We assume that, within the dense clusters of neurons that can be found in nuclei, cells may interconnect via soma-to-soma interactions, in addition to conventional synaptic connections. We illustrate this idea with a multi-layer architecture (MLA) composed of multiple clusters of recurrent sub-networks of spiking Random Neural Networks (RNN) with dense soma-to-soma interactions, and use this RNN-MLA architecture for deep learning. The inputs to the clusters are first normalised by adjusting the external arrival rates of spikes to each cluster. Then we apply this architecture to learning from multi-channel datasets. Numerical results based on both images and sensor based data, show the value of this novel architecture for deep learning.