In this paper, we consider the application of signal alignment (SA) enabled physical network coding (PNC) for the uplink of heterogeneous networks. The joint design of SA and PNC has the potential of fully exploiting the precoding space and can achieve better spatial diversity of a multi-input multi-output (MIMO) networks that provides higher system degrees of freedom (DoF), than the case where only PNC or interference alignment (IA) is employed individually. We consider a scenario where a set of small-cells coexist under the same spectrum with the macro-cell. For this scenario, we design new joint SA and PNC based schemes under different levels of inter-tier coordination. We compare the proposed joint SA-PNC schemes with the IA based techniques, recently designed for uplink heterogeneous systems. Simulation results show that the proposed SA-PNC is quite efficient to remove the inter-tier/system interference while allowing to increase the overall data rate, by serving more users, as compared with the IA based methods.