Neurovascular and metabolic dysfunction with cell type-specific transcriptomic changes in presymptomatic 5XFAD mice
Yao, M., Sun, N., Linville, R., Wei, Z., Kakazu, A., Ouyang, Y., Li, R., Du, L., Wang, H., Zhou, Y., Jiang, Y., Zhang, Z., Li, A., Garcia, F. J., Lu, H., Xu, J., Kellis, M., Heiman, M., and Duan, W. (2026). Fluids Barriers CNS 23, 3.
Read PDFProteogenomics in cerebrospinal fluid and plasma reveals new biological fingerprint of cerebral small vessel disease
Caro, I., Western, D., Namba, S., Sun, N., Kawaguchi, S., He, Y., Fujita, M., Roshchupkin, G., D’Aoust, T., Duperron, M.G., Sargurupremraj, M., Tsuchida, A., Koido, M., Ahmadi, M., Yang, C., Timsina, J., Ibanez, L., Matsuda, K., Suzuki, Y., Oda, Y., Kanai, A., Jandaghi, P., Munter, M., Auld, D., Astafeva, I., Puerta, R., Rotter, J.I., Psaty, B.M., Bis, J.C., Longstreth, W.T. Jr, Couffinhal, T., García-González, P., Pytel, V., Marquié, M., Cano, A., Boada, M., Joliot, M., Lathrop, M., Le Grand, Q., Launer, L.J., Wardlaw, J.M., Heiman, M., Ruiz, A., Matthews, P.M., Seshadri, S., Fornage, M., Adams, H., Mishra, A., Trégouët, D.A., Okada, Y., Kellis, M., De Jager, P.L., Tzourio, C., Kamatani, Y., Matsuda, F., Cruchaga, C., and Debette, S. (2025). Nat Aging, 5(12):2514-2531.
Astrogliosis Occurs Selectively in Amygdala of Adolescent Primate and Rodent Following Daily Δ9-Tetrahydrocannabinol, Prevented by Cannabidiol Co-Treatment
Sun, Y., Sivasubramanian, M., Milenkovic, M., Gumbert, A., Bergman, J., Ge, P., Heiman, M., Di Raddo, M.E., Withey, S.L., Madras, B.K., and George, S.R. (2025). Biol Psychiatry Glob Open Sci, 29;5(4):100496.
Brain-wide mapping of immune receptors uncovers a neuromodulatory role of IL-17E and the receptor IL-17RB
Lee, Y., Ishikawa T., Lee, H., Lee, B., Ryu, C., Davila Mejia, I., Kim, M., Lu, G., Hong, Y., Feng, M., Shin, H., Meloche, S., Locksley, R.M., Koltsova, E., Grivennikov, S.I., Heiman, M., Choi, G.B., and Huh, J.R. (2025). Cell, 188(8):2203-2217.e17.
Glycocalyx dysregulation impairs blood-brain barrier in ageing and disease
Shi, S.M., Suh, R.J., Shon D.J., Garcia, F.J., Buff, J.K., Atkins, M., Li, L., Lu N., Sun, B., Luo, J., To, N.S., Cheung, T.H., McNerney, M.W., Heiman, M., Bertozzi, C.R., and Wyss-Coray, T. (2025). Nature, 639(2) 985–994.
Defining genes and pathways that modify huntingtin CAG repeat somatic instability in vivo
Sathitloetsakun, S. and Heiman, M. (2025). Nature Genetics, 57(2):281-282.
Molecular and cellular characteristics of cerebrovascular cell types and their contribution to neurodegenerative diseases
Garcia, F.J. and Heiman, M. (2025). Molecular Neurodegeneration, 20(1):13.
SLC25A38 is required for mitochondrial pyridoxal 5′-phosphate (PLP) accumulation
Pena, I.A., Shi, J.S., Chang, S.M., Yang, J., Block, S., Adelmann, C.H., Keys, H.R., Ge, P., Bathla, S., Witham, I.H., Sienski, G., Nairn, A.C., Sabatini, D.M., Lewis, C.A., Kory, N., Vander Heiden, M.G., and Heiman, M. (2025). Nature Communications, 16(1):978
Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery
Bonev, B., Castelo-Branco, G., Chen F., Codeluppi, S., Corces, M.R., Fan, J., Heiman, M., Harris, K., Inoue, F., Kellis, M., Levine, A., Lotfollahi, M., Luo, C., Maynard, K.R., Nitzan, M., Ramani, V., Satijia, R., Schirmer, L., Shen, Y., Sun, N., Green, G.S., Theis, F., Wang, X., Welch, J.D., Gokce, O., Konopka, G., Liddelow, S., Macosko, E., Ali Bayraktar, O., Habib, N., and Nowakowski, T.J. (2024). Nature Neuroscience, 27(12):2292-2309.
The Single-Cell Opioid Responses in the Context of HIV (SCORCH) Consortium
Ament, S., Campbell, R., Lobo, M.K., Receveur, J., Agrawal, K., Borjabad, A., Chang, L., Clarke, D., Cleary, J., Byrareddy, S., Emani, P., Gabuzda, D., Gaulton, K., Giglio, M., Giorgi, F., Gok, B., Guda, C., Hadas, E., Herb, B.R., Hu, W., Huttner, A., Ishmam, M., Jacobs, M., Kelschenbach, J., Kim, D.-W., Lee, C., Liu, X., Liu, S., Madras, B., Mahurkar, A., Mash, D., Mukamel, E., Niu, M., O’Connor, R., Pagan, C., Pang, A., Pillai, P., Repunte-Canonigo, V., Ruzicka, W.R., Stanley, J., Tickle, T., Tsai, S.-Y., Wang, A., Wills, L., Wilson, A., Wright, S., Xu, S., Yang, J., Zand, M., Zhang, L., Zhang, J., Akbarian, S., Buch, S., Cheng, C., Corley, M., Fox, H., Gerstein, M., Gummuluru, S., Heiman, M., Ho, Y.-C., Kellis, M., Kenny, P., Kluger, Y., Milner, T., Moore, D., Morgello, S., Ndhlovu, L., Rana, T., Sanna, P.P., Satterlee, J., Sestan, N., Spector, S., Spudich, S., Tilgner, H., Volsky, D., White, O., Williams, D., and Zeng, H. (2024). Molecular Psychiatry, 29(12):3950-3961.
TDP-43 Proteinopathy in ALS is Triggered by Loss of ASRGL1 and Associated with HML-2 Expression
Garcia-Montojo, M., Fathi, S., Rastegar C, Simula, E.R., Doucet-O’Hare, T., Cheng, Y.H.H., Abrams, R.P.M., Pasternack, N., Malik, N., Bachani, M., Disanza, B., Maric, D., Lee, M.H., Wang, H., Santamaria, U., Li, W., Sampson, K., Lorenzo, J.R., Sanchez, I.E., Mezghrani, A., Li, Y., Sechi, L.A., Pineda, S., Heiman, M., Kellis, M., Steiner, J., and Nath, A. (2024). Nature Communications, 15(1):4163.
Single-Cell Dissection of the Human Motor and Prefrontal Cortices in ALS and FTLD
Pineda, S.S., Lee, H., Ulloa-Navas, M.J., Linville, R.M., Garcia, F.J., Galani, K., Engelberg-Cook, E., Castanedes, M.C., Fitzwalter, B.E., Pregent, L.J., Gardashli, M.E., Morales-Gallel, R., Garcia-Verdugo, J.M., DeTure, M., Vera-Garcia, D.V., Hucke, A.T.S., Oskarsson, B.E., Murray, M.E., Dickson, D.W., Heiman, M., Belzil, V.V., and Kellis, M. (2024). Cell, 187(8):1971-1989.e16.
Huntington’s Disease: Pathogenic Mechanisms and Implications for Therapeutics
Editors: X. Yang, W., Thompson, L.M., and Heiman, M. 1st Edition – February 7, 2024; Elsevier; ISBN: 9780323956727.
Defining Diurnal Fluctuations in Mouse Choroid Plexus and CSF at High Molecular, Spatial, and Temporal Resolution
Fame, R.M., Kalugin, P.N., Petrova, B., Xu, H., Soden, P.A., Shipley, F.B, Dani, N., Grant, B., Pragana, A., Head, J.P., Gupta, S., Shannon, M.L., Chifamba, F.F., Hawks-Mayer, H., Vernon, A., Gao, F., Zhang, Y., Holtzman, M.J., Heiman, M., Andermann, M.L., Kanarek, N., Lipton, J.O., and Lehtinen, M.K. (2023). Nature Communications, 14 (1), 3720.
Transcriptional Vulnerabilities of Striatal Neurons in Human and Rodent Models of Huntington’s Disease
Matsushima, A., Pineda, S.S., Crittenden, J.R., Lee, H., Galani, K., Mantero, J., Tombaugh, G., Kellis, M., Heiman, M., and Graybiel, A.M. (2023) Nature Communications 14, 282.
A Partnership Between the Lipid Scramblase XK and the Lipid Transfer Protein VPS13A at the Plasma Membrane
Guillén-Samander, A., Wu, Y., Pineda, S.S., Garcia, F.J., Eisen, J.N., Leonzino, M., Ugur, B., Kellis, M., Heiman, M., and De Camilli, P. (2022) Proceedings of the National Academy of Sciences of the USA, 119(35):e2205425119.
Back-to-BACs in Huntington’s Disease Modeling
Lee, H. and Heiman, M. (2022). Neuron, 110(7):1087-1089.
Single-Cell Dissection of the Human Brain Vasculature
Garcia, F.J., Sun, N., Lee, H., Godlewski, B., Mathys, H., Galani, K., Zhou, B., Jiang, X., Ng, A.P., Mantero, J., Tsai, L.-H., Bennett, D.A., Sahin, M., Kellis, M. and Heiman, M. (2022). Nature, 603(7903):893-899.
An Amygdala Circuit That Suppresses Social Engagement
Kwon, J-T., Ryu, C., Lee, H., Sheffield, A., Fan, J., Cho, D.H., Bigler, S., Sullivan, H. A., Choe, H. K., Wickersham, I. R., Heiman, M., and Choi, G. B. (2021). Nature, 593(7857):114-118.
Shape Deformation Analysis Reveals the Temporal Dynamics of Cell-type-specific Homeostatic and Pathogenic Responses to Mutant Huntingtin
Megret, L., Gris, B., Nair, S.S., Cevost, J., Wertz, M., Aaronson, J., Rosinski, J., Vogt, T.F., Wilkinson, H., Heiman, M., Neri, C. (2021). eLife, 10:e64984
Choroid Plexus NKCC1 Mediates Cerebrospinal Fluid Clearance During Mouse Early Postnatal Development
Xu, H., Fame, R.M., Sadegh, C., Sutin, J., Naranjo, C., Syau, D., Cui, J., Shipley, F.B., Vernon, A., Gao, F., Zhang, Y., Holtzman, M., Heiman, M., Warf, B.C., Lin, P.-Y, and Lehtinen, M.K. (2021). Nature Communications, 12(1):447.
Cell Type-Specific Transcriptomics Reveals that Mutant Huntingtin Leads to Mitochondrial RNA Release and Neuronal Innate Immune Activation
Lee, H., Fenster, R.J., Pineda, S.S.P., Gibbs, W.S., Mohammadi, S., Davila-Velderrain, J., Garcia, F.G., Therrien, M., Novis, H.S., Gao, F., Wilkinson, H., Vogt, T., Kellis, M, LaVoie, M.J., Heiman M. (2020). Neuron 107, 1-18.
Selective Neuronal Vulnerability in Alzheimer’s Disease: A Network-Based Analysis
Roussarie, J-P., Yao, V., Rodriguez-Rodriguez, P., Oughtred, R., Rust, J., Plautz, Z., Kasturia, S., Albornoz, C., Wang, W., Schmidt, E.F., Dannenfelser, R., Tadych, A., Brichta, L., Barnea-Cramer, A., Heintz, N., Hof, P.R., Heiman, M., Dolinski, K., Flajolet, M., Troyanskaya, O.G., Greengard P. (2020). Neuron 107, 1-15.
Interleukin-6 Deficiency Exacerbates Huntington’s Disease Model Phenotypes
Wertz, M. H., Pineda, S. S., Lee H., Kulicke, R., Kellis, M., Heiman, M. (2020). Molecular Neurodegeneration. 15(1):29.
Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity
Wertz, M. H., Mitchem, M. R., Pineda, S. S., Hachigia, L. J. , Lee, H., Lau, V., Powers, A., Kulicke, R., Madan, G. K., Colic, M., Therrien, M., Vernon, A., Beja-Glasser, V. F., Hegde, M., Gao, F., Kellis, M., Hart, T., Doench, J. G., Heiman, M. (2020). Neuron 106, 1-14.
A Cortical-Brainstem Circuit Predicts and Governs Compulsive Alcohol Drinking
Siciliano, C.A., Noamany, H., Chang, C.-J., Brown, A.R., Chen, X., Leible, X., Lee J.J., Wang, J., Vernon, A.N., Vander Weele, C.M., Kimchi, E.Y., Heiman, M., and Tye, K.M. (2019). Science 366, 1008-1012.
Small Molecule Targets TMED9 and Promotes Lysosomal Degradation to Reverse Proteinopathy
Dvela-Levitt, M., Kost-Alimova, M., Emani, M., Kohnert, E., Thompson, R., Sidhom, E.-H., Rivadeneira, A., Sahakian, N., Roignot, J., Papagregoriou, G., Montesinos, M.S., Clark, A.R., McKinney, D., Gutierrez, J., Rot,h M., Ronco, L., Elonga, E., Carter, T.A., Gnirke, A., Melanson, M., Hartland, K., Wieder, N., Hsu, J.C.H., Deltas, C., Hughey, R., Bleyer, A.J., Kmoch, S., Živná, M., Barešova, V., Kota, S., Schlondorff, J., Heiman, M., Alper, S.L., Wagner, F., Weins, A., Golub, T.R., Lander, E.S., and Greka, A. (2019). Cell 178, 521–535.
Widespread Accumulation of Ribosome-Associated Isolated 3′ UTRs in Neuronal Cell Populations of the Aging Brain
Sudmant, P.H., Lee, H., Dominguez, D., Heiman, M., and Burge. C,B. (2018). Cell Reports 9, 2447-2456
Normal Aging Induces A1-like Astrocyte Reactivity
Clarke, L.E., Liddelow, S.A., Chakraborty, C., Münch, A.E., Heiman, M., and Barres, B.A. (2018). Proceedings of the National Academy of Sciences of the United States of America 115, E1896-E1905.
Control of Huntington’s Disease-Associated Phenotypes by the Striatum-Enriched Transcription Factor Foxp2
Hachigian, L.J., Carmona, V., Fenster, R.J., Kulicke, R., Heilbut, A., Sittler, A., Pereira de Almeida, L., Mesirov, J.P., Gao, F., Kolaczyk, E.D., and Heiman, M. (2017). Cell Reports 21, 2688-2695.
Identifying Novel Therapeutic Targets by Combining Transcriptional Data with Ordinal Clinical Measurements
Pirhaji, L., Milani, P., Dalin, S., Wassie, B.T., Dunn, D., Fenster, R.J., Avila-Pacheco, J., Greengard, P., Clish, C.B., Heiman, M., Lo, D., and Fraenkel, E. (2017). Nature Communications 8, 623.
Resolving CNS mRNA Heterogeneity: Examining mRNA Alternative Polyadenylation at a Cell Type-Specific Level
Therrien, M. and Heiman, M. (2017). Neuron 95, 1232-1233.
Genome-Wide Genetic Screening in the Mammalian Central Nervous System
Wertz, M., and Heiman, M. Genome Editing in Neurosciences, Springer. In Press.
Hypothalamic Amylin Acts in Concert with Leptin to Regulate Food Intake
Li, Z., Kelly, L., Heiman, M., Greengard, P., and Friedman, J.M. (2016). Cell Metabolism 23, 945.
The Stress-Induced Atf3-Gelsolin Cascade Underlies Dendritic Spine Deficits in Neuronal Models of Tuberous Sclerosis Complex
Nie, D., Chen, Z., Ebrahimi-Fakhari, D., Di Nardo, A., Julich, K., Robson, V.K., Cheng, Y.C., Woolf, C.J., Heiman, M., and Sahin, M. (2015). Journal of Neuroscience 35, 10762-72.
Protein Kinase A Directly Phosphorylates Metabotropic Glutamate Receptor 5 to Modulate its Function
Uematsu, K., Heiman, M., Zelenina, M., Padovan, J., Chait, B.T., Aperia, A., Nishi, A., and Greengard, P. (2015). Journal of Neurochemistry 132, 677-86.
Synthetic Lethal Screening in the Mammalian Central Nervous System Identifies Gpx6 as a Modulator of Huntington’s Disease
Shema, R., Kulicke, R., Cowley, G.S., Stein, R., Root, D.E., and Heiman, M. (2015) Proceedings of the National Academy of Sciences of the USA 112, 268-72.
Nitric Oxide Regulates Synaptic Transmission Between Spiny Projection Neurons
Sagi, Y., Heiman, M., Peterson, J.D., Musatov, S., Scarduzio, M., Logan, S.M., Kaplitt, M.G., Surmeier, D.J., Heintz, N., and Greengard, P. (2014) Proceedings of the National Academy of Sciences of the USA 111, 17636-41.
Cell Type-Specific Plasticity of Striatal Projection Neurons in Parkinsonism and L-DOPA-Induced Dyskinesia
Fieblinger, T., Graves, S.M., Sebel, L.E., Alcacer, C., Plotkin, J.L., Gertler, T.S., Chan, C.S., Heiman, M., Greengard, P., Cenci, M.A., and Surmeier, D.J. (2014). Nature Communications 5, 5316.
Cell Type-Specific mRNA Purification by Translating Ribosome Affinity Purification (TRAP)
Heiman, M., Kulicke, R., Fenster, R.J., Greengard, P., and Heintz, N. (2014) Nature Protocols 9, 1282-91.
Molecular Adaptations of Striatal Spiny Projection neurons During Levodopa-Induced Dyskinesia
Heiman, M., Heilbut, A., Francardo, V., Kulicke, R., Fenster, R.J., Kolaczyk, E.D., Mesirov, J.P., Surmeier, D.J., Cenci, M.A., and Greengard, P. (2014) Proceedings of the National Academy of Sciences of the USA. 111, 4578-83.
Differential Effects of Cocaine on Histone Posttranslational Modifications in Identified Populations of Striatal Neurons
Jordi, E., Heiman, M., Marion-Poll, L., Guermonprez, P., Cheng, S.K., Nairn, A.C., Greengard, P., and Girault, J.A. (2013) Proceedings of the National Academy of Sciences of the USA 110, 9511-6.
IRE1α Induces Thioredoxin-Interacting Protein to Activate the NLRP3 Inflammasome and Promote Programmed Cell Death Under Irremediable ER Stress
Lerner, A.G., Upton, J.P., Praveen, P.V., Ghosh, R., Nakagawa, Y., Igbaria, A., Shen, S., Nguyen, V., Backes, B.J., Heiman, M., Heintz, N., Greengard, P., Hui, S., Tang, Q., Trusina, A., Oakes, S.A., and Papa, F.R. (2012) Cell Metabolism 16, 250-64.
Strain-Specific Regulation of Striatal Phenotype in Drd2-eGFP BAC Transgenic Mice
Chan, C.S., Peterson, J.D., Gertler, T.S., Glajch, K.E., Quintana, R.E., Cui, Q., Sebel, L.E., Plotkin, J.L., Shen, W., Heiman, M., Heintz, N., Greengard, P., and Surmeier, D.J. (2012) Journal of Neuroscience 32, 9124-32.
Inhibition of mTOR Signaling in Parkinson’s Disease Prevents L-DOPA-Induced Dyskinesia
Santini, E., Heiman, M., Greengard, P., Valjent, E., and Fisone, G. (2009) Science Signaling 2, ra36.
L-DOPA Activates ERK Signaling and Phosphorylates Histone H3 in the Striatonigral Medium Spiny Neurons of Hemiparkinsonian Mice
Santini, E., Alcacer, C., Cacciatore, S., Heiman, M., Hervé, D., Greengard, P., Girault, J.A., Valjent, E., and Fisone, G. (2009) Journal of Neurochemistry 108, 621-33.
A Translational Profiling Approach for the Molecular Characterization of CNS Cell Types
Heiman, M., Schaefer, A., Gong, S., Peterson, J.D., Day, M., Ramsey, K.E., Suárez-Fariñas, M., Schwarz, C., Stephan, D.A., Surmeier, D.J., Greengard, P., and Heintz, N. (2008) Cell 135, 738-48.
Application of a Translational Profiling Approach for the Comparative Analysis of CNS Cell Types
Doyle, J.P., Dougherty, J.D., Heiman, M., Schmidt, E.F., Stevens, T.R., Ma, G., Bupp, S., Shrestha, P., Shah, R.D., Doughty, M.L., Gong, S., Greengard, P., and Heintz, N. (2008) Cell 135, 749-62.