The (X;1)(p11;q21) translocation is a recurrent chromosomal abnormality in a subset of human papillary renal cell carcinomas, and is sometimes the sole cytogenetic abnormality present. Via positional cloning, we were able to identify the genes involved. The translocation results in a fusion of the transcription factor TFE3 gene on the X chromosome to a novel gene, designated PRCC, on chromosome 1. Through this fusion, reciprocal translocation products are formed, which are both expressed in papillary renal cell carcinomas. PRCC is ubiquitously expressed in normal adult and fetal tissues and encodes a putative protein of 491 aa with a relatively high content of prolines. No relevant homologies with known sequences at either the DNA or the protein level were found.

Several human renal cell carcinomas with X;autosome translocations have been reported in recent years. The t(X ; I )(p 11.2;q21) appears to be a specific primary anomaly, suggesting that tumors with this translocation form a distinct subgroup of R C C Here we report tw o new cases, one with a t(X ;IQ )(p l I.2;q23), the other with a t (X ;l)(p l I.2;p34). The common breakpoint in X p l 1.2 suggests that they belong to the above-mentioned subset of RCC. Using FISH in conjunction with X-spedfic YAC clones, we demonstrate that the two new cases exhibited distinct breakpoints within X p l 1.2.

A combination of Southern blot analysis on a lary RCCs. The cytoplasm of this tumor type shows marked panel of tumor-derived somatic cell hybrids and fluores cence in situ hybridization (FISH) techniques was used to map a series of DNA markers relative to the 1 q21 break point of the renal cell carcinoma (RCC)-associated (X;l)-(pll;q21) translocation. This breakpoint maps between several members of the S 100 family which are clustered in the lq2l region and a conserved region between man and mouse containing the markers SPTA1-CRP-APCSFcER 1 A-ATP 1A2-APO A2. The location of the break point coincides with the transition of a region of synteny of human chromosome 1 with mouse chromosomes 3 and 1.

A combination of Southern blot analysis on a panel of tumor-derived somatic cell hybrids and fluorescence in situ hybridization techniques was used to map YACs, cosmids and DNA markers from the Xp11.2 region relative to the X chromosome breakpoint of the renal cell carcinoma-associated t(X; 1 )(p 11 ;q21). The position of the breakpoint could be determined as follows: Xcen-OATL2-DXS146-DXS255-SYP-t(X;1)-TFE3-OATL1-Xpter. Fluorescence in situ hybridization experiments using TFE3-containing YACs and cosmids revealed split signals indicating that the corresponding DNA inserts span the breakpoint region. Subsequent Southern blot analysis showed that a 2.3-kb EcoRl fragment which is present in all TFE3 cosmids identified, hybridizes to aberrant restriction fragments in three independent t(X;1)-positive renal cell carcinoma DNAs. The breakpoints in these tumors are not the same, but map within a region of approximately 6.5 kb. Through preparative gel electrophoresis an (X;1) chimaeric 4.4-kb EcoRl fragment could be isolated which encompasses the breakpoint region present on der(X). Preliminary characterization of this fragment revealed the presence of a 150-bp region with a strong homology to the 5’ end of the mouse TFE3 cDNA in the X-chromosome part, and a 48-bp segment in the chromosome 1-derived part identical to the 5’ end of a known EST (accession number R93849). These observations suggest that a fusion gene is formed between the two corresponding genes in t(X;1)(p11;q21)-positive papillary renal cell carcinomas.