O-066 The naughty genes and 3D structure of the endometrium

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
T Enomoto ◽  
M Yamaguchi ◽  
K Suda ◽  
K Yoshihara
Keyword(s):  
Somatic Mutations ◽  
Pik3ca Mutation ◽  
3D Structure ◽  
Gene Mutations ◽  
Allele Frequencies ◽  
Human Endometrium ◽  
Integrated Analysis ◽  
Endometrial Gland ◽  
Uterine Endometrium ◽  
Endometrial Epithelium

Abstract The naughty genes and 3D structure of the endometrium Takayuki Enomoto, Manako Ymaguchi, Kazuaki Suda, Kosuke Yoshihara Department of Obstetrics and Gynecology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan. The human endometrium is a highly regenerative tissue and involved in menstruation and implantation of the fertilized egg, giving it a central role in women’s reproductive health. However, the regenerative nature of the endometrial glands can lead to the development and progression of “endometrium-related diseases” such as adenomyosis, endometriosis, endometriosis-associated ovarian cancer, endometrial hyperplasia, and endometrial cancer. To clarify the pathogenesis of endometrium-related diseases and develop effective preventative measures and therapeutic strategies, comprehensive understanding of molecular biological linkage between endometrium and endometrium-related diseases was crucially important. To this end, we focused on genomic alterations of endometrial epithelium which is considered the origin of endometriosis, and sequenced 107 ovarian endometriotic and 82 normal uterine endometrial epithelium samples isolated by laser-microdissection. Intriguingly, several genes recurrently mutated in endometriosis-associated ovarian cancers were frequently mutated in both endometriotic epithelium and normal uterine endometrial glands. In particular, PIK3CA mutation was detected in 41% of endometrial epithelium subjects but none of them had shared PIK3CA mutations across multiple regions collected from the same individuals. Mutation allele frequencies of somatic mutations in uterine endometrial epithelium samples were also significantly lower than those in ovarian endometriotic epithelium samples, suggesting the heterogeneous genomic compositions in uterine endometrium. To interpret this genomic heterogeneity in uterine endometrium, we focused on endometrial gland, the minimum functional unit of uterine endometrium, and conducted 109 single endometrial glands sequencing. As a result, we unveiled that each gland carried distinct somatic mutations in cancer-associated genes, such as PIK3CA, KRAS, and PTEN, with high mutant allele frequencies, suggesting the monoclonality of each gland. The presence of cancer-associated gene mutations in histologically normal endometrial glands provides important clues regarding the pathogenesis of endometrium-related diseases. However, our previous study could not determine the spread of endometrial gland harboring cancer-associated gene mutation because there is a limitation to two-dimensional assessment of the whole shapes of endometrial gland due to its complicatedly winding morphology. Therefore, we tackled with three-dimensional (3D) assessment of human endometrium. To construct a large picture of endometrial gland structure, we performed tissue-clearing-based 3D imaging of full-thickness human uterine endometrial tissue with the use of light-sheet fluorescence microscopy. Our 3D immunohistochemistry discovered some new and unique 3D morphologies of endometrial glands, including plexus network of glands or occluded glands. Notably, computational analysis of 3D layer clarified that the plexus structure of the glands was mainly located in the stratum basalis and expanded along muscular layer horizontally, similar to the so-called “rhizome of grass”. Although previous studies have shown the 3D structure of murine endometrial glands, the bottom of these glands forms a crypt but not a rhizome. This can potentially be explained by the existence of menstruation, which is the crucial difference between the human and murine endometrium. The rhizome structure of endometrial gland in the human endometrium will have a functional advantage over the crypt in terms of the conservation of progenitor/stem cells and regeneration. In addition, some endometrial glands shared the plexus and rose toward the luminal epithelium, suggesting that these glands were the same origin. The rhizome of the endometrium may be a crucial element for understanding the expansion of endometrial glands harboring cancer-associated gene mutations. Integrated analysis of the naughty gene alterations and the 3D structure in human endometrium will lead to a better understanding of the human endometrium in various fields, including histology, pathology, pathophysiology, reproduction, and oncology.

scholarly journals A simple method to estimate the in-house limit of detection for genetic mutations with low allele frequencies in whole-exome sequencing analysis by next-generation sequencing

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Takumi Miura ◽  
Satoshi Yasuda ◽  
Yoji Sato
Keyword(s):  
Next Generation Sequencing ◽  
Allele Frequency ◽  
Somatic Mutations ◽  
Limit Of Detection ◽  
Allele Frequencies ◽  
Genetic Mutations ◽  
Sequencing Data ◽  
Simple Method ◽  
Whole Exome ◽  
Generation Sequencing

Abstract Background Next-generation sequencing (NGS) has profoundly changed the approach to genetic/genomic research. Particularly, the clinical utility of NGS in detecting mutations associated with disease risk has contributed to the development of effective therapeutic strategies. Recently, comprehensive analysis of somatic genetic mutations by NGS has also been used as a new approach for controlling the quality of cell substrates for manufacturing biopharmaceuticals. However, the quality evaluation of cell substrates by NGS largely depends on the limit of detection (LOD) for rare somatic mutations. The purpose of this study was to develop a simple method for evaluating the ability of whole-exome sequencing (WES) by NGS to detect mutations with low allele frequency. To estimate the LOD of WES for low-frequency somatic mutations, we repeatedly and independently performed WES of a reference genomic DNA using the same NGS platform and assay design. LOD was defined as the allele frequency with a relative standard deviation (RSD) value of 30% and was estimated by a moving average curve of the relation between RSD and allele frequency. Results Allele frequencies of 20 mutations in the reference material that had been pre-validated by droplet digital PCR (ddPCR) were obtained from 5, 15, 30, or 40 G base pair (Gbp) sequencing data per run. There was a significant association between the allele frequencies measured by WES and those pre-validated by ddPCR, whose p-value decreased as the sequencing data size increased. By this method, the LOD of allele frequency in WES with the sequencing data of 15 Gbp or more was estimated to be between 5 and 10%. Conclusions For properly interpreting the WES data of somatic genetic mutations, it is necessary to have a cutoff threshold of low allele frequencies. The in-house LOD estimated by the simple method shown in this study provides a rationale for setting the cutoff.

scholarly journals The New Era of Three-Dimensional Histoarchitecture of the Human Endometrium

2021 ◽  
Vol 11 (8) ◽  
pp. 713
Author(s):  
Manako Yamaguchi ◽  
Kosuke Yoshihara ◽  
Nozomi Yachida ◽  
Kazuaki Suda ◽  
Ryo Tamura ◽  
...  
Keyword(s):  
3D Imaging ◽  
Relevant Literature ◽  
3D Structure ◽  
Three Dimensional ◽  
Human Endometrium ◽  
Tissue Structure ◽  
New Era ◽  
Whole Mount ◽  
Uterine Glands

The histology of the endometrium has traditionally been established by observation of two-dimensional (2D) pathological sections. However, because human endometrial glands exhibit coiling and branching morphology, it is extremely difficult to obtain an entire image of the glands by 2D observation. In recent years, the development of three-dimensional (3D) reconstruction of serial pathological sections by computer and whole-mount imaging technology using tissue clearing methods with high-resolution fluorescence microscopy has enabled us to observe the 3D histoarchitecture of tissues. As a result, 3D imaging has revealed that human endometrial glands form a plexus network in the basalis, similar to the rhizome of grass, whereas mouse uterine glands are single branched tubular glands. This review summarizes the relevant literature on the 3D structure of mouse and human endometrium and discusses the significance of the rhizome structure in the human endometrium and the expected role of understanding the 3D tissue structure in future applications to systems biology.

Abstract 057: Cellular and Genetic Causes of Idiopathic Hyperaldosteronism

Hypertension ◽  
2017 ◽  
Vol 70 (suppl_1) ◽  
Author(s):  
Kei Omata ◽  
Fumitoshi Satoh ◽  
Ryo Morimoto ◽  
Sadayoshi Ito ◽  
Yuto Yamazaki ◽  
...  
Keyword(s):  
Somatic Mutations ◽  
Clinical Manifestations ◽  
Gene Mutations ◽  
Median Number ◽  
Zona Glomerulosa ◽  
Potential Contribution ◽  
Unilateral Adrenalectomy ◽  
Aldosterone Synthase ◽  
Formalin Fixed Paraffin Embedded ◽  
Idiopathic Hyperaldosteronism

Background: Primary aldosteronism (PA) affects ~10% of hypertensive patients and has unilateral and bilateral forms (30%:70%). Unilateral PA is caused by aldosterone-producing adenomas (APA), which express CYP11B2 (aldosterone synthase) and frequently harbor somatic mutations in aldosterone regulating genes ( KCNJ5>>CACNA1D ). We recently demonstrated that adrenals from normotensive patients present with pockets of cell expressing aldosterone synthase (CYP11B2). These aldosterone-producing foci (APF) have somatic gene mutations similar to those found in APA ( CACNA1D >> KCNJ5 ). Bilateral PA, which is typically treated by mineralocorticoid receptor (MR) blockade rather than surgery, is termed idiopathic hyperaldosteronism (IHA). Its pathobiology is largely unknown but has been thought to be due to zona glomerulosa (ZG) hyperplasia. Methods: We studied 11 IHA patients (7 males, 4 females) who had unilateral adrenalectomy. Immunohistochemistry for CYP11B2 and next generation sequencing (NGS) targeting genes found in APA were performed on formalin fixed paraffin embedded adrenal tissue. Results were compared to previously described cohorts of 53 age-matched normotensive patients (29 males, 24 females) which were evaluated similarly. Results: CYP11B2 expression was absent from intervening ZG cells in 8/11 (73%) IHA adrenals, but all adrenals harbored at least one APF. The median number and size of APF per case were significantly larger in IHA than normotensive controls (6.1 vs 0 APF/cm 2 of adrenal cortex and 0.25 vs. 0.16 mm 2 , respectively; p<0.0001 and p<0.006). In this IHA cohort, NGS identified CACNA1D and KCNJ5 somatic mutations in 44/71 (62%) and 1/71 (1%) of APF, respectively. Interpretations. Diffuse CYP11B2 expression in adrenal ZG cells was only observed in 3/11 IHA cases, arguing against ZG hyperplasia as the major underlying pathobiology. Rather, we demonstrated increased and enlarged APF in IHA adrenals compared to normotensive controls, supporting potential contribution to the clinical manifestations of hyperaldosteronism. The frequent occurrence of aldosterone-dysregulating CACNA1D somatic mutations in APF support CACNA1D as a potential therapeutic target in IHA to complement current MR blockade approaches.

scholarly journals Analysis, identification and visualization of subgroups in genomics

2020 ◽  
Author(s):  
Gunnar Völkel ◽  
Simon Laban ◽  
Axel Fürstberger ◽  
Silke D Kühlwein ◽  
Nensi Ikonomi ◽  
...  
Keyword(s):  
Large Scale ◽  
Somatic Mutations ◽  
Target Selection ◽  
Gene Mutations ◽  
Use Case ◽  
The Past ◽  
Wide Availability ◽  
Approaches To Study ◽  
User Friendly ◽  
Personalized Intervention

Abstract Motivation Cancer is a complex and heterogeneous disease involving multiple somatic mutations that accumulate during its progression. In the past years, the wide availability of genomic data from patients’ samples opened new perspectives in the analysis of gene mutations and alterations. Hence, visualizing and further identifying genes mutated in massive sets of patients are nowadays a critical task that sheds light on more personalized intervention approaches. Results Here, we extensively review existing tools for visualization and analysis of alteration data. We compare different approaches to study mutual exclusivity and sample coverage in large-scale omics data. We complement our review with the standalone software AVAtar (‘analysis and visualization of alteration data’) that integrates diverse aspects known from different tools into a comprehensive platform. AVAtar supplements customizable alteration plots by a multi-objective evolutionary algorithm for subset identification and provides an innovative and user-friendly interface for the evaluation of concurrent solutions. A use case from personalized medicine demonstrates its unique features showing an application on vaccination target selection. Availability AVAtar is available at: https://github.com/sysbio-bioinf/avatar Contact [email protected], phone: +49 (0) 731 500 24 500, fax: +49 (0) 731 500 24 502

scholarly journals Molecular and Other Novel Advances in Treatment of Metastatic Epithelial and Medullary Thyroid Cancers

2010 ◽  
Vol 2010 ◽  
pp. 1-7 ◽  
Author(s):  
David Tai ◽  
Donald Poon
Keyword(s):  
Tumor Suppressor Genes ◽  
Somatic Mutations ◽  
Gene Mutations ◽  
C Cells ◽  
Therapeutic Approaches ◽  
Thyroid Cancers ◽  
Medullary Thyroid ◽  
Genetic Abnormalities ◽  
Pathologic Findings ◽  
Inherited Mutations

An understanding of the mutations of the proto-oncogenes and tumor suppressor genes that occur in thyroid cancers should eventually explain the diverse clinical characteristics of these tumors and also direct therapy. Some insights have already emerged in the last decade; some abnormalities in tumor genes are consistently associated with specific clinical and pathologic findings. These genetic abnormalities usually represent somatic mutations in tumors of follicular epithelial origin, as opposed to inherited mutations in medullary thyroid cancers of parafollicular C cells origin because most thyroid tumors are sporadic and not familial. This is different from the multiple endocrine neoplasia syndromes in which the primary tumorigenic gene mutations are inherited. This improved understanding of the molecular basis of these diseases has led to the development of novel targeted therapeutic approaches which will be discussed in this paper.

scholarly journals Clonal haematopoiesis in chronic ischaemic heart failure: prognostic role of clone size for DNMT3A- and TET2-driver gene mutations

2020 ◽  
Author(s):  
Birgit Assmus ◽  
Sebastian Cremer ◽  
Klara Kirschbaum ◽  
David Culmann ◽  
Katharina Kiefer ◽  
...  
Keyword(s):  
Heart Failure ◽  
Somatic Mutations ◽  
Prognostic Significance ◽  
Gene Mutations ◽  
Amplicon Sequencing ◽  
Driver Mutations ◽  
Driver Gene ◽  
Roc Curve Analysis ◽  
Driver Genes ◽  
Clone Size

Abstract Aims Somatic mutations of the epigenetic regulators DNMT3A and TET2 causing clonal expansion of haematopoietic cells (clonal haematopoiesis; CH) were shown to be associated with poor prognosis in chronic ischaemic heart failure (CHF). The aim of our analysis was to define a threshold of variant allele frequency (VAF) for the prognostic significance of CH in CHF. Methods and results We analysed bone marrow and peripheral blood-derived cells from 419 patients with CHF by error-corrected amplicon sequencing. Cut-off VAFs were optimized by maximizing sensitivity plus specificity from a time-dependent receiver operating characteristic (ROC) curve analysis from censored data. 56.2% of patients were carriers of a DNMT3A- (N = 173) or a TET2- (N = 113) mutation with a VAF &gt;0.5%, with 59 patients harbouring mutations in both genes. Survival ROC analyses revealed an optimized cut-off value of 0.73% for TET2- and 1.15% for DNMT3A-CH-driver mutations. Five-year-mortality was 18% in patients without any detected DNMT3A- or TET2 mutation (VAF &lt; 0.5%), 29% with only one DNMT3A- or TET2-CH-driver mutations above the respective cut-off level and 42% in patients harbouring both DNMT3A- and TET2-CH-driver mutations above the respective cut-off levels. In carriers of a DNMT3A mutation with VAF ≥ 1.15%, 5-year mortality was 31%, compared with 18% mortality in those with VAF &lt; 1.15% (P = 0.048). Likewise, in patients with TET2 mutations, 5-year mortality was 32% with VAF ≥ 0.73%, compared with 19% mortality with VAF &lt; 0.73% (P = 0.029). Conclusion The present study defines novel threshold levels for clone size caused by acquired somatic mutations in the CH-driver genes DNMT3A and TET2 that are associated with worse outcome in patients with CHF.

Abstract 2265: An integrated analysis of gene mutations and gene sets for predicting paclitaxel response in lung adenocarcinoma

2016 ◽  
Author(s):  
Chia-Yu Huang ◽  
Yu-Chiao Chiu ◽  
Tzu-Pin Lu ◽  
Liang-Chuan Lai ◽  
Mong-Hsun Tsai ◽  
...  
Keyword(s):  
Lung Adenocarcinoma ◽  
Gene Mutations ◽  
Integrated Analysis ◽  
Gene Sets

scholarly journals Frequency of somatic MEN1 gene mutations in monoclonal parathyroid tumours of patients with primary hyperparathyroidism

2000 ◽  
pp. 47-54 ◽  
Author(s):  
S Miedlich ◽  
K Krohn ◽  
P Lamesch ◽  
A Muller ◽  
R Paschke
Keyword(s):  
Primary Hyperparathyroidism ◽  
Gene Mutation ◽  
X Chromosome ◽  
Somatic Mutations ◽  
Genetic Defect ◽  
Gene Mutations ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Men1 Gene ◽  
Parathyroid Tumours

OBJECTIVES: Investigation of small numbers of parathyroid tumours by X-chromosome inactivation analysis suggests that the majority of them are monoclonal lesions most likely caused by a somatic mutation. Somatic mutations in the MEN1 gene located on chromosome 11q13 have recently been identified in 12-17% of solitary parathyroid tumours in patients with sporadic primary hyperparathyroidism, and they may be the precipitating genetic defect leading to monoclonal cell proliferation in these tumours. DESIGN: To determine the prevalence of MEN1 gene mutations in monoclonal parathyroid neoplasias we investigated 33 parathyroid tumours of patients with primary hyperparathyroidism for clonality and mutations in the MEN1 gene. METHODS: X-chromosome inactivation analysis was used to assess the clonal status of the tumours, direct sequencing of the complete coding region was applied to identify mutations in the MEN1 gene. RESULTS: Twenty-eight female patients (26 patients with solitary adenoma, 2 patients with hyperplasia) were informative for the polymorphism of the androgen receptor on the X-chromosome and could be tested for inactivation pattern. Nineteen of twenty-six (73%) solitary adenomas were monoclonal. Somatic mutations in the MEN1 gene were identified in nine cases. Six of them were found in the relatively large second exon of the MEN1 gene (A49D, 193del36, 402delC, 482del22, 547delT, W126X). One was found in exon 5 (904del9), one in exon 7 (Y327X) and one in exon 9 (R415X). Of the monoclonal tumours, 5 out of 19 (26%) harboured a somatic MEN1 gene mutation. CONCLUSIONS: In summary, 73% of the solitary parathyroid adenomas were monoclonal. In 26% of the monoclonal tumours a somatic MEN1 gene mutation has been identified. However, for 74% of monoclonal tumours of the parathyroids the underlying genetic defects are still not known.

scholarly journals Germline and somatic mutations of homologous recombination-associated genes in Japanese ovarian cancer patients

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Kentaro Sugino ◽  
Ryo Tamura ◽  
Hirofumi Nakaoka ◽  
Nozomi Yachida ◽  
Manako Yamaguchi ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Homologous Recombination ◽  
Cancer Patients ◽  
Somatic Mutations ◽  
Clear Cell ◽  
Gene Mutations ◽  
Parp Inhibitors ◽  
Low Grade ◽  
Mmr Genes ◽  
Selection Of

AbstractWe explored the frequency of germline and somatic mutations in homologous recombination (HR)-associated genes in major histological types of ovarian cancer. We performed targeted sequencing to assess germline and somatic mutations of 16 HR-associated genes and 4 mismatch repair (MMR) genes among 207 ovarian cancer patients (50 high-grade serous carcinomas (HGSC), 99 clear cell carcinomas (CCC), 39 endometrioid carcinomas (EC), 13 mucinous carcinomas (MC), and 6 low-grade serous carcinomas (LGSC)). Germline or somatic mutations of HR-associated genes were detected in 44% of HGSC, 28% of CCC, 23% of EC, 16% of MC, and 17% of LGSC patients. The profile of HR-associated gene mutations was remarkably different among each histological type. Germline BRCA1/2 mutations were frequently detected in HGSC and were rarely observed in CCC, EC, and MC patients. ATM somatic mutation was more frequently detected in CCC (9%) and EC patients (18%) than in HGSC patients (4%). There was a positive correlation between MMR gene mutations and HR-associated gene mutations (p = 0.0072). Our findings might be useful in selection of ovarian cancer patients that should be treated with PARP inhibitors.

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