Shuyuan Zhang

All Publications

• The G1-S transition is promoted by Rb degradation via the E3 ligase UBR5. Science advances Zhang, S., Valenzuela, L. F., Zatulovskiy, E., Mangiante, L., Curtis, C., Skotheim, J. M. 2024; 10 (43): eadq6858

  Abstract

  Mammalian cells make the decision to divide at the G1-S transition in response to diverse signals impinging on the retinoblastoma protein Rb, a cell cycle inhibitor and tumor suppressor. Passage through the G1-S transition is initially driven by Rb inactivation via phosphorylation and by Rb's decreasing concentration in G1. While many studies have identified the mechanisms of Rb phosphorylation, the mechanism underlying Rb's decreasing concentration in G1 was unknown. Here, we found that Rb's concentration decrease in G1 requires the E3 ubiquitin ligase UBR5. UBR5 knockout cells have increased Rb concentration in early G1, exhibited a lower G1-S transition rate, and are more sensitive to inhibition of cyclin-dependent kinase 4/6 (Cdk4/6). This last observation suggests that UBR5 inhibition can strengthen the efficacy of Cdk4/6 inhibitor-based cancer therapies.

  View details for DOI 10.1126/sciadv.adq6858

  View details for PubMedID 39441926

  View details for PubMedCentralID PMC11498223

• Genome dilution by cell growth drives starvation-like proteome remodeling in mammalian and yeast cells. Nature structural & molecular biology Lanz, M. C., Zhang, S., Swaffer, M. P., Ziv, I., Gotz, L. H., Kim, J., McCarthy, F., Jarosz, D. F., Elias, J. E., Skotheim, J. M. 2024

  Abstract

  Cell size is tightly controlled in healthy tissues and single-celled organisms, but it remains unclear how cell size influences physiology. Increasing cell size was recently shown to remodel the proteomes of cultured human cells, demonstrating that large and small cells of the same type can be compositionally different. In the present study, we utilize the natural heterogeneity of hepatocyte ploidy and yeast genetics to establish that the ploidy-to-cell size ratio is a highly conserved determinant of proteome composition. In both mammalian and yeast cells, genome dilution by cell growth elicits a starvation-like phenotype, suggesting that growth in large cells is restricted by genome concentration in a manner that mimics a limiting nutrient. Moreover, genome dilution explains some proteomic changes ascribed to yeast aging. Overall, our data indicate that genome concentration drives changes in cell composition independently of external environmental cues.

  View details for DOI 10.1038/s41594-024-01353-z

  View details for PubMedID 39048803

• The G1/S transition is promoted by Rb degradation via the E3 ligase UBR5. bioRxiv : the preprint server for biology Zhang, S., Valenzuela, L. F., Zatulovskiy, E., Skotheim, J. M. 2023

  Abstract

  Mammalian cells make the decision to divide at the G1/S transition in response to diverse signals impinging on the retinoblastoma protein Rb, a cell cycle inhibitor and tumor suppressor. Rb is inhibited by two parallel pathways. In the canonical pathway, cyclin D-Cdk4/6 kinase complexes phosphorylate and inactivate Rb. In the second, recently discovered pathway, Rb's concentration decreases during G1 through an unknown mechanism. Here, we found that regulated protein degradation via the E3 ubiquitin ligase UBR5 is responsible for Rb's concentration drop in G1. UBR5 knockout cells have increased Rb concentration in early G1, exhibited a lower G1/S transition rate, and are more sensitive to inhibition of Cdk4/6. This last observation suggests that UBR5 inhibition can strengthen the efficacy of Cdk4/6 inhibitor-based cancer therapies.

  View details for DOI 10.1101/2023.10.03.560768

  View details for PubMedID 37873473

  View details for PubMedCentralID PMC10592979

• Increasing cell size remodels the proteome and promotes senescence. Molecular cell Lanz, M. C., Zatulovskiy, E., Swaffer, M. P., Zhang, L., Ilerten, I., Zhang, S., You, D. S., Marinov, G., McAlpine, P., Elias, J. E., Skotheim, J. M. 2022

  Abstract

  Cell size is tightly controlled in healthy tissues, but it is unclear how deviations in cell size affect cell physiology. To address this, we measured how the cell's proteome changes with increasing cell size. Size-dependent protein concentration changes are widespread and predicted by subcellular localization, size-dependent mRNA concentrations, and protein turnover. As proliferating cells grow larger, concentration changes typically associated with cellular senescence are increasingly pronounced, suggesting that large size may be a cause rather than just a consequence of cell senescence. Consistent with this hypothesis, larger cells are prone to replicative, DNA-damage-induced, and CDK4/6i-induced senescence. Size-dependent changes to the proteome, including those associated with senescence, are not observed when an increase in cell size is accompanied by an increase in ploidy. Together, our findings show how cell size could impact many aspects of cell physiology by remodeling the proteome and provide a rationale for cell size control and polyploidization.

  View details for DOI 10.1016/j.molcel.2022.07.017

  View details for PubMedID 35987199

• The cell cycle inhibitor RB is diluted in G1 and contributes to controlling cell size in the mouse liver. Frontiers in cell and developmental biology Zhang, S., Zatulovskiy, E., Arand, J., Sage, J., Skotheim, J. M. 2022; 10: 965595

  Abstract

  Every type of cell in an animal maintains a specific size, which likely contributes to its ability to perform its physiological functions. While some cell size control mechanisms are beginning to be elucidated through studies of cultured cells, it is unclear if and how such mechanisms control cell size in an animal. For example, it was recently shown that RB, the retinoblastoma protein, was diluted by cell growth in G1 to promote size-dependence of the G1/S transition. However, it remains unclear to what extent the RB-dilution mechanism controls cell size in an animal. We therefore examined the contribution of RB-dilution to cell size control in the mouse liver. Consistent with the RB-dilution model, genetic perturbations decreasing RB protein concentrations through inducible shRNA expression or through liver-specific Rb1 knockout reduced hepatocyte size, while perturbations increasing RB protein concentrations in an Fah -/- mouse model increased hepatocyte size. Moreover, RB concentration reflects cell size in G1 as it is lower in larger G1 hepatocytes. In contrast, concentrations of the cell cycle activators Cyclin D1 and E2f1 were relatively constant. Lastly, loss of Rb1 weakened cell size control, i.e., reduced the inverse correlation between how much cells grew in G1 and how large they were at birth. Taken together, our results show that an RB-dilution mechanism contributes to cell size control in the mouse liver by linking cell growth to the G1/S transition.

  View details for DOI 10.3389/fcell.2022.965595

  View details for PubMedID 36092730

• Delineation of proteome changes driven by cell size and growth rate. Frontiers in cell and developmental biology Zatulovskiy, E., Lanz, M. C., Zhang, S., McCarthy, F., Elias, J. E., Skotheim, J. M. 2022; 10: 980721

  Abstract

  Increasing cell size drives changes to the proteome, which affects cell physiology. As cell size increases, some proteins become more concentrated while others are diluted. As a result, the state of the cell changes continuously with increasing size. In addition to these proteomic changes, large cells have a lower growth rate (protein synthesis rate per unit volume). That both the cell's proteome and growth rate change with cell size suggests they may be interdependent. To test this, we used quantitative mass spectrometry to measure how the proteome changes in response to the mTOR inhibitor rapamycin, which decreases the cellular growth rate and has only a minimal effect on cell size. We found that large cell size and mTOR inhibition, both of which lower the growth rate of a cell, remodel the proteome in similar ways. This suggests that many of the effects of cell size are mediated by the size-dependent slowdown of the cellular growth rate. For example, the previously reported size-dependent expression of some senescence markers could reflect a cell's declining growth rate rather than its size per se. In contrast, histones and other chromatin components are diluted in large cells independently of the growth rate, likely so that they remain in proportion with the genome. Finally, size-dependent changes to the cell's growth rate and proteome composition are still apparent in cells continually exposed to a saturating dose of rapamycin, which indicates that cell size can affect the proteome independently of mTORC1 signaling. Taken together, our results clarify the dependencies between cell size, growth, mTOR activity, and the proteome remodeling that ultimately controls many aspects of cell physiology.

  View details for DOI 10.3389/fcell.2022.980721

  View details for PubMedID 36133920

• RB depletion is required for the continuous growth of tumors initiated by loss of RB. PLoS genetics Doan, A., Arand, J., Gong, D., Drainas, A. P., Shue, Y. T., Lee, M. C., Zhang, S., Walter, D. M., Chaikovsky, A. C., Feldser, D. M., Vogel, H., Dow, L. E., Skotheim, J. M., Sage, J. 2021; 17 (12): e1009941

  Abstract

  The retinoblastoma (RB) tumor suppressor is functionally inactivated in a wide range of human tumors where this inactivation promotes tumorigenesis in part by allowing uncontrolled proliferation. RB has been extensively studied, but its mechanisms of action in normal and cancer cells remain only partly understood. Here, we describe a new mouse model to investigate the consequences of RB depletion and its re-activation in vivo. In these mice, induction of shRNA molecules targeting RB for knock-down results in the development of phenotypes similar to Rb knock-out mice, including the development of pituitary and thyroid tumors. Re-expression of RB leads to cell cycle arrest in cancer cells and repression of transcriptional programs driven by E2F activity. Thus, continuous RB loss is required for the maintenance of tumor phenotypes initiated by loss of RB, and this new mouse model will provide a new platform to investigate RB function in vivo.

  View details for DOI 10.1371/journal.pgen.1009941

  View details for PubMedID 34879057

• Cell growth dilutes the cell cycle inhibitor Rb to trigger cell division. Science (New York, N.Y.) Zatulovskiy, E., Zhang, S., Berenson, D. F., Topacio, B. R., Skotheim, J. M. 2020; 369 (6502): 466–71

  Abstract

  Cell size is fundamental to cell physiology. For example, cell size determines the spatial scale of organelles and intracellular transport and thereby affects biosynthesis. Although some genes that affect mammalian cell size have been identified, the molecular mechanisms through which cell growth drives cell division have remained elusive. We show that cell growth during the G1 phase of the cell division cycle dilutes the cell cycle inhibitor Retinoblastoma protein (Rb) to trigger division in human cells. RB overexpression increased cell size and G1 duration, whereas RB deletion decreased cell size and removed the inverse correlation between cell size at birth and the duration of the G1 phase. Thus, Rb dilution through cell growth in G1 provides one of the long-sought molecular mechanisms that promotes cell size homeostasis.

  View details for DOI 10.1126/science.aaz6213

  View details for PubMedID 32703881

• Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury GASTROENTEROLOGY Lin, Y., Zhang, S., Zhu, M., Lu, T., Chen, K., Wen, Z., Wang, S., Xiao, G., Luo, D., Jia, Y., Li, L., MacConmara, M., Hoshida, Y., Singal, A. G., Yopp, A., Wang, T., Zhu, H. 2020; 158 (6): 1698-+

  Abstract

  Thirty to 90% of hepatocytes contain whole-genome duplications, but little is known about the fates or functions of these polyploid cells or how they affect development of liver disease. We investigated the effects of continuous proliferative pressure, observed in chronically damaged liver tissues, on polyploid cells.We studied Rosa-rtTa mice (controls) and Rosa-rtTa;TRE-short hairpin RNA mice, which have reversible knockdown of anillin, actin binding protein (ANLN). Transient administration of doxycycline increases the frequency and degree of hepatocyte polyploidy without permanently altering levels of ANLN. Mice were then given diethylnitrosamine and carbon tetrachloride (CCl4) to induce mutations, chronic liver damage, and carcinogenesis. We performed partial hepatectomies to test liver regeneration and then RNA-sequencing to identify changes in gene expression. Lineage tracing was used to rule out repopulation from non-hepatocyte sources. We imaged dividing hepatocytes to estimate the frequency of mitotic errors during regeneration. We also performed whole-exome sequencing of 54 liver nodules from patients with cirrhosis to quantify aneuploidy, a possible outcome of polyploid cell divisions.Liver tissues from control mice given CCl4 had significant increases in ploidy compared with livers from uninjured mice. Mice with knockdown of ANLN had hepatocyte ploidy above physiologic levels and developed significantly fewer liver tumors after administration of diethylnitrosamine and CCl4 compared with control mice. Increased hepatocyte polyploidy was not associated with altered regenerative capacity or tissue fitness, changes in gene expression, or more mitotic errors. Based on lineage-tracing experiments, non-hepatocytes did not contribute to liver regeneration in mice with increased polyploidy. Despite an equivalent rate of mitosis in hepatocytes of differing ploidies, we found no lagging chromosomes or micronuclei in mitotic polyploid cells. In nodules of human cirrhotic liver tissue, there was no evidence of chromosome-level copy number variations.Mice with increased polyploid hepatocytes develop fewer liver tumors following chronic liver damage. Remarkably, polyploid hepatocytes maintain the ability to regenerate liver tissues during chronic damage without generating mitotic errors, and aneuploidy is not commonly observed in cirrhotic livers. Strategies to increase numbers of polypoid hepatocytes might be effective in preventing liver cancer.

  View details for Web of Science ID 000534228500017

  View details for PubMedID 31972235

  View details for PubMedCentralID PMC8902703

• SWI/SNF component ARID1A restrains pancreatic neoplasia formation GUT Wang, S. C., Nassour, I., Xiao, S., Zhang, S., Luo, X., Lee, J., Li, L., Sun, X., Nguyen, L. H., Chuang, J., Peng, L., Daigle, S., Shen, J., Zhu, H. 2019; 68 (7): 1259–70

  View details for DOI 10.1136/gutjnl-2017-315490

  View details for Web of Science ID 000471840200017

• Suppression of the SWI/SNF Component Arid1a Promotes Mammalian Regeneration. Cell stem cell Sun, X., Chuang, J. C., Kanchwala, M., Wu, L., Celen, C., Li, L., Liang, H., Zhang, S., Maples, T., Nguyen, L. H., Wang, S. C., Signer, R. A., Sorouri, M., Nassour, I., Liu, X., Xu, J., Wu, M., Zhao, Y., Kuo, Y. C., Wang, Z., Xing, C., Zhu, H. 2016; 18 (4): 456-66

  Abstract

  Mammals have partially lost the extensive regenerative capabilities of some vertebrates, possibly as a result of chromatin-remodeling mechanisms that enforce terminal differentiation. Here, we show that deleting the SWI/SNF component Arid1a substantially improves mammalian regeneration. Arid1a expression is suppressed in regenerating tissues, and genetic deletion of Arid1a increases tissue repair following an array of injuries. Arid1a deficiency in the liver increases proliferation, reduces tissue damage and fibrosis, and improves organ function following surgical resection and chemical injuries. Hepatocyte-specific deletion is also sufficient to increase proliferation and regeneration without excessive overgrowth, and global Arid1a disruption potentiates soft tissue healing in the ear. We show that Arid1a loss reprograms chromatin to restrict promoter access by transcription factors such as C/ebpα, which enforces differentiation, and E2F4, which suppresses cell-cycle re-entry. Thus, epigenetic reprogramming mediated by deletion of a single gene improves mammalian regeneration and suggests strategies to promote tissue repair after injury.

  View details for DOI 10.1016/j.stem.2016.03.001

  View details for PubMedID 27044474

  View details for PubMedCentralID PMC4826298