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A personalized PCR test for circulating tumor DNA identified cases of progressive hepatocellular carcinoma, investigators reported in the September issue of Cellular and Molecular Gastroenterology and Hepatology.
Patients with liver cancer who underwent resection or transplantation and were positive for ctDNA had significantly higher rates of recurrence (P <.0102) and metastasis (P <.0386), reported Dr. Atsushi Ono of Hiroshima (Japan) University and the RIKEN Center for Integrative Medical Sciences and associates. The study also found that transcatheter arterial chemoembolization [TACE] increased levels of ctDNA, compared with total cell-free DNA, making the marker easier to detect.
“Analyzing cell-free DNA after TACE in unresectable and recurrent cases as a liquid biopsy to establish cancer genome profiles might … guide selection of an individualized therapeutic regimen without requiring percutaneous biopsy,” they added.
Assays for ctDNA have shown promise for diagnosing other cancers and targeting their treatments, but HCC diagnosis relies primarily on imaging, and HCC ctDNA has not been well characterized, noted the investigators. They performed massively parallel whole-genome sequencing of DNA extracted from resected HCCs from 46 patients. They serially measured plasma ctDNA levels before and after surgery using personalized quantitative PCR assays that targeted somatic rearrangements. They also used chemiluminescent immunoassays to test for two conventional tumor markers, alpha-fetoprotein and des-gamma-carboxy prothrombin (Cell Mol Gastroenterol Hepatol. 2015 Jul 2 [doi: 10.1016/j.jcmgh.2015.06.009]).
In all, 25 somatic mutations were present in both primary tumor tissue and in cell-free DNA samples, and 83% of mutations in the primary tumor were detectable in cell-free DNA. Among seven patients who tested positive for ctDNA before surgery, six developed recurrent disease and four developed extrahepatic metastases, Dr. Ono and associates said.
Levels of ctDNA increased as disease progressed and dropped in response to treatment, and one case remained positive for ctDNA even after alpha-fetoprotein and des-gamma-carboxy prothrombin became negative or dropped below threshold after resection. “This suggests that, in some patients, ctDNA might be a better and more sensitive biomarker for HCC than the conventional tumor markers,” they said.
The assay analyzed plasma instead of serum because serum was likely to have more normal cell-free nucleic acids, which would make it harder to detect mutant alleles, the investigators noted. Testing for ctDNA could help address the problem of tumor heterogeneity because ctDNA contains the entire tumor genome, including variants from independent tumors, but the assay will need further validation, especially because its lower limits varied by primer sets, which reduced its sensitivity and meant that some cases went undetected, they added.
The study was funded by the government of Japan, the RIKEN President’s Fund, the Princess Takamatsu Cancer Research Fund, and the Takeda Science Foundation. The investigators declared no competing interests.
As the oncology field advances toward implementation of personalized medicine programs, molecular and genomic analysis of circulating tumor DNA (ctDNA) represents a promising approach for diagnosis, prognosis, therapy selection, and minimal residual disease monitoring of a wide array of malignancies.
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| Dr. Larissa Furtado |
With the purpose of assessing the utility of extracellular tumor DNA as a potential biomarker for hepatocellular carcinoma (HCC), Dr. Ono and colleagues analyzed serum ctDNA from 46 HCC patients using quantitative PCR assays for somatic rearrangements uncovered by whole-genome sequencing of their primary tumors.
For the seven patients with detectable ctDNA in preoperative serum, the incidence of recurrence and extrahepatic metastasis within 2 years following hepatectomy were significantly worse than in the ctDNA-negative group, although no significant difference in the cumulative survival rate was observed between these patients. The ctDNA positivity also was found to be an independent predictor of microscopic vascular invasion of the portal vein, and it correlated with larger tumor size and higher alpha-fetoprotein and des-gamma-carboxy prothrombin levels.
In addition, the investigators demonstrated that transcatheter arterial chemoembolization (TACE) enriched ctDNA levels in cell-free DNA in blood, and that serum ctDNA levels were increased with disease progression and reflected response to treatments.
 |
| Dr. Jeremy Segal |
The diagnosis of HCC is currently based on imaging and/or biopsies. Even though there are no well-established biomarkers for early detection and monitoring of HCC at present, the data presented here indicate the potential utility of personalized ctDNA testing for individualized management of hepatocellular carcinoma patients.
Dr. Larissa V. Furtado and Dr. Jeremy P. Segal are both assistant professors and assistant directors of the division of genomic and molecular pathology in the department of pathology at the University of Chicago Medical Center. Neither has conflicts of interest.
As the oncology field advances toward implementation of personalized medicine programs, molecular and genomic analysis of circulating tumor DNA (ctDNA) represents a promising approach for diagnosis, prognosis, therapy selection, and minimal residual disease monitoring of a wide array of malignancies.
|
| Dr. Larissa Furtado |
With the purpose of assessing the utility of extracellular tumor DNA as a potential biomarker for hepatocellular carcinoma (HCC), Dr. Ono and colleagues analyzed serum ctDNA from 46 HCC patients using quantitative PCR assays for somatic rearrangements uncovered by whole-genome sequencing of their primary tumors.
For the seven patients with detectable ctDNA in preoperative serum, the incidence of recurrence and extrahepatic metastasis within 2 years following hepatectomy were significantly worse than in the ctDNA-negative group, although no significant difference in the cumulative survival rate was observed between these patients. The ctDNA positivity also was found to be an independent predictor of microscopic vascular invasion of the portal vein, and it correlated with larger tumor size and higher alpha-fetoprotein and des-gamma-carboxy prothrombin levels.
In addition, the investigators demonstrated that transcatheter arterial chemoembolization (TACE) enriched ctDNA levels in cell-free DNA in blood, and that serum ctDNA levels were increased with disease progression and reflected response to treatments.
|
| Dr. Jeremy Segal |
The diagnosis of HCC is currently based on imaging and/or biopsies. Even though there are no well-established biomarkers for early detection and monitoring of HCC at present, the data presented here indicate the potential utility of personalized ctDNA testing for individualized management of hepatocellular carcinoma patients.
Dr. Larissa V. Furtado and Dr. Jeremy P. Segal are both assistant professors and assistant directors of the division of genomic and molecular pathology in the department of pathology at the University of Chicago Medical Center. Neither has conflicts of interest.
As the oncology field advances toward implementation of personalized medicine programs, molecular and genomic analysis of circulating tumor DNA (ctDNA) represents a promising approach for diagnosis, prognosis, therapy selection, and minimal residual disease monitoring of a wide array of malignancies.
|
| Dr. Larissa Furtado |
With the purpose of assessing the utility of extracellular tumor DNA as a potential biomarker for hepatocellular carcinoma (HCC), Dr. Ono and colleagues analyzed serum ctDNA from 46 HCC patients using quantitative PCR assays for somatic rearrangements uncovered by whole-genome sequencing of their primary tumors.
For the seven patients with detectable ctDNA in preoperative serum, the incidence of recurrence and extrahepatic metastasis within 2 years following hepatectomy were significantly worse than in the ctDNA-negative group, although no significant difference in the cumulative survival rate was observed between these patients. The ctDNA positivity also was found to be an independent predictor of microscopic vascular invasion of the portal vein, and it correlated with larger tumor size and higher alpha-fetoprotein and des-gamma-carboxy prothrombin levels.
In addition, the investigators demonstrated that transcatheter arterial chemoembolization (TACE) enriched ctDNA levels in cell-free DNA in blood, and that serum ctDNA levels were increased with disease progression and reflected response to treatments.
|
| Dr. Jeremy Segal |
The diagnosis of HCC is currently based on imaging and/or biopsies. Even though there are no well-established biomarkers for early detection and monitoring of HCC at present, the data presented here indicate the potential utility of personalized ctDNA testing for individualized management of hepatocellular carcinoma patients.
Dr. Larissa V. Furtado and Dr. Jeremy P. Segal are both assistant professors and assistant directors of the division of genomic and molecular pathology in the department of pathology at the University of Chicago Medical Center. Neither has conflicts of interest.
A personalized PCR test for circulating tumor DNA identified cases of progressive hepatocellular carcinoma, investigators reported in the September issue of Cellular and Molecular Gastroenterology and Hepatology.
Patients with liver cancer who underwent resection or transplantation and were positive for ctDNA had significantly higher rates of recurrence (P <.0102) and metastasis (P <.0386), reported Dr. Atsushi Ono of Hiroshima (Japan) University and the RIKEN Center for Integrative Medical Sciences and associates. The study also found that transcatheter arterial chemoembolization [TACE] increased levels of ctDNA, compared with total cell-free DNA, making the marker easier to detect.
“Analyzing cell-free DNA after TACE in unresectable and recurrent cases as a liquid biopsy to establish cancer genome profiles might … guide selection of an individualized therapeutic regimen without requiring percutaneous biopsy,” they added.
Assays for ctDNA have shown promise for diagnosing other cancers and targeting their treatments, but HCC diagnosis relies primarily on imaging, and HCC ctDNA has not been well characterized, noted the investigators. They performed massively parallel whole-genome sequencing of DNA extracted from resected HCCs from 46 patients. They serially measured plasma ctDNA levels before and after surgery using personalized quantitative PCR assays that targeted somatic rearrangements. They also used chemiluminescent immunoassays to test for two conventional tumor markers, alpha-fetoprotein and des-gamma-carboxy prothrombin (Cell Mol Gastroenterol Hepatol. 2015 Jul 2 [doi: 10.1016/j.jcmgh.2015.06.009]).
In all, 25 somatic mutations were present in both primary tumor tissue and in cell-free DNA samples, and 83% of mutations in the primary tumor were detectable in cell-free DNA. Among seven patients who tested positive for ctDNA before surgery, six developed recurrent disease and four developed extrahepatic metastases, Dr. Ono and associates said.
Levels of ctDNA increased as disease progressed and dropped in response to treatment, and one case remained positive for ctDNA even after alpha-fetoprotein and des-gamma-carboxy prothrombin became negative or dropped below threshold after resection. “This suggests that, in some patients, ctDNA might be a better and more sensitive biomarker for HCC than the conventional tumor markers,” they said.
The assay analyzed plasma instead of serum because serum was likely to have more normal cell-free nucleic acids, which would make it harder to detect mutant alleles, the investigators noted. Testing for ctDNA could help address the problem of tumor heterogeneity because ctDNA contains the entire tumor genome, including variants from independent tumors, but the assay will need further validation, especially because its lower limits varied by primer sets, which reduced its sensitivity and meant that some cases went undetected, they added.
The study was funded by the government of Japan, the RIKEN President’s Fund, the Princess Takamatsu Cancer Research Fund, and the Takeda Science Foundation. The investigators declared no competing interests.
A personalized PCR test for circulating tumor DNA identified cases of progressive hepatocellular carcinoma, investigators reported in the September issue of Cellular and Molecular Gastroenterology and Hepatology.
Patients with liver cancer who underwent resection or transplantation and were positive for ctDNA had significantly higher rates of recurrence (P <.0102) and metastasis (P <.0386), reported Dr. Atsushi Ono of Hiroshima (Japan) University and the RIKEN Center for Integrative Medical Sciences and associates. The study also found that transcatheter arterial chemoembolization [TACE] increased levels of ctDNA, compared with total cell-free DNA, making the marker easier to detect.
“Analyzing cell-free DNA after TACE in unresectable and recurrent cases as a liquid biopsy to establish cancer genome profiles might … guide selection of an individualized therapeutic regimen without requiring percutaneous biopsy,” they added.
Assays for ctDNA have shown promise for diagnosing other cancers and targeting their treatments, but HCC diagnosis relies primarily on imaging, and HCC ctDNA has not been well characterized, noted the investigators. They performed massively parallel whole-genome sequencing of DNA extracted from resected HCCs from 46 patients. They serially measured plasma ctDNA levels before and after surgery using personalized quantitative PCR assays that targeted somatic rearrangements. They also used chemiluminescent immunoassays to test for two conventional tumor markers, alpha-fetoprotein and des-gamma-carboxy prothrombin (Cell Mol Gastroenterol Hepatol. 2015 Jul 2 [doi: 10.1016/j.jcmgh.2015.06.009]).
In all, 25 somatic mutations were present in both primary tumor tissue and in cell-free DNA samples, and 83% of mutations in the primary tumor were detectable in cell-free DNA. Among seven patients who tested positive for ctDNA before surgery, six developed recurrent disease and four developed extrahepatic metastases, Dr. Ono and associates said.
Levels of ctDNA increased as disease progressed and dropped in response to treatment, and one case remained positive for ctDNA even after alpha-fetoprotein and des-gamma-carboxy prothrombin became negative or dropped below threshold after resection. “This suggests that, in some patients, ctDNA might be a better and more sensitive biomarker for HCC than the conventional tumor markers,” they said.
The assay analyzed plasma instead of serum because serum was likely to have more normal cell-free nucleic acids, which would make it harder to detect mutant alleles, the investigators noted. Testing for ctDNA could help address the problem of tumor heterogeneity because ctDNA contains the entire tumor genome, including variants from independent tumors, but the assay will need further validation, especially because its lower limits varied by primer sets, which reduced its sensitivity and meant that some cases went undetected, they added.
The study was funded by the government of Japan, the RIKEN President’s Fund, the Princess Takamatsu Cancer Research Fund, and the Takeda Science Foundation. The investigators declared no competing interests.
FROM CELLULAR AND MOLECULAR GASTROENTEROLOGY AND HEPATOLOGY
Key clinical point: The presence of circulating tumor (ct) DNA indicated progression of hepatocellular carcinoma.
Major finding: Among seven patients who tested positive for ctDNA before undergoing surgical resection, six developed recurrent HCC and four developed extrahepatic metastases.
Data source: Real-time quantitative PCR analysis of serum samples from 46 patients with HCC who underwent hepatectomy or liver transplantation.
Disclosures: The study was funded by the government of Japan, the RIKEN President’s Fund, the Princess Takamatsu Cancer Research Fund, and the Takeda Science Foundation. The investigators declared no competing interests.
