Plasma cell free DNA methylation markers for hepatocellular carcinoma surveillance in patients with cirrhosis: a case control study

Abstract

Background Hepatocellular carcinoma (HCC) is the leading cause of death in patients with cirrhosis, primarily due to failed early detection. HCC screening is recommended among individuals with cirrhosis using biannual abdominal ultrasound, for earlier tumor detection, administration of curative treatment, and improved survival. Surveillance by imaging with or without biomarkers such as alpha-fetoprotein (AFP) remains suboptimal for early stage HCC detection. Here we report on the development and assessment of methylation biomarkers from liquid biopsies for HCC surveillance in cirrhotic patients. Methods DNA methylation markers including the HCCBloodTest (Epigenomics AG) and a DNA-methylation panel established by next generation sequencing (NGS) were assessed using a training/testing design. The NGS panel algorithm was established in a training study (41 HCC patients; 46 cirrhotic non-HCC controls). For testing, plasma samples were obtained from cirrhotic patients (Child class A or B) with (60) or without (103) early stage HCC (BCLC stage 0, A, B). The assays were then tested using blinded sample sets and analyzed by preset algorithms. Results The HCCBloodTest and the NGS panel exhibited 76.7% and 57% sensitivities at 64.1% and 97% specificity, respectively. In a post-hoc analysis, a combination of the NGS panel with AFP (20 ng/mL) achieved 68% sensitivity at 97% specificity (AUC = 0.9). Conclusions Methylation biomarkers in cell free plasma DNA provide a new alternative for HCC surveillance. Multiomic panels comprising DNA methylation markers with other biological markers, such as AFP, provide an option to further increase the overall clinical performance of surveillance via minimally invasive blood samples. Trial Registration: Test set study—ClinicalTrials.gov (NCT03804593) January 11, 2019, retrospectively registered.

Diagnostic performance of circulating tumor DNA as a minimally invasive biomarker for hepatocellular carcinoma: a systematic review and meta-analysis

“…Other articles combined healthy volunteers and chronic hepatitis or liver cirrhosis patients as the control group. The majority of articles were conducted in Asia ( n = 31) ( Huang et al, 2003 ; Wong et al, 2000 ; Wong et al, 2003 ; Chu et al, 2004 ; Lin et al, 2005 ; Yeo et al, 2005 ; Wang et al, 2006 ; Zhang et al, 2007 ; Chang et al, 2008 ; Hu et al, 2010 ; Huang et al, 2011 ; Sun et al, 2013 ; Zhang et al, 2013 ; Han et al, 2014 ; Ji et al, 2014 ; Kuo et al, 2014 ; Li et al, 2014 ; Yang et al, 2014 ; Dong et al, 2015 ; Huang et al, 2015 ; Teng et al, 2016 ; Dong et al, 2017 ; Hu et al, 2017 ; Tian et al, 2017 ; Wu et al, 2017 ; Li et al, 2018 ; Wei et al, 2018 ; Bai et al, 2019 ; Liu et al, 2020 ; Qian et al, 2020 ; Akuta et al, 2021 ), five in Africa ( Igetei et al, 2008 ; Ahmed et al, 2010 ; Ramadan et al, 2015 ; Marchio et al, 2019 ; Pasha, Mohamed & Radwan, 2019 ), three in America ( Huang et al, 2014 ; Kisiel et al, 2019 ; Lewin et al, 2021 ) , and one in Europe ( Oussalah et al, 2018 ). A total of 37 studies looked at ctDNA methylation, while three evaluated single-gene mutation.…”

“…In the qualitative analysis subgroup, our study enrolled a total population of 3,072 HCC patients and 3,413 control individuals (2,064 patients with benign liver disorders or liver cirrhosis, 1,001 healthy volunteers, and 308 non-cancer controls in a combined group of patients with benign liver disorders and healthy controls). Patients with chronic hepatitis, benign hepatic lesions, and cirrhosis were selected as the control group in 13 articles ( Chu et al, 2004 ; Wang et al, 2006 ; Chang et al, 2008 ; Ahmed et al, 2010 ; Huang et al, 2011 ; Huang et al, 2014 ; Ji et al, 2014 ; Huang et al, 2015 ; Oussalah et al, 2018 ; Kisiel et al, 2019 ; Qian et al, 2020 ; Akuta et al, 2021 ; Lewin et al, 2021 ) , while eight articles with only healthy control groups were chosen in this subgroup ( Yeo et al, 2005 ; Zhang et al, 2007 ; Igetei et al, 2008 ; Hu et al, 2010 ; Zhang et al, 2013 ; Kuo et al, 2014 ; Bai et al, 2019 ; Marchio et al, 2019 ) . Other articles combined healthy volunteers and chronic hepatitis or liver cirrhosis patients as the control group.…”

Risk factors and diagnostic biomarkers for nonalcoholic fatty liver disease-associated hepatocellular carcinoma: Current evidence and future perspectives

“…DNA methylation can also be analyzed using peripheral blood. In a recent study, methylation cfDNA biomarkers provided a modest diagnostic value for NAFLD-HCC with a sensitivity of 87.5% and specificity of 39.4%[ 78 ]. The combination of this DNA methylation panel and AFP led to a better cohort wide diagnostic performance than either of them used alone.…”

Liquid Biopsy Using Cell-Free or Circulating Tumor DNA in the Management of Hepatocellular Carcinoma

“… 42 , 60 , 61 Combining methylation markers such as HOXA1, EMX1, and TSPYL5 with other biomarkers such as AFP or AFP-L3 can improve the performance for early stage HCC detection. 62 , 63 , 64 …”