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Stucky A, Viet CT, Aouizerat BE, Ye Y, Doan C, Mundluru T, Sedhiazadeh P, Sinha UK, Chen X, Zhang X, Li SC, Cai J, Zhong JF. Single-Cell Molecular Profiling of Head and Neck Squamous Cell Carcinoma Reveals Five Dysregulated Signaling Pathways Associated With Circulating Tumor Cells. Cancer Control 2024; 31:10732748241251571. [PMID: 38869038 PMCID: PMC11179551 DOI: 10.1177/10732748241251571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 04/05/2024] [Accepted: 04/11/2024] [Indexed: 06/14/2024] Open
Abstract
OBJECTIVES To determine the dysregulated signaling pathways of head and neck squamous cell carcinoma associated with circulating tumor cells (CTCs) via single-cell molecular characterization. INTRODUCTION Head and neck squamous cell carcinoma (HNSCC) has a significant global burden and is a disease with poor survival. Despite trials exploring new treatment modalities to improve disease control rates, the 5 year survival rate remains low at only 60%. Most cancer malignancies are reported to progress to a fatal phase due to the metastatic activity derived from treatment-resistant cancer cells, regarded as one of the most significant obstacles to develope effective cancer treatment options. However, the molecular profiles of cancer cells have not been thoroughly studied. METHODS Here, we examined in-situ HNSCC tumors and pairwisely followed up with the downstream circulating tumor cells (CTCs)-based on the surrogate biomarkers to detect metastasis that is established in other cancers - not yet being fully adopted in HNSCC treatment algorithms. RESULTS Specifically, we revealed metastatic HNSCC patients have complex CTCs that could be defined through gene expression and mutational gene profiling derived from completed single-cell RNASeq (scRNASeq) that served to confirm molecular pathways inherent in these CTCs. To enhance the reliability of our findings, we cross-validated those molecular profiles with results from previously published studies. CONCLUSION Thus, we identified 5 dysregulated signaling pathways in CTCs to derive HNSCC biomarker panels for screening HNSCC in situ tumors.
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Affiliation(s)
- Andres Stucky
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Chi T Viet
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Loma Linda University, Loma Linda, CA, USA
| | - Bradley E Aouizerat
- Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University, New York, NY, USA
- Bluestone Center for Clinical Research, College of Dentistry, New York University, New York, NY, USA
| | - Yi Ye
- Department of Oral and Maxillofacial Surgery, College of Dentistry, New York University, New York, NY, USA
- Bluestone Center for Clinical Research, College of Dentistry, New York University, New York, NY, USA
| | - Coleen Doan
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Loma Linda University, Loma Linda, CA, USA
| | - Tarun Mundluru
- Herman Ostrow School of Dentistry, Department of Periodontics and Diagnostic Sciences, University of Southern California, Los Angeles, CA, USA
| | - Parish Sedhiazadeh
- Herman Ostrow School of Dentistry, Department of Periodontics and Diagnostic Sciences, University of Southern California, Los Angeles, CA, USA
| | - Uttam K Sinha
- Department of Otolaryngology-Head and Neck Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xuelian Chen
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Xi Zhang
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
| | - Shengwen Calvin Li
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Research Institute, Children's Hospital of Orange County, Orange, CA, USA
- Department of Neurology, University of California-Irvine School of Medicine, Orange, CA, USA
| | - Jin Cai
- Department of Oral and Maxillofacial Surgery, Zhuhai People's Hospital, Zhuhai Clinical Medical College of Jinan University, Zhuhai, People's Republic of China
| | - Jiang F Zhong
- Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, CA, USA
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Sun L, Li X, Tu L, Stucky A, Huang C, Chen X, Cai J, Li SC. RNA-Sequencing Combined With Genome-Wide Allele-Specific Expression Patterning Identifies ZNF44 Variants as a Potential New Driver Gene for Pediatric Neuroblastoma. Cancer Control 2023; 30:10732748231175017. [PMID: 37161925 DOI: 10.1177/10732748231175017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
INTRODUCTION Neuroblastoma (NB) is one of the children's most common solid tumors, accounting for approximately 8% of pediatric malignancies and 15% of childhood cancer deaths. Somatic mutations in several genes, such as ALK, have been associated with NB progression and can facilitate the discovery of novel therapeutic strategies. However, the differential expression of mutated and wild-type alleles on the transcriptome level is poorly studied. METHODS This study analyzed 219 whole-exome sequencing datasets with somatic mutations detected by MuTect from paired normal and tumor samples. RESULTS We prioritized mutations in 8 candidate genes (RIMS4, RUSC2, ALK, MYCN, PTPN11, ALOX12B, ZNF44, and CNGB1) as potential driver mutations. We further confirmed the presence of allele-specific expression of the somatic mutations in NB with integrated analysis of 127 RNA-seq samples (of which 85 also had DNA-seq data available), including MYCN, ALK, and PTPN11. The allele-specific expression of mutations suggests that the same somatic mutation may have different effects on the clinical outcomes of tumors. CONCLUSION Our study suggests 2 novel variants of ZNF44 as a novel candidate driver gene for NB.
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Affiliation(s)
- Lan Sun
- Department of Oncology,Bishan Hospital of Chongqing Medical University, The People's Hospital of Bishan District, Chongqing, China
| | - Xiaoqing Li
- Department of Oncology,Bishan Hospital of Chongqing Medical University, The People's Hospital of Bishan District, Chongqing, China
| | - Lingli Tu
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Andres Stucky
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Chuan Huang
- Department of Oncology,Bishan Hospital of Chongqing Medical University, The People's Hospital of Bishan District, Chongqing, China
| | - Xuelian Chen
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Jin Cai
- Department of Oral and Maxillofacial Surgery, Zhuhai People's Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Shengwen Calvin Li
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Research Institute, Children's Hospital of Orange County (CHOC), Orange, CA, USA
- Department of Neurology, University of California, Irvine School of Medicine, Orange, CA, USA
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Stucky A, Gao L, Li SC, Tu L, Luo J, Huang X, Chen X, Li X, Park TH, Cai J, Kabeer MH, Plant AS, Sun L, Zhang X, Zhong JF. Molecular Characterization of Differentiated-Resistance MSC Subclones by Single-Cell Transcriptomes. Front Cell Dev Biol 2022; 10:699144. [PMID: 35356283 PMCID: PMC8959432 DOI: 10.3389/fcell.2022.699144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 02/14/2022] [Indexed: 11/25/2022] Open
Abstract
Background: The mechanism of tumorigenicity potentially evolved in mesenchymal stem cells (MSCs) remains elusive, resulting in inconsistent clinical application efficacy. We hypothesized that subclones in MSCs contribute to their tumorgenicity, and we approached MSC-subclones at the single-cell level. Methods: MSCs were cultured in an osteogenic differentiation medium and harvested on days 12, 19, and 25 for cell differentiation analysis using Alizarin Red and followed with the single-cell transcriptome. Results: Single-cell RNA-seq analysis reveals a discrete cluster of MSCs during osteogenesis, including differentiation-resistant MSCs (DR-MSCs), differentiated osteoblasts (DO), and precursor osteoblasts (PO). The DR-MSCs population resembled cancer initiation cells and were subjected to further analysis of the yes associated protein 1 (YAP1) network. Verteporfin was also used for YAP1 inhibition in cancer cell lines to confirm the role of YAP1 in MSC--involved tumorigenicity. Clinical data from various cancer types were analyzed to reveal relationships among YAP1, OCT4, and CDH6 in MSC--involved tumorigenicity. The expression of cadherin 6 (CDH6), octamer-binding transcription factor 4 (OCT4), and YAP1 expression was significantly upregulated in DR-MSCs compared to PO and DO. YAP1 inhibition by Verteporfin accelerated the differentiation of MSCs and suppressed the expression of YAP1, CDH6, and OCT4. A survey of 56 clinical cohorts revealed a high degree of co-expression among CDH6, YAP1, and OCT4 in various solid tumors. YAP1 inhibition also down-regulated HeLa cell viability and gradually inhibited YAP1 nuclear localization while reducing the transcription of CDH6 and OCT4. Conclusions: We used single-cell sequencing to analyze undifferentiated MSCs and to discover a carcinogenic pathway in single-cell MSCs of differentiated resistance subclones.
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Affiliation(s)
- Andres Stucky
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, CA, United States
| | - Li Gao
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Shengwen Calvin Li
- Neuro-oncology and Stem Cell Research Laboratory, CHOC Children’s Research Institute, Center for Neuroscience Research, Children’s Hospital of Orange County (CHOC), Orange, CA, United States
- Department of Neurology, Irvine School of Medicine, University of California, Irvine, CA, United States
- *Correspondence: Shengwen Calvin Li, ; Lan Sun, ; Xi Zhang,
| | - Lingli Tu
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, CA, United States
- Department of Oncology, Bishan, The People’s Hospital of Bishan District, Bishan, Chongqing, China
| | - Jun Luo
- Stomatological Hospital of Chongqing Medical University, Chongqing, China
| | - Xi Huang
- Department of Hematology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xuelian Chen
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, CA, United States
| | - Xiaoqing Li
- Department of Oncology, Bishan, The People’s Hospital of Bishan District, Bishan, Chongqing, China
| | - Tiffany H. Park
- School of Dental Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Jin Cai
- Department of Oral and Maxillofacial Surgery, Zhuhai People’s Hospital, Zhuhai Hospital Affiliated with Jinan University, Zhuhai, China
| | - Mustafa H. Kabeer
- Pediatric Surgery, CHOC Children’s Hospital, Department of Surgery, Irvine School of Medicine, University of California, Irvine, CA, United States
| | - Ashley S. Plant
- Division of Pediatric Oncology, Children’s Hospital of Orange County, Orange, CA, United States
| | - Lan Sun
- Department of Oncology, Bishan, The People’s Hospital of Bishan District, Bishan, Chongqing, China
- *Correspondence: Shengwen Calvin Li, ; Lan Sun, ; Xi Zhang,
| | - Xi Zhang
- Medical Center of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, China
- *Correspondence: Shengwen Calvin Li, ; Lan Sun, ; Xi Zhang,
| | - Jiang F. Zhong
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, CA, United States
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Dong Z, Wang Y, Yin D, Hang X, Pu L, Zhang J, Geng J, Chang L. Advanced techniques for gene heterogeneity research: Single‐cell sequencing and on‐chip gene analysis systems. VIEW 2022. [DOI: 10.1002/viw.20210011] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Zaizai Dong
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Yu Wang
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Dedong Yin
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Xinxin Hang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
| | - Lei Pu
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Jianfu Zhang
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Jia Geng
- Department of Laboratory Medicine State Key Laboratory of Biotherapy and Cancer Center West China Hospital Sichuan University/Collaborative Innovation Center Chengdu China
| | - Lingqian Chang
- Key Laboratory of Biomechanics and Mechanobiology, Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China
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Stucky A, Gao L, Sun L, Li SC, Chen X, Park TH, Cai J, Kabeer MH, Zhang X, Sinha UK, Zhong JF. Evidence for AJUBA-catenin-CDH4-linked differentiation resistance of mesenchymal stem cells implies tumorigenesis and progression of head and neck squamous cell carcinoma: a single-cell transcriptome approach. BLOOD AND GENOMICS 2021; 5:29-39. [PMID: 34368804 PMCID: PMC8346230 DOI: 10.46701/bg.2021012021106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
An increasing number of reports indicate that mesenchymal stem cells (MSCs) play an essential role in promoting tumorigenesis and progression of head and neck squamous cell carcinoma (HNSCC). However, the molecular mechanisms underlying this process remain unclear. Using the MSC model system, this study analyzes the molecular pathway by which differentiation resistant MSCs promote HNSCC. MSCs were cultured in osteogenic differentiation media and harvested on days 12 and 19. Cells were stained for cell differentiation analysis using Alizarin Red. The osteogenesis-resistant MSCs (OR-MSCs) and MSC-differentiation-derived osteoblasts (D-OSTBs) were identified and subjected to the single-cell transcriptome analysis. Gene-specific analyses of these two sub-populations were performed for the patterns of differential expression. A total of 1 780 differentially expressed genes were determined to distinguish OR-MSCs significantly from D-OSTB. Notably, AJUBA, β-catenin, and CDH4 expression levels were upregulated considerably within the OR-MSCs compared to D-OSTBs. To confirm their clinical relevance, a survey of a clinical cohort revealed a high correlation among the expression levels of AJUBA, β-catenin and CDH4. The results shed new light that OR-MSCs participate in the development of HNSCC via a pathway mediated by AJUBA, β-catenin, CDH4, and CTNNB1, thereby implying that MSC-based therapy is a promising therapeutic approach in the management of HNSCC.
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Affiliation(s)
- Andres Stucky
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Li Gao
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Lan Sun
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Shengwen Calvin Li
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Neuro-Oncology and Stem Cell Research Laboratory, Center for Neuroscience Research, CHOC Children's Research Institute, Children's Hospital of Orange County (CHOC), Orange, CA 92868, USA
- Department of Neurology, University of California - Irvine School of Medicine, Orange, CA 92868, USA
| | - Xuelian Chen
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Tiffany H. Park
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jin Cai
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Mustafa H. Kabeer
- Division of Pediatric General and Thoracic Surgery, Children's Hospital of Orange County, Orange, CA 92868, USA
- Department of Surgery, University of California - Irvine School of Medicine, Orange, CA 92868, USA
| | - Xi Zhang
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Uttam K. Sinha
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Jiang F. Zhong
- Department of Otolaryngology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
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Bai Z, Deng Y, Kim D, Chen Z, Xiao Y, Fan R. An Integrated Dielectrophoresis-Trapping and Nanowell Transfer Approach to Enable Double-Sub-Poisson Single-Cell RNA Sequencing. ACS NANO 2020; 14:7412-7424. [PMID: 32437127 DOI: 10.1021/acsnano.0c02953] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Current technologies for high-throughput single-cell RNA sequencing (scRNA-seq) are based upon stochastic pairing of cells and barcoded beads in nanoliter droplets or wells. They are limited by the mathematical principle of the Poisson statistics such that the utilization of either cells or beads or both is no more than ∼33%. Despite the versatile design of microfluidics or microwells for high-yield loading of beads that beats the Poisson limit, subsequent encapsulation of single cells is still determined by stochastic pairing, representing a fundamental limitation in the field of single-cell sequencing. Here, we present dTNT-seq, an integrated dielectrophoresis (DEP)-trapping-nanowell-transfer (dTNT) approach to perform cell trapping and bead loading both in a sub-Poisson manner to facilitate scRNA-seq. A larger-sized 50 μm microwell array was prealigned precisely on top of the 20 μm DEP nanowell array such that single cells trapped by DEP can be readily transferred into the underneath larger wells by flipping the device, followed by subsequent hydrodynamic bead loading and coisolation with transferred single cells. Using a dTNT device composed of 3600 electroactive DEP-nanowell units, we demonstrated a single-cell trapping rate of 91.84%, a transfer efficiency of 82%, and a routine bead loading rate of >99%, which breaks the Poisson limit for the capture of both cells and beads, thus called double-sub-Poisson distribution, prior to encapsulating them in nanoliter wells for cellular mRNA barcoding. This approach was applied to human (HEK) and mouse (3T3) cells. Comparison with a non-DEP-based method through gene expression clustering and regulatory pathway analysis demonstrates consistent patterns and negligible alternation of cellular transcriptional states by DEP. We envision the dTNT-seq device can be modified for studying cell-cell interactions and enable other applications requiring active manipulation of single cells prior to transcriptome sequencing.
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Affiliation(s)
- Zhiliang Bai
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
- State Key Laboratory of Precision Measurement Technology and Instrument, Tianjin University, Tianjin 300072, China
| | - Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Dongjoo Kim
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Zhuo Chen
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Yang Xiao
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, United States
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut 06511, United States
- Human and Translational Immunology, Yale School of Medicine, New Haven, Connecticut 06511, United States
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Liu J, Zhang X, Zhong JF, Zhang C. Use of chimeric antigen receptor T cells in allogeneic hematopoietic stem cell transplantation. Immunotherapy 2019; 11:37-44. [PMID: 30702011 DOI: 10.2217/imt-2018-0089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The chimeric antigen receptor T (CAR-T) cells play an antileukemia role, and can be used to treat or prevent relapse by targeting minimal residual disease for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, the infusion of allogeneic CAR-T cells may also cause graft-versus-host disease, which limited their applications during and after allo-HSCT. In this review, we discuss the clinical trials that applying CAR-T cells before allo-HSCT and the use of donor-derived CAR-T cells as conditioning regimen during allo-HSCT. At last, we analyzed the effect of donor-derived CAR-T cells on preventive infusion after allo-HSCT.
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Affiliation(s)
- Jun Liu
- Department of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, People's Republic of China
| | - Xi Zhang
- Department of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, People's Republic of China
| | - Jiang F Zhong
- Division of Periodontology, Diagnostic Sciences & Dental Hygiene, & Division of Biomedical Sciences, Herman Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, USA
| | - Cheng Zhang
- Department of Hematology, Xinqiao Hospital, Army Medical University, Chongqing, People's Republic of China
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