scholarly journals A Systematic Review and Meta-Analysis of Gene Expression Profiling for Primary Cutaneous Melanoma Prognosis

2020 ◽  
Vol 4 (3) ◽  
pp. 221
Author(s):  
Graham H Litchman ◽  
Giselle Prado ◽  
Rebeca W Teplitz ◽  
Darrell Rigel

To decrease morbidity and mortality from melanoma, it is imperative to identify patients who are at high risk for developing widespread disease. Gene expression profiling (GEP) technology may impact melanoma management as physicians are better equipped to measure prognosis. Many different GEP signatures have been investigated. We searched Pubmed, Cochrane CENTRAL, and Embase for studies on GEP in primary melanoma prognosis and assessed GEP signatures for prognostic and analytic validity and clinical impact. The relationship between GEP and survival was measured using hazard ratios (HR) and odds ratios (OR). We found twenty-nine articles comprising 9 gene signatures meeting inclusion criteria and conducted a meta-analysis on 6 studies on a 31-gene signature. High-risk GEP status was associated with poorer recurrence-free survival (HR=7.22; 95% CI, 4.75-10.98), distant metastasis-free survival (HR=6.62; 95% CI, 4.91-8.91), and overall survival (HR=7.06; 95% CI, 4.44-11.22); as well as sentinel lymph node biopsy positivity (OR=2.99; 95% CI, 2.15-4.15). With recent improvements in treating advanced melanoma, accurately assessing prognosis is important. This study has clinical implications for melanoma patients who may benefit from prognostic testing. These results may be useful to clinicians when ordering GEP testing and help them make better management decisions.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 162-162 ◽  
Author(s):  
Bart Barlogie ◽  
Elias J. Anaissie ◽  
John D. Shaughnessy ◽  
Frits van Rhee ◽  
Mauricio Pineda-Roman ◽  
...  

Abstract We have previously reported on the remarkable activity of the TT3 program that incorporated both bortezomib (V) and thalidomide (T) into the up-front management of 303 patients. TT3 consisted of 2 cycles each of induction prior to and of dose-reduced consolidation therapy with VTD-PACE (cisplatin, doxorubicin, cyclophosphamide, etoposide) after melphalan 200mg/m2 (M200)-based tandem transplants, followed by maintenance therapy for 3 years with VTD and, in later stages, VRD (substituting T for lenalidomide, R). Characteristics included a median age of 59yr (range, 33–75yr), B2M >=4mg/L in 37%, albumin <3.5g/dL in 26%, ISS stages II and III in 33% and 21%, cytogenetic abnormalities (CA) in 33% and gene expression profiling (GEP)-defined high-risk MM in 15% of the 275 patients with such data. With a median follow-up of 39 months, 4-yr overall survival (OS) and event-free survival (EFS) estimates were 78% and 71%, respectively, including 84% and 77% among the 85% with GEP-defined low-risk MM contrasting with 43% and 33% in the remainder with high-risk MM (both p<0.0001). Near-CR and CR, attained in 86% and 63%, were sustained at 4 years from response onset in 78% and 87%, which pertained to 83% and 90% with low-risk MM but to only 44% and 57% with high-risk MM (all p <0.0001). These results were corroborated in a TT3 extension trial (TT3E) that enrolled 175 additional patients, comprising higher proportions of CA (42%) and GEP-defined high-risk MM (21%). Two-year estimates of OS and EFS are 85% and 85%, with 94% and 92% in low-risk patients versus 61% and 62% in high-risk MM (p=0.0001, p=0.0003); the 2-yr estimate of remaining in CR is 93% including 100% in low-risk and 77% in high-risk MM (p=0.01). Multivariate analysis of features linked to OS in TT3 included GEP-defined high-risk, CA, B2M and LDH elevation, collectively accounting for 41% of outcome variability by R2 statistics; the corresponding R2 values for EFS and n-CR duration were 38% and 39%. Compared to the predecessor trial, TT2, that evaluated the role of T in a randomized trial design in 668 patients, TT3 data were superior for OS (p=0.08), EFS (<0.0001), n-CR duration (p<0.0001) and CR duration (p=0.0002). In the low-risk subgroup, EFS (p=0.0001), n-CR duration (p<0.0001) and CR duration (Figure 1a; p=0.0002) all were superior in TT3 versus TT2; whereas, in the high-risk MM group, outcomes remained poor also with TT3 despite superior EFS (Figure 1b; p=0.03). Based on these data, we have now started a GEP-risk-based algorithm of assigning separate therapies to good-risk (TT4) and poor-risk MM (TT5). As the TT3 results for low-risk are difficult to improve upon, TT4 randomizes patients between standard TT3 and TT3-LITE that employs only 1 cycle each of induction and consolidation (with anticipated further improvement in compliance) and 4-day-fractionated M50×4 to enable the addition of VTD and thus exploit synergistic drug interactions to occur. In order to sustain tolerable effective therapies for at least 3 years and prevent recurrence from previous drug-free or insufficiently effective phases in TT3, TT5 for high-risk MM employs less dose-intense and more dose-dense highly synergistic combination therapy, utilizing M10-VTD-PACE for induction, M80 (in 4 daily fractions of M20) plus VRD-PACE tandem transplants, separated by 2 cycles of M20 (in 4 daily fractions of M5) plus VTD-PACE, and followed by 2 years of monthly alternating R-VD and M-VD. Figure 1a: Superior CR duration with TT3 v TT2 in GEP-low-risk MM: Figure 1a:. Superior CR duration with TT3 v TT2 in GEP-low-risk MM: Figure 1b: Superior event-free survival with TT3 v TT2 in GEP-high-risk MM: Figure 1b:. Superior event-free survival with TT3 v TT2 in GEP-high-risk MM:


Blood ◽  
2010 ◽  
Vol 116 (23) ◽  
pp. 4874-4884 ◽  
Author(s):  
Richard C. Harvey ◽  
Charles G. Mullighan ◽  
Xuefei Wang ◽  
Kevin K. Dobbin ◽  
George S. Davidson ◽  
...  

Abstract To resolve the genetic heterogeneity within pediatric high-risk B-precursor acute lymphoblastic leukemia (ALL), a clinically defined poor-risk group with few known recurring cytogenetic abnormalities, we performed gene expression profiling in a cohort of 207 uniformly treated children with high-risk ALL. Expression profiles were correlated with genome-wide DNA copy number abnormalities and clinical and outcome features. Unsupervised clustering of gene expression profiling data revealed 8 unique cluster groups within these high-risk ALL patients, 2 of which were associated with known chromosomal translocations (t(1;19)(TCF3-PBX1) or MLL), and 6 of which lacked any previously known cytogenetic lesion. One unique cluster was characterized by high expression of distinct outlier genes AGAP1, CCNJ, CHST2/7, CLEC12A/B, and PTPRM; ERG DNA deletions; and 4-year relapse-free survival of 94.7% ± 5.1%, compared with 63.5% ± 3.7% for the cohort (P = .01). A second cluster, characterized by high expression of BMPR1B, CRLF2, GPR110, and MUC4; frequent deletion of EBF1, IKZF1, RAG1-2, and IL3RA-CSF2RA; JAK mutations and CRLF2 rearrangements (P < .0001); and Hispanic ethnicity (P < .001) had a very poor 4-year relapse-free survival (21.0% ± 9.5%; P < .001). These studies reveal striking clinical and genetic heterogeneity in high-risk ALL and point to novel genes that may serve as new targets for diagnosis, risk classification, and therapy.


2021 ◽  
Vol 39 (15_suppl) ◽  
pp. 10030-10030
Author(s):  
Jennifer Seelisch ◽  
Matthew Zatzman ◽  
Federico Comitani ◽  
Fabio Fuligni ◽  
Ledia Brunga ◽  
...  

10030 Background: Infant acute lymphoblastic leukemia (ALL) is the only subtype of childhood ALL whose outcome has not improved over the past two decades. The most important prognosticator is the presence of rearrangements in the Mixed Lineage Leukemia gene (MLL-r), however, many patients present with high-risk clinical features but without MLL-r. We recently identified two cases of infant ALL with high-risk clinical features resembling MLL-r, but were negative for MLL-r by conventional diagnostics. RNA sequencing revealed a partial tandem duplication in MLL (MLL-PTD). We thus aimed to determine if MLL-PTD, other MLL abnormalities, or other genetic or transcriptomic features were driving this subset of high-risk infant ALL without MLL-r. Methods: We obtained 19 banked patient samples from the Children’s Oncology Group (COG) infant ALL trial (AALL0631) from MLL wildtype patients as determined by FISH and cytogenetics. Utilizing deep RNA-sequencing, we manually inspected the MLL gene for MLL-PTD, while also performing automated fusion detection and gene expression profiling in search of defining features of these tumors. Results: 3 additional MLL-PTDs were identified, all in patients with infant T-cell ALL, whereas both index cases were in patients with infant B-cell ALL. Gene expression profiling analysis revealed that all five MLL-PTD infants clustered together. Eight infants (7 with B-cell ALL) were found to have Ph-like expression. Five of these 8 infants were also found to have an IKZF1/JAK2 expression profile; one of these five had a PAX5-JAK2 fusion detected. Two infants (including the one noted above) had novel PAX5 fusions, known drivers of B-cell leukemia. Additional detected fusions included TCF3-PBX1 and TCF4-ZNF384. Conclusions: MLL-PTDs were found in both B- and T-cell infant ALL. Though Ph-like ALL has been described in adolescents and young adults, we found a substantial frequency of Ph-like expression among MLL-WT infants. Further characterization of these infants is ongoing. If replicated in other infant cohorts, these two findings may help explain the poor prognosis of MLL-WT ALL when compared to children with standard risk ALL, and offer the possibility of targeted therapy for select infants.


Author(s):  
Aaron W. Kangas-Dick ◽  
Alissa Greenbaum ◽  
Victor Gall ◽  
Roman Groisberg ◽  
Janice Mehnert ◽  
...  

2019 ◽  
Vol 47 (W1) ◽  
pp. W234-W241 ◽  
Author(s):  
Guangyan Zhou ◽  
Othman Soufan ◽  
Jessica Ewald ◽  
Robert E W Hancock ◽  
Niladri Basu ◽  
...  

Abstract The growing application of gene expression profiling demands powerful yet user-friendly bioinformatics tools to support systems-level data understanding. NetworkAnalyst was first released in 2014 to address the key need for interpreting gene expression data within the context of protein-protein interaction (PPI) networks. It was soon updated for gene expression meta-analysis with improved workflow and performance. Over the years, NetworkAnalyst has been continuously updated based on community feedback and technology progresses. Users can now perform gene expression profiling for 17 different species. In addition to generic PPI networks, users can now create cell-type or tissue specific PPI networks, gene regulatory networks, gene co-expression networks as well as networks for toxicogenomics and pharmacogenomics studies. The resulting networks can be customized and explored in 2D, 3D as well as Virtual Reality (VR) space. For meta-analysis, users can now visually compare multiple gene lists through interactive heatmaps, enrichment networks, Venn diagrams or chord diagrams. In addition, users have the option to create their own data analysis projects, which can be saved and resumed at a later time. These new features are released together as NetworkAnalyst 3.0, freely available at https://www.networkanalyst.ca.


2016 ◽  
Vol 6 (9) ◽  
pp. e471-e471 ◽  
Author(s):  
Y Jethava ◽  
A Mitchell ◽  
M Zangari ◽  
S Waheed ◽  
C Schinke ◽  
...  

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