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Santinello B, Sun R, Amjad A, Hoyt SJ, Ouyang L, Courret C, Drennan R, Leo L, Larracuente AM, Core L, O'Neill RJ, Mellone BG. Transcription of a centromere-enriched retroelement and local retention of its RNA are significant features of the CENP-A chromatin landscape. bioRxiv 2024:2024.01.14.574223. [PMID: 38293134 PMCID: PMC10827089 DOI: 10.1101/2024.01.14.574223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Centromeres depend on chromatin containing the conserved histone H3 variant CENP-A for function and inheritance, while the role of centromeric DNA repeats remains unclear. Retroelements are prevalent at centromeres across taxa and represent a potential mechanism for promoting transcription to aid in CENP-A incorporation or for generating RNA transcripts to maintain centromere integrity. Here, we probe into the transcription and RNA localization of the centromere-enriched retroelement G2/Jockey-3 (hereafter referred to as Jockey-3 ) in Drosophila melanogaster , currently the only in vivo model with assembled centromeres. We find that Jockey-3 is a major component of the centromeric transcriptome and produces RNAs that localize to centromeres in metaphase. Leveraging the polymorphism of Jockey-3 and a de novo centromere system, we show that these RNAs remain associated with their cognate DNA sequences in cis , suggesting they are unlikely to perform a sequence-specific function at all centromeres. We show that Jockey-3 transcription is positively correlated with the presence of CENP-A, and that recent Jockey-3 transposition events have occurred preferentially at CENP-A-containing chromatin. We propose that Jockey-3 contributes to the epigenetic maintenance of centromeres by promoting chromatin transcription, while inserting preferentially within these regions, selfishly ensuring its continued expression and transmission. Given the conservation of retroelements as centromere components through evolution, our findings have broad implications in understanding this association in other species.
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Bahrambeigi V, Lee JJ, Branchi V, Rajapakshe KI, Xu Z, Kui N, Henry JT, Kun W, Stephens BM, Dhebat S, Hurd MW, Sun R, Yang P, Ruppin E, Wang W, Kopetz S, Maitra A, Guerrero PA. Transcriptomic Profiling of Plasma Extracellular Vesicles Enables Reliable Annotation of the Cancer-Specific Transcriptome and Molecular Subtype. Cancer Res 2024; 84:1719-1732. [PMID: 38451249 PMCID: PMC11096054 DOI: 10.1158/0008-5472.can-23-4070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/08/2024]
Abstract
Longitudinal monitoring of patients with advanced cancers is crucial to evaluate both disease burden and treatment response. Current liquid biopsy approaches mostly rely on the detection of DNA-based biomarkers. However, plasma RNA analysis can unleash tremendous opportunities for tumor state interrogation and molecular subtyping. Through the application of deep learning algorithms to the deconvolved transcriptomes of RNA within plasma extracellular vesicles (evRNA), we successfully predicted consensus molecular subtypes in patients with metastatic colorectal cancer. Analysis of plasma evRNA also enabled monitoring of changes in transcriptomic subtype under treatment selection pressure and identification of molecular pathways associated with recurrence. This approach also revealed expressed gene fusions and neoepitopes from evRNA. These results demonstrate the feasibility of using transcriptomic-based liquid biopsy platforms for precision oncology approaches, spanning from the longitudinal monitoring of tumor subtype changes to the identification of expressed fusions and neoantigens as cancer-specific therapeutic targets, sans the need for tissue-based sampling. SIGNIFICANCE The development of an approach to interrogate molecular subtypes, cancer-associated pathways, and differentially expressed genes through RNA sequencing of plasma extracellular vesicles lays the foundation for liquid biopsy-based longitudinal monitoring of patient tumor transcriptomes.
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Affiliation(s)
- Vahid Bahrambeigi
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaewon J. Lee
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Vittorio Branchi
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kimal I. Rajapakshe
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zhichao Xu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naishu Kui
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason T. Henry
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wang Kun
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Bret M. Stephens
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sarah Dhebat
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mark W. Hurd
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Peng Yang
- Department Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Statistics Rice University, Houston, TX, USA
| | - Eytan Ruppin
- Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wenyi Wang
- Department Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paola A. Guerrero
- Sheikh Ahmed Center for Pancreatic Cancer Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Hornstein NJ, Zeineddine MA, Gunes BB, Pellatt AJ, Knafl M, Zhu H, Willett AF, Yousef A, Liu S, Sun R, Futreal A, Woodman SE, Taggart MW, Overman MJ, Halperin DM, Raghav KP, Shen JP. Efficacy and safety of atezolizumab and bevacizumab in appendiceal adenocarcinoma. Cancer Res Commun 2024:745187. [PMID: 38709066 DOI: 10.1158/2767-9764.crc-24-0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/27/2024] [Accepted: 04/30/2024] [Indexed: 05/07/2024]
Abstract
PURPOSE Appendiceal Adenocarcinoma (AA) remains an orphan disease with limited treatment options for patients unable to undergo surgical resection. Evidence supporting the efficacy of combined VEGF and PD-1 inhibition in other tumor types provided a compelling rationale for investigating this combination in AA, where immune checkpoint inhibitors (ICIs) have not been previously explored. PATIENTS AND METHODS We conducted a prospective, single arm phase 2 study evaluating efficacy and safety of atezolizumab in conjunction with bevacizumab (Atezo+Bev) in advanced, unresectable AA. RESULTS Patients treated with the Atezo+Bev combination had 100% disease control rate (1 PR, 15 SD) with progression free survival (PFS) of 18.3 months and overall survival not-yet-reached with median duration of follow up of 40 months. These survival intervals were significantly longer relative to a clinically and molecularly matched synthetic control cohort treated with cytotoxic chemotherapy designed for colorectal cancer (PFS of 4.4 months, p = .041). CONCLUSIONS In light of recent data demonstrating a lack of efficacy of 5-FU based chemotherapy, Atezo+Bev is a promising treatment option for patients with low-grade unresectable AA; further study is warranted.
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Affiliation(s)
- Nicholas J Hornstein
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | | | - Betul B Gunes
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Andrew J Pellatt
- The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Mark Knafl
- University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Haifeng Zhu
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Anneleis F Willett
- University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Abdelrahman Yousef
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
| | - Suyu Liu
- The University of Texas MD Anderson Cancer Center, houston, TX, United States
| | - Ryan Sun
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Andrew Futreal
- The University of Texas MD Anderson Cancer Center, Houston, United States
| | - Scott E Woodman
- University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Melissa W Taggart
- The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Michael J Overman
- University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Daniel M Halperin
- University of Texas MD Anderson Cancer Center, Houston, United States
| | - Kanwal P Raghav
- University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - John Paul Shen
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States
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4
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Jallouk AP, Kui N, Sun R, Westin JR, Steiner RE, Nair R, Nastoupil LJ, Fayad LE, Zaki AA, Hawkins M, Adkins S, Noorani M, Das K, Henderson J, Shpall EJ, Kebriaei P, Ramdial J, Flowers CR, Neelapu SS, Ahmed S, Strati P. Effect of delayed cell infusion in patients with large B-cell lymphoma treated with chimeric antigen receptor T-cell therapy. Haematologica 2024; 109:1460-1468. [PMID: 38031807 PMCID: PMC11063866 DOI: 10.3324/haematol.2023.284453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/23/2023] [Indexed: 12/01/2023] Open
Abstract
Complications occurring after lymphodepleting chemotherapy (LDC) may delay chimeric antigen receptor (CAR) T-cell infusion. The effect of these delays on clinical outcomes is unclear. We performed a retrospective analysis of 240 patients with relapsed/refractory large B-cell lymphoma treated with standard-of-care axicabtagene ciloleucel (axi-cel) and identified 40 patients (16.7%) who had delay in axi-cel infusion. Of these, 85% had delay due to infection. At time of LDC initiation, patients with delayed infusion had lower absolute neutrophil count (P=0.006), lower platelets (P=0.004), lower hemoglobin (P<0.001) and higher C-reactive protein (P=0.001) than those with on-time infusion. Patients with delayed infusion had lower day 30 overall response rates (59.0% vs. 79.4%; P=0.008) and shorter median progression-free survival (PFS) (3.5 vs. 8.2 months; P=0.002) and overall survival (7.8 vs. 26.4 months; P=0.046) than those with on-time infusion. The association with PFS was maintained on multivariate analysis. There was also an association between extent of delay and survival, with shorter median PFS in patients who had delays of 2-5 days (1.8 vs. 8.2 months; P=0.001) and >5 days (4.6 vs. 8.2 months; P=0.036), but not 1 day (5.7 vs. 8.2 months; P=0.238). Following propensity score matching, patients with delayed infusion continued to have shorter median PFS (3.5 vs. 6.0 months; P=0.015). Levels of pro-inflammatory cytokines on day of infusion were significantly higher in patients with delayed infusion. Together, these findings suggest that delays in CAR T-cell administration after initiation of LDC are associated with inferior outcomes. Further studies are needed to guide strategies to improve efficacy in such patients.
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MESH Headings
- Humans
- Male
- Female
- Middle Aged
- Immunotherapy, Adoptive/adverse effects
- Immunotherapy, Adoptive/methods
- Aged
- Lymphoma, Large B-Cell, Diffuse/therapy
- Lymphoma, Large B-Cell, Diffuse/mortality
- Lymphoma, Large B-Cell, Diffuse/immunology
- Adult
- Retrospective Studies
- Receptors, Chimeric Antigen/immunology
- Treatment Outcome
- Biological Products/therapeutic use
- Biological Products/administration & dosage
- Aged, 80 and over
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Affiliation(s)
- Andrew P Jallouk
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX; Division of Hematology/Oncology, Vanderbilt University Medical Center, Nashville, TN
| | - Naishu Kui
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason R Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Raphael E Steiner
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ranjit Nair
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Loretta J Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luis E Fayad
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ajlan Al Zaki
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Misha Hawkins
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sherry Adkins
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mansoor Noorani
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kaberi Das
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jared Henderson
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Partow Kebriaei
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jeremy Ramdial
- Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Christopher R Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sattva S Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX; Department of Stem Cell Transplantation and Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX.
| | - Paolo Strati
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX.
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Sun R, Srivastava A, Derebail VK, Han J, Molokie RE, Gordeuk V, Saraf SL. GLP-1 agonists and SGLT-2 inhibitors in adults with sickle cell disease. Am J Hematol 2024. [PMID: 38655752 DOI: 10.1002/ajh.27348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/06/2024] [Accepted: 04/15/2024] [Indexed: 04/26/2024]
Affiliation(s)
- Ryan Sun
- Sickle Cell Center, Division of Hematology & Oncology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Anand Srivastava
- Division of Nephrology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Vimal K Derebail
- UNC Kidney Center, Division of Nephrology and Hypertension, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jin Han
- Sickle Cell Center, Division of Hematology & Oncology, University of Illinois Chicago, Chicago, Illinois, USA
- Department of Pharmacy Practice, University of Illinois Chicago, Chicago, Illinois, USA
| | - Robert E Molokie
- Sickle Cell Center, Division of Hematology & Oncology, University of Illinois Chicago, Chicago, Illinois, USA
- Department of Medicine, Jesse Brown VA Medical Center, Chicago, Illinois, USA
| | - Victor Gordeuk
- Sickle Cell Center, Division of Hematology & Oncology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Santosh L Saraf
- Sickle Cell Center, Division of Hematology & Oncology, University of Illinois Chicago, Chicago, Illinois, USA
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Choi J, Xu Z, Sun R. Variance-components tests for genetic association with multiple interval-censored outcomes. Stat Med 2024. [PMID: 38636557 DOI: 10.1002/sim.10081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 02/18/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
Massive genetic compendiums such as the UK Biobank have become an invaluable resource for identifying genetic variants that are associated with complex diseases. Due to the difficulties of massive data collection, a common practice of these compendiums is to collect interval-censored data. One challenge in analyzing such data is the lack of methodology available for genetic association studies with interval-censored data. Genetic effects are difficult to detect because of their rare and weak nature, and often the time-to-event outcomes are transformed to binary phenotypes for access to more powerful signal detection approaches. However transforming the data to binary outcomes can result in loss of valuable information. To alleviate such challenges, this work develops methodology to associate genetic variant sets with multiple interval-censored outcomes. Testing sets of variants such as genes or pathways is a common approach in genetic association settings to lower the multiple testing burden, aggregate small effects, and improve interpretations of results. Instead of performing inference with only a single outcome, utilizing multiple outcomes can increase statistical power by aggregating information across multiple correlated phenotypes. Simulations show that the proposed strategy can offer significant power gains over a single outcome approach. We apply the proposed test to the investigation that motivated this study, a search for the genes that perturb risks of bone fractures and falls in the UK Biobank.
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Affiliation(s)
- Jaihee Choi
- Department of Statistics, Rice University, Houston, Texas, USA
| | - Zhichao Xu
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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7
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Sun R, Wei LJ. Is Pertuzumab Plus Trastuzumab Without Chemotherapy a Reasonable Treatment for ERBB2-Positive Metastatic Breast Cancer? JAMA Oncol 2024; 10:537. [PMID: 38329744 DOI: 10.1001/jamaoncol.2023.6957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Affiliation(s)
- Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston
| | - Lee-Jen Wei
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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Sun R, Li T, Ren WH. [Role of liver sinusoidal endothelial cell damage in the developmental process of hepatic sinusoidal obstruction syndrome: a focus on the research progress of immune inflammatory mechanisms]. Zhonghua Gan Zang Bing Za Zhi 2024; 32:279-283. [PMID: 38584115 DOI: 10.3760/cma.j.cn501113-20231129-00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Hepatic sinusoidal obstruction syndrome (HSOS) is a type of secondary vascular disease of the liver that is mainly associated with the ingestion of pyrrole alkaloids (PAs) and hematopoietic stem cell transplantation (HSCT) treatment, resulting in severe liver dysfunction, multiple organ failure, and even death. Hepatic sinusoidal dilatation and obstruction, hepatocyte coagulative necrosis, and hepatic lobular inflammation are the main pathological manifestations of HSOS. The key initiating process for the pathogenesis of HSOS is damage to liver sinusoidal endothelial cells (LSECs). Currently, it is believed that LSECs are damaged by the involvement of multiple etiologies and mechanisms, and secondary coagulation and fibrinolysis disorders, oxidative stress, and inflammatory responses are the occurrence contributors to HSOS; however, the mechanism has not been fully elucidated. Therefore, the role of immune-inflammatory mechanisms has received increasing attention in LSEC damage. This article provides an overview of the epidemiology, etiology, and pathological changes of HSOS and reviews the physiological functions, common etiological damage mechanisms, and the key role of LSEC damage in the pathogenesis of HSOS, with a special focus on the role and research progress of immune-inflammatory mechanisms for LSEC damage in recent years. Furthermore, we believe that in-depth study and elucidation of the role of immune-inflammatory mechanisms in LSEC damage and the pathogenesis of HSOS and diagnosis will provide feasible research and development ideas for the screening and identification of new markers and drug treatment targets for HSOS.
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Affiliation(s)
- R Sun
- Department of Infectious Diseases, Shandong Provincial Hospital, Shandong University, Jinan 250021, China
| | - T Li
- Department of Infectious Diseases, Shandong Provincial Hospital, Shandong University, Jinan 250021, China
| | - W H Ren
- Department of Infectious Diseases, Shandong Provincial Hospital, Shandong University, Jinan 250021, China
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9
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Zhu H, Choi J, Kui N, Yang T, Wei P, Li D, Sun R. Identification of Pancreatic Cancer Germline Risk Variants With Effects That Are Modified by Smoking. JCO Precis Oncol 2024; 8:e2300355. [PMID: 38564682 DOI: 10.1200/po.23.00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 12/08/2023] [Accepted: 02/08/2024] [Indexed: 04/04/2024] Open
Abstract
PURPOSE Pancreatic cancer (PC) is a deadly disease most often diagnosed in late stages. Identification of high-risk subjects could both contribute to preventative measures and help diagnose the disease at earlier timepoints. However, known risk factors, assessed independently, are currently insufficient for accurately stratifying patients. We use large-scale data from the UK Biobank (UKB) to identify genetic variant-smoking interaction effects and show their importance in risk assessment. METHODS We draw data from 15,086,830 genetic variants and 315,512 individuals in the UKB. There are 765 cases of PC. Crucially, robust resampling corrections are used to overcome well-known challenges in hypothesis testing for interactions. Replication analysis is conducted in two independent cohorts totaling 793 cases and 570 controls. Integration of functional annotation data and construction of polygenic risk scores (PRS) demonstrate the additional insight provided by interaction effects. RESULTS We identify the genome-wide significant variant rs77196339 on chromosome 2 (per minor allele odds ratio in never-smokers, 2.31 [95% CI, 1.69 to 3.15]; per minor allele odds ratio in ever-smokers, 0.53 [95% CI, 0.30 to 0.91]; P = 3.54 × 10-8) as well as eight other loci with suggestive evidence of interaction effects (P < 5 × 10-6). The rs77196339 region association is validated (P < .05) in the replication sample. PRS incorporating interaction effects show improved discriminatory ability over PRS of main effects alone. CONCLUSION This study of genome-wide germline variants identified smoking to modify the effect of rs77196339 on PC risk. Interactions between known risk factors can provide critical information for identifying high-risk subjects, given the relative inadequacy of models considering only main effects, as demonstrated in PRS. Further studies are necessary to advance toward comprehensive risk prediction approaches for PC.
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Affiliation(s)
- Huili Zhu
- Section of Hematology and Oncology, Department of Medicine, Baylor College of Medicine, Houston, TX
| | - Jaihee Choi
- Department of Statistics, Rice University, Houston, TX
| | - Naishu Kui
- Department of Biostatistics, University of Texas School of Public Health, Houston, TX
| | - Tianzhong Yang
- Division of Biostatistics and Health Data Science, School of Public Health, University of Minnesota, Minneapolis, MN
| | - Peng Wei
- Department of Biostatistics, Division of Basic Science, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- Department of Biostatistics, Division of Basic Science, The University of Texas MD Anderson Cancer Center, Houston, TX
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10
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Li Y, Xiao X, Li J, Han Y, Cheng C, Fernandes GF, Slewitzke SE, Rosenberg SM, Zhu M, Byun J, Bossé Y, McKay JD, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeböller H, Wichmann HE, Christiani DC, Rennert G, Arnold SM, Goodman GE, Field JK, Davies MP, Shete S, Marchand LL, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Sun R, Zienolddiny S, Grankvist K, Johansson M, Caporaso NE, Cox A, Hong YC, Lazarus P, Schabath MB, Aldrich MC, Schwartz AG, Gorlov I, Purrington KS, Yang P, Liu Y, Bailey-Wilson JE, Pinney SM, Mandal D, Willey JC, Gaba C, Brennan P, Xia J, Shen H, Amos CI. Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies. Cancer Epidemiol Biomarkers Prev 2024; 33:389-399. [PMID: 38180474 PMCID: PMC10905670 DOI: 10.1158/1055-9965.epi-23-0613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 08/03/2023] [Accepted: 01/03/2024] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Clinical, molecular, and genetic epidemiology studies displayed remarkable differences between ever- and never-smoking lung cancer. METHODS We conducted a stratified multi-population (European, East Asian, and African descent) association study on 44,823 ever-smokers and 20,074 never-smokers to identify novel variants that were missed in the non-stratified analysis. Functional analysis including expression quantitative trait loci (eQTL) colocalization and DNA damage assays, and annotation studies were conducted to evaluate the functional roles of the variants. We further evaluated the impact of smoking quantity on lung cancer risk for the variants associated with ever-smoking lung cancer. RESULTS Five novel independent loci, GABRA4, intergenic region 12q24.33, LRRC4C, LINC01088, and LCNL1 were identified with the association at two or three populations (P < 5 × 10-8). Further functional analysis provided multiple lines of evidence suggesting the variants affect lung cancer risk through excessive DNA damage (GABRA4) or cis-regulation of gene expression (LCNL1). The risk of variants from 12 independent regions, including the well-known CHRNA5, associated with ever-smoking lung cancer was evaluated for never-smokers, light-smokers (packyear ≤ 20), and moderate-to-heavy-smokers (packyear > 20). Different risk patterns were observed for the variants among the different groups by smoking behavior. CONCLUSIONS We identified novel variants associated with lung cancer in only ever- or never-smoking groups that were missed by prior main-effect association studies. IMPACT Our study highlights the genetic heterogeneity between ever- and never-smoking lung cancer and provides etiologic insights into the complicated genetic architecture of this deadly cancer.
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Affiliation(s)
- Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Jianrong Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Chao Cheng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Gail F. Fernandes
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Shannon E. Slewitzke
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Susan M. Rosenberg
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Meng Zhu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Yohan Bossé
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Canada
| | - James D. McKay
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Stephen Lam
- Department of Integrative Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Stig E. Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria T. Landi
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, World Health Organization, Lyon, France
| | - Angela Risch
- Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany
- University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | | | - David C. Christiani
- Departments of Environmental Health and Epidemiology, Harvard TH Chan School of Public Health, Boston, Massachusetts
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | | | | | - John K. Field
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael P.A. Davies
- Institute of Translational Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sanjay Shete
- Department of Biostatistics, The University of Texas, MD Anderson Cancer Center, Houston, Texas
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Loïc Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | - Rayjean J. Hung
- Luenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Canada
| | - Angeline S. Andrew
- Departments of Epidemiology and Community and Family Medicine, Dartmouth College, Hanover, New Hampshire
| | | | - Ryan Sun
- Department of Biostatistics, The University of Texas, MD Anderson Cancer Center, Houston, Texas
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Neil E. Caporaso
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, Maryland
| | - Angela Cox
- Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of South Korea
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Matthew B. Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Melinda C. Aldrich
- Department of Thoracic Surgery, Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ann G. Schwartz
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Karmanos Cancer Institute, Detroit, Michigan
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Kristen S. Purrington
- Department of Oncology, Wayne State University School of Medicine, Detroit, Michigan
- Karmanos Cancer Institute, Detroit, Michigan
| | - Ping Yang
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota
| | - Yanhong Liu
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | | | - Susan M. Pinney
- University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Diptasri Mandal
- Louisiana State University Health Sciences Center, New Orleans, Louisiana
| | - James C. Willey
- College of Medicine and Life Sciences, University of Toledo, Toledo, Ohio
| | - Colette Gaba
- The University of Toledo College of Medicine, Toledo, Ohio
| | - Paul Brennan
- Institut universitaire de cardiologie et de pneumologie de Québec, Department of Molecular Medicine, Laval University, Quebec City, Canada
| | - Jun Xia
- Creighton University School of Medicine, Omaha, Nebraska
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, P.R. China
| | - Christopher I. Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
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11
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Hassan MM, Li D, Han Y, Byun J, Hatia RI, Long E, Choi J, Kelley RK, Cleary SP, Lok AS, Bracci P, Permuth JB, Bucur R, Yuan JM, Singal AG, Jalal PK, Ghobrial RM, Santella RM, Kono Y, Shah DP, Nguyen MH, Liu G, Parikh ND, Kim R, Wu HC, El-Serag H, Chang P, Li Y, Chun YS, Lee SS, Gu J, Hawk E, Sun R, Huff C, Rashid A, Amin HM, Beretta L, Wolff RA, Antwi SO, Patt Y, Hwang LY, Klein AP, Zhang K, Schmidt MA, White DL, Goss JA, Khaderi SA, Marrero JA, Cigarroa FG, Shah PK, Kaseb AO, Roberts LR, Amos CI. Genome-wide association study identifies high-impact susceptibility loci for HCC in North America. Hepatology 2024:01515467-990000000-00763. [PMID: 38381705 DOI: 10.1097/hep.0000000000000800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 12/18/2023] [Indexed: 02/23/2024]
Abstract
BACKGROUND AND AIMS Despite the substantial impact of environmental factors, individuals with a family history of liver cancer have an increased risk for HCC. However, genetic factors have not been studied systematically by genome-wide approaches in large numbers of individuals from European descent populations (EDP). APPROACH AND RESULTS We conducted a 2-stage genome-wide association study (GWAS) on HCC not affected by HBV infections. A total of 1872 HCC cases and 2907 controls were included in the discovery stage, and 1200 HCC cases and 1832 controls in the validation. We analyzed the discovery and validation samples separately and then conducted a meta-analysis. All analyses were conducted in the presence and absence of HCV. The liability-scale heritability was 24.4% for overall HCC. Five regions with significant ORs (95% CI) were identified for nonviral HCC: 3p22.1, MOBP , rs9842969, (0.51, [0.40-0.65]); 5p15.33, TERT , rs2242652, (0.70, (0.62-0.79]); 19q13.11, TM6SF2 , rs58542926, (1.49, [1.29-1.72]); 19p13.11 MAU2 , rs58489806, (1.53, (1.33-1.75]); and 22q13.31, PNPLA3 , rs738409, (1.66, [1.51-1.83]). One region was identified for HCV-induced HCC: 6p21.31, human leukocyte antigen DQ beta 1, rs9275224, (0.79, [0.74-0.84]). A combination of homozygous variants of PNPLA3 and TERT showing a 6.5-fold higher risk for nonviral-related HCC compared to individuals lacking these genotypes. This observation suggests that gene-gene interactions may identify individuals at elevated risk for developing HCC. CONCLUSIONS Our GWAS highlights novel genetic susceptibility of nonviral HCC among European descent populations from North America with substantial heritability. Selected genetic influences were observed for HCV-positive HCC. Our findings indicate the importance of genetic susceptibility to HCC development.
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Affiliation(s)
- Manal M Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Donghui Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
| | - Rikita I Hatia
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Erping Long
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Robin Kate Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Sean P Cleary
- Division of Hepatobiliary and Pancreas Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Anna S Lok
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Paige Bracci
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Jennifer B Permuth
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida, USA
- Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Roxana Bucur
- Princess Margaret Cancer Center and Toronto General Hospital, University Health Network, Toronto, Ontario, Canada
| | - Jian-Min Yuan
- Cancer Epidemiology and Prevention Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Amit G Singal
- Division of Digestive and Liver Diseases, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Prasun K Jalal
- Department of Gastroenterology and Hepatology, Baylor College of Medicine, Houston, Texas, USA
| | - R Mark Ghobrial
- J.C. Walter Jr. Transplant Center, Houston Methodist Hospital, Houston, Texas, USA
| | - Regina M Santella
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City, New York, USA
| | - Yuko Kono
- Division of Gastroenterology and Hepatology, University of California San Diego, San Diego, California, USA
| | - Dimpy P Shah
- Mays Cancer Center, The University of Texas Health Science Center San Antonio MD Anderson, San Antonio, Texas, USA
| | - Mindie H Nguyen
- Division of Gastroenterology and Hepatology, Department of Epidemiology and Population Health, Stanford University Medical Center, Palo Alto, California, USA
| | - Geoffrey Liu
- Medical Oncology and Hematology, Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
| | - Neehar D Parikh
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Richard Kim
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, Florida, USA
| | - Hui-Chen Wu
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York City, New York, USA
| | - Hashem El-Serag
- Department of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Ping Chang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yanan Li
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yun Shin Chun
- Division of Surgery, Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sunyoung S Lee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jian Gu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ernest Hawk
- Division of Cancer Prevention and Population Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Chad Huff
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hesham M Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laura Beretta
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samuel O Antwi
- Division of Epidemiology, Department of Quantitative Health Sciences, Mayo Clinic, Jacksonville, Florida, USA
| | - Yehuda Patt
- Division of Hematology/Oncology, Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Lu-Yu Hwang
- Department of Epidemiology, Human Genetics, and Environment Science, The University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Alison P Klein
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland, USA
| | - Karen Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Mikayla A Schmidt
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Donna L White
- Sections of Gastroenterology and Hepatology and Health Services Research, Baylor College of Medicine, Houston, Texas, USA
| | - John A Goss
- Division of Abdominal Transplantation, Michael E. DeBakey School of Medicine, Baylor College of Medicine, Houston, Texas, USA
| | - Saira A Khaderi
- Division of Abdominal Transplantation, Baylor College of Medicine, Houston, Texas, USA
| | - Jorge A Marrero
- Division of Digestive and Liver Diseases, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Francisco G Cigarroa
- Transplant Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Pankil K Shah
- Mays Cancer Center, The University of Texas Health Science Center San Antonio MD Anderson, San Antonio, Texas, USA
| | - Ahmed O Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, USA
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas, USA
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12
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Hsu EJ, Lin TA, Dabush DR, McCaw Z, Koong A, Lin C, Abi Jaoude J, Patel R, Kouzy R, El Alam MB, Noticewala S, Yang Y, Sherry AD, Fuller CD, Thomas CR, Tang C, Msaouel P, Das P, Huang B, Tian L, Sun R, Lee JJ, Meirson T, Ludmir EB. Association of differential censoring with survival and suboptimal control arms among oncology clinical trials. J Natl Cancer Inst 2024:djae028. [PMID: 38331394 DOI: 10.1093/jnci/djae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/14/2024] [Accepted: 02/01/2024] [Indexed: 02/10/2024] Open
Abstract
Differential censoring (DC), referring to censoring imbalance between treatment arms, may bias the interpretation of survival outcomes in clinical trials. In 146 phase 3 oncology trials with statistically significant time-to-event surrogate primary endpoints (PEPs), we evaluated the association between DC in the surrogate PEP, control arm adequacy, and the subsequent statistical significance of OS results. Twenty-four (16%) trials exhibited DC favoring the control arm (ConDC), while 15 (10%) exhibited experimental arm DC (ExpDC). Positive OS was more common in ConDC trials (63%) than trials without DC (37%) or with ExpDC (47%; odds ratio [OR] 2.64, 95% CI 1.10-7.20; P=.04). ConDC trials more frequently used suboptimal control arms (46%) compared to 20% without DC and 13% with ExpDC (OR 3.60, 95% CI 1.29-10.0; P=.007). The presence of ConDC in trials with surrogate PEPs, especially in those with OS conversion, may indicate an inadequate control arm and should be examined and explained.
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Affiliation(s)
- Eric J Hsu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Timothy A Lin
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dor R Dabush
- Davidoff Cancer Center, Rabin Medical Center, Petah-Tikva, Israel
| | - Zachary McCaw
- Department of Biostatistics, The University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alex Koong
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christine Lin
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joseph Abi Jaoude
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roshal Patel
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ramez Kouzy
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Molly B El Alam
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sonal Noticewala
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yumeng Yang
- School of Bioinformatics, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Alexander D Sherry
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clifton D Fuller
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Charles R Thomas
- Radiation Oncology, Dartmouth Cancer Center, Geisel School of Medicine, Lebanon, NH, USA
| | - Chad Tang
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Prajnan Das
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Lu Tian
- Department of Health Research and Policy, Stanford University, Stanford, CA, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - J Jack Lee
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tomer Meirson
- Davidoff Cancer Center, Rabin Medical Center, Petah-Tikva, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ethan B Ludmir
- Department of Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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13
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Sun R, Liu J, Wei LJ. Assessing Predictability of Pathologic Lymph Node Regression for Recurrence and Survival in Esophageal Adenocarcinoma. J Clin Oncol 2024; 42:366. [PMID: 37988644 DOI: 10.1200/jco.23.01785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/02/2023] [Indexed: 11/23/2023] Open
Affiliation(s)
- Ryan Sun
- Ryan Sun, PhD, Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX; Jingyi Liu, PhD, Eli Lilly and Company, Indianapolis, IN; and Lee-Jen Wei, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Jingyi Liu
- Ryan Sun, PhD, Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX; Jingyi Liu, PhD, Eli Lilly and Company, Indianapolis, IN; and Lee-Jen Wei, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lee-Jen Wei
- Ryan Sun, PhD, Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX; Jingyi Liu, PhD, Eli Lilly and Company, Indianapolis, IN; and Lee-Jen Wei, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
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14
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Mamlouk O, Strati P, Feng L, Sun R, Ayers A, Steiner RE, Nair R, Flowers C, Ramdial JL, Saini N, Srour SA, Champlin RE, Kebriaei P, Nastoupil LJ, Rodriguez MA, Shpall EJ, Nieto Y, Westin J, Neelapu SS, Mandayam S, Ahmed S. Real-world analysis of safety and efficacy of CAR T-cell therapy in lymphoma patients with decreased kidney function. Br J Haematol 2024; 204:e11-e16. [PMID: 37822075 DOI: 10.1111/bjh.19152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 09/29/2023] [Indexed: 10/13/2023]
Affiliation(s)
- Omar Mamlouk
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Paolo Strati
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lei Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Amy Ayers
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Raphael E Steiner
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ranjit Nair
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Christopher Flowers
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jeremy L Ramdial
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Neeraj Saini
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Samer A Srour
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard E Champlin
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Partow Kebriaei
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Loretta J Nastoupil
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Maria A Rodriguez
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Yago Nieto
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jason Westin
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sattva S Neelapu
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sreedhar Mandayam
- Section of Nephrology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sairah Ahmed
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Department of Stem Cell Transplantation & Cellular Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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15
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Sun R, Seibert TM, Wei LJ. Predictability of Olfactory Neuroblastoma Staging Systems. JAMA Otolaryngol Head Neck Surg 2024; 150:84-85. [PMID: 37971764 DOI: 10.1001/jamaoto.2023.3634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Affiliation(s)
- Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston
| | - Tyler M Seibert
- Department of Radiation Medicine, University of California San Diego, La Jolla
- Department of Radiology, University of California San Diego, La Jolla
- Department of Bioengineering, University of California San Diego, La Jolla
| | - Lee-Jen Wei
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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16
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Sun R, Shi A, Lin X. Differences in set-based tests for sparse alternatives when testing sets of outcomes compared to sets of explanatory factors in genetic association studies. Biostatistics 2023; 25:171-187. [PMID: 36000269 PMCID: PMC10724113 DOI: 10.1093/biostatistics/kxac036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 07/15/2022] [Accepted: 08/07/2022] [Indexed: 01/11/2023] Open
Abstract
Set-based association tests are widely popular in genetic association settings for their ability to aggregate weak signals and reduce multiple testing burdens. In particular, a class of set-based tests including the Higher Criticism, Berk-Jones, and other statistics have recently been popularized for reaching a so-called detection boundary when signals are rare and weak. Such tests have been applied in two subtly different settings: (a) associating a genetic variant set with a single phenotype and (b) associating a single genetic variant with a phenotype set. A significant issue in practice is the choice of test, especially when deciding between innovated and generalized type methods for detection boundary tests. Conflicting guidance is present in the literature. This work describes how correlation structures generate marked differences in relative operating characteristics for settings (a) and (b). The implications for study design are significant. We also develop novel power bounds that facilitate the aforementioned calculations and allow for analysis of individual testing settings. In more concrete terms, our investigation is motivated by translational expression quantitative trait loci (eQTL) studies in lung cancer. These studies involve both testing for groups of variants associated with a single gene expression (multiple explanatory factors) and testing whether a single variant is associated with a group of gene expressions (multiple outcomes). Results are supported by a collection of simulation studies and illustrated through lung cancer eQTL examples.
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Affiliation(s)
- Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Andy Shi
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02215, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02215, USA
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17
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Hildreth AD, Padilla ET, Gupta M, Wong YY, Sun R, Legala AR, O'Sullivan TE. Adipose cDC1s contribute to obesity-associated inflammation through STING-dependent IL-12 production. Nat Metab 2023; 5:2237-2252. [PMID: 37996702 DOI: 10.1038/s42255-023-00934-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 10/18/2023] [Indexed: 11/25/2023]
Abstract
Obesity is associated with chronic low-grade white adipose tissue (WAT) inflammation that can contribute to the development of insulin resistance in mammals. Previous studies have identified interleukin (IL)-12 as a critical upstream regulator of WAT inflammation and metabolic dysfunction during obesity. However, the cell types and mechanisms that initiate WAT IL-12 production remain unclear. Here we show that conventional type 1 dendritic cells (cDC1s) are the cellular source of WAT IL-12 during obesity through analysis of mouse and human WAT single-cell transcriptomic datasets, IL-12 reporter mice and IL-12p70 protein levels by enzyme-linked immunosorbent assay. We demonstrate that cDC1s contribute to obesity-associated inflammation by increasing group 1 innate lymphocyte interferon-γ production and inflammatory macrophage accumulation. Inducible depletion of cDC1s increased WAT insulin sensitivity and systemic glucose tolerance during diet-induced obesity. Mechanistically, endocytosis of apoptotic bodies containing self-DNA by WAT cDC1s drives stimulator of interferon genes (STING)-dependent IL-12 production. Together, these results suggest that WAT cDC1s act as critical regulators of adipose tissue inflammation and metabolic dysfunction during obesity.
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Affiliation(s)
- Andrew D Hildreth
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Eddie T Padilla
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Meha Gupta
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Yung Yu Wong
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ryan Sun
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Akshara R Legala
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Timothy E O'Sullivan
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA.
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18
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Sun R, Wei LJ. Efficacy, Safety, and Analysis Issues in a Study of Intraoperative Hyperthermic Intraperitoneal Chemotherapy for Locally Advanced Colon Cancer. JAMA Surg 2023; 158:1357-1358. [PMID: 37585200 DOI: 10.1001/jamasurg.2023.3483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Affiliation(s)
- Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston
| | - Lee-Jen Wei
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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19
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Chu F, Cao J, Liu J, Yang H, Davis TJ, Kuang SQ, Cheng X, Zhang Z, Karri S, Vien LT, Bover L, Sun R, Vega F, Green M, Davis RE, Neelapu SS. Chimeric antigen receptor T cells to target CD79b in B-cell lymphomas. J Immunother Cancer 2023; 11:e007515. [PMID: 38007239 PMCID: PMC10680003 DOI: 10.1136/jitc-2023-007515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2023] [Indexed: 11/27/2023] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR) T cells targeting CD19 mediate potent and durable effects in B-cell malignancies. However, antigen loss or downregulation is a frequent cause of resistance. Here, we report development of a novel CAR T-cell therapy product to target CD79b, a pan B-cell antigen, widely expressed in most B-cell lymphomas. METHODS We generated a novel anti-CD79b monoclonal antibody by hybridoma method. The specificity of the antibody was determined by testing against isogenic cell lines with human CD79b knock-in or knock-out. A single-chain variable fragment derived from the monoclonal antibody was used to make a panel of CD79b-targeting CAR molecules containing various hinge, transmembrane, and co-stimulatory domains. These were lentivirally transduced into primary T cells and tested for antitumor activity in in vitro and in vivo B-cell lymphoma models. RESULTS We found that the novel anti-CD79b monoclonal antibody was highly specific and bound only to human CD79b and no other cell surface protein. In testing the various CD79b-targeting CAR molecules, superior antitumor efficacy in vitro and in vivo was found for a CAR consisting CD8α hinge and transmembrane domains, an OX40 co-stimulatory domain, and a CD3ζ signaling domain. This CD79b CAR specifically recognized human CD79b-expressing lymphoma cell lines but not CD79b knock-out cell lines. CD79b CAR T cells, generated from T cells from either healthy donors or patients with lymphoma, proliferated, produced cytokines, degranulated, and exhibited robust cytotoxic activity in vitro against CD19+ and CD19- lymphoma cell lines and patient-derived lymphoma tumors relapsing after prior CD19 CAR T-cell therapy. Furthermore, CD79b CAR T cells were highly efficient at eradicating pre-established lymphoma tumors in vivo in three aggressive lymphoma xenograft models, including two cell line-derived xenografts and one patient-derived xenograft. Notably, these CAR T cells did not demonstrate any significant tonic signaling activity or markers of exhaustion. CONCLUSION Our results indicated that this novel CD79b CAR T-cell therapy product has robust antitumor activity against B-cell lymphomas. These results supported initiation of a phase 1 clinical trial to evaluate this product in patients with relapsed or refractory B-cell lymphomas.
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Affiliation(s)
- Fuliang Chu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jingjing Cao
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jingwei Liu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Haopeng Yang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Timothy J Davis
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Shao-Qing Kuang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Xiaoyun Cheng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zheng Zhang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Swathi Karri
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Long T Vien
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Laura Bover
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Michael Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Richard Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sattva S Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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20
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Strati P, Jallouk A, Deng Q, Li X, Feng L, Sun R, Adkins S, Johncy S, Cain T, Steiner RE, Ahmed S, Chihara D, Fayad LE, Iyer SP, Horowitz S, Nastoupil LJ, Nair R, Hassan A, Daoud TE, Hawkins M, Rodriguez MA, Shpall EJ, Ramdial JL, Kebriaei P, Hong DS, Westin JR, Neelapu SS, Green MR. A phase 1 study of prophylactic anakinra to mitigate ICANS in patients with large B-cell lymphoma. Blood Adv 2023; 7:6785-6789. [PMID: 37389847 PMCID: PMC10692290 DOI: 10.1182/bloodadvances.2023010653] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023] Open
Affiliation(s)
- Paolo Strati
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Andrew Jallouk
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Qing Deng
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xubin Li
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lei Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sherry Adkins
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Swapna Johncy
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Taylor Cain
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Raphael E. Steiner
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Dai Chihara
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luis E. Fayad
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Swaminathan P. Iyer
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sandra Horowitz
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Loretta J. Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ranjit Nair
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ahmed Hassan
- Department of Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Taher E. Daoud
- Department of Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Misha Hawkins
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Maria A. Rodriguez
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Elizabeth J. Shpall
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jeremy L. Ramdial
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Partow Kebriaei
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David S. Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason R. Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sattva S. Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael R. Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
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21
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Li X, Chen H, Selvaraj MS, Van Buren E, Zhou H, Wang Y, Sun R, McCaw ZR, Yu Z, Arnett DK, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Carson AP, Carlson JC, Chami N, Chen YDI, Curran JE, de Vries PS, Fornage M, Franceschini N, Freedman BI, Gu C, Heard-Costa NL, He J, Hou L, Hung YJ, Irvin MR, Kaplan RC, Kardia SL, Kelly T, Konigsberg I, Kooperberg C, Kral BG, Li C, Loos RJ, Mahaney MC, Martin LW, Mathias RA, Minster RL, Mitchell BD, Montasser ME, Morrison AC, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Rich SS, Sitlani CM, Smith JA, Taylor KD, Tiwari H, Vasan RS, Wang Z, Yanek LR, Yu B, Rice KM, Rotter JI, Peloso GM, Natarajan P, Li Z, Liu Z, Lin X. A statistical framework for powerful multi-trait rare variant analysis in large-scale whole-genome sequencing studies. bioRxiv 2023:2023.10.30.564764. [PMID: 37961350 PMCID: PMC10634938 DOI: 10.1101/2023.10.30.564764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Large-scale whole-genome sequencing (WGS) studies have improved our understanding of the contributions of coding and noncoding rare variants to complex human traits. Leveraging association effect sizes across multiple traits in WGS rare variant association analysis can improve statistical power over single-trait analysis, and also detect pleiotropic genes and regions. Existing multi-trait methods have limited ability to perform rare variant analysis of large-scale WGS data. We propose MultiSTAAR, a statistical framework and computationally-scalable analytical pipeline for functionally-informed multi-trait rare variant analysis in large-scale WGS studies. MultiSTAAR accounts for relatedness, population structure and correlation among phenotypes by jointly analyzing multiple traits, and further empowers rare variant association analysis by incorporating multiple functional annotations. We applied MultiSTAAR to jointly analyze three lipid traits (low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides) in 61,861 multi-ethnic samples from the Trans-Omics for Precision Medicine (TOPMed) Program. We discovered new associations with lipid traits missed by single-trait analysis, including rare variants within an enhancer of NIPSNAP3A and an intergenic region on chromosome 1.
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Affiliation(s)
- Xihao Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Margaret Sunitha Selvaraj
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Eric Van Buren
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yuxuan Wang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zachary R. McCaw
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhi Yu
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Donna K. Arnett
- Provost Office, University of South Carolina, Columbia, SC, USA
| | - Joshua C. Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W. Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A. Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E. Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - April P. Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Jenna C. Carlson
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Paul S. de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Barry I. Freedman
- Department of Internal Medicine, Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Charles Gu
- Division of Biology & Biomedical Sciences, Washington University School of Medicine, St. Louis, MO, USA
| | - Nancy L. Heard-Costa
- Department of Neurology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- Framingham Heart Study, Framingham, MA, USA
| | - Jiang He
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University, Chicago, IL, USA
| | - Yi-Jen Hung
- Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Robert C. Kaplan
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sharon L.R. Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Tanika Kelly
- Department of Medicine, Division of Nephrology, University of Illinois Chicago, Chicago, IL, USA
| | - Iain Konigsberg
- Department of Biomedical Informatics, University of Colorado, Aurora, CO, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian G. Kral
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Changwei Li
- Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane University Translational Science Institute, New Orleans, LA, USA
| | - Ruth J.F. Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Michael C. Mahaney
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Lisa W. Martin
- George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Rasika A. Mathias
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ryan L. Minster
- Department of Human Genetics and Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Braxton D. Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - May E. Montasser
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C. Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Patricia A. Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M. Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Alexander P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Departments of Epidemiology, University of Washington, Seattle, WA, USA
| | - Stephen S. Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Colleen M. Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Hemant Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ramachandran S. Vasan
- Framingham Heart Study, Framingham, MA, USA
- Department of Quantitative and Qualitative Health Sciences, UT Health San Antonio School of Public Health, San Antonia, TX, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lisa R. Yanek
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bing Yu
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | | | - Kenneth M. Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Gina M. Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zhonghua Liu
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Xihong Lin
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Statistics, Harvard University, Cambridge, MA, USA
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22
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Lai C, Sun R, Zhang W, Peng Y. Gastrointestinal: A case of IgG4-related disease involving intestinal tract and orbital cavity. J Gastroenterol Hepatol 2023; 38:1865. [PMID: 37340618 DOI: 10.1111/jgh.16254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 06/22/2023]
Affiliation(s)
- C Lai
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment and Standardization, Xiangya Hospital of Central South University, Changsha, China
| | - R Sun
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment and Standardization, Xiangya Hospital of Central South University, Changsha, China
| | - W Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Xiangya Hospital Central South University, Changsha, China
- International Joint Research Center of Minimally Invasive Endoscopic Technology Equipment and Standardization, Xiangya Hospital of Central South University, Changsha, China
| | - Y Peng
- Department of Gastroenterology, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Artificial Intelligence Computer Aided Diagnosis and Treatment for Digestive Disease, Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Organ Fibrosis, Changsha, China
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Sherry AD, Msaouel P, McCaw ZR, Abi Jaoude J, Hsu EJ, Kouzy R, Patel R, Yang Y, Lin TA, Taniguchi CM, Rödel C, Fokas E, Tang C, Fuller CD, Minsky B, Meirson T, Sun R, Ludmir EB. Prevalence and implications of significance testing for baseline covariate imbalance in randomised cancer clinical trials: The Table 1 Fallacy. Eur J Cancer 2023; 194:113357. [PMID: 37827064 DOI: 10.1016/j.ejca.2023.113357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/18/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND The 'Table 1 Fallacy' refers to the unsound use of significance testing for comparing the distributions of baseline variables between randomised groups to draw erroneous conclusions about balance or imbalance. We performed a cross-sectional study of the Table 1 Fallacy in phase III oncology trials. METHODS From ClinicalTrials.gov, 1877 randomised trials were screened. Multivariable logistic regressions evaluated predictors of the Table 1 Fallacy. RESULTS A total of 765 randomised controlled trials involving 553,405 patients were analysed. The Table 1 Fallacy was observed in 25% of trials (188 of 765), with 3% of comparisons deemed significant (59 of 2353), approximating the typical 5% type I error assertion probability. Application of trial-level multiplicity corrections reduced the rate of significant findings to 0.3% (six of 2345 tests). Factors associated with lower odds of the Table 1 Fallacy included industry sponsorship (adjusted odds ratio [aOR] 0.29, 95% confidence interval [CI] 0.18-0.47; multiplicity-corrected P < 0.0001), larger trial size (≥795 versus <280 patients; aOR 0.32, 95% CI 0.19-0.53; multiplicity-corrected P = 0.0008), and publication in a European versus American journal (aOR 0.06, 95% CI 0.03-0.13; multiplicity-corrected P < 0.0001). CONCLUSIONS This study highlights the persistence of the Table 1 Fallacy in contemporary oncology randomised controlled trials, with one of every four trials testing for baseline differences after randomisation. Significance testing is a suboptimal method for identifying unsound randomisation procedures and may encourage misleading inferences. Journal-level enforcement is a possible strategy to help mitigate this fallacy.
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Affiliation(s)
- Alexander D Sherry
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pavlos Msaouel
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Zachary R McCaw
- Insitro, South San Francisco, CA, USA; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joseph Abi Jaoude
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Radiation Oncology, Stanford University, Stanford, CA, USA
| | - Eric J Hsu
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ramez Kouzy
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roshal Patel
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Radiation Oncology, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - Yumeng Yang
- Department of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Timothy A Lin
- Department of Radiation Oncology and Molecular Radiation Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cullen M Taniguchi
- Department of Gastrointestinal Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Experimental Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Claus Rödel
- Department of Radiotherapy and Oncology, University of Frankfurt, Frankfurt, Germany; Frankfurt Cancer Institute, Frankfurt, Germany; German Cancer Research Center (DKFZ), Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt am Main, Frankfurt, Germany
| | - Emmanouil Fokas
- Department of Radiotherapy and Oncology, University of Frankfurt, Frankfurt, Germany; Frankfurt Cancer Institute, Frankfurt, Germany; German Cancer Research Center (DKFZ), Heidelberg, German Cancer Consortium (DKTK), Partner Site Frankfurt am Main, Frankfurt, Germany
| | - Chad Tang
- Department of Translational Molecular Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Genitourinary Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Clifton David Fuller
- Department of Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bruce Minsky
- Department of Gastrointestinal Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tomer Meirson
- Davidoff Cancer Center, Rabin Medical Center, Petach Tikva, Israel
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ethan B Ludmir
- Department of Gastrointestinal Radiation Oncology, Division of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Sun R, Sun D, Zhu L, Sun J. Regression analysis of general mixed recurrent event data. Lifetime Data Anal 2023; 29:807-822. [PMID: 37438585 DOI: 10.1007/s10985-023-09604-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 06/23/2023] [Indexed: 07/14/2023]
Abstract
In modern biomedical datasets, it is common for recurrent outcomes data to be collected in an incomplete manner. More specifically, information on recurrent events is routinely recorded as a mixture of recurrent event data, panel count data, and panel binary data; we refer to this structure as general mixed recurrent event data. Although the aforementioned data types are individually well-studied, there does not appear to exist an established approach for regression analysis of the three component combination. Often, ad-hoc measures such as imputation or discarding of data are used to homogenize records prior to the analysis, but such measures lead to obvious concerns regarding robustness, loss of efficiency, and other issues. This work proposes a maximum likelihood regression estimation procedure for the combination of general mixed recurrent event data and establishes the asymptotic properties of the proposed estimators. In addition, we generalize the approach to allow for the existence of terminal events, a common complicating feature in recurrent event analysis. Numerical studies and application to the Childhood Cancer Survivor Study suggest that the proposed procedures work well in practical situations.
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Affiliation(s)
- Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Dayu Sun
- Department of Biostatistics, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | | | - Jianguo Sun
- Department of Statistics, University of Missouri, Columbia, MO, USA
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25
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Sun R, Xi K, Song X, Yin W, Xi D, Shao Y, Gu W, Jiang J. The Effect of MDSC-Derived Exosomes Played in Esophageal Squamous Carcinoma Cells after Ionizing Radiation. Int J Radiat Oncol Biol Phys 2023; 117:e261. [PMID: 37785000 DOI: 10.1016/j.ijrobp.2023.06.1216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Radiotherapy is the main treatment for esophageal cancer. Previous studies have shown that radiotherapy not only kills tumor cells directly, but also reshapes the immune microenvironment of the tumor. It has been reported an increase in the recruitment of myeloid-derived suppressor cells (MDSC) can occur in tumor tissue after ionizing radiation. Exosomes are mediators of intercellular information exchange and are also involved in the regulation of the tumor microenvironment. In this study, we wanted to understand whether MDSC in esophageal cancer tissue are involved in the regulation of tumor cell response to ionizing radiation via exosomes. MATERIALS/METHODS KYSE-150 was used to construct a subcutaneous transplantation tumor model in nude mice. And then mice irradiated with 5 Gy×5fx and 0 Gy×5fx respectively. After irradiation, the spleens of the mice were used to isolate MDSC, and collect the cell supernatants to extract the exosomes. Based on the exosomes, we divided the experiment into three groups (control, exosomes, exosomes+radiation). Exosomes were injected into a nude mouse model of esophageal cancer via the tail vein or co-cultured with KYSE-150 cells. Mice were irradiated with a 5 Gy×5fx after completion of injection, and KYSE-150 cells were irradiated with a single dose 4 Gy. After radiation, KYSE-150 cells were used to detect cell cloning, apoptosis and cell cycle by flow cytometry, cell proliferation by CCK 8. XRCC4,XRCC5,XRCC6,γH2AX,ATM expression in cells and tumor tissue were measured by Western blot and RT-PCR. RESULTS The tumor volume was significantly reduced after 5 Gy x 5fx radiation. When exosomes co-cultured with KYSE-150 cells, decrease in apoptosis and increase in cell cloning and cell proliferation were found in the exosomes+radiation group and exosomes group after radiation when compared with the control group, with this change being more pronounced in the exosome+radiation group. The results of the cell cycle assay showed that after ionizing radiation, the proportion of cells in the G0/G1 phase was significantly lower, and the proportion of cells in the S and G2/M phases were significantly higher in the exosomes+radiation group and exosomes group when compared to the Control group. The protein and mRNA expression of XRCC4,XRCC5,XRCC6,γH2AX,ATM in cells were increased in exosomes+radiation group and exosomes group after radiation when compared with the control group, with this change being more obvious in the exosome+radiation group. After irradiation, tumor volumes were measured in nude mice and the results showed that exosomes+radiation group tumors were the largest in volume, while the control group regressed most significantly after irradiation. CONCLUSION MDSC-derived exosomes have a tumor growth-promoting effect in esophageal squamous carcinoma, which is enhanced by ionizing radiation, and this may be related to the accelerated repair of damage in tumor tissue after radiation.
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Affiliation(s)
- R Sun
- Department of Radiotherapy & Oncology, The Third Affiliated Hospital of Soochow University, Chang Zhou, China
| | - K Xi
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - X Song
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - W Yin
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - D Xi
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - Y Shao
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - W Gu
- Department of Oncology Radiotherapy, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
| | - J Jiang
- Department of Tumor Biological Treatment, the Third Affiliated Hospital of Soochow University, Changzhou, Jiangsu, China
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Antonoff MB, Kui N, Sun R, Deboever N, Hofstetter W, Mehran RJ, Morris VK, Rice DC, Swisher SG, Vaporciyan AA, Walsh GL, Rajaram R. Factors associated with receipt of pulmonary metastasectomy in patients with lung-limited metastatic colorectal cancer: Disparities in care and impact on overall survival. J Thorac Cardiovasc Surg 2023:S0022-5223(23)00766-3. [PMID: 37690624 DOI: 10.1016/j.jtcvs.2023.08.051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/21/2023] [Accepted: 08/28/2023] [Indexed: 09/12/2023]
Abstract
OBJECTIVES Pulmonary metastasectomy (PM) for colorectal cancer may provide respite from systemic therapy and prolonged disease-free intervals. We sought to identify factors associated with PM and to characterize the differential impact on overall survival for those offered lung resection. METHODS The National Cancer Database was queried for stage IV colorectal cancer patients with lung-limited metastatic disease between 2010 and 2016. Among patients who underwent primary tumor resection, those who underwent PM were compared with those who did not. Penalized regression with the least absolute selection and shrinkage operator was used to determine factors associated with receiving metastasectomy as well as overall survival. RESULTS In total, 867 (15.1%) patients underwent resection of both primary tumor and pulmonary metastases whereas 4864 (84.8%) had primary tumor resection alone. In unadjusted analyses, metastasectomy patents were younger, more often privately insured, more educated, and traveled farther to receive care (all P < .001). In multivariable analyses, younger age, traveling >25 miles, and care at high-volume hospitals were associated with PM (P < .01). In addition, primary site surgery without PM was associated with worse overall survival (hazard ratio, 1.35; confidence interval, 1.23-1.49), even after adjusting for patient, tumor, and hospital-related factors. CONCLUSIONS Patients who were older, who received care closer to home, and who were treated at low-volume hospitals were less likely to receive metastasectomy for lung-limited colorectal cancer after definitive resection of their primary tumor. Failure to receive PM resulted in worse overall survival, emphasizing the strong need for efforts to provide uniform, equitable care to all patients.
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Affiliation(s)
- Mara B Antonoff
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex.
| | - Naishu Kui
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Nathaniel Deboever
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Wayne Hofstetter
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Reza J Mehran
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Van K Morris
- Department of GI Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - David C Rice
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Stephen G Swisher
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Ara A Vaporciyan
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Garrett L Walsh
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex
| | - Ravi Rajaram
- Department of Thoracic and Cardiovascular Surgery, University of Texas MD Anderson Cancer Center, Houston, Tex
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Napolitano S, Parikh AR, Henry J, Parseghian CM, Willis J, Raghav KP, Morris VK, Johnson B, Kee BK, Dasari AN, Overman MJ, Luthra R, Drusbosky LM, Corcoran RB, Kopetz S, Sun R. Novel Clinical Tool to Estimate Risk of False-Negative KRAS Mutations in Circulating Tumor DNA Testing. JCO Precis Oncol 2023; 7:e2300228. [PMID: 37824798 DOI: 10.1200/po.23.00228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/29/2023] [Accepted: 08/03/2023] [Indexed: 10/14/2023] Open
Abstract
PURPOSE In metastatic colorectal cancer, the detection of RAS mutations by circulating tumor DNA (ctDNA) has emerged as a valid and noninvasive alternative approach to determining RAS status. However, some RAS mutations may be missed, that is, false negatives can occur, possibly compromising important treatment decisions. We propose a statistical model to assess the probability of false negatives when performing ctDNA testing for RAS. METHODS Cohorts of 172 subjects with tissue and multipanel ctDNA testing from MD Anderson Cancer Center and 146 subjects from Massachusetts General Hospital were collected. We developed a Bayesian model that uses observed frequencies of reference mutations (the maximum of APC and TP53) to provide information about the probability of KRAS false negatives. The model was alternatively trained on one cohort and tested on the other. All data were collected on Guardant assays. RESULTS The model suggests that negative KRAS findings are believable when the maximum of APC and TP53 frequencies is at least 8% (corresponding posterior probability of false negative <5%). Validation studies demonstrated the ability of our tool to discriminate between false-negative and true-negative subjects. Simulations further confirmed the utility of the proposed approach. CONCLUSION We suggest clinicians use the tool to more precisely quantify KRAS false-negative ctDNA results when at least one of the reference mutations (APC, TP53) is observed; usage may be especially important for subjects with a maximum reference frequency of <8%. Extension of the methodology to predict false negatives of other genes is possible. Additional reference genes can also be considered. Use of personal training data sets is supported. An open-source R Shiny application is available for public use.
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Affiliation(s)
- Stefania Napolitano
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Aparna R Parikh
- Department of Medicine, Division of Hematology and Oncology, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA
| | | | - Christine M Parseghian
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason Willis
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kanwal P Raghav
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Van K Morris
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Benny Johnson
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryan K Kee
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Arvind N Dasari
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Raja Luthra
- Department of Hematopathology, Division of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- Department of Biostatistics, Division of Basic Science, The University of Texas MD Anderson Cancer Center, Houston, TX
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Chamseddine S, Mohamed YI, Lee SS, Yao JC, Hu ZI, Tran Cao HS, Xiao L, Sun R, Morris JS, Hatia RI, Hassan M, Duda DG, Diab M, Mohamed A, Nassar A, Datar S, Amin HM, Kaseb AO. Clinical and Prognostic Biomarker Value of Blood-Circulating Inflammatory Cytokines in Hepatocellular Carcinoma. Oncology 2023; 101:730-737. [PMID: 37467732 PMCID: PMC10614568 DOI: 10.1159/000531870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/20/2023] [Indexed: 07/21/2023]
Abstract
INTRODUCTION Circulating inflammatory cytokines play critical roles in tumor-associated inflammation and immune responses. Recent data have suggested that several interleukins (ILs) mediate carcinogenesis in hepatocellular carcinoma (HCC). However, the predictive and prognostic value of circulating ILs is yet to be validated. Our study aimed to evaluate the association of the serum ILs with overall survival (OS) and clinicopathologic features in a large cohort of HCC patients. METHODS We prospectively collected data and serum samples from 767 HCC patients treated at the University of Texas MD Anderson Cancer Center between 2001 and 2014, with a median follow-up of 67.4 months (95% confidence interval [CI]: 52.5, 83.3). Biomarker association with OS was evaluated by the log-rank method. RESULTS The median OS in this cohort was 14.2 months (95% CI: 12, 16.1 months). Clinicopathologic features were more advanced, and OS was significantly inferior in patients with high circulating levels of IL1-R1, IL-6, IL-8, IL-10, IL-15, IL-16, and IL-18. CONCLUSION Our study shows that several serum IL levels are valid prognostic biomarker candidates and potential targets for therapy in HCC.
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Affiliation(s)
- Shadi Chamseddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA,
| | - Yehia I Mohamed
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Sunyoung S Lee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - James C Yao
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Zishuo Ian Hu
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Hop S Tran Cao
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Lianchun Xiao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jeffrey S Morris
- Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Rikita I Hatia
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Manal Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Dan G Duda
- Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Maria Diab
- Department of Hematology and Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia, USA
| | - Amr Mohamed
- Division of Hematology/Oncology, Department of Medicine, University Hospitals Cleveland Medical Center, Cleveland, Ohio, USA
| | - Ahmed Nassar
- Department of Surgery, Emory University, Atlanta, Georgia, USA
| | - Saumil Datar
- Department of Internal Medicine University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Hesham M Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Ahmed Omar Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Xiao Y, Sun Z, Sun R, Hou WY, Xu L, Lu JY. [Safety and feasibility of right colectomy via a transvaginal approach: early experience from a single center]. Zhonghua Wei Chang Wai Ke Za Zhi 2023; 26:588-594. [PMID: 37583013 DOI: 10.3760/cma.j.cn441530-20221020-00422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Objective: To investigate the safety and feasibility of performing right colectomy via a transvaginal approach. Methods: This was a retrospeltive cohort study. Data of 30 patients who had undergone transvaginal laparoscopic right colectomy (transvaginal group) and 23 women who had undergone laparoscopic right colectomy (laparoscopic group) from January 2019 to March 2022 in the Division of Colorectal Surgery, Department of General Surgery, Peking Union Medical College Hospital were collected retrospectively. The inclusion criteria for the transvaginal group were as follows: (1) post-menopausal woman; (2) transverse diameter of the tumor < 6 cm; and (3) diagnosis of benign polyps that were unresectable by endoscopy, mucinous tumors of the appendix, or confirmed right colon cancer not requiring D3 lymphadenectomy. The inclusion criteria for the laparoscopic group were as follows: (1) pathologically confirmed adenocarcinoma or high-grade intraepithelial neoplasia; (2) lesion located from the cecum to the right third of the transverse colon; and (3) clinically stage T1-4NanyM0. The exclusion criteria for the laparoscopic group were as follows: (1) distant metastasis discovered during surgical exploration; (2) multiple organ resection required or R0 resection not possible; or (3) conversion to open surgery required. Safety was evaluated on the basis of intra- and post-operative complications. Feasibility was assessed by postoperative recovery and quality of operative specimen. The body mass index was lower in the transvaginal than the laparoscopic group (22.0±3.1 kg/m2 vs. 24.1±2.6 kg/m2, t=2.617, P=0.012). Results: Among the 30 transvaginal laparoscopic right colectomies, 26 were pure transvaginal surgeries, three required laparoscopic assistance because of difficulties with anastomosis (n=2) or abdominal adhesions (n=1), and one required conversion to laparoscopic surgery because of vascular injury. Compared with the laparoscopic group, the transvaginal group had a longer surgery time (175.0 [147.5, 216.3] minutes vs. 120.0 [100.0, 120.0] minutes, U=63.000, P<0.001) and more blood loss (30.0 [10.0, 50.0] ml vs. 23.0 [10.0, 20.0] ml, U=208.000, P=0.011). The incidence of intraoperative complications (16.7% [5/30) vs. 0, P=0.061] was comparable between the two groups. In the transvaginal group, the sites of intraoperative injuries were bladder (n=3), ileocecal artery (n=1), and right uterine artery (n=1). The incidence of postoperative complications (20.0% [6/30] vs. 17.4% [4/23], χ2<0.001,P>0.999) was also comparable between the two groups. Clavien-Dindo grade III postoperative complications occurred in two patients in the transvaginal group (one patient had a pelvic hematoma that required embolization; the other had a vesico-vaginal fistula that required surgery). Postoperative visual analogue scale scores were significantly lower (P<0.001) in the transvaginal group. Times to first flatus, ambulation, and first intake and duration of postoperative hospital stay were comparable between the two groups (P>0.05). The proportion of specimens of moderate quality was 83.3% (25/30) in the transvaginal group and 100% (23/23) in the laparoscopic group; this difference is not significant (P=0.061). Among patients who underwent D2 lymph node dissection, the number of lymph nodes examined was comparable between the transvaginal (n=23) and laparoscopic groups (n=7) (18 [15, 27] vs. 20 [16, 29], U=69.500, P=0.589). Conclusion: Transvaginal right colon surgery is associated with less postoperative pain than laparoscopic surgery, but is not yet the preferred alternative because of the incidence of surgical complications.
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Affiliation(s)
- Y Xiao
- Division of Colorectal Surgery, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Z Sun
- Division of Colorectal Surgery, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - R Sun
- Division of Colorectal Surgery, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - W Y Hou
- Division of Colorectal Surgery, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - L Xu
- Division of Colorectal Surgery, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - J Y Lu
- Division of Colorectal Surgery, Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Abuhadra N, Sun R, Yam C, Rauch GM, Ding Q, Lim B, Thompson AM, Mittendorf EA, Adrada BE, Damodaran S, Virani K, White J, Ravenberg E, Sun J, Choi J, Candelaria R, Arun B, Ueno NT, Santiago L, Saleem S, Abouharb S, Murthy RK, Ibrahim N, Sahin A, Valero V, Symmans WF, Litton JK, Tripathy D, Moulder S, Huo L. Predictive Roles of Baseline Stromal Tumor-Infiltrating Lymphocytes and Ki-67 in Pathologic Complete Response in an Early-Stage Triple-Negative Breast Cancer Prospective Trial. Cancers (Basel) 2023; 15:3275. [PMID: 37444385 DOI: 10.3390/cancers15133275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/11/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
High stromal tumor-infiltrating lymphocytes (sTILs) are associated with improved pathologic complete response (pCR) in triple-negative breast cancer (TNBC). We hypothesize that integrating high sTILs and additional clinicopathologic features associated with pCR could enhance our ability to predict the group of patients on whom treatment de-escalation strategies could be tested. In this prospective early-stage TNBC neoadjuvant chemotherapy study, pretreatment biopsies from 408 patients were evaluated for their clinical and demographic features, as well as biomarkers including sTILs, Ki-67, PD-L1 and androgen receptor. Multivariate logistic regression models were developed to generate a computed response score to predict pCR. The pCR rate for the entire cohort was 41%. Recursive partitioning analysis identified ≥20% as the optimal cutoff for sTILs to denote 35% (143/408) of patients as having high sTILs, with a pCR rate of 59%, and 65% (265/408) of patients as having low sTILs, with a pCR rate of 31%. High Ki-67 (cutoff > 35%) was identified as the only predictor of pCR in addition to sTILs in the training set. This finding was verified in the testing set, where the highest computed response score encompassing both high sTILa and high Ki-67 predicted a pCR rate of 65%. Integrating Ki67 and sTIL may refine the selection of early stage TNBC patients for neoadjuvant clinical trials evaluating de-escalation strategies.
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Affiliation(s)
- Nour Abuhadra
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Clinton Yam
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Gaiane M Rauch
- Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qingqing Ding
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bora Lim
- Department of Oncology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alastair M Thompson
- Division of Surgical Oncology, Section of Breast Surgery, Baylor College of Medicine, Houston, TX 77030, USA
| | - Elizabeth A Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Beatriz E Adrada
- Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Senthil Damodaran
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kiran Virani
- Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jason White
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Elizabeth Ravenberg
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jia Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jaihee Choi
- Department of Statistics, Rice University, Houston, TX 77005, USA
| | - Rosalind Candelaria
- Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Banu Arun
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lumarie Santiago
- Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sadia Saleem
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sausan Abouharb
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rashmi K Murthy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nuhad Ibrahim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Aysegul Sahin
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Vicente Valero
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - William Fraser Symmans
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jennifer K Litton
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Stacy Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lei Huo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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McCaw ZR, Gaynor SM, Sun R, Lin X. Leveraging a surrogate outcome to improve inference on a partially missing target outcome. Biometrics 2023; 79:1472-1484. [PMID: 35218565 PMCID: PMC11023615 DOI: 10.1111/biom.13629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 12/18/2021] [Accepted: 01/11/2022] [Indexed: 11/30/2022]
Abstract
Sample sizes vary substantially across tissues in the Genotype-Tissue Expression (GTEx) project, where considerably fewer samples are available from certain inaccessible tissues, such as the substantia nigra (SSN), than from accessible tissues, such as blood. This severely limits power for identifying tissue-specific expression quantitative trait loci (eQTL) in undersampled tissues. Here we propose Surrogate Phenotype Regression Analysis (Spray) for leveraging information from a correlated surrogate outcome (eg, expression in blood) to improve inference on a partially missing target outcome (eg, expression in SSN). Rather than regarding the surrogate outcome as a proxy for the target outcome, Spray jointly models the target and surrogate outcomes within a bivariate regression framework. Unobserved values of either outcome are treated as missing data. We describe and implement an expectation conditional maximization algorithm for performing estimation in the presence of bilateral outcome missingness. Spray estimates the same association parameter estimated by standard eQTL mapping and controls the type I error even when the target and surrogate outcomes are truly uncorrelated. We demonstrate analytically and empirically, using simulations and GTEx data, that in comparison with marginally modeling the target outcome, jointly modeling the target and surrogate outcomes increases estimation precision and improves power.
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Affiliation(s)
- Zachary R. McCaw
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sheila M. Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Ryan Sun
- Department of Biostatistics, MD Anderson Cancer Center, Houston, TX
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
- Department of Statistics, Harvard University, Cambridge, MA
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Wang H, Moniruzzaman R, Li L, Ji B, Liu Y, Zuo X, Abbasgholizadeh R, Zhao J, Liu G, Wang R, Tang H, Sun R, Su X, Tan TH, Maitra A, Wang H. Hematopoietic progenitor kinase 1 inhibits the development and progression of pancreatic intraepithelial neoplasia. J Clin Invest 2023:163873. [PMID: 37140994 DOI: 10.1172/jci163873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Ras plays an essential role in the development of acinar to ductal metaplasia (ADM) and pancreatic ductal adenocarcinoma (PDAC). However, mutant Kras is an inefficient driver for PDAC development. The switching mechanisms from low Ras activity to high Ras activity that is required for development and progression of pancreatic intraepithelial neoplasia (PanIN) are unclear. In this study, we found that HPK1 was upregulated during pancreatic injury and ADM. HPK1 interacted with the SH3 domain and phosphorylated Ras GTPase activating protein (RasGAP) and upregulated RasGAP activity. Using the transgenic mouse models of HPK1 or M46, a kinase-dead mutant of HPK1, we showed that HPK1 inhibited Ras activity and its downstream signaling and regulated acinar cell plasticity. M46 promoted the development of ADM and PanINs. Expression of M46 in KrasG12D;Bac mice promoted the infiltration of myeloid-derived suppressor cells and macrophages, inhibited the infiltration of T cells, and accelerated the progression of PanINs to invasive and metastatic PDAC, while HPK1 attenuated mutant Kras-driven PanIN progression. Our results showed that HPK1 plays an important role in ADM and the progression of PanINs by regulating Ras signaling. Loss of HPK1 kinase activity promotes an immunosuppressive tumor microenvironment and accelerates the progression of PanINs to PDAC.
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Affiliation(s)
- Hua Wang
- Department of Gastrointestinal Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Rohan Moniruzzaman
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Lei Li
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Baoan Ji
- Department of Cancer Biology, Mayo Clinic Florida, Jacksonville, United States of America
| | - Yi Liu
- Department of Gastrointestinal Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Xiangsheng Zuo
- Department of Gastrointestinal Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Reza Abbasgholizadeh
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Jun Zhao
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Guangchao Liu
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Ruiqi Wang
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Hongli Tang
- The Advanced Technology Genomics Core, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Ryan Sun
- Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Xiaoping Su
- Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Tse-Hua Tan
- Immunology Research Center, National Health Research Institutes, Zhunan, Taiwan
| | - Anirban Maitra
- The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
| | - Huamin Wang
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, United States of America
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Ally SA, Han J, Sun R, Molokie RE, Gordeuk VR, Lash JP, Saraf SL. Community-level socioeconomic distress is associated with nutritional status in adults with sickle cell anemia. EJHaem 2023; 4:432-436. [PMID: 37206276 PMCID: PMC10188476 DOI: 10.1002/jha2.661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 01/30/2023] [Accepted: 02/03/2023] [Indexed: 05/21/2023]
Abstract
Sickle cell anemia (SCA) negatively impacts the ability to achieve educational and occupational goals increasing vulnerability to socioeconomic challenges. In a cross-sectional analysis of 332 SCA adults, we investigated whether the distressed community index (DCI) was associated with SCA-related complications and nutritional status. More patients with higher DCI had Medicaid insurance. A higher DCI was independently associated with tobacco use and lower body mass index, serum albumin, and vitamin D 25-OH levels after adjusting for insurance status but was not associated with SCA-related complications. Future studies investigating access to healthy foods may help improve health equity in patients with SCA.
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Affiliation(s)
- Syeda Akila Ally
- Division of Hematology and OncologyDepartment of MedicineUniversity of Illinois at ChicagoChicagoIllinoisUSA
| | - Jin Han
- Division of Hematology and OncologyDepartment of MedicineUniversity of Illinois at ChicagoChicagoIllinoisUSA
- Department of Pharmacy PracticeCollege of PharmacyUniversity of Illinois at ChicagoChicagoIllinoisUSA
| | - Ryan Sun
- Division of Hematology and OncologyDepartment of MedicineUniversity of Illinois at ChicagoChicagoIllinoisUSA
| | - Robert E. Molokie
- Division of Hematology and OncologyDepartment of MedicineUniversity of Illinois at ChicagoChicagoIllinoisUSA
- Department of MedicineJesse Brown VA Medical CenterChicagoIllinoisUSA
| | - Victor R. Gordeuk
- Division of Hematology and OncologyDepartment of MedicineUniversity of Illinois at ChicagoChicagoIllinoisUSA
| | - James P. Lash
- Division of NephrologyDepartment of MedicineUniversity of Illinois at ChicagoChicagoIllinoisUSA
| | - Santosh L. Saraf
- Division of Hematology and OncologyDepartment of MedicineUniversity of Illinois at ChicagoChicagoIllinoisUSA
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Yam C, Mittendorf EA, Garber HR, Sun R, Damodaran S, Murthy RK, Ramirez D, Karuturi M, Layman RM, Ibrahim N, Rauch GM, Adrada BE, Candelaria RP, White JB, Ravenberg E, Clayborn A, Ding QQ, Symmans WF, Prabhakaran S, Thompson AM, Valero V, Tripathy D, Huo L, Moulder SL, Litton JK. A phase II study of neoadjuvant atezolizumab and nab-paclitaxel in patients with anthracycline-resistant early-stage triple-negative breast cancer. Breast Cancer Res Treat 2023; 199:457-469. [PMID: 37061619 DOI: 10.1007/s10549-023-06929-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/30/2023] [Indexed: 04/17/2023]
Abstract
PURPOSE Neoadjuvant anti-PD-(L)1 therapy improves the pathological complete response (pCR) rate in unselected triple-negative breast cancer (TNBC). Given the potential for long-term morbidity from immune-related adverse events (irAEs), optimizing the risk-benefit ratio for these agents in the curative neoadjuvant setting is important. Suboptimal clinical response to initial neoadjuvant therapy (NAT) is associated with low rates of pCR (2-5%) and may define a patient selection strategy for neoadjuvant immune checkpoint blockade. We conducted a single-arm phase II study of atezolizumab and nab-paclitaxel as the second phase of NAT in patients with doxorubicin and cyclophosphamide (AC)-resistant TNBC (NCT02530489). METHODS Patients with stage I-III, AC-resistant TNBC, defined as disease progression or a < 80% reduction in tumor volume after 4 cycles of AC, were eligible. Patients received atezolizumab (1200 mg IV, Q3weeks × 4) and nab-paclitaxel (100 mg/m2 IV,Q1 week × 12) as the second phase of NAT before undergoing surgery followed by adjuvant atezolizumab (1200 mg IV, Q3 weeks, × 4). A two-stage Gehan-type design was employed to detect an improvement in pCR/residual cancer burden class I (RCB-I) rate from 5 to 20%. RESULTS From 2/15/2016 through 1/29/2021, 37 patients with AC-resistant TNBC were enrolled. The pCR/RCB-I rate was 46%. No new safety signals were observed. Seven patients (19%) discontinued atezolizumab due to irAEs. CONCLUSION This study met its primary endpoint, demonstrating a promising signal of activity in this high-risk population (pCR/RCB-I = 46% vs 5% in historical controls), suggesting that a response-adapted approach to the utilization of neoadjuvant immunotherapy should be considered for further evaluation in a randomized clinical trial.
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Affiliation(s)
- Clinton Yam
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA.
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Elizabeth A Mittendorf
- Division of Breast Surgery, Department of Surgery, Brigham and Women's Hospital, Boston, MA, USA
- Breast Oncology Program, Dana-Farber/Brigham Cancer Center, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - Haven R Garber
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Ryan Sun
- Department of Biostatistics, Division of Basic Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Senthil Damodaran
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Rashmi K Murthy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - David Ramirez
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Meghan Karuturi
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Rachel M Layman
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Nuhad Ibrahim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Gaiane M Rauch
- Department of Breast Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Beatriz E Adrada
- Department of Breast Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosalind P Candelaria
- Department of Breast Imaging, Division of Diagnostic Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason B White
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Elizabeth Ravenberg
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Alyson Clayborn
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Qing Qing Ding
- Department of Pathology, Division of Pathology-Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - W Fraser Symmans
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sabitha Prabhakaran
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alastair M Thompson
- Section of Breast Surgery, Division of Surgical Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Vicente Valero
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Lei Huo
- Department of Pathology, Division of Pathology-Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stacy L Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA
| | - Jennifer K Litton
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Dan L. Duncan Building (CPB5.3542), 1515 Holcombe Blvd. Unit 1354, Houston, TX, 77030, USA.
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Abuhadra N, Sun R, Bassett RL, Huo L, Chang JT, Teshome M, Clayborn AR, White JB, Ravenberg EE, Adrada BE, Candelaria RP, Yang W, Ding Q, Symmans WF, Arun B, Damodaran S, Koenig KB, Layman RM, Lim B, Litton JK, Thompson A, Ueno NT, Piwnica-Worms H, Hortobagyi GN, Valero V, Tripathy D, Rauch GM, Moulder S, Yam C. Targeting chemotherapy resistance in mesenchymal triple-negative breast cancer: a phase II trial of neoadjuvant angiogenic and mTOR inhibition with chemotherapy. Invest New Drugs 2023:10.1007/s10637-023-01357-4. [PMID: 37043123 DOI: 10.1007/s10637-023-01357-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/27/2023] [Indexed: 04/13/2023]
Affiliation(s)
- Nour Abuhadra
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Roland L Bassett
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lei Huo
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey T Chang
- Department of Integrative Biology and Pharmacology, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Mediget Teshome
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alyson R Clayborn
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Jason B White
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Elizabeth E Ravenberg
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Beatriz E Adrada
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rosalind P Candelaria
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Wei Yang
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Qingqing Ding
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - W Fraser Symmans
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Banu Arun
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Senthil Damodaran
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Kimberly B Koenig
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Rachel M Layman
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Bora Lim
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Jennifer K Litton
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Alastair Thompson
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Helen Piwnica-Worms
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel N Hortobagyi
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Vicente Valero
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA
| | - Gaiane M Rauch
- Department of Diagnostic Radiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Stacy Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
| | - Clinton Yam
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX, 77030, USA.
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Sun R, Huang B, Wei LJ. Comparing Short- and Long-Term Treatment Duration of Bevacizumab for Advanced Ovarian Cancer. J Clin Oncol 2023; 41:1952-1953. [PMID: 36763910 DOI: 10.1200/jco.22.02596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 01/12/2023] [Indexed: 02/12/2023] Open
Affiliation(s)
- Ryan Sun
- Ryan Sun, PhD, Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX; Bo Huang, PhD, Pfizer Inc, Groton, CT; and Lee-Jen Wei, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bo Huang
- Ryan Sun, PhD, Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX; Bo Huang, PhD, Pfizer Inc, Groton, CT; and Lee-Jen Wei, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lee-Jen Wei
- Ryan Sun, PhD, Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX; Bo Huang, PhD, Pfizer Inc, Groton, CT; and Lee-Jen Wei, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
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Sohn AJ, Taherian M, Katz MHG, Prakash LR, Chatterjee D, Wang H, Kim M, Tzeng CWD, Lee JE, Ikoma N, Rashid A, Wolff RA, Zhao D, Koay EJ, Sun R, Maitra A, Wang H. Integrated Pathologic Score Effectively Stratifies Patients With Pancreatic Ductal Adenocarcinoma Who Received Neoadjuvant Therapy and Pancreaticoduodenectomy. Am J Surg Pathol 2023; 47:421-430. [PMID: 36746143 PMCID: PMC10023386 DOI: 10.1097/pas.0000000000002013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Neoadjuvant therapy is increasingly used to treat patients with pancreatic ductal adenocarcinoma (PDAC). Pathologic parameters of treated PDAC, including tumor (ypT) and lymph node (ypN) stage, and tumor response grading (TRG) are important prognostic factors in this group of patients. To our knowledge, a multifactorial prognostic score combining pathologic features including ypT, ypN, and TRG in treated PDAC patients has not been reported. Our cohort consisted of 398 PDAC patients who received neoadjuvant therapy and underwent pancreaticoduodenectomy at our institution. All pancreaticoduodenectomy specimens were grossly and microscopically evaluated using a standard protocol. The integrated pathologic score (IPS) was calculated as the sum of the scores for ypT, ypN, and TRG according to either the MD Anderson grading system (IPSMDA) or the College of American Pathologists (CAP) grading system (IPSCAP). The IPSMDA and IPSCAP were correlated with clinicopathologic parameters and patient survival. Using either IPSMDA or IPSCAP, PDAC patients were stratified into 3 distinct prognostic groups for both disease-free survival (DFS) ( P <0.001) and overall survival (OS) ( P <0.001). The IPSMDA and IPSCAP correlated with tumor differentiation, margin status, the American Joint Committee on Cancer (AJCC) stage, and tumor recurrence ( P <0.05). In multivariate analysis, IPSMDA, IPSCAP, margin status, and tumor differentiation were independent prognostic factors for both DFS ( P <0.05) and OS ( P <0.05). However, patients with AJCC stage IB, IIA, or IIB disease had no significant difference in either DFS or OS ( P >0.05). The IPS appears to provide improved prognostic information compared with AJCC staging for preoperatively treated patients with PDAC.
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Affiliation(s)
- Aaron J Sohn
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mehran Taherian
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew HG Katz
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Laura R Prakash
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Deyali Chatterjee
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hua Wang
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ching-Wei D Tzeng
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jeffrey E Lee
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Naruhiko Ikoma
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Zhao
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Eugene J Koay
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anirban Maitra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huamin Wang
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Han Y, Byun J, Zhu C, Sun R, Roh JY, Cordell HJ, Lee HS, Shaw VR, Kang SW, Razjouyan J, Cooley MA, Hassan MM, Siminovitch KA, Folseraas T, Ellinghaus D, Bergquist A, Rushbrook SM, Franke A, Karlsen TH, Lazaridis KN, McGlynn KA, Roberts LR, Amos CI. Multitrait genome-wide analyses identify new susceptibility loci and candidate drugs to primary sclerosing cholangitis. Nat Commun 2023; 14:1069. [PMID: 36828809 PMCID: PMC9958016 DOI: 10.1038/s41467-023-36678-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 02/10/2023] [Indexed: 02/26/2023] Open
Abstract
Primary sclerosing cholangitis (PSC) is a rare autoimmune bile duct disease that is strongly associated with immune-mediated disorders. In this study, we implemented multitrait joint analyses to genome-wide association summary statistics of PSC and numerous clinical and epidemiological traits to estimate the genetic contribution of each trait and genetic correlations between traits and to identify new lead PSC risk-associated loci. We identified seven new loci that have not been previously reported and one new independent lead variant in the previously reported locus. Functional annotation and fine-mapping nominated several potential susceptibility genes such as MANBA and IRF5. Network-based in silico drug efficacy screening provided candidate agents for further study of pharmacological effect in PSC.
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Affiliation(s)
- Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Catherine Zhu
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas, M.D. Anderson Cancer Center, Houston, TX, USA
| | - Julia Y Roh
- Department of Pharmacy, Ochsner Health, New Orleans, LA, USA
| | - Heather J Cordell
- Population Health Sciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Hyun-Sung Lee
- David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Vikram R Shaw
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Sung Wook Kang
- David J. Sugarbaker Division of Thoracic Surgery, Michael E. DeBakey Department of Surgery, Baylor College of Medicine, Houston, TX, USA
| | - Javad Razjouyan
- VA HSR&D, Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, USA
- Big Data Scientist Training Enhancement Program (BD-STEP), VA Office of Research and Development, Washington, DC, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
- VA Quality Scholars Coordinating Center, IQuESt, Michael E. DeBakey VA Medical Center, Houston, TX, USA
| | - Matthew A Cooley
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
| | - Manal M Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Katherine A Siminovitch
- Departments of Medicine, Immunology and Medical Sciences, University of Toronto, Toronto, Ontario, Canada
- Mount Sinai Hospital, Lunenfeld-Tanenbaum Research Institute and Toronto General Research Institute, Toronto, Ontario, Canada
| | - Trine Folseraas
- Norwegian PSC Research Center, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Annika Bergquist
- Department of Medicine Huddinge, Unit of Gastroenterology and Rheumatology, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Simon M Rushbrook
- Department of Gastroenterology, Norfolk and Norwich University Hospital, Norwich, United Kingdom
- Norwich Medical School, University of East Anglia, Norfolk, United Kingdom
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
| | - Tom H Karlsen
- Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Konstantinos N Lazaridis
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Katherine A McGlynn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lewis R Roberts
- Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.
- Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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Bansal RK, Cassim R, Sun R, Mallick R, Finelli A, Tanguay S, Drachenberg DE, Pouliot F, Lavallee L, So AI, Rendon RA, Wood L, Kapoor A, Lalani AKA, Basappa NS, Bhindi B, Dean LW, Bjarnason GA, Breau RH. Outcomes of partial nephrectomy for non-metastatic cT2 renal tumors: Results from a Canadian multi-institutional collaborative. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.6_suppl.690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023] Open
Abstract
690 Background: The role of partial nephrectomy (PN) is not well defined for cT2 renal cell carcinoma (RCC) as compared to radical nephrectomy (RN). The aim of this study was to examine oncological outcomes of PN as compared to RN for non-metastatic cT2 RCC. Methods: The Canadian Kidney Cancer information system was used to define patients who underwent surgery for non-metastatic cT2 RCC from January 2011 to October 2022. Patients with clear-cell, papillary, and chromophobe RCC were included. Other histology, multiple tumours, and hereditary RCC syndrome patients were excluded. Each PN patient was individually matched to RN up to 1:4 depending on availability of patients based on tumor size (+/- 1cm), histology, grade (clear cell and papillary), and necrosis (clear cell). Matched patients were analyzed as clusters. Results: A total of 1523 patients were identified, and 50 PN patients met study criteria who were then matched to 185 RN patients. Both groups had similar age, gender, smoking status, BMI, Charlson comorbidity index score, symptoms at presentation, baseline eGFR, hemoglobin and pathological characteristics. PN patients had smaller tumors (7.6 cm [IQR 2] vs 8.4 [IQR 2.4], p=0.05), had higher likelihood of undergoing open surgery (72.9% vs 31.8%, p<0.0001) and less likely received adrenalectomy (2% vs 24.3%, p=0.0004). Positive surgical margin rates were similar in both groups (8.2% in PN vs 3.4% in RN, p=0.2). Median follow up was not significantly different in either group (3.6 yrs [IQR 4.7] in PN vs 3.3 [4.7] yrs in RN, p=0.9). During the follow up period, PN patients had higher risk of local recurrence (HR 3.0, 95%CI 1.08-8.37), lower risk of distant metastasis (HR 0.36, 95%CI 0.15-0.88), better cancer specific survival (HR 0.56, 95%CI 0.18-1.78) and overall survival (HR 0.36, 95%CI 0.11-1.19) and as compared to RN. At 6 months and beyond after surgery, PN patients had less decline in eGFR than RN patients (-16.6 [SD 21.1] vs -24.4[SD 16.2], p=0.0002). Complications rates between PN and RN were (18% vs 9%, p=0.057). Conclusions: In this multi-institutional Canadian cohort of patients with non-metastatic cT2 RCC undergoing surgery, PN compared to RN was associated with slightly higher risk of peri-operative complications, better preservation of renal function, and higher risk of local recurrence. The lower risk of distant metastasis and death was likely from residual confounding unaccounted for in the individual patient match. [Table: see text]
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Affiliation(s)
| | | | - Ryan Sun
- University of Manitoba, Winnipeg, MB, Canada
| | | | | | - Simon Tanguay
- McGill University Health Center, Montreal, QC, Canada
| | | | | | - Luke Lavallee
- Ottawa Hospital Cancer Centre, University of Ottawa, Ottawa, ON, Canada
| | - Alan I. So
- Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Lori Wood
- Queen Elizabeth II Health Sciences Centre, Dalhousie University, Halifax, NS, Canada
| | - Anil Kapoor
- St Joseph's Healthcare, McMaster University, Hamilton, ON, Canada
| | | | | | - Bimal Bhindi
- Southern Alberta Institute of Urology, Calgary, AB, Canada
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Zeineddine FA, Zeineddine MA, Yousef A, Gu Y, Chowdhury S, Dasari A, Huey RW, Johnson B, Kee B, Lee MS, Morelli MP, Morris VK, Overman MJ, Parseghian C, Raghav K, Willis J, Wolff RA, Kawaguchi Y, Vauthey JN, Sun R, Kopetz S, Shen JP. Survival improvement for patients with metastatic colorectal cancer over twenty years. NPJ Precis Oncol 2023; 7:16. [PMID: 36781990 PMCID: PMC9925745 DOI: 10.1038/s41698-023-00353-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 01/16/2023] [Indexed: 02/15/2023] Open
Abstract
Over the past two decades of successive clinical trials in metastatic colorectal cancer (CRC), the median overall survival of both control and experimental arms has steadily improved. However, the incremental change in survival for metastatic CRC patients not treated on trial has not yet been quantified. We performed a retrospective review of 1420 patients with de novo metastatic CRC who received their primary treatment at the University of Texas M.D. Anderson Cancer Center (UTMDACC) from 2004 through 2019. Median OS was roughly stable for patients diagnosed between 2004 and 2012 (22.6 months) but since has steadily improved for those diagnosed in 2013 to 2015 (28.8 months), and 2016 to 2019 (32.4 months). Likewise, 5-year survival rate has increased from 15.7% for patients diagnosed from 2004 to 2006 to 26% for those diagnosed from 2013 to 2015. Notably, survival improved for patients with BRAFV600E mutant as well as microsatellite unstable (MSI-H) tumors. Multivariate regression analysis identified surgical resection of liver metastasis (HR = 0.26, 95% CI, 0.19-0.37), use of immunotherapy (HR = 0.44, 95% CI, 0.29-0.67) and use of third line chemotherapy (regorafenib or trifluridine/tipiracil, HR = 0.74, 95% CI, 0.58-0.95), but not year of diagnosis (HR = 0.99, 95% CI, 0.98-1), as associated with better survival, suggesting that increased use of these therapies are the drivers of the observed improvement in survival.
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Affiliation(s)
- Fadl A Zeineddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mohammad A Zeineddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Abdelrahman Yousef
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Gu
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Saikat Chowdhury
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Arvind Dasari
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan W Huey
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Benny Johnson
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Bryan Kee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael S Lee
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Pia Morelli
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Van K Morris
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael J Overman
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Christine Parseghian
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kanwal Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason Willis
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yoshikuni Kawaguchi
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jean-Nicolas Vauthey
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Patni T, Lee CT, Li Y, Kaste S, Zhu L, Sun R, Hudson MM, Ness KK, Neumann A, Robison LL. Factors for poor oral health in long-term childhood cancer survivors. BMC Oral Health 2023; 23:73. [PMID: 36739372 PMCID: PMC9899385 DOI: 10.1186/s12903-023-02762-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/23/2023] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Survivors of childhood cancer are at risk for therapy-related dental diseases. The purpose of the study was to investigate the associations between clinical, socioeconomic, and demographic factors and oral diseases in the St. Jude Lifetime Cohort (SJLIFE) participants. METHODS We performed a retrospective medical chart review and evaluated longitudinal self-reported dental outcomes in 4856 childhood cancer survivors and 591 community controls participating in the St. Jude Lifetime Cohort (SJLIFE) study. Univariate and multivariable logistic regression models were used to assess the impact of socioeconomic factors, treatment exposures and patient demographics on dental outcomes. RESULTS Cancer survivors were more likely to report microdontia (odds ratio (OR) = 7.89, 95% confidence interval (CI) [4.64, 14.90]), abnormal root development (OR = 6.19, CI [3.38, 13.00]), hypodontia (OR = 2.75, CI [1.83, 4.33]), enamel hypoplasia (OR = 4.24, CI [2.9, 6.49]), xerostomia (OR = 7.72, CI [3.27, 25.10]), severe gingivitis (OR = 2.04, CI [1.43, 3.03]), and ≥ 6 missing teeth (OR = 3.73, CI [2.46, 6.00]) compared to controls without cancer history. Survivors who received classic alkylating agents (OR = 1.6, CI [1.36, 1.88]), anthracycline antibiotics (OR = 1.22, CI [1.04, 1.42] or radiation therapy potentially exposing the oral cavity (OR = 1.48, CI [1.26, 1.72]) were more likely to report at least one dental health problem after controlling for socioeconomic factors, age at last follow-up and diagnosis, other treatment exposures, and access to dental services. Survivors who had radiation therapy potentially exposing the oral cavity (OR = 1.52, CI [1.25, 1.84]) were also more likely to report at least one soft tissue abnormality after controlling for socioeconomic factors, age at last follow-up and diagnosis, other treatment exposures, and access and utilization of dental services. CONCLUSIONS Childhood cancer survivors have a higher prevalence of oral-dental abnormalities than the controls without a cancer history. Cancer treatment, socioeconomic factors, and access to oral health care contribute to the prevalence of dental abnormalities.
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Affiliation(s)
- Tushar Patni
- grid.240871.80000 0001 0224 711XDepartment of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Chun-Teh Lee
- Department of Periodontics and Dental Hygiene, The University of Texas Health Science Center at Houston School of Dentistry, Houston, TX, USA.
| | - Yimei Li
- grid.240871.80000 0001 0224 711XDepartment of Biostatistics, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Sue Kaste
- grid.240871.80000 0001 0224 711XDepartment of Diagnostic Imaging, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Liang Zhu
- grid.267308.80000 0000 9206 2401Department of Internal Medicine, The University of Texas Health Science Center at Houston, Houston, TX USA
| | - Ryan Sun
- grid.240145.60000 0001 2291 4776Department of Biostatistics, MD Anderson Cancer Center, Houston, TX USA
| | - Melissa M. Hudson
- grid.240871.80000 0001 0224 711XDepartment of Oncology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Kirsten K. Ness
- grid.240871.80000 0001 0224 711XDepartment of Epidemiology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Ana Neumann
- grid.267308.80000 0000 9206 2401Department of General Practice and Dental Public Health, The University of Texas Health Science Center at Houston School of Dentistry, Houston, TX USA
| | - Leslie L. Robison
- grid.240871.80000 0001 0224 711XDepartment of Epidemiology, St. Jude Children’s Research Hospital, Memphis, TN USA
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Westin J, Davis RE, Feng L, Hagemeister F, Steiner R, Lee HJ, Fayad L, Nastoupil L, Ahmed S, Rodriguez A, Fanale M, Samaniego F, Iyer SP, Nair R, Oki Y, Fowler N, Wang M, Ma MCJ, Vega F, McDonnell T, Pinnix C, Griffith D, Lu Y, Tewari S, Sun R, Scott DW, Flowers CR, Neelapu S, Green MR. Smart Start: Rituximab, Lenalidomide, and Ibrutinib in Patients With Newly Diagnosed Large B-Cell Lymphoma. J Clin Oncol 2023; 41:745-755. [PMID: 35952327 PMCID: PMC10489211 DOI: 10.1200/jco.22.00597] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/03/2022] [Accepted: 06/29/2022] [Indexed: 02/01/2023] Open
Abstract
PURPOSE Chemoimmunotherapy for patients with newly diagnosed diffuse large B-cell lymphoma (DLBCL) is largely unchanged for decades. Both preclinical models and clinical data suggest the combination of lenalidomide and ibrutinib may have synergy in DLBCL, particularly in the non-germinal center B-cell-like subset. METHODS We enrolled 60 patients with newly diagnosed non-germinal center B-cell-like DLBCL in this investigator-initiated, single-arm phase II trial of rituximab, lenalidomide, and ibrutinib (RLI) with the sequential addition of chemotherapy (ClinicalTrials.gov identifier: NCT02636322). Patients were treated with rituximab 375 mg/m2 intravenous once on day 1, lenalidomide 25 mg once per day on days 1-10, and ibrutinib 560 mg once daily continuously of each 21-day cycle (RLI). After two cycles, standard chemotherapy was added to RLI for six additional cycles. The primary end points were overall response rate (ORR) after two cycles of RLI alone and complete response rate after completion of RLI with chemotherapy. In evaluable samples, circulating tumor DNA and DLBCL90 assays were performed. RESULTS The median age was 63.5 years (range, 29-83 years) with 28% age 70 years or older. The revised international prognostic index identified 42% as high risk, and 62% were double expressor of MYC and BCL2 protein. The ORR after two cycles of RLI was 86.2%, and the complete response rate at the end of RLI-chemotherapy was 94.5%. With a median follow-up of 31 months, the progression-free survival and overall survival were at 91.3% and 96.6% at 2 years, respectively. CONCLUSION Smart Start is the first study, to our knowledge, to treat newly diagnosed DLBCL with a targeted therapy combination before chemotherapy. RLI produced a high ORR, and RLI with chemotherapy resulted in durable responses. This establishes the potential for developing biologically driven and noncytotoxic first-line therapies for DLBCL.
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Affiliation(s)
- Jason Westin
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - R. Eric Davis
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Lei Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fredrick Hagemeister
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Raphael Steiner
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Hun Ju Lee
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Luis Fayad
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Loretta Nastoupil
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sairah Ahmed
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alma Rodriguez
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michelle Fanale
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
- Seagen, Bothell, WA
| | - Felipe Samaniego
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Swaminathan P. Iyer
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ranjit Nair
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yasuhiro Oki
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Nathan Fowler
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael Wang
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Man Chun John Ma
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Francisco Vega
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy McDonnell
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Chelsea Pinnix
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Donna Griffith
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yang Lu
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sanjit Tewari
- Department of Nuclear Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David W. Scott
- British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Christopher R. Flowers
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sattva Neelapu
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Michael R. Green
- Department of Lymphoma and Myeloma, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
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Wu WB, Zhang XB, Liu YP, Zou X, You R, Xie YL, Duan XT, Li HF, Wen K, Peng L, Hua YJ, Huang PY, Sun R, Chen JH, Chen MY. Stent pretreatment for internal carotid artery exposed to necrotic lesions in nasopharyngeal carcinoma. Rhinology 2023; 0:3056. [PMID: 36715464 DOI: 10.4193/rhin22.451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
BACKGROUND Post radiation nasopharyngeal necrosis (PRNN) invading the internal carotid artery (ICA) contributes to the death of 69.2-72.7% of PRNN patients. ICA occlusion is an effective treatment to avoid fatal bleeding, while some patients are intolerant. We present a novel method that allows for these patients without interrupting blood flow through the ICA. METHODOLOGY This study enrolled patients with PRNN-invaded ICA who were not suitable for ICA occlusion from April 2020 to November 2022. ICA stent pretreatment was performed in the 36 patients and followed the endoscopic nasopharyngectomy (ENPG) or conservative treatment for PRNN. We report the survival outcome and incidence of complications after stent implantation and compare the survival outcomes of ENPG and conservative treatment for PRNN followed by stent implantation. RESULTS ICA stent pretreatment was performed in the 36 enrolled patients, among which 14 underwent ENPG, and 22 received conservative treatment. 27.8% patients died after a median follow-up of 15 months. The Kaplan-Meier estimates of overall survival were higher in the ENPG group than in the conservative treatment group. Karnofsky performance status (KPS) was significantly higher in the ENPG group than in the non-ENPG group. CONCLUSIONS The innovative application of ICA stents is a promising treatment to improve outcomes in patients with PRNN invading the ICA who are unsuitable for ICA embolization, especially when followed by endoscopic surgery. However, methods to avoid postoperative cerebral ischemia and nasopharyngeal hemorrhage still require further study.
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Affiliation(s)
- W-B Wu
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - X-B Zhang
- Department of Neurosurgery, The third affiliated hospital of Southern Medical University, Guangzhou, P. R. China
| | - Y-P Liu
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - X Zou
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - R You
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - Y-L Xie
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - X-T Duan
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - H-F Li
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - K Wen
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - L Peng
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - Y-J Hua
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - P-Y Huang
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - R Sun
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
| | - J-H Chen
- Department of Neurosurgery, The third affiliated hospital of Southern Medical University, Guangzhou, P. R. China
| | - M-Y Chen
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
- Sun Yat-sen University Cancer Center
- State Key Laboratory of Oncology in South China
- Collaborative Innovation Center for Cancer Medicine
- Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, P.R. China
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Raghav K, Ou FS, Venook AP, Innocenti F, Sun R, Lenz HJ, Kopetz S. Acquired Genomic Alterations on First-Line Chemotherapy With Cetuximab in Advanced Colorectal Cancer: Circulating Tumor DNA Analysis of the CALGB/SWOG-80405 Trial (Alliance). J Clin Oncol 2023; 41:472-478. [PMID: 36067452 PMCID: PMC9870237 DOI: 10.1200/jco.22.00365] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/01/2022] [Accepted: 07/18/2022] [Indexed: 01/27/2023] Open
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.Acquired genomic alterations (Acq-GAs), specifically RAS, BRAF, and EGFR-ectodomain mutations and ERBB2 and MET amplifications, are recognized as major mechanisms of resistance to later-line anti-EGFR-antibody therapy in metastatic colorectal cancer (mCRC). However, data regarding emergence of these Acq-GAs under the selective pressure of first-line anti-EGFR-chemotherapy are lacking. We performed next-generation sequencing (Guardant360) on circulating tumor DNA obtained from paired plasma samples (pretreatment and postprogression) from the CALGB/SWOG-80405 trial, which randomly assigned patients with mCRC between first-line chemotherapy with cetuximab (anti-EGFR-chemotherapy) or bevacizumab (anti-VEGF-chemotherapy). The primary objective was to determine the prevalence of Acq-GAs on anti-EGFR-chemotherapy and compare this to the prevalence with anti-VEGF-chemotherapy on trial and pooled estimates (N = 292) seen with later-line anti-EGFR-antibody therapy as reported in the literature. Among the 61 patients on anti-EGFR-chemotherapy, only four (6.6%) developed ≥ 1 Acq-GAs of interest compared with 10.1% (7) on anti-VEGF-chemotherapy (odds ratio, 0.62; 95% CI, 0.20 to 2.11) and 62.0% on anti-EGFR-antibody therapy in later lines (odds ratio, 0.09; 95% CI, 0.03 to 0.23). Acq-GAs, classically associated with anti-EGFR-antibody resistance in later lines (RAS, BRAF, and EGFR-ectodomain mutations; ERBB2 and MET amplifications), were rare with up-front use of anti-EGFR-chemotherapy indicating divergent resistance mechanisms. These findings have critical translational relevance to timing and value of circulating tumor DNA-guided anti-EGFR rechallenge in patients with mCRC, especially those treated with anti-EGFR therapy upfront.
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Affiliation(s)
- Kanwal Raghav
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fang-Shu Ou
- Alliance Statistics and Data Management Center, Mayo Clinic, Rochester, MN
| | - Alan P. Venook
- UCSF Helen Diller Family Comprehensive Cancer, San Francisco, CA
| | | | - Ryan Sun
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Heinz-Josef Lenz
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA
| | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
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Parseghian CM, Sun R, Woods M, Napolitano S, Lee HM, Alshenaifi J, Willis J, Nunez S, Raghav KP, Morris VK, Shen JP, Eluri M, Sorokin A, Kanikarla P, Vilar E, Rehn M, Ang A, Troiani T, Kopetz S. Resistance Mechanisms to Anti-Epidermal Growth Factor Receptor Therapy in RAS/RAF Wild-Type Colorectal Cancer Vary by Regimen and Line of Therapy. J Clin Oncol 2023; 41:460-471. [PMID: 36351210 PMCID: PMC9870238 DOI: 10.1200/jco.22.01423] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/30/2022] [Accepted: 11/02/2022] [Indexed: 11/11/2022] Open
Abstract
PURPOSE Acquired resistance to anti-epidermal growth factor receptor (EGFR) inhibitor (EGFRi) therapy in colorectal cancer (CRC) has previously been explained by the model of acquiring new mutations in KRAS/NRAS/EGFR, among other MAPK-pathway members. However, this was primarily on the basis of single-agent EGFRi trials and little is known about the resistance mechanisms of EGFRi combined with effective cytotoxic chemotherapy in previously untreated patients. METHODS We analyzed paired plasma samples from patients with RAS/BRAF/EGFR wild-type metastatic CRC enrolled in three large randomized trials evaluating EGFRi in the first line in combination with chemotherapy and as a single agent in third line. The mutational signature of the alterations acquired with therapy was evaluated. CRC cell lines with resistance to cetuximab, infusional fluorouracil, leucovorin, and oxaliplatin, and SN38 were developed, and transcriptional changes profiled. RESULTS Patients whose tumors were treated with and responded to EGFRi alone were more likely to develop acquired mutations (46%) compared with those treated in combination with cytotoxic chemotherapy (9%). Furthermore, contrary to the generally accepted hypothesis of the clonal evolution of acquired resistance, we demonstrate that baseline resistant subclonal mutations rarely expanded to become clonal at progression, and most remained subclonal or disappeared. Consistent with this clinical finding, preclinical models with acquired resistance to either cetuximab or chemotherapy were cross-resistant to the alternate agents, with transcriptomic profiles consistent with epithelial-to-mesenchymal transition. By contrast, commonly acquired resistance alterations in the MAPK pathway do not affect sensitivity to cytotoxic chemotherapy. CONCLUSION These findings support a model of resistance whereby transcriptomic mechanisms of resistance predominate in the presence of active cytotoxic chemotherapy combined with EGFRi, with a greater predominance of acquired MAPK mutations after single-agent EGFRi. The proposed model has implications for prospective studies evaluating EGFRi rechallenge strategies guided by acquired MAPK mutations, and highlights the need to address transcriptional mechanisms of resistance.
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Affiliation(s)
- Christine M. Parseghian
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Melanie Woods
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Stefania Napolitano
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Hey Min Lee
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jumanah Alshenaifi
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jason Willis
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Shakayla Nunez
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kanwal P. Raghav
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Van K. Morris
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John P. Shen
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Madhulika Eluri
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Alexey Sorokin
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Preeti Kanikarla
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Eduardo Vilar
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
- Division of Cancer Prevention and Population Sciences, Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Teresa Troiani
- Department of Precision Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Campania, Italy
| | - Scott Kopetz
- Division of Cancer Medicine, Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
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Li X, Quick C, Zhou H, Gaynor SM, Liu Y, Chen H, Selvaraj MS, Sun R, Dey R, Arnett DK, Bielak LF, Bis JC, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Freedman BI, Göring HHH, Guo X, Haessler J, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Manichaikul A, Martin LW, McGarvey ST, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Sitlani CM, Smith JA, Taylor KD, Vasan RS, Willer CJ, Wilson JG, Yanek LR, Zhao W, Rotter JI, Natarajan P, Peloso GM, Li Z, Lin X. Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies. Nat Genet 2023; 55:154-164. [PMID: 36564505 PMCID: PMC10084891 DOI: 10.1038/s41588-022-01225-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 10/13/2022] [Indexed: 12/24/2022]
Abstract
Meta-analysis of whole genome sequencing/whole exome sequencing (WGS/WES) studies provides an attractive solution to the problem of collecting large sample sizes for discovering rare variants associated with complex phenotypes. Existing rare variant meta-analysis approaches are not scalable to biobank-scale WGS data. Here we present MetaSTAAR, a powerful and resource-efficient rare variant meta-analysis framework for large-scale WGS/WES studies. MetaSTAAR accounts for relatedness and population structure, can analyze both quantitative and dichotomous traits and boosts the power of rare variant tests by incorporating multiple variant functional annotations. Through meta-analysis of four lipid traits in 30,138 ancestrally diverse samples from 14 studies of the Trans Omics for Precision Medicine (TOPMed) Program, we show that MetaSTAAR performs rare variant meta-analysis at scale and produces results comparable to using pooled data. Additionally, we identified several conditionally significant rare variant associations with lipid traits. We further demonstrate that MetaSTAAR is scalable to biobank-scale cohorts through meta-analysis of TOPMed WGS data and UK Biobank WES data of ~200,000 samples.
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Affiliation(s)
- Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Corbin Quick
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yaowu Liu
- School of Statistics, Southwestern University of Finance and Economics, Chengdu, China
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Margaret Sunitha Selvaraj
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rounak Dey
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Donna K Arnett
- University of Kentucky, College of Public Health, Lexington, KY, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Barry I Freedman
- Department of Internal Medicine, Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Harald H H Göring
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeffrey Haessler
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Rita R Kalyani
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian G Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lisa W Martin
- Division of Cardiology, George Washington School of Medicine and Health Sciences, Washington, DC, USA
| | - Stephen T McGarvey
- Department of Epidemiology, International Health Institute, Department of Anthropology, Brown University, Providence, RI, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore VA Medical Center, Baltimore, MD, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Departments of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Departments of Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Cristen J Willer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - James G Wilson
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Statistics, Harvard University, Cambridge, MA, USA.
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Sun R, Wei LJ. Quantifying Clinical Utility of Enzalutamide for Overall Survival in Metastatic Hormone-Sensitive Prostate Cancer. J Clin Oncol 2022; 40:4278-4279. [PMID: 35985008 DOI: 10.1200/jco.22.01084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Ryan Sun
- Ryan Sun, PhD, Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX; and Lee-Jen Wei, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
| | - Lee-Jen Wei
- Ryan Sun, PhD, Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX; and Lee-Jen Wei, PhD, Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA
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48
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Bahrambeigi V, Lee JJ, Rajapakshe KI, Stephens BM, Henry JT, Dhebat S, Hurd MW, Sun R, Kopetz S, Maitra A, Guerrero PA. Abstract PR013: Transcriptomic profiling of liquid biopsy in colorectal cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.crc22-pr013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Abstract
Objective: Consensus molecular subtype (CMS) is a predictive factor for treatment outcomes of chemotherapies for metastatic colorectal cancer (CRC). CMS classification is based on transcriptomic profiles of CRC specimens obtained by tumor biopsy. Tumor biopsy often provides limited information due to the heterogeneity within tumor and spatial heterogeneity between the primary tumor and distant metastases. In addition, repeated tissue biopsy to monitor the treatment response is not practical. Liquid biopsy is a minimally invasive method for the real-time monitoring of cancer-derived biomarkers. Among liquid biopsy biomarkers, extracellular vesicles (EVs) have a unique potential because they possess nucleic acids. We explored the use of CRC plasma EVs in predicting the molecular subtype of CRCs using RNA-seq. Methods: EVs were isolated from 10 different CMS-stratified colorectal cancer cell lines and a normal control. Whole transcriptome RNA-seq on cellular RNA (cRNA) and cell-derived evRNA was done to determine if EVs could be used to predict the CMS subtype of their cells of origin. We then sought to perform molecular subtyping of plasma EVs from patients with CRC. RNA-seq was performed on tumor tissues and matched plasma EVs from 46 patients with CRC and 59 healthy controls (age/gender matched). The bulk transcriptome from CRC plasma EVs was deconvoluted to predict the cancer percentage (CIBERSORTx) and to utilize cancer-specific transcriptome for CMS subtyping (DeMixT). Artificial neural network (ANN)-based CMS subtype classifier was used to classify molecular subtypes. Results: There was 100% concordance between CMS subtype of evRNA with that of the cRNA. We showed that, RNA mixtures containing as low as 1% cancer cell RNA could be accurately classified into the correct CMS class. Imputed proportions of cancer in plasma of CRC patients ranged from 0.89% to 2.08%. Receiver operating characteristic (ROC) curve showed area under the curve of 0.961 with specificity and sensitivity of 0.96 and 0.9, respectively. Plasma evRNA was classified into CMS classes and there was 67% (31/46) concordance between the predicted subtype of liquid biopsies and the tumor samples. In patients with tumor purity greater than 10%, the concordance was higher at 75% (27/36). Conclusions: EVs could be used to accurately predict CMS subtypes of their cells of origin. We created a pipeline using low-input RNA library preparation from plasma EV to estimate the cancer RNA portion present in the bulk transcriptome and predict the molecular subtypes of colorectal cancers. Molecular subtyping of evRNA may help to track CMS changes of the tumor in patients undergoing treatment.
Citation Format: Vahid Bahrambeigi, Jaewon J. Lee, Kimal I. Rajapakshe, Bret M. Stephens, Jason T. Henry, Sarah Dhebat, Mark W. Hurd, Ryan Sun, Scott Kopetz, Anirban Maitra, Paola A. Guerrero. Transcriptomic profiling of liquid biopsy in colorectal cancer [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr PR013.
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Affiliation(s)
| | - Jaewon J. Lee
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Jason T. Henry
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sarah Dhebat
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mark W. Hurd
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ryan Sun
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Scott Kopetz
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anirban Maitra
- 1The University of Texas MD Anderson Cancer Center, Houston, TX
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Li Z, Li X, Zhou H, Gaynor SM, Selvaraj MS, Arapoglou T, Quick C, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Auer PL, Bielak LF, Bis JC, Blackwell TW, Blangero J, Boerwinkle E, Bowden DW, Brody JA, Cade BE, Conomos MP, Correa A, Cupples LA, Curran JE, de Vries PS, Duggirala R, Franceschini N, Freedman BI, Göring HHH, Guo X, Kalyani RR, Kooperberg C, Kral BG, Lange LA, Lin BM, Manichaikul A, Manning AK, Martin LW, Mathias RA, Meigs JB, Mitchell BD, Montasser ME, Morrison AC, Naseri T, O'Connell JR, Palmer ND, Peyser PA, Psaty BM, Raffield LM, Redline S, Reiner AP, Reupena MS, Rice KM, Rich SS, Smith JA, Taylor KD, Taub MA, Vasan RS, Weeks DE, Wilson JG, Yanek LR, Zhao W, Rotter JI, Willer CJ, Natarajan P, Peloso GM, Lin X. A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies. Nat Methods 2022; 19:1599-1611. [PMID: 36303018 PMCID: PMC10008172 DOI: 10.1038/s41592-022-01640-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 09/06/2022] [Indexed: 02/07/2023]
Abstract
Large-scale whole-genome sequencing studies have enabled analysis of noncoding rare-variant (RV) associations with complex human diseases and traits. Variant-set analysis is a powerful approach to study RV association. However, existing methods have limited ability in analyzing the noncoding genome. We propose a computationally efficient and robust noncoding RV association detection framework, STAARpipeline, to automatically annotate a whole-genome sequencing study and perform flexible noncoding RV association analysis, including gene-centric analysis and fixed window-based and dynamic window-based non-gene-centric analysis by incorporating variant functional annotations. In gene-centric analysis, STAARpipeline uses STAAR to group noncoding variants based on functional categories of genes and incorporate multiple functional annotations. In non-gene-centric analysis, STAARpipeline uses SCANG-STAAR to incorporate dynamic window sizes and multiple functional annotations. We apply STAARpipeline to identify noncoding RV sets associated with four lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several of them in an additional 9,123 TOPMed samples. We also analyze five non-lipid TOPMed traits.
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Affiliation(s)
- Zilin Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Xihao Li
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Hufeng Zhou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Sheila M Gaynor
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Margaret Sunitha Selvaraj
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Theodore Arapoglou
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Corbin Quick
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yaowu Liu
- School of Statistics, Southwestern University of Finance and Economics, Chengdu, China
| | - Han Chen
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rounak Dey
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Donna K Arnett
- Dean's Office, University of Kentucky, College of Public Health, Lexington, KY, USA
| | - Paul L Auer
- Division of Biostatistics, Institute for Health & Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Lawrence F Bielak
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Thomas W Blackwell
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, USA
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Donald W Bowden
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Brian E Cade
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Adolfo Correa
- Jackson Heart Study, Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
| | - Joanne E Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Paul S de Vries
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Barry I Freedman
- Department of Internal Medicine, Nephrology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Harald H H Göring
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, The University of Texas Rio Grande Valley, Brownsville, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Rita R Kalyani
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Brian G Kral
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leslie A Lange
- Division of Biomedical Informatics and Personalized Medicine, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Bridget M Lin
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Alisa K Manning
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Metabolism Program, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA, USA
| | - Lisa W Martin
- Division in Cardiology, George Washington School of Medicine and Health Sciences, Washington, DC, USA
| | - Rasika A Mathias
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James B Meigs
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Division of General Internal Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatrics Research and Education Clinical Center, Baltimore VA Medical Center, Baltimore, MD, USA
| | - May E Montasser
- Division of Endocrinology, Diabetes, and Nutrition, Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Take Naseri
- Ministry of Health, Government of Samoa, Apia, Samoa
| | - Jeffrey R O'Connell
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Nicholette D Palmer
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Departments of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Susan Redline
- Division of Sleep and Circadian Disorders, Brigham and Women's Hospital, Boston, MA, USA
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
- Division of Pulmonary, Critical Care, and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | | | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Margaret A Taub
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ramachandran S Vasan
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Daniel E Weeks
- Department of Human Genetics and Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - James G Wilson
- Division of Cardiology, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Lisa R Yanek
- GeneSTAR Research Program, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Cristen J Willer
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA
| | - Pradeep Natarajan
- Center for Genomic Medicine and Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Gina M Peloso
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Framingham Heart Study, National Heart, Lung, and Blood Institute and Boston University, Framingham, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Statistics, Harvard University, Cambridge, MA, USA.
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Sun R, Wei LJ. Quantifying Clinical Utility of Adjuvant Abemaciclib in Patients With High-risk Early Breast Cancer Who Received Neoadjuvant Chemotherapy. JAMA Oncol 2022; 8:1701. [PMID: 36173642 DOI: 10.1001/jamaoncol.2022.4528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Ryan Sun
- Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston
| | - Lee-Jen Wei
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
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