Clear cell renal cell carcinoma ontogeny and mechanisms of lethality

Abstract

The molecular features that define clear cell renal cell carcinoma (ccRCC) initiation and progression are being increasingly defined. The TRACERx Renal studies and others that have described the interaction between tumour genomics and remodelling of the tumour microenvironment provide important new insights into the molecular drivers underlying ccRCC ontogeny and progression. Our understanding of common genomic and chromosomal copy number abnormalities in ccRCC, including chromosome 3p loss, provides a mechanistic framework with which to organize these abnormalities into those that drive tumour initiation events, those that drive tumour progression and those that confer lethality. Truncal mutations in ccRCC, including those in VHL, SET2, PBRM1 and BAP1, may engender genomic instability and promote defects in DNA repair pathways. The molecular features that arise from these defects enable categorization of ccRCC into clinically and therapeutically relevant subtypes. Consideration of the interaction of these subtypes with the tumour microenvironment reveals that specific mutations seem to modulate immune cell populations in ccRCC tumours. These findings present opportunities for disease prevention, early detection, prognostication and treatment.

Figure 1:. Timeline of key discoveries in ccRCC genomics.

Green boxes denote events related to copy number changes; orange boxes indicate key genomic findings, and blue boxes represent key transcriptomic contributions.

Figure 2:. Key events in ccRCC progression.

Tumor initiators include 3p loss and VHL mutations. Evolution is driven by DNA repair defects and errors in mitosis that create additional aneuploidy. The acquisition of key chromosomal gains and losses, mutations in PI3K pathway elements and other oncogenic driver mutations confer lethal potential to intratumoral clones, and enhance the probability of developing metastases.

Figure 3:. Non-HIF VHL Targets.

A. VHL regulates NFkB through HIF dependent and independent mechanisms. VHL loss will increase TGFA transcription which induces cell autonomous increase in NFkB activation via growth factor receptor mediated IKK inhibition. CK2 mediated CARD9 inhibition is enhanced by VHL, and ZHX2 is inhibited by VHL. B. 1. Extracellular fibronectin homeostasis is dependent on interaction with CK2-phosphorylated and neddylatedVHL and loss of VHL results in defective or deficient extracellular matrix. 2. VHL is involved in collagen IV homeostasis. 3. VHL regulates intercellular and adherens junctions. C. VHL regulates primary cilium and mitosis. 1. VHL maintains primary cilium homeostasis by blocking AURKA mediated reduction of primary ciliary stability. 2. VHL supports mitotic function by enhancing Mad2 function by downregulating Mad2 inhibitory miR-28–5p.

Figure 3:. Non-HIF VHL Targets.

A. VHL regulates NFkB through HIF dependent and independent mechanisms. VHL loss will increase TGFA transcription which induces cell autonomous increase in NFkB activation via growth factor receptor mediated IKK inhibition. CK2 mediated CARD9 inhibition is enhanced by VHL, and ZHX2 is inhibited by VHL. B. 1. Extracellular fibronectin homeostasis is dependent on interaction with CK2-phosphorylated and neddylatedVHL and loss of VHL results in defective or deficient extracellular matrix. 2. VHL is involved in collagen IV homeostasis. 3. VHL regulates intercellular and adherens junctions. C. VHL regulates primary cilium and mitosis. 1. VHL maintains primary cilium homeostasis by blocking AURKA mediated reduction of primary ciliary stability. 2. VHL supports mitotic function by enhancing Mad2 function by downregulating Mad2 inhibitory miR-28–5p.

Figure 3:. Non-HIF VHL Targets.

A. VHL regulates NFkB through HIF dependent and independent mechanisms. VHL loss will increase TGFA transcription which induces cell autonomous increase in NFkB activation via growth factor receptor mediated IKK inhibition. CK2 mediated CARD9 inhibition is enhanced by VHL, and ZHX2 is inhibited by VHL. B. 1. Extracellular fibronectin homeostasis is dependent on interaction with CK2-phosphorylated and neddylatedVHL and loss of VHL results in defective or deficient extracellular matrix. 2. VHL is involved in collagen IV homeostasis. 3. VHL regulates intercellular and adherens junctions. C. VHL regulates primary cilium and mitosis. 1. VHL maintains primary cilium homeostasis by blocking AURKA mediated reduction of primary ciliary stability. 2. VHL supports mitotic function by enhancing Mad2 function by downregulating Mad2 inhibitory miR-28–5p.

Figure 4:. Factors influencing mismatch repair in ccRCC.

Mismatch repair mechanisms are affected by multiple axes in ccRCC. 1. Loss of VHL itself alters HDAC6 regulation via AURKA, effectively suppressing MSH2 via protein degradation. 2. MLH1 may exhibit haploinsufficiency due to 3p deletion. 3. Loss of MSH6 targeting to H3K36me3 can result in uncoupling of transcription coupled repair mechanisms for efficient targeting of DNA repair mechanisms to essential segments of the genome.

Figure 5:. Factors Influencing HRR in ccRCC.

1. Loss of VHL creates glutamine dependence for nucleoside production and increased risk for nucleoside shortfall, which can create vulnerabilities during mitosis dependent DNA repair. 2. VHL loss impacts key HRR genes through a HIF dependent mechanism. 3. VHL interacts with KAT5/Tip60, which acetylates and regulates ATM, p53, and H4K16.

Figure 6:. Alterations in the immune microenvironment.

Tumor cell genomic features may influence cell surface receptor expression as well as synthesis and secretion of immunomodulatory chemokines, cytokines and proangiogenic factors. PBRM1 mutations have been shown to increase angiogenesis, and decrease chemokine and cytokine production, whereas tumors bearing BAP1 mutations are associated with an inflamed microenvironment.