Epigenetics in ovarian cancer: premise, properties, and perspectives.

Malignant ovarian tumors bear the highest mortality rate among all gynecological cancers. Both late tumor diagnosis and tolerance to available chemical therapy increase patient mortality. Therefore, it is both urgent and important to identify biomarkers facilitating early identification and novel agents preventing recurrence. Accumulating evidence demonstrates that epigenetic aberrations (particularly histone modifications) are crucial in tumor initiation and development. Histone acetylation and methylation are respectively regulated by acetyltransferases-deacetylases and methyltransferases-demethylases, both of which are implicated in ovarian cancer pathogenesis. In this review, we summarize the most recent discoveries pertaining to ovarian cancer development arising from the imbalance of histone acetylation and methylation, and provide insight into novel therapeutic interventions for the treatment of ovarian carcinoma

Preliminary expression profile of cytokines in brain tissue of BALB/c mice with Angiostrongylus cantonensis infection

BACKGROUND: Angiostrongylus cantonensis (A. cantonensis) infection can result in increased risk of eosinophilic meningitis. Accumulation of eosinophils and inflammation can result in the A. cantonensis infection playing an important role in brain tissue injury during this pathological process. However, underlying mechanisms regarding the transcriptomic responses during brain tissue injury caused by A. cantonensis infection are yet to be elucidated. This study is aimed at identifying some genomic and transcriptomic factors influencing the accumulation of eosinophils and inflammation in the mouse brain infected with A. cantonensis. METHODS: An infected mouse model was prepared based on our laboratory experimental process, and then the mouse brain RNA Libraries were constructed for deep Sequencing with Illumina Genome Analyzer. The raw data was processed with a bioinformatics’ pipeline including Refseq genes expression analysis using cufflinks, annotation and classification of RNAs, lncRNA prediction as well as analysis of co-expression network. The analysis of Refseq data provides the measure of the presence and prevalence of transcripts from known and previously unknown genes. RESULTS: This study showed that Cys-Cys (CC) type chemokines such as CCL2, CCL8, CCL1, CCL24, CCL11, CCL7, CCL12 and CCL5 were elevated significantly at the late phase of infection. The up-regulation of CCL2 indicated that the worm of A. cantonensis had migrated into the mouse brain at an early infection phase. CCL2 could be induced in the brain injury during migration and CCL2 might play a major role in the neuropathic pain caused by A. cantonensis infection. The up-regulated expression of IL-4, IL-5, IL-10, and IL-13 showed Th2 cell predominance in immunopathological reactions at late infection phase in response to infection by A. cantonensis. These different cytokines can modulate and inhibit each other and function as a network with the specific potential to drive brain eosinophilic inflammation. The increase of ATF-3 expression at 21 dpi suggested the injury of neuronal cells at late phase of infection. 1217 new potential lncRNA were candidates of interest for further research. CONCLUSIONS: These cytokine networks play an important role in the development of central nervous system inflammation caused by A. cantonensis infection. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13071-015-0939-6) contains supplementary material, which is available to authorized users

LncRNAs: the bridge linking RNA and colorectal cancer.

Long noncoding RNAs (lncRNAs) are transcribed by genomic regions (exceeding 200 nucleotides in length) that do not encode proteins. While the exquisite regulation of lncRNA transcription can provide signals of malignant transformation, lncRNAs control pleiotropic cancer phenotypes through interactions with other cellular molecules including DNA, protein, and RNA. Recent studies have demonstrated that dysregulation of lncRNAs is influential in proliferation, angiogenesis, metastasis, invasion, apoptosis, stemness, and genome instability in colorectal cancer (CRC), with consequent clinical implications. In this review, we explicate the roles of different lncRNAs in CRC, and the potential implications for their clinical application

Analysis of five deep-sequenced trio-genomes of the Peninsular Malaysia Orang Asli and North Borneo populations

BackgroundRecent advances in genomic technologies have facilitated genome-wide investigation of human genetic variations. However, most efforts have focused on the major populations, yet trio genomes of indigenous populations from Southeast Asia have been under-investigated.ResultsWe analyzed the whole-genome deep sequencing data (30x) of five native trios from Peninsular Malaysia and North Borneo, and characterized the genomic variants, including single nucleotide variants (SNVs), small insertions and deletions (indels) and copy number variants (CNVs). We discovered approximately 6.9 million SNVs, 1.2 million indels, and 9000 CNVs in the 15 samples, of which 2.7% SNVs, 2.3% indels and 22% CNVs were novel, implying the insufficient coverage of population diversity in existing databases. We identified a higher proportion of novel variants in the Orang Asli (OA) samples, i.e., the indigenous people from Peninsular Malaysia, than that of the North Bornean (NB) samples, likely due to more complex demographic history and long-time isolation of the OA groups. We used the pedigree information to identify de novo variants and estimated the autosomal mutation rates to be 0.81x10(-8) - 1.33x10(-8), 1.0x10(-9) - 2.9x10(-9), and 0.001 per site per generation for SNVs, indels, and CNVs, respectively. The trio-genomes also allowed for haplotype phasing with high accuracy, which serves as references to the future genomic studies of OA and NB populations. In addition, high-frequency inherited CNVs specific to OA or NB were identified. One example is a 50-kb duplication in DEFA1B detected only in the Negrito trios, implying plausible effects on host defense against the exposure of diverse microbial in tropical rainforest environment of these hunter-gatherers. The CNVs shared between OA and NB groups were much fewer than those specific to each group. Nevertheless, we identified a 142-kb duplication in AMY1A in all the 15 samples, and this gene is associated with the high-starch diet. Moreover, novel insertions shared with archaic hominids were identified in our samples.ConclusionOur study presents a full catalogue of the genome variants of the native Malaysian populations, which is a complement of the genome diversity in Southeast Asians. It implies specific population history of the native inhabitants, and demonstrated the necessity of more genome sequencing efforts on the multi-ethnic native groups of Malaysia and Southeast Asia

Hierarchical TiO2/C nanocomposite monoliths with a robust scaffolding architecture, mesopore-macropore network and TiO2-C heterostructure for high-performance lithium ion batteries.

Engineering hierarchical structures of electrode materials is a powerful strategy for optimizing the electrochemical performance of an anode material for lithium-ion batteries (LIBs). Herein, we report the fabrication of hierarchical TiO2/C nanocomposite monoliths by mediated mineralization and carbonization using bacterial cellulose (BC) as a scaffolding template as well as a carbon source. TiO2/C has a robust scaffolding architecture, a mesopore-macropore network and TiO2-C heterostructure. TiO2/C-500, obtained by calcination at 500 °C in nitrogen, contains an anatase TiO2-C heterostructure with a specific surface area of 66.5 m(2) g(-1). When evaluated as an anode material at 0.5 C, TiO2/C-500 exhibits a high and reversible lithium storage capacity of 188 mA h g(-1), an excellent initial capacity of 283 mA h g(-1), a long cycle life with a 94% coulombic efficiency preserved after 200 cycles, and a very low charge transfer resistance. The superior electrochemical performance of TiO2/C-500 is attributed to the synergistic effect of high electrical conductivity, anatase TiO2-C heterostructure, mesopore-macropore network and robust scaffolding architecture. The current material strategy affords a general approach for the design of complex inorganic nanocomposites with structural stability, and tunable and interconnected hierarchical porosity that may lead to the next generation of electrochemical supercapacitors with high energy efficiency and superior power density.Sincere gratitude goes to funding agencies for financially support: Y. Xu to NNSF China (2117 1067, 21373100), Jilin Provincial Talent Fund (802110000412) and Tang Aoqing Professor Fund of Jilin University (450091105161). T. Hasan to the Royal Academy of Engineering Research Fellowship. B.L. Su to the Thousand Talents Program of China (“Expert of the State” position), Clare Hall Life Membership at the Clare Hall College and the financial support of the Department of Chemistry, University of Cambridge, L.H. Chen and Y. Li to the Department of Education of Hubei Province for “Chutian Scholar” program, NNSF China (21301133), Hubei Natural Science Foundation (2014CFB1 60, 2015CFB428) and the financial support of SRF for ROCS (SEM [2015]311).This is the author accepted manuscript. The final version is available from the Royal Society of Chemistry via https://doi.org/10.1039/C5NR09149

RecAI: Leveraging Large Language Models for Next-Generation Recommender Systems

This paper introduces RecAI, a practical toolkit designed to augment or even revolutionize recommender systems with the advanced capabilities of Large Language Models (LLMs). RecAI provides a suite of tools, including Recommender AI Agent, Recommendation-oriented Language Models, Knowledge Plugin, RecExplainer, and Evaluator, to facilitate the integration of LLMs into recommender systems from multifaceted perspectives. The new generation of recommender systems, empowered by LLMs, are expected to be more versatile, explainable, conversational, and controllable, paving the way for more intelligent and user-centric recommendation experiences. We hope the open-source of RecAI can help accelerate evolution of new advanced recommender systems. The source code of RecAI is available at \url{https://github.com/microsoft/RecAI}.Comment: 4 pages. Webconf 2024 demo trac