Screening and identification of photoresponse factors in kiwifruit (Actinidia arguta) development.

BACKGROUND: Light is essential for kiwifruit development, in which photoresponse factors contributes greatly to the quality formation. 'Light sensitive hypocotyls, also known as light-dependent short hypocotyls' (LSH) gene family can participate in fruit development as photoresponse factor. However, the key LSH gene that determine kiwifruit development remains unclear. This study aim to screen and identify the key gene AaLSH9 in A. arguta. MATERIALS AND METHODS: Genome-wide identification of the LSH gene family was used to analyse LSH genes in kiwifruit. Homologous cloning was used to confirm the sequence of candidate LSH genes. qRT-PCR and cluster analysis of expression pattern were used to screen the key AaLSH9 gene. Subcellular localization of AaLSH9 in tobacco leaves and overexpression of AaLSH9 in Arabidopsis thaliana hy5 mutant plants were used to define the acting place in cell and identify molecular function, respectively. RESULTS: We identified 15 LSH genes, which were divided into two sub-families namely A and B. Domain analysis of A and B showed that they contained different domain organizations, which possibly played key roles in the evolution process. Three LSH genes, AaLSH2, AaLSH9, and AaLSH11, were successfully isolated from Actinidia arguta. The expression pattern and cluster analysis of these three AaLSH genes suggested AaLSH9 might be a key photoresponse gene participating in fruit development in A. arguta. Subcellular localization showed AaLSH9 protein was located in the nucleus. The overexpression of AaLSH9 gene in Arabidopsis thaliana hy5 mutant plants partially complemented the long hypocotyls of hy5 mutant, implying AaLSH9 played a key role as photoresponse factor in cells. In addition, the seed coat color of A. thaliana over-expressing AaLSH9 became lighter than the wide type A.thaliana. Finally, AaCOP1 was confirmed as photoresponse factor to participate in developmental process by stable transgenic A. thaliana. CONCLUSIONS: AaLSH9 can be involved in kiwifruit (A. arguta) development as key photoresponse factor. Our results not only identified the photoresponse factors AaLSH9 and AaCOP1 but also provided insights into their key role in fruit quality improvement in the process of light response.

Enhanced Data Mining and Visualization of Sensory-Graph-Modeled Datasets through Summarization.

The acquisition, processing, mining, and visualization of sensory data for knowledge discovery and decision support has recently been a popular area of research and exploration. Its usefulness is paramount because of its relationship to the continuous involvement in the improvement of healthcare and other related disciplines. As a result of this, a huge amount of data have been collected and analyzed. These data are made available for the research community in various shapes and formats; their representation and study in the form of graphs or networks is also an area of research which many scholars are focused on. However, the large size of such graph datasets poses challenges in data mining and visualization. For example, knowledge discovery from the Bio-Mouse-Gene dataset, which has over 43 thousand nodes and 14.5 million edges, is a non-trivial job. In this regard, summarizing the large graphs provided is a useful alternative. Graph summarization aims to provide the efficient analysis of such complex and large-sized data; hence, it is a beneficial approach. During summarization, all the nodes that have similar structural properties are merged together. In doing so, traditional methods often overlook the importance of personalizing the summary, which would be helpful in highlighting certain targeted nodes. Personalized or context-specific scenarios require a more tailored approach for accurately capturing distinct patterns and trends. Hence, the concept of personalized graph summarization aims to acquire a concise depiction of the graph, emphasizing connections that are closer in proximity to a specific set of given target nodes. In this paper, we present a faster algorithm for the personalized graph summarization (PGS) problem, named IPGS; this has been designed to facilitate enhanced and effective data mining and visualization of datasets from various domains, including biosensors. Our objective is to obtain a similar compression ratio as the one provided by the state-of-the-art PGS algorithm, but in a faster manner. To achieve this, we improve the execution time of the current state-of-the-art approach by using weighted, locality-sensitive hashing, through experiments on eight large publicly available datasets. The experiments demonstrate the effectiveness and scalability of IPGS while providing a similar compression ratio to the state-of-the-art approach. In this way, our research contributes to the study and analysis of sensory datasets through the perspective of graph summarization. We have also presented a detailed study on the Bio-Mouse-Gene dataset, which was conducted to investigate the effectiveness of graph summarization in the domain of biosensors.

Lsh/HELLS is required for B lymphocyte development and immunoglobulin class switch recombination.

Mutation of HELLS (Helicase, Lymphoid-Specific)/Lsh in human DNA causes a severe immunodeficiency syndrome, but the nature of the defect remains unknown. We assessed here the role of Lsh in hematopoiesis using conditional Lsh knockout mice with expression of Mx1 or Vav Cre-recombinase. Bone marrow transplantation studies revealed that Lsh depletion in hematopoietic stem cells severely reduced B cell numbers and impaired B cell development in a hematopoietic cell-autonomous manner. Lsh-deficient mice without bone marrow transplantation exhibited lower Ig levels in vivo compared to controls despite normal peripheral B cell numbers. Purified B lymphocytes proliferated normally but produced less immunoglobulins in response to in vitro stimulation, indicating a reduced capacity to undergo class switch recombination (CSR). Analysis of germline transcripts, examination of double-stranded breaks using biotin-labeling DNA break assay, and End-seq analysis indicated that the initiation of the recombination process was unscathed. In contrast, digestion-circularization PCR analysis and high-throughput sequencing analyses of CSR junctions and a chromosomal break repair assay indicated an impaired ability of the canonical end-joining pathway in Lsh-deficient B cells. Our data suggest a hematopoietic cell-intrinsic role of Lsh in B cell development and in CSR providing a potential target for immunodeficiency therapy.

The Chromatin Remodeler HELLS: A New Regulator in DNA Repair, Genome Maintenance, and Cancer.

Robust, tightly regulated DNA repair is critical to maintaining genome stability and preventing cancer. Eukaryotic DNA is packaged into chromatin, which has a profound, yet incompletely understood, regulatory influence on DNA repair and genome stability. The chromatin remodeler HELLS (helicase, lymphoid specific) has emerged as an important epigenetic regulator of DNA repair, genome stability, and multiple cancer-associated pathways. HELLS belongs to a subfamily of the conserved SNF2 ATP-dependent chromatin-remodeling complexes, which use energy from ATP hydrolysis to alter nucleosome structure and packaging of chromatin during the processes of DNA replication, transcription, and repair. The mouse homologue, LSH (lymphoid-specific helicase), plays an important role in the maintenance of heterochromatin and genome-wide DNA methylation, and is crucial in embryonic development, gametogenesis, and maturation of the immune system. Human HELLS is abundantly expressed in highly proliferating cells of the lymphoid tissue, skin, germ cells, and embryonic stem cells. Mutations in HELLS cause the human immunodeficiency syndrome ICF (Immunodeficiency, Centromeric instability, Facial anomalies). HELLS has been implicated in many types of cancer, including retinoblastoma, colorectal cancer, hepatocellular carcinoma, and glioblastoma. Here, we review and summarize accumulating evidence highlighting important roles for HELLS in DNA repair, genome maintenance, and key pathways relevant to cancer development, progression, and treatment.

Pelvic organ prolapse and uterine preservation: a cohort study (POP-UP study).

BACKGROUND: Abdominal and laparoscopic sacro-colpopexy (LSC) is considered the standard surgical option for the management of a symptomatic apical pelvic organ prolapse (POP). Women who have their uterus, and for whom an LSC is indicated, can have a laparoscopic sacro-hysteropexy (LSH), a laparoscopic supra-cervical hysterectomy and laparoscopic sacro-cervicopexy (LSCH + LSC) or a total laparoscopic hysterectomy and laparoscopic sacro-colpopexy (TLH + LSC). The main aim of this study was to compare clinical and patient reported outcomes of uterine sparing versus concomitant hysterectomy LSC procedures. METHODS: A retrospective analysis of clinical, imaging and patient reported outcomes at baseline, 3 and 12 months after LSH versus either LSCH + LSC or TLH + LSC between January 2015 and January 2019 in a tertiary referral urogynecology center in Pilsen, the Czech Republic. RESULTS: In total, 294 women were included in this analysis (LSH n = 43, LSCH + LSC n = 208 and TLH + LSC n = 43). There were no differences in the incidence of perioperative injuries and complications. There were no statistically significant differences between the concomitant hysterectomy and the uterine sparing groups in any of the operative, clinical or patient reported outcomes except for a significantly lower anterior compartment failure rate (p = 0.017) and higher optimal mesh placement rate at 12 months in women who had concomitant hysterectomy procedures (p = 0.006). CONCLUSION: LSH seems to be associated with higher incidence of anterior compartment failures and suboptimal mesh placement based on postoperative imaging techniques compared to LSC with concomitant hysterectomy.

Arabidopsis LSH8 Positively Regulates ABA Signaling by Changing the Expression Pattern of ABA-Responsive Proteins.

Phytohormone ABA regulates the expression of numerous genes to significantly affect seed dormancy, seed germination and early seedling responses to biotic and abiotic stresses. However, the function of many ABA-responsive genes remains largely unknown. In order to improve the ABA-related signaling network, we conducted a large-scale ABA phenotype screening. LSH, an important transcription factor family, extensively participates in seedling development and floral organogenesis in plants, but whether its family genes are involved in the ABA signaling pathway has not been reported. Here we describe a new function of the transcription factor LSH8 in an ABA signaling pathway. In this study, we found that LSH8 was localized in the nucleus, and the expression level of LSH8 was significantly induced by exogenous ABA at the transcription level and protein level. Meanwhile, seed germination and root length measurements revealed that lsh8 mutant lines were ABA insensitive, whereas LSH8 overexpression lines showed an ABA-hypersensitive phenotype. With further TMT labeling quantitative proteomic analysis, we found that under ABA treatment, ABA-responsive proteins (ARPs) in the lsh8 mutant presented different changing patterns with those in wild-type Col4. Additionally, the number of ARPs contained in the lsh8 mutant was 397, six times the number in wild-type Col4. In addition, qPCR analysis found that under ABA treatment, LSH8 positively mediated the expression of downstream ABA-related genes of ABI3, ABI5, RD29B and RAB18. These results indicate that in Arabidopsis, LSH8 is a novel ABA regulator that could specifically change the expression pattern of APRs to positively mediate ABA responses.

A Fast and Memory-Efficient Spectral Library Search Algorithm Using Locality-Sensitive Hashing.

With the accumulation of MS/MS spectra collected in spectral libraries, the spectral library searching approach emerges as an important approach for peptide identification in proteomics, complementary to the commonly used protein database searching approach, in particular for the proteomic analyses of well-studied model organisms, such as human. Existing spectral library searching algorithms compare a query MS/MS spectrum with each spectrum in the library with matched precursor mass and charge state, which may become computationally intensive with the rapidly growing library size. Here, the software msSLASH, which implements a fast spectral library searching algorithm based on the Locality-Sensitive Hashing (LSH) technique, is presented. The algorithm first converts the library and query spectra into bit-strings using LSH functions, and then computes the similarity between the spectra with highly similar bit-string. Using the spectral library searching of large real-world MS/MS spectra datasets, it is demonstrated that the algorithm significantly reduced the number of spectral comparisons, and as a result, achieved 2-9X speedup in comparison with existing spectral library searching algorithm SpectraST. The spectral searching algorithm is implemented in C/C++, and is ready to be used in proteomic data analyses.

SYMMETRIC PETALS 1 Encodes an ALOG Domain Protein that Controls Floral Organ Internal Asymmetry in Pea (Pisum sativum L.).

In contrast to typical radially symmetrical flowers, zygomorphic flowers, such as those produced by pea (Pisum sativum L.), have bilateral symmetry, manifesting dorsoventral (DV) and organ internal (IN) asymmetry. However, the molecular mechanism controlling IN asymmetry remains largely unclear. Here, we used a comparative mapping approach to clone SYMMETRIC PETALS 1 (SYP1), which encodes a key regulator of floral organ internal asymmetry. Phylogenetic analysis showed that SYP1 is an ortholog of Arabidopsis thaliana LIGHT-DEPENDENT SHORT HYPOCOTYL 3 (LSH3), an ALOG (Arabidopsis LSH1 and Oryza G1) family transcription factor. Genetic analysis and physical interaction assays showed that COCHLEATA (COCH, Arabidopsis BLADE-ON-PETIOLE ortholog), a known regulator of compound leaf and nodule identity in pea, is involved in organ internal asymmetry and interacts with SYP1. COCH and SYP1 had similar expression patterns and COCH and SYP1 target to the nucleus. Furthermore, our results suggested that COCH represses the 26S proteasome-mediated degradation of SYP1 and regulates its abundance. Our study suggested that the COCH-SYP1 module plays a pivotal role in floral organ internal asymmetry development in legumes.

Lymphoid-specific helicase promotes the growth and invasion of hepatocellular carcinoma by transcriptional regulation of centromere protein F expression.

Lymphoid-specific helicase (LSH) is overexpressed in tumor tissues and its overexpression is associated with poor prognosis in several cancers. However, the role and molecular mechanism of LSH in hepatocellular carcinoma (HCC) remains largely unknown. Herein, we report that LSH was overexpressed in tumor tissues of HCC, and overexpression of LSH was associated with poor prognosis from a public HCC database, and validated by clinical samples from our department. Ectopic LSH expression promoted the growth of HCC cells in vivo and in vitro. Mechanistically, LSH overexpression promoted tumor growth by activating transcription of centromere protein F (CENPF). Clinically, overexpression of LSH and/or CENPF correlated with shorter overall survival and higher cumulative recurrence rates of HCC. In conclusion, LSH promotes tumor growth of HCC through transcriptional regulation of CENPF expression. Therefore, LSH may be a novel predictor for prognosis and a potential therapeutic target for HCC.

ConvNet and LSH-Based Visual Localization Using Localized Sequence Matching.

Convolutional Network (ConvNet), with its strong image representation ability, has achieved significant progress in the computer vision and robotic fields. In this paper, we propose a visual localization approach based on place recognition that combines the powerful ConvNet features and localized image sequence matching. The image distance matrix is constructed based on the cosine distance of extracted ConvNet features, and then a sequence search technique is applied on this distance matrix for the final visual recognition. To speed up the computational efficiency, the locality sensitive hashing (LSH) method is applied to achieve real-time performances with minimal accuracy degradation. We present extensive experiments on four real world data sets to evaluate each of the specific challenges in visual recognition. A comprehensive performance comparison of different ConvNet layers (each defining a level of features) considering both appearance and illumination changes is conducted. Compared with the traditional approaches based on hand-crafted features and single image matching, the proposed method shows good performances even in the presence of appearance and illumination changes.

Case report of ovarian torsion mimicking ovarian cancer as an uncommon late complication of laparoscopic supracervical hysterectomy.

Laparoscopic supracervical hysterectomy (LSH) is an example of a partial hysterectomy, performed due to benign gynaecological complaints. Better endoscopic instruments and operational techniques have led to a great reduction in the number of abdominal hysterectomies. It is believed that LSH is a safe and minimally invasive hysterectomy technique. The Cochrane Database meta-analysis proves the benefits of minimally invasive surgery compared with abdominal gynaecological surgery, including decreased pain, surgical-site infections and hospital stay, quicker return to activity, and fewer postoperative adhesions. According to recent publications, the overall complication rate of all hysterectomy methods is about 1-4.5%. Adnexal torsion is a correlated complication. About 3-5% of patients undergoing emergency surgery due to pelvic pain are diagnosed with this condition. It may be the cause of acute abdomen and correlated symptoms such as vomiting, nausea, or severe pain. To the best of our knowledge a case of asymptomatic, delayed ovarian torsion mimicking ovarian tumour has not been reported so far. In the presented case, torsion successfully imitated neoplastic process as both ROMA score and IOTA 'simple rules' indicated a malignancy with high degree of probability. This case demonstrates that, if ovarian tumour is detected in the postoperative period, a torsion of ovarian pedicle should be taken into consideration as it may mimic malignant neoplasm.

Microlaparoscopy in urogynecology: LSH and sacrocervicopexy.

STUDY OBJECTIVE: To determine the feasibility of using only microlaparoscopic (3.5 mm) accessory instruments for performing laparoscopic supracervical hysterectomy (LSH) and sacrocervicopexy with the aid of a transcervically placed cannula for introduction of mesh and needles. DESIGN: Retrospective evaluation of the first five cases of microlaparoscopic LSH with sacrocervicopexy (Canadian Task Force classification III). SETTING: Community teaching hospital affiliated with a major teaching hospital. PATIENTS: Five women with symptomatic uterovaginal prolapse of stage II or higher. INTERVENTIONS: LSH with transcervical morcellation followed by sacrocervicopexy with all 3.5 mm instruments using synthetic mesh with anterior and posterior extensions. MEASUREMENTS AND MAIN RESULTS: Four ports were made in all patients: a 5-mm infraumbilical port for the laparoscope and three 3.5-mm ports (right and left paraumbilical and suprapubic). LSH was performed using a 3-mm bipolar grasping device and reusable monopolar scissors. Resection of the uterus was also performed using monopolar scissors. Transcervical coring through the vagina was performed using a 15-mm serrated cylindrical blade with a central rod placed upward through the cervix, and transcervical morcellation was performed using an electromechanical morcellator. In all patients, sacrocervicopexy was performed successfully using Y-shaped polypropylene mesh, with PTFE sutures on the vagina and the sacral promontory. Reperitonealization over the mesh was performed using a running barbed absorbable suture. There were no intraoperative or postoperative complications in this group of patients. CONCLUSION: LSH and sacrocervicopexy using 3.5-mm accessory ports is a feasible procedure with the use of transcervical morcellation and a transcervical access cannula.

Enhanced photocatalytic activity of hydrozincite-TiO2 nanocomposite by copper for removal of pharmaceutical pollutant mefenamic acid in aqueous solution.

Nanocomposites based on hydrozincite-TiO2 and copper-doped HZ-xCu-TiO2 (x = 0.1; 0.25; 0.35) were synthesized in a single step using the urea method. The samples were characterized by XRD, FTIR, SEM/TEM, and DRS. The study of adsorption capacity and photocatalytic efficiency of these nanocomposites have been tested on a pharmaceutical pollutant, mefenamic acid (MFA). Kinetic study of removal of MFA indicates that this pollutant was adsorbed on the surface of the synthesized phases, according to Langmuir's model. Such adsorption proved to be well adapted in a kinetic pseudo-second-order model with capacity of 13.08 mg/g for HZ-0.25Cu-TiO2. Subsequently, the kinetics of photocatalytic degradation under UV-visible irradiation was studied according to several parameters, which allowed us to optimize our experimental conditions. The nanocomposite HZ-0.25Cu-TiO2 showed significant removal efficiency of MFA. Elimination rate reached 100% after 20 min under UV-vis irradiation, and 77% after 7 h under visible light irradiation. Repeatability tests have shown that this nanocomposite is extremely stable after six photocatalytic cycles. By-products of MFA were detected by LC/MS. These photoproducts was produced by three types of reactions of hydroxylation: cyclization and cleavage of the aromatic ring. MFA underwent complete mineralization after 22 h of irradiation in the presence of the HZ-0.25Cu-TiO2.

The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome.

Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.

Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype.

Microbial organisms play important roles in many aspects of human health and diseases. Encouraged by the numerous studies that show the association between microbiomes and human diseases, computational and machine learning methods have been recently developed to generate and utilize microbiome features for prediction of host phenotypes such as disease versus healthy cancer immunotherapy responder versus nonresponder. We have previously developed a subtractive assembly approach, which focuses on extraction and assembly of differential reads from metagenomic data sets that are likely sampled from differential genomes or genes between two groups of microbiome data sets (e.g., healthy vs. disease). In this article, we further improved our subtractive assembly approach by utilizing groups of k-mers with similar abundance profiles across multiple samples. We implemented a locality-sensitive hashing (LSH)-enabled approach (called kmerLSHSA) to group billions of k-mers into k-mer coabundance groups (kCAGs), which were subsequently used for the retrieval of differential kCAGs for subtractive assembly. Testing of the kmerLSHSA approach on simulated data sets and real microbiome data sets showed that, compared with the conventional approach that utilizes all genes, our approach can quickly identify differential genes that can be used for building promising predictive models for microbiome-based host phenotype prediction. We also discussed other potential applications of LSH-enabled clustering of k-mers according to their abundance profiles across multiple microbiome samples.

Glycyrrhizin and its derivatives promote hepatic differentiation via sweet receptor, Wnt, and Notch signaling.

The acute liver disease is involved in aberrant release of high-mobility group box 1 (HMGB1). Glycyrrhizin (GL), a traditional Chinese medicine for liver disease, binds to HMGB1, thereby inhibits tissue injury. However the mode of action of GL for chronic liver disease remains unclear. We investigated the effects of glycyrrhizin (GL) and its derivatives on liver differentiation using human iPS cells by using a flow cytometric analysis. GL promoted hepatic differentiation at the hepatoblast formation stage. The GL derivatives, 3-O-mono-glucuronyl 18ß-glycyrrhetinic acid (Mono) and 3-O-[glucosyl (1 â†’ 2)-glucuronyl] 18ß-glycyrrhetinic acid increased AFP+ cell counts and albumin+ cell counts. Glucuronate conjugation seemed to be a requirement for hepatic differentiation. Mono exhibited the most significant hepatic differentiation effect. We evaluated the effects of (±)-2-(2,4-dichlorophenoxy) propionic acid (DP), a T1R3 antagonist, and sucralose, a T1R3 agonist, on hepatic differentiation, and found that DP suppressed Mono-induced hepatic differentiation, while sucralose promoted hepatic differentiation. Thus, GL promoted hepatic differentiation via T1R3 signaling. In addition, Mono increased ß-catenin+ cell count and decreased Hes5+ cell count suggesting the involvement of Wnt and Notch signaling in GL-induced hepatic differentiation. In conclusion, GL exerted a hepatic differentiation effect via sweet receptor (T1R3), canonical Wnt, and Notch signaling.

PRDM9 activity depends on HELLS and promotes local 5-hydroxymethylcytosine enrichment.

Meiotic recombination starts with the formation of DNA double-strand breaks (DSBs) at specific genomic locations that correspond to PRDM9-binding sites. The molecular steps occurring from PRDM9 binding to DSB formation are unknown. Using proteomic approaches to find PRDM9 partners, we identified HELLS, a member of the SNF2-like family of chromatin remodelers. Upon functional analyses during mouse male meiosis, we demonstrated that HELLS is required for PRDM9 binding and DSB activity at PRDM9 sites. However, HELLS is not required for DSB activity at PRDM9-independent sites. HELLS is also essential for 5-hydroxymethylcytosine (5hmC) enrichment at PRDM9 sites. Analyses of 5hmC in mice deficient for SPO11, which catalyzes DSB formation, and in PRDM9 methyltransferase deficient mice reveal that 5hmC is triggered at DSB-prone sites upon PRDM9 binding and histone modification, but independent of DSB activity. These findings highlight the complex regulation of the chromatin and epigenetic environments at PRDM9-specified hotspots.

LSH interacts with and stabilizes GINS4 transcript that promotes tumourigenesis in non-small cell lung cancer.

BACKGROUND: Elucidating mechanisms in oncogenes and epigenetic modifiers are needed to gain insights into the etiology and treatment of cancer, regulation of oncogene by chromatin modifiers at post-transcriptional level is critical and remains unclear. We have investigated the role of GINS4 in NSCLC. METHODS: The expression of chromatin modifier lymphoid-specific helicase (LSH) and GINS4 was assessed in tumor and normal tissue from 79 patients with NSCLC with clinical characteristics. HBE, A549, H358, and H522, PC9, 95C and 95D were cultured after overexpression or silencing of GIAT4RA. Cell proliferation assay, cell migration and invasion assays, plate colony formation assay, immunofluorescence assay, Operetta® high-content screening and analysis, Western blot analysis and Co-Immunoprecipitation (Co-IP) assay, RNA immunoprecipitation assay and tumor growth assay was used to address the potential interplay of between GINS4 and LSH, and the functional of GINS4. RESULTS: GINS4 is highly expressed in lung cancer cells and tissues, and GINS4 expression is not association with clinical risk factors, but linked with clinical stage and lymphatic metastasis status. Higher expression of GINS4 poorly linked with overall survival in lung adenocarcinomas. Furthermore, GINS4 promoted many characteristics of tumorigenesis including cell growth, clonal formation, migration and invasion, epithelial-mesenchymal transition, tumor sphere and tumor growth in vivo. Interestingly, our results demonstrated that LSH increases GINS4 expression through binding to 3'UTR region of GINS4 and stabilizing its mRNA levels. Finally, LSH overexpression rescues GINS4 knockdown-induced features. CONCLUSIONS: GINS4 facilitates lung cancer progression by promoting key characteristics of tumor potential, and LSH epigenetically interacts with and stabilizes GINS4 transcripts.

The chromatin remodeling protein Lsh alters nucleosome occupancy at putative enhancers and modulates binding of lineage specific transcription factors.

Dynamic regulation of chromatin accessibility is a key feature of cellular differentiation during embryogenesis, but the precise factors that control access to chromatin remain largely unknown. Lsh/HELLS is critical for normal development and mutations of Lsh in human cause the ICF (Immune deficiency, Centromeric instability, Facial anomalies) syndrome, a severe immune disorder with multiple organ deficiencies. We report here that Lsh, previously known to regulate DNA methylation level, has a genome wide chromatin remodeling function. Using micrococcal nuclease (MNase)-seq analysis, we demonstrate that Lsh protects MNase accessibility at transcriptional regulatory regions characterized by DNase I hypersensitivity and certain histone 3 (H3) tail modifications associated with enhancers. Using an auxin-inducible degron system, allowing proteolytical degradation of Lsh, we show that Lsh mediated changes in nucleosome occupancy are independent of DNA methylation level and are characterized by reduced H3 occupancy. While Lsh mediated nucleosome occupancy prevents binding sites for transcription factors in wild type cells, depletion of Lsh leads to an increase in binding of ectopically expressed tissue specific transcription factors to their respective binding sites. Our data suggests that Lsh mediated chromatin remodeling can modulate nucleosome positioning at a subset of putative enhancers contributing to the preservation of cellular identity through regulation of accessibility.

DNA methylation modifier LSH inhibits p53 ubiquitination and transactivates p53 to promote lipid metabolism.

BACKGROUND: The stability of p53 is mainly controlled by ubiquitin-dependent degradation, which is triggered by the E3 ubiquitin ligase MDM2. The chromatin modifier lymphoid-specific helicase (LSH) is essential for DNA methylation and cancer progression as a transcriptional repressor. The potential interplay between chromatin modifiers and transcription factors remains largely unknown. RESULTS: Here, we present data suggesting that LSH regulates p53 in cis through two pathways: prevention proteasomal degradation through its deubiquitination, which is achieved by reducing the lysine 11-linked, lysine 48-linked polyubiquitin chains (K11 and K48) on p53; and revival of the transcriptional activity of p53 by forming a complex with PKM2 (pyruvate kinase 2). Furthermore, we confirmed that the LSH-PKM2 interaction occurred at the intersubunit interface region of the PKM2 C-terminal region and the coiled-coil domains (CC) and ATP-binding domains of LSH, and this interaction regulated p53-mediated transactivation in cis in lipid metabolism, especially lipid catabolism. CONCLUSION: These findings suggest that LSH is a novel regulator of p53 through the proteasomal pathway, thereby providing an alternative mechanism of p53 involvement in lipid metabolism in cancer.