Mesothelioma vs. Adenocarcinoma

Immunohistochemistry
It is generally recommended to perform two mesothelioma markers and two carcinoma markers, since there is no single sensitive and specific marker for either entity.  The data below is a snapshot of several studies.
 
IHC Marker
Adenocarcinoma
Mesothelioma
8%
100%
CK5/6 (CK5)
2%
100%
0%
93%
Thrombomodulin
14%
61-77%
N-Cadherin
30%
73%
93-100%
8%
80-100%
18%
BG8
96%
7%
81-88%
0%
84%
0%
72-74%
0%
72-85%
0%
 
Obviously the main source of adenocarcinoma in this differential setting is with a primary lung adenocarcinoma and mesothelioma.  If a metastasis is likely, then the stain performance expectations for adenocarinoma may vary significantly (e.g. metastatic ovarian serous carcinoma would likely express WT-1).
References
Marchevsky AM. Application of immunohistochemistry to the diagnosis of malignant mesothelioma. Arch Pathol Lab Med. 2008;132: 397–401. 
 
Sandeck HP, Røe OD, Kjærheim K, Willén H, Larsson E. Re-evaluation of histological diagnoses of malignant mesothelioma by immunohistochemistry. Diagnostic pathology. 2010;5: 47. doi:10.1186/1746-1596-5-47
 
Ordóñez NG. Immunohistochemical diagnosis of epithelioid mesothelioma: an update. Arch Pathol Lab Med. 2005;129: 1407–1414.