Beyond mRNA: The role of non-coding RNAs in normal and aberrant hematopoiesis

The screening, identification, design and clinical application of tumor-specific neoantigens for TCR-T cells

Recent advances in neoantigen research have accelerated the development of tumor immunotherapies, including adoptive cell therapies (ACTs), cancer vaccines and antibody-based therapies, particularly for solid tumors. With the development of next-generation sequencing and bioinformatics technology, the rapid identification and prediction of tumor-specific antigens (TSAs) has become possible. Compared with tumor-associated antigens (TAAs), highly immunogenic TSAs provide new targets for personalized tumor immunotherapy and can be used as prospective indicators for predicting tumor patient survival, prognosis, and immune checkpoint blockade response. Here, the identification and characterization of neoantigens and the clinical application of neoantigen-based TCR-T immunotherapy strategies are summarized, and the current status, inherent challenges, and clinical translational potential of these strategies are discussed.

LncRNA HOXD-AS2 regulates miR-3681-5p/DCP1A axis to promote the progression of non-small cell lung cancer

Background

Non-small cell lung cancer (NSCLC) is the most common malignancy in lung cancer, with a low survival rate and unfavorable prognosis. Dysregulated long non-coding RNAs (lncRNAs) play vital functions in tumor progression. This study intended to probe the expression pattern and function of HOXD-AS2 in NSCLC.

Methods

Quantitative real-time polymerase chain reaction (qRT-PCR) was conducted to analyze the expression of HOXD-AS2, miR-3681-5p, CCR1, mRNA-decapping enzyme 1A (DCP1A), and PPP3R1. Cell viability, migration, and invasion were separately examined via 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide (MTT) and transwell experiments. Luciferase reporter assay was conducted to evaluate the binding of miR-3681-5p with HOXD-AS2 or DCP1A. Protein expression of DCP1A was assessed via Western blot. NSCLC animal models were constructed through injection of H1975 cells transfected with lentivirus (LV)-sh-HOXD-AS2 into nude mice, followed by hematoxylin and eosin (HE) staining and immunohistochemistry (IHC) analysis.

Results

In this study, HOXD-AS2 was upregulated in NSCLC tissues and cells, and high HOXD-AS2 predicted short overall survival (OS). Downregulation of HOXD-AS2 could impair the proliferation, migration, and invasion abilities of H1975 and A549 cells. MiR-3681-5p was shown to bind with HOXD-AS2 and be lowly expressed in NSCLC. Suppression of miR-3681-5p could abolish the inhibitory effect of HOXD-AS2 silencing on proliferation, migration, and invasion. DCP1A was screened as the target of miR-3681-5p and its overexpression could rescue miR-3681-5p upregulation-repressed proliferation, migration, and invasion activities. Moreover, animal experiments affirmed that HOXD-AS2 promoted tumor growth in vivo.

Conclusions

HOXD-AS2 modulates the miR-3681-5p/DCP1A axis to boost the progression of NSCLC, which founds the basis of HOXD-AS2 as a new diagnostic biomarker and molecular target for NSCLC therapy.

The Promising Role of Non-Coding RNAs as Biomarkers and Therapeutic Targets for Leukemia

Early-stage leukemia identification is crucial for effective disease management and leads to an improvement in the survival of leukemia patients. Approaches based on cutting-edge biomarkers with excellent accuracy in body liquids provide patients with the possibility of early diagnosis with high sensitivity and specificity. Non-coding RNAs have recently received a great deal of interest as possible biomarkers in leukemia due to their participation in crucial oncogenic processes such as proliferation, differentiation, invasion, apoptosis, and their availability in body fluids. Recent studies have revealed a strong correlation between leukemia and the deregulated non-coding RNAs. On this basis, these RNAs are also great therapeutic targets. Based on these advantages, we tried to review the role of non-coding RNAs in leukemia. Here, the significance of several non-coding RNA types in leukemia is highlighted, and their potential roles as diagnostic, prognostic, and therapeutic targets are covered.

Long Non-coding RNA RP11-395G23.3 Acts as a Competing Endogenous RNA of miR-124-3p to Regulate ROR1 in Anaplastic Thyroid Carcinoma

Anaplastic thyroid carcinoma (ATC) is one of the most aggressive human malignancies with poor prognosis. However, the underlying mechanisms of ATC remain to be elucidated. Recently, increasing studies have focused on competitive endogenous RNA (ceRNA) to discover valuable biomarkers for the diagnosis of ATC. The present study identified 705 differentially expressed mRNAs and 47 differentially expressed lncRNAs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also conducted. Additionally, an lncRNA/miRNA/mRNA network was constructed which included 1103 regulatory relations. The upregulation of RP11-395G23.3 in ATC cells was confirmed by quantitative reverse transcription polymerase chain reaction (qRT-PCR). In the loss of function assays, results suggested silencing of RP11-395G23.3 inhibited cell proliferation and induced cell apoptosis. Mechanically, RP11-395G23.3 could increase ROR1 via sponging miR-124-3p as a ceRNA. Moreover, ROR1 expression was decreased with the downregulation of RP11-395G23.3, but was rescued by the co-transfection of the miR-124-3p inhibitor in ATC cells. Our research suggested that the RP11-395G23.3/miR-124-3p/ROR1 axis potentially acted as a potential target for the diagnosis of ATC.

The active component of ginseng, ginsenoside Rb1, improves erythropoiesis in models of Diamond-Blackfan anemia by targeting Nemo-like kinase

Nemo-like kinase (NLK) is a member of the mitogen-activated protein kinase family of kinases and shares a highly conserved kinase domain with other mitogen-activated protein kinase family members. The activation of NLK contributes to the pathogenesis of Diamond–Blackfan anemia (DBA), reducing c-myb expression and mechanistic target of rapamycin activity, and is therefore a potential therapeutic target. Unlike other anemias, the hematopoietic effects of DBA are largely restricted to the erythroid lineage. Mutations in ribosomal genes induce ribosomal insufficiency and reduced protein translation, dramatically impacting early erythropoiesis in the bone marrow of patients with DBA. We sought to identify compounds that suppress NLK and increases erythropoiesis in ribosomal insufficiency. We report that the active component of ginseng, ginsenoside Rb1, suppresses NLK expression and improves erythropoiesis in in vitro models of DBA. Ginsenoside Rb1–mediated suppression of NLK occurs through the upregulation of miR-208, which binds to the 3′-UTR of NLK mRNA and targets it for degradation. We also compare ginsenoside Rb1–mediated upregulation of miR-208 with metformin-mediated upregulation of miR-26. We conclude that targeting NLK expression through miRNA binding of the unique 3′-UTR is a viable alternative to the challenges of developing small-molecule inhibitors to target the highly conserved kinase domain of this specific kinase.

Transposable element-derived sequences in vertebrate development

Transposable elements (TEs) are major components of all vertebrate genomes that can cause deleterious insertions and genomic instability. However, depending on the specific genomic context of their insertion site, TE sequences can sometimes get positively selected, leading to what are called "exaptation" events. TE sequence exaptation constitutes an important source of novelties for gene, genome and organism evolution, giving rise to new regulatory sequences, protein-coding exons/genes and non-coding RNAs, which can play various roles beneficial to the host. In this review, we focus on the development of vertebrates, which present many derived traits such as bones, adaptive immunity and a complex brain. We illustrate how TE-derived sequences have given rise to developmental innovations in vertebrates and how they thereby contributed to the evolutionary success of this lineage.

Long noncoding RNA CCDC26 as a modulator of transcriptional switching between fetal and embryonic globins

The CCDC26 gene is considered to encode a functional noncoding RNA associated with acute myeloid leukemia and other cancers. However, investigations into the physiological roles of CCDC26 are rare. Previously, we reported that CCDC26 regulated proliferation and cell death of leukemia cells through KIT, a receptor tyrosine kinase, by using K562 leukemia cells and their derivative CCDC26-knockdown (KD) cells. Here we propose a new role of CCDC26 in the differentiation of erythroid cells. We showed that expression of embryonic (ε- and ζ-) globins was markedly upregulated in CCDC26-KD cells compared with K562 control cells during hemin-induced differentiation. In contrast, expression of fetal-type γ-globin, a major globin expressed in original K562 cells, was decreased. These changes in the expression of globin genes mainly took place at the transcriptional level, with significant suppression of transcription of adult (β-, δ-) globins in CCDC26-KD cells. Re-introduction of exogenous CCDC26 into the CCDC26-KD cells recovered low-level expression of the embryonal globins. These results suggest CCDC26 has a role in switching transcription of globin genes in the differentiation of erythroid cells. The expression profile of the CCDC26-KD cells and control cells suggests FOG-2, a transcriptional modulator, as a candidate for a mediator of the CCDC26-associated regulation. We showed that both embryonic globins were transcriptionally activated in FOG-2-KD K562 cells. The KIT inhibitor ISCK03 suppressed the production of hemoglobin in K562 cells but did not affect transcription of globin genes. To summarize, FOG-2, but not KIT, is responsible for globin transcriptional regulation by CCDC26.

Non-coding RNAs - A primer for the laboratory scientist

Advances in molecular genetics have identified several species of RNA that fail to translate - hence the non-coding RNAs. The two major groups within this class of nucleic acids are microRNAs (miRNA) and long non-coding RNAs (lncRNA). There is growing body of evidence supporting the view that these molecules have regulatory effect on both DNA and RNA. The objective of this brief review is to explain the molecular genetic of these molecules, to summarize their potential as mediators of disease, and to highlight their value as diagnostic markers and as tools in disease management.

WGCNA Co-Expression Network Analysis Reveals ILF3-AS1 Functions as a CeRNA to Regulate PTBP1 Expression by Sponging miR-29a in Gastric Cancer

Gastric cancer (GC) is one of the most common types of human cancers worldwide. However, the detail mechanisms underlying GC progression remained to be investigated. The present study identified 2823 differently expressed mRNAs and 441 differently expressed lncRNAs in GC. WGCNA was conducted to identify highly correlated lncRNAs and mRNAs. Bioinformatics analysis observed that these dysregulated lncRNAs were significantly associated with the regulation of angiogenesis, cell division, cell-cell adhesion, blood vessel development, adaptive immune response, gastric acid secretion, immune response. Co-expression analysis identified ILF3-AS1 was a key lncRNA involved in regulating GC progression. Loss of function assays showed that knockdown of ILF3-AS1 significantly suppressed GC cell proliferation and metastasis. Mechanically, the results indicate that ILF3-AS1 could enhance PTBP3 expression as an miR-29a sponge, thereby promoting the proliferation and metastasis of GC cells. Our work suggests that the ILF3-AS1/miR-29a/PTBP3 axis may be a potential target for the clinical diagnosis and treatment of GC.

Identification of key protein-coding genes and lncRNAs in spontaneous neutrophil apoptosis

Polymorphonuclear leukocytes (PMNs) are the most abundant cells of the innate immune system in humans, and spontaneous PMN apoptosis plays crucial roles in maintaining neutrophil homeostasis and resolving inflammation. However, the detailed mechanisms of spontaneous PMN apoptosis remain to be elucidated. By analysis of the public microarray dataset GSE37416, we identified a total of 3050 mRNAs and 220 long non-coding RNAs (lncRNAs) specifically expressed during PMN apoptosis in a time-dependent manner. By short time-series expression miner (STEM) analysis, Gene Ontology analysis, and lncRNA-mRNA co-expression network analyses, we identified some key molecules specifically related to PMN apoptosis. STEM analysis identified 12 gene profiles with statistically significance, including 2 associated with apoptosis. Protein-protein interaction (PPI) network analysis of the genes from 2 profiles and lncRNA-mRNA co-expression network analysis identified a 12-gene hub (including NFκB1 and BIRC3) associated with apoptosis, as well as 2 highly correlated lncRNAs (THAP9-AS1, and AL021707.6). We experimentally examined the expression profiles of two mRNA (NFκB1 and BIRC3) and two lncRNAs (THAP9-AS1 andAL021707.6) by quantitative real-time polymerase chain reaction to confirm their time-dependent expressions. These data altogether demonstrated that these genes are involved in the regulation of spontaneous neutrophil apoptosis and the corresponding gene products could also serve as potential key regulatory molecules for PMN apoptosis and/or therapeutic targets for over-reactive inflammatory response caused by the abnormality in PMN apoptosis.

Toxicogenomics: A 2020 Vision

Toxicogenomics (TGx) has contributed significantly to toxicology and now has great potential to support moves towards animal-free approaches in regulatory decision making. Here, we discuss in vitro TGx systems and their potential impact on risk assessment. We raise awareness of the rapid advancement of genomics technologies, which generates novel genomics features essential for enhanced risk assessment. We specifically emphasize the importance of reproducibility in utilizing TGx in the regulatory setting. We also highlight the role of machine learning (particularly deep learning) in developing TGx-based predictive models. Lastly, we touch on the topics of how TGx approaches could facilitate adverse outcome pathways (AOP) development and enhance read-across strategies to further regulatory application. Finally, we summarize current efforts to develop TGx for risk assessment and set out remaining challenges.

Long non-coding RNAs in hematological malignancies: translating basic techniques into diagnostic and therapeutic strategies

Recent studies have revealed that non-coding regions comprise the vast majority of the human genome and long non-coding RNAs (lncRNAs) are a diverse class of non-coding RNAs that has been implicated in a variety of biological processes. Abnormal expression of lncRNAs has also been linked to different human diseases including cancers, yet the regulatory mechanisms and functional effects of lncRNAs are still ambiguous, and the molecular details also need to be confirmed. Unlike protein-coding gene, it is much more challenging to unravel the roles of lncRNAs owing to their unique and complex features such as functional diversity and low conservation among species, which greatly hamper their experimental characterization. In this review, we summarize and discuss both conventional and advanced approaches for the identification and functional characterization of lncRNAs related to hematological malignancies. In particular, the utility and advancement of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system as gene-editing tools are envisioned to facilitate the molecular dissection of lncRNAs via different knock-in/out strategies. Besides experimental considerations specific to lncRNAs, the roles of lncRNAs in the pathogenesis and progression of leukemia are also highlighted in the review. We expect that these insights may ultimately lead to clinical applications including development of biomarkers and novel therapeutic approaches targeting lncRNAs.