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2. Genomic signatures of past and present chromosomal instability in Barrett’s esophagus and early esophageal adenocarcinoma

Author

Bao, Chunyang, Tourdot, Richard W, Brunette, Gregory J, Stewart, Chip, Sun, Lili, Baba, Hideo, Watanabe, Masayuki, Agoston, Agoston T, Jajoo, Kunal, Davison, Jon M, Nason, Katie S, Getz, Gad, Wang, Kenneth K, Imamura, Yu, Odze, Robert, Bass, Adam J, Stachler, Matthew D, and Zhang, Cheng-Zhong

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Oncology and Carcinogenesis, Genetics, Human Genome, Rare Diseases, Cancer, Digestive Diseases, 2.1 Biological and endogenous factors, Aetiology, Humans, Barrett Esophagus, Esophageal Neoplasms, Adenocarcinoma, Chromosomal Instability, Precancerous Conditions, Genomics, Disease Progression
Abstract

The progression of precancerous lesions to malignancy is often accompanied by increasing complexity of chromosomal alterations but how these alterations arise is poorly understood. Here we perform haplotype-specific analysis of chromosomal copy-number evolution in the progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC) on multiregional whole-genome sequencing data of BE with dysplasia and microscopic EAC foci. We identify distinct patterns of copy-number evolution indicating multigenerational chromosomal instability that is initiated by cell division errors but propagated only after p53 loss. While abnormal mitosis, including whole-genome duplication, underlies chromosomal copy-number changes, segmental alterations display signatures of successive breakage-fusion-bridge cycles and chromothripsis of unstable dicentric chromosomes. Our analysis elucidates how multigenerational chromosomal instability generates copy-number variation in BE cells, precipitates complex alterations including DNA amplifications, and promotes their independent clonal expansion and transformation. In particular, we suggest sloping copy-number variation as a signature of ongoing chromosomal instability that precedes copy-number complexity. These findings suggest copy-number heterogeneity in advanced cancers originates from chromosomal instability in precancerous cells and such instability may be identified from the presence of sloping copy-number variation in bulk sequencing data.

Published
2023

19. Dual targeted extracellular vesicles regulate oncogenic genes in advanced pancreatic cancer

Author

Chiang, Chi-Ling, Ma, Yifan, Hou, Ya-Chin, Pan, Junjie, Chen, Sin-Yu, Chien, Ming-Hsien, Zhang, Zhi-Xuan, Hsu, Wei-Hsiang, Wang, Xinyu, Zhang, Jingjing, Li, Hong, Sun, Lili, Fallen, Shannon, Lee, Inyoul, Chen, Xing-Yu, Chu, Yeh-Shiu, Zhang, Chi, Cheng, Tai-Shan, Jiang, Wen, Kim, Betty Y. S., Reategui, Eduardo, Lee, Robert, Yuan, Yuan, Liu, Hsiao-Chun, Wang, Kai, Hsiao, Michael, Huang, Chi-Ying F., Shan, Yan-Shen, Lee, Andrew S., and James Lee, L.

Published
2023
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28. Influencing Factors of Scientific Data Value Increment Based on System Dynamics

Author

SUN Lili, WANG WeiJie, SHENG Jiefei

Subjects
scientific data, value increment, influencing factors, system dynamics, data elements, fair, Bibliography. Library science. Information resources, Agriculture
Abstract

[Purpose/Significance] To explore the influencing factors of the added value of scientific data and reveal the inherent development laws of the added value of scientific data. [Method/Process] First, based on the interview data of 18 experts and the research results related to the value appreciation of scientific data in existing literature, the grounded theory method was adopted. Through open coding, main-axis coding, and selective coding, 19 categories, 6 main categories, and 3 core categories were finally obtained. From this, a theoretical model of the factors influencing the value appreciation of scientific data was obtained. On this basis, the Vensim PLE tool was used to establish a dynamic model of the value appreciation system of scientific data, and the process of value appreciation of scientific data was dynamically simulated and analyzed to reveal the relationship between various influencing factors and the value appreciation of scientific data. [Results/Conclusions] In the process of increasing the value of scientific data, the quality factor of raw data is a prerequisite, and high-quality raw scientific data are conducive to the integration and secondary development of subsequent scientific data. The data literacy of data producers represented by researchers has the most significant impact on the quality of scientific data. The level of data storage and payment has a significant impact on the added value of scientific data. When the perceived effort and perceived risk of data storage and payment by researchers decrease, accompanied by the pressure of scientific data sharing policies, researchers become more likely to increase their willingness to save and pay, thereby significantly improving the scale effect of data storage and payment. The organization and integration of scientific data is the key to the formation of value-added scientific data. Overall, the metadata quality has the most significant impact on the level of scientific data organization and integration. The quality of metadata is the foundation of scientific data processing, classification, and integration. The higher the quality of metadata, the more it helps to improve the level of scientific data organization and integration. The sharing and development of scientific data is the key to realizing the value-added of scientific data. It is the final step in realizing the value-added of scientific data. In this process, the scale of scientific data openness, the quality of scientific data sharing platforms, and development capabilities all have a positive promoting effect on the level of scientific data sharing and development.

Published
2023
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37. Esophageal Epithelium and Lamina Propria Are Unevenly Involved in Eosinophilic Esophagitis

Author

Hiremath, Girish, Sun, Lili, Collins, Margaret H., Bonis, Peter A., Arva, Nicoleta C., Capocelli, Kelley E., Chehade, Mirna, Davis, Carla M., Falk, Gary W., Gonsalves, Nirmala, Gupta, Sandeep K., Hirano, Ikuo, Leung, John, Khoury, Paneez, Mukkada, Vincent A., Martin, Lisa J., Spergel, Jonathan M., Wechsler, Joshua B., Yang, Guang-Yu, Aceves, Seema S., Furuta, Glenn T., Rothenberg, Marc.E., Koyama, Tatsuki, and Dellon, Evan S.

Published
2023
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44. Abstract 15689: Ablation for Atrial Fibrillation in Patients With Rare Pathogenic Variants in Cardiomyopathy and Arrhythmia Genes

Author

El-Harasis, Majd A, Yoneda, Zachary, Anderson, Katherine, Ye, Fei, Quintana, Joseph, Martinez-Parachini, Jose R, Jackson, Gregory, Varghese, Bibin, Crawford, Diane, Sun, Lili, Williams, Hollie L, OʼNeill, Matthew, Davogustto, Giovanni E, Laws, James L, Murphy, Brittany, Tomasek, Kelsey, Su, Yan Ru, Solem, Emily, Metz, Emma, Smith, Carly, Stubbs, Douglas, Grauherr, Dakota, Wells, Quinn, Michaud, Gregory, saavedra, pablo, Estrada, Juan C, Richardson, Travis, Shen, Sharon, Kanagasundram, Arvindh, Montgomery, Jay A, Tandri, Harikrishna, Ellis, Christopher R, Crossley, George H, Kannankeril, Prince, Stevenson, Lynne W, Stevenson, William G, Lubitz, Steven A, Ellinor, Patrick T, Roden, Dan M, and Shoemaker, Ben B

Published
2023
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47. Eosinophils Exert Antitumorigenic Effects in the Development of Esophageal Squamous Cell Carcinoma

Author

Jacobse, Justin, Aziz, Zaryab, Sun, Lili, Chaparro, Jasmine, Pilat, Jennifer M., Kwag, Aaron, Buendia, Matthew, Wimbiscus, Mae, Nasu, Motomi, Saito, Tsuyoshi, Mine, Shinji, Orita, Hajime, Revetta, Frank, Short, Sarah P., Kay Washington, M., Hiremath, Girish, Gibson, Michael K., Coburn, Lori A., Koyama, Tatsuki, Goettel, Jeremy A., Williams, Christopher S., and Choksi, Yash A.

Published
2023
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49. Clinical application of 3D parametric surface planar topological guide plate in fenestrated/branched endovascular aortic repair technique

Author

FU Dongsheng, LIU Zhao, YANG Chao, LI Qin, CHEN Gezheng, SUN Lili, LI Wendong, ZHOU Minjie, LIU Chen, QIAO Tong, LI Yiqing, LI Xiaoqiang

Subjects
3d parametric surface planar topological guide plate technology, endovascular aortic repair, aortic arch, thoracoabdominal aorta, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282, Surgery, RD1-811
Abstract

Objective To summarize the experience and effect using 3D parametric surface planar topological guide plate technology in fenestrated/branched endovascular aortic repair (F/B EVAR) to repair aortic arch and thoracoabdominal aortic lesions involving important aortic branches. Methods From August 2020 through April 2022, 17 patients [14 males and 3 females, mean age of(61.06±11.23)(39-78) years] with complex aortic lesions involving important branches were treated in both Nanjing Drum Tower Hospital and Union Hospital. There were 8 cases with aortic arch aneurysms 4 cases and dissections 4 cases, respectively, and 9 cases with thoracoabdominal aortic aneurysms 5 cases and dissections 4 cases, respectively. Six cases were urgent operation and 11 cases were selective operation. Before operation, 3D parametric surface planar topological guide plate was made according to aortic computed tomography angiography. Under the guidance of planar guide plate, pre-fenestrated and external/internal branched and other endovascular aortic repair was performed. Totally, 50 fenestrated/branched stent grafts were planted. Results All operations were completed without conversion to open surgery. Average operative time was (4.57±2.29)(1.50-10.67) h. There was no renal insufficiency, paraplegia and loss of branch arteries. One patient (5.88%) died during perioperative period. Within the follow-up, there were 2 cases (11.76%) of endoleak type Ⅰc and type Ⅲc, respectively. Conclusions F/B EVAR under the guidance of 3D parametric surface planar topological guide plate is a minimally invasive treatment. The technology is more accurate than traditional measurement and positioning, faster than 3D printing guidance, and safe and reliable shown in the follow-up.

Published
2022
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