Jalal Kenji Baruni

All Publications

• Mouse lemur cell atlas informs primate genes, physiology and disease. Nature Ezran, C., Liu, S., Chang, S., Ming, J., Guethlein, L. A., Wang, M. F., Dehghannasiri, R., Olivieri, J., Frank, H. K., Tarashansky, A., Koh, W., Jing, Q., Botvinnik, O., Antony, J., Pisco, A. O., Karkanias, J., Yang, C., Ferrell, J. E., Boyd, S. D., Parham, P., Long, J. Z., Wang, B., Salzman, J., De Vlaminck, I., Wu, A. R., Quake, S. R., Krasnow, M. A. 2025

  Abstract

  Mouse lemurs (Microcebus spp.) are an emerging primate model organism, but their genetics, cellular and molecular biology remain largely unexplored. In an accompanying paper1, we performed large-scale single-cell RNA sequencing of 27 organs from mouse lemurs. We identified more than 750 molecular cell types, characterized their transcriptomic profiles and provided insight into primate evolution of cell types. Here we use the generated atlas to characterize mouse lemur genes, physiology, disease and mutations. We uncover thousands of previously unidentified lemur genes and hundreds of thousands of new splice junctions including over 85,000 primate splice junctions missing in mice. We systematically explore the lemur immune system by comparing global expression profiles of key immune genes in health and disease, and by mapping immune cell development, trafficking and activation. We characterize primate-specific and lemur-specific physiology and disease, including molecular features of the immune program, lemur adipocytes and metastatic endometrial cancer that resembles the human malignancy. We present expression patterns of more than 400 primate genes missing in mice, many with similar expression patterns to humans and some implicated in human disease. Finally, we provide an experimental framework for reverse genetic analysis by identifying naturally occurring nonsense mutations in three primate immune genes missing in mice and by analysing their transcriptional phenotypes. This work establishes a foundation for molecular and genetic analyses of mouse lemurs and prioritizes primate genes, isoforms, physiology and disease for future study.

  View details for DOI 10.1038/s41586-025-09114-8

  View details for PubMedID 40739355

• A molecular cell atlas of mouse lemur, an emerging model primate. Nature Ezran, C., Liu, S., Chang, S., Ming, J., Botvinnik, O., Penland, L., Tarashansky, A., de Morree, A., Travaglini, K. J., Zhao, J., Wang, G., Hasegawa, K., Sin, H., Sit, R., Okamoto, J., Sinha, R., Zhang, Y., Karanewsky, C. J., Pendleton, J. L., Morri, M., Perret, M., Aujard, F., Stryer, L., Artandi, S., Fuller, M. T., Weissman, I. L., Rando, T. A., Ferrell, J. E., Wang, B., De Vlaminck, I., Yang, C., Casey, K. M., Albertelli, M. A., Pisco, A. O., Karkanias, J., Neff, N., Wu, A. R., Quake, S. R., Krasnow, M. A. 2025

  Abstract

  Mouse lemurs are the smallest and fastest reproducing primates, as well as one of the most abundant, and they are emerging as a model organism for primate biology, behaviour, health and conservation. Although much has been learnt about their ecology and phylogeny in Madagascar and their physiology, little is known about their cellular and molecular biology. Here we used droplet-based and plate-based single-cell RNA sequencing to create Tabula Microcebus, a transcriptomic atlas of 226,000 cells from 27 mouse lemur organs opportunistically obtained from four donors clinically and histologically characterized. Using computational cell clustering, integration and expert cell annotation, we define and biologically organize more than 750 lemur molecular cell types and their full gene expression profiles. This includes cognates of most classical human cell types, including stem and progenitor cells, and differentiating cells along the developmental trajectories of spermatogenesis, haematopoiesis and other adult tissues. We also describe dozens of previously unidentified or sparsely characterized cell types. We globally compare expression profiles to define the molecular relationships of cell types across the body, and explore primate cell and gene expression evolution by comparing lemur transcriptomes to those of human, mouse and macaque. This reveals cell-type-specific patterns of primate specialization and many cell types and genes for which the mouse lemur provides a better human model than mouse1. The atlas provides a cellular and molecular foundation for studying this model primate and establishes a general approach for characterizing other emerging model organisms.

  View details for DOI 10.1038/s41586-025-09113-9

  View details for PubMedID 40739356

• Homeostatic Signal Convergence in Vagal Baroreceptors. The Journal of neuroscience : the official journal of the Society for Neuroscience Baruni, J. K. 2024; 44 (28)

  View details for DOI 10.1523/JNEUROSCI.0671-24.2024

  View details for PubMedID 38986580

  View details for PubMedCentralID PMC11236574

• An organism-wide atlas of hormonal signaling based on the mouse lemur single-cell transcriptome. Nature communications Liu, S., Ezran, C., Wang, M. F., Li, Z., Awayan, K., Long, J. Z., De Vlaminck, I., Wang, S., Epelbaum, J., Kuo, C. S., Terrien, J., Krasnow, M. A., Ferrell, J. E. 2024; 15 (1): 2188

  Abstract

  Hormones mediate long-range cell communication and play vital roles in physiology, metabolism, and health. Traditionally, endocrinologists have focused on one hormone or organ system at a time. Yet, hormone signaling by its very nature connects cells of different organs and involves crosstalk of different hormones. Here, we leverage the organism-wide single cell transcriptional atlas of a non-human primate, the mouse lemur (Microcebus murinus), to systematically map source and target cells for 84 classes of hormones. This work uncovers previously-uncharacterized sites of hormone regulation, and shows that the hormonal signaling network is densely connected, decentralized, and rich in feedback loops. Evolutionary comparisons of hormonal genes and their expression patterns show that mouse lemur better models human hormonal signaling than mouse, at both the genomic and transcriptomic levels, and reveal primate-specific rewiring of hormone-producing/target cells. This work complements the scale and resolution of classical endocrine studies and sheds light on primate hormone regulation.

  View details for DOI 10.1038/s41467-024-46070-9

  View details for PubMedID 38467625

  View details for PubMedCentralID 1540572

• Illuminating complexity in serotonin neurons of the dorsal raphe nucleus. Neuron Baruni, J., Luo, L. 2022; 110 (16): 2519-2521

  Abstract

  The function of serotonin in the mammalian brain has been challenging to unravel. In this issue of Neuron, Paquelet etal. (2022) employ microendoscopy to record over 2,000 dorsal raphe serotonin neurons, yielding new insights into their activity from the single neuron to the population level.

  View details for DOI 10.1016/j.neuron.2022.07.013

  View details for PubMedID 35981523

• Reward expectation differentially modulates attentional behavior and activity in visual area V4. Nature neuroscience Baruni, J. K., Lau, B., Salzman, C. D. 2015; 18 (11): 1656-63

  Abstract

  Neural activity in visual area V4 is enhanced when attention is directed into neuronal receptive fields. However, the source of this enhancement is unclear, as most physiological studies have manipulated attention by changing the absolute reward associated with a particular location as well as its value relative to other locations. We trained monkeys to discriminate the orientation of two stimuli presented simultaneously in different hemifields while we independently varied the reward magnitude associated with correct discrimination at each location. Behavioral measures of attention were controlled by the relative value of each location. By contrast, neurons in V4 were consistently modulated by absolute reward value, exhibiting increased activity, increased gamma-band power and decreased trial-to-trial variability whenever receptive field locations were associated with large rewards. These data challenge the notion that the perceptual benefits of spatial attention rely on increased signal-to-noise in V4. Instead, these benefits likely derive from downstream selection mechanisms.

  View details for DOI 10.1038/nn.4141

  View details for PubMedID 26479590

  View details for PubMedCentralID PMC4624579

• Cytokinetic furrowing in toroidal, binucleate and anucleate cells in C. elegans embryos. Journal of cell science Baruni, J. K., Munro, E. M., von Dassow, G. 2008; 121 (Pt 3): 306-16

  Abstract

  Classical experimental studies on echinoderm zygotes concluded that the juxtaposition of two astral microtubule arrays localizes the stimulus for cytokinetic furrowing. However, recent experimental and genetic studies in Caenorhabditis elegans, Drosophila and mammalian cultured cells implicate microtubules of the central spindle, and regulatory proteins associated with this structure, suggesting that the essential conditions for furrow induction may differ from one animal cell to another. We used micromanipulation and laser microsurgery to create, in three ways, the juxtaposition of astral microtubules in C. elegans embryonic cells. In toroidal cells we observe that furrows initiate both where astral microtubule arrays are juxtaposed, and where the cortex most closely approaches the central spindle. We find that binucleate cells successfully furrow not only across the spindles, but also between unconnected spindle poles. Finally, we find that anucleate cells containing only a pair of centrosomes nevertheless attempt to cleave. Therefore, in C. elegans embryonic cells, as in echinoderms, juxtaposition of two asters suffices to induce furrowing, and neither the chromatin nor the physical structure of the central spindle are indispensable for furrow initiation. However, furrows that cross a central spindle are more likely to complete than those that do not.

  View details for DOI 10.1242/jcs.022897

  View details for PubMedID 18198185