1
|
Ramesh P, Ruan D, Sheng K. Hypoxia Informed RBE-Weighted Beam Orientation Optimization for Intensity Modulated Proton Therapy Using [ 18F]-FMISO-PET Estimation of pO 2. Int J Radiat Oncol Biol Phys 2023; 117:e709. [PMID: 37786075 DOI: 10.1016/j.ijrobp.2023.06.2205] [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) Variable relative biological effectiveness (RBE) models have previously informed proton therapy dose optimization algorithms, but few models have incorporated hypoxia's increase on radioresistance. Here, we obtain voxel-based estimation of partial oxygen pressure to weigh RBE values in a single biologically informed beam orientation optimization (BOO) algorithm. MATERIALS/METHODS Four brain cancer patients with [18F]-FMISO-PET/CT images were selected from an HCP database. Oxygen values were derived from tracer uptake using a non-linear least squares curve fitting. RBE dose was then weighted using oxygen enhancement ratios (OER) for each structure and substituted into the dose fidelity term of our BOO algorithm. The nonlinear optimization problem was solved using a split-Bregman approach, with FISTA as the solver. This method (HypRBE) was compared dose fidelity terms using the Rorvik RBE model (RegRBE), without OER. Tumor homogeneity index (HI), Dmax, and D95% were evaluated along with worst-case statistics after normalization to normal tissue isotoxicity. RESULTS Compared to RegRBE, HypRBE increased tumor [HI, Dmax, D95%] on average by [0.5%, 2.0%, 2.5%] and improved worst-case tumor [HI, Dmax, D95%] by [5.3%, 16.2%, 9.6%]. HypRBE shows an increase in therapeutic ratio, and is notably robust against uncertainty scenarios. CONCLUSION We have developed an optimization algorithm whose dose fidelity term is weighted by hypoxia informed RBE values. We have shown that HypRBE selects beams that are better suited to protect low RBE, well-oxygenated normal tissue while maintaining high dose to high RBE, hypoxic tumor cells.
Collapse
Affiliation(s)
- P Ramesh
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA
| | - D Ruan
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA
| | - K Sheng
- University of California, San Francisco, San Francisco, CA
| |
Collapse
|
2
|
Jiao C, Ling DC, Bian SX, Vassantachart A, Cheng K, Mehta S, Lock D, Feng M, Thomas H, Scholey J, Sheng K, Fan Z, Yang W. Contouring Analysis on Synthetic Contrast-Enhanced MR from GRMM-GAN and Implications on MR-Guide Radiation Therapy. Int J Radiat Oncol Biol Phys 2023; 117:S117. [PMID: 37784304 DOI: 10.1016/j.ijrobp.2023.06.450] [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) MR-guided linear accelerators have been commercialized making MR-only planning and adaptation an appealing alternative circumventing MR-CT registration. However, obtaining daily contrast-enhanced MR images can be prohibitive due to the increased risk of side effects from repeated contrast injections. In this work, we evaluate the quality of contrast-enhanced multi-modal MR image synthesis network GRMM-GAN (gradient regularized multi-modal multi-discrimination sparse-attention fusion generative adversarial network) for MR-guided radiation therapy. MATERIALS/METHODS With IRB approval, we trained the GRMM-GAN based on 165 abdominal MR studies from 65 patients. Each study included T2, T1 pre-contrast (T1pre), and T1 contrast enhanced (T1ce) images. The two pre-contrast MR modalities, T2 and T1pre images were adopted as inputs for GRMM-GAN, and the T1ce image at the portal venous phase was used as an output. Ten MR scans containing 21 liver tumors were selected for contouring analysis. A Turing test was first given to six radiation oncologists, in which 100 real T1ce and synthetic T1ce image slices are randomly given to the radiation oncologists to determine the authenticity of the synthesis. We then invited two radiation oncologists (RadOnc 1 and RadOnc2) to manually contour the 21 liver tumors independently on the real T1ce images. RadOnc2 then performed contouring on the respective synthetic T1ce MRs. DICE coefficient (defined as the intersection over the average of two volumes) and Hausdorff distance (HD, measuring how far two volumes are from each other) were used as analysis metrics. The DICE coefficients were calculated from the two radiation oncologists' contours on the real T1ce MR for each tumor. The DICE coefficients were also calculated from RadOnc 2's contours on real and synthetic MRs. Besides, tumor center shifts were extracted. The tumor center of mass coordinates was extracted from real and synthetic volumes. The difference in the coordinates indicated the shifts in the superior-inferior (SI), right-left (RL), and anterior-posterior (AP) directions between real and synthetic tumor volumes. RESULTS An average of 52.3% test score was achieved from the six radiation oncologists, which is close to random guessing. RadOnc 1 and RadOnc 2, who had participated in the contouring analysis, achieved an average DICE of 0.91±0.02 from tumor volumes drawn on the real T1ce MRs. This result sets the inter-operator uncertainty baseline in the real clinical setting. RadOnc 2 achieved an average DICE (real vs. synth) of 0.90±0.04 and HD of 4.76±1.82 mm. Only sub-millimeter (SI: 0.67 mm, RL: 0.41 mm, AP: 0.39 mm) tumor center shifts were observed in all three directions. CONCLUSION The GRMM-GAN method has the potential for MR-guided liver radiation when contrast agents cannot be administered daily and provide synthetic contrast-enhanced MR for better tumor targeting. The network can produce synthetic MR images with satisfactory contour agreement and geometric integrity.
Collapse
Affiliation(s)
- C Jiao
- University of California, San Francisco, San Francisco, CA
| | - D C Ling
- University of Southern California, Los Angeles, CA
| | - S X Bian
- University of Southern California, Los Angeles, CA
| | - A Vassantachart
- Department of Radiation Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - K Cheng
- Department of Radiation Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - S Mehta
- Department of Radiation Oncology, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - D Lock
- University of Southern California, Los Angeles, CA
| | - M Feng
- University of California, San Francisco, San Francisco, CA
| | - H Thomas
- University of California, San Francisco, San Francisco, CA
| | - J Scholey
- University of California, San Francisco, San Francisco, CA
| | - K Sheng
- University of California, San Francisco, San Francisco, CA
| | - Z Fan
- University of Southern California, Los Angeles, CA
| | - W Yang
- University of California, San Francisco, San Francisco, CA
| |
Collapse
|
3
|
Liu H, Neilsen BK, Xu D, Pham J, Cao M, Ruan D, Kishan AU, Sheng K. Towards Automated Dosimetric Analysis of the Bladder Trigone: Deep-Learning-Based Joint Segmentation and Landmark Localization. Int J Radiat Oncol Biol Phys 2023; 117:S118. [PMID: 37784306 DOI: 10.1016/j.ijrobp.2023.06.452] [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) The bladder trigone dosimetry is hypothesized to have a stronger correlation with post-SBRT urinary toxicity than that of the entire bladder. However, the trigone tends to move significantly between simulation and daily treatment. Its small size, large daily motion, and proximity to the target lead to potentially consequential but unaccounted-for dosimetric uncertainties. Manual segmentation of the structure can be inconsistent and time-consuming, even with MR-guided RT. Here, we propose and demonstrate a deep-learning-based framework for joint segmentation and landmark localization to support deformable registration and comprehensive dosimetric analysis. MATERIALS/METHODS A total of 30 patients were randomly selected for training, and 20 were held out for testing. Each patient had 1 simulation and 5 daily pre-treatment images obtained from a clinical 0.35T MR Linac. The trigone is defined as the triangular bladder section among three landmarks (2 ureteral orifices and the internal urethral orifice). In the manual contouring process, the 3 landmarks were identified first, followed by trigone segmentation. The proposed joint method uses a modified 3D nnU-Net with 2 decoders, one for segmentation and the other for landmark localization. The shared encoder is expected to extract features useful for both tasks. The joint framework was compared with a baseline method using two separate 3D nnU-Nets for landmark localization and trigone segmentation, respectively. Since the trigone is small (∼2% of the bladder volume), we further experimented with a second-stage prediction mimicking the human contouring process. The predicted landmarks from the first stage were used to crop the trigone region, and a second network was trained on cropped images. Evaluation metrics included the Dice score, 95% Hausdorff distance (HD95), and average surface distance (ASD) for segmentation, and Euclidean distance (ED) between the predicted and ground truth landmarks for localization. RESULTS The quantification metrics are summarized in the table below. The joint approach shows similar Dice performance to the baseline method but markedly better HD95 by 13%. For landmark localization, the proposed method is similar to the baseline, but the integration of the segmentation task stabilizes the training process. The two-stage approach further improves HD95, ASD, and ED by 27%, 24%, and 19%. CONCLUSION Combining segmentation and landmark localization exhibits a synergistic effect. The proposed two-stage approach provided additional improvement. Future studies will explore the deformable registration of the trigone based on the segmentation and landmark detection, as well as analyze cumulated dose distribution.
Collapse
Affiliation(s)
- H Liu
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA; Physics and Biology in Medicine, University of California, Los Angeles, Los Angeles, CA
| | - B K Neilsen
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA
| | - D Xu
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA; Computer Science, University of California, Los Angeles, Los Angeles, CA
| | - J Pham
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA; Physics and Biology in Medicine, University of California, Los Angeles, Los Angeles, CA
| | - M Cao
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA
| | - D Ruan
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA; Physics and Biology in Medicine, University of California, Los Angeles, Los Angeles, CA
| | - A U Kishan
- Department of Radiation Oncology, University of California, Los Angeles, Los Angeles, CA; Department of Urology, University of California, Los Angeles, Los Angeles, CA
| | - K Sheng
- University of California, San Francisco, San Francisco, CA
| |
Collapse
|
4
|
Xu Z, Wang Y, Sheng K, Rosenthal R, Liu N, Hua X, Zhang T, Chen J, Song M, Lv Y, Zhang S, Huang Y, Wang Z, Cao T, Shen Y, Jiang Y, Yu Y, Chen Y, Guo G, Yin P, Weitz DA, Wang Y. Droplet-based high-throughput single microbe RNA sequencing by smRandom-seq. Nat Commun 2023; 14:5130. [PMID: 37612289 PMCID: PMC10447461 DOI: 10.1038/s41467-023-40137-9] [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] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 07/10/2023] [Indexed: 08/25/2023] Open
Abstract
Bacteria colonize almost all parts of the human body and can differ significantly. However, the population level transcriptomics measurements can only describe the average bacteria population behaviors, ignoring the heterogeneity among bacteria. Here, we report a droplet-based high-throughput single-microbe RNA-seq assay (smRandom-seq), using random primers for in situ cDNA generation, droplets for single-microbe barcoding, and CRISPR-based rRNA depletion for mRNA enrichment. smRandom-seq showed a high species specificity (99%), a minor doublet rate (1.6%), a reduced rRNA percentage (32%), and a sensitive gene detection (a median of ~1000 genes per single E. coli). Furthermore, smRandom-seq successfully captured transcriptome changes of thousands of individual E. coli and discovered a few antibiotic resistant subpopulations displaying distinct gene expression patterns of SOS response and metabolic pathways in E. coli population upon antibiotic stress. smRandom-seq provides a high-throughput single-microbe transcriptome profiling tool that will facilitate future discoveries in microbial resistance, persistence, microbe-host interaction, and microbiome research.
Collapse
Affiliation(s)
- Ziye Xu
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Yuting Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - Raoul Rosenthal
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA
| | - Nan Liu
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Xiaoting Hua
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tianyu Zhang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Jiaye Chen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Mengdi Song
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Yuexiao Lv
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Shunji Zhang
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
| | - Yingjuan Huang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Zhaolun Wang
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Ting Cao
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA
| | - Yifei Shen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Chen
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Guoji Guo
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
| | - David A Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA, USA.
| | - Yongcheng Wang
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China.
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China.
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, USA.
| |
Collapse
|
5
|
Tian S, Xiong X, Zeng J, Wang S, Tremblay BJM, Chen P, Chen B, Liu M, Chen P, Sheng K, Zeve D, Qi W, Breault DT, Rodríguez C, Gerhard R, Jin R, Doxey AC, Dong M. Identification of TFPI as a receptor reveals recombination-driven receptor switching in Clostridioides difficile toxin B variants. Nat Commun 2022; 13:6786. [PMID: 36351897 PMCID: PMC9646764 DOI: 10.1038/s41467-022-33964-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 04/16/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022] Open
Abstract
Toxin B (TcdB) is a major exotoxin responsible for diseases associated with Clostridioides difficile infection. Its sequence variations among clinical isolates may contribute to the difficulty in developing effective therapeutics. Here, we investigate receptor-binding specificity of major TcdB subtypes (TcdB1 to TcdB12). We find that representative members of subtypes 2, 4, 7, 10, 11, and 12 do not recognize the established host receptor, frizzled proteins (FZDs). Using a genome-wide CRISPR-Cas9-mediated screen, we identify tissue factor pathway inhibitor (TFPI) as a host receptor for TcdB4. TFPI is recognized by a region in TcdB4 that is homologous to the FZD-binding site in TcdB1. Analysis of 206 TcdB variant sequences reveals a set of six residues within this receptor-binding site that defines a TFPI binding-associated haplotype (designated B4/B7) that is present in all TcdB4 members, a subset of TcdB7, and one member of TcdB2. Intragenic micro-recombination (IR) events have occurred around this receptor-binding region in TcdB7 and TcdB2 members, resulting in either TFPI- or FZD-binding capabilities. Introduction of B4/B7-haplotype residues into TcdB1 enables dual recognition of TFPI and FZDs. Finally, TcdB10 also recognizes TFPI, although it does not belong to the B4/B7 haplotype, and shows species selectivity: it recognizes TFPI of chicken and to a lesser degree mouse, but not human, dog, or cattle versions. These findings identify TFPI as a TcdB receptor and reveal IR-driven changes on receptor-specificity among TcdB variants.
Collapse
Affiliation(s)
- Songhai Tian
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA.
| | - Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Ji Zeng
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, 510006, China
| | - Siyu Wang
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Benjamin Jean-Marie Tremblay
- Department of Biology, Cheriton School of Computer Science, and Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, N2L 3G1, Canada
| | - Peng Chen
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Baohua Chen
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Min Liu
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Kuanwei Sheng
- Wyss Institute for Bioinspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Daniel Zeve
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Wanshu Qi
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA, 02138, USA
| | - César Rodríguez
- Faculty of Microbiology & CIET, University of Costa Rica, San José, Costa Rica
| | - Ralf Gerhard
- Institute of Toxicology, Hannover Medical School, 30625, Hannover, Germany
| | - Rongsheng Jin
- Department of Physiology and Biophysics, School of Medicine, University of California Irvine, Irvine, CA, 92697, USA
| | - Andrew C Doxey
- Department of Biology, Cheriton School of Computer Science, and Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA, 02115, USA.
- Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
6
|
Du J, Zhou Y, Jin L, Sheng K. A Hybrid Tumor Model for Ultra-Large-Scale Heterogeneous Vascular Tumor Growth. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Jiao C, Lao Y, Vassantachart A, Shiroishi M, Zada G, Chang E, Fan Z, Sheng K, Yang W. Voxel-Wise GBM Recurrence Prediction Based on Sparse Attention Multi-Modal MR Image Fusion Coupling with Stem Cell Niches Proximity Estimation. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
8
|
Lao Y, Yang W, Moghanaki D, Sheng K. Biomedical Profiling of Lung Tumor via Ventilation-Induced Tumor Deformation: Implications on the Prognosis of Lung Cancer. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.1518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
9
|
Jiang L, Lyu Q, Abdelhamid A, Hui S, Sheng K. A Sparse Orthogonal Collimators System for Experiments on Small-Animal Scale. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
10
|
Xiong X, Tian S, Yang P, Lebreton F, Bao H, Sheng K, Yin L, Chen P, Zhang J, Qi W, Ruan J, Wu H, Chen H, Breault DT, Wu H, Earl AM, Gilmore MS, Abraham J, Dong M. Emerging enterococcus pore-forming toxins with MHC/HLA-I as receptors. Cell 2022; 185:1157-1171.e22. [PMID: 35259335 PMCID: PMC8978092 DOI: 10.1016/j.cell.2022.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [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: 07/02/2021] [Revised: 12/15/2021] [Accepted: 02/01/2022] [Indexed: 01/12/2023]
Abstract
Enterococci are a part of human microbiota and a leading cause of multidrug resistant infections. Here, we identify a family of Enterococcus pore-forming toxins (Epxs) in E. faecalis, E. faecium, and E. hirae strains isolated across the globe. Structural studies reveal that Epxs form a branch of β-barrel pore-forming toxins with a β-barrel protrusion (designated the top domain) sitting atop the cap domain. Through a genome-wide CRISPR-Cas9 screen, we identify human leukocyte antigen class I (HLA-I) complex as a receptor for two members (Epx2 and Epx3), which preferentially recognize human HLA-I and homologous MHC-I of equine, bovine, and porcine, but not murine, origin. Interferon exposure, which stimulates MHC-I expression, sensitizes human cells and intestinal organoids to Epx2 and Epx3 toxicity. Co-culture with Epx2-harboring E. faecium damages human peripheral blood mononuclear cells and intestinal organoids, and this toxicity is neutralized by an Epx2 antibody, demonstrating the toxin-mediated virulence of Epx-carrying Enterococcus.
Collapse
Affiliation(s)
- Xiaozhe Xiong
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Songhai Tian
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pan Yang
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Francois Lebreton
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Huan Bao
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
| | - Linxiang Yin
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jie Zhang
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA
| | - Wanshu Qi
- Division of Endocrinology, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jianbin Ruan
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Immunology, University of Connecticut Health School of Medicine, Farmington, CT 06030, USA
| | - Hao Wu
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hong Chen
- Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - David T Breault
- Division of Endocrinology, Boston Children's Hospital, and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Hao Wu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael S Gilmore
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Jonathan Abraham
- Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Infectious Diseases, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Department of Surgery, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
| |
Collapse
|
11
|
Cao M, Gao Y, Yoon S, Yang Y, Sheng K, Sachdeva A, Ballas L, Steinberg M, Kishan A. Interfractional Geometric Variations and Dosimetric Benefits of Online Adaptive Stereotactic Body Radiotherapy of Prostate Bed After Radical Prostatectomy. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
12
|
Bota-Rabassedas N, Banerjee P, Niu Y, Cao W, Luo J, Xi Y, Tan X, Sheng K, Ahn YH, Lee S, Parra ER, Rodriguez-Canales J, Albritton J, Weiger M, Liu X, Guo HF, Yu J, Rodriguez BL, Firestone JJA, Mino B, Creighton CJ, Solis LM, Villalobos P, Raso MG, Sazer DW, Gibbons DL, Russell WK, Longmore GD, Wistuba II, Wang J, Chapman HA, Miller JS, Zong C, Kurie JM. Contextual cues from cancer cells govern cancer-associated fibroblast heterogeneity. Cell Rep 2021; 35:109009. [PMID: 33882319 PMCID: PMC8142261 DOI: 10.1016/j.celrep.2021.109009] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 01/21/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022] Open
Abstract
Cancer cells function as primary architects of the tumor microenvironment. However, the molecular features of cancer cells that govern stromal cell phenotypes remain unclear. Here, we show that cancer-associated fibroblast (CAF) heterogeneity is driven by lung adenocarcinoma (LUAD) cells at either end of the epithelial-to-mesenchymal transition (EMT) spectrum. LUAD cells that have high expression of the EMT-activating transcription factor ZEB1 reprogram CAFs through a ZEB1-dependent secretory program and direct CAFs to the tips of invasive projections through a ZEB1-driven CAF repulsion process. The EMT, in turn, sensitizes LUAD cells to pro-metastatic signals from CAFs. Thus, CAFs respond to contextual cues from LUAD cells to promote metastasis. Bota-Rabassedas et al. show that EMT in lung adenocarcinoma cells activates a secretory process that governs CAF heterogeneity and, in turn, sensitizes lung adenocarcinoma cells to pro-metastatic signals from CAFs. Thus, EMT positions lung adenocarcinoma cells at the apex of a signaling hierarchy in the tumor microenvironment.
Collapse
Affiliation(s)
- Neus Bota-Rabassedas
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Priyam Banerjee
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yichi Niu
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wenjian Cao
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jiayi Luo
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Yuanxin Xi
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaochao Tan
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kuanwei Sheng
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Young-Ho Ahn
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Sieun Lee
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Edwin Roger Parra
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaime Rodriguez-Canales
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jacob Albritton
- Department of Molecular Medicine and Inflammation-Cancer Microenvironment Research Center, College of Medicine, Ewha Womans University, Seoul 07804, Korea
| | - Michael Weiger
- Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xin Liu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hou-Fu Guo
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jiang Yu
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - B Leticia Rodriguez
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Barbara Mino
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chad J Creighton
- Dan L Duncan Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Luisa M Solis
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Pamela Villalobos
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Maria Gabriela Raso
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Daniel W Sazer
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Don L Gibbons
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William K Russell
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Gregory D Longmore
- Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA; Department of Cell Biology & Physiology, Washington University in St. Louis, St. Louis, MO, USA
| | - Ignacio I Wistuba
- Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jing Wang
- Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Harold A Chapman
- Department of Medicine, University of California, San Francisco Cardiovascular Research Institute, San Francisco, CA, USA
| | - Jordan S Miller
- Department of Bioengineering, Rice University, Houston, TX, USA.
| | - Chenghang Zong
- Departments of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Jonathan M Kurie
- Departments of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
13
|
Abstract
Circulating extracellular vesicles (EVs)-biological nanomaterials shed from most mammalian cells-have emerged as promising biomarkers, drug delivery vesicles, and treatment modulators. While different types of vesicles are being explored for these applications, it is becoming clear that human EVs are quite heterogeneous even in homogeneous or monoclonal cell populations. Since it is the surface EV protein composition that will largely dictate their biological behavior, high-throughput single EV profiling methods are needed to better define EV subpopulations. Here, we present an antibody-based immunosequencing method that allows multiplexed measurement of protein molecules from individual nanometer-sized EVs. We use droplet microfluidics to compartmentalize and barcode individual EVs. The barcodes/antibody-DNA are then sequenced to determine protein composition. Using this highly sensitive technology, we detected specific proteins at the single EV level. We expect that this technology can be further adapted for multiplexed protein analysis of any nanoparticle.
Collapse
Affiliation(s)
- Jina Ko
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Yongcheng Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - David A. Weitz
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- John A. Paulson School of Engineering and Applied Sciences and Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Ralph Weissleder
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA 02114, USA
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA 02115, USA
- R. Weissleder, MD, PhD, Center for Systems Biology, Massachusetts General Hospital Research Institute, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, 617-726-8226,
| |
Collapse
|
14
|
Lao Y, Yu V, Pham A, Wang T, Ruan D, Chang E, Sheng K, Yang W. Voxel-Wise GBM Recurrence Prediction Based On Post-Operative Multiparametric MR Images Using Multidimensional SVM Coupling With Stem Cell Niches Proximity Estimation. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
15
|
Lyu Q, Neph R, Yu V, Ruan D, Boucher S, Sheng K. Non-Coplanar Many-Isocenter Optimization for Radiotherapy on Robotic Arm Platform. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
16
|
Jia Y, McKenzie E, Sheng K, Ruan D, Weidhaas J, Raldow A, Qi X. Prediction of Post-chemoradiotherapy Response for Patients with Local Advanced Rectal Cancer Using Pre-treatment CT and PET Radiomics. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.2129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
17
|
Cao Y, Vassantachart A, Ye J, Yu C, Ruan D, Sheng K, Fan Z, Bian S, Zada G, Shiu A, Chang E, Yang W. Automatic Detection and Segmentation of Multiple Brain Metastases on MR Images Using Simultaneous Optimized Double-UNET Architecture. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.860] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
18
|
Kim Y, Yaseen AB, Kishi JY, Hong F, Saka SK, Sheng K, Gopalkrishnan N, Schaus TE, Yin P. Single-strand RPA for rapid and sensitive detection of SARS-CoV-2 RNA. medRxiv 2020:2020.08.17.20177006. [PMID: 32839783 PMCID: PMC7444299 DOI: 10.1101/2020.08.17.20177006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We report the single-strand Recombinase Polymerase Amplification (ssRPA) method, which merges the fast, isothermal amplification of RPA with subsequent rapid conversion of the double-strand DNA amplicon to single strands, and hence enables facile hybridization-based, high-specificity readout. We demonstrate the utility of ssRPA for sensitive and rapid (4 copies per 50 μL reaction within 10 min, or 8 copies within 8 min) visual detection of SARS-CoV-2 RNA spiked samples, as well as clinical saliva and nasopharyngeal swabs in VTM or water, on lateral flow devices. The ssRPA method promises rapid, sensitive, and accessible RNA detection to facilitate mass testing in the COVID-19 pandemic.
Collapse
Affiliation(s)
- Youngeun Kim
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Adam B. Yaseen
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Jocelyn Y. Kishi
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Fan Hong
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Sinem K. Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Kuanwei Sheng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Nikhil Gopalkrishnan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Thomas E. Schaus
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| |
Collapse
|
19
|
Wang Y, Cao T, Ko J, Shen Y, Zong W, Sheng K, Cao W, Sun S, Cai L, Zhou Y, Zhang X, Zong C, Weissleder R, Weitz D. Dissolvable Polyacrylamide Beads for High-Throughput Droplet DNA Barcoding. Adv Sci (Weinh) 2020; 7:1903463. [PMID: 32328429 PMCID: PMC7175265 DOI: 10.1002/advs.201903463] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/16/2020] [Indexed: 05/24/2023]
Abstract
Droplet-based single cell sequencing technologies, such as inDrop, Drop-seq, and 10X Genomics, are catalyzing a revolution in the understanding of biology. Barcoding beads are key components for these technologies. What is limiting today are barcoding beads that are easy to fabricate, can efficiently deliver primers into drops, and thus achieve high detection efficiency. Here, this work reports an approach to fabricate dissolvable polyacrylamide beads, by crosslinking acrylamide with disulfide bridges that can be cleaved with dithiothreitol. The beads can be rapidly dissolved in drops and release DNA barcode primers. The dissolvable beads are easy to synthesize, and the primer cost for the beads is significantly lower than that for the previous barcoding beads. Furthermore, the dissolvable beads can be loaded into drops with >95% loading efficiency of a single bead per drop and the dissolution of beads does not influence reverse transcription or the polymerase chain reaction (PCR) in drops. Based on this approach, the dissolvable beads are used for single cell RNA and protein analysis.
Collapse
Affiliation(s)
- Yongcheng Wang
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
- Department of Chemistry and Chemical BiologyHarvard UniversityCambridgeMA02138USA
| | - Ting Cao
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
- Beijing National Laboratory for Molecular Sciences (BNLMS)MOE Key Laboratory of Bioorganic Chemistry and Molecular EngineeringCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Jina Ko
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
- Center for Systems BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
| | - Yinan Shen
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| | - Will Zong
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| | - Kuanwei Sheng
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Wenjian Cao
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Sijie Sun
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| | - Liheng Cai
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| | - Ying‐Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS)MOE Key Laboratory of Bioorganic Chemistry and Molecular EngineeringCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Xin‐Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS)MOE Key Laboratory of Bioorganic Chemistry and Molecular EngineeringCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871China
| | - Chenghang Zong
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTX77030USA
| | - Ralph Weissleder
- Center for Systems BiologyMassachusetts General HospitalHarvard Medical SchoolBostonMA02114USA
- Department of Systems BiologyHarvard Medical SchoolBostonMA02115USA
| | - David Weitz
- Wyss Institute for Biologically Inspired EngineeringHarvard UniversityBostonMA02115USA
- John A. Paulson School of Engineering and Applied Sciences and Department of PhysicsHarvard UniversityCambridgeMA02138USA
| |
Collapse
|
20
|
Lao Y, David J, Fan Z, Sheng K, Yang W, Tuli R. Discriminating Locally Advanced and Borderline Resectable Pancreatic Cancers - a Contrast CT Based Quantitative Characterization of Vascular Involvement. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
21
|
Jen HI, Hill MC, Tao L, Sheng K, Cao W, Zhang H, Yu HV, Llamas J, Zong C, Martin JF, Segil N, Groves AK. Transcriptomic and epigenetic regulation of hair cell regeneration in the mouse utricle and its potentiation by Atoh1. eLife 2019; 8:e44328. [PMID: 31033441 PMCID: PMC6504235 DOI: 10.7554/elife.44328] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 04/28/2019] [Indexed: 12/30/2022] Open
Abstract
The mammalian cochlea loses its ability to regenerate new hair cells prior to the onset of hearing. In contrast, the adult vestibular system can produce new hair cells in response to damage, or by reprogramming of supporting cells with the hair cell transcription factor Atoh1. We used RNA-seq and ATAC-seq to probe the transcriptional and epigenetic responses of utricle supporting cells to damage and Atoh1 transduction. We show that the regenerative response of the utricle correlates with a more accessible chromatin structure in utricle supporting cells compared to their cochlear counterparts. We also provide evidence that Atoh1 transduction of supporting cells is able to promote increased transcriptional accessibility of some hair cell genes. Our study offers a possible explanation for regenerative differences between sensory organs of the inner ear, but shows that additional factors to Atoh1 may be required for optimal reprogramming of hair cell fate.
Collapse
Affiliation(s)
- Hsin-I Jen
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
| | - Matthew C Hill
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
| | - Litao Tao
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Kuanwei Sheng
- Program in Integrative Molecular and Biomedical SciencesBaylor College of MedicineHoustonUnited States
| | - Wenjian Cao
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - Hongyuan Zhang
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| | - Haoze V Yu
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Juan Llamas
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Chenghang Zong
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonUnited States
| | - James F Martin
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of Molecular Physiology and BiophysicsBaylor College of MedicineHoustonUnited States
- The Texas Heart InstituteHoustonUnited States
| | - Neil Segil
- Department of Stem Cell Biology and Regenerative Medicine, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
- Caruso Department of Otolaryngology - Head and Neck Surgery, Keck School of MedicineUniversity of Southern CaliforniaLos AngelesUnited States
| | - Andrew K Groves
- Program in Developmental BiologyBaylor College of MedicineHoustonUnited States
- Department of NeuroscienceBaylor College of MedicineHoustonUnited States
| |
Collapse
|
22
|
Yu V, Cao M, Sheng K. Novel Optical Patient Surface Mapping for Robust Collision Modeling and Prevention in External Beam Radiation Therapy. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.06.364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
23
|
Lyu Q, Yu V, O'Connor D, Ruan D, Sheng K. 4πVMAT: A Novel Method to Efficiently Deliver Non-Coplanar Treatment. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
24
|
Woods K, Nguyen D, Neph R, O'Connor D, Sheng K. A Sparse Orthogonal Collimator for Small Animal IMRT Using Rectangular Aperture Optimization. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.06.368] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
25
|
Gou S, Lao Y, Fan Z, Sheng K, Sandler H, Tuli R, Yang W. Automated Vessel Segmentation in Pancreas 4D-MRI using a Novel Transferred Convolutional Neural Network. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
26
|
Scavuzzo MA, Hill MC, Chmielowiec J, Yang D, Teaw J, Sheng K, Kong Y, Bettini M, Zong C, Martin JF, Borowiak M. Endocrine lineage biases arise in temporally distinct endocrine progenitors during pancreatic morphogenesis. Nat Commun 2018; 9:3356. [PMID: 30135482 PMCID: PMC6105717 DOI: 10.1038/s41467-018-05740-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 07/20/2018] [Indexed: 12/22/2022] Open
Abstract
Decoding the molecular composition of individual Ngn3 + endocrine progenitors (EPs) during pancreatic morphogenesis could provide insight into the mechanisms regulating hormonal cell fate. Here, we identify population markers and extensive cellular diversity including four EP subtypes reflecting EP maturation using high-resolution single-cell RNA-sequencing of the e14.5 and e16.5 mouse pancreas. While e14.5 and e16.5 EPs are constantly born and share select genes, these EPs are overall transcriptionally distinct concomitant with changes in the underlying epithelium. As a consequence, e16.5 EPs are not the same as e14.5 EPs: e16.5 EPs have a higher propensity to form beta cells. Analysis of e14.5 and e16.5 EP chromatin states reveals temporal shifts, with enrichment of beta cell motifs in accessible regions at later stages. Finally, we provide transcriptional maps outlining the route progenitors take as they make cell fate decisions, which can be applied to advance the in vitro generation of beta cells. Endocrine progenitors form early in pancreatic development but the diversity of this cell population is unclear. Here, the authors use single cell RNA sequencing of the mouse pancreas at e14.5 and e16.5 to show that endocrine progenitors are temporally distinct and those formed later are more likely to become beta cells
Collapse
Affiliation(s)
- Marissa A Scavuzzo
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Matthew C Hill
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jolanta Chmielowiec
- Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Diane Yang
- Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jessica Teaw
- Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA.,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kuanwei Sheng
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yuelin Kong
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Maria Bettini
- Department of Pediatrics, Section of Diabetes and Endocrinology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, 77030, USA.,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chenghang Zong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA
| | - James F Martin
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA. .,The Texas Heart Institute, Houston, TX, 77030, USA. .,Cardiovascular Research Institute, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Malgorzata Borowiak
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, 77030, USA. .,Center for Cell and Gene Therapy, Texas Children's Hospital, and Houston Methodist Hospital, Baylor College of Medicine, Houston, TX, 77030, USA. .,Stem Cell and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,Molecular and Cellular Biology Department, Baylor College of Medicine, Houston, TX, 77030, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA. .,McNair Medical Institute, Baylor College of Medicine, Houston, TX, 77030, USA.
| |
Collapse
|
27
|
Jiang N, Cao M, Lamb J, Sheng K, Mikaeilian A, Low D, Raldow A, Steinberg M, Lee P. Outcomes Utilizing MRI-Guided and Real-Time Adaptive Pancreas Stereotactic Body Radiotherapy (SBRT). Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.338] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
28
|
Gu W, O'Connor D, Nguyen D, Yu V, Ruan D, Sheng K. Integrated Beam Angle and Scanning Spot Optimization for Intensity Modulated Proton Therapy. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
29
|
Yang Y, Gadjev I, Rosenzweig J, Sheng K. Gold Nanoparticle Dose Enhancement of Inverse-Compton Based Monoenergetic Photon Beams: A Monte Carlo Evaluation. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.2390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
30
|
Yang Y, Cao M, Gao Y, Kamrava M, Kalbasi A, Lamb J, Agazaryan N, Sheng K, Low D, Hu P. Longitudinal Diffusion MRI for Early Assessment of Treatment Response in Sarcoma Patients After Preoperative Radiation Therapy. Int J Radiat Oncol Biol Phys 2017. [DOI: 10.1016/j.ijrobp.2017.06.2389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
31
|
Sheng K. EP-1521: Non-coplanar beam orientation and fluence map optimization based on group sparsity. Radiother Oncol 2017. [DOI: 10.1016/s0167-8140(17)31956-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
32
|
Tian L, Goldstein A, Wang H, Ching Lo H, Sun Kim I, Welte T, Sheng K, Dobrolecki LE, Zhang X, Putluri N, Phung TL, Mani SA, Stossi F, Sreekumar A, Mancini MA, Decker WK, Zong C, Lewis MT, Zhang XHF. Mutual regulation of tumour vessel normalization and immunostimulatory reprogramming. Nature 2017; 544:250-254. [PMID: 28371798 PMCID: PMC5788037 DOI: 10.1038/nature21724] [Citation(s) in RCA: 495] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 02/24/2017] [Indexed: 12/16/2022]
Abstract
Blockade of angiogenesis can retard tumour growth, but may also paradoxically increase metastasis1,2. Vessel normalization (VN) may resolve this paradox3. VN involves increased pericyte coverage, improved tumour vessel perfusion, reduced vascular permeability, and consequently mitigated hypoxia3. While these processes alter tumour progression, their regulation is poorly understood. Here we show that Type 1 T helper (Th1) cells play a crucial role in VN. Bioinformatic analyses revealed that gene expression features related to VN correlate with immunostimulatory pathways, especially T lymphocyte (TL) infiltration/activities. To delineate the causal relationship, we employed various mouse models with VN or TL deficiencies. While VN disruption reduced TL infiltration as expected4, reciprocal depletion or inactivation of CD4+-TLs decreased VN, indicating a mutually-regulatory loop. Additionally, CD4+-TL activation by immune checkpoint blockade (ICB) increased VN. IFNγ+ Th1 cells are the major population associated with VN. Patient-derived xenograft (PDX) tumours growing in immunodeficient animal hosts exhibited enhanced hypoxia compared to the original tumours in immunocompetent human hosts, which was reduced by adoptive Th1 transfer. Our findings elucidate an unexpected role of Th1 in vasculature and immune reprogramming. Th1 cells may be a marker and a determinant of both ICB and anti-angiogenesis efficacies.
Collapse
Affiliation(s)
- Lin Tian
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Amit Goldstein
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Hai Wang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Hin Ching Lo
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Ik Sun Kim
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Thomas Welte
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Kuanwei Sheng
- Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Lacey E Dobrolecki
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Xiaomei Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Nagireddy Putluri
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Thuy L Phung
- Department of Pathology &Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Sendurai A Mani
- Department of Translational Molecular Pathology, MD Anderson Cancer Center, 2130 West Holcombe Boulevard, Houston, Texas 77030, USA
| | - Fabio Stossi
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Arun Sreekumar
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Verna &Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Michael A Mancini
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - William K Decker
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Pathology &Immunology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Center for Cell and Gene Therapy, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Chenghang Zong
- Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Graduate Program in Integrative Molecular and Biomedical Sciences, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Michael T Lewis
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Dan L. Duncan Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,Department of Molecular and Cellular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA.,McNair Medical Institute, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
| |
Collapse
|
33
|
Nguyen D, Thomas D, Cao M, O'Connor D, Lamb J, Sheng K. Automated Triplet Beam Orientation Optimization for Magnetic Resonance Imaging–Guided Co-60 Radiation Therapy. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
34
|
Yu V, Tran A, Nguyen D, Woods K, Kaprealian T, Chin R, Low D, Sheng K. Significant Cord and Esophagus Dose Reduction by 4π Non-Coplanar Spine Stereotactic Body Radiation Therapy and Stereotactic Radiosurgery. Int J Radiat Oncol Biol Phys 2016. [DOI: 10.1016/j.ijrobp.2016.06.2246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
35
|
Yu V, Ruan D, Nguyen D, Kaprealian T, Chin R, Sheng K. SU-F-R-17: Advancing Glioblastoma Multiforme (GBM) Recurrence Detection with MRI Image Texture Feature Extraction and Machine Learning. Med Phys 2016. [DOI: 10.1118/1.4955789] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
36
|
Zhang J, Nguyen D, Woods K, Tran A, Li X, Ding X, Kabolizadeh P, Guerrero T, Sheng K. SU-F-T-186: A Treatment Planning Study of Normal Tissue Sparing with Robustness Optimized IMPT, 4Pi IMRT, and VMAT for Head and Neck Cases. Med Phys 2016. [DOI: 10.1118/1.4956323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
37
|
Woods K, Karunamuni R, Tran A, Yu V, Nguyen D, Hattangadi-Gluth J, Sheng K. TH-EF-BRB-01: BEST IN PHYSICS (THERAPY): Dosimetric Comparison of 4π and Clinical IMRT for Cortex-Sparing High-Grade Glioma Treatment. Med Phys 2016. [DOI: 10.1118/1.4958247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
38
|
O'Connor D, Voronenko Y, Nguyen D, Yin W, Sheng K. TH-EF-BRB-05: 4pi Non-Coplanar IMRT Beam Angle Selection by Convex Optimization with Group Sparsity Penalty. Med Phys 2016. [DOI: 10.1118/1.4958251] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
39
|
Han F, Zhou Z, Yang Y, Sheng K, Hu P. SU-F-J-158: Respiratory Motion Resolved, Self-Gated 4D-MRI Using Rotating Cartesian K-Space Sampling. Med Phys 2016. [DOI: 10.1118/1.4956066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
40
|
Nguyen D, Thomas D, Cao M, O'Connor D, Lamb J, Sheng K. TH-AB-BRA-02: Automated Triplet Beam Orientation Optimization for MRI-Guided Co-60 Radiotherapy. Med Phys 2016. [DOI: 10.1118/1.4958053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
41
|
Yang Y, Cao M, Kamrava M, Low D, Sheng K, Lamb J, Agazaryan N, Thomas D, Hu P. WE-FG-202-11: Longitudinal Diffusion MRI for Treatment Assessment of Sarcoma Patients with Pre-Operative Radiation Therapy. Med Phys 2016. [DOI: 10.1118/1.4957923] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
42
|
Bai Y, Wu P, Mao T, Gong S, Wang J, Sheng K, Xie Y, Niu T. SU-D-206-04: Iterative CBCT Scatter Shading Correction Without Prior Information. Med Phys 2016. [DOI: 10.1118/1.4955658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
43
|
Sheng K. TH-AB-BRB-03: 4n Radiotherapy. Med Phys 2016. [DOI: 10.1118/1.4958049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
44
|
Wu P, Mao T, Gong S, Wang J, Sheng K, Xie Y, Niu T. SU-D-206-03: Segmentation Assisted Fast Iterative Reconstruction Method for Cone-Beam CT. Med Phys 2016. [DOI: 10.1118/1.4955657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
45
|
Woods K, Harrison M, Boucher S, McNevin J, Kutsaev S, Faillace L, Sheng K. TH-EF-BRB-07: Novel Hardware and Software Platform for Intermediate Energy 4π Radiotherapy. Med Phys 2016. [DOI: 10.1118/1.4958253] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
46
|
Qi X, Yang Y, Yang L, Low D, Sheng K. WE-FG-202-08: Assessment of Treatment Response Via Longitudinal Diffusion MRI On A MRI-Guided System: Initial Experience of Quantitative Analysis. Med Phys 2016. [DOI: 10.1118/1.4957920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
47
|
Nguyen D, Lyu Q, Ruan D, O'Connor D, Low D, Sheng K. MO-AB-BRA-01: A Global Level Set Based Formulation for Volumetric Modulated Arc Therapy. Med Phys 2016. [DOI: 10.1118/1.4957153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
48
|
Tran A, Ruan D, Woods K, Yu V, Nguyen D, Sheng K. SU-D-BRB-01: A Comparison of Learning Methods for Knowledge Based Dose Prediction for Coplanar and Non-Coplanar Liver Radiotherapy. Med Phys 2016. [DOI: 10.1118/1.4955627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
49
|
Yu V, Tran A, Nguyen D, Woods K, Cao M, Kaprealian T, Chin R, Low D, Sheng K. TH-EF-BRB-03: Significant Cord and Esophagus Dose Reduction by 4π Non-Coplanar Spine Stereotactic Body Radiation Therapy and Stereotactic Radiosurgery. Med Phys 2016. [DOI: 10.1118/1.4958249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
50
|
Nguyen D, Ruan D, O'Connor D, Low D, Sheng K. A Novel Approach to Deliver Non-Coplanar Intensity Modulated Radiation Therapy Using Simple Orthogonal Collimators. Int J Radiat Oncol Biol Phys 2015. [DOI: 10.1016/j.ijrobp.2015.07.395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|