Fusion of the transcription factor TFE3 gene to a novel gene, PRCC, in t(X;1)(p11;q21)-positive papillary renal cell carcinomas

Abstract

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.

Figure 1

RT-PCR on three different t(X;1)-positive RCCs (lanes 1–3) and t(X;1)-negative controls (lanes 4–6). Lanes: 1, CL89-12117; 2, CL89-17872; 3, RP-T; 4, RP-N; 5, normal renal tissues pooled from several persons; and 6, normal renal tissue from a patient with RCC. The marker shown is the 100-bp ladder (Life Technologies). All three RT-PCR products showed the same sequence joining 150 bp of TFE3 to 48 bp of EST R93849R93849.

Figure 2

Southern blot analysis of somatic cell hybrids using C1 as a probe. A3 and A9 are the hamster and mouse controls, X and 1 the hybrids containing these chromosomes as the only human component, and dX and d1 the CL89-12117-derived somatic cell hybrids containing either der(X) or der(1). RCC1 (CL89-12117), RCC2 (CL89-17872), and REN11-TT are the t(X;1)-positive RCCs. Lane REN11-N, normal tissue adjacent to REN11-TT; and lane NK, normal kidney tissue. HL60 is a myeloid leukemia cell line. As a molecular size marker, λ HindIII DNA was used. DNA samples were cleaved with EcoRI.

Figure 3

Northern blot analysis of t(X;1)-positive RCCs and normal kidney using C1-cDNA (a), TFE3-cDNA (b), or a 5′ fragment from C12 (positions 1–678) (c) as a probe. Lanes 1 and 2 contain total RNA from CL89-17872 and CL89-12117, respectively, lane 3 and 4 contain oligo(dT)-selected RNA from CL89-12117 (1.5 μg) and normal kidney tissue (cortex and medulla; 0.8 μg), respectively. An actin control hybridization is shown (d). As a molecular size marker glyoxylated λ HindIII DNA was used.

Figure 4

Nucleotide sequences and deducted amino acid sequences of C12/PRCC [GenBank accession no. X99720X99720 (a) and the TFE3 sequence (b)] present in C1(TFE3/PRCC) (positions 1–639) and the additional 5′ part (accession no. X99721X99721) present upstream of the known TFE3 sequence (accession no. X51330X51330). Breakpoint locations are indicated by arrows (asterisks in the margins). The first 31 nt of the known human TFE3 sequence including the primer sequence are underlined.

Figure 5

Northern blot analysis of human tissues using C12/PRCC and 3′ TFE3 as probes. Lanes 1–8 contain adult tissues, and lanes 9–12 contain fetal tissues. Lanes: 1, heart; 2, brain; 3, placenta; 4, lung; 5, liver; 6, skeletal muscle; 7, kidney; 8, pancreas; 9, kidney; 10, liver; 11, lung; and 12, brain.