Loss of CDKN1A mRNA and Protein Expression Are Independent Predictors of Poor Outcome in Chromophobe Renal Cell Carcinoma Patients

Chromophobe renal cell carcinoma (chRCC) patients have good prognosis. Only 5%–10% patients die of metastatic disease after tumorectomy, but tumor progression cannot be predicted by histopathological parameters alone. chRCC are characterized by losses of many chromosomes, whereas gene mutations are rare. In this study, we aim at identifying genes indicating chRCC progression. A bioinformatic approach was used to correlate chromosomal loss and mRNA expression from 15287 genes from The Cancer Genome Atlas (TCGA) database. All genes in TCGA chromophobe renal cancer dataset (KICH) for which a significant correlation between chromosomal loss and mRNA expression was shown, were identified and their associations with outcome was assessed. Genome-wide DNA copy-number alterations were analyzed by Affymetrix OncoScan® CNV FFPE Microarrays in a second cohort of Swiss chRCC. In both cohorts, tumors with loss of chromosomes 2, 6, 10, 13, 17 and 21 had signs of tumor progression. There were 4654 genes located on these chromosomes, and 13 of these genes had reduced mRNA levels, which was associated with poor outcome in chRCC. Decreased CDKN1A expression at mRNA (p = 0.02) and protein levels (p = 0.02) were associated with short overall survival and were independent predictors of prognosis (p < 0.01 and <0.05 respectively). CDKN1A expression status is a prognostic biomarker independent of tumor stage. CDKN1A immunohistochemistry may be used to identify chRCC patients at greater risk of disease progression.

Telomere attrition and candidate gene mutations preceding monosomy 7 in aplastic anemia

Key Points Accelerated telomere attrition precedes chromosomal loss and malignant transformation to MDS/AML arising from aplastic anemia.

Essential Thrombocytosis: Redefinition in the Genomic Era

Introduction: Essential thrombocytosis (ET) is a hematopoietic stem cell disease defined by acquired mutations in JAK2, CALR or MPL. Variability in natural history, phenotypic transformation to PV or MF, and thrombosis risk exist within ET with age, gender, disease duration, mutant allele burden and other factors operating as modifiers. Methods: We established a prospective, observational cohort of 605 ET, polycythemia vera (PV) and myelofibrosis (MF) patients enrolled between 2005 and 2013 with which to study the genomic modifiers of the MPN. We obtained neutrophil JAK2V617F allele burdens for all patients, and MPL and CALR mutation status for the JAK2V617F-negative subset. SNP-array karyotypes and ASXL1mutation analyses were obtained on a subset of the cohort. Results: Twenty-five percent of the cohort was newly diagnosed and the median MPN disease duration of the cohort was 8 years (range 1-52 years). Females comprised the majority of the entire MPN cohort, whether considering newly diagnosed (80/155;51%) or prevalent cases (370/605;62%). Females comprised the majority of ET patients, whether considering newly diagnosed (34/55;61%), or prevalent cases (71/101;70%). JAK2V617F was present in 60% of ET. While CALR mutations were present in 67% of JAK2V617F-negative ET, they comprised a smaller relative proportion in females (55%) compared to males (88%; p=0.0047), due to an excess of JAK2-CALR-MPL mutation-negative (triple negative (TN)) ET in females (34%) compared to males (8%; p=0.0142). At last follow up, females comprised 70% of JAK2V617F-positive ET, 70% of JAK2V617F-negative ET, 57% of CALR mutation-positive ET, 86% of MPL-mutation positive ET and 90% of TN ET. Similar to reported findings, JAK2V617F-positive ET patients were older at diagnosis (48.7 vs 42.5 yrs,p=0.005), had lower platelet counts and a higher prevalence of chemotherapy use compared to JAK2V617F-negative ET. Strikingly, abdominal venous thrombosis events were restricted to the JAK2V617F-positive ET cohort, occurring in 4%, and predominantly in females. A family history of an MPN was similar between groups, described in 13% of CALR and TN mutation ET compared to 11% of JAK2V617F-positive ET. ET patients had a low prevalence of chromosomal loss, gain or acquired uniparental disomy (UPD) compared to PV or MF patients. UPD occurred in 14% of JAK2V617F-negative ET, and encompassed the CALR gene in one patient with a CALR mutation, the MPL gene in a patient with an MPL mutation, and the TET2 gene in two others. UPD was present in 23% of JAK2V617F-positive ET, and did not encompass regions present in the JAK2V617F-negative ET cases. ASXL1 mutations were absent in all ET cases. While JAK2V617F-positive ET patients may transform to PV, transformation to PV in CALR, MPL or TN mutation patients was not observed. Transformation to post-ET MF occurred in all ET genotypes, and despite differences in time to transformation (mean 10.2 years in JAK2V617F-positive ET compared to 18.3 years in CALR, MPL and TN mutation ET (p=0.005)), average age at MF transformation was similar (62 years). Both UPD and chromosomal loss/gain were prevalent in ET patients who transformed to MF, regardless of genotype. However, 9pUPD was restricted to JAK2V617F-positive patients. Chromosomal loss regions in 20q and 17q were present in both JAK2V617F and CALR positive post-ETMF, as were ASXL1 mutations (40% in JAK2V617F -positive post-ETMF and 75% in JAK2V617F-negative post-ETMF). Conclusions: The genetic drivers of phenotype within ET may differ (JAK2, CALR, MPL, TN), yet all ET subtypes share female predominance, similar rates of familial clustering, and similar age at transformation and chromosomal instability lesions that accompany post-ET MF. TN ET is not yet defined by a genetic lesion, yet shares similar epidemiologic, natural history and genetic features as mutation defined ET. We conclude that TN ET is likely a clonal myeloid disease, and that either there are other ET driver lesions, or that allele burdens of JAK2, CALR or MPL lesions are below the limits of detection of standard screening assays in TN ET. Given the molecular epidemiology of MPN, it will be crucial recognize and reduce the risk factors that lead to the excess acquisition of ET in women, to identify the risk factors that lead to disease transformation, and to develop targeted therapy that can extinguish ET clones while avoiding therapy that accelerates genomic instability in ET. Disclosures Moliterno: Incyte: Consultancy.