Juan Pineda

Juan Pineda

 Juan, a junior studying Neuroscience at Macalester College, developed a tool to link cell transcriptome information with neuronal connectivity in the brain.

Dysregulation of neuronal circuits plays a crucial role in the pathology of various neurological disorders. Understanding the disruptions in these connections, particularly in a cell-type or region-specific manner, is essential for unraveling the mechanisms underlying these illnesses and identifying potential therapeutic targets. The Broad is truly a magnificent research institution that is leading cutting-edge research. There is a plethora of resources available, and everyone is always willing to collaborate and talk about anything science-related. This summer at the Broad, I have learned how to think and troubleshoot as a scientist even more, which I will carry for the rest of my scientific career. While technologies like snRNA-seq and viral tracing exist for single-cell transcriptomics and connectivity individually, a method currently needs to integrate both aspects. This knowledge gap limits our understanding of neuronal connectivity and hinders the identification of effective treatments. Consequently, our lab has developed a groundbreaking technology called Synapse-Seq, which combines single-cell transcriptomic information with neuroanatomy at single-synapse resolution by labeling each synapse with a unique RNA barcode. However, Synapse-Seq is currently unable to assess connections between neurons. In parallel, our lab has also developed dendrimers, a novel cluster of oligonucleotides capable of assaying molecules at sub-250nm resolution. We aimed to integrate dendrimers into the Synapse-Seq framework, enabling simultaneous assessment of connectomics and single-cell transcriptomics in a high-throughput manner. We used dendrimers to connect mRNA barcodes across pre- and post-synaptic compartments and then sequenced the barcodes. We developed and validated this technology through in vitro studies using neuronal cell culture and applied single-molecule FISH techniques and confocal microscopy. The outcomes of this research effort hold significant promise in two key areas: (1) a method to study connectivity and neurodevelopment in brain organoids by looking at neural networks in a physiologically relevant system and (2) facilitate the identification of therapeutic targets for neurological disorders by providing a comprehensive understanding of brain connectivity in diseased states.


Project: Simultaneous acquisition of single-cell mRNA and connectomics in the brain

Mentors: Michael Kim & Nicholas Thom

PI: Macosko Lab, Stanley Center for Psychiatric Research


August 2023