Validation Set for Prediction of Outcome in Adult Male Germ Cell Tumors
ABSTRACT: This series represents expression profiles of 34 non-seminoma germ cell tumors (NSGCTs) from patients who received cisplatin based chemotherarpy for treatment of their disease for whom full clinical follow-up information was available. These specimens were used as a validation set to test outcome prediction models using a subset of previously profiled GCT specimens (see GEO accession #GSE3218). Keywords: Disease state analysis (good vs. poor patient outcome) Overall design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 2003. The tumor samples consist of 34 NSGCT specimens. RNA was isolated, labeled, and hybridized to Affymetrix U133A and U133B microarrays using standard protocols. Data were processed by the RMA method.
INSTRUMENT(S): [HG-U133A] Affymetrix Human Genome U133A Array
Project description:This series represents expression profiles of 34 non-seminoma germ cell tumors (NSGCTs) from patients who received cisplatin based chemotherarpy for treatment of their disease for whom full clinical follow-up information was available. These specimens were used as a validation set to test outcome prediction models using a subset of previously profiled GCT specimens (see GEO accession #GSE3218). Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 2003. The tumor samples consist of 34 NSGCT specimens. RNA was isolated, labeled, and hybridized to Affymetrix U133A and U133B microarrays using standard protocols. Data were processed by the RMA method.
Project description:Expression profiling of a panel of 101 adult male germ cell tumors and 5 normal testis specimens was performed on Affymetrix U133A and U133B microarrays. This data has been used to:; 1) generate a gene classifier that predicts histology (see PMID 15870693). 2) identify candidate target genes on 12p, a region that is gained in almost 100% of germ cell tumors (see PMID 16424014); 3) identify pluripotency associated genes through comparison of pluripotent embryonal carcinoma vs. undifferentiated seminoma. ONGOING:; 4) Identification of genes associated with patient outcome and cisplatin resistance. Experiment Overall Design: Tumor tissues were collected under IRB-approved protocols at the Memorial Sloan-Kettering Cancer Center, New York, between 1987 and 1999. The tumor samples consist of 17 seminomas, 15 pure EC, 15 pure T, 10 pure YS, 2 pure CC, and 42 NSGCT with mixed histologies. There were six patients who had each had two tumors per patient that were included in this study (designated with the same number but different letter- e.g. 155A and 155C are from same patient but represent two different tumors, one being the primary testicular lesion, the other being a liver metastasis). Five normal testis specimens (and one pooled sample consisting of equal amounts of the 5 normal testis specimens) from individual of similar ages were used as controls.
Project description:The study consist of patients who presented at Memorial Sloan-Kettering Cancer Center with a colonic neoplasm between 1992 and 2004. Biological specimens used in this study include primary colon adenocarcinomas, adenomas, metastasis and corresponding normal mucosae. 390 expression arrays
Project description:Due to their rarity, little is known about prognostic factors in female germ cell tumors (GCTs) or outcomes following systemic therapy. Management is largely based on studies of male GCT and epithelial ovarian cancer.Chart review was performed for all females with GCT seen at Memorial Sloan Kettering Cancer Center (MSKCC) from 1990 to 2012. Patients receiving chemotherapy were stratified using a modification of the male IGCCCG risk system, and the classifier was correlated with outcome.Of 93 patients, 92 (99%) underwent primary surgery and 85 (92%) received chemotherapy. Modified IGCCCG classification was significantly associated with progression-free survival (PFS) and overall survival (OS), both when applied preoperatively and pre-chemotherapy (p<0.001 for all four analyses). Progression after initial chemotherapy (n=29) was detected by imaging in 14 (48%) patients, by serum tumor markers in 6 (21%) patients, and by multiple methods in the rest. Seven (29%) of 24 patients treated with salvage chemotherapy achieved long-term PFS, including 4/6 who received high-dose chemotherapy (HDCT) as initial salvage versus 3/16 treated with other initial salvage regimens. The estimated 3-year OS rate was 84% (95% CI, 76-92%), with a trend favoring dysgerminoma over non-dysgerminoma histologies (p=0.12).Modified IGCCCG classification was prognostic for female GCT patients in this cohort and identified a poor-risk group who may benefit from more intensive first-line chemotherapy. Both imaging and tumor marker evaluation were important in identifying relapses after first-line chemotherapy. The majority of long-term remissions with salvage therapy were achieved with initial salvage HDCT.
Project description:Subpopulations of MDA-MB-231 that exhibit different metastatic tropisms when injected into immuno-deficient mice. Also, a cohort of primary breast cancers surgically resected at the Memorial Sloan-Kettering Cancer Center (MSKCC).
Project description:To assess whether regional lymph node dissection could improve the prognosis of patients with metastatic renal cell carcinoma.We reviewed data on 258 patients who underwent cytoreductive nephrectomy at Memorial Sloan Kettering Cancer Center, New York, USA, some of whom received a concurrent lymph node dissection. The primary outcome measure was overall survival. A Cox proportional hazards regression model included, age, pathological stage, lymphadenopathy, tumor size, modified Memorial Sloan Kettering Cancer Center criteria, site of metastatic disease and lymph node dissection. We created a logistic regression model to evaluate risk factors for node-positive disease. Survival analyses were carried out for lymph node template (hilar vs other) and number of nodes removed (0-3, 4-7 or ?8).Of 258 patients, 177 (69%) underwent lymph node dissection, and positive nodes were found in 59 (33%). The 5-year overall survival was 21% for patients who underwent lymph node dissection and 31% for patients who did not. No significant difference in survival was found among patients receiving or not receiving lymph node dissection. The 5-year overall survival was 27% and 9% for negative and positive nodal status, respectively (P?<?0.0005). For patients who underwent lymph node dissection, the presence of lymphadenopathy was a significant predictor of node-positive disease (odds ratio 25.0, 95% confidence interval 9.04-69.4, P?<?0.0001).Lymph node dissection carried out during cytoreductive nephrectomy is not associated with a survival benefit. Lymph node-positive disease represents a poor prognostic variable; therefore, lymph node dissection should be considered as a staging procedure for clinical trials.
Project description:BACKGROUND:Patient-reported outcome measures (PROMs) have become widely adopted in the care of patients with prostate cancer, but there is no validated crosswalk between two commonly used instruments, the Expanded Prostate Cancer Index Composite Short Form (EPIC-26) and the Memorial Sloan Kettering (MSK) instrument, which consists of the International Index of Erectile Function-6 (IIEF-6) questionnaire and the MSK radical prostatectomy urinary outcome scale. OBJECTIVE:To develop and validate bidirectional crosswalks between the sexual and urinary domains (single domain in MSK, separate incontinence and irritative/obstructive domains in EPIC-26) of the MSK and EPIC-26 instruments. DESIGN, SETTING, AND PARTICIPANTS:Radical prostatectomy (RP) patients completing instruments at MSK and Michigan Urological Surgery Improvement Collaborative (MUSIC) between January and May of 2017 were invited to enroll. Stratified random sampling (by institution, MSK urinary function score, and MSK erectile function score) was used to divide patient data into training and test sets. Models were developed to predict the domain score for each instrument using the other's item responses and domain scores. Performance was evaluated using capped root-mean-squared error and accuracy at established thresholds. RESULTS AND LIMITATIONS:We received 517 instruments at MSK and 1033 within MUSIC, which were assigned to training (825), post-RP test (412), and pre-RP test (313) sets. We found the crosswalks to have low error and high accuracy. Although the crosswalks are more accurate if responses to each item are known, it is possible to convert between instruments on the basis of a total domain score. CONCLUSIONS:The crosswalks are a valid way to convert between sexual and urinary domains of the MSK and EPIC-26 instruments. PATIENT SUMMARY:We developed and validated a set of formulas that allow conversion of sexual and urinary function scores between the Memorial Sloan Kettering and Expanded Prostate Cancer Index Composite Short Form patient-reported outcome questionnaires. These crosswalks allow seamless transition between the two questionnaires.
Project description:BACKGROUNDAdoptive transfer of donor-derived EBV-specific cytotoxic T-lymphocytes (EBV-CTLs) can eradicate EBV-associated lymphomas (EBV-PTLD) after transplantation of hematopoietic cell (HCT) or solid organ (SOT) but is unavailable for most patients.METHODSWe developed a third-party, allogeneic, off-the-shelf bank of 330 GMP-grade EBV-CTL lines from specifically consented healthy HCT donors. We treated 46 recipients of HCT (n = 33) or SOT (n = 13) with established EBV-PTLD, who had failed rituximab therapy, with third-party EBV-CTLs. Treatment cycles consisted of 3 weekly infusions of EBV-CTLs and 3 weeks of observation.RESULTSEBV-CTLs did not induce significant toxicities. One patient developed grade I skin graft-versus-host disease. Complete remission (CR) or sustained partial remission (PR) was achieved in 68% of HCT recipients and 54% of SOT recipients. For patients who achieved CR/PR or stable disease after cycle 1, one year overall survival was 88.9% and 81.8%, respectively. In addition, 3 of 5 recipients with POD after a first cycle who received EBV-CTLs from a different donor achieved CR or durable PR (60%) and survived longer than 1 year. Maximal responses were achieved after a median of 2 cycles.CONCLUSIONThird-party EBV-CTLs of defined HLA restriction provide safe, immediately accessible treatment for EBV-PTLD. Secondary treatment with EBV-CTLs restricted by a different HLA allele (switch therapy) can also induce remissions if initial EBV-CTLs are ineffective. These results suggest a promising potential therapy for patients with rituximab-refractory EBV-associated lymphoma after transplantation.TRIAL REGISTRATIONPhase II protocols (NCT01498484 and NCT00002663) were approved by the Institutional Review Board at Memorial Sloan Kettering Cancer Center, the FDA, and the National Marrow Donor Program.FUNDINGThis work was supported by NIH grants CA23766 and R21CA162002, the Aubrey Fund, the Claire Tow Foundation, the Major Family Foundation, the Max Cure Foundation, the Richard "Rick" J. Eisemann Pediatric Research Fund, the Banbury Foundation, the Edith Robertson Foundation, and the Larry Smead Foundation. Atara Biotherapeutics licensed the bank of third-party EBV-CTLs from Memorial Sloan Kettering Cancer Center in June 2015.
Project description:Genomic amplification at 9p24.1, including the loci for JAK2, PD-L1, and PD-L2, has recently been described as a mechanism of resistance in postchemotherapy, triple-negative breast cancer. This genomic signature holds significant promise as a prognostic biomarker and has implications for targeted therapy with JAK2 inhibitors, as well as with immunotherapy. To guide future screening strategies, the frequency of these alterations was determined. A total of 5399 cases were included in the study. This encompassed 2890 institutional cases tested by the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets assay and 2509 cases from The Cancer Genome Atlas (TCGA). The combined incidence of 9p24.1 amplifications in both the Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets and TCGA cohorts was 1.0% (56/5399 cases) and showed a >10-fold higher incidence in triple-negative breast cancer (triple-negative: 5.1%; non-triple-negative: 0.5%). Tumor mutation burden and stromal tumor infiltrating lymphocytes, parameters used to assess response to immunotherapy, were not significantly higher for these cases. The significance of genomic losses at 9p24.1 is unclear, and further studies are needed. Herein, we studied the spectrum of copy number alterations in breast cancer cases within our institutional clinical sequencing cohort and those profiled by TCGA to determine the frequency of genomic alterations that may predict response or resistance to JAK2 inhibitors and/or immunotherapy.
Project description:This retrospective study compared the outcomes of sequential therapy using sunitinib followed by axitinib or the mammalian target of rapamycin (mTOR) inhibitors (everolimus or temsirolimus). Among 234 patients treated with molecular-targeted drugs for metastatic renal cell carcinoma, we selected 137 patients treated with sunitinib as the first-line therapy. We then compared patients treated with axitinib (n = 52) or mTOR inhibitors (n = 31), as the second-line treatment, and investigated the progression-free survival (PFS) and overall survival (OS). The PFS of axitinib-treated patients (median 8.7 months) was superior to that of mTOR inhibitors-treated patients (median 3.4 months; P = 0.001). Additionally, the OS from baseline of axitinib-treated patients (median 69 months) was superior to that of mTOR inhibitors-treated patients (median 33.4 months; P = 0.034). A multivariate analysis was performed with the following factors: the drugs used for the second-line treatment, the Memorial Sloan Kettering Cancer Center risk classification during the initial treatment, whether the discontinuation of the first-line treatment was due to adverse events, and whether the duration of response of the first-line treatment was less than 6 or 12 months. Importantly, the drugs used for the second-line treatment and Memorial Sloan Kettering Cancer Center risk classification were independent factors. Our findings suggest that axitinib works better than mTOR inhibitors after the first-line treatment with sunitinib.