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#38319496   2024/02/06 To Up

Whole-exome sequencing reveals genetic variants that may play a role in neurocytomas.

Neurocytomas (NCs) are rare intracranial tumors that can often be surgically resected. However, disease course is unpredictable in many patients and medical therapies are lacking. We have used whole exome sequencing to explore the molecular etiology for neurocytoma and assist in target identification to develop novel therapeutic interventions.
Sapna Khowal, Dongyun Zhang, William H Yong, Anthony P Heaney

2359 related Products with: Whole-exome sequencing reveals genetic variants that may play a role in neurocytomas.

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#37827097   2023/10/10 To Up

Indoor particulate matter induces epigenetic changes in companion atopic dogs.

The prevalence of atopic dermatitis (AD) is increasing and environmental factors are receiving attention as contributing causes. Indoor air pollutants (IAPs), especially particulate matter (PM) can alter epigenetic markers, DNA methylation (DNAm). Although DNAm-mediated epigenetic changes have been reported to modulate the pathogenesis of AD, their role at high risk of exposure to PM is still unclear. The study investigated the effects of exposure to IAPs in the development of AD and epigenetic changes through DNAm in companion atopic dogs that share indoor environment with their owners. Dogs were divided into two groups: AD (n = 47) and controls (n = 21). The IAPs concentration in each household was measured for 48 h, and a questionnaire on the residential environment was completed in all dogs. Eighteen dogs with AD and 12 healthy dogs were selected for DNAm analysis. In addition, clinical and immunological evaluations were conducted. The concentrations of PM, PM, and volatile organic compounds (VOCs) were significantly higher in the AD group. Moreover, there were more significant methylation differences in the LDLRAD4, KHSRP, and CTDSP2 genes in connection with PM in AD group compared to the controls. The degree of methylation of the LDLRAD4 and CTDSP2 genes was also correlated with related protein productions. The present study revealed that exposure to high indoor PM can cause epigenetic development of AD by methylation of the LDLRAD4, KHSRP, and CTDSP2 genes in dogs. Under the concept of "One Health," improving indoor environments should be considered to prevent the development of AD.
Jihyun Kim, Yeji Kim, Yunji Song, Tae Jung Kim, Seung-Hwa Lee, Ha-Jung Kim

2599 related Products with: Indoor particulate matter induces epigenetic changes in companion atopic dogs.

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#37629167   2023/08/19 To Up

Tumor Suppressor Properties of Small C-Terminal Domain Phosphatases in Clear Cell Renal Cell Carcinoma.

Clear cell renal cell carcinoma (ccRCC) accounts for 80-90% of kidney cancers worldwide. Small C-terminal domain phosphatases CTDSP1, CTDSP2, and CTDSPL (also known as SCP1, 2, 3) are involved in the regulation of several important pathways associated with carcinogenesis. In various cancer types, these phosphatases may demonstrate either antitumor or oncogenic activity. Tumor-suppressive activity of these phosphatases in kidney cancer has been shown previously, but in general case, the antitumor activity may be dependent on the choice of cell line. In the present work, transfection of the Caki-1 cell line (ccRCC morphologic phenotype) with expression constructs containing the coding regions of these genes resulted in inhibition of cell growth in vitro in the case of ( < 0.001) and ( < 0.05) but not . The analysis of The Cancer Genome Atlas (TCGA) data showed differential expression of some of genes and of their target, . These results were confirmed by quantitative RT-PCR using an independent sample of primary ccRCC tumors ( = 52). We observed downregulation and found a positive correlation of expression for two gene pairs: and ( = 0.76; < 0.001) and and ( = 0.38; < 0.05). Survival analysis based on TCGA data demonstrated a strong association of lower expression of , , , and with poor survival of ccRCC patients ( < 0.001). In addition, according to TCGA, , , and were differently expressed in two subtypes of ccRCC-ccA and ccB, characterized by different survival rates. These results confirm that and have tumor suppressor properties in ccRCC and reflect their association with the more aggressive ccRCC phenotype.
George S Krasnov, Grigory A Puzanov, Erdem B Dashinimaev, Khava S Vishnyakova, Tatiana T Kondratieva, Yegor S Chegodaev, Anton Y Postnov, Vera N Senchenko, Yegor E Yegorov

1136 related Products with: Tumor Suppressor Properties of Small C-Terminal Domain Phosphatases in Clear Cell Renal Cell Carcinoma.

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#37053215   2023/04/13 To Up

Non-allergic eye rubbing is a major behavioral risk factor for keratoconus.

Since the environmental, behavioral, and socioeconomic factors in the etiology of keratoconus (KTCN) remain poorly understood, we characterized them as features influencing KTCN phenotype, and especially affecting the corneal epithelium (CE). In this case-control study, 118 KTCN patients and 73 controls were clinically examined and the Questionnaire covering the aforementioned aspects was completed and then statistically elaborated. Selected KTCN-specific findings were correlated with the outcomes of the RNA-seq assessment of the CE samples. Male sex, eye rubbing, time of using a computer after work, and dust in the working environment, were the substantial KTCN risk factors identified in multivariate analysis, with ORs of 8.66, 7.36, 2.35, and 5.25, respectively. Analyses for genes whose expression in the CE was correlated with the eye rubbing manner showed the enrichment in apoptosis (TP53, BCL2L1), chaperon-related (TLN1, CTDSP2, SRPRA), unfolded protein response (NFYA, TLN1, CTDSP2, SRPRA), cell adhesion (TGFBI, PTPN1, PDPK1), and cellular stress (TFDP1, SRPRA, CAPZB) pathways. Genes whose expression was extrapolated to the allergy status didn't contribute to IgE-related or other inflammatory pathways. Presented findings support the hypothesis of chronic mechanical corneal trauma in KTCN. Eye-rubbing causes CE damage and triggers cellular stress which through its influence on cell apoptosis, migration, and adhesion affects the KTCN phenotype.
Katarzyna Jaskiewicz, Magdalena Maleszka-Kurpiel, Andrzej Michalski, Rafal Ploski, Malgorzata Rydzanicz, Marzena Gajecka

1443 related Products with: Non-allergic eye rubbing is a major behavioral risk factor for keratoconus.

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#34432772   // To Up

[SCP Phosphatases and Oncogenesis].

Small SCP phosphatases CTDSP1, CTDSP2, and CTDSPL specifically dephosphorylate serine and threonine residues in protein molecules. The enzymes are involved in regulating activity of RNA polymerase II at the transition from transcription initiation to elongation, regulating expression of neuron-specific genes, and activating the key cell-cycle protein pRb at the G1/S boundary. In addition, the substrates of SCP phosphatases include SMAD transcription modulators; AKT1 protein kinase, which regulates the cell cycle, apoptosis, and angiogenesis; the TWIST1 and c-MYC transcription factors; Ras family proteins, which are involved in signaling pathways regulating the cell growth and apoptosis; CDCA3, which is associated with cell division; the cyclin-dependent kinase inhibitor p21; and the promyelocytic leukemia protein (PML), which is involved in regulation of the tumor suppressors p53, PTEN, and mTOR. Dysfunction or inactivation of SCP phosphatases leads to various diseases, including cancer. Recently the increase in interest to SCP phosphatases is due to their their tumor growth-inhibiting properties or role in the development of malignant tumors of various etiology and localization. The review discusses the properties of SCP phosphatases and their role in oncogenesis. Understanding the functions of SCP phosphatases and their regulatory mechanisms can be useful in searching for efficient targets for tumor therapy.
G A Puzanov, V N Senchenko

1413 related Products with: [SCP Phosphatases and Oncogenesis].

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#34268420   // To Up

Whole-exome sequencing analysis to identify novel potential pathogenetic mutations in fetuses with abnormal brain structure.

Genetic mutations in genes related to the production, migration, or differentiation of cortical neurons can result in malformations of cortical development (MCDs). However, a large number of MCD-related pathogenetic mutations remain unknown. This study aimed to investigate the genetic cause of MCDs and to identify the new MCD-associated mutations through whole-exome sequencing (WES) in fetuses with abnormal brain structure.
Lili Shi, Ming Li, Hong Qi, Jianjiang Zhu, Jing Yang, Jie Tang, Longxia Wang

1376 related Products with: Whole-exome sequencing analysis to identify novel potential pathogenetic mutations in fetuses with abnormal brain structure.

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#34151974   2021/06/21 To Up

The miR-26 family regulates neural differentiation-associated microRNAs and mRNAs by directly targeting REST.

Repressor element 1-silencing transcription factor (REST) plays a crucial role in the differentiation of neural progenitor cells (NPCs). C-terminal domain small phosphatases (CTDSPs) are REST effector proteins that reduce RNA polymerase II activity on genes required for neurogenesis. miR-26b regulates neurogenesis in zebrafish by targeting ctdsp2 mRNA, but the molecular events triggered by this microRNA (miR) remain unknown. Here, we show in a murine embryonic stem cell differentiation paradigm that inactivation of miR-26 family members disrupts the formation of neurons and astroglia and arrests neurogenesis at the neural progenitor level. Furthermore, we show that miR-26 directly targets Rest, thereby inducing the expression of a large set of REST complex-repressed neuronal genes, including miRs required for induction of the neuronal gene expression program. Our data identify the miR-26 family as the trigger of a self-amplifying system required for neural differentiation that acts upstream of REST-controlled miRs.
Mark Sauer, Nina Was, Thomas Ziegenhals, Xiantao Wang, Markus Hafner, Matthias Becker, Utz Fischer

2519 related Products with: The miR-26 family regulates neural differentiation-associated microRNAs and mRNAs by directly targeting REST.

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#33097826   2020/10/23 To Up

Lipoblastomas presenting in older children and adults: analysis of 22 cases with identification of novel PLAG1 fusion partners.

Lipoblastomas are benign neoplasms of embryonal white fat that typically present in the first 3 years of life and show a lobular arrangement of maturing adipocytes with variable degrees of myxoid change. We systematically studied the clinicopathologic and genetic features of lipoblastomas arising in older children and adults. Cases with a diagnosis of lipoblastoma or maturing lipoblastoma in patients >3 years of age were retrieved from our archives. Immunostaining for CD34 and desmin and molecular studies (FISH, RNA sequencing) were performed. Twenty-two cases (8F; 14M) were identified in patients ranging from 4 to 44 years of age (median 10 years). Sites included extremity (n = 15), head and neck (n = 4), and trunk (n = 3) with tumor sizes varying from 1.6 to 17.5 cm (median 5). Only three tumors had histologic features of "conventional" lipoblastoma. The majority of tumors (n = 14) were composed of variably sized lobules of mature adipose tissue partitioned by thin fibrous septa ("maturing"). The remaining five cases consisted predominantly of bland spindled to plump ovoid cells embedded in a fibrous stroma, with a vaguely plexiform arrangement of small myxoid and adipocytic nodules ("fibroblastic"). CD34 was diffusely positive in all cases tested (21/21), while desmin immunoreactivity was identified in 12 of 21 cases (diffuse = 7, focal = 5). PLAG1 rearrangements were identified in 13 tumors in the entire cohort (59%), including all 5 fibroblastic tumors. RNA sequencing detected eight PLAG1 fusion partners, of which two were known (CHCHD7 and COL3A1) and six were novel (SRSF3, HNRNPC, PCMTD1, YWHAZ, CTDSP2, and PPP2R2A). Twelve cases had follow-up (1-107 months; median 21 months), and no recurrences were reported. Lipoblastomas may occur in older children and adults and may be difficult to recognize due to their predominantly adipocytic or fibrous appearance. Awareness that lipoblastomas may occur in older patients, careful evaluation for foci showing more typical morphologic features, ancillary immunohistochemistry for CD34 and desmin, and molecular genetic studies to identify PLAG1 rearrangements are the keys to recognizing these tumors.
Karen Fritchie, Lu Wang, Zhaohong Yin, Joy Nakitandwe, Dale Hedges, Andrew Horvai, Jorge Torres Mora, Andrew L Folpe, Armita Bahrami

1112 related Products with: Lipoblastomas presenting in older children and adults: analysis of 22 cases with identification of novel PLAG1 fusion partners.



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#31831742   2019/12/12 To Up

Integrated exome and RNA sequencing of dedifferentiated liposarcoma.

The genomic characteristics of dedifferentiated liposarcoma (DDLPS) that are associated with clinical features remain to be identified. Here, we conduct integrated whole exome and RNA sequencing analysis in 115 DDLPS tumors and perform comparative genomic analysis of well-differentiated and dedifferentiated components from eight DDLPS samples. Several somatic copy-number alterations (SCNAs), including the gain of 12q15, are identified as frequent genomic alterations. CTDSP1/2-DNM3OS fusion genes are identified in a subset of DDLPS tumors. Based on the association of SCNAs with clinical features, the DDLPS tumors are clustered into three groups. This clustering can predict the clinical outcome independently. The comparative analysis between well-differentiated and dedifferentiated components identify two categories of genomic alterations: shared alterations, associated with tumorigenesis, and dedifferentiated-specific alterations, associated with malignant transformation. This large-scale genomic analysis reveals the mechanisms underlying the development and progression of DDLPS and provides insights that could contribute to the refinement of DDLPS management.
Makoto Hirata, Naofumi Asano, Kotoe Katayama, Akihiko Yoshida, Yusuke Tsuda, Masaya Sekimizu, Sachiyo Mitani, Eisuke Kobayashi, Motokiyo Komiyama, Hiroyuki Fujimoto, Takahiro Goto, Yukihide Iwamoto, Norifumi Naka, Shintaro Iwata, Yoshihiro Nishida, Toru Hiruma, Hiroaki Hiraga, Hirotaka Kawano, Toru Motoi, Yoshinao Oda, Daisuke Matsubara, Masashi Fujita, Tatsuhiro Shibata, Hidewaki Nakagawa, Robert Nakayama, Tadashi Kondo, Seiya Imoto, Satoru Miyano, Akira Kawai, Rui Yamaguchi, Hitoshi Ichikawa, Koichi Matsuda

1393 related Products with: Integrated exome and RNA sequencing of dedifferentiated liposarcoma.

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#31774910   // To Up

Tumor suppressor properties of the small C-terminal domain phosphatases in non-small cell lung cancer.

Non-Small Cell Lung Cancer (NSCLC) is responsible for the majority of deaths caused by cancer. Small C-terminal domain (CTD) phosphatases (SCP), CTDSP1, CTDSP2 and CTDSPL (CTDSPs) belong to SCP/CTDSP subfamily and are involved in many vital cellular processes and tumorigenesis. High similarity of their structures suggests similar functions. However their role in NSCLC remains insufficiently understood. For the first time we revealed the suppressor function of CTDSPs leading to a significant growth slowdown and senescence of A549 lung adenocarcinoma (ADC) cells in vitro. Their tumor-suppressive activity can be realized through increasing the proportion of the active form of Rb protein dephosphorylated at Ser807/811, Ser780, and Ser795 (P<0.05) thereby negatively regulating cancer cell proliferation. Moreover, we observed that a frequent (84%, 39/46) and highly concordant (Spearman's rank correlation coefficient (rs) = 0.53-0.62, P≤0.01) down-regulation of CTDSPs and RB1 is characteristic of primary NSCLC samples (n=46). A clear difference in their mRNA levels was found between lung ADCs with and without lymph node metastases, but not in squamous cell carcinomas (SCCs) (P≤0.05). Based on The Cancer Genome Atlas (TCGA) data and the results obtained using the CrossHub tool, we suggest that the well-known oncogenic cluster miR-96/182/183 could be a common expression regulator of CTDSPs. Indeed, according to our qPCR, the expression of CTDSPs negatively correlates with these miRs, but positively correlates with their intronic miR-26a/b. Our results reflect functional association of CTDSP1, CTDSP2, and CTDSPL, expand knowledge about their suppressor properties through Rb dephosphorylation and provide new insights into the regulation of NSCLC growth.
George S Krasnov, Grigory A Puzanov, Marina A Afanasyeva, Erdem B Dashinimaev, Khava S Vishnyakova, Artemy D Beniaminov, Alexei A Adzhubei, Tatiana T Kondratieva, Yegor E Yegorov, Vera N Senchenko

1266 related Products with: Tumor suppressor properties of the small C-terminal domain phosphatases in non-small cell lung cancer.



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