Intra-tumor heterogeneity (ITH) is a key challenge in cancer treatment, but previous studies have focused mainly on the genomic alterations without exploring phenotypic (transcriptomic and immune) heterogeneity. Using one of the largest prospective surgical cohorts for Hepatocellular Carcinoma (HCC) with multi-region sampling, we sequenced whole genomes and paired transcriptomes from 67 HCC patients (331 samples). We found that while genomic ITH was rather constant across TNM stages, phenotypic ITH had a very different trajectory and quickly diversified in stage II patients. Most strikingly, 30% patients were found to contain more than one transcriptomic subtype within a single tumor. Such phenotypic ITH was found to be much more informative in predicting patient survival than genomic ITH and explains the poor efficacy of single-target systemic therapies in HCC. Taken together, we not only revealed an unprecedentedly dynamic landscape of phenotypic heterogeneity in HCC, but also highlighted the importance of studying phenotypic evolution across cancer types.

Background: The programmed death-1/programmed death-ligand-1 (PD-1/PD-L1) axis may represent a target for cervical cancer; however, it is poorly understood in human immunodeficiency virus (HIV)-infected patients. Methods: We evaluated HIV-positive ( n = 42) and HIV-negative ( n = 110) women with locally advanced cervical cancer regarding their PD-L1 expression, determined by combined positive score (CPS) ⩾ 1 and tumor proportion score (TPS) ⩾ 25%, and PD-L1 copy number alterations, assessed by fluorescence in situ hybridization. Results: Regardless of HIV status, 84.9% and 44.8% of cases were PD-L1-positive according to CPS ⩾ 1 and TPS ⩾ 25%. Per CPS ⩾ 1, PD-L1 positive rate was similar between HIV-positive and HIV-negative women, whereas a significant difference was seen per TPS ⩾ 25%. Tumor size and parametrial invasion were correlated with PD-L1 positivity in HIV-negative women, whereas anti-retroviral therapy (ART) was correlated with TPS < 25%. Low CD4-positive cell counts were associated with CPS < 1 in HIV-positive women. No significant difference was observed in PD-L1 copy number status between HIV-positive and HIV-negative women. PD-L1 amplification and polysomy were independently associated with TPS ⩾ 25%, whereas the presence of parametrial invasion was independently associated with CPS ⩾ 1. Cancer stage and PD-L1 amplification were identified as independent predictors of recurrence-free survival [hazard ratio (HR) = 2.40 (1.32–4.36) and HR = 5.33 (1.94–14.61)] and cancer-specific survival [HR = 13.62 (5.1–36.38) and HR = 3.53 (1.43–8.69)]. PD-L1 polysomy was an independent predictor of locoregional recurrence-free survival [HR = 3.27 (1.27–8.41)]. HIV status and PD-L1 expression (CPS ⩾ 1 or TPS ⩾ 25%) were not associated with poor patient outcomes. Conclusion: PD-L1 amplification and polysomy are the strongest drivers of PD-L1 expression in cervical cancer, and could represent prognostic biomarkers for anti-PD-1/PD-L1 therapy. Cervical cancer biology may be modulated by HIV infection, CD4-positive cells, and HIV treatments.

Cervical cancer has become a leading cause of death in both HIV-infected and uninfected women. Previous studies have revealed that antiretroviral therapy (ART) possesses anti-human papillomavirus (HPV) and antitumour properties, potentially serving as an anticancer agent and improving functional immunity in HIV-positive individuals. However, to the best of our knowledge, no studies have examined the association between ART and the clinical outcome of patients with pre-existing invasive cervical cancer. The current study analysed 48 HIV-positive and 123 HIV-negative patients with locally advanced stage IB2-IVA cervical cancer between December 2008 and December 2016. Tumours were categorized based on programmed cell death-ligand 1 (PD-L1) immunoreactivity and copy number alterations in the PD-L1 gene, as determined by fluorescence in situ hybridization. The results revealed that ART-treated patients exhibited a lower prevalence of PD-L1 immunopositivity, PD-L1 amplification and polysomy compared with patients that did not receive ART and those that were HIV-negative. Furthermore, ART-treated patients with PD-L1 immunonegativity exhibited an improved recurrence-free survival (RFS) compared with patients that did not receive ART and HIV-negative individuals with PD-L1 immunopositivity (P=0.041 vs. P=0.030). Additionally, ART-exposed patients with PD-L1 disomy demonstrated improved locoregional recurrence-free survival (LRR) when compared with HIV-negative patients with PD-L1 amplification and polysomy (P=0.039 vs. P=0.007), RFS (P<0.001 vs. P=0.006) and cancer-specific survival (CSS) (P=0.021 vs. P=0.025). ART-exposed patients with PD-L1 disomy also exhibited improved RFS (P<0.001) and CSS (P<0.001) compared with HIV-negative patients with PD-L1 amplification. Improved LRRs were demonstrated in ART-exposed patients with PD-L1 disomy (P=0.028) compared with non-HIV patients with polysomy. Following multivariate analysis, International Federation of Gynaecology and Obstetrics stage and PD-L1 amplification were determined to be predictors of poor a RFS [hazard ratio (HR), 2.43; 95% confidence interval (CI), 1.37–4.30; P=0.002 vs. HR, 7.03; 95% CI, 2.79–17.74; P<0.001) and CSS (HR, 11.47; 95% CI, 4.70–27.99; P<0.001 vs. HR, 4.05; 95% CI, 1.64–9.98; P=0.002). However, only PD-L1 polysomy was determined to be a predictor of poor LRR (HR, 2.50; 95% CI, 1.11–5.63; P=0.027). HIV status was not associated with poor outcomes, as determined using Cox models. The results of the current study indicated that ART may be used for the treatment of cervical cancer in both HIV-infected and uninfected patients. However, additional research is required to further elucidate these results.

Background Conventional differential expression (DE) testing compares the grouped mean value of tumour samples to the grouped mean value of the normal samples, and may miss out dysregulated genes in small subgroup of patients. This is especially so for highly heterogeneous cancer like Hepatocellular Carcinoma (HCC). Methods Using multi-region sampled RNA-seq data of 90 patients, we performed patient-specific differential expression testing, together with the patients’ matched adjacent normal samples. Results Comparing the results from conventional DE analysis and patient-specific DE analyses, we show that the conventional DE analysis omits some genes due to high inter-individual variability present in both tumour and normal tissues. Dysregulated genes shared in small subgroup of patients were useful in stratifying patients, and presented differential prognosis. We also showed that the target genes of some of the current targeted agents used in HCC exhibited highly individualistic dysregulation pattern, which may explain the poor response rate. Discussion/conclusion Our results highlight the importance of identifying patient-specific DE genes, with its potential to provide clinically valuable insights into patient subgroups for applications in precision medicine.

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