Onco-condensates: formation, multi-component organization, and biological functions

Abstract

Numerous cellular processes occur in the context of condensates, a type of large, membrane-less biomolecular assembly generated through phase separation. These condensates function as a hub of diversified cellular events by concentrating the required components. Cancer frequently coopts biomolecular condensation mechanisms to promote survival and/or proliferation. Onco-condensates, which refer to those that have causal roles or are critically involved in tumorigenicity, operate to abnormally elevate biological output of a proliferative process, or to suppress a tumor-suppressive pathway, thereby promoting oncogenesis. Here, we summarize advances regarding how multi-component onco-condensates are established and organized to promote oncogenesis, with those related to chromatin and transcription deregulation used as showcases. A better understanding should enable development of new means of targeting onco-condensates as potential therapeutics.

Keywords: biomolecular condensation; cancer; disease; intrinsically disordered region (IDR); onco-condensate; phase separation; small molecule; therapeutic.

Figure 1.. Formation and function of onco-condensates, with special emphasis on those leading to aberrant chromatin organization and/or gene-expression dysregulation.

(A) Schematic showing onco-condensates of NUP98-HOXA9 and EWS-FLI, which hijack IDRs in proteins normally confined to the nuclear pore complex (NPC, which contains wildtype NUP98) or stress granules (which contains wildtype EWS), and condensates of mutant NPM1c (NPM1c) that translocates from the nucleolus (which contains wild-type NPM1) to the nucleoplasm and then the cytosol. (B) Via LLPS, BRD4-NUT establishes transcriptional super-hubs, termed mega-domains and sub-compartment M. Top: The NUT segment recruits p300 to induce histone acetylation, which is then bound by bromodomains in BRD4-NUT to form a feedforward loop. Bottom: Bromodomain (BD)-acetylation multivalency, together with IDR-mediated self-association and heterotypic interactions, mediates condensation of BRD4-NUT and partners. (C-E) Schemes illustrating LLPS induced by oncogene overexpression (Myc; C) or mutation-associated structural change (SHP2; D); additionally, cancer-associated missense mutations recurrently target IDR of the tumor suppressor UTX, which converts the liquid-like material state of UTX condensate into a solid-like one (E). (F) Onco-fusions such as NUP98-HOXA9 and EWS-FLI gain LLPS-inducing IDRs, which mediate homotypic and heterotypic interactions with (co)activators for establishing transcriptional onco-condensates; concurrently, chromatin loops are formed at proto-oncogene promoters and enhancers due to onco-fusion LLPS.

Figure 2.. Selective recruitment and exclusion by the MED1 condensate.

The existence of alternating blocks of oppositely charged amino acids within IDRs of MED1 and positive regulators of transcription (such as PAF1 complex subunits, SPT6 and CTR9) permits selective recruitment and co-partitioning into MED1 condensates; meanwhile, negative regulators of transcription (such as NELFE) harbor IDRs lacking such a ‘blocky’ feature and are excluded from the condensates, thus allowing robust transcription.

Figure 3.. Cancer coopts LLPS of YAP/TAZ, the two mechano-transducers, to attain uncontrolled growth.

(A) Hippo signaling in mammals. Left: Upon activation of canonical Hippo signaling, NF2 phosphorylates MST1/2 and MAP4K. MST1/2, MAP4K or STK25 phosphorylates LATS1/2, which then phosphorylates cytoplasmic YAP/TAZ. Phosphorylated YAP/TAZ undergoes proteasomal degradation or binds 14-3-3 which leads to cytoplasmic sequestration. “X” indicates inhibition. Right: When Hippo signaling is off, unphosphorylated YAP/TAZ translocates to the nucleus and binds to TEAD, Smad or other transcription factors, resulting in activation of target genes such as AMOTL2, AREG, BIRC5, CTGF and CYR61. (B-C) Nuclear TAZ forms condensates (B). In response to hyperosmotic stress, YAP forms both cytoplasmic and nuclear condensates in a manner dependent on an intrinsically-disordered TAD domain (C). Nuclear TAZ/YAP condensates compartmentalize the indicated active transcription machinery to promote transcription of TAZ/YAP-specific proliferation genes. (D) Through multivalent interactions mediated by acquired IDRs, YAP-MAMLD1 or C11ORF95-YAP forms nuclear condensates, which concentrate transcriptional (co-)activators and switch the PRC2-mediated H3K27me3 to gene-active H3K27ac at target oncogenes. (E) Deficiency of a glycogenolysis enzyme in pre-malignant liver cells leads to glucose storage, which boosts glycogen accumulation. Accumulated glycogen undergoes LLPS to inactivate Hippo signaling through sequestration of Laforin and associated MST1/2. As a result, YAP translocates to the nucleus leading to activation of downstream onco-targets.