Spatial transcriptomics analysis of neoadjuvant cabozantinib and nivolumab in advanced hepatocellular carcinoma identifies independent mechanisms of resistance and recurrence

Abstract

Novel immunotherapy combination therapies have improved outcomes for patients with hepatocellular carcinoma (HCC), but responses are limited to a subset of patients and recurrence can also occur. Little is known about the inter- and intra-tumor heterogeneity in cellular signaling networks within the HCC tumor microenvironment (TME) that underlie responses to modern systemic therapy. We applied spatial transcriptomics (ST) profiling to characterize the tumor microenvironment in HCC resection specimens from a clinical trial of neoadjuvant cabozantinib, a multi-tyrosine kinase inhibitor that primarily blocks VEGF, and nivolumab, a PD-1 inhibitor in which 5 out of 15 patients were found to have a pathologic response. ST profiling demonstrated that the TME of responding tumors was enriched for immune cells and cancer associated fibroblasts (CAF) with pro-inflammatory signaling relative to the non-responders. The enriched cancer-immune interactions in responding tumors are characterized by activation of the PAX5 module, a known regulator of B cell maturation, which colocalized with spots with increased B cell markers expression suggesting strong activity of these cells. Cancer-CAF interactions were also enriched in the responding tumors and were associated with extracellular matrix (ECM) remodeling as there was high activation of FOS and JUN in CAFs adjacent to tumor. The ECM remodeling is consistent with proliferative fibrosis in association with immune-mediated tumor regression. Among the patients with major pathologic response, a single patient experienced early HCC recurrence. ST analysis of this clinical outlier demonstrated marked tumor heterogeneity, with a distinctive immune-poor tumor region that resembles the non-responding TME across patients and was characterized by cancer-CAF interactions and expression of cancer stem cell markers, potentially mediating early tumor immune escape and recurrence in this patient. These data show that responses to modern systemic therapy in HCC are associated with distinctive molecular and cellular landscapes and provide new targets to enhance and prolong responses to systemic therapy in HCC.

Heterogeneity in Liver Cancer Immune Microenvironment: Emerging Single-Cell and Spatial Perspectives

“…67 The critical roles of B cells in mediating immunotherapy response have been highlighted by spatial transcriptome analysis of resection specimens from 15 HCC patients involved in a neoadjuvant trial, five of which achieved pathological responses. 75 As expected, a lack of clinical response was tightly correlated with an absence of immune infiltration into the tumor. In the responders, activation of PAX5 signaling in the immune regions adjacent to tumor clusters was detected.…”

Transarterial therapy combined with bevacizumab plus immune checkpoint inhibitors as a neoadjuvant therapy for locally advanced hepatocellular carcinoma

“…Remarkably, our ndings unveiled that the Neo-surgery cohort exhibited prolonged OS and PFS compared to their counterparts undergoing immediate surgical intervention. Preclinical investigations and correlative analyses lend credence to the hypothesis that neoadjuvant therapy leads a localized tumor response and mitigates recurrence by modulating the tumor microenvironment, a phenomenon observed across various therapeutic modalities, including immune-based interventions 32,33 . Numerous synergistic mechanisms contributing to the effectiveness of neoadjuvant therapy in HCC have been elucidated.…”

Informing virtual clinical trials of hepatocellular carcinoma with spatial multi-omics analysis of a human neoadjuvant immunotherapy clinical trial

“…However, due to a lack of spatial resolution, outputs from QSP models cannot be fully compared with quantitatively analyzed histopathological samples from tumors, including measures of intratumoral heterogeneity 19 . Our spatial transcriptomics analysis has demonstrated that spatial heterogeneity can result in distinct tumor immune microenvironments, leading to resistance and recurrence to immunotherapy in liver cancer 20 . To fully utilize the wealth of information contained in the spatial data in the TME, we coupled an agent-based model (ABM) with our whole-patient QSP platform to formulate a spatial QSP model (spQSP).…”

“…Together, using this new computational model a virtual clinical trial is conducted that simulates both patient outcomes and spatially resolved molecular states of tumors. We benchmark our computational model by comparing the simulated state of the TME to high-dimensional spatial proteomics and transcriptomics data from post-treatment tumor resections in the original clinical trial 3,20,24 . Whereas the biospecimens for the neoadjuvant clinical trial were only obtained at the time of surgery, the spQSP model fully simulated the spatial molecular states of the tumors over time.…”