Arlotta Laboratory

Programming, Reprogramming and Modeling of the Mammalian Cerebral Cortex

The execution of critical behaviors like movement, emotion, and intelligence relies on the orchestrated integration into functional circuits of an outstanding diversity of neuronal subtypes. Focusing on excitatory pyramidal neurons of the mammalian cerebral cortex, our work aims to understand the mechanistic principles that govern the establishment and maintenance of neuronal diversity in the central nervous system, how neuronal diversity affects the behavior of other neurons and glia during cortical development, and the boundaries of neurons’ capacity to reprogram their class-specific identity in the adult brain. At a fundamental level, we are interested in understanding how cortical neurons and circuits are generated and how they subsequently remain unchanged for life. At an applied level, we aim to explore whether neuronal reprogramming can become a valuable therapeutic tool to probe brain plasticity and to replace lost neurons.

While our work is mostly rooted in development of the murine cerebral cortex, a recent interest of our lab has been building in vitro models that resemble the cellular complexity, tissue architecture and local connectivity of the developing human cerebral cortex, which can become a platform for understanding higher-order circuit function and dysfunction that is affected in neurodevelopmental and neuropsychiatric cortical disease. To this end, we are generating next-generation, long-term cultures of 3D cerebral organoids, starting from human induced pluripotent stem cells (iPSCs) derived from control individuals, from patients with neuropsychiatric or neurodevelopmental pathology, or engineered to carry specific genetic mutations associated with these diseases. 

In the long term, our work aims at developing approaches to aid neuronal regeneration in neurodegenerative diseases of the cortical output circuitry, and at understanding and modulating neuronal function in neuropsychiatric diseases affecting the cerebral cortex.


Arlotta Lab


Most of our work aims at defining the molecular rules that shape and retain neuronal diversity in the cerebral cortex; understanding how pyramidal neuron diversity affects the behavior of other neurons and glia to build functional cortical circuits; and exploring the boundaries of the stability of postmitotic neuron identity in vivo. While our work is rooted in development, we are also interested in understanding and modeling complex human cortical pathology, focusing on the development of new high-throughput in vitro models of human cortical development and neurodevelopmental disease using 3D cerebral organoids. 

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Our work spans several areas of investigation:

Molecular principles that shape neuronal diversity during cortical development

In prior work, we have contributed to defining some of the molecular rules that build neuronal diversity in the cerebral cortex, and have challenged the notion that the identity of postmitotic cortical neurons is irreversibly determined by showing that it can be changed (“reprogrammed”) in vivo. We have implemented approaches to molecularly profile individual classes of cortical projection neurons (PNs), building the first molecular map of PN diversity and defining some of the functional pathways required for its generation during embryogenesis. (See our new database DeCoN.) We are expanding this work using a “systems biology” approach that considers the combinatorial role of distinct regulatory events in shaping pyramidal neuron diversity. 

Pyramidal neuron diversity and impact on cortical interneurons and myelin distribution

We have demonstrated that correct establishment of pyramidal neuron diversity is critical in building a balanced cortical microcircuitry and to impose correct patterns of myelination, in vivo. We discovered that distinct pyramidal neuron subtypes differentially affect the laminar fate and assembly into microcircuitry of their interneuron partners. Similarly, pyramidal neurons of different neocortical layers present signature profiles of myelination along their axons that reflect idiosyncratic interactions between different neurons and oligodendrocytes. We have built the first high-resolution map of myelin distribution on single axons of pyramidal neurons and shown that, contrary to common assumptions, myelin is not uniformly distributed along the axons of all neurons. This discovery suggests that neurons may use myelin differently to generate arrays of long-distance communication mechanisms and enable highly complex network behavior. 

Reprogramming neuronal identity in vivo

Substantial work has challenged the idea that differentiated cells cannot change their identity and has underscored the powerful role played by transcription factors in instructing lineage reprogramming. We propose that despite the tight control over maintenance of neuronal identity, neurons are no exception to this mutability, and have questioned the assumption that once generated the identity of neurons cannot change. We showed that within a defined window of neuronal plasticity (closing by P21), postmitotic pyramidal neurons of the neocortex can be directly reprogrammed in vivo to acquire molecular, electrophysiological and connectivity features of alternate neuronal classes. In turn, such changes are also able to reshape afferent connectivity onto reprogrammed neurons by local interneurons. Much of our work is now focused on defining and overriding regulatory mechanisms that make adult neurons refractory to reprogramming their class-specific identity.
Human 3D cerebral organoids as next-generation models of neurodevelopmental and neuropsychiatric disease

Molecular studies of both normal human cerebral cortex development and of neurodevelopmental disorders are currently hampered by the fact that the development, architecture and function of the human brain differ significantly from commonly used animal models such as mice, while direct analysis of human cortical tissue is limited by ethical concerns and tissue availability. Mechanistic and functional analysis of living human brain is precluded by the challenge of monitoring how single-cell transcriptomes of specific neuronal and glial subtypes change dynamically in response to physiological or dysfunctional circuit activity and how these changes orchestrate long-lasting effects on the circuit. It is clear that human cortical development and neuropsychiatric disorder research need a new and robust in vitro system that allows for the simultaneous interrogation of circuit-level activity and molecular-level changes on cells participating in physiologically relevant circuits. To is end, we are working on the development of a 3D cerebral organoid system produced from human pluripotent stem cells that recapitulates key aspects of the cellular diversity, tissue architecture and circuit wiring of the endogenous human developing brain.


SCRB 160

Experimental Embryology: From Stem Cells to Tissues and Back Again

Description: This advanced laboratory course will apply experimental approaches and surgical techniques to illustrate critical events of embryonic development. Students will be trained to perform a diversified set of experiments to observe firsthand how embryos develop and how manipulations of embryonic development lead to mutant organogenesis. Attention will also be paid to illustrating how developmental mechanisms may be used to aid efforts to regenerate specific tissue types in the adult organism.

Particular emphasis will be placed on experiments covering the following topics: in vitro fertilization and pre-implantation embryology; fate specification, morphogenesis, and lineage relationships; organ development; directed differentiation of cell types from Embryonic Stem (ES) cells; tissue-specific stem cells; surgical manipulation of late stage mouse embryos in utero; and neural stem cell transplantation. Students will gain direct experience working with various species including: sea urchin, chicken, zebrafish, frog, and mouse embryos.

Lab News

Mapping the brain cell by cell

October 23, 2017

Harvard and collaborators receive $64.7 million NIH grant to build a detailed map of brain cells in mice

The human brain contains many billions of cells, and scientists are still working to assemble a comprehensive catalog of all of the different types. Neuroscientists have dreamt for years of understanding the role that each one of these cells plays, and how the cells differ, connect and function. But the number of cells has...

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