Aberrant expression of membranous carbonic anhydrase IX (CAIX) is associated with unfavorable disease course in papillary and clear cell renal cell carcinoma. 
Antibodies against carbonic anhydrase IX (CAIX) are often part of immunohistochemical panels used to assist renal cell cancer (RCC) subtyping.  This study was undertaken to determine, whether assessing CAIX expression levels could provide additional prognostic information.  More than 1,800 RCCs were analyzed in a tissue microarray (TMA) format for CAIX expression.  All tumors had been reviewed and newly classified according to the WHO 2016 classification.  Membranous CAIX expression revealed a "black and white" pattern that was strikingly dependent on the RCC subtype.  In clear cell RCC, 89.2% of cancers showed strong positivity.  The few clear cell RCC with lower CAIX expression levels were more likely to exhibit unfavorable tumor phenotype (p < 0.0001) and poor disease course (p = 0.0036).  CAIX was completely absent in 99% of chromophobe RCC and in 100% of oncocytomas.  In papillary RCC, 80.2% of cancers showed complete absence of CAIX staining.  Papillary RCC with detectable CAIX expression had a less favorable tumor phenotype (p≤0.05) and worse disease outcome (p = 0.0176).  These data are consistent with the concept, that "aberrant" CAIX staining - meaning absent or weak staining in a cancer expected to have a high level CAIX expression such as clear cell RCC or detectable CAIX expression in tumors that are typically CAIX negative such as papillary and chromophobe RCC - reflects biologic tumor dedifferentiation.  Our data demonstrate that CAIX is a highly useful diagnostic biomarker for RCC providing both diagnostic and prognostic information.