Dissecting the roles of histone deacetylase 1 and 2 in the hematopoietic system

Reversible histone acetylation on lysine residues has been intensively studied as an epigenetic mark for gene activation in a variety of eukaryotes. Histone deacetylases (HDACs) act to repress gene expression by removing acetyl groups from histones and possibly other proteins. Based on their expression pattern, distribution and biochemical activity, HDAC1 andhave been considered to be the major HDACs to regulate gene expression in a wide range of tissues in mammals. Experiments using transformed cells and HDAC inhibitors suggest that HDACs are important for cell cycle progression, apoptosis regulation and induction of differentiation; however their in vivo roles in a higher organism as well as their molecular mechanism of actions remain largely unexplored. I have generated mice conditionally targeted at the HDAC1 or HDAC2 locus and crossed these to different deleter mice in order to dissect the function of these enzymes in vivo; I focused on B cell specific inactivation in the first part of the thesis and on hematopoieticlineage specific inactivation in the second part. Mice completely lacking HDAC1 die during embryogenesis while animals lacking HDAC2 show partial perinatal mortality. In contrast, ablation of HDAC1 orin the B cell lineage led to no obvious developmental defect. Simultaneous deletion of both HDAC1 andin the B cell lineage causes a very severe blockade in the early B cell development accompanied by severe defects in cell cycle progression, apoptosis regulation and recombination of immunoglobulin heavy chain (IgH) variable (VH) segments. Using three-dimensional DNA fluorescence in situ hybridization, we show that pre-BI cells lacking HDAC1 andare severely impaired in the contraction of the IgH locus, a mechanism whereby distantly located variable genes are brought in close proximity to the rest of the locus. Analysis of histone modifications revealed that these pre-BI cells lshow global histone hyperacetylation as well as increased histone lysinemethylation. Taken together, we conclude that HDAC1 andare crucial factors for B cell development, survival and IgH recombination by modulating histone modifications which may affect gene expression and the higher order of chromatin structure. In the second part I have analyzed the roles of HDAC1 in the hematopoietic lineage. Loss of HDAC1 in the hematopoietic lineage has only minor impacts on the myeloid lineage development, but impaired IgG secretion and reduced germinal center formation were observed upon induction of a T cell dependent immune response. Using transcriptome analysis, we found that these germinal center B cells lacking HDAC1 exhibit higher expression of genes involved in cell cycle regulation as well as apoptosis. These results suggest that HDAC1 has important roles to regulate the adaptive immune response by controlling the expansion of B cells upon antigen stimulation

Generation of human GAPDH knock-in reporter iPSC lines for stable expression of tdTomato in pluripotent and differentiated culture conditions

Human induced pluripotent stem cells (iPSCs) can differentiate into multiple cell types and are utilized for research on human development and regenerative medicine. Here, we report the establishment of human GAPDH knock-in reporter iPSC lines (GAPDH-tdT1 and 2), via CRISPR/Cas9-mediated homologous recombination, that stably express tdTomato as a constitutive cell label in both iPSCs and their differentiated derivatives. These cell lines will provide useful tools to trace cell locations and fates in 2D cultures and 3D organoids and will facilitate in vivo experiments

A DNA Repair Complex Functions as an Oct4/Sox2 Coactivator in Embryonic Stem Cells

SummaryThe transcriptional activators Oct4, Sox2, and Nanog cooperate with a wide array of cofactors to orchestrate an embryonic stem (ES) cell-specific gene expression program that forms the molecular basis of pluripotency. Here, we report using an unbiased in vitro transcription-biochemical complementation assay to discover a multisubunit stem cell coactivator complex (SCC) that is selectively required for the synergistic activation of the Nanog gene by Oct4 and Sox2. Purification, identification, and reconstitution of SCC revealed this coactivator to be the trimeric XPC-nucleotide excision repair complex. SCC interacts directly with Oct4 and Sox2 and is recruited to the Nanog and Oct4 promoters as well as a majority of genomic regions that are occupied by Oct4 and Sox2. Depletion of SCC/XPC compromised both pluripotency in ES cells and somatic cell reprogramming of fibroblasts to induced pluripotent stem (iPS) cells. This study identifies a transcriptional coactivator with diversified functions in maintaining ES cell pluripotency and safeguarding genome integrity.PaperCli

A case of pulmonary tuberculosis accompanied with immune thrombocytopenic purpura

AbstractA 30-year-old Japanese woman with chest pain and nodules in the left upper lung field was diagnosed as having pulmonary tuberculosis by sputum examination. Purpura on her legs had lasted for 3 months and her platelet count was 1.9 × 104/mm3 on admission. She was also diagnosed as having immune thrombocytopenic purpura because of elevation of serum PA-IgG and proliferation of megakaryocytes in the bone marrow. Anti-tubercular therapy and steroid therapy were concurrently performed, resulted in recovery of the platelet count. Steroid therapy was gradually tapered off and then withdrawn, thereafter anti-tubercular therapy was finished. She has been relapse-free.Cases of pulmonary tuberculosis accompanied with immune thrombocytopenic purpura are rare. The pathogenesis in the present case was suggested to have occurred through an immunological mechanism

EEF1A1 Deacetylation Enables Transcriptional Activation of Remyelination

Remyelination of the peripheral and central nervous systems (PNS and CNS, respectively) is a prerequisite for functional recovery after lesion. However, this process is not always optimal and becomes inefficient in the course of multiple sclerosis. Here we show that, when acetylated, eukaryotic elongation factor 1A1 (eEF1A1) negatively regulates PNS and CNS remyelination. Acetylated eEF1A1 (Ac- eEF1A1) translocates into the nucleus of myelinating cells where it binds to Sox10, a key transcription factor for PNS and CNS myelination and remyelination, to drag Sox10 out of the nucleus. We show that the lysine acetyltransferase Tip60 acetylates eEF1A1, whereas the histone deacetylase HDAC2 deacetylates eEF1A1. Promoting eEF1A1 deacetylation maintains the activation of Sox10 target genes and increases PNS and CNS remyelination efficiency. Taken together, these data identify a major mechanism of Sox10 regulation, which appears promising for future translational studies on PNS and CNS remyelination

The incidence of drug-induced interstitial lung disease caused by epidermal growth factor receptor tyrosine kinase inhibitors or immune checkpoint inhibitors in patients with non-small cell lung cancer in presence and absence of vascular endothelial growth factor inhibitors: a systematic review

Interstitial lung disease (ILD) or pneumonitis caused by epidermal growth factor receptor (EGFR) tyrosine kinase inhibitors (TKI) or immune checkpoint inhibitors (ICI) is a major concern in the treatment of non-small cell lung cancer (NSCLC). Whether the addition of vascular endothelial growth factor (VEGF) and VEGF receptor (VEGFR) inhibitors can reduce the incidence of drug-induced ILD remains unclear. We conducted a systematic review to assess the incidence of ILD induced by EGFR-TKIs or ICIs in the presence or absence of VEGF/VEGFR inhibitors in relevant randomized trials between January 2009 and October 2023. The primary outcome was the odds ratio for the incidence of ILD in all patients worldwide and Asians. Secondary outcomes were the odds ratios (ORs) of the incidence at grade-3 or higher ILD in all patients worldwide and Asians. We identified 13 randomized studies, one sub-analysis in the EGFR-TKI group, and three randomized studies in the ICI group. In the EGFR-TKI group, the OR of ILD incidence at any grade with VEGF/VEGFR inhibitors was 0.54 (95% CI, 0.32–0.90; p = 0.02), which represented a significantly lower incidence than that without VEGF/VEGFR inhibitors. Contrarily, the OR of ILD incidence at grade ≥ 3 with VEGF/VEGFR inhibitors was 1.00 (95% CI, 0.43–2.36; p = 0.99). In all subjects in the ICI group, the OR of ILD incidence at any grade with VEGF/VEGFR inhibitors was 0.78 (95% CI, 0.51–1.21; p = 0.27). The systematic review demonstrated that the addition of VEGF/VEGFR inhibitors could reduce the incidence of drug-induced ILD at any grade caused by EGFR-TKI in patients with NSCLC but could not reduce that at grade ≥ 3. The ILD induced by ICIs remains undetermined owing to the limited number of randomized trials for which ILD data are available.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=409534, identifier CRD42023409534

Elevated β-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs

There is a high death rate of lung cancer patients. Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) are effective in some lung adenocarcinoma patients with EGFR mutations. However, a significant number of patients show primary and acquire resistance to EGFR-TKIs. Although the Akt kinase is commonly activated due to various resistance mechanisms, the key targets of Akt remain unclear. Here, we show that the Akt-β-catenin pathway may be a common resistance mechanism. We analyzed gene expression profiles of gefitinib-resistant PC9M2 cells that were derived from gefitinib-sensitive lung cancer PC9 cells and do not have known resistance mechanisms including EGFR mutation T790M. We found increased expression of Axin, a β-catenin target gene, increased phosphorylation of Akt and GSK3, accumulation of β-catenin in the cytoplasm/nucleus in PC9M2 cells. Both knockdown of β-catenin and treatment with a β-catenin inhibitor at least partially restored gefitinib sensitivity to PC9M2 cells. Lung adenocarcinoma tissues derived from gefitinib-resistant patients displayed a tendency to accumulate β-catenin in the cytoplasm. We provide a rationale for combination therapy that includes targeting of the Akt-β-catenin pathway to improve the efficacy of EGFR-TKIs

Recursive regularization for inferring gene networks from time-course gene expression profiles

<p>Abstract</p> <p>Background</p> <p>Inferring gene networks from time-course microarray experiments with vector autoregressive (VAR) model is the process of identifying functional associations between genes through multivariate time series. This problem can be cast as a variable selection problem in Statistics. One of the promising methods for variable selection is the elastic net proposed by Zou and Hastie (2005). However, VAR modeling with the elastic net succeeds in increasing the number of true positives while it also results in increasing the number of false positives.</p> <p>Results</p> <p>By incorporating relative importance of the VAR coefficients into the elastic net, we propose a new class of regularization, called recursive elastic net, to increase the capability of the elastic net and estimate gene networks based on the VAR model. The recursive elastic net can reduce the number of false positives gradually by updating the importance. Numerical simulations and comparisons demonstrate that the proposed method succeeds in reducing the number of false positives drastically while keeping the high number of true positives in the network inference and achieves two or more times higher true discovery rate (the proportion of true positives among the selected edges) than the competing methods even when the number of time points is small. We also compared our method with various reverse-engineering algorithms on experimental data of MCF-7 breast cancer cells stimulated with two ErbB ligands, EGF and HRG.</p> <p>Conclusion</p> <p>The recursive elastic net is a powerful tool for inferring gene networks from time-course gene expression profiles.</p