as well as horizontal integration of whole genome sequencing, methylation arrays, RNA-Seq, miRNA-Seq, proteomics, and phosphoproteomics, we derived an integrated and comparative map of these two closely related immune cells and identified potential molecular effectors of immune cell differentiation following antigen encounter

Maltose-binding protein switches programmed cell death in Nicotiana glutinosa leaf cells

Maltose-binding protein (MBP) is a part of the complex regulatory and transport maltose system of Escherichia coli that is responsible for the uptake and efficient catabolism of maltodextrins through the trans-membrane signaling at the expense of ATP. In the present work, this bacterial periplasmic protein was identified as a cell death inducer in Nicotiana glutinosa plant. Upon exogenous application at the concentrations more than 50 μg/mL, purified MBP protein induced wilting and localized cell death on the leaves of test plant. DNA fragmentation assay and antioxidant enzymes activity test showed that the induced cell death might be programmed. It was predicted that maltose-binding protein signals programmed cell death (PCD) upstream of reactive oxygen species (ROS) and DNA fragmentation processes in the test plant leaves. However, it needs to be clarified that how MBP switches and signals PCD in plant tissues.Белок, связывающий мальтозу (МСБ), является частью сложной системы регуляции и транспорта мальтозы у Escherichia coli. Он отвечает за поглощение и эффективный катаболизм мальтозы с помощью трансмембранной передачи сигнала за счет АТФ. В настоящей работе показано, что этот бактериальный перипластный белок является индуктором клеточ-ной гибели у Nicotiana glutinosa. При экзогенном нанесении в концентрациях более чем 50 мг/мг очищенный МСБ индуцирует увядание и локали-зованную клеточную гибель в листьях тестовых растений. Анализ фрагментации ДНК и активности антиоксидантных ферментов показал, что индуцированная гибель клеток может быть запрограммированной. Предполагается, что МСБ может влиять на развитие программированной клеточной гибели через сигналинг активных форм кислорода и регуляцию процессов фрагментации ДНК в листьях тестовых растений, однако механизм такого воздействия подлежит дальнейшему исследованию