Homozygous deletion of the chromosomal region 9p21.3 is common in urothelial carcinoma (UC) and leads to loss of several genes, including CDKN2A and MTAP, resulting in loss of MTAP protein expression. Here, we aimed to explore the diagnostic potential of MTAP immunohistochemistry (IHC) as a surrogate marker for homozygous 9p21.3 deletion (9p21 homozygous deletion [HD]) in UC. MTAP status was determined by IHC on 27 UC tissue specimens with known 9p21.3 status as defined by fluorescence in situ hybridization in matched cytological specimens, by IHC and fluorescence in situ hybridization on a tissue microarray (TMA) containing 359 UC at different stages, and by IHC on 729 consecutive UC from routine practice. Moreover, we analyzed a longitudinal series of matched specimens from 38 patients with MTAP-negative recurrent UC. MTAP loss by IHC was found in all 17 patients with 9p21 HD and in 2/8 cases without 9p21 HD. In the TMA, MTAP loss was more common in metastases (53%) than in muscle-invasive (33%) and non-muscle-invasive UC (29%) (P = .03). In the consecutive series, 164/729 (22%) cases showed loss of MTAP expression. In 41 of these 164 cases (25%), loss of MTAP expression was heterogenous. We also discovered loss of MTAP expression in flat urothelium adjacent to MTAP-negative low-grade UC, suggesting true flat low-grade neoplasia that could not be diagnosed by morphology alone. Longitudinal analysis of recurrences showed persistent negative MTAP status over time in 37/38 (97%) patients. MTAP IHC can serve as a surrogate marker for 9p21 HD in UC and as a diagnostic tool to differentiate reactive urothelium from urothelial neoplasia. It also provides a unique opportunity to study clinicopathological associations and the heterogeneity of 9p21 HD across the whole spectrum of UC manifestations.

Malignant pleural mesothelioma (MPM) is a rare and deadly disease. A precursor in situ lesion, malignant pleural mesothelioma in situ (MPMIS), has recently been proposed. On cytological examination, the distinction between reactive and malignant mesothelial cells is often challenging, and sometimes even impossible without ancillary methods. Fluorescence in situ hybridization (FISH) for detection of 9p21 deletion is a powerful diagnostic tool in this context, both in histological and in cytological specimens. Here, we present a case of MPM with initial presentation as a putative MPMIS with disomic chromosomal pattern and homozygous 9p21 deletion with subsequent development of an aneuploid pattern after whole genome duplication during tumor progression.

The ongoing approval of adjuvant systemic therapy in high-risk kidney tumor will increase the demand for prognostic assessment in these tumors. 9p21 deletion has been suggested as a possible prognostic feature in clear cell kidney cancer.
To learn more on the prognostic relevance of 9p21 deletions in clear cell and other kidney tumors, 1,809 kidney tumor specimens were analyzed by dual-labeling fluorescence in situ hybridization (FISH) with probes for 9p21 and centromere 9 in a tissue microarray format. Results were compared to histologic tumor type, pT stage, grade, and patient outcome.
A total of 1,341 (74%) of tumor samples had interpretable FISH results. 9p21 deletion was found in 4.4% of 894 clear cell, 5.1% of 197 papillary, and 4.2% of 71 chromophobe carcinomas. 9p21 deletions were not found in 112 oncocytomas and in 21 clear cell tubulo-papillary cancers. In clear cell carcinomas, 9p deletions were associated with advanced stage (P = 0.009) and nodal metastasis (P = 0.0067), but not with ISUP grade (P = 0.1039) and distant metastasis (P = 0.4809). Also, in papillary carcinomas, 9p deletions were associated with advanced stage (P = 0.0008) and nodal metastasis (P = 0.0202) but not with ISUP grade (0.0904) and distant metastasis (P = 0.2022). Follow-up data were available for 789 clear cell and 177 papillary cancers. In both tumor entities, 9p21 deletions were associated with shortened overall survival, tumor-specific death, and progression-free survival in univariate analysis (P < 0.02 each). In a multivariate analysis, 9p21 deletion was an independent predictor of early tumor recurrence (P = 0.04).
9p21 deletions, 9p21 deletions identify a small subset of aggressive renal carcinomas. 9p deletion assessment may be clinically useful to identify high-risk renal cell carcinomas.

Overexpression of the p16 tumor suppressor, but also deletion of its gene locus 9p21, is linked to unfavorable tumor phenotype and poor prognosis in breast cancer. To better understand these contradictory observations, and to clarify the prognostic impact of p16 expression and 9p21 deletion, a tissue microarray (TMA) with 2,197 breast cancers was analyzed by fluorescence in-situ hybridization and immunohistochemistry (FISH) for 9p21 deletion and p16 expression. p16 immunostaining was weak in 25.6%, moderate in 7.1%, and strong in 12.7% of 1,684 evaluable cancers. Strong p16 staining was linked to advanced tumor stage (p = 0.0003), high-grade (p < 0.0001), high tumor cell proliferation (p < 0.0001), negative hormone receptor (ER/PR) status (p < 0.0001 each), and shorter overall survival (p = 0.0038). 9p21 deletion was found in 15.3% of 1,089 analyzable breast cancers, including 1.7% homozygous and 13.6% heterozygous deletions. 9p21 deletion was linked to adverse tumor features, including high-grade (p < 0.0001) and nodal positive cancers (p = 0.0063), high cell proliferation (p < 0.0001), negative hormone receptor (ER/PR) status (p ≤ 0.0006), and HER2 amplification (p = 0.0078). Patient outcome was worse in 9p21 deleted than in undeleted cancers (p = 0.0720). p16 expression was absent in cancers harboring homozygous 9p21 deletions, but no difference in p16 expression was found between cancers with (59.2% p16 positive) and without heterozygous 9p21 deletion (51.3% p16 positive, p = 0.0256). In summary, p16 expression is unrelated to partial 9p21 deletion, but both alterations are linked to aggressive breast cancer phenotype. High-level p16 expression is a strong predictor of unfavorable disease course in breast cancer.