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X-linked lymphoproliferative syndromes (XLPs) are rare, yet often fatal primary immunodeficiency diseases, which rarely manifest as Langerhans cell histiocytosis (LCH) complicated with hemophagocytic lymphohistiocytosis (HLH). Clinical data of a case of XLP-2 manifesting as LCH complicated with HLH was retrospectively analyzed to determine the etiology and causal gene.The diagnosis of multisystem LCH was confirmed by skin biopsy and other examinations in a 13-month boy with recurrent ear discharge, fever and hemorrhagic papules for 3 months. A good therapeutic response to LCH-III protocol-directed induction chemotherapy was achieved but unremitting HLH developed 6 weeks after the initiation of induction chemotherapy. To identify possible underlying genetic causes, gene mutation analysis was undertaken. A novel XIAP gene mutation (c.99delT, p.F33fsX37) was documented.After the diagnosis of HLH had been confirmed, HLH-2004-directed chemotherapy was instituted.The clinical condition of the patient had become progressively deteriorating after 8-week chemotherapy of HLH-2004 protocol, requiring frequent infusions of RBC suspensions and apheresis platelets. His parents decided to receive no further therapy, and the patient died soon after discharge.Meticulous laboratory investigations including genetic studies should be undertaken in young children with LCH complicated with HLH and poor therapeutic response.