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Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types. This effort complements both ongoing efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at a single point in time. Generating single-cell, multiparametric, longitudinal atlases and integrating them with clinical outcomes should help identify novel predictive biomarkers and features as well as therapeutically relevant cell types, cell states, and cellular interactions across transitions. The resulting tumor atlases should have a profound impact on our understanding of cancer biology and have the potential to improve cancer detection, prevention, and therapeutic discovery for better precision-medicine treatments of cancer patients and those at risk for cancer.

Background: Multiple lung screening studies have shown a beneficial reduction in cancers specific mortality with annual low-dose computed tomography (LDCT) screening in high risk patients and resulted in a much improved probability of early stage disease at diagnosis. Nonetheless, still ~30% of such patients have a recurrence within 5 years following surgical resection. This begs the question what are the molecular determinants of cancer behavior between indolent and aggressive tumors. Methods: A targeted deep sequencing was performed on the DNA samples of 21 adenocarcinoma in situ (AIS), 27 minimally invasive adenocarcinoma (MIA) and 54 fully invasive adenocarcinoma. These cancers were classified based on the tumor size (1.5 cm) as indolent (n=42) and aggressive (n=60) tumors. We analyzed the association between tumor aggressiveness and genomic alterations of these targeted genes including frequency of gene mutations, copy number changes, mutation signatures, tumor clonality as well as overall survival. Results: Copy number loss of CRIPAK (chr4p16) and copy number gain of NOTCH1 were enriched in indolent tumors and chromosome 19q13 deletion was enriched in aggressive tumors. CRIPAK alterations including both mutations and copy number loss together were further significantly enriched in a subset of indolent tumors (16/25) that only consists of AIS/MIA. CRIPAK alterations were associated with longer survival in all population, after adjusting for histology and age (P=0.02). Interestingly, we found higher CRIPAK mRNA level was also significantly associated with better survival in a combined seven public lung adcarcinoma datasets (n=673, HR=0.37, P=1.1e-05), after adjusting for stage, gender and smoking history. In addition, both APOBEC and MMR mutation signatures were correlated with indolent tumors. Known driver genes such as KRAS, EGFR or TP53 mutations were not distinct between indolent and aggressive tumors, indicating an early role for these genes in the development of lung adenocarcinoma. Finally, we found that mutations of NCOR1, USP9X and NF1 were enriched in indolent tumors while mutations in GNAS and ATM were enriched in aggressive tumors. Conclusion: Our study suggests the genomic alterations of the chromosome 4p16 harboring a novel cancer gene CRIPAK’s deletions and mutations are predictive of indolent behavior, a finding that warrants further validation. This work was supported by UO1CA196405. Citation Format: Jun Qian, Heidi Chen, Yong Zou, Pierre Massion. CRIPAK genomic alterations are associated with indolent lung adenocarcinoma and predicts longer survival [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3413.

Background: Previous work from our laboratory has investigated the role of solute carrier family A1 member 5 (SLC1A5) as a critical modulator of glutamine (Gln) uptake, cell growth and tumor progression in non-small cell lung cancer (NSCLC). In addition, remarkable metabolic reprogramming was observed in cells from individuals at high risk of lung cancer, including an increased dependence on Gln. However, it remains unclear how these changes in Gln metabolism and other metabolic dysregulations contribute to early events of tumorigenesis such as genomic instability. Given the emerging role of Gln metabolism in cancer and the differential expression of SLC1A5 in NSCLC, we tested the hypothesis that Gln uptake is a key mechanism by which cells with oncogenic potential can transform into a malignant phenotype. Aims & Strategy: The aim of this study is to evaluate the involvement of SLC1A5 in the process of early oncogenic transformation and survival. To address this aim, we utilized four HBECs immortalized by over-expressing Cdk4 and human telomerase reverse transcriptase (hTERT), along with a series of canonical oncogenic drivers, P53-knocdown, KRAS and MYC overexpression, which drove these cells to exhibit a malignant phenotype. This successful transformation of an in vitro model could be useful in studying the metabolic dysregulation and, in particular, the role of Gln metabolism in contributing to genomic instability in an accessible and employable cell model representative of the oncogenic transformation process. Results: We found that oncogene driven HBECs exhibited a substantially higher expression of SLC1A5 than unaltered HBEC cells. Inhibition of SLC1A5 by a small molecule inhibitor, gamma-l-Glutamyl-P-NitroAnilide (GPNA), decreased cell survival, Gln uptake and markers of genotoxic stress. The sensitivity to GPNA treatment was significantly correlated with SLC1A5 RNA expression (R2=0.96, P Conclusion: Overall, Our results indicate that oncogene-transformed HBECs exhibited higher dependence on Gln uptake through SLC1A5 relative to the non-oncogenic clones. Tumor-forming HBECs exhibited higher sensitivity to SLC1A5 inhibition than non-tumorigenic ones. Furthermore, Gln deprivation was implicated in regulation of genomic integrity and apoptosis in this cell model. This works suggests that Gln metabolism regulates aspects of genomic instability and implicates its function in lung tumorigenesis. Citation Format: Omar M. Omar, Jamshedur Rahman, Pierre Massion. A human bronchial epithelial cell model demonstrates a role for glutamine regulation in genomic instability and oncogenic transformation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4354.

Malignancies of the lung are expected to be responsible for over 25% of all cancer-associated mortalities in the United States in 2019. Clinical treatment of lung cancer is complicated by both poor detection of early disease activity and relapse or unresponsiveness to administered therapy. Taken together, these realities of patient outcome underscore the need for alternative therapeutic strategies. Research efforts in the cancer immunology field focus primarily on T cells in the tumor microenvironment, however, there is evidence that B cells may impart a clinical benefit in patients. The formation of tertiary lymphoid structures and antibody secretion in lung tumors associate with positive clinical outcomes yet remain understudied and poorly characterized. In an effort to expand upon these observations, we isolated B cells from cryopreserved human lung cancer tissue and recovered B-cell receptor (BCR) sequences by paired heavy and light chain single cell RNA sequencing. From these experiments, we identified clonally expanded B-cell populations and convergent BCR sequences shared between different patients. We further demonstrated that recombinant antibodies derived from lung cancer patients bind cultured lung cancer cell lines in a dose-dependent manner. This preliminary data supports the notion that tumor-resident B-cells secrete functional antibodies that may additionally be tumor-reactive. Future characterization of these antibodies includes antigen identification and the measurement of in vitro and in vivo cytotoxic activity. Human patient-derived antibodies not only could serve as a novel source for therapeutic and diagnostic agents but may also help inform vaccine design in lung cancer indications.