BCL11B/CTIP2 is highly expressed in GABAergic interneurons of the mouse somatosensory cortex

•BCL11B is expressed within all major subgroups of GABAergic interneurons in S1.•A majority of BCL11B+ cells in neocortical layers I-IV are GABAergic interneurons.•Around 40% of all BCL11B+ cells in layer V are GABAergic interneurons.•Bcl11b mRNA is expressed at the highest level by putative neurogliaform cells.

In the nervous system, BCL11B is crucial for the development of deep layer corticospinal projection neurons and striatal medium spiny neurons and is often used as a marker for the aforementioned cell types. However, the expression of BCL11B in subtypes of non-excitatory neurons in the primary somatosensory cortex (S1) has not been reported in the mouse. In this study we show that BCL11B is extensively expressed in S1 GABAergic interneurons, throughout the three main subgroups (somatostatin-, parvalbumin- and 5HT3a-expresssing). Almost all BCL11B positive cells in the upper S1 layers were GABAergic interneurons and surprisingly, almost 40% of the BCL11B positive neurons in layer V were GABAergic interneurons. Single cell mRNA sequencing data revealed higher Bcl11b expression in S1 interneurons compared to deep layer pyramidal neurons. The highest levels of Bcl11b expression were found within the 5HT3a population, specifically in putative neurogliaform interneuron subclasses (5HT3a-positive but not expressing vasoactive intestinal peptide). In the light of our findings we suggest caution using BCL11B as a single marker to identify neurons.