Date of Award
Fall 2026
Abstract
Primary cilia are microtubule-based structures that emerge from the surface of most mammalian cells, including neurons in the brain. They function as cellular antennae and are responsible for detecting and transmitting signals. Studies have shown that changes in primary cilia structure and function cause numerous neurological diseases, such as Joubert syndrome and Bardet-Biedl syndrome. However, their function in postnatal cerebral cortices remains poorly understood. My dissertation has three main goals. First, I aimed to reveal the cilia orientation pattern across cortical regions of mice, turtles, and macaques. Second, I collected more evidence on reverse soma movement during postnatal development within the mouse cerebral cortex, to help establish the novel concept of reverse movement in principal neurons. Third, I sought to determine the effect of the AC3 ablation on Arl13b-positive cilia morphology and neuronal maturation in the hippocampus.Project 1: Our lab has previously reported that in the neocortex, which has a loosely laminated structure, the primary cilia of principal neurons are predominantly oriented toward the pial direction. In contrast, in hippocampal regions with compact laminar organization, cilia exhibit bidirectional (opposing) orientation. Here, to determine whether cilia directionality is associated with neuronal positioning and cortical evolution, I investigated the orientation of primary cilia across cortical regions in multiple species, including turtles (reptiles), mice (mammals), and macaques (mammals and primates). Using immunofluorescence imaging and custom MATLAB tools for cilia detection and orientation analysis, I found that cilia orientation patterns vary across cortical structures. In loosely laminated regions in mice, including the subiculum, layer III piriform cortex, layers II/III and layer V perirhinal cortex, layers II/III and layer V entorhinal cortex, primary cilia predominantly orient toward the pial surface, whereas in compact laminated regions in mice, such as layer II piriform cortex, layer II olfactory tubercle, cilia manifest bidirectional orientation. In contrast, primary cilia of astrocytes, or of excitatory neurons in nucleated regions do not display specific cilia directionality. Comparative analysis across species revealed that these patterns are conserved, with reptiles, such as turtles, exhibiting more bidirectional cilia orientation in the lateral, dorsal, and medial cortices, as they contain compact laminar organization. While the subiculum, CA1 region, and neocortex (sulcus and gyrus) in macaques are loosely laminated structures and cilia orientation points toward the pial surface, the dentate gyrus (DG) and CA3 region (parts of hippocampus) exhibit compact laminated organization and have bidirectional cilia orientation. These data suggest that, over the course of cortical evolution, primary cilia in principal neurons progress from having no preferred orientation in lower non-laminated brain regions to becoming increasingly aligned toward the pial surface in higher laminated cortical regions. We propose a working model of cortical evolution in which the placement of principal neurons evolves from minimal migration in lower vertebrate species with simpler cortical organization to more outward migration in higher species, which possess more complex and expanded cortical structures, and ultimately to pronounced reverse soma movement in the inside-out laminated cortices of more advanced brains. This reversal is likely driven by the accumulation of large neuronal populations in the outer cortical layers following the completion of radial migration. Project 2: The placement of principal neurons is essential for establishing the layered organization of the cerebral cortex. While radial migration during embryonic development is well studied, how neurons complete postnatal positioning remains unclear. Previously, our lab reported that the principal neurons in the cerebral cortex undergo a slow reverse movement during the early postnatal developmental stage. More evidence is needed to establish the novel concept of reverse movement. In this chapter, I continued to examine postnatal neuronal positioning and further collected evidence supporting the notion of the reverse movement of principal neurons during early postnatal development. Using CFSE labeling, cortical neuronal positioning from P1 to P9 was tracked, and a gradual redistribution of labeled neurons was observed from superficial layers to deeper layers. This finding is further supported by double-labeling dye injection experiments, which revealed distinct spatial separation between neuronal populations labeled at different time points. In parallel, analysis of axon initial segment (AIS) morphology demonstrated a transition from uniformly straight structures at early postnatal stages to layer-specific patterns, with curved AIS emerging in deeper layers at the later postnatal stages. This morphology change also suggest reverse soma movement. The orientation of primary cilia was further examined as mice aged, and I found that cilia were initially randomly oriented during early postnatal development upon cilia expression, but increasingly aligned toward the pial surface from P10 to P30. These changes matched the period of neuronal repositioning. Comparative analysis of AIS morphology in the macaque cortex revealed similar layer-dependent differences and cilia orientation, suggesting conservation across species. Additionally, in situ hybridization (ISH) data of developmental mouse brain data from the Allen Brain Institute further demonstrated progressive neuronal reorganization in the subiculum, post-subiculum, and CA1 regions during postnatal development, providing further evidence of reverse neuronal movement during this period. Together, these findings suggest that the position of principal neurons in the cerebral cortex is not fixed at birth but continues to be refined during early postnatal development. Reverse soma movement may play a crucial role in shaping cortical laminar organization, affecting neuronal maturation and circuit formation. Project 3: Primary cilia are signaling organelles that regulate neuronal development and function. While Arl13b is known to regulate ciliogenesis and Shh signaling, and AC3 mediates cAMP signaling within neuronal primary cilia, the relationship between AC3 and Arl13b within cilia remains unclear. In this study, I investigated the effect of AC3 loss on Arl13b cilia expression and neuronal maturation during postnatal development. Using AC3 conditional knockout mice (cKOs, or AC3 flox/flox Emx1-Cre mice), I analyzed Arl13b-positive cilia morphology in the hippocampal DG and CA1 regions across postnatal stages. I found that loss of AC3 resulted in increased Arl13b-positive cilia length and cilia frequency in the DG, whereas cilia length was reduced in CA1 neurons, indicating the effect differs between regions. In addition, I found that WT groups expressed more NeuN-positive neurons in both CA1 and DG regions than AC3 cKO groups at both P7 and P10, suggesting that AC3 affects neuronal maturation during early postnatal development. These findings demonstrate that AC3 regulates Arl13b cilia expression pattern and modulates neuronal maturation in the hippocampus.
Document Type
Dissertation
First Advisor
Xuanmao XC Chen
Department or Program
Genetics
Degree Name
Doctor of Philosophy
Recommended Citation
Mirhosseini, Soheila, "Primary Cilia Pattern Analysis in the Vertebrate Cerebral Cortices" (2026). Doctoral Dissertations. 3041.
https://scholars.unh.edu/dissertation/3041