scholarly journals A Novel Epigenetic Machine Learning Model to Define Risk of Progression for Hepatocellular Carcinoma Patients

2021 ◽  
Vol 22 (3) ◽  
pp. 1075
Author(s):  
Luca Bedon ◽  
Michele Dal Bo ◽  
Monica Mossenta ◽  
Davide Busato ◽  
Giuseppe Toffoli ◽  
...  

Although extensive advancements have been made in treatment against hepatocellular carcinoma (HCC), the prognosis of HCC patients remains unsatisfied. It is now clearly established that extensive epigenetic changes act as a driver in human tumors. This study exploits HCC epigenetic deregulation to define a novel prognostic model for monitoring the progression of HCC. We analyzed the genome-wide DNA methylation profile of 374 primary tumor specimens using the Illumina 450 K array data from The Cancer Genome Atlas. We initially used a novel combination of Machine Learning algorithms (Recursive Features Selection, Boruta) to capture early tumor progression features. The subsets of probes obtained were used to train and validate Random Forest models to predict a Progression Free Survival greater or less than 6 months. The model based on 34 epigenetic probes showed the best performance, scoring 0.80 accuracy and 0.51 Matthews Correlation Coefficient on testset. Then, we generated and validated a progression signature based on 4 methylation probes capable of stratifying HCC patients at high and low risk of progression. Survival analysis showed that high risk patients are characterized by a poorer progression free survival compared to low risk patients. Moreover, decision curve analysis confirmed the strength of this predictive tool over conventional clinical parameters. Functional enrichment analysis highlighted that high risk patients differentiated themselves by the upregulation of proliferative pathways. Ultimately, we propose the oncogenic MCM2 gene as a methylation-driven gene of which the representative epigenetic markers could serve both as predictive and prognostic markers. Briefly, our work provides several potential HCC progression epigenetic biomarkers as well as a new signature that may enhance patients surveillance and advances in personalized treatment.

Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 3544-3544
Author(s):  
Tingyu Wang ◽  
Ru Li ◽  
Rui Lv ◽  
Ying Yu ◽  
Jiawen Chen ◽  
...  

Abstract Background Follicular lymphoma (FL) is an incurable indolent disease with a heterogeneous course. The Follicular Lymphoma International Prognostic Index (FLIPI) is the most commonly used prognostic system to predict survival. Rituximab-based immunochemotherapy is now the standard choice for the first-line therapy of FL, followed by rituximab maintenance (RM) in patients with response, which prolongs the progression-free survival (PFS). However, the role of RM in different FLIPI risk groups has never been studied as we know. In this study, we aimed to illustrate the effect of RM in FLIPI risk groups. Methods Newly diagnosed FL patients at our center were enrolled in this analysis. All the patients received the rituximab-based chemoimmunotherapy induction regimens. Response assessments were determined according to Lugano's 2014 criteria. Patients who didn't respond to induction were excluded. Categorical variables were compared using Fisher's exact test. Overall survival (OS) and progression-free survival (PFS) were estimated using the Kaplan-Meier method and compared with the log-rank test. Results From May 2003 to September 2020, 203 newly diagnosed FL were included. 192 patients (95.0%) achieved remission (complete response, CR/partial response, PR) after immunochemotherapy induction, of whom 96 patients continued rituximab maintenance therapies every 3 months for 1-2 years (RM group) (median 7 times,range 4 to 12). 96 patients received no maintenance or fewer than 4 times (control group) (median 0 times, range 0-3). There were no significant differences in baseline characteristics other than the Ann Arbor stage and pathological grade. The RM group patients were more likely to be at low grade (71.8% vs 54.9%, P = 0.042) and advanced stage (90.6% vs 78.7% , P = 0.027) (Table 1). After a median follow-up of 36.4 months (95% confidence interval [CI], 32.2 to 40.6), median OS and PFS were not reached. The 5-year OS rates and PFS rates were 95.1% (95%CI, 90.2%-100%) and 83.0% (95%CI, 75%-91%)(Fig 1). And RM significantly prolonged the PFS, with 5-year PFS rates 92.2% (95%CI, 85.1%-99.3%) and 70.3%(95%CI, 55%-85.6%) (P = 0.0003) (Fig 2). According to FLIPI risk stratification, patients were classified into low-risk, intermediate-risk, and high-risk groups. The 5-year PFS rates were 97.7% (95%CI, 93.2%-100%), 84.7% (95%CI, 70.4%-99%), and 67.8% (95%CI, 49%-86.6%), respectively (Fig 3). For low-risk patients, there was no significant difference in PFS for the RM group vs the control group. However, for both intermediate risk and high-risk patients, PFS was significantly longer in the RM group compared to the control group (P < 0.0001). The PFS rates at 5 years in intermediate-risk patients were 100% and 77.8% (95%CI, 40.8%-92.6%), for the RM group vs control group, high risk 76.4% (95%CI, 54.3%-98.5%), and 54.9% (95%CI, 21.6%-88.2%), respectively (Fig 4). Conclusion Standard rituximab maintenance significantly prolongs progression-free survival in FLIPI intermediate risk and high-risk patients with FL, but not in the FLIPI low risk group. Figure 1 Figure 1. Disclosures Wang: AbbVie: Consultancy; Astellas Pharma, Inc.: Research Funding.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 3778-3778 ◽  
Author(s):  
Mario Tiribelli ◽  
Massimiliano Bonifacio ◽  
Elisabetta Calistri ◽  
Gianni Binotto ◽  
Elena Maino ◽  
...  

Abstract Abstract 3778 Introduction. The EUTOS score has recently been developed by the European Leukemia-Net (ELN) to predict the achievement of an 18-month complete cytogenetic response (CCyR) and progression-free survival in imatinib-treated early chronic phase (ECP) chronic myeloid leukemia (CML) patients. The score uses the percentage of basophils and spleen size to divide patients in 2 groups of low- and high-risk. Since its publication in 2011, however, there have been conflicting reports about the efficacy of EUTOS score. Moreover, scanty data are available on the power of this scoring system to foresee optimal response to imatinib, as defined by ELN recommendations. Aims and Methods. To test the power of EUTOS score in predicting achievement of optimal response to imatinib, as defined by ELN, time to imatinib failure (TTF) and progression-free survival (PFS), we evaluated 265 ECP CML patients treated with front-line standard dose imatinib (400 mg daily) at 5 major hematology centres in the north-eastern area of Italy. Partial cytogenetic response (PCyR) and CCyR were defined as 1–35% and 0% Ph+ metaphases, respectively; major molecular response (MMR) was defined as BCR-ABL <0.1%IS. TTF was measured from the start of imatinib to the date of any of the following events: progression to accelerated or blastic phase, death for any cause at any time, imatinib dose increase (≥ 600 mg/day) for primary or secondary hematologic or cytogenetic resistance. PFS was measured from the start of imatinib to the date of progression to accelerated or blastic phase or death for any cause at any time. Survival probabilities were estimated by the Kaplan-Meier method and compared by log rank test; differences among variables were evaluated by the Fisher's exact test or by Student's t-distribution. Results. A total of 265 consecutive patients with ECP CML were included in this study. The median age was 55 years (range 19–84), with 149 males and 116 females. The median follow-up was 61 months (range 6–136). The median time from diagnosis to imatinib therapy was 0.7 months (range 0 – 7.6). The distribution according to the EUTOS score was: 248 patients (93.6%) in the low risk group and 17 patients (6.4%) in the high risk group. The “optimal response” endpoints to imatinib (i.e. PCyR at 6th months, CCyR at 12th months and MMR at 18th months) were higher in low-risk patients, but did not achieve statistical significance. Specifically, the values were as following: PCyR 86% vs 67% (p=0.055), CCyR 80% vs 63% (p=0.117) and MMR 61% vs 36% (p=0.126). Cumulative incidence of CCyR was comparable in the two groups (88%% in low-risk and 80% in high risk), but time to CCyR was shorter in low-risk patients (6 months) compared to the one in high-risk patients (9 months) (p=0.048) [figure 1]. More importantly, EUTOS score was able to predict long term response to therapy. Indeed, 59% of patients in the high-risk group experienced imatinib failure, compared to 30% in the low-risk group (p=0.027). Moreover also TTF was significant shorter in the high-risk group [figure 2]. Fifty-three patients in the low-risk group (21%) were switched to 2nd-generation TKIs (29 dasatinib, 22 nilotinib, 1 bosutinib, 1 ponatinib), compared to six (35%) in the high-risk group (4 dasatinib, 2 nilotinib). Also PFS rate was significantly worse in patients with high EUTOS score, with 11/248 events (4%) in the low-risk group and 4/17 (23%) in the high-risk cases (p=0.01) [figure 3]. Conclusions. In our study group, the EUTOS score was predictive for long-term outcome of imatinib therapy, both in terms of treatment failure and of progression-free survival. Taking into consideration the ELN definitions of optimal response, there was a trend toward better cytogenetic and molecular response in low-risk patients; the lack of statistical significance could be due to the relatively small number of high-risk cases. Disclosures: No relevant conflicts of interest to declare.


2020 ◽  
Vol 8 (1) ◽  
pp. e000205 ◽  
Author(s):  
Sai-Lan Liu ◽  
Li-Juan Bian ◽  
Ze-Xian Liu ◽  
Qiu-Yan Chen ◽  
Xue-Song Sun ◽  
...  

BackgroundThe tumor immune microenvironment has clinicopathological significance in predicting prognosis and therapeutic efficacy. We aimed to develop an immune signature to predict distant metastasis in patients with nasopharyngeal carcinoma (NPC).MethodsUsing multiplexed quantitative fluorescence, we detected 17 immune biomarkers in a primary screening cohort of 54 NPC tissues presenting with/without distant metastasis following radical therapy. The LASSO (least absolute shrinkage and selection operator) logistic regression model used statistically significant survival markers in the training cohort (n=194) to build an immune signature. The prognostic and predictive accuracy of it was validated in an external independent group of 304 patients.ResultsEight statistically significant markers were identified in the screening cohort. The immune signature consisting of four immune markers (PD-L1+ CD163+, CXCR5, CD117) in intratumor was adopted to classify patients into high and low risk in the training cohort and it showed a high level of reproducibility between different batches of samples (r=0.988 for intratumor; p<0.0001). High-risk patients had shorter distant metastasis-free survival (HR 5.608, 95% CI 2.619 to 12.006; p<0.0001) and progression-free survival (HR 2.798, 95% CI 1.498 to 5.266; p=0·001). The C-indexes which reflected the predictive capacity in training and validation cohort were 0.703 and 0.636, respectively. Low-risk patients benefited from induction chemotherapy plus concurrent chemoradiotherapy (IC+CCRT) (HR 0.355, 95% CI 0.147 to 0.857; p=0·021), while high-risk patients did not (HR 1.329, 95% CI 0.543 to 3.253; p=0·533). To predict the individual risk of distant metastasis, nomograms with the integration of both immune signature and clinicopathological risk factors were developed.ConclusionsThe immune signature provided a reliable estimate of distant metastasis risk in patients with NPC and might be applied to identify the cohort which benefit from IC+CCRT.


Blood ◽  
2011 ◽  
Vol 118 (17) ◽  
pp. 4547-4553 ◽  
Author(s):  
María-Victoria Mateos ◽  
Norma C. Gutiérrez ◽  
María-Luisa Martín-Ramos ◽  
Bruno Paiva ◽  
María-Angeles Montalbán ◽  
...  

Abstract Cytogenetic abnormalities (CAs) such as t(4;14), t(14;16) or del(17p), and nonhyperdiploidy are associated with poor prognosis in multiple myeloma. We evaluated the influence of CAs by FISH and DNA ploidy by flow cytometry on response and survival in 232 elderly, newly diagnosed multiple myeloma patients receiving an induction with weekly bortezomib followed by maintenance therapy with bortezomib-based combinations. Response was similar in the high-risk and standard-risk CA groups, both after induction (21% vs 27% complete responses [CRs]) and maintenance (39% vs 45% CR). However, high-risk patients showed shorter progression-free survival (PFS) than standard-risk patients, both from the first (24 vs 33 months; P = .04) and second randomization (17 vs 27 months; P = .01). This also translated into shorter overall survival (OS) for high-risk patients (3-year OS: 55% vs 77%; P = .001). This adverse prognosis applied to either t(4;14) or del(17p). Concerning DNA ploidy, hyperdiploid patients showed longer OS than nonhyperdiploid patients (77% vs 63% at 3 years; P = .04), and this was more evident in patients treated with bortezomib, thalidomide, and prednisone (77% vs 53% at 3 years; P = .02). The present schema does not overcome the negative prognosis of high-risk CAs and nonhyperdiploidy. This trial was registered with www.ClinicalTrials.gov as NCT00443235.


Blood ◽  
2004 ◽  
Vol 104 (11) ◽  
pp. 3308-3308
Author(s):  
Maria Luisa Moleti ◽  
Anna Maria Testi ◽  
Luigi Malandruccolo ◽  
Elisabetta Todisco ◽  
Edoardo Pescarmona ◽  
...  

Abstract Over the last 14 years, at our Institute, we have used the NCI 89-C-41 protocol designed by I. Magrath in children and adolescents with small non-cleaved cell (SNCL) and large B-cell (LBCL) lymphomas. In the 1996 paper (J Clin Oncol 1996, 14: 925–34), Magrath et al reported an event-free survival of 92% at 2 years, in adults and children with SNCL. In this protocol, patients with a single extra-abdominal mass or completely resected abdominal disease and LDH <350 IU/L are classified as low-risk; all other patients are defined as high-risk. Low-risk patients receive 3 cycles of the CODOX-M regimen, a combination of cyclophosphamide, doxorubicin, prednisone, vincristine, high-dose methotrexate and intrathecal therapy. High-risk patients receive 4 alternating CODOX-M and IVAC regimens. The IVAC protocol includes ifosfamide, etoposide, high-dose cytarabine and intrathecal methotrexate. We describe hereby the results obtained in 35 patients younger than 21 years with SNCL and LCBL, seronegative for the HIV, treated with the NCI 89-C-41 protocol between September 1989 and March 2003 at our Institute. Median age at presentation was 12.1 years, ranging form 2.6 to 21 years. Thirty patients had SNCL and 5 LBCL. According to Murphy’s staging system, 17 were classified as stage II, 9 as stage III and 9 as stage IV (all with bone marrow involvement that was >25% in 3; 1 with associated CNS disease). Two patients were defined as low risk, while 33 were high-risk. The CNS+ patient received additional IT therapy. G-CSF was given in case of neutropenia associated to severe infections. Thirty-two of the 35 patients (91%) achieved a CR. The remaining 3 patients (SNCL, stages II, III and IV) obtained a PR after the first 2 cycles, but the disease rapidly progressed and led to death in all 3. One patient with stage IV SNCL died in CR of fungal meningitis, during the fourth cycle neutropenia. Three complete responders (SNCL, stage III) relapsed after 2, 2 and 33 months from the end of therapy. Only 1 of them is alive and well in second CR after a stem cell transplant. A life-threatening tumor lysis syndrome was observed in 2 patients; metabolic alterations caused seizures in 1 of them that resolved without sequelae. The hematological toxicity was acceptable; in low-risk patients no thrombocytopenias were observed and neutropenia lasted from 0 to 3 days. For high-risk patients, the median time to PMN >0.5 x 109/L after each cycle was 7, 6, 6 and 6 days (range 0–19), respectively, and to PLTS >50 x 109/L was 6 days (range 0–36). Infections were observed only in high-risk patients with 13 bacterial sepsis, 1 disseminated fungal infection and 12 localized infections. Mucositis (WHO >2) was the main extra-hematological side-effect occurring usually after the CODOX-M regimen; transient peripheral neuropathy occurred in 4 patients after the CODOX-M cycle. No acute and late liver, pulmonary and cardiac toxicities were registered. The 7-years overall survival and event free-survival are 83 and 80%. The results of our study indicate that the NCI 89-C-41 protocol, originally designed for SNCL patients, has confirmed its feasibility and documented its long-term efficacy in a series of children and adolescents with both SNCL and LBCL managed at a single center and with a median follow-up extended to 10 years.


Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 1150-1150 ◽  
Author(s):  
Maria-Victoria Mateos ◽  
Jane Estell ◽  
Wolney Barreto ◽  
Paolo Corradini ◽  
Chang-Ki Min ◽  
...  

Abstract Introduction: Daratumumab is a first-in-class monoclonal antibody targeting the plasma cell antigen, CD38, that demonstrated significant activity in combination with bortezomib and dexamethasone (DVd) compared with bortezomib and dexamethasone alone (Vd) in a pre-specified interim analysis of CASTOR, a randomized phase 3 study of relapsed or refractory multiple myeloma (RRMM; Palumbo A. N Engl J Med 2016; in press). In this abstract, we report on subgroup analyses according to the number of prior lines of therapy received, and include outcomes based on cytogenetic status, in order to identify the patient population who derived the most benefit from the DVd combination. Methods: Eligible patients (pts) received at least 1 prior line of therapy and were randomized (1:1) to 8 cycles (q3w) of Vd with or without daratumumab (16 mg/kg IV qw in Cycles 1-3, Day 1 of Cycles 4-8, then q4w until progression). For each cycle, bortezomib 1.3 mg/m2 SC was administered on Days 1, 4, 8, and 11, and dexamethasone 20 mg PO was given on Days 1, 2, 4, 5, 8, 9, 11, 12. Progression-free survival (PFS) was the primary endpoint. Numbers of prior lines of therapy were determined by the site investigator according to the IMWG consensus guidelines. High-risk cytogenetic status based on local laboratory assessments was defined as having at least one of the following abnormalities via karyotyping or fluorescence in-situ hybridization: del17p, t(4;14), or t(14;16). Minimal residual disease (MRD) was evaluated on bone marrow aspirate samples that had been prepared with Ficoll using three different thresholds (10-4, 10-5, and 10-6) based on the ClonoSEQ assay (Adaptive Biotechnologies, Seattle, WA, USA). Results: Median follow-up was 7.4 months. In the 1 to 3 prior lines (1-3 PL) subgroup (DVd, n=229; Vd, n=219), PFS was significantly longer with DVd vs Vd (median: not reached [NR] vs 7.3 mo; HR, 0.39; 95% CI, 0.28-0.55; P<0.0001); estimated 12-month PFS rates were 62.2% vs 29.3%, respectively. Median time to progression (TTP) among 1-3 PL pts was NR vs 7.4 months, respectively (HR, 0.29; 95% CI, 0.20-0.43; P<0.0001). Overall response rate (ORR) was significantly higher with DVd vs Vd (84% vs 67%; P<0.0001) and was associated with higher rates of very good partial response (VGPR) or better (62% vs 32%; P<0.0001). Among 1-3 PL pts with standard-risk cytogenetic status, PFS was significantly prolonged in DVd vs Vd (HR, 0.38; 95% CI, 0.25-0.58; P<0.0001), and estimated 12-month PFS rates were 58.7% vs 27.0%, respectively. PFS was also significantly longer in pts with high-risk cytogenetics who received DVd vs Vd (HR, 0.46; 95% CI, 0.22-0.97; P=0.0367; Figure), with estimated 12-month PFS rates of 63.2% vs 26.7%, respectively. Lastly, the rate of MRD-negative patients was significantly higher (4 fold or greater) at all evaluated thresholds (10-4, 10-5, and 10-6) among the 1-3 PL subgroup. In the 1 prior line (1 PL) subgroup (DVd, n=122; Vd, n=113), PFS was also significantly improved for DVd vs Vd (median: NR vs 7.5 mo; HR, 0.31; 95% CI, 0.18-0.52; P<0.0001); estimated 12-month PFS rates were 77.5% vs 29.4%, respectively. Median TTP among 1 PL pts was NR vs 8.4 months, respectively (HR, 0.28; 95% CI, 0.16-0.49; P<0.0001). ORR in pts with 1 PL was significantly higher for DVd vs Vd (89% vs 74%; P=0.0029), including higher rates of VGPR or better being observed for DVd vs Vd (71% vs 42%; P<0.0001). Updated efficacy and safety data, including analyses of MRD status across different sensitivity thresholds (10-4, 10-5, and 10-6), will be presented at the meeting. Conclusions: The treatment benefit of DVd vs Vd was maintained across 1-3 PL and 1 PL pts. Responses for DVd were deep and durable and correlated with significantly improved outcomes vs Vd. Despite small group sizes, treatment benefit of DVd vs Vd was also observed in high-risk cytogenetic pts receiving 1-3 PL. These data continue to support the addition of daratumumab to a standard-of-care regimen in RRMM. Figure Progression-free Survival in High-risk Patients (Defined by Cytogenetic Abnormalities) who Received 1 to 3 Prior Lines of Therapy Figure. Progression-free Survival in High-risk Patients (Defined by Cytogenetic Abnormalities) who Received 1 to 3 Prior Lines of Therapy Disclosures Mateos: Janssen, Celgene, Amgen, Takeda, BMS: Honoraria. Estell:Janssen: Membership on an entity's Board of Directors or advisory committees. Corradini:Celgene, Janssen, Novartis, Roche, Takeda, Sanofi, Servier, Gilead: Honoraria; Takeda: Consultancy. Medvedova:Oregon Health and Science University: Employment. Qi:Janssen: Employment. Schecter:Janssen: Employment, Equity Ownership. Amin:Janssen: Employment. Qin:Janssen: Employment. Deraedt:Janssen: Employment; Johnson & Johnson: Equity Ownership. Casneuf:Johnson & Johnson: Equity Ownership; Janssen R&D, Beerse, Belgium: Employment. Chiu:Janssen: Employment. Sasser:Janssen: Employment; Johnson & Johnson: Equity Ownership. Nooka:Amgen, Novartis, Spectrum: Consultancy.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shuo Zhang ◽  
Beichen Liu ◽  
Mengli Zhou ◽  
Jintian Wang ◽  
Jinzhao Liu ◽  
...  

AbstractRecurIndex, a multigene profiling assay, can predict the risk of local recurrence and distant metastasis in female breast cancer (FBC), but its role in male breast cancer (MBC) remains unclear. In this study, the clinicopathological data of 43 consecutive MBC patients undergoing surgeries between 2009 and 2018 were retrospectively analysed. Their paraffin-embedded tissue sections were examined by RecurIndex test which comprised 2 models: recurrence index for local recurrence (RI-LR) and recurrence index for distant recurrence (RI-DR). Of 43 patients, there were 26 low-risk and 17 high-risk patients assessed by RI-LR, while 17 low-risk and 26 high-risk patients by RI-DR. For RI-LR, tumor N stage showed statistically significant (P < 0.001) between low- and high-risk patients; for RI-DR, differences were pronounced in tumor grade (P = 0.033), T stage (P = 0.043) and N stage (P = 0.003). In terms of clinical outcomes, the overall survival (OS) of low- and high-risk patients stratified by RI-LR showed no statistically significant differences (P = 0.460), while high-risk patients identified by RI-DR had a significantly worse distant recurrence-free survival (DRFS) (P = 0.035), progression-free survival (PFS) (P = 0.019) and OS (P = 0.044) than low-risk patients. Overall, RI-DR can effectively predict the DRFS, PFS and OS of MBC patients and identify those at low risk of recurrence, which may serve as a potential prognostic tool for MBC.


2021 ◽  
Vol 10 ◽  
Author(s):  
Zhongsong Man ◽  
Yongqiang Chen ◽  
Lu Gao ◽  
Guowei Xei ◽  
Quanfu Li ◽  
...  

Dysregulation of RNA binding proteins (RBPs) is closely associated with tumor events. However, the function of RBPs in hepatocellular carcinoma (HCC) has not been fully elucidated. The RNA sequences and relevant clinical data of HCC were retrieved from the The Cancer Genome Atlas (TCGA) database to identify distinct RBPs. Subsequently, univariate and multivariate cox regression analysis was performed to evaluate the overall survival (OS)-associated RBPs. The expression levels of prognostic RBP genes and survival information were analyzed using a series of bioinformatics tool. A total of 365 samples with 1,542 RBPs were included in this study. One hundred and eighty-seven differently RBPs were screened, including 175 up-regulated and 12 down-regulated. The independent OS-associated RBPs of NHP2, UPF3B, and SMG5 were used to develop a prognostic model. Survival analysis showed that low-risk patients had a significantly longer OS and disease-free survival (DFS) when compared to high-risk patients (HR: 2.577, 95% CI: 1.793–3.704, P &lt; 0.001 and HR: 1.599, 95% CI: 1.185–2.159, P = 0.001, respectively). The International Cancer Genome Consortium (ICGC) database was used to externally validate the model, and the OS of low-risk patients were found to be longer than that of high-risk patients (P &lt; 0.001). The Nomograms of OS and DFS were plotted to help in clinical decision making. These results showed that the model was effective and may help in prognostic stratification of HCC patients. The prognostic prediction model based on RBPs provides new insights for HCC diagnosis and personalized treatment.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 125-125
Author(s):  
Christoph Heuck ◽  
Pingping Qu ◽  
Frits van Rhee ◽  
Sarah Waheed ◽  
Saad Z Usmani ◽  
...  

Abstract Gene expression profiling (GEP) reliably predicts overall and progression free survival in multiple myeloma. Driven by the concept that therapy will reveal biology, we applied the GEP70 risk model to 56 patients enrolled in Total Therapy 6 (TT6), a phase 2 trial for previously treated patients. One year survival estimates were 62% vs.97%, p<0.0001, Figure 1A). To investigate whether fewer than the 70 genes could predict this difference in outcomes, the probe sets of the GEP70 risk model were ranked by p-values, based on univariate Cox regression analysis for OS. The five probe sets with the smallest P values (corresponding to genes ENO1, FABP5, TRIP13, TAGLN2, and RFC4) were combined to create a continuous score (Figure1B). Association of several of these genes with different cancers has previously been reported by others. We re-trained this 5 gene model (GEP5) on a dataset of 275 uniformly treated patients on Total Therapy 3A (TT3A) and identified a new optimal cutoff of 10.68. We validated this new cutoff with patients enrolled in Total Therapy 2 (TT2) (n=351) and Total Therapy 3B (TT3B) (n=166). For TT2 patients, the dataset from which the GEP70 model was developed, clinical outcomes of the GEP5defined low risk patients were very similar to the GEP70 defined low risk patients. Survival estimates were higher for GEP5-defined high risk than for GEP70 high risk patients (5-year estimated OS: 40%, GEP5; 28%, GEP70; 5-year estimated PFS: 26%, GEP5; 15%, GEP70) (Figure 2A and 2B). This was also seen in both TT2 treatment arms. For the second validation cohort (TT3B), GEP5 and GEP70 risk distinction were similar to the TT3A discovery cohort (Figures 2C and 2D). On multivariate analysis, the GEP5-defined high-risk designation was the most adverse variable for PFS, with an estimated hazard ratio of 3.44 (95% CI: 2.02-5.86), whereas the GEP70 model was selected first for OS. (Table 1).Table 1.Multivariate stepwise Cox regression analysis performed on the TT3B validation setOverall survivalProgression-free survivalVariablen/N (%)HR (95% CI)P-valueHR (95% CI)P-valueMultivariateGEP70 high-risk36/159 (23%)4.45 (2.47, 8.02)<.001B2M > 5.5 mg/L49/159 (31%)1.73 (1.01, 2.95)0.045GEP5 high-risk42/159 (26%)3.44 (2.02, 5.86)<.001 Applied to the publicly available dataset from the HOVON group, GEP5 identified a high risk group with a 3-year estimate OS survival of 52% compared to 75% for the low risk group (p<0.001). TT4 and TT5 are phase 2 trials for previously untreated GEP70 defined low-risk and high-risk patients, respectively. GEP5 identified in TT4 a subset (17/303) of high risk patients with significantly worse 3-year estimated OS (69% vs. 86%, p=0.03), and in TT5 GEP5 identifies a low-risk subset (22/57) of patients with significantly better 3-year estimate OS (94% vs. 59%, p=0.01). Recently a large-scale proteomics experiment involving 85 patients with MM identified ENO1, FABP5, and TAGLN2 among a set of 24 proteins that are associated with short OS. It was further shown that gene expression levels correlated closely with protein abundance. In summary, we have identified 5 genes that have the greatest influence on GEP defined risk. The GEP5 score maintains prognostic power even in patients who have been risk stratified using other risk models. The correlation of expression at both mRNA and protein levels indicate that the genes identified in GEP5 are not simply an artifact of the microarray methodology, but rather supports their biologic relevance. This simplified risk model with a reduced number of genes has the potential to open molecular risk testing to a larger audience. Figure 1. Figure 1. Overall Survival in TT6 according to A) GEP70 risk score and B) GEP5 risk score Figure 2. Figure 2. Overall survival (left panels) and progression-free survival (right panels) according to GEP5 risk score in A) TT3A training set set, B) TT2 test set and C) a second test set TT3B Figure 3. Figure 3. Overall survival (left panels) and progression-free survival (right panels) according to GEP5 in A) the publicly available HOVON dataset B) TT4, for previously untreated GEP70 defined low-risk myeloma and C) TT5, for previously untreated GEP70 defined high-risk myeloma Disclosures: van Rhee: Jansen & Jansen: Research Funding. Usmani:Celgene: Consultancy, Research Funding, Speakers Bureau; Onyx: Research Funding, Speakers Bureau. Epstein:University of Arkansas for Medical Sciences: Co-inventor of the DNA probes for FISH of IGHC/IGHV (14q32), MMSET/FGFR3 (4p16), CCND3 (6p21), CCND1 (11q13), MAF (16q23), and MAFB (20q12) loci, sub. to the US Patent & Trademark Office as Prov. App# 61/726,327: Methods of Detecting 14q32 Translocations, Co-inventor of the DNA probes for FISH of IGHC/IGHV (14q32), MMSET/FGFR3 (4p16), CCND3 (6p21), CCND1 (11q13), MAF (16q23), and MAFB (20q12) loci, sub. to the US Patent & Trademark Office as Prov. App# 61/726,327: Methods of Detecting 14q32 Translocations Patents & Royalties. Zhang:University of Arkansas for Medical Sciences: Co-inventor of the DNA probes for FISH of IGHC/IGHV (14q32), MMSET/FGFR3 (4p16), CCND3 (6p21), CCND1 (11q13), MAF (16q23), and MAFB (20q12) loci, sub. to the US Patent & Trademark Office as Prov. App# 61/726,327: Methods of Detecting 14q32 Translocations, Co-inventor of the DNA probes for FISH of IGHC/IGHV (14q32), MMSET/FGFR3 (4p16), CCND3 (6p21), CCND1 (11q13), MAF (16q23), and MAFB (20q12) loci, sub. to the US Patent & Trademark Office as Prov. App# 61/726,327: Methods of Detecting 14q32 Translocations Patents & Royalties. Barlogie:Celgene: Consultancy, Honoraria, Research Funding; Myeloma Health, LLC: Patents & Royalties.


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