Publications by authors named "Ruiying Zhao"

74 Publications

Identification of NTRK gene fusions in lung adenocarcinomas in the Chinese population.

J Pathol Clin Res 2021 Mar 26. Epub 2021 Mar 26.

Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, PR China.

The molecular profile of neurotrophic tyrosine kinase receptor (NTRK) gene fusions in lung adenocarcinoma (LUAD) is not fully understood. Next-generation sequencing (NGS) and pan-tyrosine kinase receptor (TRK) immunohistochemistry (IHC) are powerful tools for NTRK fusion detection. In this study, a total of 4,619 LUAD formalin-fixed, paraffin-embedded tissues were collected from patients who underwent biopsy or resection at the Shanghai Chest Hospital during 2017-2019. All specimens were screened for NTRK1 rearrangements using DNA-based NGS. Thereafter, the cases with NTRK1 rearrangements and cases negative for common driver mutations were analyzed for NTRK1/2/3 fusions using total nucleic acid (TNA)-based NGS and pan-TRK IHC. Overall, four NTRK1/2 fusion events were identified, representing 0.087% of the original sample set. At the DNA level, seven NTRK1 rearrangements were identified, while only two TPM3-NTRK1 fusions were confirmed on TNA-based NGS as functional. In addition, two NTRK2 fusions (SQSTM1-NTRK2 and KIF5B-NTRK2) were identified by TNA-based NGS in 350 'pan-negative' cases. Two patients harboring NTRK1/2 fusions were diagnosed with invasive adenocarcinoma, while the other two were diagnosed with adenocarcinoma in situ and minimally invasive adenocarcinoma. All four samples with NTRK fusions were positive for the expression of pan-TRK. The two samples with NTRK2 fusions showed cytoplasmic staining alone, while the other two samples with NTRK1 fusions exhibited both cytoplasmic and membranous staining. In summary, functional NTRK fusions are found in early-stage LUAD; however, they are extremely rare. According to this study's results, they are independent oncogenic drivers, mutually exclusive with other driver mutations. We demonstrated that NTRK rearrangement analysis using a DNA-based approach should be verified with an RNA-based assay.
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http://dx.doi.org/10.1002/cjp2.208DOI Listing
March 2021

Impact of diabetes on promoting the growth of breast cancer.

Cancer Commun (Lond) 2021 Feb 20. Epub 2021 Feb 20.

Department of Molecular and Cellular Oncology, the University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.

Background: Type II diabetes mellitus (DM2) is a significant risk factor for cancers, including breast cancer. However, a proper diabetic breast cancer mouse model is not well-established for treatment strategy design. Additionally, the precise diabetic signaling pathways that regulate cancer growth remain unresolved. In the present study, we established a suitable mouse model and demonstrated the pathogenic role of diabetes on breast cancer progression.

Methods: We successfully generated a transgenic mouse model of human epidermal growth factor receptor 2 positive (Her2 or ERBB2) breast cancer with DM2 by crossing leptin receptor mutant (Lepr ) mice with MMTV-ErbB2/neu) mice. The mouse models were administrated with antidiabetic drugs to assess the impacts of controlling DM2 in affecting tumor growth. Magnetic resonance spectroscopic imaging was employed to analyze the tumor metabolism.

Results: Treatment with metformin/rosiglitazone in MMTV-ErbB2/Lepr mouse model reduced serum insulin levels, prolonged overall survival, decreased cumulative tumor incidence, and inhibited tumor progression. Anti-insulin resistance medications also inhibited glycolytic metabolism in tumors in vivo as indicated by the reduced metabolic flux of hyperpolarized C pyruvate-to-lactate reaction. The tumor cells from MMTV-ErbB2/Lepr transgenic mice treated with metformin had reprogrammed metabolism by reducing levels of both oxygen consumption and lactate production. Metformin decreased the expression of Myc and pyruvate kinase isozyme 2 (PKM2), leading to metabolism reprogramming. Moreover, metformin attenuated the mTOR/AKT signaling pathway and altered adipokine profiles.

Conclusions: MMTV-ErbB2/Lepr mouse model was able to recapitulate diabetic HER2 human breast cancer. Additionally, our results defined the signaling pathways deregulated in HER2 breast cancer under diabetic condition, which can be intervened by anti-insulin resistance therapy.
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http://dx.doi.org/10.1002/cac2.12147DOI Listing
February 2021

Catalytic Nanozyme for Radiation Protection.

Bioconjug Chem 2021 03 11;32(3):411-429. Epub 2021 Feb 11.

Department of Physics and Tianjin Key Laboratory of Low Dimensional Materials Physics and Preparing Technology, Institute of Advanced Materials Physics, School of Science, Tianjin University, Tianjin 300350, China.

Radiotherapy has been widely used in clinical cancer treatment. However, the ionizing radiation required to kill the tumor will inevitably cause damage to the surrounding normal tissues. To minimize the radiation damage and side effects, small molecular radioprotective agents have been used as clinical adjuvants for radiation protection of healthy tissues. However, the shortcomings of small molecules such as short circulation time and rapid kidney clearance from the body greatly hinder their biomedical applications. In recent years, nanozymes have attracted much attention because of their potential to treat a variety of diseases. Nanozymes exhibit catalytic properties and antioxidant capabilities to provide a potential solution for the development of high-efficiency radioprotective agents in radiotherapy and nuclear radiation accidents. Therefore, in this review, we systematically summarize the catalytic nanozymes used for radiation protection of healthy tissues and discuss the challenges and future prospects of nanomaterials in the field of radiation protection.
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http://dx.doi.org/10.1021/acs.bioconjchem.0c00648DOI Listing
March 2021

LncRNA H19 Suppresses Osteosarcomagenesis by Regulating snoRNAs and DNA Repair Protein Complexes.

Front Genet 2020 15;11:611823. Epub 2021 Jan 15.

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, United States.

Osteosarcoma is one of the most frequent common primary malignant tumors in childhood and adolescence. Long non-coding RNAs (lncRNAs) have been reported to regulate the initiation and progression of tumors. However, the exact molecular mechanisms involving lncRNA in osteosarcomagenesis remain largely unknown. Li-Fraumeni syndrome (LFS) is a familial cancer syndrome caused by germline p53 mutation. We investigated the tumor suppressor function of lncRNA H19 in LFS-associated osteosarcoma. Analyzing H19-induced transcriptome alterations in LFS induced pluripotent stem cell (iPSC)-derived osteoblasts, we unexpectedly discovered a large group of snoRNAs whose expression was significantly affected by H19. We identified SNORA7A among the H19-suppressed snoRNAs. SNORA7A restoration impairs H19-mediated osteogenesis and tumor suppression, indicating an oncogenic role of SNORA7A. TCGA analysis indicated that SNORA7A expression is associated with activation of oncogenic signaling and poor survival in cancer patients. Using an optimized streptavidin-binding RNA aptamer designed from H19 lncRNA, we revealed that H19-tethered protein complexes include proteins critical for DNA damage response and repair, confirming H19's tumor suppressor role. In summary, our findings demonstrate a critical role of H19-modulated SNORA7A expression in LFS-associated osteosarcomas.
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http://dx.doi.org/10.3389/fgene.2020.611823DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7844330PMC
January 2021

Morphological, immunohistochemical, and genetic analyses of bronchiolar adenoma and its putative variants.

J Pathol Clin Res 2021 May 5;7(3):287-300. Epub 2021 Jan 5.

Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, PR China.

We collected 26 cases of bronchiolar adenoma (BA) and its variants, and performed a comprehensive characterization using a combination of morphological, immunohistochemical, and genetic assessments. Of these 26, 13 were classic bilayered cases, including 10 proximal and 3 distal-type BAs. Of note, we also identified 13 cases that lacked a continuous basal cell layer. In five cases, the adenomas were partially classic bilayered, leaving a single layer of columnar or cuboidal epithelial cells in some areas of the lesion (BA with monolayered cell lesions). In the other eight cases, the glandular or papillary structures were entirely composed of monolayered columnar or cuboidal epithelial cells, which were morphologically identical to the luminal epithelial cells of classic BA (monolayered BA-like lesions). Immunohistochemical analysis revealed thyroid transcription factor 1 expression by ciliated columnar epithelial cells, basal cells, and nonciliated columnar and cuboidal epithelial cells. Basal cells also expressed p40 and p63. Twenty-five cases underwent next-generation sequencing using a 422-cancer-gene panel (GeneseeqPrime). Oncogenic driver mutations were detected in 23 cases, including 13 (52%) with EGFR mutations, 4 (16%) with KRAS G12D/V mutations, 3 (12%) with BRAF V600E mutations, 2 (8%) with ERBB2 exon 20 insertions, and 1 (4%) with a RET fusion. EGFR exon 20 insertions were present in 100% of BAs with monolayered cell lesions, 37.5% of monolayered BA-like lesions, and 8% of classic BA (Fisher's exact test, p = 0.002, false discovery rate = 0.014). Collectively, our study revealed a gradual morphological transition between BA and its variants. The genetic composition of BAs with monolayered structures differed significantly from those of classic BAs or lung adenocarcinoma.
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http://dx.doi.org/10.1002/cjp2.197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8072999PMC
May 2021

Comprehensive Molecular Characterizations of Chinese Patients With Different Subtypes of Lung Squamous Cell Carcinoma.

Front Oncol 2020 10;10:607130. Epub 2020 Dec 10.

Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.

Background: This study aims to profile integrative genomic spectra of Chinese patients with different subtypes of lung squamous cell carcinoma (LUSC) and explore potential molecular prognosis factors.

Methods: We retrospectively identified 204 surgically resected LUSC patients in Shanghai Chest Hospital who underwent capture-based targeted next-generation sequencing (NGS) with a panel of 68 lung cancer-related genes from September 2017 to January 2019. NGS was used to profile comprehensive molecular characterizations.

Results: Of 204 cases, 114 (55.9%) were keratinizing squamous cell carcinoma (KSCC), 77 (37.7%) were non-keratinizing squamous cell carcinoma (NKSCC), 13 (6.4%) were basaloid squamous cell carcinoma (BSCC), respectively. All subtypes presented similarly high proportions of mutations, including TP53, CDKN2A, and NOTCH1. A comparable prevalence of FGFR1 amplifications was identified between KSCC and NKSCC (11.4 26.9%, p = 0.007). Compared with NKSCC, IGF1R amplifications were more frequent in BSCC (0 15.4%, p = 0.019). We found cases with TP53 alterations had less EGFR alterations in KSCC (P = 0.013, OR = 0.158). Compared with TCGA cohorts, our Chinese cohorts exhibited statistic differences in both somatic mutations and signaling pathways. We found that STK 11 alterations and TOP2A alterations were significantly associated with higher risk of recurrence in patients with LUSC.

Conclusions: Significant differences exist among three subtypes of LUSC in molecular characterizations.
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http://dx.doi.org/10.3389/fonc.2020.607130DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7758445PMC
December 2020

Modeling of osteosarcoma with induced pluripotent stem cells.

Stem Cell Res 2020 12 22;49:102006. Epub 2020 Sep 22.

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. Electronic address:

Osteosarcoma is the most common type of bone cancer. Osteosarcoma is commonly associated with TP53 inactivation (around 95% of cases) and RB1 inactivation (around 28% of cases). With the discovery of reprogramming factors to induce pluripotency even in terminally differentiated cells, induced pluripotent stem cells (iPSCs) have emerged as a promising disease model. iPSC-based disease modeling uniquely recapitulates disease phenotypes and can support discoveries into disease etiology and is used extensively today to study a variety of diseases, including cancers. This paper focuses on iPSC-based modeling of Li-Fraumeni syndrome (LFS), an autosomal dominant disorder commonly associated with TP53 mutation and high osteosarcoma incidence. As iPSCs are increasingly utilized as a platform for cancer modeling, the experimental approaches that we discuss here may serve as a guide for future studies.
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http://dx.doi.org/10.1016/j.scr.2020.102006DOI Listing
December 2020

Molecular and clinicopathological characteristics of ROS1-rearranged non-small-cell lung cancers identified by next-generation sequencing.

Mol Oncol 2020 11 14;14(11):2787-2795. Epub 2020 Sep 14.

Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou University, China.

ROS1 gene rearrangements have been reported in diverse cancer types including non-small-cell lung cancer (NSCLC), and with a notably higher prevalence in lung adenocarcinoma. The tyrosine kinase inhibitors, crizotinib, lorlatinib, and entrectinib, have demonstrated favorable efficacy in treating ROS1-rearranged NSCLCs. Herein, we retrospectively reviewed 17 158 NSCLC patients whose tumor specimen and/or circulating cell-free DNA underwent comprehensive genomic profiling. A total of 258 unique patients were identified with ROS1 rearrangements, representing an overall prevalence of approximately 1.5% of ROS1 fusions in newly diagnosed and relapsed NSCLC patients. CD74 (38%) was the most common fusion partner of ROS1, followed by EZR (13%), SDC4 (13%), SLC34A2 (10%), and other recurrent fusion partners with lower frequencies, including TPM3, MYH9, and CCDC6. Variant breakpoints occurred in ROS1 introns 33 (37%), 31 (25%), 32 (17%), and 34 (11%) with no obvious hotspots. CD74 (63%) and EZR (50%) were more frequently fused to ROS1 intron 33 than other introns, while ROS1 intron 31 was most frequently fused with SDC4 (79%) and SLC34A2 (81%). Crizotinib progression-free survival (PFS) was not significantly different between fusion variants involving breakpoints in different ROS1 introns, nor was there a significant difference in PFS between CD74-ROS1 and non-CD74-ROS1 groups of patients. Furthermore, TP53 was most frequently mutated in patients who progressed on crizotinib, and TP53 mutations were significantly associated with shorter crizotinib PFS. ROS1 mutations, including G2032R, were observed in approximately 33% of post-crizotinib samples. Collectively, we report the prevalence of ROS1 fusions in a large-scale NSCLC population and the efficacy of crizotinib in treating patients with ROS1-rearranged NSCLC.
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http://dx.doi.org/10.1002/1878-0261.12789DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7607175PMC
November 2020

[Progress in metabolic engineering of biosynthesis of 3-hydroxypropionic acid].

Sheng Wu Gong Cheng Xue Bao 2020 Jun;36(6):1101-1112

College of Life Sciences, Northeast Forestry University, Harbin 150040, Heilongjiang, China.

As an important platform compound, 3-hydroxypropionic acid (3-HP) can be used as a substrate to synthesize a variety of biological products with commercial potential. The titer of 3-HP by wild-type bacteria is low, which severely limits the large-scale application and production of 3-HP. By modifying the genes related to the metabolic pathway, engineered bacteria using cheap substrates as carbon sources are constructed, the aim of reducing production cost and increasing output is realized. In this paper, the recent progress in the synthesis of 3-HP by metabolic engineering at home and abroad is reviewed. The advantages and disadvantages of glycerol pathway, malonyl-CoA pathway and beta-alanine pathway for synthesis of 3-HP are also summarized and analyzed, and the future development of 3-HP is prospected.
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http://dx.doi.org/10.13345/j.cjb.190398DOI Listing
June 2020

Circulating Myeloid-derived Suppressor Cells Facilitate Invasion of Thyroid Cancer Cells by Repressing miR-486-3p.

J Clin Endocrinol Metab 2020 08;105(8)

Department of Endocrinology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.

Background: Myeloid-derived suppressor cells (MDSCs) have become increasingly recognized as facilitators of tumor development. However, the role of MDSCs in papillary thyroid carcinoma (PTC) progression has not been clearly explored.

Objective: We aimed to evaluate the levels and function of circulating MDSCs in PTC.

Methods: The proportion of circulating polymorphonuclear (PMN)-MDSCs and mononuclear-MDSCs from patients with PTC or benign thyroid nodules and healthy controls was measured using flow cytometry. For immunosuppressive activity analysis, sorted circulating MDSCs were cocultured with CD3/CD28-costimulated T lymphocytes and the proliferation of T cells was determined. PTC cell lines (TPC-1 and BC-PAP) were cocultured with PMN-MDSCs, and the effects on cell migration, invasion, proliferation, and apoptosis were evaluated. The differential expressed microribonucleic acids (RNAs) and messenger RNAs and their function were also explored in TPC-1 cells cocultured with or without PMN-MDSCs.

Results: PMN-MDSCs were increased in peripheral blood mononuclear cells of patients with PTC. Circulating PMN-MDSCs displayed strong T cell suppressive activity. PTC cells demonstrated enhanced invasive capabilities in vitro and in vivo when cocultured with sorted PMN-MDSCs. PMN-MDSCs decreased expression of miR-486-3p and activated nuclear factor kappa B2 (NF-κB2), a direct target of miR-486-3p. Rescue of miR-486-3p diminished the cell migration and invasion induced by PMN-MDSCs.

Conclusion: Collectively, our work indicates that circulating PMN-MDSCs promote PTC progression. By suppressing miR-486-3p, PMN-MDSCs promote the activity of the NF-κB2 signaling pathway, resulting in accelerated invasion of PTC cells, which may provide new therapeutic strategies for treatment of thyroid cancer.
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http://dx.doi.org/10.1210/clinem/dgaa344DOI Listing
August 2020

Clinicopathologic features and genomic analysis of pulmonary blastomatoid carcinosarcoma.

BMC Cancer 2020 Mar 24;20(1):248. Epub 2020 Mar 24.

Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, Shanghai, 200030, China.

Background: This study was designed to investigate the clinicopathologic features of pulmonary blastomatoid carcinosarcoma and explore the genomic profiles of epithelial and mesenchymal components in this tumor.

Methods: Three cases of pulmonary blastomatoid carcinosarcoma were enrolled in this study. Clinicopathologic information and prognostic data were retrospectively reviewed. Diagnostic immunohistochemistry was performed. The epithelial and mesenchymal components were microdissected to investigate the genomic profiles by performing capture-based targeted next generation sequencing.

Results: The epithelial components in patient one consisted of low-grade and high-grade fetal lung adenocarcinoma. Low-grade epithelial cells showed nuclear expression of β-catenin and missense mutation of CTNNB1. The epithelial components in another two patients consisted of high-grade fetal lung adenocarcinoma/enteric adenocarcinoma. The epithelial cells showed membrane staining of β-catenin and harbored no mutation of CTNNB1. The mesenchymal components in all three tumors were composed of primitive round/spindle cells without definite differentiation and showed cytoplasmic dot positive of β-catenin and no corresponding mutation. Within a tumor, both components exhibited relatively comparable molecular profile. In patient one, 4 mutations: RB1, FAT3, PTCH1 and LRP1B were shared by both epithelial and mesenchymal components. Epithelial component had additional mutations in BCOR, CTNNB1, CTCF, FAT1 and DICER1. In patient two, 12 mutations were shared. The epithelial component had BRCA2 mutation and the mesenchymal had mutations in CREBBP, ALK, DNMT3A, ASXL2, MYCN and RICTOR. Patient three had 6 shared mutations. The epithelial component had an additional mutation in KAT6A and the mesenchymal had an additional mutation in APC. Collectively, we observed heterogeneity between epithelial and mesenchymal components of the same tumor.

Conclusions: Blastomatoid carcinosarcoma showed characteristic morphology and immunophenotype. Parallel detection of genetic abnormalities in epithelial and mesenchymal components could provide further evidence for tumor differentiation, molecular targeting and differential diagnosis.
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http://dx.doi.org/10.1186/s12885-020-06748-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092447PMC
March 2020

Expression Profiling of Driver Genes in Female Never-smokers With Non-adenocarcinoma Non-small-cell Lung Cancer in China.

Clin Lung Cancer 2020 09 10;21(5):e355-e362. Epub 2020 Feb 10.

Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China. Electronic address:

Background: Although smoking is a primary cause of lung cancer, females are overrepresented among never-smokers with the disease. The mutational landscape of adenocarcinoma in never-smoking females has been extensively profiled; however, there is little knowledge about genomic alterations in non-adenocarcinoma non-small-cell lung cancer (NA-NSCLC). In the study, we reviewed the status of oncogenic drivers of NA-NSCLC in these populations.

Materials And Methods: Comprehensive genomic profiling was performed on DNA extracted from formalin-fixed, paraffin-embedded sections of 52 NA-NSCLC tissues, including 35 squamous cell carcinomas (SQCCs), 11 adenosquamous carcinomas, 5 pulmonary sarcomatoid carcinoma, and 1 large cell carcinoma by next-generation sequencing within a panel of 68 cancer-related genes.

Results: Mutations of the common oncogenic drivers (EGFR, KRAS, ALK, ROS1, MET, RET, and ERBB2) occurred in 61.5% of cases. The frequency of well-established targets (EGFR and ALK), new targets without widely available therapies (MET and ERBB2), and potentially actionable targets (RET and DDR2) in SQCCs of female never-smokers was significantly higher than that in The Cancer Genome Atlas dataset. There were 31%, 82%, and 80% of cases with SQCC, adenosquamous carcinoma, and pulmonary sarcomatoid carcinoma, respectively, harboring at least one of the following targets: EGFR, ALK, ERBB2, and MET. Approximately 78% (7/9) of the patients responded to various targeted treatments.

Conclusion: Female never-smokers with NA-NSCLC in this study had a high frequency of currently known or potentially actionable oncogenic alterations and could benefit from targeted therapy. Our study also provides evidence for the recommendation of molecular analysis in never-smoking female SQCC.
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http://dx.doi.org/10.1016/j.cllc.2020.02.005DOI Listing
September 2020

Molecular Profiling for Supernatants and Matched Cell Pellets of Pleural Effusions in Non-Small-Cell Lung Cancer.

J Mol Diagn 2020 04 7;22(4):513-522. Epub 2020 Feb 7.

Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, People's Republic of China. Electronic address:

Pleural effusion (PE) is commonly observed in advanced lung cancer patients. Cell-free total nucleic acid (cfTNA) isolated from cancer patients' plasma has allowed noninvasive tumor genome analyses; however, there are limited studies of detection and characterization of cfTNA in PE. Herein, we included 47 advanced non-small-cell lung cancer patients with PE, who had lung cancer driver mutations tested on tumor tissue specimens either at diagnosis or during disease progression. The supernatant and cell pellet of each PE were evaluated for molecular profiles in parallel on an Ion Torrent next-generation sequencing platform. Somatic mutations were detected in 89.1% supernatant cfTNA, but in only 54.3% of cell pellets. The overall concordance rate between supernatants and formalin-fixed, paraffin-embedded cell pellets at the mutation level was 53.3%. By contrast, 41.7% and 5.0% of somatic alterations were detected in supernatants and cell pellets, respectively. Furthermore, joint analysis of supernatants and cell pellets from PE showed a high concordance (88.3%) of variant detection with their respective tumor tissue specimens. Low-frequency T790M mutations in three cases (0.29%, 0.41%, and 1.56%) were detected in supernatants but not in the matched cell pellets or tumor tissues. In conclusion, pleural effusion-derived cfTNA can effectively be used in clinical practice for molecular analysis by next-generation sequencing, even in cases where corresponding cell pellets or tumor tissues yield insufficient material.
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http://dx.doi.org/10.1016/j.jmoldx.2020.01.011DOI Listing
April 2020

Engineering Mutation Clones in Mammalian Cells with CRISPR/Cas9.

Methods Mol Biol 2020 ;2108:355-369

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.

CRISPR, Clustered Regularly Interspaced Short Palindromic Repeat, as a powerful genome engineering system has been widely accepted and employed in gene editing of a vast range of cell types. Comparing to zinc finger nucleases (ZFNs) or transcription-activator-like effector nucleases (TALENs), CRISPR shows less complicated process and higher efficiency. With the development of different CRISPR systems, it can be used not only to knock out a gene, but also to make precise modifications, activate or repress target genes with epigenetic modifications, and even for genome-wide screening. Here we will describe the procedure of generating stable cell lines with a knock-in mutation created by CRISPR. Specifically, this protocol demonstrated how to apply CRISPR to create the point mutation of R249 to S249 on TP53 exon 7 in human embryonic stem cells (hESC) H9 line, which includes three major steps: (1) design CRISPR system targeting TP53 genomic region, (2) deliver the system to H9 hESC and clone selection, and (3) examination and selection of positive clones.
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http://dx.doi.org/10.1007/978-1-0716-0247-8_29DOI Listing
January 2021

Genomic Integrity Safeguards Self-Renewal in Embryonic Stem Cells.

Cell Rep 2019 08;28(6):1400-1409.e4

Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. Electronic address:

A multitude of signals are coordinated to maintain self-renewal in embryonic stem cells (ESCs). To unravel the essential internal and external signals required for sustaining the ESC state, we expand upon a set of ESC pluripotency-associated phosphoregulators (PRs) identified previously by short hairpin RNA (shRNA) screening. In addition to the previously described Aurka, we identify 4 additional PRs (Bub1b, Chek1, Ppm1g, and Ppp2r1b) whose depletion compromises self-renewal and leads to consequent differentiation. Global gene expression profiling and computational analyses reveal that knockdown of the 5 PRs leads to DNA damage/genome instability, activating p53 and culminating in ESC differentiation. Similarly, depletion of genome integrity-associated genes involved in DNA replication and checkpoint, mRNA processing, and Charcot-Marie-Tooth disease lead to compromise of ESC self-renewal via an increase in p53 activity. Our studies demonstrate an essential link between genomic integrity and developmental cell fate regulation in ESCs.
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http://dx.doi.org/10.1016/j.celrep.2019.07.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6708277PMC
August 2019

Characterising dryland salinity in three dimensions.

Sci Total Environ 2019 Sep 6;682:190-199. Epub 2019 May 6.

Institute of Agricultural Remote Sensing and Information Technology Application, College of Environment and Resource Sciences, Zhejiang University, Hangzhou 310058, China. Electronic address:

Due to frequent salt migration and large spatial variability within soil profiles, salinity characterisation by traditional drilling sampling methods is time-consuming and labour-intensive. Thus, it is necessary to develop monitoring technology and three-dimensional (3D) characterisation methods for rapid, non-invasive, and accurate soil salinity measurement. This study presents a new framework combining sensor technology and an inversion algorithm to characterise 3D soil salinity. Four typical land-use types (natural desert, natural vegetation, apple orchard, and winter wheat farmland) in the Aksu region of southern Xinjiang were surveyed and apparent conductivity (ECa) data were recorded at depths of 0.75 m and 1.50 m. ECa data were converted to electrical conductivity and salinity characterisation was conducted following U.S. Salinity Laboratory recommendations. Ordinary Kriging interpolation was used to map the spatial distribution and an iterative inversion model was used to map the vertical distribution of soil salinity. Model parameters were adjusted several times and the accuracy of different inversion algorithms was compared to obtain the best inversion effect. As a result, the Multilevel Orthogonal Inversion model was developed to characterise 3D soil salinity for different land-use types. Due to crop activities including irrigation, managed land use types (apple orchard and winter wheat plots) typically exhibited weaker salinity than natural systems (desert and vegetation plots) but greater spatial variability overall. The proposed framework combining EM (electromagnetic) sensing and the 3D inversion algorithm can effectively characterise and visualise soil salinity for the entire soil profile, which is important for land evaluation and improvement.
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http://dx.doi.org/10.1016/j.scitotenv.2019.05.037DOI Listing
September 2019

Irradiation-induced dynamic changes of gene signatures reveal gain of metastatic ability in nasopharyngeal carcinoma.

Am J Cancer Res 2019 1;9(3):479-495. Epub 2019 Mar 1.

Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-sen University Guangzhou 510080, P. R. China.

Nasopharyngeal carcinoma (NPC), arising from the nasopharynx epithelium, is prevalent among South and East Asia. The radiotherapy is the primary treatment for NPC patients. However, the acquired radioresistance dramatically diminishes the therapeutic effect of radiotherapy. Meanwhile, recurrence and metastasis always occur in line with the radioresistance, but the underlying mechanisms are still unclear. In this study, we established two radioresistant NPC cell lines, CNE1R and SUNE1R, by sequentially irradiated parental CNE1 and SUNE1 cells up to a clinical treatment dose of 72 Gy. A transcriptome profile analysis of CNE1R and CNE1 reveals that activated oncogenic pathways are highly enriched in CNE1R. As the result, CNE1R showed higher proliferation rate but lower apoptosis rate after irradiation, and enhanced metastasis ability in comparison with CNE1. Significantly, a group of metastasis associated genes were increased in CNE1R while the irradiation proceeded, including several matrix metallopeptidase (MMP) members, especially MMP10 and MMP13. With further analysis, we found both MMP10 and MMP13 are highly upregulated in metastatic head and neck cancer specimens compared to non-metastatic ones. More importantly, patients with lower expression of both MMP10 and MMP13 showed a better five-year survival than the double high group. Our findings unveiled the potential mechanisms of radioresistance related metastasis in NPC patients, and the increase of MMP10 and MMP13 may serve as high risk factors for metastasis during radiotherapy.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448059PMC
March 2019

Next-Generation Sequencing for Genotyping of Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration Samples in Lung Cancer.

Ann Thorac Surg 2019 07 15;108(1):219-226. Epub 2019 Mar 15.

Department of Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China; Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, P.R. China. Electronic address:

Background: Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) can obtain a small amount of specimen. This study aims to evaluate the feasibility and robustness of using EBUS-EBNA samples to perform capture-based targeted next-generation sequencing (NGS).

Methods: Tissue samples from patients with advanced non-small cell lung cancer were collected by EBUS-TBNA and were formalin-fixed paraffin-embedded. Three representative genes, EGFR, ALK, and ROS1, were examined by amplification refractory mutation system polymerase chain reaction, immunohistochemistry, and quantitative reverse transcription polymerase chain reaction. The remaining samples were processed with NGS assay with a 56-gene panel. Classic driver mutations detected by NGS were verified by conventional methods.

Results: Of the 85 samples from patients with advanced non-small cell lung cancer, 77 were performed successfully with all assays. Forty-one mutations in EGFR, ALK, and ROS1 were detected in both conventional methods and NGS, representing a 100% concordance. In contrast, four EGFR mutations detected by NGS were not covered in the targeted regions of amplification refractory mutation system polymerase chain reaction, leading to a negative call in these patients. Altogether, NGS detected 12 additional variants, including six KRAS mutations, one BRAF mutation, one RET fusion, one MET amplification concurrent with EGFR L858R, one KRAS amplification together with EGFR 19del, and one ERBB2 amplification. The mean number of needle passes per lymph node was 5.2 in samples successfully applied in all assays.

Conclusions: NGS assay can be successfully conducted with limited tissue samples obtained from EBUS-TBNA. Compared with conventional methods, NGS assay provides more comprehensive information on genetic alterations in tumors, which greatly assists therapeutic decision making for advanced lung cancer.
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http://dx.doi.org/10.1016/j.athoracsur.2019.02.010DOI Listing
July 2019

Malignant perivascular epithelioid cell tumor of the lung synchronous with a primary adenocarcinoma: one case report and review of the literature.

BMC Cancer 2019 Mar 15;19(1):235. Epub 2019 Mar 15.

Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241 West Huaihai Road, Shanghai, 200030, China.

Background: Perivascular Epithelioid Cell Tumors (PEComa) is an extraordinarily rare mesenchymal neoplasm especially the malignant type originating from the lung. To date, only 8 cases of malignant or malignant potential pulmonary PEComa had been documented. Firm diagnostic criteria for malignant pulmonary PEComa need urgently to be established.

Case Presentation: We report a challenging case of malignant pulmonary PEComa combined with a primary adenocarcinoma in a 54-year-old man. The PEComa-like tumor showed strong Melan-A and weak transcription factor E3 (TFE3) protein expression but no TFE3 gene rearrangement. The carcinoma-like nodule was recognized as a poorly differentiated primary lung adenocarcinoma.

Discussion And Conclusions: Our case report was the first case of malignant pulmonary PEComa synchronous with a primary adenocarcinoma and studied the dilemma of diagnosing benign versus malignant criteria for this uncommon tumor.
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http://dx.doi.org/10.1186/s12885-019-5383-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419825PMC
March 2019

Clinicopathological Features of ALK Expression in 9889 Cases of Non-small-Cell Lung Cancer and Genomic Rearrangements Identified by Capture-Based Next-Generation Sequencing: A Chinese Retrospective Analysis.

Mol Diagn Ther 2019 06;23(3):395-405

Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, No. 241, West Huai Hai Road, Xv Hui District, Shanghai, 200030, China.

Background: The clinicopathological features and genomic rearrangements of anaplastic lymphoma kinase (ALK) fusion cases have not been fully identified.

Objective: Our objective was to explore the status of ALK in non-small-cell lung cancer (NSCLC) specimens, to explore the relationships between ALK status and clinicopathological features and to identify genomic rearrangements via capture-based next-generation sequencing (NGS).

Methods: We tested 9889 NSCLC specimens for ALK status using the Ventana anti-ALK (D5F3) antibody. Clinicopathological features were analyzed and genomic rearrangements identified using capture-based NGS in 76 ALK-positive cases.

Results: In total, 485 specimens (4.90%) tested positive for ALK. The positivity rate was higher for adenocarcinoma samples than for non-adenocarcinoma samples (6.03 vs. 1.47%; p < 0.001) and for biopsies/cell blocks than for surgical specimens (7.00 vs. 4.16%; p < 0.001). Patient age, patient sex, specimen type, specimen histotype, and patient smoking history were all significantly correlated with ALK status. Genomic rearrangements were detected in 98.68% (75/76) of the ALK-positive samples; 89.33% (67/75) carried the canonical EML4-ALK, and the remaining samples carried only noncanonical ALK rearrangements. Four of these noncanonical ALK fusion samples were identified as carrying EML4-ALK transcripts at the RNA level. A novel fusion variant, SRD5A2-ALK, was revealed.

Conclusions: Younger patients with NSCLC, especially those aged < 30 years, were more likely to test positive for ALK. Positive ALK test results were more common in patients with invasive mucinous adenocarcinoma and solid-predominant invasive adenocarcinoma than in patients with other histotypes. Samples that carried only noncanonical ALK rearrangements may also have carried the canonical EML4-ALK, which was not detected by capture-based NGS. EML4-ALK transcripts might result from rare splicing mechanisms without genomic rearrangements.
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http://dx.doi.org/10.1007/s40291-019-00389-yDOI Listing
June 2019

Generation of a heterozygous p53 R249S mutant human embryonic stem cell line by TALEN-mediated genome editing.

Stem Cell Res 2019 01 30;34:101360. Epub 2018 Nov 30.

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. Electronic address:

As one of the most essential genome guardians, p53 and its mutants have been suggested associated with many types of cancers. Many p53 mutants function induce unique phenotypes, including carcinogenesis, metastasis, and drug resistance. The p53(R249S) mutation is the most prevalent and specific mutation associated with liver cancer development. Here, we demonstrate the generation of a heterozygous p53(R249S) mutation in the H9 human embryonic stem cell line using TALEN-mediated genome editing. The generated cell line maintains a normal karyotype, a pluripotent state and the in vivo capacity to develop a teratoma containing all three germ layer tissues.
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http://dx.doi.org/10.1016/j.scr.2018.101360DOI Listing
January 2019

Different characteristics and survival in non-small cell lung cancer patients with primary and acquired EGFR T790M mutation.

Int J Cancer 2019 06 3;144(11):2880-2886. Epub 2019 Jan 3.

Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.

Primary epidermal growth factor receptor (EGFR) T790M mutation can be occasionally identified in previous untreated nonsmall cell lung cancer (NSCLC) patients. To compare clinical characteristics and outcomes in patients with primary and acquired EGFR T790M mutation, we collected the data of patients diagnosed with EGFR mutation from 2012 to 2017 in Shanghai Chest Hospital. Primary EGFR T790M mutation was identified in 61 patients (1.1%; 95% confidence interval (CI): 0.8%-1.3%) of 5685 TKI-naive EGFR mutant patients. Acquired T790M mutation was detected in 98 patients (50.3%; 95%CI: 43.2%-57.3%) of 195 TKI-treated patients. T790M mutation always coexisted with sensitizing EGFR mutations. Primary EGFR T790M always coexisted with 21L858R (46/61) whereas acquired T790M coexisted with 19del (68/98), (p < 0.001). Among them, 18 patients with primary T790M mutation received osimertinib and 72 patients with acquired T790M mutation received osimertinib. The median progression-free survival (PFS) of osimertinib was significantly longer in primary T790M group (17.0 months, 95%CI:14.0-20.0 months) compared to acquired T790M group (10.0 months, 95%CI:8.6-11.4 months, p = 0.022). However, the median overall survival (OS) of acquired T790M mutation patients was significantly longer compared to that of primary T790M mutation patients who received osimertinib (50.4 months vs. 29.9 months, p = 0.016). Our findings suggest that primary T790M mutation likely coexists with 21L858R while acquired mutation likely coexists with 19del. Both mutations showed good response to osimertinib. Patients with primary T790M mutation experienced greater benefits from osimertinib. However, patients with acquired T790M mutation had a better overall survival during the entire clinical treatment.
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http://dx.doi.org/10.1002/ijc.32015DOI Listing
June 2019

Proposal on incorporating lymphovascular invasion as a T-descriptor for stage I lung cancer.

Lung Cancer 2018 11 1;125:245-252. Epub 2018 Oct 1.

Department of Pulmonary, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai, 230032, China. Electronic address:

Background: Lymphovascular invasion (LVI) and Visceral Pleural Invasion (VPI) have been reported to be risk factors for stage I Non-Small Cell Lung Cancer (NSCLC). However, only VPI was incorporated into the current 8th Tumor-Node-Metastasis (TNM) classification. This study aimed to explore the prognostic effect of LVI and VPI on TNM staging in pathological stage I NSCLC.

Method: We retrospectively reviewed 2633 consecutive p-stage I NSCLC patients in the Shanghai Chest Hospital (2008-2012). By using the Kaplan-Meier method and Cox proportional hazard regression model, we identified the correlations between LVI, VPI, and clinical outcomes in p-stage 1 NSCLC.

Results: Of all 2633 p-stage I NSCLC patients, 222 were pathologically diagnosed with LVI and 836 pathologically with VPI. The 5-year recurrence free survival (RFS) and overall survival (OS) rates of patients with LVI was significantly worse compared to those without LVI (61.2% vs 82.0%, p < 0.001; 73.3% vs 88.1%, p < 0.001). The same results emerged for patients with VPI (70.1% vs 85.9%, p < 0.001; 82.3% vs 90.0%, p < 0.001). Using the univariable and multivariable analysis, we found that when tumor diameter was 3 cm or smaller, LVI (RFS: hazard ratio [HR], 2.54; 95% confidence interval [CI], 1.86-3.50; p < .001; OS: HR, 2.53; 95% CI, 1.72-3.71; p < .001) and VPI (RFS: HR, 2.14; 95% CI, 1.71-2.67; p < .001; OS: HR, 1.56; 95% CI, 1.12-2.04; p = 0.01) were significant prognostic factors for RFS and OS. When tumor size was between 3-4 cm, LVI (HR, 1.84; 95% CI, 1.03-3.29; p = 0.039) and VPI (HR, 2.56; 95% CI, 1.61-4.07; p < .001) were associated with inferior OS.

Conclusions: The presence of LVI significantly affected OS and RFS in stage I NSCLC patients. Our results suggested that it might be better to incorporate LVI as a T descriptor as VPI in the further TNM classification.
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http://dx.doi.org/10.1016/j.lungcan.2018.09.024DOI Listing
November 2018

Generation of an induced pluripotent stem cell line from an individual with a heterozygous RECQL4 mutation.

Stem Cell Res 2018 12 2;33:36-40. Epub 2018 Oct 2.

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Center for Precision Health, School of Biomedical Informatics and School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA. Electronic address:

The DNA helicase RECQL4 is known for its roles in DNA replication and repair. RECQL4 mutations cause several genetic disorders including Rothmund-Thomson syndrome (RTS), characterized by developmental defects and predisposition to osteosarcoma. Here we reprogrammed fibroblasts with a heterozygous RECQL4 mutation (c.1878 + 32_1878 + 55del24) to induced pluripotent stem cells (iPSCs). These iPSCs are pluripotent and are able to be differentiated into all three germ layers, providing a novel tool to further interrogate the role of RECQL4 DNA helicase in vitro.
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http://dx.doi.org/10.1016/j.scr.2018.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6317900PMC
December 2018

Solitary pulmonary capillary hemangioma: Clinicopathologic and radiologic characteristics of nine surgically resected cases.

Pathol Res Pract 2018 Nov 20;214(11):1885-1891. Epub 2018 Sep 20.

Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200030, China. Electronic address:

Background: Solitary pulmonary capillary hemangioma (SPCH) is an extraordinarily rare capillary derived mesenchymal neoplasm. Although routine morphology and immunohistochemistry are adequate for the diagnosis of classical SPCH in surgical specimens, true gross appearance identification of most tumor themselves and diagnosis for some exceptional cases are still very difficult. Furthermore, preoperative imaging and frozen diagnosis remain a challenge.

Methods: We reported nine original cases of solitary pulmonary capillary hemangioma and summarized the clinical characteristics of twenty-one reported lesions. Imaging materials were reviewed by the image experts of our hospital. Quick hematoxylin-eosin stained intraoperative frozen sections and routine histological diagnosis were re-confirmed by 3 specialist pathologists with at least 10 years of diagnostic experience in our department. Immunohistochemistry analysis was performed on formalin fixed archival tissue. The surgical methods, following up information and prognosis were retrospectively analyzed.

Results: In imaging, three tumors showed solid nodules, three cases displayed mix ground glass nodules, two nodules were pure ground glass density, and one case was a cystic-solid mass. Macroscopically, solitary pulmonary capillary hemangiomas were ill-defined soft hemorrhagic lesion with pale yellow or dark brownish cut surface. Two cases had a clear boundary and seven lesions were poorly demarcated. Typical morphological features were densely proliferating thin-walled capillaries composing of single layer of flatten or cuboidal endothelial cells within the thickened alveolar septa. One case was mistaken for a histiocytogenic lesion during freezing. The cystic-solid lesion showed a hyperplasia capillary network along the submucosal interstitium of bronchioles. Immunohistochemically, tumor endothelial cells were positive for ERG, Fli-1, CD31, CD34 and Vimentin and negative for CK, α-SMA, TTF-1, HMB45, S-100 and CD68. Lobectomy was performed on seven cases, wedge resection and segmentectomy were proceeded in two patients respectively. Follow up information showed no evidence of complication or recurrence.

Conclusions: Solitary pulmonary capillary hemangioma has special imaging and various histological features and must be distinguished from small benign lung lesions and preinvasive cancer. Although the prognosis of this tumor is good after surgical resection, the correct interpretation of the gross appearance and radiographic findings are still important. Choosing appropriate resection mode depends on accurate evaluation preoperative and intraoperative.
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http://dx.doi.org/10.1016/j.prp.2018.09.014DOI Listing
November 2018

Corrigendum to "Identifying localized and scale-specific multivariate controls of soil organic matter variations using multiple wavelet coherence" [Sci. Total Environ. 643 (2018) 548-558].

Sci Total Environ 2019 02 19;649:1661-1662. Epub 2018 Sep 19.

Department of Land Resource Management, School of Tourism and Urban Management, Jiangxi University of Finance and Economics, Nanchang 330013, China.

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http://dx.doi.org/10.1016/j.scitotenv.2018.09.065DOI Listing
February 2019

Induced Pluripotent Stem Cells and Induced Pluripotent Cancer Cells in Cancer Disease Modeling.

Adv Exp Med Biol 2018;1119:169-183

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA.

In 2006, Noble Prize laureate Shinya Yamanaka discovered that a set of transcription factors can reprogram terminally differentiated somatic cells to a pluripotent stem cell state. Since then, induced pluripotent stem cells (iPSCs) have come into the public spotlight. Amidst a growing field of promising clinical uses of iPSCs in recent years, cancer disease modeling has emerged as a particularly promising and rapidly translatable application of iPSCs. Technological advances in genome editing over the past few years have facilitated increasingly rapid progress in generation of iPSCs with clearly defined genetic backgrounds to complement existing patient-derived models. Improved protocols for differentiation of iPSCs, engineered iPSCs and embryonic stem cells (ESCs) now permit the study of disease biology in the majority of somatic cell types. Here, we highlight current efforts to create patient-derived iPSC disease models to study various cancer types. We review the advantages and current challenges of using iPSCs in cancer disease modeling.
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http://dx.doi.org/10.1007/5584_2018_257DOI Listing
July 2019

Modeling Osteosarcoma Using Li-Fraumeni Syndrome Patient-derived Induced Pluripotent Stem Cells.

J Vis Exp 2018 06 13(136). Epub 2018 Jun 13.

Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston; Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center UTHealth; Center for Stem Cell and Regenerative Medicine, The Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, The University of Texas Health Science Center at Houston; Center for Precision Health, School of Biomedical Informatics and School of Public Health, The University of Texas Health Science Center at Houston;

Li-Fraumeni syndrome (LFS) is an autosomal dominant hereditary cancer disorder. Patients with LFS are predisposed to a various type of tumors, including osteosarcoma--one of the most frequent primary non-hematologic malignancies in the childhood and adolescence. Therefore, LFS provides an ideal model to study this malignancy. Taking advantage of iPSC methodologies, LFS-associated osteosarcoma can be successfully modeled by differentiating LFS patient iPSCs to mesenchymal stem cells (MSCs), and then to osteoblasts--the cells of origin for osteosarcomas. These LFS osteoblasts recapitulate oncogenic properties of osteosarcoma, providing an attractive model system for delineating the pathogenesis of osteosarcoma. This manuscript demonstrates a protocol for the generation of iPSCs from LFS patient fibroblasts, differentiation of iPSCs to MSCs, differentiation of MSCs to osteoblasts, and in vivo tumorigenesis using LFS osteoblasts. This iPSC disease model can be extended to identify potential biomarkers or therapeutic targets for LFS-associated osteosarcoma.
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http://dx.doi.org/10.3791/57664DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6101728PMC
June 2018

Identifying localized and scale-specific multivariate controls of soil organic matter variations using multiple wavelet coherence.

Sci Total Environ 2018 Dec 23;643:548-558. Epub 2018 Jun 23.

Department of Land Resource Management, School of Tourism and Urban Management, Jiangxi University of Finance and Economics, Nanchang 330013, China. Electronic address:

Environmental factors have shown localized and scale-dependent controls over soil organic matter (SOM) distribution in the landscape. Previous studies have explored the relationships between SOM and individual controlling factors; however, few studies have indicated the combined control from multiple environmental factors. In this study, we compared the localized and scale-dependent univariate and multivariate controls of SOM along two long transects (northeast, NE transect and north, N transect) from China. Bivariate wavelet coherence (BWC) between SOM and individual factors and multiple wavelet coherence (MWC) between SOM and factor combinations were calculated. Average wavelet coherence (AWC) and percent area of significant coherence (PASC) were used to assess the relative dominance of individual and a combination of factors to explain SOM variations at different scales and locations. The results showed that (in BWC analysis) mean annual temperature (MAT) with the largest AWC (0.39) and PASC (16.23%) was the dominant factor in explaining SOM variations along the NE transect. The topographic wetness index (TWI) was the dominant factor (AWC = 0.39 and PASC = 20.80%) along the N transect. MWC identified the combination of Slope, net primary production (NPP) and mean annual precipitation (MAP) as the most important combination in explaining SOM variations along the NE transect with a significant increase in AWC and PASC at different scales and locations (e.g. AWC = 0.91 and PASC = 58.03% at all scales). The combination of TWI, NPP and normalized difference vegetation index (NDVI) was the most influential along the N transect (AWC = 0.83 and PASC = 32.68% at all scales). The results indicated that the combined controls of environmental factors on SOM variations at different scales and locations in a large area can be identified by MWC. This is promising for a better understanding of the multivariate controls in SOM variations at larger spatial scales and may improve the capability of digital soil mapping.
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http://dx.doi.org/10.1016/j.scitotenv.2018.06.210DOI Listing
December 2018

Comparison of genetic profiles among primary lung tumor, metastatic lymph nodes and circulating tumor DNA in treatment-naïve advanced non-squamous non-small cell lung cancer patients.

Lung Cancer 2018 07 5;121:54-60. Epub 2018 May 5.

Department of Endoscopy, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, PR China; Department of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, 241 West Huaihai Road, Shanghai 200030, PR China. Electronic address:

Objectives: Genetic profiles of primary and metastatic lung tumor have been investigated by previous studies. However, whether they can be replaced by each other to guide treatment remains controversial. Moreover, it is unclear that whether genetic profiles of plasma can reflect genetic divergence between primary and metastatic lesions.

Materials And Methods: In this prospective study, we collected 35 pairs of matched primary tumor tissue, metastatic lymph nodes and plasma from treatment-naïve patients with advanced non-squamous non-small cell lung cancer (NSCLC) and applied to capture-based sequencing using a panel consisting 56 NSCLC-related genes to interrogate the heterogeneity and similarity among the 3 sites.

Results: We observed 62.0% (67/108) by-variant concordance rate among primary tumor, metastatic lymph nodes and plasma as well as 76.4% (81/106) by-variant concordance rate between primary tumor and metastatic lymph nodes. When the analysis restricted to driver genes, we achieved 60.9% (28/46) and 77.3% (34/44) concordance, respectively. Furthermore, there is no statistically significant difference in progression-free survival (PFS) of 17 patients who used matched targeted therapy between patients having 100% concordance rate between primary tumor and metastatic lymph nodes and patients having partially matched mutational profiles.

Conclusion: Collectively, our study revealed a similar genetic profile shared between primary tumor and metastatic lymph nodes. The limited discordance observed can be partially reflected by plasma. Sequencing results obtained from either site can be utilized for providing treatment guidance.
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http://dx.doi.org/10.1016/j.lungcan.2018.05.002DOI Listing
July 2018