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Yao H, Pan Z, Ma W, Zhao Z, Su Z, Yang J. Whole-Genome Resequencing Analysis of the Camelus bactrianus (Bactrian Camel) Genome Identifies Mutations and Genes Affecting Milk Production Traits. Int J Mol Sci 2024; 25:7836. [PMID: 39063078 PMCID: PMC11277051 DOI: 10.3390/ijms25147836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Milk production is an important trait that influences the economic value of camels. However, the genetic regulatory mechanisms underlying milk production in camels have not yet been elucidated. We aimed to identify candidate molecular markers that affect camel milk production. We classified Junggar Bactrian camels (9-10-year-old) as low-yield (<1.96 kg/d) or high-yield (>2.75 kg/d) based on milk production performance. Milk fat (5.16 ± 0.51 g/100 g) and milk protein (3.59 ± 0.22 g/100 g) concentrations were significantly lower in high-yielding camels than those in low-yielding camels (6.21 ± 0.59 g/100 g, and 3.93 ± 0.27 g/100 g, respectively) (p < 0.01). There were no apparent differences in gland tissue morphology between the low- and high-production groups. Whole-genome resequencing of 12 low- and 12 high-yield camels was performed. The results of selection mapping methods, performed using two methods (FST and θπ), showed that 264 single nucleotide polymorphism sites (SNPs) overlapped between the two methods, identifying 181 genes. These genes were mainly associated with the regulation of oxytocin, estrogen, ErbB, Wnt, mTOR, PI3K-Akt, growth hormone synthesis/secretion/action, and MAPK signaling pathways. A total of 123 SNPs were selected, based on significantly associated genomic regions and important pathways for SNP genotyping, for verification in 521 additional Bactrian camels. This analysis showed that 13 SNPs were significantly associated with camel milk production yield and 18 SNPs were significantly associated with camel milk composition percentages. Most of these SNPs were located in coding regions of the genome. However, five and two important mutation sites were found in the introns of CSN2 (β-casein) and CSN3 (κ-casein), respectively. Among the candidate genes, NR4A1, ADCY8, PPARG, CSN2, and CSN3 have previously been well studied in dairy livestock. These observations provide a basis for understanding the molecular mechanisms underlying milk production in camels as well as genetic markers for breeding programs aimed at improving milk production.
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Affiliation(s)
- Huaibing Yao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
| | - Zhangyuan Pan
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China;
| | - Wanpeng Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; (W.M.); (Z.S.)
| | - Zhongkai Zhao
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
| | - Zhanqiang Su
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi 830052, China; (W.M.); (Z.S.)
| | - Jie Yang
- Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi 830017, China; (H.Y.); (Z.Z.)
- Xinjiang Camel Industry Engineering Technology Research Center, Urumqi 830017, China
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2
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Kavitha L, Priyadharsini J V, P A, A P. Targeting compensatory proliferation signals in oral cancer. J Oral Biol Craniofac Res 2024; 14:461-464. [PMID: 38946920 PMCID: PMC11214308 DOI: 10.1016/j.jobcr.2024.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 05/12/2024] [Accepted: 05/16/2024] [Indexed: 07/02/2024] Open
Abstract
Apoptosis is an orchestrated phenomenon that regulates cell populations in physiological and pathological conditions. Carcinogenesis involves a state of disequilibrium between cell proliferation and cell death. The resistance to conventional therapeutic modalities of cancer, including surgery, radiotherapy, and chemotherapy, can be explained by the compensatory repair and regeneration that occurs in the tumor microenvironment following apoptosis through the apoptotic compensatory proliferation signaling microvesicles (ACPSVs) or apoptotic extracellular microvesicles (ApoEVs). These microvesicles provide proliferative signals and act as mutagens, triggering cell proliferation, angiogenesis, immune evasion, metastasis, and invasion. This review discusses the phenomenon of apoptosis-induced proliferation and the role of ApoEVs in establishing an oncoregenerative niche, resulting in therapeutic resistance and recurrence of malignancies.
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Affiliation(s)
- Loganathan Kavitha
- Department of Oral and Maxillofacial Pathology, Ragas Dental College and Hospital (Affiliated to The Tamil Nadu Dr. MGR Medical University), ECR, Uthandi, Chennai-600119, India
| | - Vijayashree Priyadharsini J
- Clinical Genetics Lab, Centre for Cellular and Molecular Research (The Blue Lab), Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Poonamallee High Road, Chennai, Tamil Nadu, 600077, India
| | - Anitha P
- Clinical Genetics Lab, Centre for Cellular and Molecular Research (The Blue Lab), Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Poonamallee High Road, Chennai, Tamil Nadu, 600077, India
| | - Paramasivam A
- Molecular Biology Lab, Centre for Cellular and Molecular Research (The Blue Lab), Saveetha Dental College & Hospital, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, Poonamallee High Road, Chennai, Tamil Nadu, 600077, India
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Wei Z, Zhou C, Shen Y, Deng H, Shen Z. Identification of a new anoikis-related gene signature for prognostic significance in head and neck squamous carcinomas. Medicine (Baltimore) 2023; 102:e34790. [PMID: 37682196 PMCID: PMC10489427 DOI: 10.1097/md.0000000000034790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/26/2023] [Indexed: 09/09/2023] Open
Abstract
Anoikis, a mode of programmed cell death, is essential for normal development and homeostasis in the organism and plays an important role in the onset and progression of cancers. The authors of this research sought to establish a gene signature associated with anoikis to predict therapy outcomes and patient prognosis for individuals with head and neck squamous cell carcinoma (HNSCC). Transcriptome data of anoikis-related genes (ARGs) in individuals with HNSCC were retrieved from public databases to aid in the formulation of the gene signature. A novel ARG signature was then created using a combination of the Least Absolute Shrinkage and Selection Operator regression and Cox regression analysis. The relationship between ARGs and tumor immune microenvironment in HNSCC was explored using single-cell analysis. HNSCC individuals were classified into high-risk and low-risk groups as per the median value of risk score. The study also investigated the variations in the infiltration status of immune cells, tumor microenvironment, sensitivity to immunotherapy and chemotherapeutics, as well as functional enrichment between the low-risk and high-risk categories. A total of 18 ARGs were incorporated in the formulation of the signature. Our signature's validity as a standalone predictive predictor was validated by multivariate Cox regression analysis and Kaplan-Meier survival analysis. Generally, the prognosis was worse for high-risk individuals. Subjects in the low-risk groups had a better prognosis and responded in a better way to combination immunotherapy, had higher immunological ratings and activity levels, and had more immune cell infiltration. In addition, gene set enrichment analysis findings showed that the low-risk subjects exhibited heightened activity in several immune-related pathways. However, the high-risk patients responded better to chemotherapy. The aim of this research was to develop a new ARG signature to predict the prognosis and sensitivity to immunotherapeutic and chemotherapeutic schemes for HNSCC patient. As a result, this could help spur the creation of new chemotherapeutics and immunotherapeutic approaches for patients with HNSCC.
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Affiliation(s)
- Zhengyu Wei
- Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, China
| | - Chongchang Zhou
- Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo, China
| | - Yi Shen
- Health Science Center, Ningbo University, Ningbo, China
| | - Hongxia Deng
- Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo, China
| | - Zhisen Shen
- Department of Otorhinolaryngology Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, China
- Department of Otorhinolaryngology Head and Neck Surgery, Ningbo Medical Centre Lihuili Hospital, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, China
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Lai TY, Ko YC, Chen YL, Lin SF. The Way to Malignant Transformation: Can Epigenetic Alterations Be Used to Diagnose Early-Stage Head and Neck Cancer? Biomedicines 2023; 11:1717. [PMID: 37371812 DOI: 10.3390/biomedicines11061717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 06/05/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Identifying and treating tumors early is the key to secondary prevention in cancer control. At present, prevention of oral cancer is still challenging because the molecular drivers responsible for malignant transformation of the 11 clinically defined oral potentially malignant disorders are still unknown. In this review, we focused on studies that elucidate the epigenetic alterations demarcating malignant and nonmalignant epigenomes and prioritized findings from clinical samples. Head and neck included, the genomes of many cancer types are largely hypomethylated and accompanied by focal hypermethylation on certain specific regions. We revisited prior studies that demonstrated that sufficient uptake of folate, the primary dietary methyl donor, is associated with oral cancer reduction. As epigenetically driven phenotypic plasticity, a newly recognized hallmark of cancer, has been linked to tumor initiation, cell fate determination, and drug resistance, we discussed prior findings that might be associated with this hallmark, including gene clusters (11q13.3, 19q13.43, 20q11.2, 22q11-13) with great potential for oral cancer biomarkers, and successful examples in screening early-stage nasopharyngeal carcinoma. Although one-size-fits-all approaches have been shown to be ineffective in most cancer therapies, the rapid development of epigenome sequencing methods raises the possibility that this nonmutagenic approach may be an exception. Only time will tell.
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Affiliation(s)
- Ting-Yu Lai
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu 30013, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Ying-Chieh Ko
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Yu-Lian Chen
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan
| | - Su-Fang Lin
- National Institute of Cancer Research, National Health Research Institutes, Miaoli 35053, Taiwan
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Rosenbaum E, Antonescu CR, Smith S, Bradic M, Kashani D, Richards AL, Donoghue M, Kelly CM, Nacev B, Chan JE, Chi P, Dickson MA, Keohan ML, Gounder MM, Movva S, Avutu V, Thornton K, Zehir A, Bowman AS, Singer S, Tap W, D'Angelo S. Clinical, genomic, and transcriptomic correlates of response to immune checkpoint blockade-based therapy in a cohort of patients with angiosarcoma treated at a single center. J Immunother Cancer 2022; 10:jitc-2021-004149. [PMID: 35365586 PMCID: PMC8977792 DOI: 10.1136/jitc-2021-004149] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/12/2022] [Indexed: 12/15/2022] Open
Abstract
Background Angiosarcoma is a histologically and molecularly heterogeneous vascular neoplasm with aggressive clinical behavior. Emerging data suggests that immune checkpoint blockade (ICB) is efficacious against some angiosarcomas, particularly cutaneous angiosarcoma of the head and neck (CHN). Methods Patients with histologically confirmed angiosarcoma treated with ICB-based therapy at a comprehensive cancer center were retrospectively identified. Clinical characteristics and the results of targeted exome sequencing, transcriptome sequencing, and immunohistochemistry analyses were examined for correlation with clinical benefit. Durable clinical benefit was defined as a progression-free survival (PFS) of ≥16 weeks. Results For the 35 patients included in the analyses, median PFS and median overall survival (OS) from the time of first ICB-based treatment were 11.9 (95% CI 7.4 to 31.9) and 42.5 (95% CI 19.6 to 114.2) weeks, respectively. Thirteen patients (37%) had PFS ≥16 weeks. Clinical factors associated with longer PFS and longer OS in multivariate analyses were ICB plus other therapy regimens, CHN disease, and white race. Three of 10 patients with CHN angiosarcoma evaluable for tumor mutational burden (TMB) had a TMB ≥10. Five of six patients with CHN angiosarcoma evaluable for mutational signature analysis had a dominant mutational signature associated with ultraviolet (UV) light. No individual gene or genomic pathway was significantly associated with PFS or OS; neither were TMB or UV signature status. Analyses of whole transcriptomes from nine patient tumor samples found upregulation of angiogenesis, inflammatory response, and KRAS signaling pathways, among others, in patients with PFS ≥16 weeks, as well as higher levels of cytotoxic T cells, dendritic cells, and natural killer cells. Patients with PFS <16 weeks had higher numbers of cancer-associated fibroblasts. Immunohistochemistry findings for 12 patients with baseline samples available suggest that neither PD-L1 expression nor presence of tumor-infiltrating lymphocytes at baseline appears necessary for a response to ICB-based therapy. Conclusions ICB-based therapy benefits only a subset of angiosarcoma patients. Patients with CHN angiosarcoma are more likely to have PFS ≥16 weeks, a dominant UV mutational signature, and higher TMB than angiosarcomas arising from other primary sites. However, clinical benefit was seen in other angiosarcomas also and was not restricted to tumors with a high TMB, a dominant UV signature, PD-L1 expression, or presence of tumor infiltrating lymphocytes at baseline.
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Affiliation(s)
- Evan Rosenbaum
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA .,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Cristina R Antonescu
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Shaleigh Smith
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Martina Bradic
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Kashani
- Department of Medicine, SUNY Downstate Medical Center, New York City, New York, USA
| | - Allison L Richards
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark Donoghue
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciara M Kelly
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Benjamin Nacev
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Jason E Chan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Ping Chi
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark A Dickson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Mary L Keohan
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Mrinal M Gounder
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Sujana Movva
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Viswatej Avutu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Katherine Thornton
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Anita S Bowman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Samuel Singer
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - William Tap
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
| | - Sandra D'Angelo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, New York, USA.,Department of Medicine, Weill Cornell Medical College, New York City, New York, USA
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6
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Farshidfar F, Rhrissorrakrai K, Levovitz C, Peng C, Knight J, Bacchiocchi A, Su J, Yin M, Sznol M, Ariyan S, Clune J, Olino K, Parida L, Nikolaus J, Zhang M, Zhao S, Wang Y, Huang G, Wan M, Li X, Cao J, Yan Q, Chen X, Newman AM, Halaban R. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nat Commun 2022; 13:898. [PMID: 35197475 PMCID: PMC8866401 DOI: 10.1038/s41467-022-28566-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2022] [Indexed: 12/11/2022] Open
Abstract
Acral melanoma, the most common melanoma subtype among non-White individuals, is associated with poor prognosis. However, its key molecular drivers remain obscure. Here, we perform integrative genomic and clinical profiling of acral melanomas from 104 patients treated in North America (n = 37) or China (n = 67). We find that recurrent, late-arising focal amplifications of cytoband 22q11.21 are a leading determinant of inferior survival, strongly associated with metastasis, and linked to downregulation of immunomodulatory genes associated with response to immune checkpoint blockade. Unexpectedly, LZTR1 - a known tumor suppressor in other cancers - is a key candidate oncogene in this cytoband. Silencing of LZTR1 in melanoma cell lines causes apoptotic cell death independent of major hotspot mutations or melanoma subtypes. Conversely, overexpression of LZTR1 in normal human melanocytes initiates processes associated with metastasis, including anchorage-independent growth, formation of spheroids, and an increase in MAPK and SRC activities. Our results provide insights into the etiology of acral melanoma and implicate LZTR1 as a key tumor promoter and therapeutic target.
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Affiliation(s)
- Farshad Farshidfar
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | | | | | - Cong Peng
- Xiangya Hospital, Central South University, Changsha, China
| | - James Knight
- Yale Center for Genome Analysis, Yale University, New Haven, CT, 06520, USA
| | | | - Juan Su
- Xiangya Hospital, Central South University, Changsha, China
| | - Mingzhu Yin
- Xiangya Hospital, Central South University, Changsha, China
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Mario Sznol
- Department of Internal Medicine, Section of Medical Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephan Ariyan
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - James Clune
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | - Kelly Olino
- Department of Surgery, Yale University School of Medicine, New Haven, CT, USA
| | | | - Joerg Nikolaus
- Department of Molecular and Cellular Physiology, Yale University School of Medicine, New Haven, CT, USA
| | - Meiling Zhang
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Shuang Zhao
- Xiangya Hospital, Central South University, Changsha, China
| | - Yan Wang
- Department of Dermatologic Surgery Institute of Dermatology, Chinese Academy of Medical Sciences & Peking Union Medical College, Nanjing, China
| | - Gang Huang
- Department of Bone and Soft Tissue oncology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, Hunan, China
| | - Miaojian Wan
- Department of Dermatology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xianan Li
- Department of Bone and Soft Tissue oncology, Hunan Cancer Hospital, Affiliated Tumor Hospital of Xiangya Medical School of Central South University, Changsha, Hunan, China
| | - Jian Cao
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Qin Yan
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Xiang Chen
- Xiangya Hospital, Central South University, Changsha, China.
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
| | - Ruth Halaban
- Department of Dermatology, Yale University School of Medicine, New Haven, CT, USA.
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