Identification of Novel Micropeptides Derived from Hepatocellular Carcinoma-Specific Long Noncoding RNA.

Identification of cancer-specific target molecules and biomarkers may be useful in the development of novel treatment and immunotherapeutic strategies. We have recently demonstrated that the expression of long noncoding (lnc) RNAs can be cancer-type specific due to abnormal chromatin remodeling and alternative splicing. Furthermore, we identified and determined that the functional small protein C20orf204-189AA encoded by long intergenic noncoding RNA Linc00176 that is expressed predominantly in hepatocellular carcinoma (HCC), enhances transcription of ribosomal RNAs and supports growth of HCC. In this study we combined RNA-sequencing and polysome profiling to identify novel micropeptides that originate from HCC-specific lncRNAs. We identified nine lncRNAs that are expressed exclusively in HCC cells but not in the liver or other normal tissues. Here, DNase-sequencing data revealed that the altered chromatin structure plays a key role in the HCC-specific expression of lncRNAs. Three out of nine HCC-specific lncRNAs contain at least one open reading frame (ORF) longer than 50 amino acid (aa) and enriched in the polysome fraction, suggesting that they are translated. We generated a peptide specific antibody to characterize one candidate, NONHSAT013026.2/Linc013026. We show that Linc013026 encodes a 68 amino acid micropeptide that is mainly localized at the perinuclear region. Linc013026-68AA is expressed in a subset of HCC cells and plays a role in cell proliferation, suggesting that Linc013026-68AA may be used as a HCC-specific target molecule. Our finding also sheds light on the role of the previously ignored 'dark proteome', that originates from noncoding regions in the maintenance of cancer.

Genome-Wide Methylation Mapping Using Nanopore Sequencing Technology Identifies Novel Tumor Suppressor Genes in Hepatocellular Carcinoma.

Downregulation of multiple tumor suppressor genes (TSGs) plays an important role in cancer formation. Recent evidence has accumulated that cancer progression involves genome-wide alteration of epigenetic modifications, which may cause downregulation of the tumor suppressor gene. Using hepatocellular carcinoma (HCC) as a system, we mapped 5-methylcytosine signal at a genome-wide scale using nanopore sequencing technology to identify novel TSGs. Integration of methylation data with gene transcription profile of regenerated liver and primary HCCs allowed us to identify 10 potential tumor suppressor gene candidates. Subsequent validation led us to focus on functionally characterizing one candidate-glucokinase (GCK). We show here that overexpression of GCK inhibits the proliferation of HCC cells via induction of intracellular lactate accumulation and subsequently causes energy crisis due to NAD+ depletion. This suggests GCK functions as a tumor suppressor gene and may be involved in HCC development. In conclusion, these data provide valuable clues for further investigations of the process of tumorigenesis in human cancer.

THOC5 controls 3'end-processing of immediate early genes via interaction with polyadenylation specific factor 100 (CPSF100).

Transcription of immediate early genes (IEGs) in response to extrinsic and intrinsic signals is tightly regulated at multiple stages. It is known that untranslated regions of the RNA can play a role in these processes. Here we show that THOC5, a member of the TREX (transcription/export) complex, plays a role in expression of only a subset of constitutively active genes, however transcriptome analysis reveals that more than 90% of IEG were not induced by serum in THOC5 depleted cells. Furthermore, THOC5 depletion does not influence the expression of the most rapidly induced IEGs, e.g. Fos and Jun. One group of THOC5 target genes, including Id1, Id3 and Wnt11 transcripts, were not released from chromatin in THOC5 depleted cells. Genes in another group, including Myc and Smad7 transcripts, were released with shortening of 3'UTR by alternative cleavage, and were spliced but export was impaired in THOC5 depleted cells. By interactome analysis using THOC5 as bait, we show that upon stimulation with serum THOC5 forms a complex with polyadenylation-specific factor 100 (CPSF100). THOC5 is required for recruitment of CPSF100 to 3'UTR of THOC5 target genes. These data suggest the presence of a novel mechanism for the control of IEG response by THOC5 via 3'end-processing.

Murine precision-cut liver slices (PCLS): a new tool for studying tumor microenvironments and cell signaling ex vivo.

BACKGROUND: One of the most insidious characteristics of cancer is its spread to and ability to compromise distant organs via the complex process of metastasis. Communication between cancer cells and organ-resident cells via cytokines/chemokines and direct cell-cell contacts are key steps for survival, proliferation and invasion of metastasized cancer cells in organs. Precision-cut liver slices (PCLS) are considered to closely reflect the in vivo situation and are potentially useful for studying the interaction of cancer cells with liver-resident cells as well as being a potentially useful tool for screening anti-cancer reagents. Application of the PCLS technique in the field of cancer research however, has not yet been well developed. RESULTS: We established the mouse PCLS system using perfluorodecalin (PFD) as an artificial oxygen carrier. Using this system we show that the adherence of green fluorescent protein (GFP) labeled MDA-MB-231 (highly invasive) cells to liver tissue in the PCLS was 5-fold greater than that of SK-BR-3 (less invasive) cells. In addition, we generated PCLS from THOC5, a member of transcription/export complex (TREX), knockout (KO) mice. The PCLS still expressed Gapdh or Albumin mRNAs at normal levels, while several chemokine/growth factor or metalloprotease genes, such as Cxcl12, Pdgfa, Tgfb, Wnt11, and Mmp1a genes were downregulated more than 2-fold. Interestingly, adhesion of cancer cells to THOC5 KO liver slices was far less (greater than 80% reduction) than to wild-type liver slices. CONCLUSION: Mouse PCLS cultures in the presence of PFD may serve as a useful tool for screening local adherence and invasiveness of individual cancer cells, since single cells can be observed. This method may also prove useful for identification of genes in liver-resident cells that support cancer invasion by using PCLS from transgenic liver.

Synthesis of new bioisosteric hemiasterlin analogues with extremely high cytotoxicity.

In this Letter, the synthesis and the evaluation of the cytotoxicity of new hemiasterlin analogues were reported. The indole moiety was replaced respectively by benzofurane, naphthalene and 4-bromobenzene groups. Most of these derivatives possess strong cytotoxic activity on two human tumour cell lines (KB and Hep-G2), and some analogues showed comparable cytotoxic activity to that observed for paclitaxel and ellipticine, against KB and Hep-G2 cancer cell lines.

Synthesis of new simplified hemiasterlin derivatives with α,ß-unsaturated carbonyl moiety.

In this Letter, we report a convenient and efficient method for the synthesis of new simplified derivatives of hemiasterlin in which the α,α-dimethylbenzylic moiety A is replaced by α,ß-unsaturated aryl groups as Michael acceptor. Most of these derivatives have a strong cytotoxic activity on three human tumor cell lines (KB, Hep-G2 and MCF7). Analogs 17b and 17f showed a high cytotoxicity against KB and Hep-G2 cancer cell lines comparable to paclitaxel and ellipticine.

Synthesis and cytotoxic evaluation of novel ester-triazole-linked triterpenoid-AZT conjugates.

Betulinic acid and analogous naturally occurring triterpenoid acids were transformed into the corresponding propargyl esters and subsequently deployed as substrates for a click chemistry-mediated coupling with azidothymidine (AZT) en route to novel 1,2,3-triazole-tethered triterpenoid-AZT conjugates. Twelve new hybrids were thus prepared and assessed in terms of their cytotoxic activity, revealing an interesting anticancer activity of five triterpenoid-AZT hybrids on KB and Hep-G2 tumor cell lines.

Pseudothrombosis due to blood-contrast level in the infrarenal vena cava.

Filling defects within the inferior vena cava (IVC) are common findings on computed tomography (CT); nevertheless, a majority of these defects are attributed to artifacts. The documentation pertaining to pseudothrombosis specifically affecting the infrarenal vena cava is notably insufficient in current literature. The aim of this study is to present a case demonstrating a blood-contrast level in the infrarenal vena cava, resembling an intraluminal filling defect.

Acute acalculous cholecystitis with portal cavernoma: A case report with literature review.

Portal cavernoma cholangiopathy (PCC) refers to morphological changes in the intrahepatic, extrahepatic biliary system, along with the gallbladder (GB), induced by portal cavernoma (PC). Acute acalculous cholecystitis (AAC) represents an infrequent clinical manifestation of PCC. Given the inadequacy of documentation within medical literature, AAC may go undiagnosed among patients with PC presenting symptoms of right upper quadrant pain. The current study aims to report a case of acute acalculous cholecystitis secondary to portal cavernoma, focusing on radiological findings, with a brief review of literature.

Maturity of Food Safety Management Systems in the Vietnamese Seafood Processing Industry.

Fifty-nine percent (59%) of the reported food safety issues in Vietnam are related to seafood products, mainly fish and fish products. The international export of seafood products continues to grow due to intensification of the production in the Vietnamese seafood processing industry. To ensure the production of safe food, a company-specific, effective food safety management system is essential. This research explores the maturity of food safety management systems in a convenience sample of the Vietnamese seafood processing industry to identify potential gaps and interventions for improvement. The food safety management system diagnostic instrument was used to assess the context riskiness, maturity of control and assurance activities and food safety performance of 11 companies. Maturity of their food safety management systems was further explored through hierarchical cluster analysis, and the differences in maturity between clusters were statistically tested through Mann-Whitney U tests (nonparametric). The influence of companies' organizational characteristics on the maturity of control and assurance activities was assessed through nonparametric K independent tests. A variability in the maturity of food safety management systems between the eleven Vietnamese companies was measured. Cluster analysis revealed two clusters, Cluster I (six companies) and Cluster II (five companies). The companies in both these clusters operate under a moderate level context riskiness and average to advanced level of food safety performance. However, control and assurance activities are at a lower maturity in Cluster I compared to Cluster II. None of the companies' organizational characteristics (i.e. certification level) have a statistically significant influence on the maturity of control and assurance activities. However, compliance with multiple food safety standards and the presence of physical intervention system(s) have a positive influence on food safety performance.

Prevalence and factors associated with malnutrition among hemodialysis patients in a single hemodialysis center in Vietnam: A cross-sectional study.

Malnutrition is a common problem among hemodialysis patients that increases morbidity and mortality and decreases the quality of life. This study aimed to assess the prevalence of malnutrition and associated factors and survey the consumption of energy and several nutrients among hemodialysis patients. A prospective observational study with a cross-sectional design was conducted on 76 patients on hemodialysis therapy at Nguyen Tri Phuong Hospital, Ho Chi Minh City, Vietnam, for 2 months (from May to July 2022). Dialysis malnutrition score was used to determine patients' nutritional status. Data about their biochemical parameters were retrieved from records with the newest results. Among the 76 patients, 38 (50.0%) were female. The mean age of the patients was 55.0 ±â€…13.5 years. Based on the dialysis malnutrition score, 56 (73.7%) patients had mild to moderate malnutrition, while 2 (2.6%) had severe malnutrition. The average energy intake was 21.5 kcal/kg/day, with only 3.9% meeting the recommended intake. The average protein intake was 1.0 g/kg/day, and about 10.5% of participants complied with the recommended protein level. In addition, the majority of patients did not reach the recommendations for sodium (56.6%), potassium (88.2%), phosphate (75.0%), and calcium (82.9%). We found a significant association between patients' occupation (P < .05), dialysis vintage (P < .001), and malnutrition status. Malnutrition is widespread among Vietnamese hemodialysis patients, which necessitates regular assessment and monitoring. We recommend paying more attention to the nutritional status of patients who are unemployed, retired, or stopped working and those with ≥ 5 years of hemodialysis.

Automated Machine Learning for Predicting Diabetic Retinopathy Progression From Ultra-Widefield Retinal Images.

Importance: Machine learning (ML) algorithms have the potential to identify eyes with early diabetic retinopathy (DR) at increased risk for disease progression. Objective: To create and validate automated ML models (autoML) for DR progression from ultra-widefield (UWF) retinal images. Design, Setting and Participants: Deidentified UWF images with mild or moderate nonproliferative DR (NPDR) with 3 years of longitudinal follow-up retinal imaging or evidence of progression within 3 years were used to develop automated ML models for predicting DR progression in UWF images. All images were collected from a tertiary diabetes-specific medical center retinal image dataset. Data were collected from July to September 2022. Exposure: Automated ML models were generated from baseline on-axis 200° UWF retinal images. Baseline retinal images were labeled for progression based on centralized reading center evaluation of baseline and follow-up images according to the clinical Early Treatment Diabetic Retinopathy Study severity scale. Images for model development were split 8-1-1 for training, optimization, and testing to detect 1 or more steps of DR progression. Validation was performed using a 328-image set from the same patient population not used in model development. Main Outcomes and Measures: Area under the precision-recall curve (AUPRC), sensitivity, specificity, and accuracy. Results: A total of 1179 deidentified UWF images with mild (380 [32.2%]) or moderate (799 [67.8%]) NPDR were included. DR progression was present in half of the training set (590 of 1179 [50.0%]). The model's AUPRC was 0.717 for baseline mild NPDR and 0.863 for moderate NPDR. On the validation set for eyes with mild NPDR, sensitivity was 0.72 (95% CI, 0.57-0.83), specificity was 0.63 (95% CI, 0.57-0.69), prevalence was 0.15 (95% CI, 0.12-0.20), and accuracy was 64.3%; for eyes with moderate NPDR, sensitivity was 0.80 (95% CI, 0.70-0.87), specificity was 0.72 (95% CI, 0.66-0.76), prevalence was 0.22 (95% CI, 0.19-0.27), and accuracy was 73.8%. In the validation set, 6 of 9 eyes (75%) with mild NPDR and 35 of 41 eyes (85%) with moderate NPDR progressed 2 steps or more were identified. All 4 eyes with mild NPDR that progressed within 6 months and 1 year were identified, and 8 of 9 (89%) and 17 of 20 (85%) with moderate NPDR that progressed within 6 months and 1 year, respectively, were identified. Conclusions and Relevance: This study demonstrates the accuracy and feasibility of automated ML models for identifying DR progression developed using UWF images, especially for prediction of 2-step or greater DR progression within 1 year. Potentially, the use of ML algorithms may refine the risk of disease progression and identify those at highest short-term risk, thus reducing costs and improving vision-related outcomes.

An ataxia-telangiectasia-mutated (ATM) kinase mediated response to DNA damage down-regulates the mRNA-binding potential of THOC5.

In response to DNA damage, transcription is blocked by inhibition of RNA polymerase II activity. The regulation of a preexisting pool of mRNAs, therefore, plays a key role in DNA repair, cell cycle arrest, or inhibition of differentiation. THOC5 is a member of the THO complex and plays a role in the export of a subset of mRNA, which plays an important role in hematopoiesis and maintaining primitive cells. Since three serine residues in the PEST domain of THOC5 have been shown to be directly phosphorylated by ataxia-telangiectasia-mutated (ATM) kinase, we examined the THOC5-dependent mRNA export under DNA damage. We show here that DNA damage drastically decreased the cytoplasmic pool of a set of THOC5-dependent mRNAs and impaired the THOC5/mRNA complex formation. The mRNP complex formed with nonphosphorylation mutant (S307/312/314A) THOC5, but not with a C-terminal deletion mutant after DNA damage, suggesting that the C-terminal domain of THOC5, but not its phosphorylation in the PEST domain, is necessary for the regulation of the mRNA-binding potency of THOC5. The cytoplasmic THOC5-dependent mRNAs were recovered by treatment with ATM kinase-specific or p53-specific siRNA, as well as by treatment with ATM kinase inhibitor, KU55933, under DNA damage conditions, suggesting that the ATM-kinase-p53 pathway is involved in this response to the DNA damage. Furthermore, the treatment with KU55933 blocked DNA damage-induced THOC5mRNP complex dissociation, indicating that activation of ATM kinase suppresses the ability of THOC5 to bind to its target mRNAs.

Identification of mRNAs that are spliced but not exported to the cytoplasm in the absence of THOC5 in mouse embryo fibroblasts.

The TREX (transcription/export) complex has been conserved throughout evolution from yeast to man and is required for coupled transcription elongation and nuclear export of mRNAs. The TREX complex in mammals and Drosophila is composed of the THO subcomplex (THOC1, THOC2, THOC5, THOC6, and THOC7), THOC3, UAP56, and Aly/THOC4. In human and Drosophila, various studies have shown that THO is required for the export of heat shock mRNAs, but nothing is known about other mRNAs. Our previous study using conditional THOC5 (or FMIP) knockout mice revealed that the presence of THOC5 is critical in hematopoietic cells but not for terminally differentiated cells. In this study, we describe the establishment of a mouse embryo fibroblast cell line (MEF), THOC5 flox/flox. Four days after infection of MEF THOC5 flox/flox with adenovirus carrying Cre-recombinase gene (Ad-GFP-Cre), THOC5 is down-regulated >95% at the protein level, and cell growth is strongly suppressed. Transcriptome analysis using cytoplasmic RNA isolated from cells lacking functional THOC5 reveals that only 2.9% of all genes were down-regulated more than twofold. Although we examined these genes in fibroblasts, one-fifth of all down-regulated genes (including HoxB3 and polycomb CBX2) are known to play a key role in hematopoietic development. We further identified 10 genes that are spliced but not exported to the cytoplasm in the absence of THOC5. These mRNAs were copurified with THOC5. Furthermore, Hsp70 mRNA was exported in the absence of THOC5 at 37°C, but not under heat shock condition (42°C), suggesting that THOC5 may be required for mRNA export under stress and/or upon signaling-induced conditions.

TSSUNet-MB - ab initio identification of σ70 promoter transcription start sites in Escherichia coli using deep multitask learning.

MOTIVATION: Computational promoter prediction (CPP) tools designed to classify prokaryotic promoter regions usually assume that a transcription start site (TSS) is located at a predefined position within each promoter region. Such CPP tools are sensitive to any positional shifting of the TSS in a windowed region, and they are unsuitable for determining the boundaries of prokaryotic promoters. RESULTS: TSSUNet-MB is a deep learning model developed to identify the TSSs of σ70 promoters. Mononucleotide and bendability were used to encode input sequences. TSSUNet-MB outperforms other CPP tools when assessed using the sequences obtained from the neighborhood of real promoters. TSSUNet-MB achieved a sensitivity of 0.839 and specificity of 0.768 on sliding sequences, while other CPP tool cannot maintain both sensitivities and specificities in a compatible range. Furthermore, TSSUNet-MB can precisely predict the TSS position of σ70 promoter-containing regions with a 10-base accuracy of 77.6%. By leveraging the sliding window scanning approach, we further computed the confidence score of each predicted TSS, which allows for more accurately identifying TSS locations. Our results suggest that TSSUNet-MB is a robust tool for finding σ70 promoters and identifying TSSs.

Identifying temporal sensory drivers of liking of biscuit supplemented with brewer's spent grain for young consumers.

Brewer's spent grain (BSG), a by-product of the brewing industry, has great potential as food additive. BSG is particularly rich in protein and fibre content which makes it an ideal nutritional fortifier for biscuits. However, adding BSG to biscuits can lead to changes in sensory perception and consumer acceptance. This study explored the temporal sensory profiles and drivers/inhibitors of liking in BSG-fortified biscuits. Six biscuit formulations were obtained from a design with factors oat flake particle size (three levels: 0.5 mm, small commercial flakes, large commercial flakes) and baking powder (two levels: with, without). Consumers (n = 104) tasted the samples, described their dynamic sensory perception using the Temporal Check-All-That-Apply (TCATA) method, and rated their liking on a 7-point categorical scale. The Clustering around Latent Variables (CLV) approach was used to group consumers into two clusters based on their preferences. The temporal sensory profiles and drivers/inhibitors of liking were investigated within each cluster. Foamy and Easy-to-swallow were sensory drivers of liking for both groups of consumers. However, inhibitors of liking were different in the two clusters: Dense and Hard-to-swallow for one cluster and Chewy, Hard-to-swallow and Hard for the other cluster. These findings give evidence that manipulating oat particle size and presence/absence of baking powder changes BSG-fortified biscuits' sensory profiles and consumer preferences. A complementary analysis of the area-under-curve of the TCATA data and inspection of individual temporal curves showed the dynamics of perception and showed how oat particle size and presence/absence of baking powder affected consumer perception and acceptance of BSG-fortified biscuits. The methods proposed in this paper can be further applied to understand how enriching products with ingredients that would otherwise go to waste affects acceptance in different consumer segments.

Mapping alternative polyadenylation in human cells using direct RNA sequencing technology.

Alternative cleavage and polyadenylation (APA) is a widespread mechanism to generate mRNA isoforms with alternative 3' untranslated regions. Here, we detail a protocol for detecting APA genome wide using direct RNA sequencing technology including computational analysis. We describe steps for RNA sample and library preparation, nanopore sequencing, and data analysis. Experiments and data analysis can be performed over a period of 6-8 days and require molecular biology and bioinformatics skills. For complete details on the use and execution of this protocol, please refer to Polenkowski et al.1.

Performance of Automated Machine Learning for Diabetic Retinopathy Image Classification from Multi-field Handheld Retinal Images.

PURPOSE: To create and validate code-free automated deep learning models (AutoML) for diabetic retinopathy (DR) classification from handheld retinal images. DESIGN: Prospective development and validation of AutoML models for DR image classification. PARTICIPANTS: A total of 17 829 deidentified retinal images from 3566 eyes with diabetes, acquired using handheld retinal cameras in a community-based DR screening program. METHODS: AutoML models were generated based on previously acquired 5-field (macula-centered, disc-centered, superior, inferior, and temporal macula) handheld retinal images. Each individual image was labeled using the International DR and diabetic macular edema (DME) Classification Scale by 4 certified graders at a centralized reading center under oversight by a senior retina specialist. Images for model development were split 8-1-1 for training, optimization, and testing to detect referable DR ([refDR], defined as moderate nonproliferative DR or worse or any level of DME). Internal validation was performed using a published image set from the same patient population (N = 450 images from 225 eyes). External validation was performed using a publicly available retinal imaging data set from the Asia Pacific Tele-Ophthalmology Society (N = 3662 images). MAIN OUTCOME MEASURES: Area under the precision-recall curve (AUPRC), sensitivity (SN), specificity (SP), positive predictive value (PPV), negative predictive value (NPV), accuracy, and F1 scores. RESULTS: Referable DR was present in 17.3%, 39.1%, and 48.0% of the training set, internal validation, and external validation sets, respectively. The model's AUPRC was 0.995 with a precision and recall of 97% using a score threshold of 0.5. Internal validation showed that SN, SP, PPV, NPV, accuracy, and F1 scores were 0.96 (95% confidence interval [CI], 0.884-0.99), 0.98 (95% CI, 0.937-0.995), 0.96 (95% CI, 0.884-0.99), 0.98 (95% CI, 0.937-0.995), 0.97, and 0.96, respectively. External validation showed that SN, SP, PPV, NPV, accuracy, and F1 scores were 0.94 (95% CI, 0.929-0.951), 0.97 (95% CI, 0.957-0.974), 0.96 (95% CI, 0.952-0.971), 0.95 (95% CI, 0.935-0.956), 0.97, and 0.96, respectively. CONCLUSIONS: This study demonstrates the accuracy and feasibility of code-free AutoML models for identifying refDR developed using handheld retinal imaging in a community-based screening program. Potentially, the use of AutoML may increase access to machine learning models that may be adapted for specific programs that are guided by the clinical need to rapidly address disparities in health care delivery. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found after the references.

THOC5 complexes with DDX5, DDX17, and CDK12 to regulate R loop structures and transcription elongation rate.

THOC5, a member of the THO complex, is essential for the 3'processing of some inducible genes, the export of a subset of mRNAs and stem cell survival. Here we show that THOC5 depletion results in altered 3'cleavage of >50% of mRNAs and changes in RNA polymerase II binding across genes. THOC5 is recruited close to high-density polymerase II sites, suggesting that THOC5 is involved in transcriptional elongation. Indeed, measurement of elongation rates in vivo demonstrated decreased rates in THOC5-depleted cells. Furthermore, THOC5 is preferentially recruited to its target genes in slow polymerase II cells compared with fast polymerase II cells. Importantly chromatin-associated THOC5 interacts with CDK12 (a modulator of transcription elongation) and RNA helicases DDX5, DDX17, and THOC6 only in slow polymerase II cells. The CDK12/THOC5 interaction promotes CDK12 recruitment to R-loops in a THOC6-dependent manner. These data demonstrate a novel function of THOC5 in transcription elongation.

C20orf204, a hepatocellular carcinoma-specific protein interacts with nucleolin and promotes cell proliferation.

In most human cancers, a large number of proteins with driver mutations are involved in tumor development, implying that multiple fine tuners are involved in cancer formation and/or maintenance. A useful strategy for cancer therapy may therefore be to target multiple cancer type-specific fine tuners. Furthermore, genome-wide association studies of tumor samples have identified a large number of long noncoding (lnc)RNA associated with various types of tumor. In this context we have previously found that C20orf204 (a splice variant of Linc00176) RNA contains a 189 amino acid (AA) long open reading frame (C20orf204-189AA) that is expressed predominantly in hepatocellular carcinoma (HCC). We report here that a protein, C20orf204-189AA, was detected in the nucleus of 14 out of 20 primary HCC, but not in control livers. Strikingly, overexpression of C20orf204-189AA enhanced cell proliferation and ribosomal RNA transcription. C20orf204-189AA is co-localized, and interacted with nucleolin via the C-terminal and with ribosomal RNA via the N-terminal domain. Furthermore, the expression of C20orf204-189AA upregulates the protein level of nucleolin. Nucleolin and C20orf204 mRNA levels in HCC are correlated with tumor differentiation grade and patient survival, suggesting that C20orf204-189AA is a cancer type-specific fine tuner in some HCC that presents itself for potential targeting therapy and cancer biomarker. Thus, cancer cells exhibit remarkable transcriptome alterations partly by adopting cancer-specific splicing isoforms of noncoding RNAs and may participate in tumor development.