Zach Pennington, PhD

Neuroscientist at the Icahn School of Medicine at Mount Sinai

Zachary.Pennington@mssm.edu
CV / Resume
Resources

About Me

A neuroscientist at the Icahn School of Medicine at Mount Sinai, my research is focused on uncovering how traumatic psychological experiences leave a lasting imprint on the brain. The central aim of this work is to understand how trauma leads to devastating afflictions like PTSD and addiction, and how we can harness these insights to advance new treatments.

My research employs a multi-level approach to understanding trauma. Techniques involved include in vivo calcium imaging of neural activity, whole-brain analysis of stress responses in cleared tissue, persistent labeling of stress-reactive cells in the service of molecular profiling and manipulation, chemogenetic/optogenetic circuit mapping, and behavioral models of neuropsychiatric dysfunction.

I am also devoted to creating convenient open-source tools that allow the neuroscience community to more readily adopt modern technologies. I am lead developer of the behavior tracking software ezTrack, contributor to the calcium imaging analysis software Minian, have built open-source tools for counting cells in microscopy images, and share protocols for these and other neuroscience techniques here.

When I’m not in the lab, I love going on food adventures with my wife, riding my bike and skateboard, going to punk rock shows, and baking bread.

Awards and Honors

Professional Activities and Service

Publications

Research Reports

Pennington ZT, LaBanca AR, Abdel-Raheim SD, Bacon ME, Mahmoud, Sompolpong P, Baggetta AM, Zaki Y, Ko b, Dong Z, Smith ACW, Kenny PJ, Cai DJ (2024). An anterior hypothalamic circuit gates stress vulnerability. BioRxiv, 2024.10.28.620614v1. [link]

Pennington ZT, LaBanca A, Sompolpong P, Christenson Wick Z, Feng Y, Dong Z, Francisco TR, Chen L, Fulton SL, Maze I, Shuman T, Cai DJ (in press). Dissociable contributions of the amygdala and ventral hippocampus to stress-induced changes in defensive behavior. Cell Reports. [pdf]

Zaki Y, Pennington ZT, Morales-Rodriguez D, Francisco TR, LaBanca AR, Dong Z, Carrillo Segura S, Silva AJ, Shuman T, Fenton A, Rajan K, Cai DJ (in press). Aversive experience drives offline ensemble reactivation to link memories across days. Nature. [link]

Feng Y, Diego KS, Dong Z, Christenson Wick Z, Page-Harley L, Page-Harley, V, Schnipper J, Lamsifer SI, Pennington ZT, Vetere LM, Philipsberg PA, Soler I, Jurkowski A, Rosado CJ, Khan NN, Cai DJ, Shuman, T (in press). Distinct changes to hippocampal and medial entorhinal circuits emerge across the progression of cognitive deficits in epilepsy. Cell Reports. [link]

Dong Z, Feng Y, Diego K, Baggettaa A, Sweis BM, Pennington ZT, Lamsifer SI, Zaki Y, Sangiuliano F, Philipsberg PA, Morales-Rodriguez, Kircher D, Slesinger P, Shuman T, Aharoni D, Cai CJ (2024). Simultaneous dual-color calcium imaging in freely-behaving mice. BioRxiv, 2024.07.03.601770. [link]

Dong Z, Mau W, Feng Y, Pennington ZT, Chen L, Zaki Y, Rajan K, Shuman T, Aharoni D, Cai DJ (2022). Minian, an open-source miniscope analysis pipeline. eLife, 11:e70661. [pdf]

Pennington ZT, Diego KS, Francisco TR, LaBanca AR, Lamsifer SI, Liobimova O, Shuman T, Cai DJ (2021). ezTrack Ð A step by step by step guide to behavior tracking. Current Protocols in Neuroscience, 1(10): e255. [pdf]

Blaze J, Navickas A, Phillips HL, Heissel S, Plaza-Jennings A, Miglani A, Asgharian H, Foo M, Katanski CD, Watkins CP, Pennington ZT, Javidfar B, Espeso-Gil S, Rostandy B, Alwaseem H, Hahn CG, Molina H, Cai DJ, Pan T, Yao WD, Goodarzi H, Haghighi F, Akbarian S (2021). Neuronal Nsun2 deficiency produces tRNA epitranscriptomic alterations and proteomic shifts impacting synaptic signaling and behavior. Nature Communications, 12(1): 4913. [pdf]

Lichtenberg NT, Sepe-Forrest L, Pennington ZT, Lamparelli AC, Greenfield VY, Wassum KM (2021). The medial orbitofrontal cortex → basolateral amygdala circuit regulates the influence of reward cues on adaptive behavior and choice. Journal of Neuroscience, 41(34): 7267-7277. [pdf]

Rajbhandari AK, Octeau JC, Gonzalez S, Pennington ZT, Mohamed F, Trott J, Chavez J, Ngyuen E, Keces N, Hong WZ, Heve RL, Waschek J, Khakh BS, Fanselow MS (2021). A basomedial amygdala to intercalated cells microcircuit expressing PACAP and its receptor PAC1 regulates contextual fear. Journal of Neuroscience, 41(15): 3446-61. [pdf]

Shuman T, Aharoni D, Cai DJ, Lee CR, Chavlis S, Page-Harley L, Vetere LM, Feng Y, Yang CY, Mollinedo-Gajate I, Chen L, Pennington ZT, Taxidis J, Flores SE, Cheng K, Javaherian M, Kaba CC, Rao N, La-Vu M, Pandi I, Shtrahman M, Bakhurin KI, Masmanidis SC, Khakh BS, Poirazi P, Silva AJ, Golshani P (2020). Breakdown of spatial coding and neural synchronization in pilocarpine-treated epileptic mice. Nature Neuroscience, 23(2): 229-238. [pdf]

Pennington ZT, Trott JM, Rajbhandari AK, Li K, Walwyn WM, Evans CJ, Fanselow MS (2020). Chronic opioid pretreatment potentiates the sensitization of fear learning by trauma. Neuropsychopharmacology, 45(3): 482-490. [pdf]

Pennington ZT, Dong Z, Feng Y, Vetere LM, Page-Harley L, Shuman T, Cai DJ (2019). ezTrack: An open-source video analysis pipeline for the investigation of animal behavior. Scientific Reports, 9(1): 19979. [pdf]

Kosarussavadi S*, Pennington ZT*, Covel C, Schlinger BA (2017). Across sex and age: Learning and memory and patterns of avian hippocampal gene expression. Behavioral Neuroscience, 131(6): 483-491. [pdf]
*Equal contribution

Pennington ZT, Anderson AS, Fanselow MS (2017). The ventromedial prefrontal cortex in a model of traumatic stress: Fear inhibition or contextual processing? Learning & Memory, 24(9): 400-406. [pdf]

Lichtenberg NT, Pennington ZT, Holley SM, Greenfield VY, Cepeda C, Levine MS, Wassum KM (2017). Basolateral amygdala to orbitofrontal cortex projections enable cue-triggered reward expectations. Journal of Neuroscience, 37(35): 8374-8384. [pdf]

James AS, Pennington ZT, Tran P, Jentsch JD (2015). Compromised NMDA/glutamate receptor expression in dopaminergic neurons impairs instrumental learning, but not Pavlovian goal-tracking or sign-tracking. eNeuro, 2(3): e0040-14. [pdf]

Reviews and Commentaries

Pennington ZT, Cai DJ (2021). Propanolol inhibits reactivation of fear memory. Biolological Psychiatry, 89(12):1111-12. [pdf]

Fanselow MS, Pennington ZT (2018). A return to the dark ages of psychiatry with a two-system framework for the study of fear. Behaviour Research and Therapy, 100:24-29. [pdf]

Pennington ZT, Fanselow MS (2018). Indirect targeting of sub-superficial brain structures with transcranial magnetic stimulation reveals a promising way forward in the treatment of fear. Biological Psychiatry, 84(2): 80-81. [pdf]

Fanselow MS, Pennington ZT (2017). The Danger of LeDoux & Pine’s Two System Framework for Fear. American Journal of Psychiatry, 174(11): 1120-1121. [pdf]

Jentsch JD, Ashenhurst JR, Cervantes MC, Groman SM, James AS, Pennington ZT (2014). Dissecting Impulsivity and its relationship to addictions. Annals of the New York Academy of Sciences, 1327(1): 1-26. [pdf]

Jentsch JD, Pennington ZT (2014). Reward, interrupted: inhibitory control and its relevance to addictions. Neuropharmacology, 76B: 479-486. [pdf]