Academic Appointments


All Publications


  • The Mettl3 epitranscriptomic writer amplifies p53 stress responses. Molecular cell Raj, N., Wang, M., Seoane, J. A., Zhao, R. L., Kaiser, A. M., Moonie, N. A., Demeter, J., Boutelle, A. M., Kerr, C. H., Mulligan, A. S., Moffatt, C., Zeng, S. X., Lu, H., Barna, M., Curtis, C., Chang, H. Y., Jackson, P. K., Attardi, L. D. 2022

    Abstract

    The p53 transcription factor drives anti-proliferative gene expression programs in response to diverse stressors, including DNA damage and oncogenic signaling. Here, we seek to uncover new mechanisms through which p53 regulates gene expression using tandem affinity purification/mass spectrometry to identify p53-interacting proteins. This approach identified METTL3, an m6A RNA-methyltransferase complex (MTC) constituent, as a p53 interactor. We find that METTL3 promotes p53 protein stabilization and target gene expression in response to DNA damage and oncogenic signals, by both catalytic activity-dependent and independent mechanisms. METTL3 also enhances p53 tumor suppressor activity in invivo mouse cancer models and human cancer cells. Notably, METTL3 only promotes tumor suppression in the context of intact p53. Analysis of human cancer genome data further supports the notion that the MTC reinforces p53 function in human cancer. Together, these studies reveal a fundamental role for METTL3 in amplifying p53 signaling in response to cellular stress.

    View details for DOI 10.1016/j.molcel.2022.04.010

    View details for PubMedID 35512709

  • A p53-dependent translational program directs tissue-selective phenotypes in a model of ribosomopathies. Developmental cell Tiu, G. C., Kerr, C. H., Forester, C. M., Krishnarao, P. S., Rosenblatt, H. D., Raj, N., Lantz, T. C., Zhulyn, O., Bowen, M. E., Shokat, L., Attardi, L. D., Ruggero, D., Barna, M. 2021

    Abstract

    In ribosomopathies, perturbed expression of ribosome components leads to tissue-specific phenotypes. What accounts for such tissue-selective manifestations as a result of mutations in the ribosome, a ubiquitous cellular machine, has remained a mystery. Combining mouse genetics and in vivo ribosome profiling, we observe limb-patterning phenotypes in ribosomal protein (RP) haploinsufficient embryos, and we uncover selective translational changes of transcripts that controlling limb development. Surprisingly, both loss of p53, which is activated by RP haploinsufficiency, and augmented protein synthesis rescue these phenotypes. These findings are explained by the finding that p53 functions as a master regulator of protein synthesis, at least in part, through transcriptional activation of 4E-BP1. 4E-BP1, a key translational regulator, in turn, facilitates selective changes in the translatome downstream of p53, and this thereby explains how RP haploinsufficiency may elicit specificity to gene expression. These results provide an integrative model to help understand how in vivo tissue-specific phenotypes emerge in ribosomopathies.

    View details for DOI 10.1016/j.devcel.2021.06.013

    View details for PubMedID 34242585

  • p53 deficiency triggers dysregulation of diverse cellular processes in physiological oxygen. The Journal of cell biology Valente, L. J., Tarangelo, A. n., Li, A. M., Naciri, M. n., Raj, N. n., Boutelle, A. M., Li, Y. n., Mello, S. S., Bieging-Rolett, K. n., DeBerardinis, R. J., Ye, J. n., Dixon, S. J., Attardi, L. D. 2020; 219 (11)

    Abstract

    The mechanisms by which TP53, the most frequently mutated gene in human cancer, suppresses tumorigenesis remain unclear. p53 modulates various cellular processes, such as apoptosis and proliferation, which has led to distinct cellular mechanisms being proposed for p53-mediated tumor suppression in different contexts. Here, we asked whether during tumor suppression p53 might instead regulate a wide range of cellular processes. Analysis of mouse and human oncogene-expressing wild-type and p53-deficient cells in physiological oxygen conditions revealed that p53 loss concurrently impacts numerous distinct cellular processes, including apoptosis, genome stabilization, DNA repair, metabolism, migration, and invasion. Notably, some phenotypes were uncovered only in physiological oxygen. Transcriptomic analysis in this setting highlighted underappreciated functions modulated by p53, including actin dynamics. Collectively, these results suggest that p53 simultaneously governs diverse cellular processes during transformation suppression, an aspect of p53 function that would provide a clear rationale for its frequent inactivation in human cancer.

    View details for DOI 10.1083/jcb.201908212

    View details for PubMedID 32886745

  • Reciprocal Crosstalk Between YAP1/Hippo Pathway and the p53 Family Proteins: Mechanisms and Outcomes in Cancer FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY Raj, N., Bam, R. 2019; 7
  • Reciprocal Crosstalk Between YAP1/Hippo Pathway and the p53 Family Proteins: Mechanisms and Outcomes in Cancer. Frontiers in cell and developmental biology Raj, N., Bam, R. 2019; 7: 159

    Abstract

    The YAP1/Hippo and p53 pathways are critical protectors of genome integrity in response to DNA damage. Together, these pathways secure cellular adaptation and maintain overall tissue integrity through transcriptional re-programing downstream of various environmental and biological cues generated during normal tissue growth, cell proliferation, and apoptosis. Genetic perturbations in YAP1/Hippo and p53 pathways are known to contribute to the cells' ability to turn rogue and initiate tumorigenesis. The Hippo and p53 pathways cooperate on many levels and are closely coordinated through multiple molecular components of their signaling pathways. Several functional and physical interactions have been reported to occur between YAP1/Hippo pathway components and the three p53 family members, p53, p63, and p73. Primarily, functional status of p53 family proteins dictates the subcellular localization, protein stability and transcriptional activity of the core component of the Hippo pathway, Yes-associated protein 1 (YAP1). In this review, we dissect the critical points of crosstalk between the YAP1/Hippo pathway components, with a focus on YAP1, and the p53 tumor suppressor protein family. For each p53 family member, we discuss the biological implications of their interaction with Hippo pathway components in determining cell fate under the conditions of tissue homeostasis and cancer pathogenesis.

    View details for DOI 10.3389/fcell.2019.00159

    View details for PubMedID 31448276

    View details for PubMedCentralID PMC6695833

  • Genome Edited Human Hematopoietic Stem Cells Correct Lysosomal Storage Disorders: Proof-of-Concept and Safety Studies for Mucopolysaccharidosis Type I and Gaucher Disease Gomez-Ospina, N., Scharenberg, S., Mostrel, N., Raj, N., Attardi, L., Khan, S., Tomatsu, S., Lee, C., Bao, G., Porteus, M. H. CELL PRESS. 2019: 329
  • Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I. Nature communications Gomez-Ospina, N. n., Scharenberg, S. G., Mostrel, N. n., Bak, R. O., Mantri, S. n., Quadros, R. M., Gurumurthy, C. B., Lee, C. n., Bao, G. n., Suarez, C. J., Khan, S. n., Sawamoto, K. n., Tomatsu, S. n., Raj, N. n., Attardi, L. D., Aurelian, L. n., Porteus, M. H. 2019; 10 (1): 4045

    Abstract

    Lysosomal enzyme deficiencies comprise a large group of genetic disorders that generally lack effective treatments. A potential treatment approach is to engineer the patient's own hematopoietic system to express high levels of the deficient enzyme, thereby correcting the biochemical defect and halting disease progression. Here, we present an efficient ex vivo genome editing approach using CRISPR-Cas9 that targets the lysosomal enzyme iduronidase to the CCR5 safe harbor locus in human CD34+ hematopoietic stem and progenitor cells. The modified cells secrete supra-endogenous enzyme levels, maintain long-term repopulation and multi-lineage differentiation potential, and can improve biochemical and phenotypic abnormalities in an immunocompromised mouse model of Mucopolysaccharidosis type I. These studies provide support for the development of genome-edited CD34+ hematopoietic stem and progenitor cells as a potential treatment for Mucopolysaccharidosis type I. The safe harbor approach constitutes a flexible platform for the expression of lysosomal enzymes making it applicable to other lysosomal storage disorders.

    View details for DOI 10.1038/s41467-019-11962-8

    View details for PubMedID 31492863

  • Deconstructing p53 pathways in tumor suppression. Mello, S., Bieging-Rolett, K., Kaiser, A., Valente, E., Raj, N., McClendon, J., Flowers, B., Morgens, D., Bassik, M., Attardi, L. AMER ASSOC CANCER RESEARCH. 2018: 17
  • The Transactivation Domains of the p53 Protein. Cold Spring Harbor perspectives in medicine Raj, N., Attardi, L. D. 2017; 7 (1)

    Abstract

    The p53 tumor suppressor is a transcriptional activator, with discrete domains that participate in sequence-specific DNA binding, tetramerization, and transcriptional activation. Mutagenesis and reporter studies have delineated two distinct activation domains (TADs) and specific hydrophobic residues within these TADs that are critical for their function. Knockin mice expressing p53 mutants with alterations in either or both of the two TADs have revealed that TAD1 is critical for responses to acute DNA damage, whereas both TAD1 and TAD2 participate in tumor suppression. Biochemical and structural studies have identified factors that bind either or both TADs, including general transcription factors (GTFs), chromatin modifiers, and negative regulators, helping to elaborate a model through which p53 activates transcription. Posttranslational modifications (PTMs) of the p53 TADs through phosphorylation also regulate TAD activity. Together, these studies on p53 TADs provide great insight into how p53 serves as a tumor suppressor.

    View details for DOI 10.1101/cshperspect.a026047

    View details for PubMedID 27864306

  • A p53 Super-tumor Suppressor Reveals a Tumor Suppressive p53-Ptpn14-Yap Axis in Pancreatic Cancer. Cancer cell Mello, S. S., Valente, L. J., Raj, N. n., Seoane, J. A., Flowers, B. M., McClendon, J. n., Bieging-Rolett, K. T., Lee, J. n., Ivanochko, D. n., Kozak, M. M., Chang, D. T., Longacre, T. A., Koong, A. C., Arrowsmith, C. H., Kim, S. K., Vogel, H. n., Wood, L. D., Hruban, R. H., Curtis, C. n., Attardi, L. D. 2017; 32 (4): 460–73.e6

    Abstract

    The p53 transcription factor is a critical barrier to pancreatic cancer progression. To unravel mechanisms of p53-mediated tumor suppression, which have remained elusive, we analyzed pancreatic cancer development in mice expressing p53 transcriptional activation domain (TAD) mutants. Surprisingly, the p5353,54 TAD2 mutant behaves as a "super-tumor suppressor," with an enhanced capacity to both suppress pancreatic cancer and transactivate select p53 target genes, including Ptpn14. Ptpn14 encodes a negative regulator of the Yap oncoprotein and is necessary and sufficient for pancreatic cancer suppression, like p53. We show that p53 deficiency promotes Yap signaling and that PTPN14 and TP53 mutations are mutually exclusive in human cancers. These studies uncover a p53-Ptpn14-Yap pathway that is integral to p53-mediated tumor suppression.

    View details for PubMedID 29017057

  • Neat1 is a p53-inducible lincRNA essential for transformation suppression. Genes & development Mello, S. S., Sinow, C. n., Raj, N. n., Mazur, P. K., Bieging-Rolett, K. n., Broz, D. K., Imam, J. F., Vogel, H. n., Wood, L. D., Sage, J. n., Hirose, T. n., Nakagawa, S. n., Rinn, J. n., Attardi, L. D. 2017; 31 (11): 1095–1108

    Abstract

    The p53 gene is mutated in over half of all cancers, reflecting its critical role as a tumor suppressor. Although p53 is a transcriptional activator that induces myriad target genes, those p53-inducible genes most critical for tumor suppression remain elusive. Here, we leveraged p53 ChIP-seq (chromatin immunoprecipitation [ChIP] combined with high-throughput sequencing) and RNA-seq (RNA sequencing) data sets to identify new p53 target genes, focusing on the noncoding genome. We identify Neat1, a noncoding RNA (ncRNA) constituent of paraspeckles, as a p53 target gene broadly induced by mouse and human p53 in different cell types and by diverse stress signals. Using fibroblasts derived from Neat1(-/-) mice, we examined the functional role of Neat1 in the p53 pathway. We found that Neat1 is dispensable for cell cycle arrest and apoptosis in response to genotoxic stress. In sharp contrast, Neat1 plays a crucial role in suppressing transformation in response to oncogenic signals. Neat1 deficiency enhances transformation in oncogene-expressing fibroblasts and promotes the development of premalignant pancreatic intraepithelial neoplasias (PanINs) and cystic lesions in Kras(G12D)-expressing mice. Neat1 loss provokes global changes in gene expression, suggesting a mechanism by which its deficiency promotes neoplasia. Collectively, these findings identify Neat1 as a p53-regulated large intergenic ncRNA (lincRNA) with a key role in suppressing transformation and cancer initiation, providing fundamental new insight into p53-mediated tumor suppression.

    View details for PubMedID 28698299

  • Tumor suppression: p53 alters immune surveillance to restrain liver cancer. Current biology Raj, N., Attardi, L. D. 2013; 23 (12): R527-30

    Abstract

    The p53 tumor suppressor governs multiple cell-intrinsic programs, including cell-cycle arrest and apoptosis, to curb neoplastic growth. A new study reveals that p53 also acts through a novel non-cell-autonomous mechanism, by stimulating the innate immune system to maintain tissue homeostasis and suppress tumorigenesis.

    View details for DOI 10.1016/j.cub.2013.04.076

    View details for PubMedID 23787049