scholarly journals Tumor gene expression signatures of BCR/PI3K dependence in association with copanlisib monotherapy activity in heavily pretreated patients with indolent NHL and follicular lymphoma

2017 ◽  
Vol 28 ◽  
pp. v358
Author(s):  
L. Liu ◽  
K. Köchert ◽  
H. Seidel ◽  
J. Garcia-Vargas ◽  
B.H. Childs ◽  
...  
2020 ◽  
Vol 38 (15_suppl) ◽  
pp. 8052-8052
Author(s):  
Patrizia Mondello ◽  
Angelo Fama ◽  
Melissa C. Larson ◽  
Andew L. Feldman ◽  
Zhi-Zhang J Yang ◽  
...  

8052 Background: A significant proportion of patients with FL experience an early relapse and a subsequent poor outcome. While several prognostic indices have been developed, none were designed to predict early failure. Recently, we established that lack of intrafollicular CD4+ T-cell expression predicted risk of early failure, and integrating this microenvironment biomarker with the Follicular Lymphoma International Prognostic Index, termed BioFLIPI, further improved identification of FL patients at risk of early failure ( Blood 2019;134(suppl1):121). However, the microenvironment may be influenced by the genetic composition of tumor. We investigated whether the CD4 biomarker and BioFLIPI were impacted by genetic features of the tumor as assessed by a 23-gene expression prognostic score ( Lancet Oncol 2018;19:549-61). Methods: Of the 186 cases with FL grade 1-3A treated with immunochemotherapy (IC) in our prior study, 152 had digital expression quantification of 23 selected genes (23-GEP score), which used RNA from formalin-fixed, paraffin-embedded samples. Event-free survival (EFS) was defined as time from diagnosis to progression, relapse, retreatment, or death. Early failure was defined as failing to achieve EFS at 24 months. Risk of early failure was estimated using odds ratios (ORs) and 95% confidence intervals from logistic regression models. We also used Cox regression to assess associations with continuous EFS and overall survival (OS). Results: 28% of patients failed to achieve EFS24. Lack of CD4+ intrafollicular expression (38% of patients, OR = 2.33, p = 0.024) and high risk 23-GEP score (26% of patients, OR = 3.52, p = 0.001) each predicted early failure, and in a multivariable model that included FLIPI, both CD4+ (OR = 2.26, p = 0.046) and 23-GEP score (OR = 2.26, p = 0.0.057) remained predictors. Similarly, BioFLIPI modeled as a continuous score (1-4, OR per one point increase = 2.31, p < 0.001) predicted early failure, and the association remained (OR = 2.14, p < 0.001) when the high risk 23-GEP score (OR = 2.79, p = 0.013) was included in the model. When stratified on 23-GEP score, BioFLIPI was a stronger predictor of early failure in low risk (74%, OR = 2.51, p = 0.002) relative to high risk (26%, OR = 1.55, p = 0.27) patients. Similar patterns were observed for EFS and OS. Conclusions: CD4+ T-cell infiltrate and tumor gene expression appear to be independently predictive of early failure in newly diagnosed FL patients treated with IC. Future studies should integrate and validate these measures.


2003 ◽  
Vol 19 (14) ◽  
pp. 1800-1807 ◽  
Author(s):  
A. M. Bagirov ◽  
B. Ferguson ◽  
S. Ivkovic ◽  
G. Saunders ◽  
J. Yearwood

2001 ◽  
Vol 98 (26) ◽  
pp. 15149-15154 ◽  
Author(s):  
S. Ramaswamy ◽  
P. Tamayo ◽  
R. Rifkin ◽  
S. Mukherjee ◽  
C.-H. Yeang ◽  
...  

2017 ◽  
Vol 40 (2) ◽  
pp. 140-145 ◽  
Author(s):  
Joseba Rebollo ◽  
Manuel Sureda ◽  
Elena M. Martinez ◽  
Francisco J. Fernández-Morejón ◽  
José Farré ◽  
...  

2019 ◽  
Vol 31 (12) ◽  
pp. 2292-2303 ◽  
Author(s):  
Xuesong Wang ◽  
Jian Liu ◽  
Yuhu Cheng ◽  
Aiping Liu ◽  
Enhong Chen

2015 ◽  
Vol 15 (6) ◽  
pp. 789-797 ◽  
Author(s):  
Yukinaga Miyata ◽  
Kenichi Kumagai ◽  
Tomoko Nagaoka ◽  
Kazutaka Kitaura ◽  
Goro Kaneda ◽  
...  

HemaSphere ◽  
2019 ◽  
Vol 3 (S1) ◽  
pp. 1
Author(s):  
C. Bolen ◽  
W. Hiddemann ◽  
R. Marcus ◽  
M. Herold ◽  
S. Huet ◽  
...  

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Julien Racle ◽  
Kaat de Jonge ◽  
Petra Baumgaertner ◽  
Daniel E Speiser ◽  
David Gfeller

Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type-specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens. Altogether, our work not only improves accuracy but also broadens the scope of absolute cell fraction predictions from tumor gene expression data, and provides a unique novel experimental benchmark for immunogenomics analyses in cancer research (http://epic.gfellerlab.org).


2019 ◽  
Vol 20 (9) ◽  
pp. 2131 ◽  
Author(s):  
Michelle A. Glasgow ◽  
Peter Argenta ◽  
Juan E. Abrahante ◽  
Mihir Shetty ◽  
Shobhana Talukdar ◽  
...  

The majority of patients with high-grade serous ovarian cancer (HGSOC) initially respond to chemotherapy; however, most will develop chemotherapy resistance. Gene signatures may change with the development of chemotherapy resistance in this population, which is important as it may lead to tailored therapies. The objective of this study was to compare tumor gene expression profiles in patients before and after treatment with neoadjuvant chemotherapy (NACT). Tumor samples were collected from six patients diagnosed with HGSOC before and after administration of NACT. RNA extraction and whole transcriptome sequencing was performed. Differential gene expression, hierarchical clustering, gene set enrichment analysis, and pathway analysis were examined in all of the samples. Tumor samples clustered based on exposure to chemotherapy as opposed to patient source. Pre-NACT samples were enriched for multiple pathways involving cell cycle growth. Post-NACT samples were enriched for drug transport and peroxisome pathways. Molecular subtypes based on the pre-NACT sample (differentiated, mesenchymal, proliferative and immunoreactive) changed in four patients after administration of NACT. Multiple changes in tumor gene expression profiles after exposure to NACT were identified from this pilot study and warrant further attention as they may indicate early changes in the development of chemotherapy resistance.


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