Multi-omics is a cutting-edge approach that combines data from different biomolecular levels, such as DNA, RNA, proteins, metabolites, and epigenetic marks, to obtain a holistic view of how living systems work and interact. Multi-omics has been used for various purposes in biomedical research, such as identifying new diseases, discovering new drugs, personalizing treatments, and optimizing therapies. This review summarizes the latest progress and challenges of multi-omics for designing new treatments for human diseases, focusing on how to integrate and analyze multiple proteome data and examples of how to use multi-proteomics data to identify new drug targets. We also discussed the future directions and opportunities of multi-omics for developing innovative and effective therapies by deciphering proteome complexity.

Background: Bladder cancer (BC) is the most common malignant disease of the urinary tract. Recurrent high grade non muscle invasive BC carries a serious risk for progression and subsequent metastases. The most common preclinical mouse model for bladder cancer relies on administration of N-butyl-N-(4-hydroxybutyl) nitrosamine (BBN) to mice. BBN-induced tumors in mice recapitulate the histology of human BC and were characterized with an overexpression of markers typical for basal-like cancer subtype in addition to a high mutational burden with frequent mutations in Trp53, similar to human muscle invasive BC. Methods: Bladder cancer was induced in C57BL/6J male mice by administering the BBN in the drinking water. A thorough histopathological analysis of bladder specimen during and post BBN treatment was performed at 2, 4, 16, 20 and 25 weeks. RNA sequencing and qPCR was performed to assess the levels of expression of immunologically relevant genes at 2 weeks and 20 weeks during and post BBN treatment. Results: We characterized the dynamics of the inflammatory response in the BBN-induced BC in mice. The treatment with BBN had gradually induced a robust inflammation in the first 2 weeks of administration, however, the inflammatory response was progressively silenced in the following weeks of the treatment, until the progression of the primary carcinoma. Tumors at 20 weeks were characterized with a marked upregulation of IL18 when compared to premalignant inflammatory response at 2 weeks. In accordance with this, we observed an increase in expression of IFNγ-responsive genes coupled to a pronounced lymphocytic infiltrate during the early stages of malignant transformation in bladder. Similar to human basal-like BC, BBN-induced murine tumors displayed an upregulated expression of immunoinhibitory molecules such as CTLA-4, PD-L1, and IDO1 which can lead to cytotoxic resistance and tumor escape. Conclusions: Despite the recent advances in bladder cancer therapy which include the use of checkpoint inhibitors, the treatment options for patients with locally advanced and metastatic BC remain limited. BBN-induced BC in mice displays an immunological profile which shares similarities with human MIBC thus representing an optimal model for preclinical studies on immunomodulation in management of BC.

A total of 30% of lung adenocarcinoma are driven by activating KRAS mutations. The treatment options for KRAS-mutant lung cancer are still limited as a challenge for therapy is the high heterogeneity within KRAS mutant tumors. Co-existing genetic events alter RAS signaling, such as the genetic alteration of the ubiquitin ligase leucine zipper-like transcriptional regulator 1 (LZTR1). LZTR1 is an adaptor of CUL3 E3 ligase that controls the localization and expression levels of RAS proteins by regulating their ubiquitination. Recent studies demonstrated that the loss of LZTR1 leads to resistance to the tyrosine kinase inhibitor and the multi-kinase inhibitor, suggesting that LZTR1 loss might be associated with the drug resistance of KRAS-mutated lung tumors. TCGA analysis indicated that LZTR1 loss affected progression survival in KRAS mutant LUAD patients, with a significant co-occurrence of LZTR1 loss and KRAS mutations. While LZTR1 depletion in LUAD cell lines did not affect proliferation in the cell culture, the knock-out (KO) of Lztr1 in a mouse model with Kras G12D oncogenic mutations caused a clear and significant acceleration of tumor progression in the Lztr1 loss groups, indicating that Lztr1 can affect tumor onset and progression. To study the alterations of the RAS pathway triggered by LZTR1 loss, we performed a global OMICS analysis on both in vitro and in vivo systems, identifying potential therapeutic targets. The characterization of immune populations in the tumors of flow cytometry also revealed changes in immune infiltrate in the KO mouse. We are now investigating how the changes caused by Lztr1 deletion on KRAS signaling heterogeneity within tumor cells can affect the tumor microenvironment composition. Our results suggest that the dysregulation of KRAS function by Lztr1 deletion contributes to cancer progression by affecting tumor cell communication with the microenvironment. Our work could explain how Lztr1 loss can affect drug response and lead to therapy resistance.

Lung cancer is the most frequent cancer with an aggressive clinical course and high mortality rates. About 30% of non-small lung cancer is driven by activating mutations in KRAS (Kirsten rat sarcoma virus). KRAS signaling is tightly controlled through a series of post-transcriptional mechanisms, whereas dysregulation of KRAS activity is translated into heterogeneous clinical behavior. We, and others, have recently implicated leucine zipper-like transcriptional regulator 1 (LZTR1), an adaptor of the CUL3-containing E3 ligase complex, in the control of RAS ubiquitination. Heterozygous loss of LZTR1 is found in one-third of lung adenocarcinomas and co-occurs with oncogenic KRAS mutations, suggesting that LZTR1 loss could contribute to lung cancer by modulating KRAS signaling and affecting the drug response. Both WT and oncogenic KRAS mutant protein levels were modulated by LZTR1 according to a Global protein screen (GPS) scoring regulators of KRAS stability. LZTR1 also directly ubiquitinated mutant KRAS in lung cancer cells. To assess the impact of LZTR1 on KRAS-driven lung cancer, we then used the Kras-G12D mouse model. We found that either homozygous, or heterozygous knockout of Lztr1 cooperates with oncogenic KRAS and promotes tumor initiation and progression at early stages of lung cancer development. The observed phenotype arises from the changes of the immune tumor microenvironment mediated by the differential activation of RAL-B (Ras-related protein Ral-b) signaling in the absence of LZTR1. These results shed a novel light on the crosstalk between dysregulation of KRAS ubiquitination, paracrine communication exerted by the cancer cells through secreted cytokines, and the immune response in lung cancer, which has thwarted the effectiveness of therapy to date. Citation Format: Tonci Ivanisevic. The role of KRAS ubiquitination in lung cancer heterogeneity [abstract]. In: Proceedings of the AACR Special Conference: Targeting RAS; 2023 Mar 5-8; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Res 2023;21(5_Suppl):Abstract nr A019.