Supplementary Material for: Multimodal integrative genomics and pathology analyses in neoadjuvant nivolumab treatment for intermediate and locally-advanced HCC

Introduction: Immunotherapy has resulted in pathologic responses in hepatocellular carcinoma (HCC) but the benefits and molecular mechanisms of neoadjuvant immune checkpoint blockade are largely unknown. Methods: In this study, we evaluated the efficacy and safety of pre-operative nivolumab (anti-PD1) in patients with intermediate and locally-advanced HCC and determined the molecular markers for predicting treatment response. Results: Between July 2020 and November 2021, 20 treatment-naïve HCC patients with intermediate and locally advanced tumors received preoperative nivolumab at 3 mg/kg for 3 cycles prior to surgical resection. Nineteen patients underwent surgical resection on-trial. Seven (36.8%) of the 19 patients had major pathologic tumor necrosis (≥60%) in the post-nivolumab resection specimens, with 3 having almost complete (>90%) tumor necrosis. The tumor necrosis was hemorrhagic and often accompanied with increased or dense immune cell infiltrate at the border of the tumors. None of the patients developed major adverse reactions contradicting hepatectomy. RNA-sequencing analysis on both pre-nivolumab tumor biopsies and post- nivolumab resected specimens showed, in cases with major pathologic necrosis, the proportion of CD8 T cells in the HCC tissues predominantly increased after treatment. Moreover, to investigate non-invasive biomarker for nivolumab response, we evaluated the copy number variation (CNV) using target-panel sequencing on plasma cell-free DNA of the patients and derived a CNV-based anti-PD1 score. The score correlated with the extent of tumor necrosis and was validated in a Korean patient cohort with anti-PD1 treatment. Conclusion: Neoadjuvant nivolumab demonstrated promising clinical activity in intermediate and locally-advanced HCC patients. We also identified useful non-invasive biomarker predicting responsiveness.