An allele on chromosome 5 residing within the ZSWIM6 region distinguishes patients with basal-like human breast cancer.

Patients diagnosed with basal-like (also known as basal) subtype breast cancer face a more aggressive disease course and more dismal prognosis than patients diagnosed with luminal A and luminal B breast cancer molecular subtypes (1-4). We mined published microarray data (5, 6) to understand in an unbiased fashion the most distinguishing genetic and transcriptional features of tumors from patients with basal or basal-like subtype breast cancer. We identified a single nucleotide polymorphism, rs6449531 in ZSWIM6 as among the most significant genetic differences in the tumors of patients with basal-like breast cancer. In a separate cohort of patients with basal subtype breast cancer, we observed transcriptome-wide differential expression of a ZSWIM6 transcript. Analysis of patient survival data revealed that ZSWIM6 primary tumor expression was correlated with overall survival in patients with basal subtype breast cancer. Sequence variation in the ZSWIM6 gene may be important in understanding differences in genetic background that favor development of basal subtype human breast cancer.

Three-antibody classifier for muscle invasive urothelial carcinoma and its correlation with p53 expression

AimsTo assess the utility of a three-antibody immunohistochemistry panel to classify muscle invasive bladder cancers (MIBCs) in correlation with morphological features and p53 status.MethodsA retrospective review of 243 chemotherapy naïve MIBC cystectomy specimens was performed to assess morphological features. A tissue microarray was sequentially stained with CK5/6, GATA-3 and p16. Subgroups were assigned as basal-like (CK5/6+, GATA3−) and luminal (CK5/6−, GATA3+), with the latter subdivided into genomically unstable (GU, p16+) and urothelial like (Uro, p16−) subgroups. p53 staining was assessed as abnormal/wild type. Cases from the The Cancer Genome Atlas (TCGA) portal were assessed as external validation.ResultsWe identified 78.8% luminal, 21.2% basal cases within our cohort and 63.4% luminal, 36.6% basal in the TCGA dataset. Divergent differentiation (p<0.001) was significantly associated with basal-subtype cases in both cohorts. Within the luminal subgroup (n=186), 81 cases were classified as GU and 105 as Uro. Abnormal p53 staining was noted in 48.0% of basal, 80.2% GU and 38.1% Uro cases. Further, basal-subtype tumours significantly correlated with disease-specific death compared with Uro cases in multivariate survival analysis.ConclusionsThis retrospective study demonstrates the potential utility of a three-antibody immunohistochemistry panel to differentiate luminal and basal MIBC.

Randomized Phase III Postoperative Trial of Platinum-Based Chemotherapy Versus Capecitabine in Patients With Residual Triple-Negative Breast Cancer Following Neoadjuvant Chemotherapy: ECOG-ACRIN EA1131

PURPOSE Patients with triple-negative breast cancer (TNBC) and residual invasive disease (RD) after completion of neoadjuvant chemotherapy (NAC) have a high-risk for recurrence, which is reduced by adjuvant capecitabine. Preclinical models support the use of platinum agents in the TNBC basal subtype. The EA1131 trial hypothesized that invasive disease-free survival (iDFS) would not be inferior but improved in patients with basal subtype TNBC treated with adjuvant platinum compared with capecitabine. PATIENTS AND METHODS Patients with clinical stage II or III TNBC with ≥ 1 cm RD in the breast post-NAC were randomly assigned to receive platinum (carboplatin or cisplatin) once every 3 weeks for four cycles or capecitabine 14 out of 21 days every 3 weeks for six cycles. TNBC subtype (basal v nonbasal) was determined by PAM50 in the residual disease. A noninferiority design with superiority alternative was chosen, assuming a 4-year iDFS of 67% with capecitabine. RESULTS Four hundred ten of planned 775 participants were randomly assigned to platinum or capecitabine between 2015 and 2021. After median follow-up of 20 months and 120 iDFS events (61% of full information) in the 308 (78%) patients with basal subtype TNBC, the 3-year iDFS for platinum was 42% (95% CI, 30 to 53) versus 49% (95% CI, 39 to 59) for capecitabine. Grade 3 and 4 toxicities were more common with platinum agents. The Data and Safety Monitoring Committee recommended stopping the trial as it was unlikely that further follow-up would show noninferiority or superiority of platinum. CONCLUSION Platinum agents do not improve outcomes in patients with basal subtype TNBC RD post-NAC and are associated with more severe toxicity when compared with capecitabine. Participants had a lower than expected 3-year iDFS regardless of study treatment, highlighting the need for better therapies in this high-risk population.

A randomized phase III post-operative trial of platinum-based chemotherapy (P) versus capecitabine (C) in patients (pts) with residual triple-negative breast cancer (TNBC) following neoadjuvant chemotherapy (NAC): ECOG-ACRIN EA1131

605 Background: Pts with TNBC who have residual invasive disease (RD) after completion of NAC have a very high risk for recurrence, which is reduced by adjuvant capecitabine (C). Pre-clinical models support the use of platinum agents (P) in the TNBC basal subtype. EA1131 tested the hypothesis that invasive disease-free survival (iDFS) would not be inferior but improved in pts with basal subtype TNBC after NAC with the adjuvant use of a P instead of C (primary objective). Methods: Pts with clinical stage II/III TNBC post neoadjuvant taxane +/- anthracycline-based chemotherapy with at least 1 cm RD in the surgical specimen were randomized (1:1) to receive P (carboplatin or cisplatin once every 3 weeks for 4 cycles) or C (14/7d every 3 weeks for 6 cycles). TNBC subtype (basal vs. non-basal) was analyzed in the surgical specimen by PAM50. A non-inferiority design (non-inferiority margin of hazard ratio [HR] of 1.154) with superiority alternative (alternative HR of 0.754) was chosen, assuming a 4-year iDFS of 67% for the C arm. Non-inferiority was tested first. If non-inferiority was shown, a formal test for superiority of P compared to C would be conducted. Results: 401 participants were randomized to P or C between 2015 and 2020 (recruitment goal, 775), 310 (77%) had TNBC basal subtype disease (primary analysis population). Pts’ median age was 52 years, 71% were White and 19% Black. At diagnosis, most tumors were high grade (78%), T2 (59%), 47% N0, and 40% N1. Residual tumors were 37% ypT1, 44% ypT2, and 47% ypN0. Overall incidence of any toxicity was similar (83% with P, 80% with C), but grade 3 and 4 toxicities (no grade 5) were more common with P (25% vs 15%). After median follow-up of 18 months, 113 iDFS events (58% of full information) had occurred. 3-year iDFS for P arm was 40% (95%CI, 29%-51%) and 44% (95%CI, 32%-55%) for C arm. The HR for arms P/C was 1.09 (95% Repeated Confidence Interval, 0.62-1.90) and the probability of eventually rejecting the null of inferiority (i.e., conditional power) was 6%. The Data Safety and Monitoring Committee recommended stopping the trial at the 5th interim analysis in March 2021 since it was unlikely that the trial would be able to show non-inferiority or superiority of the P arm. Conclusions: Participants with TNBC with RD after NAC had a lower than expected 3-year iDFS regardless of study treatment. Available data show that it is very unlikely that the study would be able to establish non-inferiority of P to C. In addition, severe toxicities were more common with P. In pts with TNBC, particularly basal subtype, with at least 1 cm RD after NAC and high-risk of recurrence, adjuvant P use does not improve outcomes. Correlative analyses of RD tissue (NGS), circulating markers (ctDNA and CTC pre/post treatment), and patient-reported outcomes (PRO) questionnaires will now occur. Clinical trial information: NCT02445391.

Pparg drives luminal differentiation and luminal tumor formation in the urothelium

Pparg, a nuclear receptor, is downregulated in basal subtype bladder cancers that tend to be muscle invasive and amplified in luminal subtype bladder cancers that tend to be non-muscle invasive. Bladder cancers derive from the urothelium, one of the most quiescent epithelia in the body which is composed of basal, intermediate, and superficial cells. We find that expression of an activated form of Pparg (VP16;Pparg) in basal progenitors induces formation of superficial cells in situ, that exit the cell cycle, and do not form tumors. Expression in basal progenitors that have been activated by mild injury however, results in luminal tumor formation. We find that tumors are immune deserted, which may be linked to downregulation of Nf-kb, a Pparg target. Interestingly, some luminal tumors begin to shift to basal subtype tumors with time, downregulating Pparg and other luminal markers. Our findings have important implications for treatment and diagnosis bladder cancer.

Investigation of a 22-gene genomic classifier (GC) for risk stratification and molecular subtyping in an Asian prostate cancer (PCa) cohort.

249 Background: A 22-gene GC has been proposed to refine risk stratification of localized PCa by conventional NCCN criteria, and this may potentially influence treatment recommendations. Nonetheless, majority of studies looking at the utility of GC were conducted in White and non-White men from Western cohorts. We therefore investigated the association of GC with NCCN risk groups (RG) in an Asian PCa cohort. Additionally, we examined for inter-racial differences in molecular subtyping between Asian and White/non-White PCa. Methods: GC (Decipher Biosciences Inc., CA) was performed on diagnostic biopsies of men who were treated with radiotherapy +/- hormonal therapy at a single institution (N = 75). ISUP Gleason’s grade (GG) and tumor cellularity were reviewed by an expert GU pathologist. RNA was extracted from 2 x 2.0-mm tumor cores using Qiagen AllPrep DNA/RNA FFPE Kit (Qiagen, Germany) and gene expression was performed on Affymetrix Human Exon 1.0 ST Array (ThermoFischer, CA). PAM50 molecular subtyping was derived using the DecipherGRID database. Results: We profiled 80 tumors from 75 patients, comprising of 18 (24.0%), 9 (12.0%), 21 (28.0%), and 19 (25.3%) NCCN low-/favorable intermediate-, unfavorable intermediate-, high- and very high-RG, respectively; of note, 8 (10.7%) patients had regional/metastatic disease at diagnosis. Using the GC, 27 (33.8%), 14 (17.5%) and 39 (48.8%) were classified as low- (<0.45), intermediate- (0.45-0.6) and high-RG, respectively (>0.6). When stratified using a three-tier clinico-genomic (CG) classification system (Spratt et al. 2017), 6 of 21 (28.6%) NCCN-defined high-risk and 4 of 19 (21.1%) very high-risk patients were downgraded to CG-defined intermediate-/low-risk, while 2 of 27 (7.4%) NCCN low-/intermediate-risk patients were in fact upgraded to CG high-risk. Next, we interrogated the PAM50 basal-luminal signature in our cohort. Interestingly, when matched to White (N = 5762) and non-White (N = 155) for NCCN RG, ISUP GG and age, we observed a high proportion of basal subtype (62.7%) in Asians, which contrasted the prevalence observed in White (16.7%) and non-White (15.9%) North American patients (Chi-sq P <0.001). Conclusions: Here, we demonstrated the utility of the 22-gene GC for refining the NCCN risk stratification in a largest Asian PCa dataset to-date. An unexpectedly high proportion of PAM50 basal-subtype was observed, suggesting race-specific differences of the tumor transcriptome.

Long noncoding RNA MIR31HG and its splice variants regulate proliferation and migration: prognostic implications for muscle invasive bladder cancer

Background Growing evidence supports the pivotal role of long non-coding RNAs (lncRNAs) in the regulation of cancer development and progression. Their expression patterns and biological function in muscle invasive bladder cancer (MIBC) remain elusive. Methods Transcript levels of lncRNA miR-31 host gene (MIR31HG) and its splice variants were measured in our MIBC cohort (n = 102) by qRT-PCR, and validated in silico by the TCGA cohort (n = 370). Kaplan-Meier and multiple Cox regression analysis were conducted to evaluate the survival significance of MIR31HG and its splice variants. Functional experiments were performed to examine the proliferation and migration abilities of MIR31HG and its splice variants by knockdown approaches. Results In this study, a decreased expression of MIR31HG was found in bladder cancer cells and tissues, except in the basal subtype. Survival analysis showed that high expression of MIR31HG was associated with poor overall survival (OS) and disease-free survival (DFS) in patients with MIBC of basal subtype. Two splice variants of MIR31HG lacking exon 1 (MIR31HGΔE1) and exon 3 (MIR31HGΔE3) were identified to have specific expression patterns in different molecular subtypes of our MIBC cohort. MIR31HGΔE3 was highly expressed in basal subtype tumors. A high expression of MIR31HGΔE1 and MIR31HGΔE3 was associated with worse OS and DFS in our cohort. In vitro experiments revealed that knockdown of MIR31HG inhibits cell proliferation, colony formation, and migration in bladder cancer. Cell proliferation and migration assays after knockdown of splice variants of MIR31HG showed corresponding roles for the full-length transcript. Conclusions Our study demonstrates that MIR31HG and its splice variants could serve as biomarkers for the classification and prognosis prediction of patients with MIBC.