In this paper we consider the application of joint signal alignment (SA) and physical network coding (PNC) for the uplink of heterogeneous networks. The joint design of SA and PNC provides higher system degrees of freedom (DoF), than the case where only PNC or interference alignment (IA) is employed. The concept of SA-PNC is inspired by the recent advances in IA, where SA aligns signals not the interference. In fact, in SA design, there is no interference and all data transmissions are treated as signals. 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 ones.