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The diversity in somatic variation across human tissues outshining human cancers has only recently been started to be appreciated. In particular, healthy individuals carry large numbers of cells and clonal expansions with mutations in driver genes commonly observed in cancer. We previously demonstrated that the majority of epithelial cells in the proximal airway accumulate DNA damage proportionally to an individual's smoking habits. However, the analysis of whole genomes indicated the abundance of a population of cells with a near-normal mutation burden, mirroring cellular populations found in never-smoking individuals. In contrast to the proximal airway, the genomics of cells in the distal airway of healthy individuals with diverse smoking histories, and thus the foundation of lung adenocarcinoma (LUAD), has not been investigated yet. To assess the influence of smoking on the distal airway and to compare the genomics of proximal and distal airway in the lung, we established an experimental procedure to create single-cell derived alveolar type II (AT2) organoids from primary human tissue of 9 patients. In particular, we focus on AT2 cells, given their hypothesised role as a potential cell of origin for LUAD. Whole genome sequencing (WGS) of >400 organoids was utilised to assess the landscape of somatic variation, including single nucleotide variants (SNVs), insertions and deletions (indels), copy number and structural variation (CNVs, SVs). Focusing on SNVs, we found that the mutation burden of never-smokers is significantly lower compared to ex- and current-smokers. Emphasising the effect of tobacco smoking on the distal airway, this difference was driven by the presence of mutations related to SBS4 and SBS92, mutational signatures associated with tobacco smoking. Interestingly, and in contrast to the proximal airway, we did not find a difference in the mutation burden of ex- and current-smokers, suggesting that smoking damage to alveolar cells is more severe and long-term. Lastly, to characterise the driver mutation landscape in depth, we used targeted single-molecule sequencing of 250 known cancer genes to profile 15 AT2 single-cell suspensions as well as 22 frozen parenchyma biopsies. To date, our preliminary results indicate positive selection on lineage defining mutations including SFTPB and SFTPC, coding for surfactant as well as TP53. As we begin to explore these data further, we expect this work to provide unprecedented insights into the contribution of somatic and driver mutations to the earliest stages of lung cancer development. Citation Format: Moritz Jakob Przybilla, Amany Ammar, Ryan Chuen Khaw, Andrew R. Lawson, Pantelis Nicola, Kate Davies, Zoe Frazer, Kate H. Gowers, Timothy M. Butler, Sarah E. Clarke, Inigo Martincorena, Sam M. Janes, Peter J. Campbell. Somatic mutations in single-cell derived alveolar organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 218.

Patient-derived xenograft (PDX) models have become important models in cancer biology. They are thought to mimic tumor biology more closely than traditional cell lines as a consequence of their in vivo heterocellularity and cell-matrix interactions, their 3D architecture and their relatively recent derivation. The genomic fidelity of PDXs is integral to their applications in both basic research and in translational medicine. We derived multi-region PDX models from patients enrolled in TRACERx - a study of the evolutionary dynamics of non-small cell lung cancer (NSCLC) that uses a multi-region deep whole-exome sequencing (WES) approach - using more extensive spatial sampling to better understand the histological and genomic fidelity of the PDX approach. We transplanted regional NSCLC tumor tissue subcutaneously into immunocompromised NSG mice. 134 regions were attempted, resulting in 60 passagable xenografts (44.8%). Of these, 44 regional xenografts (32.8% of all regions) were NSCLC-derived, while 16 (11.9% of all regions) were B-cell lymphoproliferative disease. Multi-region sampling revealed heterogeneous success of PDX derivation between regions within individual patient tumors. There was correlation between PDX derivation and tumor purity by WES. Overall, NSCLC PDX models were established for 22 patients (50%; range 1-5 regional models per patient; Table 1). Histologically, broad similarity was observed between PDX models and corresponding patient tumor regions, although in a small number of models, variability was noted between the patient tumor and the corresponding PDX model, or during PDX passaging. PDXs were subjected to WES for comparison with matched patient tumor regions. Overall, our study demonstrates the feasibility of systematic multi-region PDX derivation and suggests that multiple spatial sampling of tumors could improve PDX take rates and generate PDXs that represent the intratumor diversity of heterogenous NSCLCs. Table 1. Engraftment rates of multiple spatial regions from non-small cell lung cancer tumors. Attempted NSCLC PDX B-Lymphoproliferations No Xenograft: Regions No Xenograft: Any Region LUAD 48 (21) 12 (7) 9 (7) 27 (10) LUSC 61 (17) 20 (11) 6 (5) 35 (4) Other 25 (6) 12 (4) 1 (1) 12 (1) TOTAL 134 (44) 44 (22) 16 (13) 74 (15) Citation Format: Robert E. Hynds, David R. Pearce, Ayse U. Akarca, Sophia Ward, Ariana Huebner, Oriol Pich, Gareth A. Wilson, Kate H. Gowers, Rebecca Towns, Assma Ben Aissa, Selvaraju Veeriah, Sergio A. Quezada, Mariam Jamal-Hanjani, Sam M. Janes, Nicholas McGranahan, David A. Moore, Teresa Marafioti, Charles Swanton. Multi-region patient-derived xenograft models from non-small cell lung cancer patients enrolled in lung 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 3096.

Introduction: Airway basal cells isolated from histologically normal epithelium in current and former smokers demonstrate a significantly higher mutation burden than those in never-smokers. However, a proportion of basal cells with lower (“near normal”) mutation burden are observed, which show preferential expansion in response to smoking cessation(1). We believe this expansion represents a “cancer protective” process, reducing the risk of future malignancy. However, mechanisms determining the dynamic balance of high versus low mutant basal cells throughout the bronchial tree are unclear. We have developed protocols that enable systematic scanning of airway epithelium in resected lung specimens, through which we aim to elucidate the mutation burden and spatial clonal architecture across contiguous regions of normal epithelium through the bronchial tree. Study design: 5-10 current or former smokers undergoing curative lobectomy for peripheral lung cancer with histologically normal airways will be consented to the study. To date, two participants have donated their samples. Fresh lobectomies were collected at the point of resection and kept on wet ice until pathological examination. All samples undergo examination within 1 hour of resection. The lobe is orientated, and the tumour and segmental bronchi identified. A sterile metal cannula is inserted through the airway lumen and sterile pathology scissors are used to carefully isolate the airways from the surrounding parenchyma. Upon macro-dissection, airway branches are immediately placed into transport media containing antibiotics. Samples are gently washed using transport media to remove residual blood, then sectioned into 1 cm3 segments, which are orientated, embedded and frozen in room-temperature Optimal Cutting Temperature compound. An 8 μM section is cut and stained with haematoxylin and eosin from each block immediately after a “full-face” tissue confirmation is observed.These will be used as guiding slides for laser capture microdissection of the regions of epithelium prior to downstream sequencing pathway. Conclusion: We have developed a pathological approach in which we can define somatic mutations in normal epithelium along the bronchial tree. We will use these data to determine basal cell clonal relationships and interpret these in a spatial context, creating a more detailed map of the smoking-induced changes that occur in the airway epithelium and how these may contribute to early carcinogenesis. References1.Yoshida K, Gowers KHC, Lee-Six H, Chandrasekharan DP, Coorens T, Maughan EF, et al. Tobacco smoking and somatic mutations in human bronchial epithelium. Nature. 2020;578(7794):266-72. Citation Format: Kate E. Davies, Helen Hall, Zoe Frazer, Kate Gowers, David Moore, Fleur Monk, Moritz J. Przybilla, Peter J. Campbell, Sam M. Janes. Contiguous airway sampling for basal cell isolation [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 2202.

Background: Bronchial pre-malignant lesions (PMLs) are the putative precursors for bronchial squamous cell carcinoma. PMLs represent a spectrum of histologies, from low-grade lesions (hyperplasia, metaplasia) to high-grade lesions (dysplasia, carcinoma in situ). The majority of these lesions will regress or remain stable without clinical intervention while a subset of lesions will progress to invasive carcinoma. We performed single-cell RNA sequencing (scRNAseq) of these lesions to elucidate the cross-talk between epithelial, stromal, and immune populations in lesions of increasing histological grade. Methods: Thirty lesions from seventeen participants were biopsied via bronchoscopy. Cells were sorted by CD45+/- FACS gating and sequenced with the Cel-Seq2 protocol. Celda was used to bi-cluster genes into modules and cells into clusters. Cells were filtered by mitochondrial percentage (%mito < 50%), minimum UMI counts (nUMI > 300), and doublet detection. Cell types were labeled by marker gene expression. Results: After filtering low quality cells, we analyzed 4,382 cells. We observed expected smoking related shifts in epithelial cell type proportions, including an increase in secretory cells (χ2 = 31.39, p = 2.11 X 10-8) and a decrease in ciliated cells (χ2 = 4.83, p = 0.028) among current smokers. Distinct differences in expression of transcriptional modules were observed between KRT5+ (basal) cells from different histologic grades. Basal cells from high grade lesions expressed smoking detoxification and cell cycle gene programs, while low grade lesion basal cells expressed differentiation gene programs. We also identified a group of cells from CIS lesions involved in an epithelial-to-mesenchymal transition, marked by an increase in SPARC and COL4A1 expression and a decrease in CDH1 expression. Subpopulations of immune cells identified include macrophages, CD4/8+ T, B, dendritic cells, and natural killer cells. Several clusters of CD4+ and CD8+ T cells displayed an exhausted phenotype, marked by the expression of PD-1, CTLA4, LAG3, and TIGIT. Samples with high grade histology (dysplasia, carcinoma in situ) were enriched in CD4+ Tregs and myeloid cells compared to low grade histology samples (hyperplasia, metaplasia), which were enriched in Natural Killer and cytotoxic CD8+ T cells (χ2 = 298.95, p = 0.001). Discussion: Our results suggest that changes in specific transcriptional programs are associated with the transition of epithelial cells to more invasive states and that changes in immune populations are associated with increasing histological grade. These signatures can suggest novel avenues for chemoprevention and cancer interception. Citation Format: Conor Shea, Lukas Kalinke, Kitty De Jong, Kate Gowers, Diane Ding, Sherry Zhang, Gang Liu, Jack Cunningham, Ipsita Dey-Guha, Mark Hennon, Sai Yendamuri, Christopher Stevenson, Avrum Spira, Mary E. Reid, Marc E. Lenburg, Sam M. Janes, Jennifer E. Beane, Sarah A. Mazzilli, Joshua D. Campbell. Epithelial, stromal, and immune changes associated with lung squamous premalignant lesion severity identified by single-cell RNA-seq [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 2201.

It is well established that tobacco smoking causes lung cancer and this is thought to be the result of a progressive accumulation of genomic mutations induced by tobacco smoke exposure; however, until recently a detailed understanding of the effects of smoke exposure on the genomes of cells in the normal bronchial epithelium was lacking. To address this, we defined the genomic architecture of normal airway basal cells in children and non-smoking, smoking and ex-smoking adults. We discovered two populations of basal cells in individuals with a smoking history: those with high mutational burden, driver gene mutations and tobacco-associated mutational signatures, and those with low mutational burden, similar to basal cells from never smokers and with an absence of mutational signatures associated with tobacco exposure. These cells expand preferentially in ex-smokers, accounting for 20-40% of basal cells compared with 2-5% in current smokers. We hypothesise that these cells are cancer-protective and their expansion reduces the risk of lung cancer development after smoking cessation. Understanding the functional differences between high- and low-mutant airway basal cells and the mechanisms by which some cells resist the accumulation of smoking-induced mutations will be crucial to understanding the earliest stages of lung carcinogenesis. To address this, we performed RNAseq on a subset of whole-genome sequenced airway basal cells. Preliminary data show that expression of markers of stemness is significantly different between high- and low-mutant basal cells. In addition, initial analysis shows that pathways such as carcinogen metabolism and MHC class I antigen presentation are higher in high-mutant basal cells. Further analysis in more patients is ongoing. To complement these data, we expanded whole-genome sequenced basal cell clones in culture and performed a range of assays to assess their progenitor and differentiation capacity. We assessed proliferation, colony-forming efficiency, longevity and differentiation and found no apparent differences between low- and high-mutant basal cells. Initial analysis suggests that carcinogen metabolism and MHC class I antigen presentation may be key pathways in establishing heterogeneity in mutational burden and clonal dynamics in the normal airway epithelium. Additional assays and analysis are ongoing and will be the focus of future research. Citation Format: Kate H. Gowers, Sarah E. Clarke, Ayu Hutami Syaraf, Kenichi Yoshida, Moritz J. Przybilla, Hugh Selway, Adam Pennycuick, Peter J. Campbell, Sam M. Janes. Defining the mechanisms that lead to mutational heterogeneity in the normal respiratory epithelium [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 3158.

Background: Sampling the bronchial airway during bronchoscopies in screening populations at high risk for lung cancer has increased detection of squamous bronchial pre-malignant lesions (PML). The majority of these lesions will regress or remain stable without any clinical intervention. However, a subset of lesions will progress to invasive malignancy. In this work, we investigate the gene expression changes in epithelial cell states and immune cell proportion shifts associated with premalignant histologic stage using single-cell RNA sequencing to begin to identify molecular features associated with PML regression or progression. Methods: Cells (n=3,325) were isolated from 11 endobronchial biopsies from 9 patients, where biopsy histology range from normal, dysplasia, carcinoma in situ (CIS) and squamous cell carcinoma. Immune cells (CD45+) and epithelial cells (CD45− EPCAM+) were sorted into separate 96-well plates using fluorescence activated cell sorting (FACS) and sequenced using CEL-Seq2 single cell RNA seq protocol. Results: After filtering low quality cells, we profiled 2,998 cells (1,052 CD45+ and 1,946 CD45−) with an average of 1,190 genes per cell. Within the epithelial cells, we focused on basal cells as they are the airway progenitor cells. We observed distinct differences in expression of KRT5+ (basal) cells between different histologic grades, where KRT5+ cells present in a hyperplasic lesion expressed multiple secretory cell markers suggesting they were transitioning to a secretory cell phenotype and KRT5+ cells from a CIS lesion from a current smoker expressed higher levels of smoking inducible genes, such as GSTM1 and CYP1A1. Lastly, KRT5+ cells from a lung squamous carcinoma tumor expressed higher levels of many genes related to cell cycle progression. Among the immune populations, low-grade PMLs with non-dysplastic histology were enriched for CD8+ T cells, whereas higher-grade PMLs and an invasive tumor were enriched for myeloid cells. Conclusions: To date, we have begun to identify histology-associated cellular and molecular profiles in bronchial premalignancy and early-stage carcinoma. Future resampling of these patients and expansion of cases will allow us to discover biomarkers associated with lesion progression and molecular targets for lung cancer interception. Citation Format: Conor Shea, Lukas Kalinke, Kitty De Jong, Kate Gowers, Diane Ding, Sherry Zhang, Gang Liu, Jack Cunningham, Ipsita Dey-Guha, Mark Hennon, Sai Yendumuri, Christopher Stevenson, Steven Dubinett, Avrum Spira, Marc Lenburg, Samuel Janes, Mary Reid, Jennifer Beane, Sarah Mazzilli, Joshua D. Campbell. Cellular and molecular changes associated with lung squamous premalignant lesion severity identified by single-cell RNA-seq [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2212.

Mesothelioma is a rapidly lethal cancer with limited treatment options. Spindle poisons have demonstrated clinical usefulness in mesothelioma, however, predictive biomarkers are lacking. Anetumab ravtansine (ARav) is an antibody drug-conjugate (ADC) comprising a mesothelin targeting antibody coupled to the payload, DM4, a microtubule destabilizer. We have recently identified BRCA1 as a direct regulator of the spindle assembly checkpoint (SAC), which is activated by spindle poisons and mediates mitotic arrest. BAP1 is one of the most frequently inactivated tumor suppressors in mesothelioma and it interacts with and regulates expression of BRCA1. We therefore hypothesized that BAP1 inactivation may confer resistance to ARav, highlighting a potential opportunity to refine personalization with this ADC. Three primary cell lines were derived from mesotheliomas resected during pleurectomy decortication expressed mesothelin (MSLN) and further characterized via whole exome sequencing. Two of the three primary cell lines have BAP1 mutation (R417 frameshift (fs); E631fs) and show reduced BRCA1/MAD2 protein expression. MSLN expression was found to be independent of BAP1 inactivation status or BRCA1 expression level. BAP1 mutant primary cell lines exhibited resistance to ARav by overriding the mitotic arrest with continued cell cycle progression, indicating a defective SAC whereas the cell line with wt BAP1 underwent mitotic arrest followed by cell death. Increase in mitotic index was also observed in primary cell line with wt BAP1 following ARav treatment without any significant change in BAP1 mutant cell lines. Resistance to ARav in BAP1 deleted cell line NCI-H226 was reversed by stable expression of wildtype BAP1 in NCI-H226 indicating critical regulation of SAC by BAP1. Vinorelbine resistant cell line RVR with a defective SAC also exhibited resistance to ARav compared to the parental REN with no change in MSLN expression suggesting that an active SAC is required for prolonged mitotic arrest and subsequent cell death. Wildtype BAP1 and MSLN is critical for efficacy of ARav. Inactivation of BAP1 correlates with loss of BRCA1 expression and dysregulation of the SAC. Citation Format: Anita Singh, Jin-li Luo, Sara Busacca, Alan Dawson, Krishna Kalyan Kolluri, Samuel Janes, Andrew Fry, Anette Sommer, Dean Fennell. Loss of BAP1/BRCA1 counteracts spindle assembly checkpoint activation by the anti-mesothelin antibody drug-conjugate anetumab ravtansine [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1808.

Background Lung cancer is the leading cause of cancer death, of which 80-90% are attributed to tobacco smoking. Our understanding of how tobacco exposure affects mutational burden, mutational signatures, driver mutations and clonal dynamics in normal lung tissue is limited. Also, genetic differences between normal cells and cancer cells in lung has not been fully elucidated. Methods To access the landscape of somatic mutations in normal bronchial epithelia, we sequenced whole genomes of 632 single-cell-derived colonies of lung basal cells from 16 patients, including 3 children, 4 never-smokers, 6 ex-smokers and 3 current smokers. Five patients had squamous cell carcinomas or carcinoma in situ, which we also sequenced to compare the genetic alteration between normal and cancer cells. Results A positive correlation between the number of base substitutions and age was observed, and 22 somatic mutations accumulated per year (95% confidence interval:20-25; P=10−8). Previous or current smoking significantly increased mutational burden: 2330 substitutions in ex-smokers and 5300 in current smokers. In addition, tobacco smoking is massively increasing both between-subject and within-subject variance of mutation burden. A population of cells in subjects with smoking history had mutation burdens equivalent to that expected for never-smokers: these cells had less damage from tobacco-specific mutational processes, and were four-fold more frequent in ex-smokers than current smokers. Signature analysis revealed that the same mutational signatures seen in lung cancers operate both in patients with and without smoking history: endogeneous signatures, including COSMIC signatures 1 and 5, and APOBEC-related signatures. Three mutational signatures were largely restricted to current or ex-smokers, including known smoking-related COSMIC signature 4 characterized by C>A transversions, signature 16 characterized by T>C mutations with extremely strong transcription strand bias and a new signature characterized by T>A and T>C mutations. dN/dS method identified driver genes in normal bronchial epithelium, including NOTCH1, TP53 and FAT1, which were overlapped with those seen in squamous cell lung cancers and other normal squamous tissues such as esophagus and skin. Driver mutations increased in frequency with age, affecting 4-14% of cells in middle-aged never-smokers. In current smokers, ≥25% of cells carried driver mutations and 0-6% cells had 2 or even 3 drivers. Layering driver mutations onto phylogenetic trees revealed that driver mutations occurred in early life. Compared to the normal bronchial epithelial cells, lung cancers and precancerous lesions were characterized by extensive copy number changes or structural variants and distinct set of driver mutations. Conclusions Tobacco smoking increases mutation burden, cell-to-cell heterogeneity and driver mutations. Our data of genetic lesions in normal bronchial cells provides insights into genetic alterations that drive carcinogenesis in lung. Citation Format: Kenichi Yoshida, Kate HC Gowers, Henry Lee-Six, Deepak P. Chandrasekharan, Tim Coorens, Elizabeth F. Maughan, Kathryn Beal, Andrew Menzies, Fraser R. Millar, Elizabeth Anderson, Sarah E. Clarke, Adam Pennycuick, Ricky M. Thackeray, Colin R. Butler, Nobuyuki Kakiuchi, Tomonori Hirano, Robert E. Hynds, Michael R. Stratton, Inigo Martincorena, Sam M. Janes, Peter J. Campbell. Tobacco exposure and somatic mutations in normal bronchial epithelia [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2342.

The ability of mesenchymal stem cells (MSC) to specifically home to tumors has suggested their potential use as a delivery vehicle for cancer therapeutics. MSC integration into tumors has been shown in animal models using histopathologic techniques after animal sacrifice. Tracking the delivery and engraftment of MSCs into human tumors will need in vivo imaging techniques. We hypothesized that labeling MSCs with iron oxide nanoparticles would enable in vivo tracking with magnetic resonance imaging (MRI). Human MSCs were labeled in vitro with superparamagnetic iron oxide nanoparticles, with no effect on differentiation potential, proliferation, survival, or migration of the cells. In initial experiments, we showed that as few as 1,000 MSCs carrying iron oxide nanoparticles can be detected by MRI one month after their coinjection with breast cancer cells that formed subcutaneous tumors. Subsequently, we show that i.v.- injected iron-labeled MSCs could be tracked in vivo to multiple lung metastases using MRI, observations that were confirmed histologically. This is the first study to use MRI to track MSCs to lung metastases in vivo. This technique has the potential to show MSC integration into human tumors, allowing early-phase clinical studies examining MSC homing in patients with metastatic tumors. [Cancer Res 2009;69(23):8862–7]