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Cognitive processing is a product of neuronal communication. A key component of neuronal communication is that each neuron can receive external signals from thousands of other neurons, connecting to different physical positions on the neuron surface. The neuron’s ability to receive external signals is achieved by spatially distinct signaling domains, or compartments, such as the neuron’s dendritic spines and growth cones. The signaling capacity of the compartments, and as a result the neuron’s ability to respond to spatially different stimulations, is realized by precise subcellular distribution of proteins and messenger RNA (mRNA) — the genetic blueprints for protein production. 

The disruption of RNA binding proteins, which transport and localize RNA throughout cellular compartments, has been implicated in autism spectrum disorders, such as Fragile X syndrome. However, the relationship between RNA mislocalization and disease remains unexplored because of molecular and spatial limitation - optical methods maintain the spatial location of molecules, but are limited in the number of molecules that can be studied simultaneously. On the other hand, current transcriptomic approaches allow the multiplexed measurement of potentially all the RNA molecules, but spatial information is lost in the process.

Using a new technology that expands brain tissue to four times its original size we can spot and sequence individual mRNAs. The sequencing works by binding a series of colorfully labeled bases to the mRNA; by recording the resulting sequence of colors, it is possible to deduce the mRNA sequence. This technology (expansion sequencing; Alon et al., 2021), can reveal how a single neuron makes thousands of connections, called synapses, which can be functionally different. Moreover, as long term synaptic plasticity is realized by local synthesis of proteins from mRNA at the synapse, the subcellular location and identity of RNA is crucial for understanding of learning and memory.


In situ cancer genomics


Genome-wide in situ characterization of tissues can be transformative in the field of cancer biology. Potentially, this will reveal the complex interaction between cells and the microenvironment within cancer tissues, by characterizing cell types and cell states while maintaining the morphological details of the tissues. One key question, for example, is to understand how tumor microenvironments, such as the state of local immune cells, govern tumor initiation, progression, metastasis, and treatment resistance. 


Rather than dissociating the tumor tissue and studying cells in isolation, our technology identifies the RNA content of the cells in situ, inside their natural tissue environment. We are generating comprehensive maps of tumor spatial heterogeneity and structure (Alon et al., 2021). The resulting maps illuminate the molecular and morphological phenotypes of tumor invasion and pathology, which will help guide future therapeutic interventions.


RNA complexity and physiology


The central dogma of biology maintains that genetic information passes faithfully from DNA to RNA to proteins; however, with the help of mechanisms such as alternative splicing, organisms use RNA as a canvas to modify and enrich this flow of information. RNA editing by deamination of adenosine to inosine (A-to-I) is another process that alters genetic information. Unlike alternative splicing, which shuffles relatively large regions of RNA, editing targets single bases. A-to-I RNA editing is catalyzed by the ADAR (adenosine deaminase that acts on RNA) family of enzymes, expressed in all eumetazoans, from cnidarians to mammals. Because inosine is interpreted as guanosine by the cellular machinery, this process can recode codons, possibly fine-tuning protein function. In the nervous system recoding affects the physiological activities of several ion channels and receptors with critical implications on brain function. Using computational tools and new sequencing technologies, we have discovered RNA editing events in the human brain and in the squid (Alon et al., 2015, Liscovitch et al., 2017), demonstrating that RNA editing can allow massive tweaking of the nervous system. 

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