scholarly journals Deciphering high risk molecular alterations in gastrointestinal malignancy utilizing an extreme outlier strategy

Oncoscience ◽  
2020 ◽  
Vol 7 (5-6) ◽  
pp. 26-29
Author(s):  
Austin R. Dosch ◽  
Siddharth Mehra ◽  
Nipun B. Merchant ◽  
Jashodeep Datta
2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi152-vi153
Author(s):  
Ryan Rui Yang ◽  
Kay Ka-Wai Li ◽  
Ho-Keung Ng

Abstract In the 2016 WHO classification of tumors of the CNS, isocitrate dehydrogenase (IDH) mutation is a main classifier for lower-grade astrocytomas and IDH mutated astrocytomas is now regarded as a single group with good prognosis. However, the molecular and clinical heterogeneity among IDH-mutant lower-grade astrocytomas have only rarely been investigated. In this study, we recruited 161 IDH-mutant lower-grade astrocytomas, and examined PDGFRA amplification, CDKN2A deletion, and CDK4 amplification by FISH analysis, TERT promoter mutation by Sanger sequencing, and ATRX loss and p53 expression by immunohistochemistry. We identified PDGFRA amplification, CDKN2A deletion, and CDK4 amplification in 18.6%, 14.9%, and 18.0% of our cohort respectively, and these alterations occurred in a mutually exclusive fashion. PDGFRA amplification was associated with shorter PFS (p< 0.0001) and OS (p< 0.0001). In tumors without PDGFRA amplification, CDKN2A deletion was associated with a shorter PFS (p=0.0332). Tumors were then divided into three risk groups based on the presence of molecular alterations: high-risk (PDGFRA amplification), intermediate-risk (CDKN2A deletion or CDK4 amplification) and low-risk (neither CDKN2A deletion, CDK4 amplification nor PDGFRA amplification). These three risk groups were significantly different in overall survival with mean survivals of 40.2, 62.9, and 71.8 months. The high-risk group also demonstrated a shorter PFS compared to intermediate- (p=0.036) and low-risk (p< 0.0001) groups. Our data illustrate that IDH-mutant lower-grade astrocytomas is not a homogeneous group and should be molecularly stratified for risk.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 1336-1336
Author(s):  
Jeremy R Graff ◽  
Ann M McNulty ◽  
Chad Dumstorf ◽  
Bruce Konicek ◽  
Chad Hall ◽  
...  

Abstract Abstract 1336 Enzastaurin (Enza) is an ATP-competitive inhibitor of PKCβ and related AGC family kinases and blocks signaling through the PI3K/AKT/TOR pathway. Accordingly, in preclinical tumor models, clinically achievable Enza doses suppress phosphorylation of AKT, GSK3β, ribosomal protein S6, mTOR, p70S6 Kinase and 4EBP1. Enza has shown significant activity in Diffuse Large B Cell Lymphoma (DLBCL) patients under clinical study. 4/55 DLBCL patients treated with Enza were progression- free after prolonged, continuous oral enza therapy, with 3/4 confirmed as complete responders (Robertson et al., JCO, 2007). Furthermore, preliminary analyses of intermediate or high-risk DLBCL patients treated with R-CHOP vs. Enza + R-CHOP suggest that Enza improves both progression-free survival and complete response rates (Hainsworth et al., JCO, 29: 2011, suppl; abstract 8016). Enza is currently being investigated in a phase 3 registration trial for DLBCL patients at high risk of relapse following R-CHOP therapy. Gene expression profiling studies have revealed molecular alterations involved in DLBCL. For example, overexpression of PKCβ is particularly evident in recurrent DLBCL and has been associated with reduced patient survival. Similarly, BCL-6, a transcriptional repressor likely involved in the corruption of appropriate B Cell differentiation, is overexpressed in ∼ 70% of DLBCL and the target of translocation in nearly 40% of DLBCL. From these studies, distinct molecular subtypes of DLBCL have emerged. The Activated B Cell (ABC) subtype, which carries the poorest prognosis, is defined by constitutive activation of NFκB whereas the Germinal Center (GC) subtype, which carries a better prognosis, is not. 10% of ABC DLBCLs harbor CARD11 mutations leading to constitutive NFκB activation, while another 20% have mutations in CD79A/B, enabling chronic B Cell receptor signaling. In both ABC and GC subtypes, chronic activation of the B Cell receptor complex signals through PKCβ and the PI3K/AKT pathway. Given its activity in DLBCL patients and its molecular mechanism of action, we chose to investigate the molecular basis for the direct anti-cancer activity of Enza, specifically in DLBCL, and to discern whether sensitivity to Enza is associated with distinct DLBCL subtypes. In multiple DLBCL lines, we show that Enza treatment at clinically achievable concentrations significantly reduces BCL-6 expression. We also show that Enza robustly induces apoptosis in both GC and ABC models, blocking signaling throughout the PI3K/AKT pathway. Moreover, we show in the same DLBCL models that the primary metabolite of enza (LY326020.HCl), which comprises ∼50% of circulating drug levels in patients, more potently inhibits these same signaling pathways and more robustly induces apoptosis. Importantly, we have also identified cell lines that are resistant to both enza and its metabolite. Profiling differences between these resistant and sensitive DLBCL lines, we now show that the pro-apoptotic activity of Enza and LY326020 requires control of the eIF4F translation initiation complex- the complex responsible for enabling translation of critical, malignancy-related mRNAs (e.g. VEGF, BCL-2, c-myc). In insensitive DLBCL cells, 4EBP1 expression levels are low to non-existent, even prior to treatment. In sensitive DLBCL cells, Enza and LY326020 reduce 4EBP1ser65 phosphorylation in a dose and time-dependent manner, increasing 4EBP1: eIF4E binding thereby precluding eIF4E:eIF4G binding and preventing eIF4F complex assembly. Furthermore, selection of DLBCL cells for resistance yields cells with reduced 4EBP1 expression, increased eIF4G expression, or both, highlighting the critical importance of this complex for Enza activity. Collectively, these data show that: 1) Enza and LY326020 have direct anti-cancer activity in DLBCL cells regardless of ABC or GC subtype; 2) Enza and LY326020 directly impact numerous molecular alterations driving DLBCL (BCL-6 expression, PKCβ and PI3K-AKT pathway signaling); 3) the ability to control eIF4F complex assembly is critical for enza and LY326020 –induced apoptosis; and 4) LY326020 is more potent than Enza at blocking signaling and inducing apoptosis. Moreover, these data suggest that baseline expression levels of 4EBP1 and/or levels of phosphorylated eIF4E (an indicator of active eIF4F complex) may be particularly informative in delineating patients most sensitive to treatment. Disclosures: Graff: Eli Lilly and Company: Employment. McNulty:Eli Lilly and Company: Employment. Dumstorf:Eli Lilly and Company: Employment. Konicek:Eli Lilly and Company: Employment. Hall:Eli Lilly and Company: Employment. Parsons:Eli Lilly and Company: Employment.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 2601-2601
Author(s):  
Guardo Daniela ◽  
Fabio Guolo ◽  
Paola Minetto ◽  
Marino Clavio ◽  
Livia Giannoni ◽  
...  

Abstract BACKGROUND AND AIMS Non high risk acute promyelocytic leukemia (APL) patients, as defined by WBC count at diagnosis, have nowadays a very good prognosis when treated with ATRA plus chemotherapy based protocols, with high rate of complete molecular remission after consolidation therapy. However, a small proportion of patients (roughly 10-15%) will eventually relapse, despite the achievement of molecular CR. In the past years, some groups showed that relapse risk could be predicted by testing for some gene alterations, such as FLT3-ITD, or by break point cluster region (BCR) analysis. However, those results were not confirmed in prospective trials. We retrospectively applied a simple 3 gene based molecular panel to low-intermediate risk acute promyelocytic patients, alongside with BCR analysis, in order to develop a risk score. MATERIALS AND METHODS Fifty-nine low/intermediate risk APL patients, treated with the Italian age-adapted AIDA protocol from January 1st 2004 to December 31st 2014 in our center were retrospectively included in this study. Median age was 47 years (range 19-88), 16 patients were older than 60 years (27%). BCR analysis was available in all patients, 41 patients showed BCR1/2, whereas 18 patients had BCR3 (30%). Molecular profile included determination of FLT3-ITD mutation, WT1 and BAALC gene expression levels and was available in 38/59 patients (64%); bone marrow sample of diagnosis is available for all other 21 patients for further analysis. Cut-off values for WT1 (20000/abl x 104) and BAALC (450/abl x 104) were arbitrarily chosen after pre-analysis and comparison with our published data. Five patients had FLT3-ITD mutation (13%), 18 (45%) patients had higher WT1 expression levels and BAALC was overexpressed in 9 (24%) patients. Pre-analysis showed that FLT3-ITD, low WT1 levels, high BAALC levels but not the presence of BCR3 were associated with higher relapse risk. A molecular score including those 3 genes was built: 16 patients had no risk factors (42%), 17 patients had one risk factor (45%), 5 had two risk factors (13%). RESULTS Fifty-four patients survived induction, all of them achieved CR, in 52 PML/RARα transcript was undetectable after last consolidation therapy. The two patients with molecular persistence of disease received further therapy and then achieved molecular CR. Nine patients (15%) relapsed after a median follow-up of 56 months, 45 patients are alive at the time of analysis (76%). Relapse risk was influenced only by the presence of at least one molecular risk factor (p<0.05), whereas age at diagnosis older than 60 years had only a borderline impact (p=0.105); none of the molecular alterations reached statistical significance if taken alone. Disease free survival (DFS) duration was significantly higher in patients who had none of the molecular risk factor, when compared to patients with at least one (3-years DFS of 100% and 70.8%, respectively, p<0.05, Figure 1). Younger patients had also a longer DFS, with a 3-years DFS of 90.7% and 72% for patients younger or older than 60 years, respectively (p<0.03). Overall survival (OS) analysis led to similar results: patients with no molecular risk factors had a very good outcome when compared to patients with at least one alteration (3-years OS of 100% and 71.5%, respectively, p<0.03). Survival was also influenced by age at diagnosis, as younger patients did significantly better, with 3-years OS of 90% (p<0.05). Again, none of the molecular alterations, if taken alone, had a significant impact on DFS or OS. CONCLUSIONS Even in our small cohort, molecular profile could identify a subset of low-intermediate APL patients at higher risk of relapse, who may take benefit from an intensified consolidation therapy, as it is currently applied to high risk patients defined by WBC at diagnosis. Figure 1. DFS according to molecular risk score Figure 1. DFS according to molecular risk score Disclosures No relevant conflicts of interest to declare.


2021 ◽  
Author(s):  
Abdalla Chacur ◽  
Juliana Couto-Vieira ◽  
Anna Okorokova-Facanha ◽  
Glenerson Baptista ◽  
Arnoldo Rocha Facanha

Comparative analysis of expression patterns of ATP6V1C1 encoding C1 subunit of V-H+-ATPase revealed that molecular alterations correlated with endometrial cancer of better prognosis were grouped with low ATP6V1C1 expression while those correlated with worse prognosis were clustered with high ATP6V1C1 expression levels. Expression patterns of C1 subunit in endometrial adenocarcinoma are associated with molecular malignancy signatures shared by histological subtypes of highest mortality rate and suggest that G3 adenocarcinoma exhibit molecular changes resembling endometrial serous carcinoma. ATP6V1C1 might serve as novel prognostic marker allowing identification of targetable pathways for high-risk endometrial cancer.


2021 ◽  
Author(s):  
Yanyan Li ◽  
Lin Shen ◽  
Na Li ◽  
Yajie Zhao ◽  
Qin Zhou ◽  
...  

Purpose: Integrative analysis was performed in the Chinese Glioma Genome Atlas and The Cancer Genome Atlas to describe the pyroptosis-associated molecular classification and prognostic signature in glioma. Experimental Design: Pyroptosis-related genes were used for consensus clustering and to develop a prognostic signature. The immune statuses, molecular alterations and clinical features of differentially expressed genes were analyzed among different subclasses and risk groups. A lncRNA-miRNA-mRNA network was built, and drug sensitivity analysis was used to identify small molecular drugs for the identified genes. Results: Glioma can be divided into two subclasses using 30 pyroptosis-related genes. Cluster 1 displayed high immune signatures and poor prognosis as well as high immune-related function scores. A prognostic signature based on 15 pyroptosis-related genes of the CGGA cohort can predict the overall survival of glioma and was well validated in the TCGA cohort. Cluster 1 had higher risk scores. The high-risk group had high immune cell and function scores and low DNA methylation of pyroptosis-related genes. The differences in pyroptosis-related gene mutations and somatic copy numbers were significant between the high-risk and low-risk groups. The ceRNA regulatory network uncovered the regulatory patterns of different risk groups in glioma. Nine pairs of target genes and drugs were identified. Conclusions: Pyroptosis-related genes can reflect the molecular biological and clinical features of glioma subclasses. The established prognostic signature can predict prognosis and distinguish molecular alterations in glioma patients. Our comprehensive analyses provide valuable guidelines for improving glioma patient management and individualized therapy.


2021 ◽  
Vol 11 ◽  
Author(s):  
Adrián Mosquera Orgueira ◽  
Andrés Peleteiro Raíndo ◽  
Miguel Cid López ◽  
José Ángel Díaz Arias ◽  
Marta Sonia González Pérez ◽  
...  

Acute Myeloid Leukemia (AML) is a heterogeneous neoplasm characterized by cytogenetic and molecular alterations that drive patient prognosis. Currently established risk stratification guidelines show a moderate predictive accuracy, and newer tools that integrate multiple molecular variables have proven to provide better results. In this report, we aimed to create a new machine learning model of AML survival using gene expression data. We used gene expression data from two publicly available cohorts in order to create and validate a random forest predictor of survival, which we named ST-123. The most important variables in the model were age and the expression of KDM5B and LAPTM4B, two genes previously associated with the biology and prognostication of myeloid neoplasms. This classifier achieved high concordance indexes in the training and validation sets (0.7228 and 0.6988, respectively), and predictions were particularly accurate in patients at the highest risk of death. Additionally, ST-123 provided significant prognostic improvements in patients with high-risk mutations. Our results indicate that survival of patients with AML can be predicted to a great extent by applying machine learning tools to transcriptomic data, and that such predictions are particularly precise among patients with high-risk mutations.


2019 ◽  
Vol 3 (11) ◽  
pp. 1778-1787 ◽  
Author(s):  
Carlos Murga-Zamalloa ◽  
Kedar V. Inamdar ◽  
Ryan A. Wilcox

Abstract High-risk lymphomas (HRLs) are associated with dismal outcomes and remain a therapeutic challenge. Recurrent genetic and molecular alterations, including c-myc expression and aurora A kinase (AAK) and polo-like kinase-1 (PLK1) activation, promote cell proliferation and contribute to the highly aggressive natural history associated with these lymphoproliferative disorders. In addition to its canonical targets regulating mitosis, the AAK/PLK1 axis directly regulates noncanonical targets, including c-myc. Recent studies demonstrate that HRLs, including T-cell lymphomas and many highly aggressive B-cell lymphomas, are dependent upon the AAK/PLK1 axis. Therefore, the AAK/PLK1 axis has emerged as an attractive therapeutic target in these lymphomas. In addition to reviewing these recent findings, we summarize the rationale for targeting AAK/PLK1 in high-risk and c-myc–driven lymphoproliferative disorders.


Author(s):  
Adam J. Lamble ◽  
Lisa Eidenschink Brodersen ◽  
Todd A. Alonzo ◽  
Jim Wang ◽  
Laura Pardo ◽  
...  

PURPOSE Increased CD123 surface expression has been associated with high-risk disease characteristics in adult acute myeloid leukemia (AML), but has not been well-characterized in childhood AML. In this study, we defined CD123 expression and associated clinical characteristics in a uniformly treated cohort of pediatric patients with newly diagnosed AML enrolled on the Children's Oncology Group AAML1031 phase III trial ( NCT01371981 ). MATERIALS AND METHODS AML blasts within diagnostic bone marrow specimens (n = 1,040) were prospectively analyzed for CD123 protein expression by multidimensional flow cytometry immunophenotyping at a central clinical laboratory. Patients were stratified as low-risk or high-risk on the basis of (1) leukemia-associated cytogenetic and molecular alterations and (2) end-of-induction measurable residual disease levels. RESULTS The study population was divided into CD123 expression–based quartiles (n = 260 each) for analysis. Those with highest CD123 expression (quartile 4 [Q4]) had higher prevalence of high-risk KMT2A rearrangements and FLT3-ITD mutations ( P < .001 for both) and lower prevalence of low-risk t(8;21), inv(16), and CEBPA mutations ( P < .001 for all). Patients in lower CD123 expression quartiles (Q1-3) had similar relapse risk, event-free survival, and overall survival. Conversely, Q4 patients had a significantly higher relapse risk (53% v 39%, P < .001), lower event-free survival (49% v 69%, P < .001), and lower overall survival (32% v 50%, P < .001) in comparison with Q1-3 patients. CD123 maintained independent significance for outcomes when all known contemporary high-risk cytogenetic and molecular markers were incorporated into multivariable Cox regression analysis. CONCLUSION CD123 is strongly associated with disease-relevant cytogenetic and molecular alterations in childhood AML. CD123 is a critical biomarker and promising immunotherapeutic target for children with relapsed or refractory AML, given its prevalent expression and enrichment in patients with high-risk genetic alterations and inferior clinical outcomes with conventional therapy.


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