BACKGROUND: Micropapillary variant of urothelial carcinoma (MPUC) showed distinct pathologic features and aggressive behavior. The cytologic findings of MPUC are still indistinct. In this study, we evaluated the cytological findings of MPUC compared with those of high-grade urothelial carcinoma (HGUC). METHODS: The voided urine cytology of 8 cases of MPUC and 8 cases of HGUC was reviewed. Following cytological parameters were evaluated: cellularity, background, number of small, tight papillary clusters, small acinar structure, scattered single cells, cytoplasmic features, nuclear-to-cytoplasmic ratio, nuclear pleomorphism, nuclear membrane irregularity, hyperchromasia, chromatin pattern and nucleoli. RESULTS: Compared to that of HGUC, cytology of MPUC showed large numbers of small, tight papillary clusters, small acinar structure, few numbers of single cells, and hyperchromatic nuclei. Other parameters were similar between the two groups; both groups showed similar cellularity, dense or vacuolated cytoplasm, moderate to severe nuclear pleomorphism, irregular nuclear membrane, coarse granular chromatin, and small and prominent nucleoli. CONCLUSIONS: The urine cytology of MPUCs showed smaller and tighter papillary cell clusters, more small acinar structures, fewer numbers of scattered single cells, and more hyperchromatic nuclei than that of HGUC. These features can help to distinguish MPUC and HGUC and offer an early cytological diagnosis of MPUC.
Chromatin ; Cytoplasm ; Nuclear Envelope

Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. ‘dada2’ performs trimming of the high-throughput sequencing data. ‘QuasR’ and ‘mosaics’ perform quality control and mapping of the input reads to the reference genome and peak calling, respectively. Finally, ‘ChIPseeker’ performs annotation and visualization of the called peaks. This workflow runs well independently of operating systems (e.g., Windows, Mac, or Linux) and processes the input fastq files into various results in one run. R code is available at github: https://github.com/ddhb/Workflow_of_Chipseq.git.
Chromatin ; Chromatin Immunoprecipitation ; Genome ; Quality Control ; Statistics as Topic*

No abstract available.
Chromatin* ; DNA* ; Epigenomics* ; Histones* ; Methylation*

It is becoming increasingly clear that eukaryotic genomes are subjected to higher-order chromatin organization by the CCCTC-binding factor/cohesin complex. Their dynamic interactions in three dimensions within the nucleus regulate gene transcription by changing the chromatin architecture. Such spatial genomic organization is functionally important for the spatial disposition of chromosomes to control cell fate during development and differentiation. Thus, the dysregulation of proper long-range chromatin interactions may influence the development of tumorigenesis and cancer progression.
Carcinogenesis ; Chromatin* ; Gene Expression Regulation ; Genome ; Humans*

We present the cytologic features of a case of solid and papillary neoplasm of the pancreas. Cytologically, the tumor was composed of a monotonous population of polygonal cells containing eccentrically located round nuclei with one or two distinct small nucleoli and a finely stippled chromatin pattern. The tumor cells were similar to those of the islet cell tumor and showed isolated loosely aggregated and solid sheets or large cell clumps. The large cell clumps revealed a branching papillary structure containing fibrovascular central core, which is characteristic histologic feature of solid and papillary neoplasm of the pancreas. This case was confirmed by tissue examination including histochemical, immunohistochemical and electron microscopical studies. Ultrastructurally, the tumor cells contained a few membrane-bound electron dense granules.
Adenoma, Islet Cell ; Chromatin ; Pancreas ; Urinary Tract*

We found an unusual morphology of eosinophil nucleus having longer chromatin filament in addition to a single narrow chromatin bridge. The nucleus having two chromatin filament bridge looked like two legged eosinophil, instead of usual glasses shape. As the physiologic function of the nucleus of granulocyte segmentation and the mechanism by which the lobes are formed during differention is still unknown, we could not know the definite nature and significance of these double chromatin filament. However we could suggest that they may be a reactive change of eosinophilia. This not uncommon morphology has not been described as yet. Here we report three cases of unusual morphology of eosinophil nucleus presenting double chromatin filament bridge, one case with a band form nucleus looked like ring shape, with brief review of literatures.
Chromatin* ; Eosinophilia ; Eosinophils* ; Eyeglasses ; Glass ; Granulocytes ; Leg

Several genetic and epigenetic theories have been suggested to explain the intricacies of life and death. However, several questions remain unsettled regarding cellular death events, particularly of living tissue in the case of cancer patients, such as the fate and adaptation of cancer cells after biological death. It is possible that cancer cells can display the intent to communicate with the external environment after biological death by means of molecular, genetic, and epigenetic pathways. Whether these cancer cells contain special information in the form of coding that may help them survive beyond the biological death of cancer patients is unknown. To understand these queries in the cancer field, we hypothesize the epigenomic hard drive (EHD) as a cellular component to record and store global epigenetic events in cancerous and non-cancerous tissues of cancer patients. This mini-review presents the novel concept of EHD that is reinforced with the existing knowledge of genetic and epigenetic events in cancer. Further, we summarize the EHD understanding that may impart much potential and interest for basic and clinical scientists to unravel mechanisms of carcinogenesis, therapeutic markers, and differential drug responses.
Carcinogenesis ; Chromatin ; Clinical Coding ; Epigenomics* ; Humans

Cytologic features of a poorly differentiated "insular" carcinoma of the thyroid are presented. In fine needle aspiration cytology, the aspirates were highly cellular and tumor cells were arranged in loose clusters or singly dispersed on focally necrotic background. Occasional microfollicles were evident. The tumor cells had poorly defined, scanty cytoplasm and most of the nuclei were fairly uniform with coarse chromatin pattern. A few large pleomorphic cells were also noted. The cytologic findings of the present case were correlated well with the histologic findings, which showed typical insular pattern and the presence of uniform cells with occasional pleomorphism.
Biopsy, Fine-Needle* ; Chromatin ; Cytoplasm ; Thyroid Gland*

Recent technical advances, such as chromatin immunoprecipitation combined with DNA microarrays (ChIp-chip) and chromatin immunoprecipitation-sequencing (ChIP-seq), have generated large quantities of high-throughput data. Considering that epigenomic datasets are arranged over chromosomes, their analysis must account for spatial or temporal characteristics. In that sense, simple clustering or classification methodologies are inadequate for the analysis of multi-track ChIP-chip or ChIP-seq data. Approaches that are based on hidden Markov models (HMMs) can integrate dependencies between directly adjacent measurements in the genome. Here, we review three HMM-based studies that have contributed to epigenetic research, from a computational perspective. We also give a brief tutorial on HMM modelling-targeted at bioinformaticians who are new to the field.
Chromatin ; Chromatin Immunoprecipitation ; Classification ; Dataset ; Epigenomics* ; Genome ; Oligonucleotide Array Sequence Analysis

The pathological hallmarks of psoriasis involve alterations in T cell genes associated with transcriptional levels, which are determined by chromatin accessibility. However, to what extent these alterations in T cell transcriptional levels recapitulate the epigenetic features of psoriasis remains unknown. Here, we systematically profiled chromatin accessibility on Th1, Th2, Th1-17, Th17, and Treg cells and found that chromatin remodeling contributes significantly to the pathogenesis of the disease. The chromatin remodeling tendency of different subtypes of Th cells were relatively consistent. Next, we profiled chromatin accessibility and transcriptional dynamics on memory Th/Treg cells. In the memory Th cells, 803 increased and 545 decreased chromatin-accessible regions were identified. In the memory Treg cells, 713 increased and 1206 decreased chromatin-accessible regions were identified. A total of 54 and 53 genes were differentially expressed in the peaks associated with the memory Th and Treg cells. FOSL1, SPI1, ATF3, NFKB1, RUNX, ETV4, ERG, FLI1, and ETC1 were identified as regulators in the development of psoriasis. The transcriptional regulatory network showed that NFKB1 and RELA were highly connected and central to the network. NFKB1 regulated the genes of CCL3, CXCL2, and IL1RN. Our results provided candidate transcription factors and a foundational framework of the regulomes of the disease.
Chromatin/genetics* ; Chromatin Assembly and Disassembly ; Gene Regulatory Networks ; Humans ; Psoriasis/genetics* ; T-Lymphocytes, Regulatory