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Estienne T, Lerousseau M, Vakalopoulou M, Alvarez Andres E, Battistella E, Carré A, Chandra S, Christodoulidis S, Sahasrabudhe M, Sun R, Robert C, Talbot H, Paragios N, Deutsch E. Deep Learning-Based Concurrent Brain Registration and Tumor Segmentation. Front Comput Neurosci 2020; 14:17. [PMID: 32265680 PMCID: PMC7100603 DOI: 10.3389/fncom.2020.00017] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 02/11/2020] [Indexed: 01/30/2023] Open
Abstract
Image registration and segmentation are the two most studied problems in medical image analysis. Deep learning algorithms have recently gained a lot of attention due to their success and state-of-the-art results in variety of problems and communities. In this paper, we propose a novel, efficient, and multi-task algorithm that addresses the problems of image registration and brain tumor segmentation jointly. Our method exploits the dependencies between these tasks through a natural coupling of their interdependencies during inference. In particular, the similarity constraints are relaxed within the tumor regions using an efficient and relatively simple formulation. We evaluated the performance of our formulation both quantitatively and qualitatively for registration and segmentation problems on two publicly available datasets (BraTS 2018 and OASIS 3), reporting competitive results with other recent state-of-the-art methods. Moreover, our proposed framework reports significant amelioration (p < 0.005) for the registration performance inside the tumor locations, providing a generic method that does not need any predefined conditions (e.g., absence of abnormalities) about the volumes to be registered. Our implementation is publicly available online at https://github.com/TheoEst/joint_registration_tumor_segmentation.
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Xiao X, Yuan T, Meng JX, Jiang YY, Cao YQ, Li Q, Sun R, Zhao MF. [Analysis on poor efficacy factors in the treatment of recurrent/refractory B-cell lymphoma with CD19 CAR-T cells]. ZHONGHUA YI XUE ZA ZHI 2020; 100:593-598. [PMID: 32164113 DOI: 10.3760/cma.j.issn.0376-2491.2020.08.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the factors influencing the efficacy of CD19 chimeric antigen receptor T (CAR-T) cells in the treatment of patients with relapsed refractory B cell lymphoma and to provide evidence for further improvement of CAR-T efficacy. Methods: A total of 34 patients with relapsed and refractory B-cell lymphoma were recruited from the Department of Hematology of Tianjin First Central Hospital from February 2017 to January 2019. All patients received CD19 CAR-T cell therapy. These patients were evaluated for efficacy, factors with poor efficacyand adverse effects. Results: The overall response rate was 58.8% (20/34) and the complete remission rate was 41.2% (14/34) after infusion of CD19 CAR-T cells in 34 patients with relapsed refractory B cell lymphoma. According to the efficacy of CAR-T cells, patients were divided into two groups, 20 in the effective group and 14 in the poorly effective group. The median am ount of CD19 CAR-T cell infusions in these two groups were 8.6 (5.0-12.7)×10(6)/kg and 9.7 (5.8-15.0) × 10(6)/kg, respectively, and the difference was not statistically significant (P=0.654). The percentage of CD19 CAR-T cells in the effective group and the poorly treated group was 10.28% (3.92%-44.16%) and 4.05% (0.92%-28.63%), respectively.The effective group had a higher proportion of CAR-T cells than the poorly treated group, but the difference was not statistically significant (P=0.371).The presence of massive mass was an unfavorable factor affecting the efficacy of CD19 CAR-T cells and the difference was statistically significant (P=0.001). Logistic regression multivariate analysis showed that the characteristics of massive tumors were still independent prognostic factors for poor efficacy of CD19 CAR-T cells (P=0.005, OR=0.039). Of all 34 patients, there were 70.6% (24/34) who showed varying degrees of adverse reactions after the infusion of CD19 CAR-T cells, mainly cytokines release syndrome (CRS). The median time of occurrence of fever was on the third day after infusion (0-11th) day. 16 patients were with grade 1 CRS, 7 with grade 2, and 1 with grade 3. After glucocorticoids and support treatment, they all showed improvements. Conclusions: CD19 CAR-T cell therapy has achieved a certain effect in CD19(+)B cell lymphoma, but has poor efficacy on some patients. Large mass tumors may be an adverse factors to CAR-T cell treatment.
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He XY, Sun R, Wei YX, Lü HR, Xiao X, Li Q, Jiang YL, Zhang H, Feng J, Zhao MF. [The value of rapid on-site evaluation (ROSE) of bronchoscopy in the diagnosis of pulmonary complications after allogeneic hematopoietic stem cell transplantation]. ZHONGHUA YI XUE ZA ZHI 2020; 99:3775-3780. [PMID: 31874513 DOI: 10.3760/cma.j.issn.0376-2491.2019.48.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the value of rapid on-site evaluation (ROSE) of bronchoscopy in the diagnosis of pulmonary complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Methods: A retrospective analysis was conducted on the diagnosis and treatment process before and after ROSE examination of 12 patients with pulmonary complications after allo-HSCT who were admitted to the Department of hematology, Tianjin First Central Hospital from January 2017 to June 2019. The diagnostic accuracy of the ROSE was evaluated by comparing the initial diagnosis of ROSE with the final clinical diagnosis. At the same time, the safety of ROSE examination was evaluated and two typical cases were shared. Results: In the 12 transbronchial lung biopsies, there were 5 cases of organizing pneumonia, 3 cases of bronchiolitis obliterans with organizing pneumonia, 1 case of pulmonary fibrosis, 1 case of acute fibrinous and organizing pneumonia, 1 case of pseudomembranous tracheobronchial aspergillosis and 1 case of uncertain diagnosis evaluated by ROSE. Compared with the final clinical diagnosis, there were 10 cases of accurate diagnosis made by ROSE (10/12). All patients were well tolerant to the operation of bronchoscopy. There was only a small amount of bleeding observed during the operation, without pneumothorax and hemoptysis. And no complications related to ROSE occurred. According to the initial diagnosis of ROSE, 10 cases of non-infectious pulmonary complications were treated with methylprednisolone or other immunosuppressive agents and 1 case of Aspergillus infection was given antifungal therapy. Seven patients with non-infectious pulmonary complications improved after treatment. One patient obtained uncertain diagnosis by ROSE was later diagnosed with virus infection by next generation sequencing technology and improved after treatment with foscarnet sodium and immunoglobulin. As of June 30, 2019, 7 patients improved and 5 died. Conclusion: ROSE has the advantages of diagnostic accuracy and rapidity, and is very suitable for patients with critical illness after hematopoietic stem cell transplantation, who are in urgent need of definite diagnosis and prompt treatment, which is beneficial to improve the prognosis of patients.
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Lancia A, Becherini C, Detti B, Bottero M, Baki M, Cancelli A, Ferlosio A, Scoccianti S, Sun R, Livi L, Ingrosso G. Radiotherapy for papillary tumor of the pineal region: A systematic review of the literature. Clin Neurol Neurosurg 2019; 190:105646. [PMID: 31896492 DOI: 10.1016/j.clineuro.2019.105646] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 11/10/2019] [Accepted: 12/19/2019] [Indexed: 11/29/2022]
Abstract
Papillary tumor of the pineal region (PTPR) is a rare neuroepithelial brain tumor, characterized by a high risk of local recurrence (greater than 70 % at 6 years). The aim of our study was to review the available literature on radiotherapy for PTPR in order to evaluate timings, schedules, outcomes and toxicities of this treatment modality. In our review, 72.4 % (84) of the patients diagnosed with PTPR received radiation therapy. There is heterogeneity in the dose prescription, ranging from 45 Gy (25 × 1.8 Gy) to 60 Gy (30 × 2 Gy) for 3D Conformal Radiation Therapy and from 12 Gy to 36 Gy for Stereotactic Radiosurgery. Being considered as a grade II or III tumor, PTPR should receive higher total radiation dose in the adjuvant setting. Our analysis showed a very limited treatment-related toxicity with an expected 10-y OS of 72.5 %. At 5-years from the diagnosis, about 60 % of the patients experienced a local recurrence, whereas at 10 years the rate is higher than 80 %. In the literature, conflicting data about radiotherapy for PTPR are reported, in particular regarding disease progression. Although radiotherapy represents a fundamental treatment in the management of PTPR, prospective studies are required to better define its impact on overall survival and progression-free survival.
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Kim J, Carmona C, Farrell K, Zhang T, Chen H, Dimpasoc M, Soliman M, Marsden M, Sun R, Zack J. Effect of natural killer cells on viral rebound in HIV-1-infected humanized mice. J Virus Erad 2019. [DOI: 10.1016/s2055-6640(20)30117-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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81
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Tselikas L, Sun R, Ammari S, Dercle L, Yevich S, Hollebecque A, Ngo-Camus M, Nicotra C, Deutsch E, Deschamps F, de Baere T. Role of image-guided biopsy and radiomics in the age of precision medicine. Chin Clin Oncol 2019; 8:57. [DOI: 10.21037/cco.2019.12.02] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/02/2019] [Indexed: 11/06/2022]
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Sun R, Cao YQ, Ma JX, Yin SY, Zhang M, Song R, Jiang H, Gao Y, Zhang HY, Feng Z, Liu J, Liu ZX, Wang YB. [Construction and identification of mouse model with conditional knockout of p75 neurotrophin receptor gene in epidermal cells by Cre-loxP system]. ZHONGHUA SHAO SHANG ZA ZHI = ZHONGHUA SHAOSHANG ZAZHI = CHINESE JOURNAL OF BURNS 2019; 35:740-745. [PMID: 31658545 DOI: 10.3760/cma.j.issn.1009-2587.2019.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To construct and identify a mouse model with conditional knockout (cKO) of p75 neurotrophin receptor (p75NTR-cKO) gene in epidermis cells by Cre-loxP system. Methods: Five p75NTR(flox/flox) transgenic C57BL/6J mice (aged 6-8 weeks, male and female unlimited, the age and sex of mice used for reproduction were the same below) and five keratin 14 promotor-driven (KRT14-) Cre(+ /-) transgenic C57BL/6J mice were bred and hybridized via Cre-loxP system. Five p75NTR(flox/+) ·KRT14-Cre(+ /-) mice selected from the first generation of mice were mated with five p75NTR(flox/flox) mice to obtain the second generation hybrids. After the second generation mice were born 20-25 days, the parts of the mice tail were cut off to identify the genotype by polymerase chain reaction method. Four p75NTR gene complete cKO mice (6 weeks old) and 4 wild-type mice (6 weeks old) were selected and sacrificed respectively. The abdominal skin tissue and brain tissue were excised to observe the expression of p75NTR in the two tissue of two types of mice by immunohistochemical staining. The abdominal skin tissue of two types of mice was obtained to observe the histomorphological changes by hematoxylin and eosin staining. Results: (1) Twenty second generation mice were bred. The genotype of 4 mice was p75NTR(flox/flox)·KRT14-Cre(+ /-)(p75NTR(-/-)), i. e. p75NTR gene complete cKO mice; the genotype of 5 mice was p75NTR(flox/+) ·KRT14-Cre(+ /-), i. e. p75NTR gene partial cKO mice; the genotype of 5 mice was p75NTR(flox/flox)·KRT14-Cre(-/-), and that of 6 mice was p75NTR(flox/+) ·KRT14-Cre(-/-), all of which were wild-type mice. (2) The expression of p75NTR was negative in skin epidermis tissue of p75NTR gene complete cKO mice, while numerous p75NTR positive expression was observed in skin epidermis tissue of wild-type mice. Abundant p75NTR positive expression was observed in brain tissue of both wild-type mice and p75NTR gene complete cKO mice. (3) There was no abnormal growth of skin epidermis tissue in both wild-type mice and p75NTR gene complete cKO mice, with intact hair follicle structure. Conclusions: Applying Cre-loxP system can successfully construct a p75NTR-cKO mice model in epidermis cells without obvious changes in skin histomorphology.
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Boutros C, Chaput N, Lanoy E, Larive A, Mateus C, Routier E, Roy S, Sun R, Lancia A, Tao Y, Ibrahim N, Khoury-Abboud R, Massard C, Bahleda R, Schwob D, Caramella C, Cassard L, Soria JC, Robert C, Deutsch E. Ancillary evaluation of systemic immune antitumour response (SIAR) and tumour growth rate (TGR) of patients (pts) with metastatic melanoma (MM) treated with radiotherapy (RT) combined with ipilimumab (ipi) in the phase I study Mel-Ipi-Rx. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz255.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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84
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Vanacker H, Angevin E, Hollebecque A, Sun R, Deutsch E, Zynovyev A, Calzone L, Barillot E, Massard C, Verlingue L. Enhanced performance of prognostic estimation from TCGA RNAseq data using transfer learning. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239.073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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85
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Sun R, Lancia A, Sundahl N, Milic M, Carre A, Lerousseau M, Estienne T, Battistella E, Klausner G, Bahleda R, Alvarez-Andres E, Robert C, Boutros C, Vakalopoulou M, Paragios N, Ost P, Massard C, Deutsch E. Evaluation of a radiomic signature of CD8 cells in patients treated with immunotherapy-radiotherapy in three clinical trials. Ann Oncol 2019. [DOI: 10.1093/annonc/mdz239.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Zhang Z, Yang K, Huang J, Wu B, Qin Y, Peng G, Wu G, Sun R, Wang W. Association of Plasma Epstein–Barr Virus DNA with Morphology of Primary Tumor and Lymph Node in Nasopharyngeal Carcinoma and its Prognostic Value. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.1581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Li Y, Zhang W, Li N, Sun R, Tang J, Gong ZZ, Li Y, Yang X, Xie ZK, Gul Q, Zhang XQ, He W, Cheng ZH. Optical determination of spin diffusion length and interfacial spin mixing conductance in epitaxial Pd/Fe bilayers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:305802. [PMID: 30995617 DOI: 10.1088/1361-648x/ab1a99] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We present a detailed study of the photoinduced magnetization precession and magnetic relaxation in epitaxial Pd/Fe films on MgO(0 0 1) substrates via all-optical pump-probe techniques. We explicitly formulate the correlation between the Gilbert damping and the effective damping in the optical approach. Furthermore, a non-local Gilbert damping induced by spin pumping is demonstrated self-consistently by the Gilbert damping dependence on Pd thickness and the [Formula: see text] relationship of damping with Fe thickness [Formula: see text]. The non-local Gilbert damping enables the determination of spin diffusion length [Formula: see text] in Pd and interfacial spin mixing conductance [Formula: see text]. Our work paves the way toward the optical determination of spin transport parameters.
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Shengchen D, Gu X, Fan G, Sun R, Wang Y, Yu D, Li H, Zhou F, Xiong Z, Lu B, Zhu G, Cao B. Evaluation of a molecular point-of-care testing for viral and atypical pathogens on intravenous antibiotic duration in hospitalized adults with lower respiratory tract infection: a randomized clinical trial. Clin Microbiol Infect 2019; 25:1415-1421. [PMID: 31229593 PMCID: PMC7173318 DOI: 10.1016/j.cmi.2019.06.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/06/2019] [Accepted: 06/13/2019] [Indexed: 01/03/2023]
Abstract
Objectives The primary objective was to evaluate whether a molecular point-of-care test (POCT) for viral and atypical pathogens added to routine real-time PCR could reduce duration of intravenous antibiotics in hospitalized patients with lower respiratory tract infection (LRTI) compared with routine real-time PCR. Methods In this single-centre, open-label, randomized controlled study, we enrolled hospitalized adults diagnosed with LRTI. Patients were randomized to an intervention group (POCT FilmArray Panel for 20 viruses, atypical pathogens and bacteria plus routine real-time PCR) or a control group (routine real-time PCR for ten pathogens). The primary outcome was duration of intravenous antibiotics during hospitalization. The secondary outcomes included length of stay, cost of hospitalization and de-escalation within 72 hours and between 72 hours and 7 days. Intention-to-treat analysis was used. Results Between October 2017 and July 2018, we enrolled 800 eligible patients (398 in the intervention group and 402 in the control group). Duration of intravenous antibiotics in the intervention group was shorter than in the control (7.0 days (interquartile range (IQR) 5.0–9.0) versus 8.0 days (IQR 6.0–11.0); p <0.001). Length of hospital stay in the intervention group was significantly shorter (8.0 days (IQR 7.0–11.0) versus 9.0 days (IQR 7.0–12.0; p <0.001) and the cost of hospitalization in the intervention group was significantly lower ($1804.7 (IQR 1298.4–2633.8) versus $2042.5 (IQR 1427.4–2926.2); p 0.002) than control group. More patients in the intervention group achieved de-escalation within 72 hours (7.9%, 29/367 versus 3.2%, 12/377; p 0.005) and between 72 hours and 7 days (29.7%, 109/367 versus 22.0%, 83/377; p 0.024). Conclusions Use of molecular POCT testing for respiratory viruses and atypical pathogens might help to reduce intravenous antibiotic use in hospitalized LRTI patients. Clinical Trial Registration clinicaltrials.gov Identifier: NCT03391076.
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Li X, Sun R, Geng X, Wang S, Zen D, Pei J, Yang J, Fan Y, Jiang H, Yang P, Li C. A comprehensive analysis of candidate gene signatures in oral squamous cell carcinoma. Neoplasma 2019; 64:167-174. [PMID: 28043142 DOI: 10.4149/neo_2017_201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
This study aimed to unravel the molecular mechanism of oral squamous cell carcinoma (OSCC). With microarray dataset GSE30784, differentially expressed genes (DEGs) were identified between OSCC and control samples. The DEGs overlapped with genes obtained from online database MalaCards were determined as OSCCDEG, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. A total of 5177 up-regulated and 6081 down-regulated DEGs were identified between OSCC and control. Out of the DEGs, 451 genes were overlapped with the 704 genes gained from MalaCards and regarded as "OSCCDEG". Up-regulated OSCCDEG were associated with cell cycle pathway, while down-regulated OSCCDEG were linked to ErbB pathway. ANGPT1, ANGPT2 and 3 hub proteins (EGFR, HSP90AA1, RB1) in the PPI network were associated with the survival rates of several tumors. The largest network module with the hub protein EGFR was associated with positive regulation of cell communication. The second largest module with the hub node FN1 was related to angiogenesis. For the third network module in connection with DNA metabolism, the hub protein was PCNA. ErbB and cell cycle pathways were crucial for OSCC. EGFR, FN1, PCNA, ANGPT1 and ANGPT2 might be potential biomarkers for OSCC. These findings help provide guidelines for treating OSCC.
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Seban RD, Robert C, Dercle L, Yeh R, Dunant A, Reuze S, Schernberg A, Sun R, Mignot F, Terroir M, Schlumberger M, Haie-Meder C, Chargari C, Deutsch E. Increased bone marrow SUVmax on 18F-FDG PET is associated with higher pelvic treatment failure in patients with cervical cancer treated by chemoradiotherapy and brachytherapy. Oncoimmunology 2019; 8:e1574197. [PMID: 31069132 PMCID: PMC6492982 DOI: 10.1080/2162402x.2019.1574197] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/07/2019] [Accepted: 01/10/2019] [Indexed: 01/19/2023] Open
Abstract
The aim of this study was to evaluate if bone marrow (BM) SUVmax measured on pre-treatment 18F-FDG PET/CT predicts the clinical outcome of locally advanced cervical cancer (LACC). We recruited retrospectively patients with LACC who underwent staging 18F-FDG PET/CT and had baseline blood tests, then treated by chemoradiation therapy (CRT), followed by image-guided adaptive brachytherapy (IGABT). BM SUVmax was calculated and correlated to inflammatory blood markers. Tumor size and pelvic lymph node involvement were evaluated on baseline MRI. Prognostic value of SUV uptake and blood markers regarding overall survival (OS), pelvic and extra-pelvic recurrence-free survival (PRFS and EPRFS respectively) was assessed using Cox models with adjusted p-values. 116 patients with FIGO stage Ib-IVa cervical cancer, treated between 2005 and 2014, were analyzed. The median follow-up was 75.5 months. BM SUVmax was significantly correlated to tumor SUVmax. In multivariate analysis, PRFS was significantly poorer in patients with high BM SUVmax (>2.8) and neutrophilia (p < .05). Tumor size (>5 vs ≤5 cm) could predict PRFS, EPRFS and OS (p < .05). In our cohort, FIGO stage (I-II vs III-IV), pelvic lymph node involvement and tumor SUVmax (>12 vs ≤12) were not prognostic for OS or pelvic and extra-pelvic relapses. Patients with LACC and high BM SUVmax on 18F-FDG PET have worse PFRS following CRT plus IGABT. These results can be potentially explained by the pro-inflammatory role of the tumor microenvironment and G-CSF expressed by tumor cells. These data support the role of PET as a potential indicator of disease aggressiveness beyond tumor staging.
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Caswell-Jin JL, McNamara K, Reiter JG, Sun R, Hu Z, Ma Z, Suarez CJ, Tilk S, Raghavendra A, Forte V, Chin SF, Bardwell H, Provenzano E, Caldas C, Lang J, West R, Tripathy D, Press MF, Curtis C. Abstract P3-06-01: Clonal evolution and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-p3-06-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Understanding to what extent a breast tumor's genetic composition may change over the course of a few months of neoadjuvant therapy has implications for optimal therapeutic approach. However, genomic changes observed across treatment may result from either treatment-induced clonal evolution or geographically disparate sampling of a heterogeneous tumor. We sought to characterize the geographic heterogeneity in primary breast tumors, and to incorporate this information into analysis of clonal evolution with neoadjuvant therapy.
Methods: We assembled the largest cohort to date of multi-region (n=2-3) whole-exome sequenced (WES) or whole-genome sequenced untreated primary breast tumors with matched normal and adequate tumor purity for analysis: four tumors with data generated for this study and five tumors compiled from three previous studies. We also generated the first cohort of multi-region (n=2-6) WES breast tumors post-neoadjuvant HER2-targeted therapy and chemotherapy, sequencing one region from a pre-treatment diagnostic specimen, multiple regions from the post-treatment surgical specimen, and matched normal for five HER2+ breast tumors that did not achieve a pathologic complete response. We used an agent-based model of spatial tumor growth to investigate whether the mutational patterns we observed with treatment were consistent with pre-existing heterogeneity or treatment-induced selection.
Results: In untreated primary breast tumors, on average 30% (range 1-70%) of apparently clonal mutations from a single region were absent or rare in a second, spatially disparate region (high-frequency regional, or HFR). Intra-tumor heterogeneity was similar post-treatment (HFR 28%, range 10-54%), and was higher in breast tumors than in previously analyzed colon, brain, lung, and esophageal tumors. Simulation studies confirmed that with high heterogeneity as observed in breast tumors, analysis of one pre-treatment and one post-treatment region could not distinguish treatment-induced clonal evolution from pre-existing heterogeneity; however, obtaining at least two post-treatment regions allowed for detection of clonal shifts with treatment. Analysis of multi-region data revealed that clonal replacement occurred with neoadjuvant therapy in two of the five tumors. Candidate causes of therapeutic resistance included amplifications in CCND1, ERBB4, and MYC in one subclone, and functional protein-altering mutations in ERCC2, SMO, and WT1 in another. Mathematical modeling suggested that these putative resistant subclones comprised 0.02-12.5% of the overall pre-treatment cell population, substantially larger than previous estimates of resistant tumor clone size.
Conclusions: WES data from multiple regions of untreated and treated primary breast tumors revealed considerable heterogeneity that remained present throughout treatment with chemotherapy and HER2-targeted therapy, even while major clonal sweeps took place in a minority of tumors. Obtaining at least two samples for analysis from breast tumors post-neoadjuvant therapy may reveal the tumor's evolutionary path and, especially as increasing numbers of molecular and immune therapeutic targets are identified, inform new clinical strategies.
Citation Format: Caswell-Jin JL, McNamara K, Reiter JG, Sun R, Hu Z, Ma Z, Suarez CJ, Tilk S, Raghavendra A, Forte V, Chin S-F, Bardwell H, Provenzano E, Caldas C, Lang J, West R, Tripathy D, Press MF, Curtis C. Clonal evolution and heterogeneity in breast tumors treated with neoadjuvant HER2-targeted therapy [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-06-01.
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Sun R, Aldunate R, Ratnam R, Jain S, Morrow D, Sosnoff J. VALIDITY AND USABILITY OF AN AUTOMATED FALL RISK ASSESSMENT TOOL FOR OLDER ADULTS. Innov Aging 2018. [DOI: 10.1093/geroni/igy023.1338] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Hua X, Chen L, Zhu Q, Hu W, Lin C, Long Z, Wen W, Sun X, Lu Z, Chen Q, Luo D, Sun R, Mo H, Tang L, Zhang W, He Z, Mai H, Lin H, Guo L. Efficacy of controlled-release oxycodone for reducing pain due to oral mucositis in nasopharyngeal carcinoma patients treated with concurrent chemoradiotherapy: A prospective clinical trial. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy438.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Benhmida S, Sun R, Gherga E, Hammoud Y, Lestrade L, Boulbair F, Mauvais O, Bontemps P, Thariat J, Bourhis J, Sun X. Radiothérapie hypofractionnée en split course de patients âgés et fragiles atteints d’un cancer de la tête et du cou localement évolué : étude de 58 cas. Cancer Radiother 2018. [DOI: 10.1016/j.canrad.2018.07.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Pu Y, Sun R, Sun F, Zhang J, Yin L, Man Z, Pu Y. Role of Hif-1a and its target gene PTP4A3 in regulating cell proliferation during benzene exposure. Toxicol Lett 2018. [DOI: 10.1016/j.toxlet.2018.06.862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Lyu X, Zeng L, Yuan J, Meng X, Sun R, Liu B, Bai Y, Liu X, Li Z, Yang S. P2.13-37 Chloroquine overcomes acquired resistance to icotinib in vitro and in vivo through STAT3/STMN1 pathway. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Sun R, Limkin EJ, Vakalopoulou M, Dercle L, Champiat S, Han SR, Verlingue L, Brandao D, Lancia A, Ammari S, Hollebecque A, Scoazec JY, Marabelle A, Massard C, Soria JC, Robert C, Paragios N, Deutsch E, Ferté C. A radiomics approach to assess tumour-infiltrating CD8 cells and response to anti-PD-1 or anti-PD-L1 immunotherapy: an imaging biomarker, retrospective multicohort study. Lancet Oncol 2018; 19:1180-1191. [PMID: 30120041 DOI: 10.1016/s1470-2045(18)30413-3] [Citation(s) in RCA: 710] [Impact Index Per Article: 118.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 05/18/2018] [Accepted: 05/23/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Because responses of patients with cancer to immunotherapy can vary in success, innovative predictors of response to treatment are urgently needed to improve treatment outcomes. We aimed to develop and independently validate a radiomics-based biomarker of tumour-infiltrating CD8 cells in patients included in phase 1 trials of anti-programmed cell death protein (PD)-1 or anti-programmed cell death ligand 1 (PD-L1) monotherapy. We also aimed to evaluate the association between the biomarker, and tumour immune phenotype and clinical outcomes of these patients. METHODS In this retrospective multicohort study, we used four independent cohorts of patients with advanced solid tumours to develop and validate a radiomic signature predictive of immunotherapy response by combining contrast-enhanced CT images and RNA-seq genomic data from tumour biopsies to assess CD8 cell tumour infiltration. To develop the radiomic signature of CD8 cells, we used the CT images and RNA sequencing data of 135 patients with advanced solid malignant tumours who had been enrolled into the MOSCATO trial between May 1, 2012, and March 31, 2016, in France (training set). The genomic data, which are based on the CD8B gene, were used to estimate the abundance of CD8 cells in the samples and data were then aligned with the images to generate the radiomic signatures. The concordance of the radiomic signature (primary endpoint) was validated in a Cancer Genome Atlas [TGCA] database dataset including 119 patients who had available baseline preoperative imaging data and corresponding transcriptomic data on June 30, 2017. From 84 input variables used for the machine-learning method (78 radiomic features, five location variables, and one technical variable), a radiomics-based predictor of the CD8 cell expression signature was built by use of machine learning (elastic-net regularised regression method). Two other independent cohorts of patients with advanced solid tumours were used to evaluate this predictor. The immune phenotype internal cohort (n=100), were randomly selected from the Gustave Roussy Cancer Campus database of patient medical records based on previously described, extreme tumour-immune phenotypes: immune-inflamed (with dense CD8 cell infiltration) or immune-desert (with low CD8 cell infiltration), irrespective of treatment delivered; these data were used to analyse the correlation of the immune phenotype with this biomarker. Finally, the immunotherapy-treated dataset (n=137) of patients recruited from Dec 1, 2011, to Jan 31, 2014, at the Gustave Roussy Cancer Campus, who had been treated with anti-PD-1 and anti-PD-L1 monotherapy in phase 1 trials, was used to assess the predictive value of this biomarker in terms of clinical outcome. FINDINGS We developed a radiomic signature for CD8 cells that included eight variables, which was validated with the gene expression signature of CD8 cells in the TCGA dataset (area under the curve [AUC]=0·67; 95% CI 0·57-0·77; p=0·0019). In the cohort with assumed immune phenotypes, the signature was also able to discriminate inflamed tumours from immune-desert tumours (0·76; 0·66-0·86; p<0·0001). In patients treated with anti-PD-1 and PD-L1, a high baseline radiomic score (relative to the median) was associated with a higher proportion of patients who achieved an objective response at 3 months (vs those with progressive disease or stable disease; p=0·049) and a higher proportion of patients who had an objective response (vs those with progressive disease or stable disease; p=0·025) or stable disease (vs those with progressive disease; p=0·013) at 6 months. A high baseline radiomic score was also associated with improved overall survival in univariate (median overall survival 24·3 months in the high radiomic score group, 95% CI 18·63-42·1; vs 11·5 months in the low radiomic score group, 7·98-15·6; hazard ratio 0·58, 95% CI 0·39-0·87; p=0·0081) and multivariate analyses (0·52, 0·35-0·79; p=0·0022). INTERPRETATION The radiomic signature of CD8 cells was validated in three independent cohorts. This imaging predictor provided a promising way to predict the immune phenotype of tumours and to infer clinical outcomes for patients with cancer who had been treated with anti-PD-1 and PD-L1. Our imaging biomarker could be useful in estimating CD8 cell count and predicting clinical outcomes of patients treated with immunotherapy, when validated by further prospective randomised trials. FUNDING Fondation pour la Recherche Médicale, and SIRIC-SOCRATE 2.0, French Society of Radiation Oncology.
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Horn P, Haschemi J, Scheiber D, Szendroedi J, Zweck E, Sun R, Luppa PB, Saeed D, Boeken U, Kelm M, Roden M, Boege F, Westenfeld R. P2781Sympathomimetic beta-1AR autoantibodies in patients after heart transplantation are associated with higher mitochondrial coupling efficiency. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p2781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Sun R, Wang Y, Jin M, Chen L, Cao Y, Chen F. Identification and Functional Studies of MYO1H for Mandibular Prognathism. J Dent Res 2018; 97:1501-1509. [PMID: 29986156 DOI: 10.1177/0022034518784936] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mandibular prognathism (MP) is regarded as a craniofacial deformity resulting from the combined effects of environmental and genetic factors, while the genetically predetermined component is considered to play an important role to develop MP. Although linkage and association studies for MP have identified multiple strongly associated regions and genes, the causal genes and variants responsible for the deformity remain largely undetermined. To address this, we performed targeted sequencing of 396 genes selected from previous studies as well as genes and pathways related with craniofacial development as primary candidates in 199 MP cases and 197 controls and carried out a series of statistical and functional analyses. A nonsynonymous common variant of MYO1H rs3825393, C>T, p.Pro1001Leu, was identified to be significantly associated with MP. During zebrafish embryologic development, expression of MYO1H orthologous genes were detected at mandibular jaw. Furthermore, jaw cartilage defects were observed in zebrafish knockdown models. Collectively, these data demonstrate that MYO1H is required for proper jaw growth and contributes to MP pathogenesis, expanding our knowledge of the genetic basis of MP.
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Fanning SW, Hodges-Gallagher L, Myles DC, Sun R, Fowler CE, Plant IN, Green BD, Harmon CL, Greene GL, Kushner PJ. Specific stereochemistry of OP-1074 disrupts estrogen receptor alpha helix 12 and confers pure antiestrogenic activity. Nat Commun 2018; 9:2368. [PMID: 29915250 PMCID: PMC6006285 DOI: 10.1038/s41467-018-04413-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 04/27/2018] [Indexed: 11/09/2022] Open
Abstract
Complex tissue-specific and cell-specific signaling by the estrogen receptor (ER) frequently leads to the development of resistance to endocrine therapy for breast cancer. Pure ER antagonists, which completely lack tissue-specific agonist activity, hold promise for preventing and treating endocrine resistance, however an absence of structural information hinders the development of novel candidates. Here we synthesize a small panel of benzopyrans with variable side chains to identify pure antiestrogens in a uterotrophic assay. We identify OP-1074 as a pure antiestrogen and a selective ER degrader (PA-SERD) that is efficacious in shrinking tumors in a tamoxifen-resistant xenograft model. Biochemical and crystal structure analyses reveal a structure activity relationship implicating the importance of a stereospecific methyl on the pyrrolidine side chain of OP-1074, particularly on helix 12. Estrogen receptor alpha (ERα) plays critical roles in the etiology and treatment of breast cancer. Here the authors synthesize benzopyrans with variable side chains to identify antiestrogenic compounds and characterize OP-1074, a compound that exhibits pure antiestrogenic activity by inducing the degradation of ERα and possesses greater potency than tamoxifen or fulvestrant in a xenograft model.
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