Bio

Honors & Awards


  • Elizabeth Young New Investigator Award, Organization for the Study of Sex Differences (2015)
  • Presidential Fellowship, Massachusetts Institute of Technology (2012-2013)
  • Sigma Xi Research Society, Princeton University (2012)

Professional Education


  • Bachelor of Arts, Princeton University (2012)
  • Doctor of Philosophy, Massachusetts Institute of Technology (2019)
  • PhD, Massachusetts Institute of Technology, Biology (2019)
  • AB, Princeton University, Molecular and Cellular Biology (2012)

Stanford Advisors


Research & Scholarship

Lab Affiliations


Publications

All Publications


  • Quantitative analysis of Y-Chromosome gene expression across 36 human tissues. Genome research Godfrey, A. K., Naqvi, S., Chmátal, L., Chick, J. M., Mitchell, R. N., Gygi, S. P., Skaletsky, H., Page, D. C. 2020

    Abstract

    Little is known about how human Y-Chromosome gene expression directly contributes to differences between XX (female) and XY (male) individuals in nonreproductive tissues. Here, we analyzed quantitative profiles of Y-Chromosome gene expression across 36 human tissues from hundreds of individuals. Although it is often said that Y-Chromosome genes are lowly expressed outside the testis, we report many instances of elevated Y-Chromosome gene expression in a nonreproductive tissue. A notable example is EIF1AY, which encodes eukaryotic translation initiation factor 1A Y-linked, together with its X-linked homolog EIF1AX Evolutionary loss of a Y-linked microRNA target site enabled up-regulation of EIF1AY, but not of EIF1AX, in the heart. Consequently, this essential translation initiation factor is nearly twice as abundant in male as in female heart tissue at the protein level. Divergence between the X and Y Chromosomes in regulatory sequence can therefore lead to tissue-specific Y-Chromosome-driven sex biases in expression of critical, dosage-sensitive regulatory genes.

    View details for DOI 10.1101/gr.261248.120

    View details for PubMedID 32461223

  • Conservation, acquisition, and functional impact of sex-biased gene expression in mammals. Science (New York, N.Y.) Naqvi, S., Godfrey, A. K., Hughes, J. F., Goodheart, M. L., Mitchell, R. N., Page, D. C. 2019; 365 (6450)

    Abstract

    Sex differences abound in human health and disease, as they do in other mammals used as models. The extent to which sex differences are conserved at the molecular level across species and tissues is unknown. We surveyed sex differences in gene expression in human, macaque, mouse, rat, and dog, across 12 tissues. In each tissue, we identified hundreds of genes with conserved sex-biased expression-findings that, combined with genomic analyses of human height, explain ~12% of the difference in height between females and males. We surmise that conserved sex biases in expression of genes otherwise operating equivalently in females and males contribute to sex differences in traits. However, most sex-biased expression arose during the mammalian radiation, which suggests that careful attention to interspecies divergence is needed when modeling human sex differences.

    View details for DOI 10.1126/science.aaw7317

    View details for PubMedID 31320509

  • Mammalian germ cells are determined after PGC colonization of the nascent gonad. Proceedings of the National Academy of Sciences of the United States of America Nicholls, P. K., Schorle, H., Naqvi, S., Hu, Y. C., Fan, Y., Carmell, M. A., Dobrinski, I., Watson, A. L., Carlson, D. F., Fahrenkrug, S. C., Page, D. C. 2019

    Abstract

    Mammalian primordial germ cells (PGCs) are induced in the embryonic epiblast, before migrating to the nascent gonads. In fish, frogs, and birds, the germline segregates even earlier, through the action of maternally inherited germ plasm. Across vertebrates, migrating PGCs retain a broad developmental potential, regardless of whether they were induced or maternally segregated. In mammals, this potential is indicated by expression of pluripotency factors, and the ability to generate teratomas and pluripotent cell lines. How the germline loses this developmental potential remains unknown. Our genome-wide analyses of embryonic human and mouse germlines reveal a conserved transcriptional program, initiated in PGCs after gonadal colonization, that differentiates germ cells from their germline precursors and from somatic lineages. Through genetic studies in mice and pigs, we demonstrate that one such gonad-induced factor, the RNA-binding protein DAZL, is necessary in vivo to restrict the developmental potential of the germline; DAZL's absence prolongs expression of a Nanog pluripotency reporter, facilitates derivation of pluripotent cell lines, and causes spontaneous gonadal teratomas. Based on these observations in humans, mice, and pigs, we propose that germ cells are determined after gonadal colonization in mammals. We suggest that germ cell determination was induced late in embryogenesis-after organogenesis has begun-in the common ancestor of all vertebrates, as in modern mammals, where this transition is induced by somatic cells of the gonad. We suggest that failure of this process of germ cell determination likely accounts for the origin of human testis cancer.

    View details for DOI 10.1073/pnas.1910733116

    View details for PubMedID 31754036

  • Conserved microRNA targeting reveals preexisting gene dosage sensitivities that shaped amniote sex chromosome evolution. Genome research Naqvi, S., Bellott, D. W., Lin, K. S., Page, D. C. 2018; 28 (4): 474–83

    Abstract

    Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals. Preexisting heterogeneities in dosage sensitivity, manifesting as differences in the extent of miRNA-mediated repression, predicted either the retention of a Y homolog or the acquisition of XCI following Y gene decay. Analogous heterogeneities among avian Z-linked genes predicted either the retention of a W homolog or gene-specific dosage compensation following W gene decay. Genome-wide analyses of human copy number variation indicate that these heterogeneities consisted of sensitivity to both increases and decreases in dosage. We propose a model of XY/ZW evolution incorporating such preexisting dosage sensitivities in determining the evolutionary fates of individual genes. Our findings thus provide a more complete view of the role of dosage sensitivity in shaping the mammalian and avian sex chromosomes and reveal an important role for post-transcriptional regulatory sequences (miRNA target sites) in sex chromosome evolution.

    View details for DOI 10.1101/gr.230433.117

    View details for PubMedID 29449410

    View details for PubMedCentralID PMC5880238

  • Chemical sensing by nonequilibrium cooperative receptors. Physical review letters Skoge, M., Naqvi, S., Meir, Y., Wingreen, N. S. 2013; 110 (24): 248102

    Abstract

    Cooperativity arising from local interactions in equilibrium receptor systems provides gain, but does not increase sensory performance, as measured by the signal-to-noise ratio (SNR) due to a fundamental tradeoff between gain and intrinsic noise. Here we allow sensing to be a nonequilibrium process and show that energy dissipation cannot circumvent the fundamental tradeoff, so that the SNR is still optimal for independent receptors. For systems requiring high gain, nonequilibrium 2D-coupled receptors maximize the SNR, revealing a new design principle for biological sensors.

    View details for DOI 10.1103/PhysRevLett.110.248102

    View details for PubMedID 25165963

    View details for PubMedCentralID PMC4114058

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