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A 44-year-old male presented with a 19-year history of urinary calculi and a 1-year history of polydipsia and weight loss. Laboratory tests revealed hyperparathyroidism and evidence of glucagonoma-associated diabetes. Imaging studies identified masses in the pancreatic head and body/tail, suggestive of glucagonoma and a parathyroid adenoma. Furthermore, the patient exhibited hypercalcitoninemia and elevated cortisol and adrenocorticotropic hormone levels. Genetic testing revealed a heterozygous MEN1 mutation [c.65T>G (p.Leu22Arg)], confirming the diagnosis of multiple endocrine neoplasia type 1 (MEN-1). The patient subsequently underwent near-total parathyroidectomy and total pancreatectomy. Postoperative immunohistochemical staining of the pancreatic tail tumor was positive for glucagon and calcitonin. The patient's postoperative hormone levels (calcitonin, glucagon, adrenocorticotropic hormone, cortisol) normalized, suggesting a rare pancreatic neuroendocrine tumor (pNET) that was co-secreting multiple hormones. Postoperative management included pancreatic enzyme supplementation, calcium supplementation, vitamin D supplementation, and insulin for glycemic control. Follow-up evaluations at 10 months demonstrated a stable clinical condition, well-controlled blood glucose and biochemical parameters, and an acceptable quality of life. This case study highlights that the presence of pNETs should be considered in patients with MEN-1 and multiple abnormal hormone levels. Timely surgical management of the involved glands and postoperative complications can effectively improve prognosis.