Areas of Research

The current focus of the Maniatis lab is on molecular neuroscience: Molecular genetic approaches to the understanding neural circuit development and neurodegenerative diseases.

The protocadherin gene cluster:

In 1999 we discovered the remarkable genomic organization of the protocadherin (Pcdh) gene cluster, which consists of three clusters (ɑ, ß and γ)  ɑ spanning nearly 1 million base pairs of DNA, and encoding over 50 distinct Pcdh protein isoforms. Subsequently detailed studies in cell culture and mice revealed the mechanism by which Pcdh gene activation occurs in individual neurons. We identified transcription promoters located immediately upstream of the coding sequences of individual Pcdh isoforms, and transcriptional enhancer elements located hundreds of thousands of base pairs away. We showed that these enhancer elements stochastically engage individual promoters through long range DNA looping, in a process requiring the DNA binding protein CTCF and cohesin, the sister chromatid cohesion complex. This process generates a cell surface identity “code” that functions in self vs non-self recognition.

The human Pcdh gene cluster

The structure and function of protocadherin proteins was determined in collaboration with the laboratories of Barry Honig and Larry Shapiro. The insights from these studies revealed how a relatively small number of protein isoforms can generated enormous functional cell surface diversity through nearly random formation of Pcdhɑ, ß and γ and γ cis-dimers, and engage at the cell surface as cis/trans tetramers. Biophysical, structural and functional studies have led to the proposal that Pcdhs form a protein lattice of cis/trans-tetramers:

The structure of Pcdh proteins

The in vivo function of the clustered Pcdhs

Genetic studies in mice have revealed that the clustered Pcdhs function in neurite self-avoidance and axonal tiling.

Loss of Pcdhg results in a defect in neurite self avoidance in mouse starburst amacrine cells (Lefevbre et al, Nature 488, 517, 2012).

Chen et al., 2017 Science 356, 411.

Loss of entire Pcdh gene cluster results in defects in olfactory sensory neuron wiring.

Visualization of individual olfactory sensory neuron in wild type and Pcdhabg^-/- mice

Mountoufaris et al., Science 356, 411, 2017

ALS disease mechanisms

We study disease mechanisms of Amyotrophic Latera Sclerosis (ALS) using mouse models, mouse embryonic stem cells and human induced pluripotent stem cells. Our current focus is on the role of autophagy, based on genetic studies showing that sequence variant in any one of several autophagy genes cause familial ALS or associate with sporadic ALS. 

Mouse models

We are introducing conditional deletion mutations of autophagy genes such as ATG7 and TBK1 into existing mouse models such as SOD1, TDP43 and C9orf72 to identify the role of affected cell types, and to investigate genetic and functional interactions between different ALS-causing mutations. 

The first example was ATG7 deletion in motor neurons in the SOD1 mouse model. Remarkably, we found that loss of autophagy function exclusively in motor neurons of the SOD1 mouse accelerated disease progression early in the disease, and diminished progression later. The diminished disease progression late correlated with a decrease in the spread of  p62 positive aggregates and phopho-CJun from the ventral to dorsal spinal cord.

Rudnick et al., Proc. Natl. Acad. Sci 114, E8924, 2017.

Mechanistic Studies of Neuronal Ensembles:  One Cell at a Time.

The aforementioned biological problems motivate a deeper understanding of cellular heterogeneity.  By way of example, given the uniqueness in protocadherin choice, how then are cell type specific patterns of expression reconciled with the stereotyped structure and function of neural circuits?  Furthermore, given the preponderance of cell autonomous and non-cell autonomous effects on ALS disease progression, can we identify cell type specific contributions to disease progression?  Can we further elucidate intrinsic and extrinsic cellular effects and their impact on cellular fate and disease?  To answer these questions, we build tools and methods of analysis to study these biological questions in depth and with single cell resolution, in both human and mouse models.

We have studied mouse and human motor neurons generated from stem cells.  As a proof of concept, we have optimizing single cell sequencing and, in collaboration with Raul Rabadan, coupled the output with topological data analysis.  This workflow enables unfettered access to heterogeneous cellular responses, through the direct detection of transcriptional co-regulation.  As a proof of concept, we have applied this to the in vitro differentiation of motor neurons from mouse embryonic stem cells.  From this work, we are well poised to identify key regulators and pivotal mechanisms associated with protocadherin based neural circuit assembly, and the molecular basis for the onset and progression of ALS.

Rizvi et al. Nature Biotechnology, 35,551 (2017)