An HLA-DR alpha promoter DNA-binding protein is expressed ubiquitously and maps to human chromosomes 22 and 5

Multi-omics profiling of cholangiocytes reveals sex-specific chromatin state dynamics during hepatic cystogenesis in polycystic liver disease

BACKGROUND & AIMS

Cholangiocytes transit from quiescence to hyperproliferation during cystogenesis in polycystic liver disease (PLD), the severity of which displays prominent sex differences. Epigenetic regulation plays important roles in cell state transition. We aimed to investigate the sex-specific epigenetic basis of hepatic cystogenesis and to develop therapeutic strategies targeting epigenetic modifications for PLD treatment.

METHODS

Normal and cystic primary cholangiocytes were isolated from wild-type and PLD mice of both sexes. Chromatin states were characterized by analyzing chromatin accessibility (ATAC sequencing) and multiple histone modifications (chromatin immunoprecipitation sequencing). Differential gene expression was determined by transcriptomic analysis (RNA sequencing). Pharmacologic inhibition of epigenetic modifying enzymes was undertaken in PLD model mice.

RESULTS

Through genome-wide profiling of chromatin dynamics, we revealed a profound increase of global chromatin accessibility during cystogenesis in both male and female PLD cholangiocytes. We identified a switch from H3K9me3 to H3K9ac on cis-regulatory DNA elements of cyst-associated genes and showed that inhibition of H3K9ac acetyltransferase or H3K9me3 demethylase slowed cyst growth in male, but not female, PLD mice. In contrast, we found that H3K27ac was specifically increased in female PLD mice and that genes associated with H3K27ac-gained regions were enriched for cyst-related pathways. In an integrated epigenomic and transcriptomic analysis, we identified an estrogen receptor alpha-centered transcription factor network associated with the H3K27ac-regulated cystogenic gene expression program in female PLD mice.

CONCLUSIONS

Our findings highlight the multi-layered sex-specific epigenetic dynamics underlying cholangiocyte state transition and reveal a potential epigenetic therapeutic strategy for male PLD patients.

IMPACT AND IMPLICATIONS

In the present study, we elucidate a sex-specific epigenetic mechanism underlying the cholangiocyte state transition during hepatic cystogenesis and identify epigenetic drugs that effectively slow cyst growth in male PLD mice. These findings underscore the importance of sex difference in the pathogenesis of PLD and may guide researchers and physicians to develop sex-specific personalized approaches for PLD treatment.

Dysregulation of Transcription Factors: A Key Culprit Behind Neurodegenerative Disorders

Neurodegenerative diseases (NDs) are considered heterogeneous disorders characterized by progressive pathological changes in neuronal systems. Transcription factors are protein molecules that are important in regulating the expression of genes. Although the clinical manifestations of NDs vary, the pathological processes appear similar with regard to neuroinflammation, oxidative stress, and proteostasis, to which, as numerous studies have discovered, transcription factors are closely linked. In this review, we summarized and reviewed the roles of transcription factors in NDs, and then we elucidated their functions during pathological processes, and finally we discussed their therapeutic values in NDs.

Potential for therapeutic manipulation of the UPR in disease

Increased endoplasmic reticulum (ER) stress and the activated unfolded protein response (UPR) signaling associated with it play key roles in physiological processes as well as under pathological conditions. The UPR normally protects cells and re-establishes cellular homeostasis, but prolonged UPR activation can lead to the development of various pathologies. These features make the UPR signaling pathway an attractive target for the treatment of diseases whose pathogenesis is characterized by chronic activation of this pathway. Here, we focus on the molecular signaling pathways of the UPR and suggest possible ways to target this response for therapeutic purposes.

Evidence for two susceptibility loci on chromosomes 22q12 and 6p21-p22 in Chinese generalized vitiligo families

Vitiligo is an acquired depigmentation disorder of the skin and hair caused by the selective destruction of melanocytes from the epidermis that gives rise to well-defined depigmented patches. Strong genetic predisposition has been well recognized. Previous reports have described five significant vitiligo susceptibility loci spread over five different chromosomes, 1p31 (AIS1), 7q (AIS2), 8p (AIS3), 4q13-q21 (AIS4), and 17p (SLEV1). In addition, our previous genome-wide scan of 106 Chinese vitiligo families presented suggestive linkages on five additional chromosome segments, 1p36, 6p21-p22, 6q24-q25, 14q12-q13, and 22q12. To clarify the significance of these suggestive loci, we have now extended this study to a total of 143 Chinese vitiligo families and increased the marker density. Two linkage signals on 6p21-p22 and 22q12 that were previously only suggestive now meet genome-wide criteria for significant linkage, establishing their importance as major vitiligo susceptibility loci. Linkage signals on 1p36 and 6q24-q25 did not improve our previous findings, but on 14q showed negative in the 143 family cohorts. The results presented here further demonstrate the genetic complexity of vitiligo pathogenesis and point to new chromosomal locations for further research to identify the specific genes involved in this process.

Association study of a functional promoter polymorphism in the XBP1 gene and schizophrenia

A functional promoter polymorphism (-116C/G) of the X-box binding protein 1 gene (XBP1) gene was reported to be associated with schizophrenia in Asian subjects. In a replication attempt, three European case-control samples comprising 2,182 German, Polish, and Swedish subjects, were genotyped for the XBP1 -116C/G polymorphism. Allele and genotype frequencies were compared between schizophrenic patients and control subjects. There were no significant case-control differences in any of the three samples, although in a meta-analysis with previous results comprising 3,612 subjects there was a borderline association between the -116G-containing genotypes and schizophrenia. We conclude that the functional XBP1 gene polymorphism is not of major importance to schizophrenia in the European populations investigated. It cannot be excluded, however, that the XBP1 polymorphism is involved in schizophrenia in other populations or adds minor susceptibility to the disorder.

Targeting Positive Regulatory Domain I-Binding Factor 1 and X Box-Binding Protein 1 Transcription Factors by Multiple Myeloma-Reactive CTL

Growing evidence indicates that multiple myeloma (MM) and other malignancies are susceptible to CTL-based immune interventions. We studied whether transcription factors inherently involved in the terminal differentiation of mature B lymphocytes into malignant and nonmalignant plasma cells provide MM-associated CTL epitopes. HLA-A*0201 (A2.1) transgenic mice were used to identify A2.1-presented peptide Ag derived from the plasma cell-associated transcriptional regulators, positive regulatory domain I-binding factor 1 (PRDI-BF1) and X box-binding protein 1 (XBP-1). A2.1-restricted CTL specific for PRDI-BF1 and XBP-1 epitopes efficiently killed a variety of MM targets. PRDI-BF1- and XBP-1-reactive CTL were able to recognize primary MM cells from A2.1(+) patients. Consistent with the expression pattern of both transcription factors beyond malignant and nonmalignant plasma cells, PRDI-BF1- and XBP-1-specific CTL activity was not entirely limited to MM targets, but was also associated with lysis of certain other malignancies and, in defined instances, with low-to-intermediate level recognition of a few types of normal cells. Our results also indicate that the A2.1-restricted, PRDI-BF1- and XBP-1-specific human CD8(+) T cell repertoire is affected by partial self tolerance and may thus require the transfer of high-affinity TCR to break tolerance. We conclude that transcription factors governing terminal cellular differentiation may provide MM- and tumor-associated CTL epitopes.

Identity between rat htf and human xbp-1 genes: determination of gene structure, target sequence, and transcription promotion function for HTF

Hepatocarcinogenesis-related transcription factor (HTF) was originally isolated from rats in which the expression was enhanced in hepatocellular carcinomas. Rat HTF (rHTF) is structurally similar to human X-box-binding protein-1 (hXBP-1), and both factors are unique in respective genomes. A previous study showed that hXBP-1 mRNA is detectable ubiquitously but is enriched in the human liver as rHTF. In this study, we demonstrated the analogous exon-intron organization and significant sequence homology for rhtf and hxbp-1 genes. Alignment of amino acid sequences of rHTF and hXBP-1 revealed that all the characteristic motifs in rHTF were conserved in hXBP-1. Moreover, Southern blotting patterns provided with the rHTF and hXBP-1 probes were basically the same. These two genes were thus thought to belong to the same evolutional lineage. We determined the consensus binding sequence (CRCGTCA) for rHTF by CASTing, and it was found to be nearly the same as that for hXBP-1. Transactivation ability of rHTF was also demonstrated. The rhtf gene generates two types of mRNAs (2.0 kb and 2.5 kb), both of which encode identical rHTF protein. These transcripts had distinct transcription initiation sites. The 2.0 kb promoter, that was revealed by the transient luciferase assay, contained GC-box and CAAT-box. Sequences around the transcription initiation site for the 2.0 kb transcript were similar in rhtf and hxbp-1 genes. Our observations suggest that HTF is a rat homolog of hXBP-1.

Polymorphism in the upstream regulatory region of DQA1 gene in the Italian population

Polymorphism in the 5'-upstream regulatory region of the DQA1 gene has been recently described. Using PCR-SSO method and SSCP analysis we have investigated this polymorphism in a group of 111 Italian blood donors which had been oligotyped for DRB1, DQA1 and DQB1 genes. Eight allelic variants were detected. Looking at the relationships among QAP sequences and DQA1 and DRB1 genes, three alternative situations were found: 1. a one-to-one relation between QAP and DQA1 alleles, independently of the other class II genes; 2. the same QAP allele in association with different DQA1-DRB1 haplotypes; 3. the same DQA1 allele with different QAP sequences according to the DRB1 specificity. No unexpected associations with DQB1 gene were found. These results must be interpreted considering that DQA1 and DRB1 genes are transcribed in opposite directions so that the promoter region of DQA1 gene lies between DQA1 and DRB1, close to the former but several hundreds kb away from the latter.

Regulation of MHC gene expression

This review focuses on recent progress made in MHC regulation. The better characterization of proteins that interact with MHC class I and II promoters and the isolation of genes encoding several of these transcription factors, such as H-2RIIBP/RXR beta, NK kappa B, I-kappa B, hXBP-1 and NF-Y, allow the functional analysis of these molecules in MHC gene regulation. The application of new techniques, such as genomic in vivo footprinting analysis, to the study of these promoters provides insights into the status of in vivo protein-DNA interaction over these promoters. New insights have also been gained in the understanding of MHC-associated genes.