Genomic mapping of metastatic organotropism in lung adenocarcinoma

We analyzed 2,532 lung adenocarcinomas (LUAD) to identify the clinicopathological and genomic features associated with metastasis, metastatic burden, organotropism, and metastasis-free survival. Patients who develop metastasis are younger and male, with primary tumors enriched in micropapillary or solid histological subtypes and with a higher mutational burden, chromosomal instability, and fraction of genome doublings. Inactivation of TP53, SMARCA4, and CDKN2A are correlated with a site-specific shorter time to metastasis. The APOBEC mutational signature is more prevalent among metastases, particularly liver lesions. Analyses of matched specimens show that oncogenic and actionable alterations are frequently shared between primary tumors and metastases, whereas copy number alterations of unknown significance are more often private to metastases. Only 4% of metastases harbor therapeutically actionable alterations undetected in their matched primaries. Key clinicopathological and genomic alterations in our cohort were externally validated. In summary, our analysis highlights the complexity of clinicopathological features and tumor genomics in LUAD organotropism.

Artificial intelligence in microbial natural product drug discovery: current and emerging role

Covering: up to the end of 2022Microorganisms are exceptional sources of a wide array of unique natural products and play a significant role in drug discovery. During the golden era, several life-saving antibiotics and anticancer agents were isolated from microbes; moreover, they are still widely used. However, difficulties in the isolation methods and repeated discoveries of the same molecules have caused a setback in the past. Artificial intelligence (AI) has had a profound impact on various research fields, and its application allows the effective performance of data analyses and predictions. With the advances in omics, it is possible to obtain a wealth of information for the identification, isolation, and target prediction of secondary metabolites. In this review, we discuss drug discovery based on natural products from microorganisms with the help of AI and machine learning.

A germline SNP in BRMS1 predisposes patients with lung adenocarcinoma to metastasis and can be ameliorated by targeting c-fos

About 50% of patients with early-stage, surgically resected lung cancer will develop distant metastasis. There remains an unmet need to identify patients likely to develop recurrence and to design innovative therapies to decrease this risk. Two primary isoforms of BRMS1, v1 and v2, are present in humans. Using next-generation sequencing of BRMS1 on matched human noncancerous lung tissue and non-small cell lung cancer (NSCLC) specimens, we identified single-nucleotide polymorphism (SNP) rs1052566 that results in an A273V mutation of BRMS1v2. This SNP is homozygous (BRMS1v2^A273V/A273V) in 8% of the population and correlates with aggressive biology in lung adenocarcinoma (LUAD). Mechanistically, we show that BRMS1v2 A273V abolishes the metastasis suppressor function of BRMS1v2 and promotes robust cell invasion and metastases by activation of c-fos-mediated gene-specific transcriptional regulation. BRMS1v2 A273V increases cell invasion in vitro and increases metastases in both tail-vein injection xenografts and LUAD patient-derived organoid (PDO) intracardiac injection metastasis in vivo models. Moreover, we show that BRMS1v2 A273V fails to interact with nuclear Src, thereby activating intratumoral c-fos in vitro. Higher c-fos results in up-regulation of CEACAM6, which drives metastases in vitro and in vivo. Using both xenograft and PDO metastasis models, we repurposed T5224 for treatment, a c-fos pharmacologic inhibitor investigated in clinical trials for arthritis, and observed suppression of metastases in BRMS1v2^A273V/A273V LUAD in mice. Collectively, we elucidate the mechanism of BRMS1v2^A273V/A273V-induced metastases and offer a putative therapeutic strategy for patients with LUAD who have this germline alteration.

Abstract 3142: BRMS1 alters the tumor inflammatory signature and immune infiltration in lung adenocarcinoma

Background: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related deaths. Metastatic cancer is highly fatal which contributes to at least 90% of cancer-associated morbidities and mortalities. During metastasis, tumor cells alter their signaling cascade and interact with the immune cells in the tumor microenvironment Therefore, it is necessary to characterize and understand how these cancer cells influence tumor-infiltrating immune cells to facilitate and even enhance their ability to metastasize. BRMS1 is a metastasis suppressor gene which is frequently downregulated in LUAD. We, and others, have shown that loss of BRMS1 results in distant metastatic disease. Given the strong correlation between immune suppression, metastasis, and therapy resistance we sought to elucidate if BRMS1 contributes to these processes. Specifically, we hypothesized that LUAD cells downregulate BRMS1 which influences the immune cell composition in the tumor. This creates an immune-suppressive tumor microenvironment aiding in metastasis.

Methods: To test our hypothesis, we generated KrasG12D P53fl/fl Brms1-/- mice which spontaneously develop tumors with Ad-Cre intratracheal inoculation. To elucidate the role of BRMS1 in the context of cancer, we performed RNA sequencing on tumors from Brms1 wild type and knockout background. We used MCP counter, an in silico cellular deconvolution algorithm on our bulk RNA seq data to identify various subsets of tumor-infiltrating immune cells. Furthermore, our observations were validated by immunofluorescence and flow cytometry.

Results: Differential gene expression analysis using RNA seq data revealed a reduction in CXCL9, CCL5, CLEC1B, CCL9, CCL7 and other proinflammatory molecules in the Brms1-/- tumors. Gene ontology and gene set enrichment analysis highlighted a diminished immune response signature in Brms1-/- tumors. Hallmarks like interferon and IL6 signaling, complement and inflammation are highly enriched in Brms1+/+ tumors. MCP counter also suggested a significant increase in NK cells and reduction in CD8+ T cell population in the Brms1-/- tumors. To validate our observation, we performed immunofluorescence and flow cytometry to assess the number of infiltrating immune cells in the tumor microenvironment. Immunofluorescence data showed reduced cytotoxic T cells (CD8+ T cells) in Brms1-/- mice. The flow cytometric analysis also revealed a reduction in the proliferative potential of these CD8+ T cells along with the increased presence of myeloid-derived suppressor cells in the Brms1-/- mice.

Conclusion: Our data suggest for the first time that reduced BRMS1 expression which is generally observed in multiple tumors not only influences metastasis but also alters tumor-infiltrating immune cell composition. Thus, BRMS1 downregulation presents as one of the potential immune evasion mechanisms that could be targeted for an improved therapy outcome in LAUD.

Citation Format: Manendra B. Lankadasari, Yuan Liu, Di He, Samhita Bapat, Brooke Mastrogiacomo, Harry B. Lengel, David R. Jones. BRMS1 alters the tumor inflammatory signature and immune infiltration in lung adenocarcinoma [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 3142.