The Mann–Whitney U test showed that the pNEN characterized by lymph node metastasis (N1, n = 14) showed a lower expression of most autophagy-associated genes compared to pNEN without lymph node metastasis (N0, n = 26), with SQSTM1 (p = 0.01), TFEB (p = 0.023) and PRKAA1 (p = 0.025) being significantly lower. Here, TFEB is linked to metastatic malignant neoplasm in the lymph nodes.