Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma
Background and rationaleLiver derived messenger ribonucleic acid (mRNA) transcripts were reported to be elevated in the circulation of hepatocellular carcinoma (HCC) patients. We now report the detection of high-risk mRNA variants exclusively in the circulation of HCC patients. Numerous genomic alle...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Oncology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fonc.2022.963641/full |
| _version_ | 1811294347513036800 |
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| author | Timothy Block Daniel Zezulinski David E. Kaplan Jingqiao Lu Samantha Zanine Tingting Zhan Cataldo Doria Aejaz Sayeed |
| author_facet | Timothy Block Daniel Zezulinski David E. Kaplan Jingqiao Lu Samantha Zanine Tingting Zhan Cataldo Doria Aejaz Sayeed |
| author_sort | Timothy Block |
| collection | DOAJ |
| description | Background and rationaleLiver derived messenger ribonucleic acid (mRNA) transcripts were reported to be elevated in the circulation of hepatocellular carcinoma (HCC) patients. We now report the detection of high-risk mRNA variants exclusively in the circulation of HCC patients. Numerous genomic alleles such as single nucleotide polymorphisms (SNPs), nucleotide insertions and deletions (called Indels), splicing variants in many genes, have been associated with elevated risk of cancer. Our findings potentially offer a novel non-invasive platform for HCC surveillance and early detection.ApproachRNAseq analysis was carried out in the plasma of 14 individuals with a diagnosis of HCC, 8 with LC and no HCC, and 6 with no liver disease diagnosis. RNA from 6 matching tumors and 5 circulating extracellular vesicle (EV) samples from 14 of those with HCC was also analyzed. Specimens from two cholangiocarcinoma (CCA) patients were also included in our study. HCC specific SNPs and Indels referred as “variants” were identified using GATK HaplotypeCaller and annotated by SnpEff to filter out high risk variants.ResultsThe variant calling on all RNA samples enabled the detection of 5.2 million SNPs, 0.91 million insertions and 0.81 million deletions. RNAseq analyses in tumors, normal liver tissue, plasma, and plasma derived EVs led to the detection of 5480 high-risk tumor specific mRNA variants in the circulation of HCC patients. These variants are concurrently detected in tumors and plasma samples or tumors and EVs from HCC patients, but none of these were detected in normal liver, plasma of LC patients or normal healthy individuals. Our results demonstrate selective detection of concordant high-risk HCC-specific mRNA variants in free plasma, plasma derived EVs and tumors of HCC patients. The variants comprise of splicing, frameshift, fusion and single nucleotide alterations and correspond to cancer and tumor metabolism pathways. Detection of these high-risk variants in matching specimens from same subjects with an enrichment in circulating EVs is remarkable. Validation of these HCC selective ctmRNA variants in larger patient cohorts is likely to identify a predictive set of ctmRNA with high diagnostic performance and thus offer a novel non-invasive serology-based biomarker for HCC. |
| first_indexed | 2024-04-13T05:15:54Z |
| format | Article |
| id | doaj.art-fd9f333714c442118b135b9366fe32c1 |
| institution | Directory Open Access Journal |
| issn | 2234-943X |
| language | English |
| last_indexed | 2024-04-13T05:15:54Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Oncology |
| spelling | doaj.art-fd9f333714c442118b135b9366fe32c12022-12-22T03:00:54ZengFrontiers Media S.A.Frontiers in Oncology2234-943X2022-12-011210.3389/fonc.2022.963641963641Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinomaTimothy Block0Daniel Zezulinski1David E. Kaplan2Jingqiao Lu3Samantha Zanine4Tingting Zhan5Cataldo Doria6Aejaz Sayeed7Department of Translational Medicine, Baruch S. Blumberg Institute, Doylestown, PA, United StatesDepartment of Translational Medicine, Baruch S. Blumberg Institute, Doylestown, PA, United StatesDivision of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine and The Corporal Michael J. Crescenz Veterans Administration Hospital, Philadelphia, PA, United StatesRay Biotech Life Inc., Peachtree Corners, GA, United StatesDepartment of Mechanical Engineering, Pennsylvania State University, PA, United StatesDivision of Biostatistics, Department of Pharmacology and Experimental Therapeutics, Thomas Jefferson University, Philadelphia PA, United StatesCHS Liver and Pancreas Centers of Excellence, Capital Health Cancer Center, One Capital Way, Pennington, NJ, United StatesDepartment of Translational Medicine, Baruch S. Blumberg Institute, Doylestown, PA, United StatesBackground and rationaleLiver derived messenger ribonucleic acid (mRNA) transcripts were reported to be elevated in the circulation of hepatocellular carcinoma (HCC) patients. We now report the detection of high-risk mRNA variants exclusively in the circulation of HCC patients. Numerous genomic alleles such as single nucleotide polymorphisms (SNPs), nucleotide insertions and deletions (called Indels), splicing variants in many genes, have been associated with elevated risk of cancer. Our findings potentially offer a novel non-invasive platform for HCC surveillance and early detection.ApproachRNAseq analysis was carried out in the plasma of 14 individuals with a diagnosis of HCC, 8 with LC and no HCC, and 6 with no liver disease diagnosis. RNA from 6 matching tumors and 5 circulating extracellular vesicle (EV) samples from 14 of those with HCC was also analyzed. Specimens from two cholangiocarcinoma (CCA) patients were also included in our study. HCC specific SNPs and Indels referred as “variants” were identified using GATK HaplotypeCaller and annotated by SnpEff to filter out high risk variants.ResultsThe variant calling on all RNA samples enabled the detection of 5.2 million SNPs, 0.91 million insertions and 0.81 million deletions. RNAseq analyses in tumors, normal liver tissue, plasma, and plasma derived EVs led to the detection of 5480 high-risk tumor specific mRNA variants in the circulation of HCC patients. These variants are concurrently detected in tumors and plasma samples or tumors and EVs from HCC patients, but none of these were detected in normal liver, plasma of LC patients or normal healthy individuals. Our results demonstrate selective detection of concordant high-risk HCC-specific mRNA variants in free plasma, plasma derived EVs and tumors of HCC patients. The variants comprise of splicing, frameshift, fusion and single nucleotide alterations and correspond to cancer and tumor metabolism pathways. Detection of these high-risk variants in matching specimens from same subjects with an enrichment in circulating EVs is remarkable. Validation of these HCC selective ctmRNA variants in larger patient cohorts is likely to identify a predictive set of ctmRNA with high diagnostic performance and thus offer a novel non-invasive serology-based biomarker for HCC.https://www.frontiersin.org/articles/10.3389/fonc.2022.963641/fullcirculating mRNA variantshepatocellular carcinomaliver cirrhosisextracellular vesiclesHCC surveillance and early detection |
| spellingShingle | Timothy Block Daniel Zezulinski David E. Kaplan Jingqiao Lu Samantha Zanine Tingting Zhan Cataldo Doria Aejaz Sayeed Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma Frontiers in Oncology circulating mRNA variants hepatocellular carcinoma liver cirrhosis extracellular vesicles HCC surveillance and early detection |
| title | Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma |
| title_full | Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma |
| title_fullStr | Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma |
| title_full_unstemmed | Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma |
| title_short | Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma |
| title_sort | circulating messenger rna variants as a potential biomarker for surveillance of hepatocellular carcinoma |
| topic | circulating mRNA variants hepatocellular carcinoma liver cirrhosis extracellular vesicles HCC surveillance and early detection |
| url | https://www.frontiersin.org/articles/10.3389/fonc.2022.963641/full |
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