Assessments of TP53 and CTNNB1 gene hotspot mutations in circulating tumour DNA of hepatitis B virus-induced hepatocellular carcinoma
Background: Hepatitis B virus (HBV) infection is one of the major causes of chronic liver disease, which progresses from chronic hepatitis B (CHB) to fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Early detection and laboratory-based screening of hepatocellular carcinoma are still major ch...
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Frontiers Media S.A.
2023-08-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1235260/full |
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| author | Sonu Kumar Neeti Nadda Afnan Quadri Rahul Kumar Shashi Paul Pranay Tanwar Shivanand Gamanagatti Nihar Ranjan Dash Anoop Saraya Shalimar Baibaswata Nayak |
| author_facet | Sonu Kumar Neeti Nadda Afnan Quadri Rahul Kumar Shashi Paul Pranay Tanwar Shivanand Gamanagatti Nihar Ranjan Dash Anoop Saraya Shalimar Baibaswata Nayak |
| author_sort | Sonu Kumar |
| collection | DOAJ |
| description | Background: Hepatitis B virus (HBV) infection is one of the major causes of chronic liver disease, which progresses from chronic hepatitis B (CHB) to fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Early detection and laboratory-based screening of hepatocellular carcinoma are still major challenges. This study was undertaken to determine whether the cancer hallmark gene signatures that are released into circulation as circulating tumour DNA (ctDNA) can be used as a liquid biopsy marker for screening, early detection, and prognosis of HCC.Methods: A total of 130 subjects, including HBV-HCC (n = 80), HBV-cirrhotic and non-cirrhotic (n = 35), and healthy (n = 15) controls, were evaluated for TP53 and beta-catenin (CTNNB1) gene hotspot mutations in ctDNA by Sanger-based cycle sequencing and droplet digital PCR (ddPCR) assays. Mutation detection frequency, percentage mutant fractions, and their association with tumour stage, mortality, and smoking habits were determined.Results: Sanger-based cycle sequencing was carried out for 32 HCC patients. Predict SNP Tools analysis indicated several pathogenic driver mutations in the ctDNA sequence, which include p.D228N, p.C229R, p.H233R, p.Y234D, p.S240T, p.G245S, and p.R249M for TP53 gene exon 7 and p.S33T for CTNNB1 gene exon 3. The TP53 c.746G>T (p.R249M) mutation was detected predominately (25% cases) by sequencing, but there was no dominant mutation at position c.747G>T (p.R249S) that was reported for HBV-HCC patients. A dual-probe ddPCR assay was developed to determine mutant and wild-type copy numbers of TP53 (p.R249M and p.R249S) and CTNNB1 (p.S45P) and their percentage mutant fraction in all 130 subjects. The TP53 R249M and CTNNB1 S45P mutations were detected in 31.25% and 26.25% of HCC patients, respectively, with a high mutant-to-wild-type fraction percentage (1.81% and 1.73%), which is significant as compared to cirrhotic and non-cirrhotic patients. Poor survival was observed in HCC patients with combined TP53 and CTNNB1 gene driver mutations. The TP53 R249M mutation was also significantly (p < 0.0001) associated with smoking habits (OR, 11.77; 95% CI, 3.219–36.20), but not the same for the TP53 R249S mutation.Conclusion: Screening of ctDNA TP53 and CTNNB1 gene mutations by ddPCR may be helpful for early detection and identifying the risk of HCC progression. |
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| last_indexed | 2024-03-12T20:34:29Z |
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| spelling | doaj.art-a2c1672112ad45bba087a4a957e259b22023-08-01T15:17:30ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-08-011410.3389/fgene.2023.12352601235260Assessments of TP53 and CTNNB1 gene hotspot mutations in circulating tumour DNA of hepatitis B virus-induced hepatocellular carcinomaSonu Kumar0Neeti Nadda1Afnan Quadri2Rahul Kumar3Shashi Paul4Pranay Tanwar5Shivanand Gamanagatti6Nihar Ranjan Dash7Anoop Saraya8 Shalimar9Baibaswata Nayak10Department of Gastroenterology, All India Institute of Medical Sciences, New Delhi, IndiaDepartment of Gastroenterology, All India Institute of Medical Sciences, New Delhi, IndiaDepartment of Gastroenterology, All India Institute of Medical Sciences, New Delhi, IndiaLaboratory Oncology Unit (BRA-IRCH), All India Institute of Medical Sciences, New Delhi, IndiaRadiodiagnosis, All India Institute of Medical Sciences, New Delhi, IndiaLaboratory Oncology Unit (BRA-IRCH), All India Institute of Medical Sciences, New Delhi, IndiaRadiodiagnosis, All India Institute of Medical Sciences, New Delhi, IndiaGastrointestinal Surgery, All India Institute of Medical Sciences, New Delhi, IndiaDepartment of Gastroenterology, All India Institute of Medical Sciences, New Delhi, IndiaDepartment of Gastroenterology, All India Institute of Medical Sciences, New Delhi, IndiaDepartment of Gastroenterology, All India Institute of Medical Sciences, New Delhi, IndiaBackground: Hepatitis B virus (HBV) infection is one of the major causes of chronic liver disease, which progresses from chronic hepatitis B (CHB) to fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). Early detection and laboratory-based screening of hepatocellular carcinoma are still major challenges. This study was undertaken to determine whether the cancer hallmark gene signatures that are released into circulation as circulating tumour DNA (ctDNA) can be used as a liquid biopsy marker for screening, early detection, and prognosis of HCC.Methods: A total of 130 subjects, including HBV-HCC (n = 80), HBV-cirrhotic and non-cirrhotic (n = 35), and healthy (n = 15) controls, were evaluated for TP53 and beta-catenin (CTNNB1) gene hotspot mutations in ctDNA by Sanger-based cycle sequencing and droplet digital PCR (ddPCR) assays. Mutation detection frequency, percentage mutant fractions, and their association with tumour stage, mortality, and smoking habits were determined.Results: Sanger-based cycle sequencing was carried out for 32 HCC patients. Predict SNP Tools analysis indicated several pathogenic driver mutations in the ctDNA sequence, which include p.D228N, p.C229R, p.H233R, p.Y234D, p.S240T, p.G245S, and p.R249M for TP53 gene exon 7 and p.S33T for CTNNB1 gene exon 3. The TP53 c.746G>T (p.R249M) mutation was detected predominately (25% cases) by sequencing, but there was no dominant mutation at position c.747G>T (p.R249S) that was reported for HBV-HCC patients. A dual-probe ddPCR assay was developed to determine mutant and wild-type copy numbers of TP53 (p.R249M and p.R249S) and CTNNB1 (p.S45P) and their percentage mutant fraction in all 130 subjects. The TP53 R249M and CTNNB1 S45P mutations were detected in 31.25% and 26.25% of HCC patients, respectively, with a high mutant-to-wild-type fraction percentage (1.81% and 1.73%), which is significant as compared to cirrhotic and non-cirrhotic patients. Poor survival was observed in HCC patients with combined TP53 and CTNNB1 gene driver mutations. The TP53 R249M mutation was also significantly (p < 0.0001) associated with smoking habits (OR, 11.77; 95% CI, 3.219–36.20), but not the same for the TP53 R249S mutation.Conclusion: Screening of ctDNA TP53 and CTNNB1 gene mutations by ddPCR may be helpful for early detection and identifying the risk of HCC progression.https://www.frontiersin.org/articles/10.3389/fgene.2023.1235260/fullHBVHCCCtDNAddPCRdriver mutationcirculatory tumor DNA (ctDNA) |
| spellingShingle | Sonu Kumar Neeti Nadda Afnan Quadri Rahul Kumar Shashi Paul Pranay Tanwar Shivanand Gamanagatti Nihar Ranjan Dash Anoop Saraya Shalimar Baibaswata Nayak Assessments of TP53 and CTNNB1 gene hotspot mutations in circulating tumour DNA of hepatitis B virus-induced hepatocellular carcinoma Frontiers in Genetics HBV HCC CtDNA ddPCR driver mutation circulatory tumor DNA (ctDNA) |
| title | Assessments of TP53 and CTNNB1 gene hotspot mutations in circulating tumour DNA of hepatitis B virus-induced hepatocellular carcinoma |
| title_full | Assessments of TP53 and CTNNB1 gene hotspot mutations in circulating tumour DNA of hepatitis B virus-induced hepatocellular carcinoma |
| title_fullStr | Assessments of TP53 and CTNNB1 gene hotspot mutations in circulating tumour DNA of hepatitis B virus-induced hepatocellular carcinoma |
| title_full_unstemmed | Assessments of TP53 and CTNNB1 gene hotspot mutations in circulating tumour DNA of hepatitis B virus-induced hepatocellular carcinoma |
| title_short | Assessments of TP53 and CTNNB1 gene hotspot mutations in circulating tumour DNA of hepatitis B virus-induced hepatocellular carcinoma |
| title_sort | assessments of tp53 and ctnnb1 gene hotspot mutations in circulating tumour dna of hepatitis b virus induced hepatocellular carcinoma |
| topic | HBV HCC CtDNA ddPCR driver mutation circulatory tumor DNA (ctDNA) |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1235260/full |
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