Lack of coordination between network layers limits the performance of most proposed solution for new challenges posed by wireless networks. To overcome such limitations, cross-layer physical and medium access (PHY-MAC) design for multi-input-multi-output orthogonal frequency division multiple access system in heterogeneous networks (HetNETs) is proposed. In this paper, we formulate an optimization problem for hybrid beamforming, in a multi-user HetNET scenario aiming to maximize the total system throughput. Furthermore, analog beamforming is selected from a codebook containing a limited number of candidates for steering vectors. The proposed problem is non-convex and hard to solve. Thus it is relaxed by transforming it into a subtraction form of two convex funcions. Afterward we apply a group of well-known metaheuristic algorithms to calculate the normalized hybrid beamforming vectors. The optimal solution is obtained using an exhaustive search (ES) algorithm that provides an ideal solution, but with high complexity. In addition, zero-forcing-based approach (ZFA), matched filter (MF), and QR-based approach (QR) are applied to get quick sub-optimal solutions. Hence, we analyze the performance of our systems using the throughput metric. The simulation results show that QR algorithm outperforms ZFA and MF in low and middle signal-tonoise ratio (SNR) regime, while ZFA outperforms QR and MF at higher SNRs. Moreover, QR is close to the optimal solution ES.