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1. Optimizing Sample Size for Supervised Machine Learning with Bulk Transcriptomic Sequencing: A Learning Curve Approach

Author

Qi, Yunhui, Wang, Xinyi, and Qin, Li-Xuan

Subjects
Statistics - Methodology, Quantitative Biology - Genomics
Abstract

Accurate sample classification using transcriptomics data is crucial for advancing personalized medicine. Achieving this goal necessitates determining a suitable sample size that ensures adequate statistical power without undue resource allocation. Current sample size calculation methods rely on assumptions and algorithms that may not align with supervised machine learning techniques for sample classification. Addressing this critical methodological gap, we present a novel computational approach that establishes the power-versus-sample-size relationship by employing a data augmentation strategy followed by fitting a learning curve. We comprehensively evaluated its performance for microRNA and RNA sequencing data, considering diverse data characteristics and algorithm configurations, based on a spectrum of evaluation metrics. To foster accessibility and reproducibility, the Python and R code for implementing our approach is available on GitHub. Its deployment will significantly facilitate the adoption of machine learning in transcriptomics studies and accelerate their translation into clinically useful classifiers for personalized treatment., Comment: 34 pages, 6 figures and extended data

Published
2024

2. Long-Term Results of Organ Preservation in Patients With Rectal Adenocarcinoma Treated With Total Neoadjuvant Therapy: The Randomized Phase II OPRA Trial

Author

Verheij, Floris S, Omer, Dana M, Williams, Hannah, Lin, Sabrina T, Qin, Li-Xuan, Buckley, James T, Thompson, Hannah M, Yuval, Jonathan B, Kim, Jin K, Dunne, Richard F, Marcet, Jorge, Cataldo, Peter, Polite, Blase, Herzig, Daniel O, Liska, David, Oommen, Samuel, Friel, Charles M, Ternent, Charles, Coveler, Andrew L, Hunt, Steven, Gregory, Anita, Varma, Madhulika G, Bello, Brian L, Carmichael, Joseph C, Krauss, John, Gleisner, Ana, Guillem, José G, Temple, Larissa, Goodman, Karyn A, Segal, Neil H, Cercek, Andrea, Yaeger, Rona, Nash, Garrett M, Widmar, Maria, Wei, Iris H, Pappou, Emmanouil P, Weiser, Martin R, Paty, Philip B, Smith, J Joshua, Wu, Abraham J, Gollub, Marc J, Saltz, Leonard B, and Garcia-Aguilar, Julio

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Cancer, Rare Diseases, Radiation Oncology, Clinical Trials and Supportive Activities, Clinical Research, Orphan Drug, Patient Safety, 6.1 Pharmaceuticals, Evaluation of treatments and therapeutic interventions, Humans, Adenocarcinoma, Chemoradiotherapy, Neoadjuvant Therapy, Neoplasm Recurrence, Local, Neoplasm Staging, Organ Preservation, Rectal Neoplasms, Treatment Outcome, Oncology & Carcinogenesis, Oncology and carcinogenesis
Abstract

Clinical trials frequently include multiple end points that mature at different times. The initial report, typically based on the primary end point, may be published when key planned co-primary or secondary analyses are not yet available. Clinical Trial Updates provide an opportunity to disseminate additional results from studies, published in JCO or elsewhere, for which the primary end point has already been reported.To assess long-term risk of local tumor regrowth, we report updated organ preservation rate and oncologic outcomes of the OPRA trial (ClinicalTrials.gov identifier: NCT02008656). Patients with stage II/III rectal cancer were randomly assigned to receive induction chemotherapy followed by chemoradiation (INCT-CRT) or chemoradiation followed by consolidation chemotherapy (CRT-CNCT). Patients who achieved a complete or near-complete response after finishing treatment were offered watch-and-wait (WW). Total mesorectal excision (TME) was recommended for those who achieved an incomplete response. The primary end point was disease-free survival (DFS). The secondary end point was TME-free survival. In total, 324 patients were randomly assigned (INCT-CRT, n = 158; CRT-CNCT, n = 166). Median follow-up was 5.1 years. The 5-year DFS rates were 71% (95% CI, 64 to 79) and 69% (95% CI, 62 to 77) for INCT-CRT and CRT-CNCT, respectively (P = .68). TME-free survival was 39% (95% CI, 32 to 48) in the INCT-CRT group and 54% (95% CI, 46 to 62) in the CRT-CNCT group (P = .012). Of 81 patients with regrowth, 94% occurred within 2 years and 99% occurred within 3 years. DFS was similar for patients who underwent TME after restaging (64% [95% CI, 53 to 78]) and patients in WW who underwent TME after regrowth (64% [95% CI, 53 to 78]; P = .94). Updated analysis continues to show long-term organ preservation in half of the patients with rectal cancer treated with total neoadjuvant therapy. In patients who enter WW, most cases of tumor regrowth occur in the first 2 years.

Published
2024

3. BatMan: Mitigating Batch Effects via Stratification for Survival Outcome Prediction

Author

Ni, Ai, Liu, Mengling, and Qin, Li-Xuan

Subjects
Statistics - Methodology
Abstract

Reproducible translation of transcriptomics data has been hampered by the ubiquitous presence of batch effects. Statistical methods for managing batch effects were initially developed in the setting of sample group comparison and later borrowed for other settings such as survival outcome prediction. The most notable such method is ComBat, which adjusts for batches by including it as a covariate alongside sample groups in a linear regression. In survival prediction, however, ComBat is used without definable groups for survival outcome and is done sequentially with survival regression for a potentially confounded outcome. To address these issues, we propose a new method, called BatMan ("BATch MitigAtion via stratificatioN"). It adjusts batches as strata in survival regression and utilize variable selection methods such as LASSO to handle high dimensionality. We assess the performance of BatMan in comparison with ComBat, each used either alone or in conjunction with data normalization, in a re-sampling-based simulation study under various levels of predictive signal strength and patterns of batch-outcome association. Our simulations show that (1) BatMan outperforms ComBat in nearly all scenarios when there are batch effects in the data, and (2) their performance can be worsened by the addition of data normalization. We further evaluate them using microRNA data for ovarian cancer from the Cancer Genome Atlas, and find that BatMan outforms ComBat while the addition of data normalization worsens the prediction. Our study thus shows the advantage of BatMan and raises caution about the naive use of data normalization in the context of developing survival prediction models. The BatMan method and the simulation tool for performance assessment are implemented in R and publicly available at https://github.com/LXQin/PRECISION.survival.

Published
2022

4. A randomised phase II trial of a trivalent ganglioside vaccine targeting GM2, GD2 and GD3 combined with immunological adjuvant OPT-821 versus OPT-821 alone in metastatic sarcoma patients rendered disease-free by surgery.

Author

Rosenbaum, Evan, Chugh, Rashmi, Ryan, Christopher, Agulnik, Mark, Milhem, Mohammed, George, Suzanne, Jones, Robin, Chmielowski, Bartosz, Van Tine, Brian, Tawbi, Hussein, Elias, Anthony, Read, William, Budd, G, Qin, Li-Xuan, Rodler, Eve, Hirman, Joe, Weiden, Paul, Bennett, Cathryn, Livingston, Philip, Ragupathi, Govind, Hansen, David, DAngelo, Sandra, Tap, William, Schwartz, Gary, Maki, Robert, and Carvajal, Richard

Subjects
Adjuvant, Ganglioside, Sarcoma, Vaccine, Humans, Male, Female, G(M2) Ganglioside, Injection Site Reaction, Sarcoma, Vaccines, Adjuvants, Immunologic, Soft Tissue Neoplasms, Neoplasms, Second Primary
Abstract

BACKGROUND: Recurrence after resection of metastatic sarcoma is common. The gangliosides GM2, GD2 and GD3 are strongly expressed across sarcoma subtypes. We hypothesised that generation of anti-ganglioside antibodies would control micrometastases and improve outcomes in sarcoma patients who were disease-free after metastasectomy. METHODS: We conducted a randomised phase II trial of the immunological adjuvant OPT-821 with a KLH-conjugated ganglioside vaccine targeting GM2, GD2 and GD3, versus OPT-821 alone in patients with metastatic sarcoma following complete metastasectomy. Patients received 10 subcutaneous injections at Weeks 1, 2, 3, 8, 16, 28, 40, 52, 68 and 84 and were followed for evidence of recurrent disease. The primary end-point was relapse-free survival. Secondary end-points included overall survival and serologic response. RESULTS: A total of 136 patients were randomised, 68 to each arm. The mean age was 51.2, 52.2% were male, 90.4% had relapsed disease, 86.8% had high-grade tumours and 14% had ≥4 metastases resected. Histologies included leiomyosarcoma (33%), spindle cell sarcoma (14%), undifferentiated pleomorphic sarcoma (13%), osteosarcoma (10%), synovial sarcoma (9%), liposarcoma (9%) and others (12%). Most adverse events were Grade ≤2 (83.8% and 70.6% in the vaccine and adjuvant arms, respectively). The most common (≥20% of patients) were injection site reaction (89.7%), fatigue (44.1%) and pyrexia (27.9%) on the vaccine arm, and injection site reaction (69.1%) on the adjuvant only arm. The 1-year relapse-free survival rate (34.5% and 34.8% in the vaccine and OPT-821 monotherapy arm, respectively) did not differ between arms (P = 0.725). One-year overall survival rates were 93.1% and 91.5% in the vaccine and OPT-821 monotherapy arm, respectively (P = 0.578). Serologic responses at week 9 were more frequent on the vaccine arm (96.5% of patients) than in the adjuvant arm (32.8%), and the difference between groups was durable. CONCLUSIONS: A sustained serologic response to vaccination was induced with the vaccine, but no difference in recurrence-free or overall survival was observed between treatment arms. CLINICALTRIALS: gov identifier: NCT01141491.

Published
2022

5. Chemoradiotherapy plus induction or consolidation chemotherapy as total neoadjuvant therapy for locally advanced rectal cancer: Pooled analysis of the CAO/ARO/AIO-12 and the OPRA randomized phase 2 trials

Author

Fokas, Emmanouil, Williams, Hannah, Diefenhardt, Markus, Lin, Sabrina, Qin, Li-Xuan, Piso, Pompiliu, Dapper, Hendrik, Germer, Christoph-Thomas, Grützmann, Robert, Tim Friede, J., Joshua Smith, J., Saltz, Leonard B., Wu, Abraham J., Weiser, Martin R., Omer, Dana, Ghadimi, Michael, Hofheinz, Ralf-Dieter, Garcia-Aguilar, Julio, and Rödel, Claus

Published
2024
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6. Depth Normalization of Small RNA Sequencing: Using Data and Biology to Select a Suitable Method

Author

Düren, Yannick, Lederer, Johannes, and Qin, Li-Xuan

Subjects
Quantitative Biology - Genomics, Quantitative Biology - Quantitative Methods, Statistics - Methodology
Abstract

Deep sequencing has become one of the most popular tools for transcriptome profiling in biomedical studies. While an abundance of computational methods exists for "normalizing" sequencing data to remove unwanted between-sample variations due to experimental handling, there is no consensus on which normalization is the most suitable for a given data set. To address this problem, we developed "DANA" - an approach for assessing the performance of normalization methods for microRNA sequencing data based on biology-motivated and data-driven metrics. Our approach takes advantage of well-known biological features of microRNAs for their expression pattern and chromosomal clustering to simultaneously assess (1) how effectively normalization removes handling artifacts, and (2) how aptly normalization preserves biological signals. With DANA, we confirm that the performance of eight commonly used normalization methods vary widely across different data sets and provide guidance for selecting a suitable method for the data at hand. Hence, it should be adopted as a routine preprocessing step (preceding normalization) for microRNA sequencing data analysis. DANA is implemented in R and publicly available at https://github.com/LXQin/DANA., Comment: 16 pages, 6 figures

Published
2022

7. Performance Evaluation of Transcriptomics Data Normalization for Survival Risk Prediction

Author

Ni, Ai and Qin, Li-Xuan

Subjects
Quantitative Biology - Genomics
Abstract

One pivotal feature of transcriptomics data is the unwanted variations caused by disparate experimental handling, known as handling effects. Various data normalization methods were developed to alleviate the adverse impact of handling effects in the setting of differential expression analysis. However, little research has been done to evaluate their performance in the setting of survival outcome prediction, an important analysis goal for transcriptomics data in biomedical research. Leveraging a unique pair of datasets for the same set of tumor samples-one with handling effects and the other without, we developed a benchmarking tool for conducting such an evaluation in microRNA microarrays. We applied this tool to evaluate the performance of three popular normalization methods-quantile normalization, median normalization, and variance stabilizing normalization-in survival prediction using various approaches for model building and designs for sample assignment. We showed that handling effects can have a strong impact on survival prediction, and that quantile normalization, a most popular method in current practice, tends to underperform median normalization and variance stabilizing normalization. We demonstrated with a small example the reason for quantile normalization's poor performance in this setting. Our finding highlights the importance of putting normalization evaluation in the context of the downstream analysis setting and the potential of improving the development of survival predictors by applying median normalization. We make available our benchmarking tool for performing such evaluation on additional normalization methods in connection with prediction modeling approaches.

Published
2021

8. Nonoperative management of the primary tumor in patients with unresectable stage IV colon cancer treated with systemic chemotherapy: Higher complication rates for left-sided colon tumors

Author

Verheij, Floris S., Yuval, Jonathan B., Kok, Niels F.M., Lin, Sabrina T., Qin, Li-Xuan, Omer, Dana M., Thompson, Hannah M., Wei, Iris H., Widmar, Maria, Pappou, Emmanouil P., Weiser, Martin R., Nash, Garrett M., Smith, J. Joshua, Paty, Philip B., Beets, Geerard L., and Garcia-Aguilar, Julio

Published
2024
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10. Pilot study of bempegaldesleukin in combination with nivolumab in patients with metastatic sarcoma

Author

D’Angelo, Sandra P., Richards, Allison L., Conley, Anthony P., Woo, Hyung Jun, Dickson, Mark A., Gounder, Mrinal, Kelly, Ciara, Keohan, Mary Louise, Movva, Sujana, Thornton, Katherine, Rosenbaum, Evan, Chi, Ping, Nacev, Benjamin, Chan, Jason E., Slotkin, Emily K., Kiesler, Hannah, Adamson, Travis, Ling, Lilan, Rao, Pavitra, Patel, Shreyaskumar, Livingston, Jonathan A., Singer, Samuel, Agaram, Narasimhan P., Antonescu, Cristina R., Koff, Andrew, Erinjeri, Joseph P., Hwang, Sinchun, Qin, Li-Xuan, Donoghue, Mark T. A., and Tap, William D.

Published
2022
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11. Cureit : An End-to-End Pipeline for Implementing Mixture Cure Models With an Application to Liposarcoma Data.

Author

Whiting, Karissa, Fei, Teng, Singer, Samuel, and Qin, Li-Xuan

Subjects
LIPOSARCOMA, RATE setting, ODDS ratio
Abstract

PURPOSE: Cure models are a useful alternative to Cox proportional hazards models in oncology studies when there is a subpopulation of patients who will not experience the event of interest. Although software is available to fit cure models, there are limited tools to evaluate, report, and visualize model results. This article introduces the cureit R package, an end-to-end pipeline for building mixture cure models, and demonstrates its use in a data set of patients with primary extremity and truncal liposarcoma. METHODS: To assess associations between liposarcoma histologic subtypes and disease-specific death (DSD) in patients treated at Memorial Sloan Kettering Cancer Center between July 1982 and September 2017, mixture cure models were fit and evaluated using the cureit package. Liposarcoma histologic subtypes were defined as well-differentiated, dedifferentiated, myxoid, round cell, and pleomorphic. RESULTS: All other analyzed liposarcoma histologic subtypes were significantly associated with higher DSD in cure models compared with well-differentiated. In multivariable models, myxoid (odds ratio [OR], 6.25 [95% CI, 1.32 to 29.6]) and round cell (OR, 16.2 [95% CI, 2.80 to 93.2]) liposarcoma had higher incidences of DSD compared with well-differentiated patients. By contrast, dedifferentiated liposarcoma was associated with the latency of DSD (hazard ratio, 10.6 [95% CI, 1.48 to 75.9]). Pleomorphic liposarcomas had significantly higher risk in both incidence and the latency of DSD (P <.0001). Brier scores indicated comparable predictive accuracy between cure and Cox models. CONCLUSION: We developed the cureit pipeline to fit and evaluate mixture cure models and demonstrated its clinical utility in the liposarcoma disease setting, shedding insights on the subtype-specific associations with incidence and/or latency. Cure models are useful in settings with high rates of long-term survivors. The "cureit" pipeline can simplify cure analyses, as shown with a liposarcoma example. [ABSTRACT FROM AUTHOR]

Published
2024
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13. Supplementary Table S3 from Therapy-Induced Senescence Contributes to the Efficacy of Abemaciclib in Patients with Dedifferentiated Liposarcoma

Author

Gleason, Caroline E., primary, Dickson, Mark A., primary, Klein (Dooley), Mary E., primary, Antonescu, Cristina R., primary, Gularte-Mérida, Rodrigo, primary, Benitez, Marimar, primary, Delgado, Juliana I., primary, Kataru, Raghu P., primary, Tan, Mark Wei Yi, primary, Bradic, Martina, primary, Adamson, Travis E., primary, Seier, Kenneth, primary, Richards, Allison L., primary, Palafox, Marta, primary, Chan, Eric, primary, D'Angelo, Sandra P., primary, Gounder, Mrinal M., primary, Keohan, Mary Louise, primary, Kelly, Ciara M., primary, Chi, Ping, primary, Movva, Sujana, primary, Landa, Jonathan, primary, Crago, Aimee M., primary, Donoghue, Mark T.A., primary, Qin, Li-Xuan, primary, Serra, Violetta, primary, Turkekul, Mesruh, primary, Barlas, Afsar, primary, Firester, Daniel M., primary, Manova-Todorova, Katia, primary, Mehrara, Babak J., primary, Kovatcheva, Marta, primary, Tan, Nguan Soon, primary, Singer, Samuel, primary, Tap, William D., primary, and Koff, Andrew, primary

Published
2024
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14. Supplementary Figure S15 from Therapy-Induced Senescence Contributes to the Efficacy of Abemaciclib in Patients with Dedifferentiated Liposarcoma

Author

Gleason, Caroline E., primary, Dickson, Mark A., primary, Klein (Dooley), Mary E., primary, Antonescu, Cristina R., primary, Gularte-Mérida, Rodrigo, primary, Benitez, Marimar, primary, Delgado, Juliana I., primary, Kataru, Raghu P., primary, Tan, Mark Wei Yi, primary, Bradic, Martina, primary, Adamson, Travis E., primary, Seier, Kenneth, primary, Richards, Allison L., primary, Palafox, Marta, primary, Chan, Eric, primary, D'Angelo, Sandra P., primary, Gounder, Mrinal M., primary, Keohan, Mary Louise, primary, Kelly, Ciara M., primary, Chi, Ping, primary, Movva, Sujana, primary, Landa, Jonathan, primary, Crago, Aimee M., primary, Donoghue, Mark T.A., primary, Qin, Li-Xuan, primary, Serra, Violetta, primary, Turkekul, Mesruh, primary, Barlas, Afsar, primary, Firester, Daniel M., primary, Manova-Todorova, Katia, primary, Mehrara, Babak J., primary, Kovatcheva, Marta, primary, Tan, Nguan Soon, primary, Singer, Samuel, primary, Tap, William D., primary, and Koff, Andrew, primary

Published
2024
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15. Data from Therapy-Induced Senescence Contributes to the Efficacy of Abemaciclib in Patients with Dedifferentiated Liposarcoma

Author

Gleason, Caroline E., primary, Dickson, Mark A., primary, Klein (Dooley), Mary E., primary, Antonescu, Cristina R., primary, Gularte-Mérida, Rodrigo, primary, Benitez, Marimar, primary, Delgado, Juliana I., primary, Kataru, Raghu P., primary, Tan, Mark Wei Yi, primary, Bradic, Martina, primary, Adamson, Travis E., primary, Seier, Kenneth, primary, Richards, Allison L., primary, Palafox, Marta, primary, Chan, Eric, primary, D'Angelo, Sandra P., primary, Gounder, Mrinal M., primary, Keohan, Mary Louise, primary, Kelly, Ciara M., primary, Chi, Ping, primary, Movva, Sujana, primary, Landa, Jonathan, primary, Crago, Aimee M., primary, Donoghue, Mark T.A., primary, Qin, Li-Xuan, primary, Serra, Violetta, primary, Turkekul, Mesruh, primary, Barlas, Afsar, primary, Firester, Daniel M., primary, Manova-Todorova, Katia, primary, Mehrara, Babak J., primary, Kovatcheva, Marta, primary, Tan, Nguan Soon, primary, Singer, Samuel, primary, Tap, William D., primary, and Koff, Andrew, primary

Published
2024
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16. Supplementary Table S3 from PDGFRβ Signaling Cooperates with β-Catenin to Modulate c-Abl and Biologic Behavior of Desmoid-Type Fibromatosis

Author

Hu, Jia, primary, Hameed, Meera R., primary, Agaram, Narasimhan P., primary, Whiting, Karissa A., primary, Qin, Li-Xuan, primary, Villano, Anthony M., primary, O'Connor, Rachael B., primary, Rozenberg, Julian M., primary, Cohen, Sonia, primary, Prendergast, Katherine, primary, Kryeziu, Sara, primary, White, Richard L., primary, Posner, Mitchell C., primary, Socci, Nicholas D., primary, Gounder, Mrinal M., primary, Singer, Samuel, primary, and Crago, Aimee M., primary

Published
2024
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17. Data from PDGFRβ Signaling Cooperates with β-Catenin to Modulate c-Abl and Biologic Behavior of Desmoid-Type Fibromatosis

Author

Hu, Jia, primary, Hameed, Meera R., primary, Agaram, Narasimhan P., primary, Whiting, Karissa A., primary, Qin, Li-Xuan, primary, Villano, Anthony M., primary, O'Connor, Rachael B., primary, Rozenberg, Julian M., primary, Cohen, Sonia, primary, Prendergast, Katherine, primary, Kryeziu, Sara, primary, White, Richard L., primary, Posner, Mitchell C., primary, Socci, Nicholas D., primary, Gounder, Mrinal M., primary, Singer, Samuel, primary, and Crago, Aimee M., primary

Published
2024
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18. Supplementary Data 1 from PDGFRβ Signaling Cooperates with β-Catenin to Modulate c-Abl and Biologic Behavior of Desmoid-Type Fibromatosis

Author

Hu, Jia, primary, Hameed, Meera R., primary, Agaram, Narasimhan P., primary, Whiting, Karissa A., primary, Qin, Li-Xuan, primary, Villano, Anthony M., primary, O'Connor, Rachael B., primary, Rozenberg, Julian M., primary, Cohen, Sonia, primary, Prendergast, Katherine, primary, Kryeziu, Sara, primary, White, Richard L., primary, Posner, Mitchell C., primary, Socci, Nicholas D., primary, Gounder, Mrinal M., primary, Singer, Samuel, primary, and Crago, Aimee M., primary

Published
2024
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19. PDGFRβ signaling cooperates with β-catenin to modulate c-Abl and biologic behavior of desmoid-type fibromatosis

Author

Hu, Jia, primary, Hameed, Meera R., additional, Agaram, Narasimhan P., additional, Whiting, Karissa A., additional, Qin, Li-Xuan, additional, Villano, Anthony M., additional, O'Connor, Rachael B., additional, Rozenberg, Julian M., additional, Cohen, Sonia, additional, Prendergast, Katherine, additional, Kryeziu, Sara, additional, White, Richard L., additional, Posner, Mitchell C., additional, Socci, Nicholas D., additional, Gounder, Mrinal M., additional, Singer, Samuel, additional, and Crago, Aimee M., additional

Published
2023
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20. Nonoperative management of the primary tumor in patients with unresectable stage IV colon cancer treated with systemic chemotherapy: Higher complication rates in left-sided colon tumors

Author

Verheij, Floris S., primary, Yuval, Jonathan B., additional, Kok, Niels F.M., additional, Lin, Sabrina T., additional, Qin, Li-Xuan, additional, Omer, Dana M., additional, Thompson, Hannah M., additional, Wei, Iris H., additional, Widmar, Maria, additional, Pappou, Emmanouil P., additional, Weiser, Martin R., additional, Nash, Garrett M., additional, Smith, J. Joshua, additional, Paty, Philip B., additional, Beets, Geerard L., additional, and Garcia-Aguilar, Julio, additional

Published
2023
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21. Genetic Evidence That Intratumoral T-cell Proliferation and Activation Are Associated with Recurrence and Survival in Patients with Resected Colorectal Liver Metastases

Author

Maker, Ajay V, Ito, Hiromichi, Mo, Qianxing, Weisenberg, Elliot, Qin, Li-Xuan, Turcotte, Simon, Maithel, Shishir, Shia, Jinru, Blumgart, Leslie, Fong, Yuman, Jarnagin, William R, DeMatteo, Ronald P, and D'Angelica, Michael I

Subjects
Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Immunology, Liver Disease, Digestive Diseases, Cancer, Clinical Research, Genetics, Colo-Rectal Cancer, 2.1 Biological and endogenous factors, Aetiology, Biomarkers, Tumor, Cell Proliferation, Colorectal Neoplasms, Female, Gene Expression Regulation, Neoplastic, Humans, Kaplan-Meier Estimate, Liver Neoplasms, Lymphocyte Activation, Lymphocytes, Tumor-Infiltrating, Male, Middle Aged, Neoplasm Proteins, Recurrence, Retrospective Studies, Survival Analysis, Tissue Array Analysis, Tumor Microenvironment, Tumor Necrosis Factor Ligand Superfamily Member 14, Pharmacology and Pharmaceutical Sciences, Oncology and carcinogenesis
Abstract

Though immune responses correlate with prognosis in primary colorectal cancer, the role of tumor immunity in metastatic disease is less clear. We hypothesized that patient survival and tumor recurrence correlate with transcriptional evidence of lymphocyte proliferation/activation in resected colorectal cancer liver metastases (CRLM). Microarray gene analysis was performed on liver tumor specimens from 96 patients who underwent resection for CRLM. A Cox proportional hazards model identified genes associated with overall survival (OS) and recurrence-free survival (RFS). Conventional gene ontology (GO) enrichment analysis ranked biologically relevant processes. Survival probabilities of prioritized processes were assessed. Protein expression was validated with immunohistochemistry in an independent set of patients. GO analysis identified and ranked unique biologic processes that correlated with survival. Genes that specifically functioned in the biologic process of "T-cell proliferation" were significant predictors of OS (P = 0.01), and both "T-cell proliferation" and "activation" were highly associated with RFS (P ≤ 0.01). Analysis of genes in these GO categories identified increased TNFSF14/LIGHT expression to be most associated with improved OS and RFS (P ≤ 0.0006). Immunohistochemistry of an independent validation set of CRLM confirmed that both increased tumor-infiltrating lymphocytes (TIL) and higher LIGHT expression on TILs were associated with improved OS and RFS. Differential expression of genes involved in T-cell proliferation/activation was associated with survival outcomes in a large number of surgical patients who underwent resection of CRLM. These biologic functions determined by GO analysis of the tumor microenvironment have identified specific immune-related genes that may be involved in an antitumor immune response.

Published
2015

24. Long-Term Results of Organ Preservation in Patients With Rectal Adenocarcinoma Treated With Total Neoadjuvant Therapy: The Randomized Phase II OPRA Trial

Author

Verheij, Floris S., primary, Omer, Dana M., additional, Williams, Hannah, additional, Lin, Sabrina T., additional, Qin, Li-Xuan, additional, Buckley, James T., additional, Thompson, Hannah M., additional, Yuval, Jonathan B., additional, Kim, Jin K., additional, Dunne, Richard F., additional, Marcet, Jorge, additional, Cataldo, Peter, additional, Polite, Blase, additional, Herzig, Daniel O., additional, Liska, David, additional, Oommen, Samuel, additional, Friel, Charles M., additional, Ternent, Charles, additional, Coveler, Andrew L., additional, Hunt, Steven, additional, Gregory, Anita, additional, Varma, Madhulika G., additional, Bello, Brian L., additional, Carmichael, Joseph C., additional, Krauss, John, additional, Gleisner, Ana, additional, Guillem, José G., additional, Temple, Larissa, additional, Goodman, Karyn A., additional, Segal, Neil H., additional, Cercek, Andrea, additional, Yaeger, Rona, additional, Nash, Garrett M., additional, Widmar, Maria, additional, Wei, Iris H., additional, Pappou, Emmanouil P., additional, Weiser, Martin R., additional, Paty, Philip B., additional, Smith, J. Joshua, additional, Wu, Abraham J., additional, Gollub, Marc J., additional, Saltz, Leonard B., additional, and Garcia-Aguilar, Julio, additional

Published
2023
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25. Supplementary Data from Immune-related Adverse Events after Immune Checkpoint Blockade–based Therapy Are Associated with Improved Survival in Advanced Sarcomas

Author

Rosenbaum, Evan, primary, Seier, Kenneth, primary, Bradic, Martina, primary, Kelly, Ciara, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Gounder, Mrinal M., primary, Keohan, Mary L., primary, Avutu, Viswatej, primary, Chi, Ping, primary, Thornton, Katherine A., primary, Chan, Jason E., primary, Dickson, Mark A., primary, Donoghue, Mark T.A., primary, Tap, William D., primary, Qin, Li-Xuan, primary, and D'Angelo, Sandra P., primary

Published
2023
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26. TABLE 3 from Immune-related Adverse Events after Immune Checkpoint Blockade–based Therapy Are Associated with Improved Survival in Advanced Sarcomas

Author

Rosenbaum, Evan, primary, Seier, Kenneth, primary, Bradic, Martina, primary, Kelly, Ciara, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Gounder, Mrinal M., primary, Keohan, Mary L., primary, Avutu, Viswatej, primary, Chi, Ping, primary, Thornton, Katherine A., primary, Chan, Jason E., primary, Dickson, Mark A., primary, Donoghue, Mark T.A., primary, Tap, William D., primary, Qin, Li-Xuan, primary, and D'Angelo, Sandra P., primary

Published
2023
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27. TABLE 4 from Immune-related Adverse Events after Immune Checkpoint Blockade–based Therapy Are Associated with Improved Survival in Advanced Sarcomas

Author

Rosenbaum, Evan, primary, Seier, Kenneth, primary, Bradic, Martina, primary, Kelly, Ciara, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Gounder, Mrinal M., primary, Keohan, Mary L., primary, Avutu, Viswatej, primary, Chi, Ping, primary, Thornton, Katherine A., primary, Chan, Jason E., primary, Dickson, Mark A., primary, Donoghue, Mark T.A., primary, Tap, William D., primary, Qin, Li-Xuan, primary, and D'Angelo, Sandra P., primary

Published
2023
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28. Data from Immune-related Adverse Events after Immune Checkpoint Blockade–based Therapy Are Associated with Improved Survival in Advanced Sarcomas

Author

Rosenbaum, Evan, primary, Seier, Kenneth, primary, Bradic, Martina, primary, Kelly, Ciara, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Gounder, Mrinal M., primary, Keohan, Mary L., primary, Avutu, Viswatej, primary, Chi, Ping, primary, Thornton, Katherine A., primary, Chan, Jason E., primary, Dickson, Mark A., primary, Donoghue, Mark T.A., primary, Tap, William D., primary, Qin, Li-Xuan, primary, and D'Angelo, Sandra P., primary

Published
2023
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29. TABLE 2 from Immune-related Adverse Events after Immune Checkpoint Blockade–based Therapy Are Associated with Improved Survival in Advanced Sarcomas

Author

Rosenbaum, Evan, primary, Seier, Kenneth, primary, Bradic, Martina, primary, Kelly, Ciara, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Gounder, Mrinal M., primary, Keohan, Mary L., primary, Avutu, Viswatej, primary, Chi, Ping, primary, Thornton, Katherine A., primary, Chan, Jason E., primary, Dickson, Mark A., primary, Donoghue, Mark T.A., primary, Tap, William D., primary, Qin, Li-Xuan, primary, and D'Angelo, Sandra P., primary

Published
2023
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30. TABLE 1 from Immune-related Adverse Events after Immune Checkpoint Blockade–based Therapy Are Associated with Improved Survival in Advanced Sarcomas

Author

Rosenbaum, Evan, primary, Seier, Kenneth, primary, Bradic, Martina, primary, Kelly, Ciara, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Gounder, Mrinal M., primary, Keohan, Mary L., primary, Avutu, Viswatej, primary, Chi, Ping, primary, Thornton, Katherine A., primary, Chan, Jason E., primary, Dickson, Mark A., primary, Donoghue, Mark T.A., primary, Tap, William D., primary, Qin, Li-Xuan, primary, and D'Angelo, Sandra P., primary

Published
2023
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31. Immune-related Adverse Events after Immune Checkpoint Blockade–based Therapy Are Associated with Improved Survival in Advanced Sarcomas

Author

Rosenbaum, Evan, primary, Seier, Kenneth, additional, Bradic, Martina, additional, Kelly, Ciara, additional, Movva, Sujana, additional, Nacev, Benjamin A., additional, Gounder, Mrinal M., additional, Keohan, Mary L., additional, Avutu, Viswatej, additional, Chi, Ping, additional, Thornton, Katherine A., additional, Chan, Jason E., additional, Dickson, Mark A., additional, Donoghue, Mark T.A., additional, Tap, William D., additional, Qin, Li-Xuan, additional, and D'Angelo, Sandra P., additional

Published
2023
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32. Therapy-Induced Senescence Contributes to the Efficacy of Abemaciclib in Patients with Dedifferentiated Liposarcoma

Author

Gleason, Caroline E., primary, Dickson, Mark A., additional, Klein (Dooley), Mary E., additional, Antonescu, Cristina R., additional, Gularte-Mérida, Rodrigo, additional, Benitez, Marimar, additional, Delgado, Juliana I., additional, Kataru, Raghu P., additional, Tan, Mark Wei Yi, additional, Bradic, Martina, additional, Adamson, Travis E., additional, Seier, Kenneth, additional, Richards, Allison L., additional, Palafox, Marta, additional, Chan, Eric, additional, D'Angelo, Sandra P., additional, Gounder, Mrinal M., additional, Keohan, Mary Louise, additional, Kelly, Ciara M., additional, Chi, Ping, additional, Movva, Sujana, additional, Landa, Jonathan, additional, Crago, Aimee M., additional, Donoghue, Mark T.A., additional, Qin, Li-Xuan, additional, Serra, Violetta, additional, Turkekul, Mesruh, additional, Barlas, Afsar, additional, Firester, Daniel M., additional, Manova-Todorova, Katia, additional, Mehrara, Babak J., additional, Kovatcheva, Marta, additional, Tan, Nguan Soon, additional, Singer, Samuel, additional, Tap, William D., additional, and Koff, Andrew, additional

Published
2023
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33. Compliance and Toxicity of Total Neoadjuvant Therapy for Rectal Cancer: A Secondary Analysis of the OPRA Trial

Author

Verheij, Floris S., primary, Omer, Dana M., additional, Lin, Sabrina T., additional, Yuval, Jonathan B., additional, Thompson, Hannah M., additional, Kim, Jin K., additional, Valdivieso, Sebastian C., additional, Qin, Li-Xuan, additional, Wu, Abraham J., additional, Saltz, Leonard B., additional, and Garcia-Aguilar, Julio, additional

Published
2023
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34. Gene Expression Profiles Accurately Predict Outcome Following Liver Resection in Patients with Metastatic Colorectal Cancer

Author

Ito, Hiromichi, Mo, Qianxing, Qin, Li-Xuan, Viale, Agnes, Maithel, Shishir K, Maker, Ajay V, Shia, Jinru, Kingham, Peter, Allen, Peter, DeMatteo, Ronald P, Fong, Yuman, Jarnagin, William R, and D’Angelica, Michael

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Colo-Rectal Cancer, Clinical Research, Clinical Trials and Supportive Activities, Genetics, Digestive Diseases, Liver Disease, Cancer, 4.1 Discovery and preclinical testing of markers and technologies, Detection, screening and diagnosis, Adult, Aged, Aged, 80 and over, Biomarkers, Tumor, Cohort Studies, Colorectal Neoplasms, Female, Gene Expression Profiling, Genetic Predisposition to Disease, Hepatectomy, Humans, Liver Neoplasms, Male, Middle Aged, Prognosis, General Science & Technology
Abstract

PurposeThe aim of this study was to build a molecular prognostic model based on gene signatures for patients with completely resected hepatic metastases from colorectal cancer (MCRC).MethodsUsing the Illumina HumanHT-12 gene chip, RNA samples from the liver metastases of 96 patients who underwent R0 liver resection were analyzed. Patients were randomly assigned to a training (n = 60) and test (n = 36) set. The genes associated with disease-specific survival (DSS) and liver-recurrence-free survival (LRFS) were identified by Cox-regression and selected to construct a molecular risk score (MRS) using the supervised principle component method on the training set. The MRS was then evaluated in the independent test set.ResultsNineteen and 115 genes were selected to construct the MRS for DSS and LRFS, respectively. Each MRS was validated in the test set; 3-year DSS/LRFS rates were 42/32% and 79/80% for patients with high and low MRS, respectively (p = 0.007 for DSS and p = 0.046 for LRFS). In a multivariate model controlling for a previously validated clinical risk score (CRS), the MRS remained a significant predictor of DSS (p = 0.001) and LRFS (p = 0.03). When CRS and MRS were combined, the patients were discriminated better with 3-year DSS/LRFS rates of 90/89% in the low risk group (both risk scores low) vs 42/26% in the high risk group (both risk scores high), respectively (p = 0.002/0.004 for DSS/LRFS).ConclusionMRS based on gene expression profiling has high prognostic value and is independent of CRS. This finding provides a potential strategy for better risk-stratification of patients with liver MCRC.

Published
2013

35. A phase Ib study of BGJ398, a pan-FGFR kinase inhibitor in combination with imatinib in patients with advanced gastrointestinal stromal tumor

Author

Kelly, Ciara M., Shoushtari, Alexander N., Qin, Li-Xuan, D’Angelo, Sandra P., Dickson, Mark A., Gounder, Mrinal M., Keohan, Mary Louise, Mcfadyen, Chloe, Sjoberg, Ana, Singer, Samuel, DeMatteo, Ronald P., Hwang, Sinchun, Heinemann, M. H., Francis, Jasmine H., Antonescu, Cristina R., Chi, Ping, and Tap, William D.

Published
2019
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40. Supplementary Data 2 from A Phase II Study of Epacadostat and Pembrolizumab in Patients with Advanced Sarcoma

Author

Kelly, Ciara M., primary, Qin, Li-Xuan, primary, Whiting, Karissa A., primary, Richards, Allison L., primary, Avutu, Viswatej, primary, Chan, Jason E., primary, Chi, Ping, primary, Dickson, Mark A., primary, Gounder, Mrinal M., primary, Keohan, Mary Louise, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Rosenbaum, Evan, primary, Adamson, Travis, primary, Singer, Samuel, primary, Bartlett, Edmund K., primary, Crago, Aimee M., primary, Yoon, Sam S., primary, Hwang, Sinchun, primary, Erinjeri, Joseph P., primary, Antonescu, Cristina R., primary, Tap, William D., primary, and D'Angelo, Sandra P., primary

Published
2023
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41. A phase II study of talimogene laherparepvec (T-VEC) and pembrolizumab in patients with advanced sarcoma: Results of expansion cohorts.

Author

Kelly, Ciara Marie, primary, Avutu, Viswatej, additional, Chi, Ping, additional, Dickson, Mark Andrew, additional, Gounder, Mrinal M., additional, Keohan, Mary Louise, additional, Movva, Sujana, additional, Rosenbaum, Evan, additional, Cordover, Emma, additional, Ariyan, Charlotte Eielson, additional, Bartlett, Edmund, additional, Crago, Aimee Marie, additional, Singer, Samuel, additional, Antonescu, Cristina R., additional, Hwang, Sinchun, additional, Erinjeri, Joseph Patrick, additional, Seier, Kenneth, additional, Qin, Li-Xuan, additional, Tap, William D., additional, and D'Angelo, Sandra P., additional

Published
2023
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42. Supplementary Data 1 from A Phase II Study of Epacadostat and Pembrolizumab in Patients with Advanced Sarcoma

Author

Kelly, Ciara M., primary, Qin, Li-Xuan, primary, Whiting, Karissa A., primary, Richards, Allison L., primary, Avutu, Viswatej, primary, Chan, Jason E., primary, Chi, Ping, primary, Dickson, Mark A., primary, Gounder, Mrinal M., primary, Keohan, Mary Louise, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Rosenbaum, Evan, primary, Adamson, Travis, primary, Singer, Samuel, primary, Bartlett, Edmund K., primary, Crago, Aimee M., primary, Yoon, Sam S., primary, Hwang, Sinchun, primary, Erinjeri, Joseph P., primary, Antonescu, Cristina R., primary, Tap, William D., primary, and D'Angelo, Sandra P., primary

Published
2023
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43. Supplementary Data 3 from A Phase II Study of Epacadostat and Pembrolizumab in Patients with Advanced Sarcoma

Author

Kelly, Ciara M., primary, Qin, Li-Xuan, primary, Whiting, Karissa A., primary, Richards, Allison L., primary, Avutu, Viswatej, primary, Chan, Jason E., primary, Chi, Ping, primary, Dickson, Mark A., primary, Gounder, Mrinal M., primary, Keohan, Mary Louise, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Rosenbaum, Evan, primary, Adamson, Travis, primary, Singer, Samuel, primary, Bartlett, Edmund K., primary, Crago, Aimee M., primary, Yoon, Sam S., primary, Hwang, Sinchun, primary, Erinjeri, Joseph P., primary, Antonescu, Cristina R., primary, Tap, William D., primary, and D'Angelo, Sandra P., primary

Published
2023
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48. Data from A Phase II Study of Epacadostat and Pembrolizumab in Patients with Advanced Sarcoma

Author

Kelly, Ciara M., primary, Qin, Li-Xuan, primary, Whiting, Karissa A., primary, Richards, Allison L., primary, Avutu, Viswatej, primary, Chan, Jason E., primary, Chi, Ping, primary, Dickson, Mark A., primary, Gounder, Mrinal M., primary, Keohan, Mary Louise, primary, Movva, Sujana, primary, Nacev, Benjamin A., primary, Rosenbaum, Evan, primary, Adamson, Travis, primary, Singer, Samuel, primary, Bartlett, Edmund K., primary, Crago, Aimee M., primary, Yoon, Sam S., primary, Hwang, Sinchun, primary, Erinjeri, Joseph P., primary, Antonescu, Cristina R., primary, Tap, William D., primary, and D'Angelo, Sandra P., primary

Published
2023
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49. Supplementary Tables S1 - S7 from Integrin-α10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma

Author

Okada, Tomoyo, primary, Lee, Ann Y., primary, Qin, Li-Xuan, primary, Agaram, Narasimhan, primary, Mimae, Takahiro, primary, Shen, Yawei, primary, O'Connor, Rachael, primary, López-Lago, Miguel A., primary, Craig, Amanda, primary, Miller, Martin L., primary, Agius, Phaedra, primary, Molinelli, Evan, primary, Socci, Nicholas D., primary, Crago, Aimee M., primary, Shima, Fumi, primary, Sander, Chris, primary, and Singer, Samuel, primary

Published
2023
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50. Data from Integrin-α10 Dependency Identifies RAC and RICTOR as Therapeutic Targets in High-Grade Myxofibrosarcoma

Author

Okada, Tomoyo, primary, Lee, Ann Y., primary, Qin, Li-Xuan, primary, Agaram, Narasimhan, primary, Mimae, Takahiro, primary, Shen, Yawei, primary, O'Connor, Rachael, primary, López-Lago, Miguel A., primary, Craig, Amanda, primary, Miller, Martin L., primary, Agius, Phaedra, primary, Molinelli, Evan, primary, Socci, Nicholas D., primary, Crago, Aimee M., primary, Shima, Fumi, primary, Sander, Chris, primary, and Singer, Samuel, primary

Published
2023
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