Whole genome sequencing refines stratification and therapy of patients with clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common form of kidney cancer, but a comprehensive description of its genomic landscape is lacking. We report the whole genome sequencing of 778 ccRCC patients enrolled in the 100,000 Genomes Project, providing the most detailed somatic mutational landscape to date. We identify new driver genes, which as well as emphasising the major role of epigenetic regulation in ccRCC highlight additional biological pathways extending opportunities for drug repurposing. Genomic characterisation identified patients with divergent clinical outcome; higher number of structural copy number alterations associated with poorer prognosis, whereas VHL mutations were independently associated with a better prognosis. The twin observations that higher T-cell infiltration is associated with better outcome and that genetically predicted immune evasion is not common supports the rationale for immunotherapy. These findings should inform personalised surveillance and treatment strategies for ccRCC patients.

The evolution of lung cancer and impact of subclonal selection in TRACERx

Lung cancer is the leading cause of cancer-associated mortality worldwide1. Here we analysed 1,644 tumour regions sampled at surgery or during follow-up from the first 421 patients with non-small cell lung cancer prospectively enrolled into the TRACERx study. This project aims to decipher lung cancer evolution and address the primary study endpoint: determining the relationship between intratumour heterogeneity and clinical outcome. In lung adenocarcinoma, mutations in 22 out of 40 common cancer genes were under significant subclonal selection, including classical tumour initiators such as TP53 and KRAS. We defined evolutionary dependencies between drivers, mutational processes and whole genome doubling (WGD) events. Despite patients having a history of smoking, 8% of lung adenocarcinomas lacked evidence of tobacco-induced mutagenesis. These tumours also had similar detection rates for EGFR mutations and for RET, ROS1, ALK and MET oncogenic isoforms compared with tumours in never-smokers, which suggests that they have a similar aetiology and pathogenesis. Large subclonal expansions were associated with positive subclonal selection. Patients with tumours harbouring recent subclonal expansions, on the terminus of a phylogenetic branch, had significantly shorter disease-free survival. Subclonal WGD was detected in 19% of tumours, and 10% of tumours harboured multiple subclonal WGDs in parallel. Subclonal, but not truncal, WGD was associated with shorter disease-free survival. Copy number heterogeneity was associated with extrathoracic relapse within 1 year after surgery. These data demonstrate the importance of clonal expansion, WGD and copy number instability in determining the timing and patterns of relapse in non-small cell lung cancer and provide a comprehensive clinical cancer evolutionary data resource.

Abstract 6080: The heterogeneity and evolution of lung neuroendocrine tumors within TRACERx

Introduction: Primary pulmonary neuroendocrine tumors (NETs) contribute to 20-25% of all lung cancer diagnoses and lie on a spectrum of malignant behavior, ranging from low grade classical carcinoid tumors to high grade, aggressive small cell carcinomas. The evolutionary relationships between NETs of different grades remain poorly understood, here we seek to use the TRACERx study to explore the genomic evolution of these lung cancers.

Methods: Tissue and blood samples were taken from a cohort of 20 patients with pulmonary NETs in a sub-study within TRACERx. Multi-region sampling (84 total regions) and whole exome sequencing was performed on fresh frozen tissue from each tumor. Histological classification of each tumor region was confirmed and scoring of tumor infiltrating lymphocytes (TILs) was performed. The data were then analyzed using the established TRACERx bioinformatics pipeline.

Results: Phylogenetic evolutionary histories were generated, illustrating the genomic divergence in each tumor and identifying points at which specific known drivers were acquired during tumor evolution. Lower grade classical and atypical carcinoids were characterized by a low mutational and copy number burden with a high fraction of subclonal mutations, with 5/12 cases having no apparent somatic mutational driver mutation. In contrast higher grade large cell neuroendocrine carcinomas and small cell carcinomas had higher mutational and copy number burden, as well as higher rates of genome instability and whole genome doubling. We identified no evolutionary link between subtypes such as commonly shared clonal drivers, suggesting that atypical or classical carcinoids later evolve into higher grade carcinomas. Dn/ds was used to investigate for evidence of selection in the carcinoid tumors; while there was no evidence for selection in known cancer driver genes associated with NETs or lung cancer, there was a high global dn/ds value suggesting the existence of unknown drivers for this cancer type. Furthermore, there was evidence of parallel evolution in one atypical carcinoid case with two distinct subclonal MEN1 frameshift mutations co-occurring with loss of the other allele. One small cell carcinoma patient was identified as having two genetically unrelated tumors. A germline predisposition for this tumor was suspected since we identified a variant in BRCA2 (rs11571833) that was maintained under loss of heterozygosity in one tumor with a corresponding somatic BRCA2 mutation in the other, suggesting two independent double hit events.

Conclusions: Genomic differences are identifiable between different members of the pulmonary NET family, with high grade tumors showing increased whole genome instability indices and phylogenetic divergence than low grade tumors. This work has shed light on the genomic landscape of pulmonary NETs and enabled the identification of distinct evolutionary trajectories in the different subtypes.

Citation Format: Robert Bentham, David A. Moore, Lorelle Brownlee, Raju Veeriah, Lizi Manzano, Fiona Blackhall, Colin R. Lindsay, TRACERx Consortium, Nicholas McGranahan, Charles Swanton, Mariam Jamal-Hanjani. The heterogeneity and evolution of lung neuroendocrine tumors within TRACERx [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6080.

Abstract 1394: Pervasive allele specific transcriptional repression of the class I and II HLA genes in TRACERx non-small cell lung cancer

Background: The adaptive immune system plays an important role in tumor evolution. A key source of cytotoxic T cell response in cancer is neoantigens, cancer cell specific mutations that result in mutant peptides that elicit a T cell mediated immune response. However, a mutation can only engender a neoantigen if the associated mutant peptide is presented to T cells by HLA molecules, and, as such, transcriptional repression or loss of the HLA genes can have important implications for immune evasion.

Methods: We elucidate allele specific genomic and transcriptomic disruption to class I and II HLA genes. In whole exome sequencing (WES) data, our new tool (LOHHLA2.0) assesses loss of heterozygosity (LOH) status and somatic mutations. In RNA sequencing (RNAseq) data, LOHHLA2.0 quantifies allele specific expression and transcriptional repression referencing matched tumor adjacent normal samples. We applied LOHHLA2.0 to the TRACERx421 dataset, including 1554 WES tumor regions from 421 patients and 941 RNAseq regions from 357 tumor patients, 96 of which also had RNAseq from tumor adjacent normal samples.

Results: We find that our method is more accurate than existing tools (RSEM) at calling gene level expression, e.g. in HLA-DPB1, RSEM under-calls HLA expression by a factor of two. 36% of TRACERx421 primary tumors harbored HLA LOH of at least one class I HLA gene, validating our previous findings in the TRACERx100 cohort. Strikingly, we found that 74% (71/96) of primary tumors with matched tumor adjacent normal tissue exhibited transcriptional repression of one or more class I HLA alleles, and 81% (78/96) exhibited class II allele transcriptional repression. Class I HLA transcriptional repression was more likely to occur subclonally than LOH. In a subset of tumors, we observed convergence upon disruption of the same allele through alternative mechanisms; with genomic loss in one tumor region and transcriptional repression in another region of the same tumor. Across the tumor regions, we found a concordance between HLA expression and immune infiltrate levels, with immune hot tumors exhibiting higher HLA class I expression.

Conclusions: In this study, we find significant disruption to class I and II HLA expression adding to the diversity of immune evasion processes evident in early stage treatment naive NSCLC.

Citation Format: Clare Puttick, Oriol Pich, Michelle Leung, Carlos Martinez-Ruiz, Robert Bentham, Rachel Rosenthal, Sonya Hessey, James R. Black, Emilia L. Lim, Katey Enfield, Emma Colliver, Krijn Dijkstra, Crispin T. Hiley, Takahiro Karasaki, Ariana Huebner, Maise Al Bakir, Thomas B. Watkins, Alexander M. Frankell, Simone Zaccaria, Mariam Jamal-Hanjani, Nicholas McGranahan, Charles Swanton. Pervasive allele specific transcriptional repression of the class I and II HLA genes in TRACERx non-small cell lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1394.

Using DNA sequencing data to quantify T cell fraction and therapy response

The immune microenvironment influences tumour evolution and can be both prognostic and predict response to immunotherapy1,2. However, measurements of tumour infiltrating lymphocytes (TILs) are limited by a shortage of appropriate data. Whole-exome sequencing (WES) of DNA is frequently performed to calculate tumour mutational burden and identify actionable mutations. Here we develop T cell exome TREC tool (T cell ExTRECT), a method for estimation of T cell fraction from WES samples using a signal from T cell receptor excision circle (TREC) loss during V(D)J recombination of the T cell receptor-α gene (TCRA (also known as TRA)). TCRA T cell fraction correlates with orthogonal TIL estimates and is agnostic to sample type. Blood TCRA T cell fraction is higher in females than in males and correlates with both tumour immune infiltrate and presence of bacterial sequencing reads. Tumour TCRA T cell fraction is prognostic in lung adenocarcinoma. Using a meta-analysis of tumours treated with immunotherapy, we show that tumour TCRA T cell fraction predicts immunotherapy response, providing value beyond measuring tumour mutational burden. Applying T cell ExTRECT to a multi-sample pan-cancer cohort reveals a high diversity of the degree of immune infiltration within tumours. Subclonal loss of 12q24.31-32, encompassing SPPL3, is associated with reduced TCRA T cell fraction. T cell ExTRECT provides a cost-effective technique to characterize immune infiltrate alongside somatic changes.

Meta-analysis of tumor- and T cell-intrinsic mechanisms of sensitization to checkpoint inhibition

Checkpoint inhibitors (CPIs) augment adaptive immunity. Systematic pan-tumor analyses may reveal the relative importance of tumor-cell-intrinsic and microenvironmental features underpinning CPI sensitization. Here, we collated whole-exome and transcriptomic data for >1,000 CPI-treated patients across seven tumor types, utilizing standardized bioinformatics workflows and clinical outcome criteria to validate multivariable predictors of CPI sensitization. Clonal tumor mutation burden (TMB) was the strongest predictor of CPI response, followed by total TMB and CXCL9 expression. Subclonal TMB, somatic copy alteration burden, and histocompatibility leukocyte antigen (HLA) evolutionary divergence failed to attain pan-cancer significance. Dinucleotide variants were identified as a source of immunogenic epitopes associated with radical amino acid substitutions and enhanced peptide hydrophobicity/immunogenicity. Copy-number analysis revealed two additional determinants of CPI outcome supported by prior functional evidence: 9q34 (TRAF2) loss associated with response and CCND1 amplification associated with resistance. Finally, single-cell RNA sequencing (RNA-seq) of clonal neoantigen-reactive CD8 tumor-infiltrating lymphocytes (TILs), combined with bulk RNA-seq analysis of CPI-responding tumors, identified CCR5 and CXCL13 as T-cell-intrinsic markers of CPI sensitivity.

Mitochondria form contact sites with the nucleus to couple prosurvival retrograde response

Mitochondria drive cellular adaptation to stress by retro-communicating with the nucleus. This process is known as mitochondrial retrograde response (MRR) and is induced by mitochondrial dysfunction. MRR results in the nuclear stabilization of prosurvival transcription factors such as the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB). Here, we demonstrate that MRR is facilitated by contact sites between mitochondria and the nucleus. The translocator protein (TSPO) by preventing the mitophagy-mediated segregation o mitochonria is required for this interaction. The complex formed by TSPO with the protein kinase A (PKA), via the A-kinase anchoring protein acyl-CoA binding domain containing 3 (ACBD3), established the tethering. The latter allows for cholesterol redistribution of cholesterol in the nucleus to sustain the prosurvival response by blocking NF-κB deacetylation. This work proposes a previously unidentified paradigm in MRR: the formation of contact sites between mitochondria and nucleus to aid communication.

The presence of opportunistic pathogens, Legionella spp., L. pneumophila and Mycobacterium avium complex, in South Australian reuse water distribution pipelines

Water reuse has become increasingly important for sustainable water management. Currently, its application is primarily constrained by the potential health risks. Presently there is limited knowledge regarding the presence and fate of opportunistic pathogens along reuse water distribution pipelines. In this study opportunistic human pathogens Legionella spp., L. pneumophila and Mycobacterium avium complex were detected using real-time polymerase chain reaction along two South Australian reuse water distribution pipelines at maximum concentrations of 10⁵, 10³ and 10⁵ copies/mL, respectively. During the summer period of sampling the concentration of all three organisms significantly increased (P < 0.05) along the pipeline, suggesting multiplication and hence viability. No seasonality in the decrease in chlorine residual along the pipelines was observed. This suggests that the combination of reduced chlorine residual and increased water temperature promoted the presence of these opportunistic pathogens.

Mycobacterium avium complex--the role of potable water in disease transmission

Mycobacterium avium complex (MAC) is a group of opportunistic pathogens of major public health concern. It is responsible for a wide spectrum of disease dependent on subspecies, route of infection and patients pre-existing conditions. Presently, there is limited research on the incidence of MAC infection that considers both pulmonary and other clinical manifestations. MAC has been isolated from various terrestrial and aquatic environments including natural waters, engineered water systems and soils. Identifying the specific environmental sources responsible for human infection is essential in minimizing disease prevalence. This paper reviews current literature and case studies regarding the wide spectrum of disease caused by MAC and the role of potable water in disease transmission. Potable water was recognized as a putative pathway for MAC infection. Contaminated potable water sources associated with human infection included warm water distribution systems, showers, faucets, household drinking water, swimming pools and hot tub spas. MAC can maintain long-term contamination of potable water sources through its high resistance to disinfectants, association with biofilms and intracellular parasitism of free-living protozoa. Further research is required to investigate the efficiency of water treatment processes against MAC and into construction and maintenance of warm water distribution systems and the role they play in MAC proliferation.

Determination of faecal pollutants in Torrens and Patawalonga catchment waters in South Australia using faecal sterols

This research investigated faecal pollution by sterol profiling in two Adelaide metropolitan catchments in winter 2000 and summer 2001. Water was sampled from five sites on the River Torrens and two sites on Patawalonga river catchment. The steroids detected were coprostanol, epicoprostanol, cholesterol, cholestanol, stigmasterol, betasitosterol, and stigmastanol. The concentrations range from 5 ng/L (of coprostanol) to 34 microg/L (of stigmasterol), with cholesterol detected more frequently at relatively high concentrations (approximately 2 microg/L). Sterol profiling suggested two sites on two occasions may have been impacted by human faecal contamination. Other steroid profiles suggested that sources of pollution consistently included dogs and birds. The steroid concentrations in the Torrens catchment were higher in winter, however, this was not observed in the Patawalonga catchment.