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Journal of Cutaneous Pathology Nov 2023Giant cell tumor of soft tissue (GCT-ST) is a rare soft tissue neoplasm that is morphologically similar to but genetically distinct from giant cell tumor of bone. A...
BACKGROUND
Giant cell tumor of soft tissue (GCT-ST) is a rare soft tissue neoplasm that is morphologically similar to but genetically distinct from giant cell tumor of bone. A novel keratin-positive GCT-ST (KPGCT-ST) harboring HMGA2::NCOR2 fusions was recently discovered. Fewer than 30 cases have been described; herein is reported an additional seven.
METHODS
Cases diagnosed as GCT-ST were retrieved from institutional archives and consultation files. The histopathologic characteristics were assessed, and the electronic medical record was reviewed.
RESULTS
Seven tumors were identified in six women and one man with a median age of 23 years. All patients underwent excision; no recurrences or metastases were noted during a median follow-up period of 7 months. Histopathologically, the tumors were characterized by a multinodular proliferation of keratin-positive mononuclear cells with evenly admixed osteoclast-like giant cells and absent neoplastic bone. A fibrous capsule with lymphoid cuffing was frequently seen. Foamy macrophages, inflammation, hemorrhage, and hemosiderin were variably present. The HMGA2::NCOR2 fusion was detected in all cases.
CONCLUSIONS
Our findings support previously reported hypotheses that KPGCT-ST is a spectrum of the same entity as the recently described xanthogranulomatous epithelial tumor. Although follow-up data are limited, to date, KPGCT-ST appears to follow an indolent course.
Topics: Male; Humans; Female; Young Adult; Adult; Keratins; Giant Cell Tumors; Soft Tissue Neoplasms; Diagnosis, Differential; Giant Cells; Nuclear Receptor Co-Repressor 2
PubMed: 37496152
DOI: 10.1111/cup.14497 -
MBio Dec 2021The life cycle of human papillomavirus (HPV) depends on keratinocyte differentiation as the virus modulates and takes advantage of cellular pathways to replicate its...
The life cycle of human papillomavirus (HPV) depends on keratinocyte differentiation as the virus modulates and takes advantage of cellular pathways to replicate its genome and assemble viral particles in differentiated cells. Viral genomes are amplified in nuclear replication foci in differentiated keratinocytes, and DNA repair factors from the DNA damage response signaling pathway are recruited to replicate viral DNA. The HPV genome is associated with cellular histones at all stages of the infectious cycle, and here, we show that the histone variant macroH2A1 is bound to the HPV genome and enriched in viral replication foci in differentiated cells. macroH2A1 isoforms play important roles in cellular transcriptional repression, double-strand break repair, and replication stress. The viral E8^E2 protein also binds to the HPV genome and inhibits viral replication and gene expression by recruiting NCoR/SMRT complexes. We show here that E8^E2 and SMRT also localize within replication foci, though independently from macroH2A1. Conversely, transcription complexes containing RNA polymerase II and Brd4 are located on the surface of the foci. Foci generated with an HPV16 E8^E2 mutant genome are not enriched for SMRT or macroH2A1 but contain transcriptional complexes throughout the foci. We propose that both the cellular macroH2A1 protein and viral E8^E2 protein help to spatially separate replication and transcription activities within viral replication foci. Human papillomaviruses are small DNA viruses that cause chronic infection of cutaneous and mucosal epithelium. In some cases, persistent infection with HPV can result in cancer, and 5% of human cancers are the result of HPV infection. In differentiated cells, HPV amplifies viral DNA in nuclear replication factories and transcribes late mRNAs to produce capsid proteins. However, very little is known about the spatial organization of these activities in the nucleus. Here, we show that repressive viral and cellular factors localize within the foci to suppress viral transcription, while active transcription takes place on the surface. The cellular histone variant macroH2A1 is important for this spatial organization.
Topics: Alphapapillomavirus; Genome, Viral; Histones; Host-Pathogen Interactions; Humans; Nuclear Receptor Co-Repressor 1; Nuclear Receptor Co-Repressor 2; Oncogene Proteins, Viral; Papillomavirus Infections; Virus Replication
PubMed: 34749533
DOI: 10.1128/mBio.02684-21 -
G3 (Bethesda, Md.) Feb 2021Ascochyta lentis causes ascochyta blight in lentil (Lens culinaris Medik.) and yield loss can be as high as 50%. With careful agronomic management practices, fungicide...
Ascochyta lentis causes ascochyta blight in lentil (Lens culinaris Medik.) and yield loss can be as high as 50%. With careful agronomic management practices, fungicide use, and advances in breeding resistant lentil varieties, disease severity and impact to farmers have been largely controlled. However, evidence from major lentil producing countries, Canada and Australia, suggests that A. lentis isolates can change their virulence profile and level of aggressiveness over time and under different selection pressures. In this paper, we describe the first genome assembly for A. lentis for the Australian isolate Al4, through the integration of data from Illumina and PacBio SMRT sequencing. The Al4 reference genome assembly is almost 42 Mb in size and encodes 11,638 predicted genes. The Al4 genome comprises 21 full-length and gapless chromosomal contigs and two partial chromosome contigs each with one telomere. We predicted 31 secondary metabolite clusters, and 38 putative protein effectors, many of which were classified as having an unknown function. Comparison of A. lentis genome features with the recently published reference assembly for closely related A. rabiei show that genome synteny between these species is highly conserved. However, there are several translocations and inversions of genome sequence. The location of secondary metabolite clusters near transposable element and repeat-rich genomic regions was common for A. lentis as has been reported for other fungal plant pathogens.
Topics: Ascomycota; Australia; Plant Breeding; Plant Diseases
PubMed: 33604672
DOI: 10.1093/g3journal/jkab006 -
Endocrinology Oct 2020The Silencing Mediator of Retinoid and Thyroid Hormone Receptors (SMRT) is a nuclear corepressor, regulating the transcriptional activity of many transcription factors...
The Silencing Mediator of Retinoid and Thyroid Hormone Receptors (SMRT) is a nuclear corepressor, regulating the transcriptional activity of many transcription factors critical for metabolic processes. While the importance of the role of SMRT in the adipocyte has been well-established, our comprehensive understanding of its in vivo function in the context of homeostatic maintenance is limited due to contradictory phenotypes yielded by prior generalized knockout mouse models. Multiple such models agree that SMRT deficiency leads to increased adiposity, although the effects of SMRT loss on glucose tolerance and insulin sensitivity have been variable. We therefore generated an adipocyte-specific SMRT knockout (adSMRT-/-) mouse to more clearly define the metabolic contributions of SMRT. In doing so, we found that SMRT deletion in the adipocyte does not cause obesity-even when mice are challenged with a high-fat diet. This suggests that adiposity phenotypes of previously described models were due to effects of SMRT loss beyond the adipocyte. However, an adipocyte-specific SMRT deficiency still led to dramatic effects on systemic glucose tolerance and adipocyte insulin sensitivity, impairing both. This metabolically deleterious outcome was coupled with a surprising immune phenotype, wherein most genes differentially expressed in the adipose tissue of adSMRT-/- mice were upregulated in pro-inflammatory pathways. Flow cytometry and conditioned media experiments demonstrated that secreted factors from knockout adipose tissue strongly informed resident macrophages to develop a pro-inflammatory, MMe (metabolically activated) phenotype. Together, these studies suggest a novel role for SMRT as an integrator of metabolic and inflammatory signals to maintain physiological homeostasis.
Topics: Adipocytes; Adipose Tissue; Animals; Cell Differentiation; Energy Metabolism; Homeostasis; Macrophages; Male; Mice; Mice, Inbred C57BL; Mice, Knockout; Nuclear Receptor Co-Repressor 2; Obesity; Organ Specificity; Phenotype
PubMed: 32770234
DOI: 10.1210/endocr/bqaa132 -
Journal of the Science of Food and... Feb 2022Feed shortage is a factor restricting animal production in the tropics, therefore how to use natural woody plant resources as animal feed is an important strategy.
BACKGROUND
Feed shortage is a factor restricting animal production in the tropics, therefore how to use natural woody plant resources as animal feed is an important strategy.
RESULTS
Under the dual stress of an anaerobic and acidic environment, the microbial response during the fermentation of paper mulberry (PM) silage was found to be sensitive. The Gram-negative bacteria and mould died, and the dominant microbial community rapidly shifted to Gram-positive bacteria, resulting in a large reduction in microbial diversity and abundance. Exogenous bran additives interfered with the stress effects of the woody silage environment. Wheat bran (WB) accelerated the response of microorganisms to the anaerobic stress, and lactic acid bacteria became the dominant microbial community, thereby enhancing the lactic acid fermentation of silage, affecting the metabolic pathways of microorganisms, and improving the flavour and quality of the silage. Addition of rice bran made Enterobacter and Clostridium species quickly respond to the stress of the silage environment and become the predominant bacterial groups. In particular, anaerobic and spore-forming Clostridium species showed a strong tolerance to the silage environment, leading to butyric acid fermentation and protein degradation of the silage, and reducing its fermentation quality.
CONCLUSION
The PacBio single-molecule real-time (SMRT) sequencing technology accurately revealed the microbial co-occurrence network and fermentation mechanism of silage. Our results indicate that PM can be used in combination with WB to prepare high-quality silage for animal production. © 2021 Society of Chemical Industry.
Topics: Animal Feed; Animals; Bacteria; Butyric Acid; Fermentation; Fungi; Lactic Acid; Microbiota; Morus; Silage; Wood
PubMed: 34343355
DOI: 10.1002/jsfa.11457 -
BMC Plant Biology Dec 2022Posttranscriptional processing of precursor mRNAs contributes to transcriptome and protein diversity and gene regulatory mechanisms in eukaryotes. However, this...
BACKGROUND
Posttranscriptional processing of precursor mRNAs contributes to transcriptome and protein diversity and gene regulatory mechanisms in eukaryotes. However, this posttranscriptional mechanism has not been studied in the marine macroalgae Gracilariopsis lemaneiformis, which is the most cultivated red seaweed species in China.
RESULTS
In the present study, third-generation sequencing (Pacific Biosciences single-molecule real-time long-read sequencing, SMRT-Seq) was used to sequence the full-length transcriptome of G. lemaneiformis to identify alternatively spliced transcripts and alternative polyadenylation (APA) sites in this species. RNAs were isolated from G. lemaneiformis under various treatments including abiotic stresses and exogenous phytohormones, and then equally pooled for SMRT-Seq. In summary, 346,544 full-length nonchimeric reads were generated, from which 13,630 unique full-length transcripts were obtained in G. lemaneiformis. Compared with the known splicing events in the gene models, more than 3000 new alternative splicing (AS) events were identified in the SMRT-Seq reads. Additionally, 810 genes were found to have poly (A) sites and 91 microRNAs (miRNAs), 961 long noncoding RNAs and 1721 novel genes were identified in G. lemaneiformis. Moreover, validation experiments showed that abiotic stresses and phytohormones could induce some specific AS events, especially intron retain isoforms, cause some alterations to the relative ratios of transcripts annotated to the same gene, and generate novel 3' ends because of differential APA. The growth of G. lemaneiformis was inhibited by Cu stress, while this inhibition was alleviated by ACC treatment. RNA-Seq analysis further revealed that 211 differential alternative splicing (DAS) events and 142 DAS events was obtained in CK vs Cu and Cu vs Cu + ACC, respectively, suggesting that AS of functional genes could be regulated by Cu stress and ACC. Compared with Cu stress, the expression of transcripts with DAS events mainly involved in the carbon fixation in photosynthetic organisms and oxidative phosphorylation pathway was upregulated in Cu + ACC treatment, revealing that ACC alleviated the growth inhibition by Cu stress by increasing carbon fixation and oxidative phosphorylation.
CONCLUSIONS
Our results provide the first comprehensive picture of the full-length transcriptome and posttranscriptional mechanism in red macroalgae, including transcripts that appeared in the presence of common abiotic stresses and phytohormones, which will improve the gene annotations of Gracilariopsis and contribute to the study of gene regulation in this important cultivated seaweed.
Topics: Alternative Splicing; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Plant Growth Regulators; RNA Splicing; Transcriptome
PubMed: 36536287
DOI: 10.1186/s12870-022-03992-0 -
Clinica Chimica Acta; International... Jul 2023The sequence similarity between CYP21A2 gene and its inactive pseudogene CYP21A1P, and copy number variation (CNV) caused by unequal crossover, make it challenging to...
BACKGROUND
The sequence similarity between CYP21A2 gene and its inactive pseudogene CYP21A1P, and copy number variation (CNV) caused by unequal crossover, make it challenging to characterize the CYP21A2 gene through traditional methods. This study aimed to evaluate the clinical utility of the long-read sequencing (LRS) method in carrier screening and genetic diagnosis of congenital adrenal hyperplasia (CAH) by comparing the efficiency of the LRS method with the conventional multiplex ligation-dependent probe amplification (MLPA) plus Sanger sequencing approaches in CYP21A2 analysis.
METHODS
In a retrospective study, full sequence analysis of the CYP21A2 and CYP21A1P was performed for three pedigrees through long-range locus-specific PCR followed by LRS based on the Pacific Biosciences (PacBio, California, USA) single-molecule real-time (SMRT) platform, and the results were compared with those obtained from next-generation sequencing (NGS)-based whole exome sequencing (WES) and the traditional methods of MLPA plus Sanger sequencing.
RESULTS
The LRS method successfully identified seven CYP21A2 variants, including three single nucleotide variants (NM_000500.9:c.1451G > C p.(Arg484Pro), c.293-13A/C > G (IVS2-13A/C > G), c.518 T > A p.(Ile173Asn)), one 111-bp polynucleotide insertion, one set of 3'URT variants (NM_000500.9:c.*368 T > C, c.*390A > G, c.*440C > T, c.*443 T > C) and two types of chimeric genes and straightforwardly depicted the inheritance patterns of these variants within families. Moreover, the LRS method enabled us to determine the cis-trans configuration of multiple variants in one assay, without the need to analyze additional family samples. Compared with traditional methods, this LRS method can achieve a precise, comprehensive and intuitive result in the genetic diagnosis of 21-hydroxylase deficiency (21-OHD).
CONCLUSION
The LRS method is comprehensive in CYP21A2 analysis and intuitive in result presentation, which holds substantial promise in clinical application as a crucial tool for carrier screening and genetic diagnosis of CAH.
Topics: Humans; Adrenal Hyperplasia, Congenital; Steroid 21-Hydroxylase; DNA Copy Number Variations; Retrospective Studies; Multiplex Polymerase Chain Reaction; High-Throughput Nucleotide Sequencing; Mutation
PubMed: 37276943
DOI: 10.1016/j.cca.2023.117419 -
Frontiers in Veterinary Science 2022(lenok) is a rare cold-water fish native to China that is of high meat quality. Its wild population has declined sharply in recent years, and therefore, exploring the...
(lenok) is a rare cold-water fish native to China that is of high meat quality. Its wild population has declined sharply in recent years, and therefore, exploring the molecular mechanisms underlying the development and reproduction of lenoks for the purposes of artificial breeding and genetic improvement is necessary. The lenok comparative transcriptome was analyzed by combining single molecule, real-time, and next generation sequencing (NGS) technology. Differentially expressed genes (DEGs) were identified in five tissues (head kidney, spleen, liver, muscle, and gonad) between immature [300 days post-hatching (dph)] and mature [three years post-hatching (ph)] lenoks. In total, 234,124 and 229,008 full-length non-chimeric reads were obtained from the immature and mature sequencing data, respectively. After NGS correction, 61,405 and 59,372 non-redundant transcripts were obtained for the expression level and pathway enrichment analyses, respectively. Compared with the mature group, 719 genes with significantly increased expression and 1,727 genes with significantly decreased expression in all five tissues were found in the immature group. Furthermore, DEGs and pathways involved in the endocrine system and gonadal development were identified, and p38 mitogen-activated protein kinases (MAPKs) were identified as potentially regulating gonadal development in lenok. Inhibiting the activity of p38 MAPKs resulted in abnormal levels of gonadotropin-releasing hormone, follicle-stimulating hormone, and estradiol, and affected follicular development. The full-length transcriptome data obtained in this study may provide a valuable reference for the study of gene function, gene expression, and evolutionary relationships in and may illustrate the basic regulatory mechanism of ovarian development in teleosts.
PubMed: 35252414
DOI: 10.3389/fvets.2022.752521 -
Physiologia Plantarum Sep 2022Terpenoids are the most important natural products collected from conifer species. However, the molecular mechanisms and core factors underlying terpenoid biosynthesis...
Terpenoids are the most important natural products collected from conifer species. However, the molecular mechanisms and core factors underlying terpenoid biosynthesis in Pinus massoniana remain unclear. To clarify these mechanisms, this study aimed to identify potential genes that might participate in the terpenoid biosynthesis of P. massoniana. In this study, single molecule real-time (SMRT) sequencing and expression analysis were used to confirm the expression patterns of genes involved in the cones, immature needles, mature needles, immature branches, and mature branches of P. massoniana. A total of 31,331 lncRNAs and 71,240 mRNAs were identified from these organs, and the greatest number of differentially expressed genes (DEGs) was discovered between needles and branches. Weighted gene coexpression network analysis (WGCNA) classified all expressed genes into nine typical modules with 11 kinds of transcription factors (TFs), namely, AP2-ERF, ARF, AUX-IAA, C2H2, Dof, F-box, SBP, WRKY, bHLH, bZIP, and GRAS, and seven kinds of functional genes, namely, ABC transporter, cellulose synthase (CesA), leucine-rich repeats (LRR), cytochrome P450 (CYT P450), pathogenesis-related protein (PR), terpene synthase (TPS), and chlorophyllase enzyme. A molecular network was constructed for hub genes, TFs, and functional genes in three modules. The potential function of eight candidate genes, including PmbHLH2, PmERF1, PmRGA, PmGAI, PmbZIP1, PmLOB1, PmMADS1, and PmMYB1, was validated through correlation analysis between terpenoid contents and expression levels, subcellular localization, and transcriptional activation activity, which provides us with probable regulators of terpenoid biosynthesis in conifers.
Topics: Transcriptome; Pinus; RNA, Long Noncoding; Leucine; Terpenes; Tracheophyta; Transcription Factors; Cytochrome P-450 Enzyme System; ATP-Binding Cassette Transporters; Biological Products; Gene Expression Regulation, Plant
PubMed: 36169876
DOI: 10.1111/ppl.13791 -
Molecular Cell Mar 2021While the role of transcription factors and coactivators in controlling enhancer activity and chromatin structure linked to gene expression is well established, the...
While the role of transcription factors and coactivators in controlling enhancer activity and chromatin structure linked to gene expression is well established, the involvement of corepressors is not. Using inflammatory macrophage activation as a model, we investigate here a corepressor complex containing GPS2 and SMRT both genome-wide and at the Ccl2 locus, encoding the chemokine CCL2 (MCP-1). We report that corepressors co-occupy candidate enhancers along with the coactivators CBP (H3K27 acetylase) and MED1 (mediator) but act antagonistically by repressing eRNA transcription-coupled H3K27 acetylation. Genome editing, transcriptional interference, and cistrome analysis reveals that apparently related enhancer and silencer elements control Ccl2 transcription in opposite ways. 4C-seq indicates that corepressor depletion or inflammatory signaling functions mechanistically similarly to trigger enhancer activation. In ob/ob mice, adipose tissue macrophage-selective depletion of the Ccl2 enhancer-transcribed eRNA reduces metaflammation. Thus, the identified corepressor-eRNA-chemokine pathway operates in vivo and suggests therapeutic opportunities by targeting eRNAs in immuno-metabolic diseases.
Topics: Adipose Tissue; Animals; CRISPR-Cas Systems; Chemokine CCL2; Co-Repressor Proteins; Enhancer Elements, Genetic; Gene Editing; Gene Expression Regulation; HEK293 Cells; Histone Acetyltransferases; Histones; Humans; Intracellular Signaling Peptides and Proteins; Lipopolysaccharides; Macrophage Activation; Male; Mediator Complex Subunit 1; Mice; Mice, Obese; Nuclear Receptor Co-Repressor 2; Obesity; RAW 264.7 Cells; RNA, Untranslated; Signal Transduction; Silencer Elements, Transcriptional
PubMed: 33503407
DOI: 10.1016/j.molcel.2020.12.040