Gene Expression Signature of Endometrial Samples from Women with and without Endometriosis

Adamyan, L. V.; Aznaurova, Y.B.; Stepanian, A.A.; Nikitin, Daniil; Garazha, Andrew; Suntsova, Maria; Sorokin, Maxim; Buzdin, Anton

doi:10.1016/j.jmig.2021.03.011

Cited by 18 publications

(12 citation statements)

References 28 publications

(22 reference statements)

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“…It can reliably estimate concentrations of cancer drug targets ( 53 ), which is also true for the emerging non-protein molecular target ganglioside GD2 ( 27 ). In addition, RNAseq data obtained for FFPE biosamples may be used to identify clinically actionable or new fusion oncogenes ( 26 ) and to generate gene signatures that can establish statuses of important tumor biomarkers like microsatellite instability ( 25 , 54 , 55 ) and oncogenic mutations ( 56 ) or that can predict individual sensitivity of a tumor to targeted ( 28 , 57 , 58 ) and non-targeted ( 59 ) therapies. Thus, adding a new option of TMB level assessment may strongly benefit this approach.…”

Section: Discussionmentioning

confidence: 99%

“…RNA sequencing was performed according to the previous protocol used to generate ANTE collection of healthy tissue RNAseq profiles (23) and several cancer expression collections (22,(24)(25)(26)(27)(28). To isolate RNA preps, 10-mM-thick paraffin slices were trimmed from each FFPE tissue block with a microtome.…”

Section: Rnaseq: Library Preparation and Sequencingmentioning

confidence: 99%

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RNA Sequencing Data for FFPE Tumor Blocks Can Be Used for Robust Estimation of Tumor Mutation Burden in Individual Biosamples

et al. 2021

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Tumor mutation burden (TMB) is a well-known efficacy predictor for checkpoint inhibitor immunotherapies. Currently, TMB assessment relies on DNA sequencing data. Gene expression profiling by RNA sequencing (RNAseq) is another type of analysis that can inform clinical decision-making and including TMB estimation may strongly benefit this approach, especially for the formalin-fixed, paraffin-embedded (FFPE) tissue samples. Here, we for the first time compared TMB levels deduced from whole exome sequencing (WES) and RNAseq profiles of the same FFPE biosamples in single-sample mode. We took TCGA project data with mean sequencing depth 23 million gene-mapped reads (MGMRs) and found 0.46 (Pearson)–0.59 (Spearman) correlation with standard mutation calling pipelines. This was converted into low (<10) and high (>10) TMB per megabase classifier with area under the curve (AUC) 0.757, and application of machine learning increased AUC till 0.854. We then compared 73 experimental pairs of WES and RNAseq profiles with lower (mean 11 MGMRs) and higher (mean 68 MGMRs) RNA sequencing depths. For higher depth, we observed ~1 AUC for the high/low TMB classifier and 0.85 (Pearson)–0.95 (Spearman) correlation with standard mutation calling pipelines. For the lower depth, the AUC was below the high-quality threshold of 0.7. Thus, we conclude that using RNA sequencing of tumor materials from FFPE blocks with enough coverage can afford for high-quality discrimination of tumors with high and low TMB levels in a single-sample mode.

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Section: Discussionmentioning

confidence: 99%

Section: Rnaseq: Library Preparation and Sequencingmentioning

confidence: 99%

RNA Sequencing Data for FFPE Tumor Blocks Can Be Used for Robust Estimation of Tumor Mutation Burden in Individual Biosamples

et al. 2021

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“…Mutations that have been observed, almost exclusively, in the KRAS genes, in the presence of adenomyosis, underscore the importance of these genes in the pathogenesis of the disease at the genetic level. This discovery of the cause-effect relationship between the presence of mutations in the aforementioned [7][8][9] KRAS genes and adenomyosis refuted the recent theory that the reported molecular abnormalities in adenomyosis are mainly epigenetic or associated with abnormal expression in different genes [7][8][9]. Most recognized abnormalities regarding gene expression, were associated with excess estrogen formation, progesterone resistance and were related to steroid hormone receptors and other transcription factors.…”

Section: Genetic Predispositionmentioning

confidence: 91%

“…Adenomyosis, one of the most common diseases in gynecology with a frequency ranging between 5% and 70% , can significantly affect the quality of life of women with clinical symptoms such as menorrhagia, dysmenorrhea and infertility [7][8][9]. There are two prevailing theories concerning the origin of adenomyosis.…”

Section: Genetic Predispositionmentioning

confidence: 99%

Uterine Embolization as a New Treatment Option in Adenomyosis Uteri

Tsikouras¹,

Gaitatzi²,

Filiou³

et al. 2022

Endometriosis - Recent Advances, New Perspectives and Treatments

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Adenomyosis is characterized by the development of endometrial ectopic glands and tissue in the myometrium layer in depth greater than 2.5 mm from the endometrial surface of the separative area by -myomas well as by hypertrophy and hyperplasia of the smooth muscles of the myometrium. This is filtration, not mere displacement, of the myometrium, from the endometrium. Clinical symptoms include dysmenorrhea and menorrhagia. It is diffuse (adenomyosis) or focal (adenomyoma), asymmetrically affects the uterine wall of premenopausal women (usually the posterior) and often coexists with myomas. The pathogenesis of adenomyosis remains unknown. The treatment options are: drug therapy, invasive treatment of fibroids: myomectomy (open—intra-abdominal, laparoscopic, hysteroscopic), hysterectomy, myolysis—cryocatalysis, microwave or radiofrequency thermal catalysis (RF-ablation), ultrasound focus catalysis (FUS), laser photocatalysis and percutaneous selective uterine artery embolization (UAE). Embolization remains an alternative and not a substitute of hysterectomy. The medical indication is made on a case-by-case basis, depending on age, desire for pregnancy and the clinical symptoms of adenomyosis.

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“…We also measured the expression of the genes that may play a role in the pathogenesis of adenomyosis (Oh et al, 2013; Artymuk et al, 2019;Inoue et al, 2019;Kim et al, 2020;Adamyan et al, 2021). Kras and Tgb1 stayed at the same level in control and tamoxifen-treated mice at both ages (Figure 3C).…”

Section: Pathological Features and Gene Expression Profile In Tamoxifen-induced Adenomyotic Micementioning

confidence: 95%

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Gene Expression Signature of Endometrial Samples from Women with and without Endometriosis

Cited by 18 publications

References 28 publications

RNA Sequencing Data for FFPE Tumor Blocks Can Be Used for Robust Estimation of Tumor Mutation Burden in Individual Biosamples

RNA Sequencing Data for FFPE Tumor Blocks Can Be Used for Robust Estimation of Tumor Mutation Burden in Individual Biosamples

Uterine Embolization as a New Treatment Option in Adenomyosis Uteri

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