Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

Long Non-Coding RNAs, Cell Cycle, and Human Breast Cancer

The long non-coding RNAs (lncRNAs) constitute an important class of the human transcriptome. The discovery of lncRNAs provided one of many unexpected results of the post-genomic era and uncovered a huge number of previously ignored transcriptional events. In recent years, lncRNAs are known to be linked with human diseases, with particular focus on cancer. Growing evidence has indicated that dysregulation of lncRNAs in breast cancer (BC) is strongly associated with the occurrence, development, and progress. Increasing numbers of lncRNAs have been found to interact with cell cycle progression and tumorigenesis in BC. The lncRNAs can exert their effect as a tumor suppressor or oncogene and regulate tumor development through direct or indirect regulation of cancer-related modulators and signaling pathways. What is more, lncRNAs are excellent candidates for promising therapeutic targets in BC due to the features of high tissue and cell-type specific expression. However, the underlying mechanisms of lncRNAs in BC still remain largely undefined. Here, we concisely summarize and sort out the current understanding of research progress in relationships of the roles for lncRNA in regulating the cell cycle. We also summarize the evidence for aberrant lncRNA expression in BC, and the potential for lncRNA to improve BC therapy is also discussed. Together, lncRNAs can be considered as exciting therapeutic candidates whose expression can be altered to impede BC progression.

Long non-coding RNAs: definitions, functions, challenges and recommendations

Genes specifying long non-coding RNAs (lncRNAs) occupy a large fraction of the genomes of complex organisms. The term 'lncRNAs' encompasses RNA polymerase I (Pol I), Pol II and Pol III transcribed RNAs, and RNAs from processed introns. The various functions of lncRNAs and their many isoforms and interleaved relationships with other genes make lncRNA classification and annotation difficult. Most lncRNAs evolve more rapidly than protein-coding sequences, are cell type specific and regulate many aspects of cell differentiation and development and other physiological processes. Many lncRNAs associate with chromatin-modifying complexes, are transcribed from enhancers and nucleate phase separation of nuclear condensates and domains, indicating an intimate link between lncRNA expression and the spatial control of gene expression during development. lncRNAs also have important roles in the cytoplasm and beyond, including in the regulation of translation, metabolism and signalling. lncRNAs often have a modular structure and are rich in repeats, which are increasingly being shown to be relevant to their function. In this Consensus Statement, we address the definition and nomenclature of lncRNAs and their conservation, expression, phenotypic visibility, structure and functions. We also discuss research challenges and provide recommendations to advance the understanding of the roles of lncRNAs in development, cell biology and disease.

The Emerging Role of LncRNA FENDRR in Multiple Cancers: A Review

Long noncoding RNAs (lncRNAs) are prominent as crucial regulators of tumor establishment and are repeatedly dysregulated in multiple cancers. Therefore, lncRNAs have been identified to play an essential function in carcinogenesis and progression of cancer at genetic and epigenetic levels. FENDRR (fetal-lethal noncoding developmental regulatory RNA) as a LncRNA is a hallmark of various malignancies. FENDRR is crucial for multiple organs' development, such as the lung and heart. The effects of FENDRR under signaling pathways in different cancers have been identified. In addition, it has been verified that FENDRR can affect the development and progression of various cancers. In addition, FENDRR expression has been associated with epigenetic regulation of target genes participating in tumor immunity. Furthermore, FENDRR downregulation was observed in various types of cancers, including colorectal cancer, gastric cancer, pancreatic cancer, cholangiocarcinoma, liver cancer, gallbladder cancer, lung cancer, breast cancer, endometrial cancer, prostate cancer, chronic myeloid leukemia, osteosarcoma, and cutaneous malignant melanoma cells. Here, we review the biological functions and molecular mechanisms of FENDRR in several cancers, and we will discuss its potential as a cancer biomarker and as a probable option for cancer treatment.

The role of lncRNAs/miRNAs/Sirt1 axis in myocardial and cerebral injury

In recent years, researchers have begun to realize the importance of the role of non-coding RNAs in the treatment of cancer and cardiovascular and neurological diseases. LncRNAs and miRNAs are important non-coding RNAs, which regulate gene expression and activate mRNA translation through binding to diverse target sites. Their involvement in the regulation of protein function and the modulation of physiological and pathological conditions continues to be investigated. Sirtuins, especially Sirt1, have a critical function in regulating a variety of physiological processes such as oxidative stress, inflammation, apoptosis, and autophagy. The lncRNAs/miRNAs/Sirt1 axis may be a novel regulatory mechanism, which is involved in the progression and/or prevention of numerous diseases. This review focuses on recent findings on the crosstalk between non-coding RNAs and Sirt1 in myocardial and cerebral injuries and may provide some insight into the development of novel approaches in the treatment of these disorders.Abbreviation: BMECs, brain microvascular endothelial cells; C2dat1, calcium/calmodulin-dependent protein kinase type II subunit delta (CAMK2D)-associated transcript 1; EPCs, endothelial progenitor cells; FOXOs, forkhead transcription factors; GAS5, growth arrest-specific 5; HAECs, human aortic endothelial cells; HAND2-AS1, HAND2 Antisense RNA 1; HIF-1α, hypoxia-inducible factor-1α; ILF3-AS1, interleukin enhancer-binding factor 3-antisense RNA 1; KLF3-AS1, KLF3 antisense RNA 1; LncRNA, long noncoding RNA; LUADT1, Lung Adenocarcinoma Associated Transcript 1; MALAT1, Metastasis-associated lung adenocarcinoma transcript 1; miRNA, microRNA; NEAT1, nuclear enriched abundant transcript 1; NF-κB, nuclear factor kappa B; OIP5-AS1, Opa-interacting protein 5-antisense transcript 1; Sirt1-AS, Sirt1 Antisense RNA; SNHG7, small nucleolar RNA host gene 7; SNHG8, small nucleolar RNA host gene 8; SNHG12, small nucleolar RNA host gene 12; SNHG15, small nucleolar RNA host gene 15; STAT3, signal transducers and activators of transcription 3; TUG1, taurine up-regulated gene 1; VSMCs, vascular smooth muscle cells; XIST, X inactive specific transcript; ZFAS1, ZNFX1 Antisense RNA 1.

Transcriptomics analysis reveals key lncRNAs and genes related to the infection of feline kidney cell line by panleukopenia virus

Feline panleukopenia virus (FPV) can cause a viral disease and is responsible for severe leukopenia, gastroenteritis, and nervous signs with significant economic losses. Biochemically long non-coding RNAs (lncRNAs) can regulate the expression of mRNA in different ways, thereby causing the functional changes in host cells in response to viral infection. However, no attention has been paid until now to investigate the link between FPV pathogenesis and lncRNA. Here, through RNA sequencing, we performed a comprehensive analysis of lncRNA and mRNA in F81 cells after FPV-BJ04 strain infection. Consistent with previous studies, our data showed that lncRNAs have distinct features from mRNA. A total of 291 lncRNAs and 873 mRNAs were differentially expressed in F81 cells after FPV-BJ04 infection. GO and KEGG enrichment analysis showed that the differentially upregulated lncRNAs target genes were mainly involved in the positive regulation of transcription by RNA polymerase II and MAPK signaling pathway. The differentially downregulated lncRNAs target genes were mainly involved in the mRNA splicing and endocytosis. In addition, the differentially expressed immune pathway related genes that are targeted by lncRNA were also screened out to construct a lncRNA-miRNA-mRNA axes as a potential novel biomarkers in regulating the immune response of feline against FPV infection. Our results contribute to understand the basic role of lncRNA in F81 cells during FPV infection and lay the foundation for following research.

Complexities of mammalian transcriptome revealed by targeted RNA enrichment techniques

Studies using highly sensitive targeted RNA enrichment methods have shown that a large portion of the human transcriptome remains to be discovered and that most of the genome is transcribed in a complex, interleaved fashion characterized by a complex web of transcripts emanating from protein coding and noncoding loci. These results resonate with those from single-cell transcriptome profiling endeavors that reveal the existence of multiple novel, cell type-specific transcripts and clearly demonstrate that our understanding of the complexities of the human transcriptome is far from being complete. Here, we review the current status of the targeted RNA enrichment techniques, their application to the discovery of novel cell type-specific transcripts, and their impact on our understanding of the human genome and transcriptome.

LncDLSM: Identification of Long Non-Coding RNAs With Deep Learning-Based Sequence Model

Long non-coding RNAs (LncRNAs) serve a vital role in regulating gene expressions and other biological processes. Differentiation of lncRNAs from protein-coding transcripts helps researchers dig into the mechanism of lncRNA formation and its downstream regulations related to various diseases. Previous works have been proposed to identify lncRNAs, including traditional bio-sequencing and machine learning approaches. Considering the tedious work of biological characteristic-based feature extraction procedures and inevitable artifacts during bio-sequencing processes, those lncRNA detection methods are not always satisfactory. Hence, in this work, we presented lncDLSM, a deep learning-based framework differentiating lncRNA from other protein-coding transcripts without dependencies on prior biological knowledge. lncDLSM is a helpful tool for identifying lncRNAs compared with other biological feature-based machine learning methods and can be applied to other species by transfer learning achieving satisfactory results. Further experiments showed that different species display distinct boundaries among distributions corresponding to the homology and the specificity among species, respectively.

Genetic deficiency of protein inhibitor of activated STAT3 suppresses experimental abdominal aortic aneurysms

Aim

Signal transducer and activator of transcription (STAT) signaling is critical for the pathogenesis of abdominal aortic aneurysms (AAAs). Though protein inhibitor of activated STAT3 (PIAS3) negatively modulates STAT3 activity, but its role in AAA disease remains undefined.

Method

AAAs were induced in PIAS3 deficient (PIAS3−/−) and wild type (PIAS3+/+) male mice via transient intra-aortic elastase infusion. AAAs were assessed by in situ measurements of infrarenal aortic external diameters prior to (day 0) and 14 days after elastase infusion. Characteristic aneurysmal pathologies were evaluated by histopathology.

Results

Fourteen days following elastase infusion, aneurysmal aortic diameter was reduced by an approximately 50% in PIAS3−/− as compared to PIAS3+/+ mice. On histological analyses, PIAS3−/− mice showed less medial elastin degradation (media score: 2.5) and smooth muscle cell loss (media score: 3.0) than those in PIAS3+/+ mice (media score: 4 for both elastin and SMC destruction). Aortic wall leukocyte accumulation including macrophages, CD4+ T cells, CD8+ T cells and B cells as well as mural neovessel formation were significantly reduced in PIAS3−/− as compared to PIAS3+/+ mice. Additionally, PIAS3 deficiency also downregulated the expression levels of matrix metalloproteinases 2 and 9 by 61% and 70%, respectively, in aneurysmal lesion.

Conclusion

PIAS3 deficiency ameliorated experimental AAAs in conjunction with reduced medial elastin degradation and smooth muscle cell depletion, mural leukocyte accumulation and angiogenesis.

Approaches for Modes of Action Study of Long Non-Coding RNAs: From Single Verification to Genome-Wide Determination

Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides (nt) that are not translated into known functional proteins. This broad definition covers a large collection of transcripts with diverse genomic origins, biogenesis, and modes of action. Thus, it is very important to choose appropriate research methodologies when investigating lncRNAs with biological significance. Multiple reviews to date have summarized the mechanisms of lncRNA biogenesis, their localization, their functions in gene regulation at multiple levels, and also their potential applications. However, little has been reviewed on the leading strategies for lncRNA research. Here, we generalize a basic and systemic mind map for lncRNA research and discuss the mechanisms and the application scenarios of ‘up-to-date’ techniques as applied to molecular function studies of lncRNAs. Taking advantage of documented lncRNA research paradigms as examples, we aim to provide an overview of the developing techniques for elucidating lncRNA interactions with genomic DNA, proteins, and other RNAs. In the end, we propose the future direction and potential technological challenges of lncRNA studies, focusing on techniques and applications.

RNA out of the mist

RNA has long been regarded primarily as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences interrupted by large tracts of transcribed but untranslated sequences, and that multicellular organisms also express many long 'intergenic' and antisense noncoding RNAs (lncRNAs). The identification of small RNAs that regulate mRNA translation and half-life did not disturb the prevailing view that animals and plant genomes are full of evolutionary debris and that their development is mainly supervised by transcription factors. Gathering evidence to the contrary involved addressing the low conservation, expression, and genetic visibility of lncRNAs, demonstrating their cell-specific roles in cell and developmental biology, and their association with chromatin-modifying complexes and phase-separated domains. The emerging picture is that most lncRNAs are the products of genetic loci termed 'enhancers', which marshal generic effector proteins to their sites of action to control cell fate decisions during development.

Nuclear and cytoplasmic lncRNAs in root tips of the model legume Medicago truncatula under control and submergence

In this study, we aimed to identify long noncoding RNAs (lncRNAs) in root tips of the model legume Medicago truncatula using previously generated nuclear, total polyA, ribosome-associated polyA, and Riboseq RNA datasets, which might shed light on their localization and potential regulatory roles. RNA-seq data were mapped to the version 5 of the M. truncatula A17 genome and analyzed to identify genome annotated lncRNAs and putative new root tip (NRT) lncRNAs. lncRNAs were classified according to their genomic location relative to chromatin accessible regions, protein-coding genes and transposable elements (TE), finding differences between annotated lncRNAs and NRT lncRNAs, both in their genomic position as well as in the type of TEs in their vicinity. We investigated their response to submergence and found a set of regulated lncRNAs that were preferentially upregulated in the nucleus, some of which were located nearby genes of the conserved submergence upregulated gene families, and chromatin accessible regions suggesting a potential regulatory role. Finally, the accumulation of lncRNAs under submergence was validated by reverse transcription quantitative polymerase chain reaction on nuclear RNA, providing additional evidence of their localization, which could ultimately be required for their function.

Evidence for Existence of Multiple Functional Human Small RNAs Derived from Transcripts of Protein-Coding Genes

The human genome encodes a multitude of different noncoding transcripts that have been traditionally separated on the basis of their lengths into long (>200 nt) or small (<200 nt) noncoding RNAs. The functions, mechanisms of action, and biological relevance of the vast majority of both long and short noncoding transcripts remain unknown. However, according to the functional understanding of the known classes of long and small noncoding RNAs (sncRNAs) that have been shown to play crucial roles in multiple biological processes, it is generally assumed that many unannotated long and small transcripts participate in important cellular functions as well. Nevertheless, direct evidence of functionality is lacking for most noncoding transcripts, especially for sncRNAs that are often dismissed as stable degradation products of longer RNAs. Here, we developed a high-throughput assay to test the functionality of sncRNAs by overexpressing them in human cells. Surprisingly, we found that a significant fraction (>40%) of unannotated sncRNAs appear to have biological relevance. Furthermore, contrary to the expectation, the potentially functional transcripts are not highly abundant and can be derived from protein-coding mRNAs. These results strongly suggest that the small noncoding transcriptome can harbor multiple functional transcripts that warrant future studies.

Full-Length Transcriptome Analysis of the Ichthyotoxic Harmful Alga Heterosigma akashiwo (Raphidophyceae) Using Single-Molecule Real-Time Sequencing

The raphidophyte Heterosigma akashiwo is a harmful algal species. The bloom of this organism has been associated with the massive mortality of fish in many coastal waters. To investigate the molecular mechanism of H. akashiwo blooms, having a reliable reference transcriptome of this species is essential. Therefore, in this study, a full-length transcriptome of H. akashiwo was obtained by single-molecule real-time sequencing. In total, 45.44 Gb subread bases were generated, and 16,668 unigenes were obtained after the sequencing data processing. A total of 8666 (52.00%) unigenes were successfully annotated using seven public databases. Among them, mostly phosphorus and nitrogen metabolism genes were detected. Moreover, there were 300 putative transcription factors, 4392 putative long non-coding RNAs, and 7851 simple sequence repeats predicted. This study provides a valuable reference transcriptome for understanding how H. akashiwo blooms at a molecular level.

Glucose metabolism and lncRNAs in breast cancer: Sworn friend

BACKGROUND

Glucose metabolism disorder is a common feature in cancer. Cancer cells generate much energy through anaerobic glycolysis, which promote the development of tumors. However, long non-coding RNA may play an important role in this process. Our aim is to explore a prognostic risk model based on the glucose metabolism-related lncRNAs which provides clues that lncRNAs predict a clinical outcome through glucose metabolism in breast cancer.

METHODS

1222 RNA-seq were extracted from the TCGA database, and 74 glucose metabolism-related genes were loaded from the GSEA website. Then, 7 glucose metabolism-related lncRNAs risk score model was developed by univariate, Lasso, and multivariate regression analysis. The lncRNA risk model showed that high-risk patients predict a poor clinical outcome with high reliability (P=2.838×10-6). Univariate and multivariate independent prognostic analysis and ROC curve analysis proved that the risk score was an independent prognostic factor in breast cancer with an AUC value of 0.652. Finally, Gene set enrichment analysis showed that cell cycle-related pathways were significantly enriched in a high-risk group.

RESULTS

Our results showed that glucose metabolism-related lncRNAs can affect breast cancer progression. 7 glucose metabolism-related lncRNAs prognostic signature was established to evaluate the OS of patients with breast cancer. PICSAR, LINC00839, AP001505.1, LINC00393 were risk factors and expressed highly in the high-risk group. A Nomogram was made based on this signature to judge patients' living conditions and prognosis.

CONCLUSION

7 glucose metabolism-related lncRNAs risk score model had a high prognostic value in breast cancer. PICSAR, LINC00839, AP001505.1, LINC00393 were risk factors. AP001505.1 expression was increased in most triple-negative breast cancer cells treated with high glucose, which may also take part in breast cancer progression and potential therapeutic targets.

Comprehensive analysis of long noncoding RNAs and lncRNA-mRNA networks in snakehead (Channa argus) response to Nocardia seriolae infection

Evidence has been demonstrated that lncRNAs are involved in a variety of immune responses in vertebrate. It has been demonstrated that immune-related lncRNAs play vital functions in immune regulation against infections in teleost. Nocardia seriolae, as one of the Gram-positive bacteria, can cause chronic systemic granulomatous disease for snakehead (Channa argus). However, how lncRNAs function in the immune regulation process once snakehead was infected with N. seriolae infection has not been studied so far. Accordingly, transcription landscapes of lncRNAs and mRNAs in snakehead were investigated. A total of 1,991 lncRNA were obtained. Totally, we predicted 57,584 co-expression and 16,047 co-location lncRNA-mRNA pairs. To further analyze the potential function of these lncRNAs, GO enrichment analysis and KEGG signal pathways were performed on the target mRNAs of these differently expressed lncRNAs, suggesting that lncRNAs may play essential roles in modulating mRNA expression levels, and subsequently trigger downstream immune signaling pathways to regulate the immune response in snakehead. In addition, 9 DEmRNA and 3 lncRNAs were randomly selected for qRT-PCR analyzed, which confirmed the accuracy of transcriptome data. These results can provide novel knowledge about lncRNAs in immune responses process in snakehead, and can serve as important resources for further investigating the roles of lncRNAs during pathogen infections in teleost.

Recent Advances and Future Potential of Long Non-Coding RNAs in Insects

Over the last decade, long non-coding RNAs (lncRNAs) have witnessed a steep rise in interest amongst the scientific community. Because of their functional significance in several biological processes, i.e., alternative splicing, epigenetics, cell cycle, dosage compensation, and gene expression regulation, lncRNAs have transformed our understanding of RNA's regulatory potential. However, most knowledge concerning lncRNAs comes from mammals, and our understanding of the potential role of lncRNAs amongst insects remains unclear. Technological advances such as RNA-seq have enabled entomologists to profile several hundred lncRNAs in insect species, although few are functionally studied. This article will review experimentally validated lncRNAs from different insects and the lncRNAs identified via bioinformatic tools. Lastly, we will discuss the existing research challenges and the future of lncRNAs in insects.

Identification of a cellular senescence-related-lncRNA (SRlncRNA) signature to predict the overall survival of glioma patients and the tumor immune microenvironment

Background: Gliomas are brain tumors that arise from glial cells, and they are the most common primary intracranial tumors with a poor prognosis. Cellular senescence plays a critical role in cancer, especially in glioma. In this study, we constructed a senescence-related lncRNA (SRlncRNA) signature to assess the prognosis of glioma. Methods: The Cancer Genome Atlas was used to collect SRlncRNA transcriptome profiles and clinical data about glioma. Patients were randomized to training, testing, and whole cohorts. LASSO and Cox regression analyses were employed to construct the SRlncRNA signature, and Kaplan-Meier (K-M) analysis was performed to determine each cohort's survival. Receiver operating characteristic (ROC) curves were applied to verify the accuracy of this signature. Gene set enrichment analysis was used to visualize functional enrichment (GSEA). The CIBERSORT algorithm, ESTIMATE and TIMER databases were utilized to evaluate the differences in the infiltration of 22 types of immune cells and their association with the signature. RT-qPCR and IHC were used to identify the consistency of the signature in tumor tissue. Results: An SRlncRNA signature consisting of six long non-coding RNAs (lncRNAs) was constructed, and patients were divided into high-risk and low-risk groups by the median of their riskscore. The KM analysis showed that the high-risk group had worse overall survival, and the ROC curve confirmed that the riskscore had more accurate predictive power. A multivariate Cox analysis and its scatter plot with clinical characteristics confirmed the riskscore as an independent risk factor for overall survival. GSEA showed that the GO and KEGG pathways were mainly enriched in the immune response to tumor cells, p53 signaling pathway, mTOR signaling pathway, and Wnt signaling pathway. Further validation also yielded significant differences in the risk signature in terms of immune cell infiltration, which may be closely related to prognostic differences, and qRT-PCR and IHC confirmed the consistency of the expression differences in the major lncRNAs with those in the prediction model. Conclusion Our findings indicated that the SRlncRNA signature might be used as a predictive biomarker and that there is a link between it and immune infiltration. This discovery is consistent with the present categorization system and may open new avenues for research and personalized therapy.

Testican-2 Is Associated with Reduced Risk of Incident ESKD

BACKGROUND

Testican-2 was recently identified as a podocyte-derived protein that is released into circulation by the kidneys and is positively correlated with eGFR and eGFR slope. However, whether higher testican-2 levels are associated with lower risk of ESKD is unknown.

METHODS

Aptamer-based proteomics assessed blood testican-2 levels among participants in the African American Study of Kidney Disease and Hypertension (AASK, n =703), the Chronic Renal Insufficiency Cohort (CRIC) study ( n =3196), and the Atherosclerosis Risk in Communities (ARIC) study ( n =4378). We compared baseline characteristics by testican-2 tertile and used Cox proportional hazards models to study the association of testican-2 with incident ESKD.

RESULTS

Higher testican-2 levels were associated with higher measured GFR (mGFR) in AASK, higher eGFR in the CRIC and ARIC studies, and lower albuminuria in all cohorts. Baseline testican-2 levels were significantly associated with incident ESKD in Cox proportional hazards models adjusted for age, sex, and race (model 1) and model 1+mGFR or eGFR+comorbidities (model 2). In model 3 (model 2+proteinuria), the associations between testican-2 (per SD increase) and incident ESKD were AASK (hazard ratio [HR]=0.84 [0.72 to 0.98], P =0.023), CRIC (HR=0.95 [0.89 to 1.02], P =0.14), ARIC (HR=0.54 [0.36 to 0.83], P =0.0044), and meta-analysis (HR=0.92 [0.86 to 0.98], P =0.0073).

CONCLUSIONS

Across three cohorts spanning >8000 individuals, testican-2 is associated with kidney health and prognosis, with higher levels associated with reduced risk of ESKD.

Long non‐coding RNA, a supreme post‐transcriptional immune regulator of bacterial or virus‐driven immune evolution in teleost

The global aquaculture boom, fuelled by a reduction in wild population and detection of novel viruses, has created a demanding market, hence, there is a pressing need to investigate the immune system of fish, further. As the most diverse community of vertebrates and a central contributor to the progressing global aquaculture market, teleost continues to draw vast scientific interest. Recent breakthroughs in multi‐omics technologies have provided a platform to understand the role of long non‐coding RNA (lncRNA) in the host immune system during infection. Emerging evidence shows that teleost lncRNA might have a regulatory role in immune responses, mostly through lncRNA–microRNA (miRNA) sponging. Teleost lncRNA shares a functionally active short sequence complement to target the miRNA which is conserved among the several fish species. Recent report suggests that rhabdovirus exploits a lncRNA in teleost and, to dodge the host immune mechanism and negatively regulate the immune system. This observation reveals the essentiality of lncRNA in pathogen‐driven immunity in teleost. Reports available on the function of teleost lncRNA are still in early stages and experimental verifications are a limiting factor. Unravelling the lncRNA‐mediated immune regulation in fishes could be used against the invading pathogens to strengthen the aquaculture production. This review elaborates on the experimentally identified and functionally characterized lncRNA and its regulatory role in the teleost immune response during infection and pathogen‐driven host immune evolution, which could eventually lead to achieving high standards in aquaculture productivity.

Overview of single-cell RNA sequencing analysis and its application to spermatogenesis research

Background

Single-cell transcriptomics allows parallel analysis of multiple cell types in tissues. Because testes comprise somatic cells and germ cells at various stages of spermatogenesis, single-cell RNA sequencing is a powerful tool for investigating the complex process of spermatogenesis. However, single-cell RNA sequencing analysis needs extensive knowledge of experimental technologies and bioinformatics, making it difficult for many, particularly experimental biologists and clinicians, to use it.

Methods

Aiming to make single-cell RNA sequencing analysis familiar, this review article presents an overview of experimental and computational methods for single-cell RNA sequencing analysis with a history of transcriptomics. In addition, combining the PubMed search and manual curation, this review also provides a summary of recent novel insights into human and mouse spermatogenesis obtained using single-cell RNA sequencing analyses.

Main Findings

Single-cell RNA sequencing identified mesenchymal cells and type II innate lymphoid cells as novel testicular cell types in the adult mouse testes, as well as detailed subtypes of germ cells. This review outlines recent discoveries into germ cell development and subtypes, somatic cell development, and cell-cell interactions.

Conclusion

The findings on spermatogenesis obtained using single-cell RNA sequencing may contribute to a deeper understanding of spermatogenesis and provide new directions for male fertility therapy.

Advances in peptides encoded by non-coding RNAs: A cargo in exosome

The metastasis of malignant tumors determines patient prognosis. This is the main reason for the poor prognosis of patients with cancer and the most challenging aspect of treating malignant tumors. Therefore, it is important to identify early tumor markers and molecules that can predict patient prognosis. However, there are currently no molecular markers with good clinical accuracy and specificity. Many non-coding RNA (ncRNAs)have been identified, which can regulate the process of tumor development at multiple levels. Interestingly, some ncRNAs are translated to produce functional peptides. Exosomes act as signal carriers, are encapsulated in nucleic acids and proteins, and play a messenger role in cell-to-cell communication. Recent studies have identified exosome peptides with potential diagnostic roles. This review aims to provide a theoretical basis for ncRNA-encoded peptides or proteins transported by exosomes and ultimately to provide ideas for further development of new diagnostic and prognostic cancer markers.

New Insights into lncRNAs in Aβ Cascade Hypothesis of Alzheimer's Disease

Alzheimer's disease (AD) is the most common type of dementia, but its pathogenesis is not fully understood, and effective drugs to treat or reverse the progression of the disease are lacking. Long noncoding RNAs (lncRNAs) are abnormally expressed and deregulated in AD and are closely related to the occurrence and development of AD. In addition, the high tissue specificity and spatiotemporal specificity make lncRNAs particularly attractive as diagnostic biomarkers and specific therapeutic targets. Therefore, an in-depth understanding of the regulatory mechanisms of lncRNAs in AD is essential for developing new treatment strategies. In this review, we discuss the unique regulatory functions of lncRNAs in AD, ranging from Aβ production to clearance, with a focus on their interaction with critical molecules. Additionally, we highlight the advantages and challenges of using lncRNAs as biomarkers for diagnosis or therapeutic targets in AD and present future perspectives in clinical practice.

Insights into the role of long non-coding RNAs in DNA methylation mediated transcriptional regulation

DNA methylation is one of the most important epigenetic mechanisms that governing regulation of gene expression, aberrant DNA methylation patterns are strongly associated with human malignancies. Long non-coding RNAs (lncRNAs) have being discovered as a significant regulator on gene expression at the epigenetic level. Emerging evidences have indicated the intricate regulatory effects between lncRNAs and DNA methylation. On one hand, transcription of lncRNAs are controlled by the promoter methylation, which is similar to protein coding genes, on the other hand, lncRNA could interact with enzymes involved in DNA methylation to affect the methylation pattern of downstream genes, thus regulating their expression. In addition, circular RNAs (circRNAs) being an important class of noncoding RNA are also found to participate in this complex regulatory network. In this review, we summarize recent research progress on this crosstalk between lncRNA, circRNA, and DNA methylation as well as their potential functions in complex diseases including cancer. This work reveals a hidden layer for gene transcriptional regulation and enhances our understanding for epigenetics regarding detailed mechanisms on lncRNA regulatory function in human cancers.

Role of lncRNA LIPE-AS1 in adipogenesis

Recent studies have identified long non-coding RNAs (lncRNAs) as potential regulators of adipogenesis. In this study, we have characterized a lncRNA, LIPE-AS1, that spans genes CEACAM1 to LIPE in man with conservation of genomic organization and tissue expression between mouse and man. Tissue-specific expression of isoforms of the murine lncRNA were found in liver and adipose tissue, one of which, designated mLas-V3, overlapped the Lipe gene encoding hormone-sensitive lipase in both mouse and man suggesting that it may have a functional role in adipose tissue. Knock down of expression of mLas-V3 using anti-sense oligos (ASOs) led to a significant decrease in the differentiation of the OP9 pre-adipocyte cell line through the down regulation of the major adipogenic transcription factors Pparg and Cebpa. Knock down of mLas-V3 induced apoptosis during the differentiation of OP9 cells as shown by expression of active caspase-3, a change in the localization of LIP/LAP isoforms of C/EBPβ, and expression of the cellular stress induced factors CHOP, p53, PUMA, and NOXA. We conclude that mLas-V3 may play a role in protecting against stress associated with adipogenesis, and its absence leads to apoptosis.

Scoring model based on the signature of non-m6A-related neoantigen-coding lncRNAs assists in immune microenvironment analysis and TCR-neoantigen pair selection in gliomas

Background

Small peptides encoded by long non-coding RNAs (lncRNAs) have attracted attention for their various functions. Recent studies indicate that these small peptides participate in immune responses and antigen presentation. However, the significance of RNA modifications remains unclear.

Methods

Thirteen non-m6A-related neoantigen-coding lncRNAs were selected for analysis from the TransLnc database. Next, a neoantigen activation score (NAS) model was established based on the characteristics of the lncRNAs. Machine learning was employed to expand the model to two additional RNA-seq and two single-cell sequencing datasets for further validation. The DLpTCR algorithm was used to predict T cell receptor (TCR)-peptide binding probability.

Results

The non-m6A-related NAS model predicted patients’ overall survival outcomes more precisely than the m6A-related NAS model. Furthermore, the non-m6A-related NAS was positively correlated with tumor cells’ evolutionary level, immune infiltration, and antigen presentation. However, high NAS gliomas also showed more PD-L1 expression and high mutation frequencies of T-cell positive regulators. Interestingly, results of intercellular communication analysis suggest that T cell-high neoplastic cell interaction is weaker in both of the NAS groups which might arise from decreased IFNGR1 expression. Moreover, we identified unique TCR-peptide pairs present in all glioma samples based on peptides encoded by the 13 selected lncRNAs. And increased levels of neoantigen-active TCR patterns were found in high NAS gliomas.

Conclusions

Our work suggests that non-m6A-related neoantigen-coding lncRNAs play an essential role in glioma progression and that screened TCR clonotypes might provide potential avenues for chimeric antigen receptor T cell (CAR-T) therapy for gliomas.

Notch-associated lncRNAs profiling circuiting epigenetic modification in colorectal cancer

Background

Colorectal cancer (CRC) is one of the most prevalent digestive cancers, ranking the 2nd cause of cancer-related fatality worldwide. The worldwide burden of CRC is predicted to rise by 60% by 2030. Environmental factors drive, first, inflammation and hence, cancer incidence increase.

Main

The Notch-signaling system is an evolutionarily conserved cascade, has role in the biological normal developmental processes as well as malignancies. Long non-coding RNAs (LncRNAs) have become major contributors in the advancement of cancer by serving as signal pathways regulators. They can control gene expression through post-translational changes, interactions with micro-RNAs or down-stream effector proteins. Recent emerging evidence has emphasized the role of lncRNAs in controlling Notch-signaling activity, regulating development of several cancers including CRC.

Conclusion

Notch-associated lncRNAs might be useful prognostic biomarkers or promising potential therapeutic targets for CRC treatment.

Therefore, here-in we will focus on the role of “Notch-associated lncRNAs in CRC” highlighting “the impact of Notch-associated lncRNAs as player for cancer induction and/or progression.”

Graphical Abstract

Unraveling diverse roles of noncoding RNAs in various human papillomavirus negative cancers

Human papillomavirus (HPV)-negative tumors distinguish from cancers associated with HPV infection. Due to its high rate of lymph node metastasis and difficulty in inchoate discover and diagnosis, the treatment efficacy of HPV-negative cancers is unsatisfactory. Epidemiological evidence suggests that HPV-negative tumor patients have a poor prognosis, and the mortality is higher than that of cancer patients caused by HPV infection. Evidence has demonstrated that noncoding RNAs (ncRNAs) play a crucial role in regulation of physiological and developmental processes. Therefore, dysregulated ncRNAs are involved in the occurrence of diversified diseases, including cancer. In cumulative studies, ncRNAs are concerned with pathogenetic mechanisms of HPV-negative tumors via regulating gene expression and signal transduction. It is important to decipher the functions of ncRNAs in HPV-negative cancers and identify the potential biomarkers, which will bring new treatment strategies for improving outcome of cancer therapy. In this review, we demonstrated the effects of ncRNAs via regulating the development and progression of HPV- negative tumors by directly or indirectly acting on target molecules, which provide a basis for future tumor targeted therapy by targeting ncRNAs for HPV-negative cancers.

LncRNA H19 Promotes Lung Adenocarcinoma Progression via Binding to Mutant p53 R175H

Simple Summary

This research explored the association and interaction between lncRNA H19 and mutant p53 (R175H) in lung adenocarcinoma development and progression. H19 over-expression may induce the elevated expression of mtp53 and interact with mtp53, which prolongs the p53 half-life and promotes transcriptional activity, leading to the progression of lung adenocarcinoma. The simultaneous inhibition of H19 and mtp53 may provide a novel strategy.

Abstract

Background: Accumulating data suggest that long non-coding RNA (lncRNA) H19 and p53are closely related to the prognosis of lung cancer. This study aims to analyze the association and interaction betweenH19 and mutant p53 R175H in lung adenocarcinoma (LAC). Methods: Mutant-type (Mt) p53 R175H was assessed by using RT-PCR in LAC cells and 100 cases of LAC tissue samples for association with H19 expression. Western blot, RNA-pull down, immunoprecipitation-Western blot and animal experiments were used to evaluate the interaction between H19 and mtp53. Results: Mtp53 R175H and H19 were over-expressed in LAC tissues and cells, while H19 over-expression extended the p53 half-life and enhanced transcriptional activity. Combined with anti-p53, ShH19 can significantly inhibit tumor growth in vivo. Conclusions: H19 over-expression may induce the elevated expression of mtp53 and interact with mtp53, leading to LAC progression. In addition, the high expression of mtp53 R175H is associated with poor overall survival inpatients. The simultaneous inhibition of H19 and mtp53 may provide a novel strategy for the effective control of LAC clinically.

High temporal resolution RNA-seq time course data reveals widespread synchronous activation between mammalian lncRNAs and neighboring protein-coding genes

The advent of massively parallel sequencing revealed extensive transcription beyond protein-coding genes, identifying tens of thousands of long noncoding RNAs (lncRNAs). Selected functional examples raised the possibility that lncRNAs, as a class, may maintain broad regulatory roles. Expression of lncRNAs is strongly linked with adjacent protein-coding gene expression, suggesting potential cis-regulatory functions. A more detailed understanding of these regulatory roles may be obtained through careful examination of the precise timing of lncRNA expression relative to adjacent protein-coding genes. Despite the diversity of reported lncRNA regulatory mechanisms, where causal cis-regulatory relationships exist, lncRNA transcription is expected to precede changes in target gene expression. Using a high temporal resolution RNA-seq time course, we profiled the expression dynamics of several thousand lncRNAs and protein-coding genes in synchronized, transitioning human cells. Our findings reveal that lncRNAs are expressed synchronously with adjacent protein-coding genes. Analysis of lipopolysaccharide-activated mouse dendritic cells revealed the same temporal relationship observed in transitioning human cells. Our findings suggest broad-scale cis-regulatory roles for lncRNAs are not common. The strong association between lncRNAs and adjacent genes may instead indicate an origin as transcriptional by-products from active protein-coding gene promoters and enhancers.

The multifaceted actions of the lncRNA H19 in cardiovascular biology and diseases

Cardiovascular diseases are the leading cause of death and debility worldwide. Various molecular mechanisms have been studied to better understand the development and progression of cardiovascular pathologies with hope to eradicate these diseases. With the advancement of the sequencing technology, it is revealed that the majority of our genome is non-coding. A growing body of literature demonstrates the critical role of long non-coding RNAs (lncRNAs) as epigenetic regulators of gene expression. LncRNAs can regulate cellular biological processes through various distinct molecular mechanisms. The abundance of lncRNAs in the cardiovascular system indicates their significance in cardiovascular physiology and pathology. LncRNA H19, in particular, is a highly evolutionarily conserved lncRNA that is enriched in cardiac and vascular tissue, underlining its importance in maintaining homeostasis of the cardiovascular system. In this review, we discuss the versatile function of H19 in various types of cardiovascular diseases. We highlight the current literature on H19 in the cardiovascular system and demonstrate how dysregulation of H19 induces the development of cardiovascular pathophysiology.

Germline genetic biomarkers to stratify patients for personalized radiation treatment

Background

Precision medicine incorporating genetic profiling is becoming a standard of care in medical oncology. However, in the field of radiation oncology there is limited use of genetic profiling and the impact of germline genetic biomarkers on radiosensitivity, radioresistance, or patient outcomes after radiation therapy is poorly understood. In HNSCC, the toxicity associated with treatment can cause delays or early cessation which has been associated with worse outcomes. Identifying potential biomarkers which can help predict toxicity, as well as response to treatment, is of significant interest.

Methods

Patients with HNSCC who received RT and underwent next generation sequencing of somatic tumor samples, transcriptome RNA-seq with matched normal tissue samples were included. Patients were then grouped by propensity towards increased late vs. early toxicity (Group A) and those without (Group B), assessed by CTCAE v5.0. The groups were then analyzed for association of specific germline variants with toxicity and clinical outcomes.

Results

In this study we analyzed 37 patients for correlation between germline variants and toxicity. We observed that TSC2, HLA-A, TET2, GEN1, NCOR2 and other germline variants were significantly associated with long term toxicities. 34 HNSCC patients treated with curative intent were evaluated for clinical outcomes. Group A had significantly improved overall survival as well as improved rates of locoregional recurrence and metastatic disease. Specific variants associated with improved clinical outcomes included TSC2, FANCD2, and PPP1R15A, while the HLA-A and GEN1 variants were not correlated with survival or recurrence. A group of five HLA-DMA/HLA-DMB variants was only found in Group B and was associated with a higher risk of locoregional recurrence.

Conclusions

This study indicates that germline genetic biomarkers may have utility in predicting toxicity and outcomes after radiation therapy and deserve further investigation in precision radiation medicine approaches.

Suppression of Long Noncoding RNA SNHG1 Inhibits the Development of Hypopharyngeal Squamous Cell Carcinoma via Increasing PARP6 Expression

Purpose

This study aimed to explore the function and molecular mechanism of long noncoding RNA Small Nucleolar RNA Host Gene 1 (SNHG1) in the development of hypopharyngeal squamous cell carcinoma (HSCC).

Methods

Human HSCC cell line FaDu was used in this study. Cell viability and apoptosis were detected using CCK-8 assay and flow cytometry, respectively. Cell migration and invasion were measured by Transwell assay. The expression of PARP6, XRCC6, β-catenin, and EMT-related proteins (E-cadherin and N-cadherin) were determined using western blotting. Moreover, the regulatory relationship between SNHG1 and PARP6 was investigated. Furthermore, the effects of the SNHG1/PARP6 axis on tumorigenicity were explored in vivo.

Results

Suppression of SNHG1 suppressed the viability, migration, and invasion but promoted apoptosis of FaDu cells in vitro (P < 0.01). PARP6 is a target of SNHG1, which was upregulated by SNHG1 knockdown in FaDu cells (P < 0.01). SNHG1 suppression and RARP6 overexpression inhibited FaDu cell proliferation, migration, and invasion (P < 0.05). SNHG1 suppression and RARP6 overexpression also inhibited tumorigenicity of HSCC in vivo. Furthermore, the protein expression of E-cadherin was significantly increased and that of N-cadherin, β-catenin, and XRCC6 was dramatically decreased in HSCC after SNHG1 suppression or/and RARP6 overexpression both in vitro and in vivo (P < 0.01).

Conclusions

SNHG1 silencing inhibits HSCC malignant progression via upregulating PARP6. XRCC6/β-catenin/EMT axis may be a possible downstream mechanism of the SNHG1/PARP6 axis in HSCC. SNHG1/PARP6 can be used as a promising target for the treatment of HSCC.

Discovering functional motifs in long noncoding RNAs

Long noncoding RNAs (lncRNAs) are products of pervasive transcription that closely resemble messenger RNAs on the molecular level, yet function through largely unknown modes of action. The current model is that the function of lncRNAs often relies on specific, typically short, conserved elements, connected by linkers in which specific sequences and/or structures are less important. This notion has fueled the development of both computational and experimental methods focused on the discovery of functional elements within lncRNA genes, based on diverse signals such as evolutionary conservation, predicted structural elements, or the ability to rescue loss-of-function phenotypes. In this review, we outline the main challenges that the different methods need to overcome, describe the recently developed approaches, and discuss their respective limitations. This article is categorized under: RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs.

Systematic Functional Annotation Workflow for Insects

Next-generation sequencing has revolutionized entomological study, rendering it possible to analyze the genomes and transcriptomes of non-model insects. However, use of this technology is often limited to obtaining the nucleotide sequences of target or related genes, with many of the acquired sequences remaining unused because other available sequences are not sufficiently annotated. To address this issue, we have developed a functional annotation workflow for transcriptome-sequenced insects to determine transcript descriptions, which represents a significant improvement over the previous method (functional annotation pipeline for insects). The developed workflow attempts to annotate not only the protein sequences obtained from transcriptome analysis but also the ncRNA sequences obtained simultaneously. In addition, the workflow integrates the expression-level information obtained from transcriptome sequencing for application as functional annotation information. Using the workflow, functional annotation was performed on the sequences obtained from transcriptome sequencing of the stick insect (Entoria okinawaensis) and silkworm (Bombyx mori), yielding richer functional annotation information than that obtained in our previous study. The improved workflow allows the more comprehensive exploitation of transcriptome data and is applicable to other insects because the workflow has been openly developed on GitHub.

Murine Falcor/LL35 lncRNA Contributes to Glucose and Lipid Metabolism In Vitro and In Vivo

Glucose and lipid metabolism are crucial functional systems in eukaryotes. A large number of experimental studies both in animal models and humans have shown that long non-coding RNAs (lncRNAs) play an important role in glucose and lipid metabolism. Previously, human lncRNA DEANR1/linc00261 was described as a tumor suppressor that regulates a variety of biological processes such as cell proliferation, apoptosis, glucose metabolism and tumorigenesis. Here we report that murine lncRNA Falcor/LL35, a proposed functional analog of human DEANR1/linc00261, is predominantly expressed in murine normal hepatocytes and downregulated in HCC and after partial hepatectomy. The application of high-throughput approaches such as RNA-seq, LC-MS proteomics, lipidomics and metabolomics analysis allowed changes to be found in the transcriptome, proteome, lipidome and metabolome of hepatocytes after LL35 depletion. We revealed that LL35 is involved in the regulation of glycolysis and lipid biosynthesis in vitro and in vivo. Moreover, LL35 affects Notch and NF-κB signaling pathways in normal hepatocytes. All observed changes result in the decrease in the proliferation and migration of hepatocytes. We demonstrated similar phenotype changes between murine LL35 and human linc00261 depletion in vitro and in vivo that opens the opportunity to translate results for LL35 from a liver murine model to possible functions of human lncRNA linc00261.

Open reading frame dominance indicates protein‐coding potential of RNAs

Recent studies have identified numerous RNAs with both coding and noncoding functions. However, the sequence characteristics that determine this bifunctionality remain largely unknown. In the present study, we develop and test the open reading frame (ORF) dominance score, which we define as the fraction of the longest ORF in the sum of all putative ORF lengths. This score correlates with translation efficiency in coding transcripts and with translation of noncoding RNAs. In bacteria and archaea, coding and noncoding transcripts have narrow distributions of high and low ORF dominance, respectively, whereas those of eukaryotes show relatively broader ORF dominance distributions, with considerable overlap between coding and noncoding transcripts. The extent of overlap positively and negatively correlates with the mutation rate of genomes and the effective population size of species, respectively. Tissue‐specific transcripts show higher ORF dominance than ubiquitously expressed transcripts, and the majority of tissue‐specific transcripts are expressed in mature testes. These data suggest that the decrease in population size and the emergence of testes in eukaryotic organisms allowed for the evolution of potentially bifunctional RNAs.

LncRNA LOC105378097 inhibits cardiac mitophagy in natural ageing mice

BACKGROUND

The development of heart ageing is the main cause of chronic disability, disease and death in the elderly. Ample evidence has established a pivotal role for significantly reduced mitophagy in the ageing heart. However, the underlying mechanisms of mitophagy deficiency in ageing heart are little known. The present study aimed to explore the underlying mechanisms of lncRNA LOC105378097 (Senescence-Mitophagy Associated LncRNA, lncR-SMAL) actions on mitophagy in the setting of heart ageing.

METHODS

The expression of lncR-SMAL was measured in serum from different ages of human and heart from different ages of mice through a quantitative real-time polymerase chain reaction. The effects of lncR-SMAL on heart function of mice were assessed by echocardiography and pressure-volume measurements system. Cardiac senescence was evaluated by hematoxylin-eosin staining, senescence-associated β-galactosidase staining, flow cytometry and western blot analysis of expression of ageing related markes p53 and p21. Cardiomyocyte mitophagy was assessed by western blot, mRFP-GFP-LC3 adenovirus particles transfection and mito-Keima staining. Interaction between lncR-SMAL and Parkin was validated through molecular docking, RNA immunoprecipitation (RIP) and RNA pull-down assay. Ubiquitination assay was performed to explore the molecular mechanism of Parkin inhibition. The effects of lncR-SMAL on mitochondrial function were investigated through electron microscopic examination, JC-1 staining and oxygen consumption rates analysis.

RESULTS

The heart-enriched lncR-SMAL reached the expression crest in the serum of human at an age of 60. Exogenously overexpression of lncRNA SMAL deteriorated cardiac function exactly as natural ageing and inhibited the associated cardiomyocytes mitophagy by depressing Parkin protein level. Improved heart ageing and mitophagy caused by Parkin overexpression were reversed by lncR-SMAL in mice. In contrast, the loss of lncR-SMAL in AC16 cells induced the upregulation of Parkin protein and ameliorated mitophagy and mitochondrial dysfunction, resulting in alleviated cardiac senescence. Besides, we found the interaction between lncR-SMAL and Parkin protein through computational docking analysis, pull-down and RIP assay. This would contribute to the promotive effect of lncR-SMAL on Parkin ubiquitination and decrease Parkin protein stability.

CONCLUSIONS

The present study for the first time demonstrates a heart-enriched lncRNA, SMAL, that inhibits the mitophagy of cardiomyocytes via the downregulation of Parkin protein, which further contributes to heart ageing and cardiac dysfunction in natural ageing mice.

The potential role of eyestalk in the immunity of Litopenaeus vannamei to Vibrio parahaemolyticus infection II. From the perspective of long non-coding RNA

Long non-coding RNAs (lncRNAs) have been linked to immunological modulation. Unfortunately, little is known about the processes of immune control in shrimp. In crustaceans such as Litopenaeus vannamei, a prominent aquaculture species, the X-organ-sinus gland complex (XO-SG) in the eyestalk is an essential neuroendocrine regulatory organ. Eyestalk ablation is commonly employed in aquaculture to accelerate ovarian maturation in shrimp. It does, however, have a negative impact on the shrimps' immunocompetence and causes death. As a result, we used RNA-seq to profile the transcriptomes of L. vannamei hemocytes infected with Vibrio parahaemolyticus after the eyestalk ablation. Following strict transcript screening procedures, 2307 lncRNAs were identified from L. vannamei hemocytes in this study. Pearson correlation analysis was finally used to uncover 535 DElncRNAs and 1566 DEmRNA targets. According to the Venn diagram analysis, 326 non-eyestalk regulatory lncRNAs (NElncRNAs) with a target of 1014 non-eyestalk regulatory genes (NEmRNAs), 47 eyestalk negative regulatory lncRNAs (ENRlncRNAs) with a target of 95 eyestalk negative regulatory genes (ENRmRNAs), and 162 eyestalk positive regulatory lncRNAs (EPRlncRNAs) with a target of 457 eyestalk positive regulatory genes (EPRmRNAs) were screened. The bioinformatics analysis revealed that lncRNAs were associated with Axon regeneration, Rap1 signaling pathway, Thyroid hormone signaling pathway, TGF-beta signaling pathway, and PI3K-Akt signaling pathway, implying that lncRNAs may play a role in the regulation of the neuroendocrine-immune (NEI) system. Furthermore, several lncRNAs targeting HSP70, YWHAZ, FER2, HIF1α, and Notch were discovered and verified by qRT-PCR. These findings showed that regulation of lncRNAs in hemocytes which were controlled by the eyestalk might be one of the impact variables in controlling the differential expression of mRNAs associated with immune response in L. vannamei infected with V. parahaemolyticus.

The role and mechanism of noncoding RNAs in regulation of metabolic reprogramming in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer. Metabolic reprogramming is considered to be an important hallmark of cancer. Emerging studies have demonstrated that noncoding RNAs (ncRNAs) are closely associated with metabolic reprogramming of HCC. NcRNAs can directly regulate the expressions or functions of metabolic enzymes or indirectly regulate the metabolism of HCC cells through some vital signaling pathways. Until now, the mechanisms of HCC development and progression remain largely unclear, and understanding the regulatory mechanism of ncRNAs on metabolic reprogramming of HCC may provide an important basis for breakthrough progress in the treatment of HCC. In this review, we summarize the ncRNAs involved in regulating metabolic reprogramming of HCC. Specifically, the regulatory roles of ncRNAs in glucose, lipid and amino acid metabolism are elaborated. In addition, we discuss the molecular mechanism of ncRNAs in regulation of metabolic reprogramming and possible therapeutic strategies that target the metabolism of cancer cells by modulating the expressions of specific ncRNAs.

Progress in Expression Pattern and Molecular Regulation Mechanism of LncRNA in Bovine Mastitis

Simple Summary

Bovine mastitis is an inflammatory disease of the mammary glands that causes serious harm to cow health and huge economic losses. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate a variety of diseases of humans and animals, especially the immune response and inflammatory disease process. This paper reviews the role of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of lncRNA expression and the molecular regulatory mechanism in bovine mastitis, and looks forward to the research and application prospect of lncRNA in bovine mastitis, intending to provide a reference for scientific researchers to systematically understand this research field.

Abstract

Bovine mastitis is an inflammatory disease caused by pathogenic microbial infection, trauma, or other factors. Its morbidity is high, and it is difficult to cure, causing great harm to the health of cows and the safety of dairy products. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are a class of endogenous non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate the immune response of humans and animals on three levels (transcription, epigenetic modification, and post-transcription), and are widely involved in the pathological process of inflammatory diseases. Over the past few years, extensive findings revealed basic roles of lncRNAs in inflammation, especially bovine mastitis. This paper reviews the expression pattern and mechanism of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of the lncRNA expression pattern and molecular regulatory mechanism in bovine mastitis, analyzes the molecular regulatory network of differentially expressed lncRNAs, and looks forward to the research and application prospect of lncRNA in bovine mastitis, laying a foundation for molecular breeding and the biological therapy of bovine mastitis.

From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo

Genome-wide sequencing has led to the discovery of thousands of long non-coding RNA (lncRNA) loci in the human genome, but evidence of functional significance has remained controversial for many lncRNAs. Genetically engineered model organisms are considered the gold standard for linking genotype to phenotype. Recent advances in CRISPR-Cas genome editing have led to a rapid increase in the use of mouse models to more readily survey lncRNAs for functional significance. Here, we review strategies to investigate the physiological relevance of lncRNA loci by highlighting studies that have used genetic mouse models to reveal key in vivo roles for lncRNAs, from fertility to brain development. We illustrate how an investigative approach, starting with whole-gene deletion followed by transcription termination and/or transgene rescue strategies, can provide definitive evidence for the in vivo function of mammalian lncRNAs.

Short open reading frames (sORFs) and microproteins: an update on their identification and validation measures

A short open reading frame (sORFs) constitutes ≤ 300 bases, encoding a microprotein or sORF-encoded protein (SEP) which comprises ≤ 100 amino acids. Traditionally dismissed by genome annotation pipelines as meaningless noise, sORFs were found to possess coding potential with ribosome profiling (RIBO-Seq), which unveiled sORF-based transcripts at various genome locations. Nonetheless, the existence of corresponding microproteins that are stable and functional was little substantiated by experimental evidence initially. With recent advancements in multi-omics, the identification, validation, and functional characterisation of sORFs and microproteins have become feasible. In this review, we discuss the history and development of an emerging research field of sORFs and microproteins. In particular, we focus on an array of bioinformatics and OMICS approaches used for predicting, sequencing, validating, and characterizing these recently discovered entities. These strategies include RIBO-Seq which detects sORF transcripts via ribosome footprints, and mass spectrometry (MS)-based proteomics for sequencing the resultant microproteins. Subsequently, our discussion extends to the functional characterisation of microproteins by incorporating CRISPR/Cas9 screen and protein–protein interaction (PPI) studies. Our review discusses not only detection methodologies, but we also highlight on the challenges and potential solutions in identifying and validating sORFs and their microproteins. The novelty of this review lies within its validation for the functional role of microproteins, which could contribute towards the future landscape of microproteomics.

Methods to Analyze the Non-Coding RNA Interactome—Recent Advances and Challenges

Most of the human genome is transcribed to generate a multitude of non-coding RNAs. However, while these transcripts have generated an immense amount of scientific interest, their biological function remains a subject of an intense debate. Understanding mechanisms of action of non-coding RNAs is a key to addressing the issue of biological relevance of these transcripts. Based on some well-understood non-coding RNAs that function inside the cell by interacting with other molecules, it is generally believed many other non-coding transcripts could also function in a similar fashion. Therefore, development of methods that can map RNA interactome is the key to understanding functionality of the extensive cellular non-coding transcriptome. Here, we review the vast progress that has been made in the past decade in technologies that can map RNA interactions with different sites in DNA, proteins or other RNA molecules; the general approaches used to validate the existence of novel interactions; and the challenges posed by interpreting the data obtained using the interactome mapping methods.

Regioselectivity of an arachidonate 9S-lipoxygenase from Sphingopyxis macrogoltabida that biosynthesizes 9S,15S- and 11S,17S-dihydroxy fatty acids from C20 and C22 polyunsaturated fatty acids

Lipoxygenases (LOXs) biosynthesize lipid mediators (LMs) as human signaling molecules. Among LMs, specialized pro-resolving mediators (SPMs) are involved in the resolution of inflammation and infection in humans. Here, the putative LOX from the bacterium Sphingopyxis macrogoltabida was identified as arachidonate 9S-LOX. The enzyme catalyzed oxygenation at the n-12 position of C20 and C22 polyunsaturated fatty acids (PUFAs) to form 9S- and 11S-hydroperoxy fatty acids, which were reduced to 9S- and 11S-hydroxy fatty acids (HFAs) by cysteine, respectively, and it catalyzed again oxygenation at the n-6 position of HFAs to form 9S,15S- and 11S,17S-DiHFAs, respectively. The regioselective residues of 9S-LOX were determined as lle395 and Val569 based on the amino acid alignment and homology models. The regioselectivity of the I395F variant was changed from the n-12 position on C20 PUFA to the n-6 position to form 15S-HFAs. This may be due to the reduction of the substrate-binding pocket by replacing the smaller Ile with a larger Phe. The V569W variant had a significantly lower second‑oxygenating activity compared to wild-type 9S-LOX because the insertion of the hydroxyl group of the first‑oxygenating products at the active site was seemed to be hindered by substituting a larger Trp for a smaller Val. The compounds, 11S-hydroxydocosapentaenoic acid, 9S,15S-dihydroxyeicosatetraenoic acid, 9S,15S-dihydroxyeicosapentaenoic acid, 11S,17S-hydroxydocosapentaenoic acid, and 11S,17S-dihydroxydocosahexaenoic acid, were newly identified by polarimeter, LC-MS/MS, and NMR. 11S,17S-DiHFAs as SPM isomers biosynthesized from C22 PUFAs showed anti-inflammatory activities in mouse and human cells. Our study contributes may stimulate physiological studies by providing new LMs.

γδ T cells in artiodactyls: Focus on swine

Vaccination is the most effective medical strategy for disease prevention but there is a need to improve livestock vaccine efficacy. Understanding the structure of the immune system of swine, which are considered a γδ T cell "high" species, and thus, particularly how to engage their γδ T cells for immune responses, may allow for development of vaccine optimization strategies. The propensity of γδ T cells to home to specific tissues, secrete pro-inflammatory and regulatory cytokines, exhibit memory or recall responses and even function as antigen-presenting cells for αβ T cells supports the concept that they have enormous potential for priming by next generation vaccine constructs to contribute to protective immunity. γδ T cells exhibit several innate-like antigen recognition properties including the ability to recognize antigen in the absence of presentation via major histocompatibility complex (MHC) molecules enabling γδ T cells to recognize an array of peptides but also non-peptide antigens in a T cell receptor-dependent manner. γδ T cell subpopulations in ruminants and swine can be distinguished based on differential expression of the hybrid co-receptor and pattern recognition receptors (PRR) known as workshop cluster 1 (WC1). Expression of various PRR and other innate-like immune receptors diversifies the antigen recognition potential of γδ T cells. Finally, γδ T cells in livestock are potent producers of critical master regulator cytokines such as interferon (IFN)-γ and interleukin (IL)-17, whose production orchestrates downstream cytokine and chemokine production by other cells, thereby shaping the immune response as a whole. Our knowledge of the biology, receptor expression and response to infectious diseases by swine γδ T cells is reviewed here.

Decoding Insulin-Like Growth Factor Signaling Pathway From a Non-coding RNAs Perspective: A Step Towards Precision Oncology in Breast Cancer

Breast cancer (BC) is a highly complex and heterogenous disease. Several oncogenic signaling pathways drive BC oncogenic activity, thus hindering scientists to unravel the exact molecular pathogenesis of such multifaceted disease. This highlights the urgent need to find a key regulator that tunes up such intertwined oncogenic drivers to trim the malignant transformation process within the breast tissue. The Insulin-like growth factor (IGF) signaling pathway is a tenacious axis that is heavily intertwined with BC where it modulates the amplitude and activity of vital downstream oncogenic signaling pathways. Yet, the complexity of the pathway and the interactions driven by its different members seem to aggravate its oncogenicity and hinder its target-ability. In this review, the authors shed the light on the stubbornness of the IGF signaling pathway and its potential regulation by non-coding RNAs in different BC subtypes. Nonetheless, this review also spots light on the possible transport systems available for efficient delivery of non-coding RNAs to their respective targets to reach a personalized treatment code for BC patients.

DLX6-AS1: A Long Non-coding RNA With Oncogenic Features

Long non-coding RNAs (lncRNAs) are a heterogeneous group of ncRNAs with characteristic size of more than 200 nucleotides. An increasing number of lncRNAs have been found to be dysregulated in many human diseases particularly cancer. However, their role in carcinogenesis is not precisely understood. DLX6-AS1 is an lncRNAs which has been unveiled to be up-regulated in various number of cancers. In different cell studies, DLX6-AS1 has shown oncogenic role via promoting oncogenic phenotype of cancer cell lines. Increase in tumor cell proliferation, migration, invasion, and EMT while suppressing apoptosis in cancer cells are the effects of DLX6-AS1 in development and progression of cancer. In the majority of cell experiment, mediator miRNAs have been identified which are sponged and negatively regulated by DLX6-AS1, and they in turn regulate expression of a number of transcription factors, eventually affecting signaling pathways involved in carcinogenesis. These pathways form axes through which DLX6-AS1 promotes carcinogenicity of cancer cells. Xenograft animal studies, also have confirmed enhancing effect of DLX6-AS1 on tumor growth and metastasis. Clinical evaluations in cancerous patients have also shown increased expression of DLX6-AS1 in tumor tissues compared to healthy tissues. High DLX6-AS1 expression has shown positive association with advanced clinicopathological features in cancerous patients. Survival analyses have demonstrated correlation between high DLX6-AS1 expression and shorter survival. In cox regression analysis, DLX6-AS1 has been found as an independent prognostic factor for patients with various types of cancer.