Identifying and targeting vulnerabilities in cancers that metastasize to the bone and bone marrow

Evolving technologies enable scientist to ask and seek answers to advanced questions, above and beyond. During the past decade single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of biology, in particular within cancer research. Contributing with its high-resolution has unraveled complicated biological circuits, along with a profound understanding of heterogeneity, cellular and molecular processes, including gene expression profiles and transcriptional states. Especially in the quest of understanding cancer metastasis, aggressive disease phenotype and treatment resistance.

In Paper I we utilize scRNA-seq on tissue material from untreated human primary clear cell renal cell carcinoma (ccRCC) patients. We dissect the tumor microenvironment (TME) and discover a metastatic gene signature that is upregulated in bone metastatic ccRCC patients that could serve as a predictive tool. We describe an immunosuppressive microenvironment with tumor associated macrophages (TAMs) with a M2 phenotype overexpressing TREM2, further associated with low survival outcome. Computational interactive receptor-ligand analysis reveals CD70 (on tumor) and CD27 (on cytotoxic T cells and regulatory T cells) as a potential pharmaceutical target. In Paper II, a continuation of Paper I, we aimed to understand genetic alterations involved in metastatic disease from the primary site, namely bone metastatic ccRCC, including comparison of a normal bone marrow to malignant. Scrutinizing the complex TME we detect, as well here, an immunosuppressive microenvironment with transcriptionally different TAMs, exhausted T cell phenotype and a tumor associated mesenchymal stem/stromal cell (TA-MSC) population that upregulates bone remodeling genes. Concluding that the relevance of TA-MSC subset causes excessive bone resorption via RANK/RANKL/OPG signaling pathway. Finally, in Paper III, we evaluate brequinar, a DHODH inhibitor, as a therapeutic agent in high-risk neuroblastoma (NB). We find DHODH as an independent risk factor in high-risk NB demonstrating prolonged survival in preclinical models when inhibited. In combination with temozolomide, already in clinical use for these children, a synergistic effect is achieved in vivo, proposing a promising approach to validate clinically.

Taken together, the presented thesis has provided comprehensive insights in the progression of ccRCC in a primary and a metastatic setting, including the identification of potential vulnerable targets. Additionally, a potential combination treatment in vitro and in vivo is presented as a promising treatment option in high-risk NB by inhibiting DHODH together with standard care of treatment agent temozolomide.

List of scientific papers

I. Alchahin AM*, Mei S*, Tsea I, Hirz T, Kfoury Y, Dahl D, Wu CL, Subtelny AO, Wu S, Scadden DT, Shin JH, Saylor PJ, Sykes DB, Kharchenko PV, Baryawno N. A transcriptional metastatic signature predicts survival in clear cell renal cell carcinoma. Nat Communications. 2022 Sep 30;13(1):5747. *Equal contribution.
https://doi.org/10.1038/s41467-022-33375-w

II. Mei S*, Alchahin AM*, Tea I*, Kfoury Y, Hirz T, Sarkar H, Wu S, Subtelny AO, Zhang Y, Salari K, Wu CL, Randolph MA, Scadden DT, Dahl DM, Shin J, Kharchenko PV, Saylor PJ, Sykes DB, Baryawno N. Single-cell analysis of immune and stroma cell remodeling in renal cell carcinoma primary tumors and bone metastatic lesions. *Equal contribution. [Manuscript]

III. Olsen TK*, Dyberg C*, Embaie BT, Alchahin AM, Milosevic J, Ding J, Otte J, Tümmler C, Hed Myrberg I, Westerhout EM, Koster J, Versteeg R, Ding HF, Kogner P, Johnsen JI, Sykes DB, Baryawno N. DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma. JCI Insight. 2022 Aug 9;7(17):e153836. *Equal contribution.
https://doi.org/10.1172/jci.insight.153836