IMPDH-Based Cytoophidium Structures as Potential Theranostics in Cancer

Abstract

We read with great interest the paper by Ruan et al.,1Ruan H. Song Z. Cao Q. Ni D. Xu T. Wang K. Bao L. Tong J. Xiao H. Xiao W. et al.IMPDH1/YB-1 Positive Feedback Loop Assembles Cytoophidia and Represents a Therapeutic Target in Metastatic Tumors.Mol Ther. 2020; 28: 1299-1313Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar who elegantly show that inosine monophosphate dehydrogenase 1 (IMPDH1)-based cytoophidia are present at a high frequency in clear cell renal cell carcinoma (ccRCC) and that IMPDH1 physically associates with and plays a role in a positive autoregulatory loop with the metastasis-related gene Y-box binding protein 1 (YB-1). This interaction favors IMPDH1 cytoophidium-mediated translocation of YB-1 into the cell nucleus, and this process correlates with ccRCC metastasis. By providing comprehensive evidence for the participation of IMPDH cytoophidia in the progression of metastatic renal cell carcinoma, this study reveals IMPDH-YB-1 as a potential therapeutic target in this disease. This study extends and enriches the study of cytoophidium structures in diverse metabolic conditions, including cancer. In a recent publication,2Keppeke G.D. Barcelos D. Fernandes M. Comodo A.N. Guimarães D.P. Cardili L. Carapeto F.C.L. Andrade L.E.C. Landman G. IMP dehydrogenase rod/ring structures in acral melanomas.Pigment Cell Melanoma Res. 2020; 33: 490-497Crossref PubMed Scopus (6) Google Scholar we analyzed IMPDH-based cytoophidium structures in the aggressive acral lentiginous melanoma (ALM) tumor and in benign melanocytic nevi specimens. The proportion of cells with cytoophidia ranged from 0% up to 80%, and the average was about 5× higher in ALM compared to nevi. Thus, using a cutoff of 5.5% of cells with cytoophidia to define as a positive sample, we found 80% of specimens to be cytoophidium-positive in the ALM group, but only 15% in the Nevi group. Additionally, receiver operator characteristic (ROC) curve analysis showed an area under the curve (AUC) of 0.88 for the differentiation of ALM and nevi, and ALM could be identified with a sensitivity and specificity above 80%. Looking only at the AML specimens, over 70% of cytoophidium-positive samples presented Breslow thickness >4.0 mm, compared to about 30% in the cytoophidium-low/negative group. Breslow thickness is one of the main indicators of malignancy in ALM and a turning point in treatment decision. IMPDH is not the only enzyme to assemble into cytoophidia. Cytidine triphosphate synthase (CTPS) forms independent cytoophidium fibers, very often aligned side-by-side with IMPDH cytoophidium structures, but still independent.3Chang C.C. Keppeke G.D. Sung L.Y. Liu J.L. Interfilament interaction between IMPDH and CTPS cytoophidia.FEBS J. 2018; 285: 3753-3768Crossref PubMed Scopus (39) Google Scholar CTPS cytoophidia were observed in 28% of 203 tissue samples of hepatocellular carcinoma, and their presence correlates with heat shock protein 90 (HSP90) staining intensity, which is linked to tumor aggressiveness. Additionally, 44% of 81 human cancer tissue samples from 11 different cancer types exhibited very high levels of CTPS cytoophidia.4Chang C.C. Jeng Y.M. Peng M. Keppeke G.D. Sung L.Y. Liu J.L. CTP synthase forms the cytoophidium in human hepatocellular carcinoma.Exp. Cell Res. 2017; 361: 292-299Crossref PubMed Scopus (41) Google Scholar Several recent publications have explored the functional implications of the assembly of IMPDH into cytoophidia. Using natural IMPDH cytoophidum-presenting stem cells as a model, we originally demonstrated that such structures produce a boost of IMPDH activity, which is convenient to supply the high consumption of guanosine-triphosphate (GTP) nucleotides in the highly proliferative stem cells.5Keppeke G.D. Chang C.C. Peng M. Chen L.Y. Lin W.C. Pai L.M. Andrade L.E.C. Sung L.Y. Liu J.L. IMP/GTP balance modulates cytoophidium assembly and IMPDH activity.Cell Div. 2018; 13: 5Crossref PubMed Scopus (38) Google Scholar Lymphocytes undergo intense proliferation with high guanine nucleotide consumption in response to antigenic challenge. IMPDH polymerization into cytoophidium structures is observed in T cells undergoing antigen-activated proliferation.6Calise S.J. Abboud G. Kasahara H. Morel L. Chan E.K.L. Immune Response-Dependent Assembly of IMP Dehydrogenase Filaments.Front. Immunol. 2018; 9: 2789Crossref PubMed Scopus (24) Google Scholar,7Duong-Ly K.C. Kuo Y.M. Johnson M.C. Cote J.M. Kollman J.M. Soboloff J. Rall G.F. Andrews A.J. Peterson J.R. T cell activation triggers reversible inosine-5′-monophosphate dehydrogenase assembly.J. Cell Sci. 2018; 131: 131Crossref Scopus (30) Google Scholar These findings were corroborated by two independent groups studying the structural modifications of IMPDH assembled into filaments,8Fernández-Justel D. Núñez R. Martín-Benito J. Jimeno D. González-López A. Soriano E.M. Revuelta J.L. Buey R.M. A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity.J. Mol. Biol. 2019; 431: 956-969Crossref PubMed Scopus (22) Google Scholar,9Johnson M.C. Kollman J.M. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation.eLife. 2020; 9: 9Crossref Scopus (28) Google Scholar IMPDH cytoophidium assembly renders the enzyme more resistant to guanosine-di/triphosphate (GDP/GTP) allosteric feedback inhibition, thereby facilitating the accumulation of the guanine nucleotide pool. Recently, a number of proteins have been shown to form either homogeneous filaments or heterogenous filaments, including either IMPDH or CTPS. For example, YB-1, ankyrin repeat domain 9 (ANKRD9), ADP-ribosylation factor-like protein 2 (ALR2), ribose-phosphate pyrophosphokinase 1 (PRPS1), asparagine synthetase (ASNS) and delta-1-pyrroline-5-carboxylate synthase (P5CS) are able to form cytoophidium-like filamentous structures in vivo and in cultured cells from mammals, Drosophila, yeast, and others, highlighting cytoophidia assembly as an important mechanism for regulation of enzyme activity.10Simonet J.C. Burrell A.L. Kollman J.M. Peterson J.R. Freedom of assembly: metabolic enzymes come together.Mol. Biol. Cell. 2020; 31: 1201-1205Crossref PubMed Scopus (1) Google Scholar,11Park C.K. Horton N.C. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation.Biophys. Rev. 2019; 11: 927-994Crossref PubMed Scopus (38) Google Scholar At least in mammals both IMPDH and CTPS seem to assemble into cytoophidia in their active conformation, resulting in increased enzyme activity.9Johnson M.C. Kollman J.M. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation.eLife. 2020; 9: 9Crossref Scopus (28) Google Scholar,12Lynch E.M. Hicks D.R. Shepherd M. Endrizzi J.A. Maker A. Hansen J.M. Barry R.M. Gitai Z. Baldwin E.P. Kollman J.M. Human CTP synthase filament structure reveals the active enzyme conformation.Nat. Struct. Mol. Biol. 2017; 24: 507-514Crossref PubMed Scopus (101) Google Scholar The effect of polymerization on enzymatic activity of other proteins remains to be explored. Cytoophidium assembly usually correlates with intense cell proliferation, which implies consumption of nucleotides for nucleic acids synthesis and as energy carriers. Intriguingly, assembly into macrostructures has not been reported for the adenylate and uridylate pathways, suggesting alternate mechanisms of regulation. However, it is also possible that this mechanism has not been sufficiently explored for these pathways or perhaps that micropolymers not visible under regular optical microscopy are involved. Further studies using the new cryo-electron microscopy approach may be rewarding in exploring this possibility. Although both IMPDH isoforms assemble into identical microfiber structures,5Keppeke G.D. Chang C.C. Peng M. Chen L.Y. Lin W.C. Pai L.M. Andrade L.E.C. Sung L.Y. Liu J.L. IMP/GTP balance modulates cytoophidium assembly and IMPDH activity.Cell Div. 2018; 13: 5Crossref PubMed Scopus (38) Google Scholar IMPDH1 predominates in the retina, while IMPDH2 is constitutively expressed throughout the body. Overexpression of IMPDH1 results in cytoophidium assembly in vitro.5Keppeke G.D. Chang C.C. Peng M. Chen L.Y. Lin W.C. Pai L.M. Andrade L.E.C. Sung L.Y. Liu J.L. IMP/GTP balance modulates cytoophidium assembly and IMPDH activity.Cell Div. 2018; 13: 5Crossref PubMed Scopus (38) Google Scholar A recent publication demonstrates that photoreceptor cells in the retina constitutively present IMPDH1 cytoophidia and that the in vivo rate of IMPDH1 filament formation in the outer segment layer correlates with increase in the synthesis of GTP and ATP.13Plana-Bonamaisó A. López-Begines S. Fernández-Justel D. Junza A. Soler-Tapia A. Andilla J. Loza-Alvarez P. Rosa J.L. Miralles E. Casals I. et al.Post-translational regulation of retinal IMPDH1 in vivo to adjust GTP synthesis to illumination conditions.eLife. 2020; 9: 9Crossref Scopus (21) Google Scholar Taken together, these data indicate that the increased IMPDH1 expression, observed by Ruan et al.,1Ruan H. Song Z. Cao Q. Ni D. Xu T. Wang K. Bao L. Tong J. Xiao H. Xiao W. et al.IMPDH1/YB-1 Positive Feedback Loop Assembles Cytoophidia and Represents a Therapeutic Target in Metastatic Tumors.Mol Ther. 2020; 28: 1299-1313Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar in ccRCC could contribute to the formation of IMPDH cytoophidia in these cells and that the gain of function associated with these cytoophidium structures could contribute to match the increased guanine nucleotide consumption owing to uncontrolled cellular proliferation. It has long been known that IMPDH expression is increased in tumor tissues.14Collart F.R. Chubb C.B. Mirkin B.L. Huberman E. Increased inosine-5′-phosphate dehydrogenase gene expression in solid tumor tissues and tumor cell lines.Cancer Res. 1992; 52: 5826-5828PubMed Google Scholar In fact, the de novo GTP biosynthesis pathway is of great importance for the progression of several tumors, such as glioblastoma, a subset of small cell lung cancer, mTORC1-related tumors, tuberous sclerosis complex (TSC)-associated tumors, solid and hematologic malignancies, ccRCC, among others.14Collart F.R. Chubb C.B. Mirkin B.L. Huberman E. Increased inosine-5′-phosphate dehydrogenase gene expression in solid tumor tissues and tumor cell lines.Cancer Res. 1992; 52: 5826-5828PubMed Google Scholar,15Naffouje R. Grover P. Yu H. Sendilnathan A. Wolfe K. Majd N. Smith E.P. Takeuchi K. Senda T. Kofuji S. Sasaki A.T. Anti-Tumor Potential of IMP Dehydrogenase Inhibitors: A Century-Long Story.Cancers (Basel). 2019; 11: 11Crossref Scopus (49) Google Scholar Inhibition of IMPDH was proposed as an anti-cancer therapy about 50 years ago, but, to date, no such drug has been approved, mainly due to inconsistent efficacy or adverse effects, although IMPDH inhibitors are widely used as immunosuppressants.15Naffouje R. Grover P. Yu H. Sendilnathan A. Wolfe K. Majd N. Smith E.P. Takeuchi K. Senda T. Kofuji S. Sasaki A.T. Anti-Tumor Potential of IMP Dehydrogenase Inhibitors: A Century-Long Story.Cancers (Basel). 2019; 11: 11Crossref Scopus (49) Google Scholar One could argue that targeting IMPDH as anti-cancer therapy could be a “double-edged sword” situation, due to the dependence of proliferating immune cells on guanosine nucleotides. In fact, proliferating antigen-activated T cells present abundant cytoophidium structures,6Calise S.J. Abboud G. Kasahara H. Morel L. Chan E.K.L. Immune Response-Dependent Assembly of IMP Dehydrogenase Filaments.Front. Immunol. 2018; 9: 2789Crossref PubMed Scopus (24) Google Scholar,7Duong-Ly K.C. Kuo Y.M. Johnson M.C. Cote J.M. Kollman J.M. Soboloff J. Rall G.F. Andrews A.J. Peterson J.R. T cell activation triggers reversible inosine-5′-monophosphate dehydrogenase assembly.J. Cell Sci. 2018; 131: 131Crossref Scopus (30) Google Scholar and immunosuppression is not a goal when treating cancer. In light of the recent discoveries, including IMPDH regulation through cytoophidium assembly, the possibility of allosteric inhibition of these enzymes, and the critical differences between IMPDH isoforms,1Ruan H. Song Z. Cao Q. Ni D. Xu T. Wang K. Bao L. Tong J. Xiao H. Xiao W. et al.IMPDH1/YB-1 Positive Feedback Loop Assembles Cytoophidia and Represents a Therapeutic Target in Metastatic Tumors.Mol Ther. 2020; 28: 1299-1313Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar,5Keppeke G.D. Chang C.C. Peng M. Chen L.Y. Lin W.C. Pai L.M. Andrade L.E.C. Sung L.Y. Liu J.L. IMP/GTP balance modulates cytoophidium assembly and IMPDH activity.Cell Div. 2018; 13: 5Crossref PubMed Scopus (38) Google Scholar,8Fernández-Justel D. Núñez R. Martín-Benito J. Jimeno D. González-López A. Soriano E.M. Revuelta J.L. Buey R.M. A Nucleotide-Dependent Conformational Switch Controls the Polymerization of Human IMP Dehydrogenases to Modulate their Catalytic Activity.J. Mol. Biol. 2019; 431: 956-969Crossref PubMed Scopus (22) Google Scholar, 9Johnson M.C. Kollman J.M. Cryo-EM structures demonstrate human IMPDH2 filament assembly tunes allosteric regulation.eLife. 2020; 9: 9Crossref Scopus (28) Google Scholar, 10Simonet J.C. Burrell A.L. Kollman J.M. Peterson J.R. Freedom of assembly: metabolic enzymes come together.Mol. Biol. Cell. 2020; 31: 1201-1205Crossref PubMed Scopus (1) Google Scholar specifically designed molecules might be developed to target IMPDH with minimal immunosuppressive action but maximal tumorigenic inhibition, perhaps by modulating polymerization of specific IMPDH isoforms or drugs with differentiated tissue penetration capabilities. The study by Ruan et al.1Ruan H. Song Z. Cao Q. Ni D. Xu T. Wang K. Bao L. Tong J. Xiao H. Xiao W. et al.IMPDH1/YB-1 Positive Feedback Loop Assembles Cytoophidia and Represents a Therapeutic Target in Metastatic Tumors.Mol Ther. 2020; 28: 1299-1313Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar expands the panorama of cytoophidium structures in cancer as a generalized phenomenon, with multiple potential translational applications comprising diverse molecular players. Although cytoophidium-targeted therapy is a promising idea, early diagnosis is, without doubt, the main contributor for the success of any anti-cancer therapy. In that sense, the screening for cytoophidium structures in cancer tissue samples represents a potential diagnostic and prognostic tool for tumors. Therefore, the cytoophidium structures have a promising role in fulfilling the theranostics concept by addressing the diagnostic and therapeutic aspects of cancer patient management.