Identification of a long non-coding RNA regulator of liver carcinoma cell survival

ABSTRACTGenomic studies have significantly improved our understanding of hepatocellular carcinoma (HCC) biology and have led to the discovery of multiple protein-coding genes driving hepatocarcinogenesis. In addition, these studies have identified thousands of new non-coding transcripts deregulated in HCC. We hypothesize that some of these transcripts may be involved in disease progression. Long non-coding RNAs are a large class of non-coding transcripts which participate in the regulation of virtually all cellular functions. However, a majority of lncRNAs remain dramatically understudied. Here, we applied a pooled shRNA-based screen to identify lncRNAs essential for HCC cell survival. We validated our screening results using RNAi, CRISPRi, and antisense oligonucleotides. We found a lncRNA, termed ASTILCS, that is critical for HCC cell growth and is overexpressed in tumors from HCC patients. We demonstrated that HCC cell death upon ASTILCS knockdown is associated with apoptosis induction and downregulation of a neighboring gene, Protein Tyrosine Kinase 2 (PTK2), a crucial protein for HCC cell survival. Taken together, our study describes a new, non-coding RNA regulator of HCC.

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Identification of a long non-coding RNA regulator of liver carcinoma cell survival

Cell Death and Disease ◽

10.1038/s41419-021-03453-w ◽

2021 ◽

Vol 12 (2) ◽

Author(s):

Yulia Rybakova ◽

John T. Gonzalez ◽

Roman Bogorad ◽

Vikash P. Chauhan ◽

Yize L. Dong ◽

...

Keyword(s):

Cell Survival ◽

Protein Tyrosine Kinase ◽

Liver Carcinoma ◽

Cellular Functions ◽

Neighboring Gene ◽

Protein Coding ◽

Tyrosine Kinase 2 ◽

Non Coding Rna ◽

Multiple Protein ◽

Genomic Studies

AbstractGenomic studies have significantly improved our understanding of hepatocellular carcinoma (HCC) biology and have led to the discovery of multiple protein-coding genes driving hepatocarcinogenesis. In addition, these studies have identified thousands of new non-coding transcripts deregulated in HCC. We hypothesize that some of these transcripts may be involved in disease progression. Long non-coding RNAs are a large class of non-coding transcripts which participate in the regulation of virtually all cellular functions. However, a majority of lncRNAs remain dramatically understudied. Here, we applied a pooled shRNA-based screen to identify lncRNAs essential for HCC cell survival. We validated our screening results using RNAi, CRISPRi, and antisense oligonucleotides. We found a lncRNA, termed ASTILCS, that is critical for HCC cell growth and is overexpressed in tumors from HCC patients. We demonstrated that HCC cell death upon ASTILCS knockdown is associated with apoptosis induction and downregulation of a neighboring gene, protein tyrosine kinase 2 (PTK2), a crucial protein for HCC cell survival. Taken together, our study describes a new, non-coding RNA regulator of HCC.

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Dosage-sensitivity of human transcription factor genes

10.1101/528554 ◽

2019 ◽

Cited By ~ 1

Author(s):

Zhihua Ni ◽

Xiao-Yu Zhou ◽

Sidra Aslam ◽

Deng-Ke Niu

Keyword(s):

Transcription Factor ◽

Copy Number ◽

Large Scale ◽

Gene Dosage ◽

Dependent Manner ◽

Cellular Functions ◽

Protein Coding ◽

Genomic Study ◽

Genomic Studies ◽

Dosage Sensitivity

AbstractChanges in the copy number of protein-coding genes would lead to detrimental effects if the consequent changes in protein concentration disrupt essential cellular functions. Large-scale genomic studies have identified thousands of dosage-sensitive genes in human genome. We are interested in the dosage-sensitivity of transcription factor (TF) genes whose products are essential for the growth, division and differentiation of cells by regulating the expression of the genetic information encoded in the genome. We first surveyed the enrichment of human TF genes in four recently curated datasets of dosage-sensitive genes, including the haploinsufficient genes identified by a large-scale genomic study, the haploinsufficient genes predicted by a machine learning approach, the genes with conserved copy number across mammals, and the ohnologs. Then we selected the dosage-sensitive genes that are present in all the four dataset and regarded them as the most reliable dosage-sensitive genes, and the genes that are absent from any one of the four datasets as the most reliable dosage-insensitive genes, and surveyed the enrichments of TFs genes in these two datasets. A large number of TF genes were found to be dosage-insensitive, which is beyond the expectation based on the role of TFs. In spite of this, the likeness of TF genes to be dosage-sensitive were supported by five datasets, with the conserved-copy-number genes as the exception. The nuclear receptors are the only one family of TFs whose dosage-sensitivity was consistently supported by all the six datasets. In addition, we found that TF families with very few members are also more likely to be dosage-sensitive while the largest TF family, C2H2-ZF, are most likely dosage-insensitive. The most extensively studied TFs, p53, are not special in dosage-sensitivity. They are significantly enriched in only three datasets. We also confirmed that dosage-sensitive genes generally have long coding sequences, high expression levels and experienced stronger selective pressure. Our results indicate some TFs function in a dose-dependent manner while some other not. Gene dosage changes in some TF families like nuclear receptor would result in disease phenotypes while the effects of such changes in some TFs like C2H2-ZF would be mild.

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Long non-coding RNA LINC00665 promotes gemcitabine resistance of Cholangiocarcinoma cells via regulating EMT and stemness properties through miR-424-5p/BCL9L axis

Cell Death and Disease ◽

10.1038/s41419-020-03346-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Min Lu ◽

Xinglei Qin ◽

Yajun Zhou ◽

Gang Li ◽

Zhaoyang Liu ◽

...

Keyword(s):

Acquired Resistance ◽

Transcriptional Regulators ◽

First Line ◽

Protein Coding ◽

Gemcitabine Resistance ◽

Non Coding Rna ◽

Sphere Formation ◽

Long Non Coding Rna ◽

Line Chemotherapy

AbstractGemcitabine is the first-line chemotherapy drug for cholangiocarcinoma (CCA), but acquired resistance has been frequently observed in CCA patients. To search for potential long noncoding RNAs (lncRNAs) involved in gemcitabine resistance, two gemcitabine resistant CCA cell lines were established and dysregulated lncRNAs were identified by lncRNA microarray. Long intergenic non-protein coding RNA 665 (LINC00665) were found to rank the top 10 upregulated lncRNAs in our study, and high LINC00665 expression was closely associated with poor prognosis and chemoresistance of CCA patients. Silencing LINC00665 in gemcitabine resistant CCA cells impaired gemcitabine tolerance, while enforced LINC00665 expression increased gemcitabine resistance of sensitive CCA cells. The gemcitabine resistant CCA cells showed increased EMT and stemness properties, and silencing LINC00665 suppressed sphere formation, migration, invasion and expression of EMT and stemness markers. In addition, Wnt/β-Catenin signaling was activated in gemcitabine resistant CCA cells, but LINC00665 knockdown suppressed Wnt/β-Catenin activation. B-cell CLL/lymphoma 9-like (BCL9L), the nucleus transcriptional regulators of Wnt/β-Catenin signaling, plays a key role in the nucleus translocation of β-Catenin and promotes β-Catenin-dependent transcription. In our study, we found that LINC00665 regulated BCL9L expression by acting as a molecular sponge for miR-424-5p. Moreover, silencing BCL9L or miR-424-5p overexpression suppressed gemcitabine resistance, EMT, stemness and Wnt/β-Catenin activation in resistant CCA cells. In conclusion, our results disclosed the important role of LINC00665 in gemcitabine resistance of CCA cells, and provided a new biomarker or therapeutic target for CCA treament.

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Identification of novel heat shock-induced long non-coding RNA in human cells

The Journal of Biochemistry ◽

10.1093/jb/mvaa126 ◽

2020 ◽

Author(s):

Rena Onoguchi-Mizutani ◽

Yoshihiro Kishi ◽

Yoko Ogura ◽

Yuuki Nishimura ◽

Naoto Imamachi ◽

...

Keyword(s):

Heat Shock ◽

Heat Shock Response ◽

A549 Cells ◽

Heat Shock Factor 1 ◽

Protein Coding ◽

Heat Shock Stress ◽

Non Coding Rna ◽

Shock Response ◽

Inducible Protein ◽

Inducible Genes

Abstract The heat-shock response is a crucial system for survival of organisms under heat stress. During heat-shock stress, gene expression is globally suppressed, but expression of some genes, such as chaperone genes, is selectively promoted. These selectively activated genes have critical roles in the heat-shock response, so it is necessary to discover heat-inducible genes to reveal the overall heat-shock response picture. The expression profiling of heat-inducible protein-coding genes has been well-studied, but that of non-coding genes remains unclear in mammalian systems. Here, we used RNA-seq analysis of heat shock-treated A549 cells to identify seven novel long non-coding RNAs that responded to heat shock. We focussed on CTD-2377D24.6 RNA, which is most significantly induced by heat shock, and found that the promoter region of CTD-2377D24.6 contains the binding site for transcription factor HSF1 (heat shock factor 1), which plays a central role in the heat-shock response. We confirmed that HSF1 knockdown cancelled the induction of CTD-2377D24.6 RNA upon heat shock. These results suggest that CTD-2377D24.6 RNA is a novel heat shock-inducible transcript that is transcribed by HSF1.

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Alu RNA Modulates the Expression of Cell Cycle Genes in Human Fibroblasts

International Journal of Molecular Sciences ◽

10.3390/ijms20133315 ◽

2019 ◽

Vol 20 (13) ◽

pp. 3315 ◽

Cited By ~ 3

Author(s):

Simona Cantarella ◽

Davide Carnevali ◽

Marco Morselli ◽

Anastasia Conti ◽

Matteo Pellegrini ◽

...

Keyword(s):

Cell Cycle ◽

Cell Cycle Progression ◽

Human Fibroblasts ◽

Rna Polymerase Iii ◽

Protein Coding ◽

Non Coding Rna ◽

Genome Wide ◽

Hela Cell Lines ◽

Significant Enrichment ◽

Alu Rna

Alu retroelements, whose retrotransposition requires prior transcription by RNA polymerase III to generate Alu RNAs, represent the most numerous non-coding RNA (ncRNA) gene family in the human genome. Alu transcription is generally kept to extremely low levels by tight epigenetic silencing, but it has been reported to increase under different types of cell perturbation, such as viral infection and cancer. Alu RNAs, being able to act as gene expression modulators, may be directly involved in the mechanisms determining cellular behavior in such perturbed states. To directly address the regulatory potential of Alu RNAs, we generated IMR90 fibroblasts and HeLa cell lines stably overexpressing two slightly different Alu RNAs, and analyzed genome-wide the expression changes of protein-coding genes through RNA-sequencing. Among the genes that were upregulated or downregulated in response to Alu overexpression in IMR90, but not in HeLa cells, we found a highly significant enrichment of pathways involved in cell cycle progression and mitotic entry. Accordingly, Alu overexpression was found to promote transition from G1 to S phase, as revealed by flow cytometry. Therefore, increased Alu RNA may contribute to sustained cell proliferation, which is an important factor of cancer development and progression.

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Commuting to Work: Nucleolar Long Non-Coding RNA Control Ribosome Biogenesis from Near and Far

Non-Coding RNA ◽

10.3390/ncrna7030042 ◽

2021 ◽

Vol 7 (3) ◽

pp. 42

Author(s):

Victoria Mamontova ◽

Barbara Trifault ◽

Lea Boten ◽

Kaspar Burger

Keyword(s):

Gene Expression ◽

Rna Polymerase Ii ◽

Ribosome Biogenesis ◽

Intergenic Spacer ◽

Cellular Growth ◽

Rrna Synthesis ◽

Protein Coding ◽

Non Coding Rna ◽

And Function ◽

In Cis

Gene expression is an essential process for cellular growth, proliferation, and differentiation. The transcription of protein-coding genes and non-coding loci depends on RNA polymerases. Interestingly, numerous loci encode long non-coding (lnc)RNA transcripts that are transcribed by RNA polymerase II (RNAPII) and fine-tune the RNA metabolism. The nucleolus is a prime example of how different lncRNA species concomitantly regulate gene expression by facilitating the production and processing of ribosomal (r)RNA for ribosome biogenesis. Here, we summarise the current findings on how RNAPII influences nucleolar structure and function. We describe how RNAPII-dependent lncRNA can both promote nucleolar integrity and inhibit ribosomal (r)RNA synthesis by modulating the availability of rRNA synthesis factors in trans. Surprisingly, some lncRNA transcripts can directly originate from nucleolar loci and function in cis. The nucleolar intergenic spacer (IGS), for example, encodes nucleolar transcripts that counteract spurious rRNA synthesis in unperturbed cells. In response to DNA damage, RNAPII-dependent lncRNA originates directly at broken ribosomal (r)DNA loci and is processed into small ncRNA, possibly to modulate DNA repair. Thus, lncRNA-mediated regulation of nucleolar biology occurs by several modes of action and is more direct than anticipated, pointing to an intimate crosstalk of RNA metabolic events.

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Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia

International Journal of Molecular Sciences ◽

10.3390/ijms22052683 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2683

Author(s):

Princess D. Rodriguez ◽

Hana Paculova ◽

Sophie Kogut ◽

Jessica Heath ◽

Hilde Schjerven ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

B Cell ◽

Molecular Mechanisms ◽

Lymphoblastic Leukemia ◽

Transcriptome Profiling ◽

Rna Seq ◽

Protein Coding ◽

Non Coding Rna ◽

Technological Developments ◽

Cell Acute Lymphoblastic Leukemia

Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.

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Screening and survival analysis of melanoma immunodrug response-related genes and the function of magnetic nanoparticles in gene extraction

Materials Express ◽

10.1166/mex.2021.2037 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1306-1312

Author(s):

Li Song ◽

Ningchao Du ◽

Haitao Luo ◽

Furong Li

Keyword(s):

Survival Analysis ◽

Magnetic Nanoparticles ◽

Drug Response ◽

High Throughput Sequencing ◽

Cox Proportional Hazards ◽

Sequencing Data ◽

Protein Coding ◽

Non Coding Rna ◽

Long Non Coding Rna ◽

Rna Genes

This study aimed to identify the association of protein coding and long non coding RNA genes with immunotherapy response in melanoma. Based on RNA sequencing data of melanoma specimens, the expression levels of protein coding and long non coding RNA genes were calculated using the Kallisto RNA-seq quantification method, and differently expressed genes were detected using the DESeq2 method. Cox proportional hazards regression was used to evaluate the effects of gene expression on survival. According to the clinical data of 14 patients with drug response and 11 patients without drug response, 18 protein coding genes and 14 long non coding RNAs showed differential expressions (multiple of difference > 2 and P < 0.01 after correction), among which the coding genes of differential expression were significantly enriched through the process of cell adhesion (P < 0.01). The results of survival analysis showed that 18 coding genes and 14 long non coding RNA genes had significant effects on patient survival (P < 0.01). In this study, magnetic nanoparticles can be used to extract genomic DNA and total RNA due to their paramagnetism and biocompatibility, then transcriptome high-throughput sequencing was performed. The method has the advantages of removing dangerous reagents such as phenol and chloroform, replacing inorganic coating such as silica with organic oil, and shortening reaction time. Protein coding and long non coding RNA genes as well as magnetic nanoparticles may serve as potential cancer immune biomarker targets for developing future oncological treatments.

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Dual Isoform Sequencing Reveals a Multifaceted Transcriptional Architecture of a Prototype Baculovirus

10.21203/rs.3.rs-637036/v1 ◽

2021 ◽

Author(s):

Gábor Torma ◽

Dóra Tombácz ◽

Norbert Moldován ◽

Ádám Fülöp ◽

István Prazsák ◽

...

Keyword(s):

Protein Coding ◽

Rna Molecules ◽

Non Coding Rna ◽

Oxford Nanopore ◽

The Pacific ◽

Viral Genes ◽

Long Read ◽

Oxford Nanopore Technologies ◽

Overlapping Transcripts

Abstract In this study, we used two long-read sequencing (LRS) techniques, Sequel from the Pacific Biosciences and MinION from Oxford Nanopore Technologies, for the transcriptional characterization of a prototype baculovirus, Autographacalifornica multiple nucleopolyhedrovirus. LRS is able to read full-length RNA molecules, and thereby to distinguish between transcript isoforms, mono- and polycistronic RNAs, and overlapping transcripts. Altogether, we detected 875 transcripts, of which 759 are novel and 116 have been annotated previously. These RNA molecules include 41 novel putative protein coding transcript (each containing 5’-truncated in-frame ORFs), 14 monocistronic transcripts, 99 multicistronic RNAs, 101 non-coding RNA, and 504 length isoforms. We also detected RNA methylation in 12 viral genes and RNA hyper-editing in the longer 5’-UTR transcript isoform of ORF 19 gene.

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