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3. Establishment and validation of preclinical models of SMARCA4-inactivated and ARID1A/ARID1B co-inactivated dedifferentiated endometrial carcinoma

Author

Wong, Nelson K.Y., Llaurado Fernandez, Marta, Kommoss, Felix K.F., Praveen Kumar, Pooja, Kim, Hannah, Liu, Jiahui, Zhang, Guihua, Coatham, Mackenzie, Lin, Yen-Yi, Haegert, Anne M., Volik, Stanislav, Le Bihan, Stephane, Collins, Colin C., Fu, Yangxin, Postovit, Lynne M., von Deimling, Andreas, Wu, Rebecca, Xue, Hui, Wang, Yuzhuo, Köbel, Martin, Carey, Mark S., and Lee, Cheng-Han

Published
2023
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4. Identification of gene signature for treatment response to guide precision oncology in clear-cell renal cell carcinoma

Author

D’Costa, Ninadh M, Cina, Davide, Shrestha, Raunak, Bell, Robert H, Lin, Yen-Yi, Asghari, Hossein, Monjaras-Avila, Cesar U, Kollmannsberger, Christian, Hach, Faraz, Chavez-Munoz, Claudia I, and So, Alan I

Subjects
Biomedical and Clinical Sciences, Clinical Sciences, Oncology and Carcinogenesis, Immunology, Kidney Disease, Biotechnology, Cancer, Clinical Research, Genetics, Detection, screening and diagnosis, 4.1 Discovery and preclinical testing of markers and technologies, 4.2 Evaluation of markers and technologies, Good Health and Well Being, Angiogenesis Inhibitors, Antineoplastic Agents, Immunological, Biomarkers, Tumor, Carcinoma, Renal Cell, Clinical Decision-Making, Cluster Analysis, Cohort Studies, Datasets as Topic, Feasibility Studies, Female, Gene Expression Profiling, Humans, Kidney Neoplasms, Male, Medical Oncology, Middle Aged, Patient Selection, Precision Medicine, Prognosis, Transcriptome
Abstract

Clear-cell renal cell carcinoma (ccRCC) is a common therapy resistant disease with aberrant angiogenic and immunosuppressive features. Patients with metastatic disease are treated with targeted therapies based on clinical features: low-risk patients are usually treated with anti-angiogenic drugs and intermediate/high-risk patients with immune therapy. However, there are no biomarkers available to guide treatment choice for these patients. A recently published phase II clinical trial observed a correlation between ccRCC patients' clustering and their response to targeted therapy. However, the clustering of these groups was not distinct. Here, we analyzed the gene expression profile of 469 ccRCC patients, using featured selection technique, and have developed a refined 66-gene signature for improved sub-classification of patients. Moreover, we have identified a novel comprehensive expression profile to distinguish between migratory stromal and immune cells. Furthermore, the proposed 66-gene signature was validated using a different cohort of 64 ccRCC patients. These findings are foundational for the development of reliable biomarkers that may guide treatment decision-making and improve therapy response in ccRCC patients.

Published
2020

7. Data from Modeling Androgen Deprivation Therapy–Induced Prostate Cancer Dormancy and Its Clinical Implications

Author

Dong, Xin, primary, Xue, Hui, primary, Mo, Fan, primary, Lin, Yen-yi, primary, Lin, Dong, primary, Wong, Nelson K.Y., primary, Sun, Yingqiang, primary, Wilkinson, Scott, primary, Ku, Anson T., primary, Hao, Jun, primary, Ci, Xinpei, primary, Wu, Rebecca, primary, Haegert, Anne, primary, Silver, Rebecca, primary, Taplin, Mary-Ellen, primary, Balk, Steven P., primary, Alumkal, Joshi J., primary, Sowalsky, Adam G., primary, Gleave, Martin, primary, Collins, Colin, primary, and Wang, Yuzhuo, primary

Published
2023
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8. Supplementary Data from Modeling Androgen Deprivation Therapy–Induced Prostate Cancer Dormancy and Its Clinical Implications

Author

Dong, Xin, primary, Xue, Hui, primary, Mo, Fan, primary, Lin, Yen-yi, primary, Lin, Dong, primary, Wong, Nelson K.Y., primary, Sun, Yingqiang, primary, Wilkinson, Scott, primary, Ku, Anson T., primary, Hao, Jun, primary, Ci, Xinpei, primary, Wu, Rebecca, primary, Haegert, Anne, primary, Silver, Rebecca, primary, Taplin, Mary-Ellen, primary, Balk, Steven P., primary, Alumkal, Joshi J., primary, Sowalsky, Adam G., primary, Gleave, Martin, primary, Collins, Colin, primary, and Wang, Yuzhuo, primary

Published
2023
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10. Supplementary Table S1 from Mutational Analysis of Gene Fusions Predicts Novel MHC Class I–Restricted T-Cell Epitopes and Immune Signatures in a Subset of Prostate Cancer

Author

Kalina, Jennifer L., primary, Neilson, David S., primary, Lin, Yen-Yi, primary, Hamilton, Phineas T., primary, Comber, Alexandra P., primary, Loy, Emma M.H., primary, Sahinalp, S. Cenk, primary, Collins, Colin C., primary, Hach, Faraz, primary, and Lum, Julian J., primary

Published
2023
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11. Supplementary Data from Multiomics Characterization of Low-Grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK Inhibitor Sensitivity and Therapeutic Vulnerability

Author

Shrestha, Raunak, primary, Llaurado Fernandez, Marta, primary, Dawson, Amy, primary, Hoenisch, Joshua, primary, Volik, Stanislav, primary, Lin, Yen-Yi, primary, Anderson, Shawn, primary, Kim, Hannah, primary, Haegert, Anne M., primary, Colborne, Shane, primary, Wong, Nelson K.Y., primary, McConeghy, Brian, primary, Bell, Robert H., primary, Brahmbhatt, Sonal, primary, Lee, Cheng-Han, primary, DiMattia, Gabriel E., primary, Le Bihan, Stephane, primary, Morin, Gregg B., primary, Collins, Colin C., primary, and Carey, Mark S., primary

Published
2023
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12. Supplementary Data from Upregulation of Scavenger Receptor B1 Is Required for Steroidogenic and Nonsteroidogenic Cholesterol Metabolism in Prostate Cancer

Author

Gordon, Jacob A., primary, Noble, Jake W., primary, Midha, Ankur, primary, Derakhshan, Fatemeh, primary, Wang, Gang, primary, Adomat, Hans H., primary, Tomlinson Guns, Emma S., primary, Lin, Yen-Yi, primary, Ren, Shancheng, primary, Collins, Collin C., primary, Nelson, Peter S., primary, Morrissey, Colm, primary, Wasan, Kishor M., primary, and Cox, Michael E., primary

Published
2023
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13. CLIIQ: Accurate Comparative Detection and Quantification of Expressed Isoforms in a Population

Author

Lin, Yen-Yi, Dao, Phuong, Hach, Faraz, Bakhshi, Marzieh, Mo, Fan, Lapuk, Anna, Collins, Colin, Sahinalp, S. Cenk, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael S., editor, Raphael, Ben, editor, and Tang, Jijun, editor

Published
2012
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18. Modeling Androgen Deprivation Therapy–Induced Prostate Cancer Dormancy and Its Clinical Implications

Author

Dong, Xin, primary, Xue, Hui, additional, Mo, Fan, additional, Lin, Yen-yi, additional, Lin, Dong, additional, Wong, Nelson K.Y., additional, Sun, Yingqiang, additional, Wilkinson, Scott, additional, Ku, Anson T., additional, Hao, Jun, additional, Ci, Xinpei, additional, Wu, Rebecca, additional, Haegert, Anne, additional, Silver, Rebecca, additional, Taplin, Mary-Ellen, additional, Balk, Steven P., additional, Alumkal, Joshi J., additional, Sowalsky, Adam G., additional, Gleave, Martin, additional, Collins, Colin, additional, and Wang, Yuzhuo, additional

Published
2022
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22. Establishment and characterization of a novel treatment‐related neuroendocrine prostate cancer cell line KUCaP13

Author

Okasho, Kosuke, primary, Mizuno, Kei, additional, Fukui, Tomohiro, additional, Lin, Yen‐Yi, additional, Kamiyama, Yuki, additional, Sunada, Takuro, additional, Li, Xin, additional, Kimura, Hiroko, additional, Sumiyoshi, Takayuki, additional, Goto, Takayuki, additional, Kobayashi, Takashi, additional, Lin, Dong, additional, Wang, Yuzhuo, additional, Collins, Colin C., additional, Inoue, Takahiro, additional, Ogawa, Osamu, additional, and Akamatsu, Shusuke, additional

Published
2021
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23. Establishment and characterization of a novel treatment‐related neuroendocrine prostate cancer cell line KUCaP13

Author

Okasho, Kosuke, Mizuno, Kei, Fukui, Tomohiro, Lin, Yen‐Yi, Kamiyama, Yuki, Sunada, Takuro, Li, Xin, Kimura, Hiroko, Sumiyoshi, Takayuki, Goto, Takayuki, Kobayashi, Takashi, Lin, Dong, Wang, Yuzhuo, Collins, Colin C., Inoue, Takahiro, Ogawa, Osamu, Akamatsu, Shusuke, Okasho, Kosuke, Mizuno, Kei, Fukui, Tomohiro, Lin, Yen‐Yi, Kamiyama, Yuki, Sunada, Takuro, Li, Xin, Kimura, Hiroko, Sumiyoshi, Takayuki, Goto, Takayuki, Kobayashi, Takashi, Lin, Dong, Wang, Yuzhuo, Collins, Colin C., Inoue, Takahiro, Ogawa, Osamu, and Akamatsu, Shusuke

Abstract

The prevalence of neuroendocrine prostate cancer (NEPC) arising from adenocarcinoma (AC) upon potent androgen receptor (AR) pathway inhibition is increasing. Deeper understanding of NEPC biology and development of novel therapeutic agents are needed. However, research is hindered by the paucity of research models, especially cell lines developed from NEPC patients. We established a novel NEPC cell line, KUCaP13, from tissue of a patient initially diagnosed with AC which later recurred as NEPC. The cell line has been maintained permanently in vitro under regular cell culture conditions and is amenable to gene engineering with lentivirus. KUCaP13 cells lack the expression of AR and overexpress NEPC-associated genes, including SOX2, EZH2, AURKA, PEG10, POU3F2, ENO2, and FOXA2. Importantly, the cell line maintains the homozygous deletion of CHD1, which was confirmed in the primary AC of the index patient. Loss of heterozygosity of TP53 and PTEN, and an allelic loss of RB1 with a transcriptomic signature compatible with Rb pathway aberration were revealed. Knockdown of PEG10 using shRNA significantly suppressed growth in vivo. Introduction of luciferase allowed serial monitoring of cells implanted orthotopically or in the renal subcapsule. Although H3K27me was reduced by EZH2 inhibition, reversion to AC was not observed. KUCaP13 is the first patient-derived, treatment-related NEPC cell line with triple loss of tumor suppressors critical for NEPC development through lineage plasticity. It could be valuable in research to deepen the understanding of NEPC.

Published
2021

24. Novel lignin-capped silver nanoparticles against multidrug resistant bacteria

Author

Universitat Politècnica de Catalunya. Departament d'Enginyeria Química, Universitat Politècnica de Catalunya. GBMI - Grup de Biotecnologia Molecular i Industrial, Slavin, Yael N., Ivanova, Kristina Dimitrova, Hoyo Pérez, Javier, Perelshtein, Ilana, Owen, Gethin, Haegert, Anne, Lin, Yen-Yi, LeBihan, Stephane, Gedanken, Aharon, Häfeli, Urs O., Tzanov, Tzanko, Bach, Horacio, Universitat Politècnica de Catalunya. Departament d'Enginyeria Química, Universitat Politècnica de Catalunya. GBMI - Grup de Biotecnologia Molecular i Industrial, Slavin, Yael N., Ivanova, Kristina Dimitrova, Hoyo Pérez, Javier, Perelshtein, Ilana, Owen, Gethin, Haegert, Anne, Lin, Yen-Yi, LeBihan, Stephane, Gedanken, Aharon, Häfeli, Urs O., Tzanov, Tzanko, and Bach, Horacio

Abstract

The emergence of bacteria resistant to antibiotics and the resulting infections are increasingly becoming a public health issue. Multidrug-resistant (MDR) bacteria are responsible for infections leading to increased morbidity and mortality in hospitals, prolonged time of hospitalization, and additional burden to financial costs. Therefore, there is an urgent need for novel antibacterial agents that will both treat MDR infections and outsmart the bacterial evolutionary mechanisms, preventing further resistance development. In this study, a green synthesis employing nontoxic lignin as both reducing and capping agents was adopted to formulate stable and biocompatible silver–lignin nanoparticles (NPs) exhibiting antibacterial activity. The resulting silver–lignin NPs were approximately 20 nm in diameter and did not agglomerate after one year of storage at 4 °C. They were able to inhibit the growth of a panel of MDR clinical isolates, including Staphylococcus aureus, Staphylococcus epidermidis, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii, at concentrations that did not affect the viability of a monocyte-derived THP-1 human cell line. Furthermore, the exposure of silver–lignin NPs to the THP-1 cells led to a significant increase in the secretion of the anti-inflammatory cytokine IL-10, demonstrating the potential of these particles to act as an antimicrobial and anti-inflammatory agent simultaneously. P. aeruginosa genes linked with efflux, heavy metal resistance, capsular biosynthesis, and quorum sensing were investigated for changes in gene expression upon sublethal exposure to the silver–lignin NPs. Genes encoding for membrane proteins with an efflux function were upregulated. However, all other genes were membrane proteins that did not efflux metals and were downregulated., Peer Reviewed, Postprint (published version)

Published
2021

25. Novel Lignin-Capped Silver Nanoparticles against Multidrug-Resistant Bacteria

Author

Slavin, Yael N., primary, Ivanova, Kristina, additional, Hoyo, Javier, additional, Perelshtein, Ilana, additional, Owen, Gethin, additional, Haegert, Anne, additional, Lin, Yen-Yi, additional, LeBihan, Stephane, additional, Gedanken, Aharon, additional, Häfeli, Urs O., additional, Tzanov, Tzanko, additional, and Bach, Horacio, additional

Published
2021
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27. Multiomics Characterization of Low-Grade Serous Ovarian Carcinoma Identifies Potential Biomarkers of MEK Inhibitor Sensitivity and Therapeutic Vulnerability

Author

Shrestha, Raunak, primary, Llaurado Fernandez, Marta, additional, Dawson, Amy, additional, Hoenisch, Joshua, additional, Volik, Stanislav, additional, Lin, Yen-Yi, additional, Anderson, Shawn, additional, Kim, Hannah, additional, Haegert, Anne M., additional, Colborne, Shane, additional, Wong, Nelson K.Y., additional, McConeghy, Brian, additional, Bell, Robert H., additional, Brahmbhatt, Sonal, additional, Lee, Cheng-Han, additional, DiMattia, Gabriel E., additional, Le Bihan, Stephane, additional, Morin, Gregg B., additional, Collins, Colin C., additional, and Carey, Mark S., additional

Published
2021
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28. Multiomics Characterization of Potential Therapeutic Vulnerabilities in Low-grade Serous Ovarian Carcinoma

Author

Shrestha, Raunak, primary, Fernandez, Marta Llaurado, additional, Dawson, Amy, additional, Hoenisch, Joshua, additional, Volik, Stanislav, additional, Lin, Yen-Yi, additional, Anderson, Shawn, additional, Kim, Hannah, additional, Haegert, Anne, additional, Colborne, Shane, additional, McConeghy, Brian, additional, Bell, Robert H., additional, Brahmbhatt, Sonal, additional, DiMattia, Gabriel E., additional, Le Bihan, Stephane, additional, Morin, Gregg B., additional, Collins, Colin C., additional, and Carey, Mark S., additional

Published
2020
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31. Electrical properties of the positive temperature coefficient of resistivity materials with 490 degrees C critical temperature

Author

Lin, Yen-Yi, Hu, Chen-Ti, Chang, Horng-Yi, and Lin, I-Nan

Subjects
Lead compounds -- Research, Temperature measurements -- Research, Semiconductors -- Thermal properties, Physics
Abstract

The positive temperature coefficient of resistivity (PTCR) of two semiconductor materials, PbTiO3 (PT) and (Pb0.9Sr0.1)TiO3 (PST), were characterized within the critical temperature range of 490 degrees C. The resistivity-temperature characteristics of PT were different compared to PST. The rapid thermal sintering process was efficient in densifying the materials and determining the PTRC behavior. The temperature for sintering PST was 1210 degrees C for 10 min while PT materials required only a temperature of 1170 degrees C at the same period.

Published
1998

32. Pentacene-based organic thin-film transistors

Author

Lin, Yen-Yi, Gundlach, David J., Nelson, Shelby F., and Jackson, Thomas N.

Subjects
Thin films -- Research, Transistors -- Research, Amorphous semiconductors -- Research, Business, Electronics, Electronics and electrical industries
Abstract

Organic thin-film transistors (TFTs) with the fused-ring polycyclic aromatic hydrocarbon pentacene as the active electronic material have exhibited mobility as much as 0.7 cm2/V-s and on/off current ratio larger than 10(super 8). These values were comparable to hydrogenated amorphous silicon devices. However, these TFTs exhibit undesirably large subthreshold slope, which is not an intrinsic property of the organic semiconducting material.

Published
1997

33. Identification of gene signature for treatment response to guide precision oncology in clear-cell renal cell carcinoma.

Author

D'Costa, Ninadh M, D'Costa, Ninadh M, Cina, Davide, Shrestha, Raunak, Bell, Robert H, Lin, Yen-Yi, Asghari, Hossein, Monjaras-Avila, Cesar U, Kollmannsberger, Christian, Hach, Faraz, Chavez-Munoz, Claudia I, So, Alan I, D'Costa, Ninadh M, D'Costa, Ninadh M, Cina, Davide, Shrestha, Raunak, Bell, Robert H, Lin, Yen-Yi, Asghari, Hossein, Monjaras-Avila, Cesar U, Kollmannsberger, Christian, Hach, Faraz, Chavez-Munoz, Claudia I, and So, Alan I

Abstract

Clear-cell renal cell carcinoma (ccRCC) is a common therapy resistant disease with aberrant angiogenic and immunosuppressive features. Patients with metastatic disease are treated with targeted therapies based on clinical features: low-risk patients are usually treated with anti-angiogenic drugs and intermediate/high-risk patients with immune therapy. However, there are no biomarkers available to guide treatment choice for these patients. A recently published phase II clinical trial observed a correlation between ccRCC patients' clustering and their response to targeted therapy. However, the clustering of these groups was not distinct. Here, we analyzed the gene expression profile of 469 ccRCC patients, using featured selection technique, and have developed a refined 66-gene signature for improved sub-classification of patients. Moreover, we have identified a novel comprehensive expression profile to distinguish between migratory stromal and immune cells. Furthermore, the proposed 66-gene signature was validated using a different cohort of 64 ccRCC patients. These findings are foundational for the development of reliable biomarkers that may guide treatment decision-making and improve therapy response in ccRCC patients.

Published
2020

34. Upregulation of Scavenger Receptor B1 Is Required for Steroidogenic and Nonsteroidogenic Cholesterol Metabolism in Prostate Cancer

Author

Gordon, Jacob A., primary, Noble, Jake W., additional, Midha, Ankur, additional, Derakhshan, Fatemeh, additional, Wang, Gang, additional, Adomat, Hans H., additional, Tomlinson Guns, Emma S., additional, Lin, Yen-Yi, additional, Ren, Shancheng, additional, Collins, Collin C., additional, Nelson, Peter S., additional, Morrissey, Colm, additional, Wasan, Kishor M., additional, and Cox, Michael E., additional

Published
2019
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35. Computational Discovery of Splicing Events from High-Throughput Omics Data

Author

Lin, Yen Yi

Abstract

The splicing mechanism, the process of forming mature messenger RNA (mRNA) by only concatenating exons and removing introns, is an essential step in gene expression. It allows a single gene to have multiple RNA isoforms which potentially code different proteins. In addition, aberrant transcripts generated from non-canonical splicing events (e.g. gene fusions) are believed to be potential drivers in many tumor types and human diseases. Thus, identification and quantification of expressed RNAs from RNA-Seq data become fundamental steps in many clinical studies. For that reason, number of methods have been developed. Most popular computational methods designed for these high-throughput omics data start by analyzing the datasets based on existing gene annotations. However, these tools (i) do not detect novel RNA isoforms and low abundance transcripts; (ii) do not incorporate multi-mapping reads in their read counting strategies in quantifications; (iii) are sensitive to sequencing artifacts. In this thesis, we will address these computational problems for analyzing splicing events from high-throughput omics data. For identification and quantification of expressed RNAs from RNA-Seq data, we introduce CLIIQ, a unified framework to solve these two problems simultaneously. This framework also supports data from multiple samples to improve accuracy. To better incorporate multi-mapping reads into the framework, we design ORMAN, a combinatorial optimization formulation to resolve their mapping ambiguity by assigning single best location for each read. For aberrant transcript detections, we present a computational strategy ProTIE to integratively analyze proteomics and transcriptomic data from the same individual. This strategy provides proteome-level evidence for aberrant transcripts that can be used to eliminate false positives reported solely based on sequencing data.

Published
2017

36. BAP1 haploinsufficiency predicts a distinct immunogenic class of malignant peritoneal mesothelioma

Author

Shrestha, Raunak, primary, Nabavi, Noushin, additional, Lin, Yen-Yi, additional, Mo, Fan, additional, Anderson, Shawn, additional, Volik, Stanislav, additional, Adomat, Hans H., additional, Lin, Dong, additional, Xue, Hui, additional, Dong, Xin, additional, Shukin, Robert, additional, Bell, Robert H., additional, McConeghy, Brian, additional, Haegert, Anne, additional, Brahmbhatt, Sonal, additional, Li, Estelle, additional, Oo, Htoo Zarni, additional, Hurtado-Coll, Antonio, additional, Fazli, Ladan, additional, Zhou, Joshua, additional, McConnell, Yarrow, additional, McCart, Andrea, additional, Lowy, Andrew, additional, Morin, Gregg B., additional, Chen, Tianhui, additional, Daugaard, Mads, additional, Sahinalp, S. Cenk, additional, Hach, Faraz, additional, Le Bihan, Stephane, additional, Gleave, Martin E., additional, Wang, Yuzhuo, additional, Churg, Andrew, additional, and Collins, Colin C., additional

Published
2019
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37. Structural variation and fusion detection using targeted sequencing data from circulating cell free DNA

Author

Gawroński, Alexander R, primary, Lin, Yen-Yi, additional, McConeghy, Brian, additional, LeBihan, Stephane, additional, Asghari, Hossein, additional, Koçkan, Can, additional, Orabi, Baraa, additional, Adra, Nabil, additional, Pili, Roberto, additional, Collins, Colin C, additional, Sahinalp, S Cenk, additional, and Hach, Faraz, additional

Published
2019
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38. Abstract A033: Identity fraud: Lineage plasticity as a mechanism of antiandrogen resistance and target for therapy

Author

Davies, Alastair, primary, Bostock, Chiara, additional, Ahmed, Musaddeque, additional, Lin, Yen-Yi, additional, Johnson, Fraser, additional, Nip, Ka Mun, additional, Ketola, Kirsi, additional, Bishop, Jennifer, additional, Fazli, Ladan, additional, Goodrich, David, additional, Hach, Faraz, additional, He, Hansen, additional, Beltran, Himisha, additional, and Zoubeidi, Amina, additional

Published
2018
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39. Abstract 4995: Identity fraud: Lineage plasticity as a mechanism of anti-androgen resistance and target for therapy

Author

Davies, Alastair H., primary, Bostock, Chiara, additional, Ahmed, Musaddeque, additional, Lin, Yen-Yi, additional, Johnson, Fraser, additional, Nip, Ka Mun, additional, Ketola, Kirsi, additional, Bishop, Jennifer, additional, Fazli, Ladan, additional, Huang, Haojie, additional, Goodrich, David, additional, Hach, Faraz, additional, He, Hansen, additional, Beltran, Himisha, additional, and Zoubeidi, Amina, additional

Published
2018
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42. BAP1 Loss Predicts Therapeutic Vulnerability in Malignant Peritoneal Mesothelioma

Author

Shrestha, Raunak, primary, Nabavi, Noushin, additional, Lin, Yen-Yi, additional, Mo, Fan, additional, Anderson, Shawn, additional, Volik, Stanislav, additional, Adomat, Hans H., additional, Lin, Dong, additional, Xue, Hui, additional, Dong, Xin, additional, Shukin, Robert, additional, Bell, Robert H., additional, McConeghy, Brian, additional, Haegert, Anne, additional, Brahmbhatt, Sonal, additional, Li, Estelle, additional, Oo, Htoo Zarni, additional, Hurtado-Coll, Antonio, additional, Fazli, Ladan, additional, Zhou, Joshua, additional, McConnell, Yarrow, additional, McCart, Andrea, additional, Lowy, Andrew, additional, Morin, Gregg B., additional, Daugaard, Mads, additional, Sahinalp, S. Cenk, additional, Hach, Faraz, additional, Bihan, Stephane Le, additional, Gleave, Martin E., additional, Wang, Yuzhuo, additional, Churg, Andrew, additional, and Collins, Colin C., additional

Published
2018
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44. Computational identification of micro-structural variations and their proteogenomic consequences in cancer

Author

Lin, Yen-Yi, primary, Gawronski, Alexander, additional, Hach, Faraz, additional, Li, Sujun, additional, Numanagić, Ibrahim, additional, Sarrafi, Iman, additional, Mishra, Swati, additional, McPherson, Andrew, additional, Collins, Colin C, additional, Radovich, Milan, additional, Tang, Haixu, additional, and Sahinalp, S Cenk, additional

Published
2017
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47. Computational proteogenomic identification and functional interpretation of translated fusions and micro structural variations in cancer

Author

Lin, Yen Yi, primary, Gawronski, Alexander, additional, Hach, Faraz, additional, Li, Sujun, additional, Numanagić, Ibrahim, additional, Sarrafi, Iman, additional, Mishra, Swati, additional, McPherson, Andrew, additional, Collins, Colin, additional, Radovich, Milan, additional, Tang, Haixu, additional, and Sahinalp, S. Cenk, additional

Published
2017
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49. The Antiproliferation Activity of Ganoderma formosanumExtracts on Prostate Cancer Cells

Author

Chiang, Cheng-Yen, Hsu, Kai-Di, Lin, Yen-Yi, Hsieh, Chang-Wei, Liu, Jui-Ming, Lu, Tze-Ying, and Cheng, Kuan-Chen

Abstract

AbstractAndrogen-independent prostate cancer accounts for mortality in the world. In this study, various extracts of a medical fungus dubbed Ganoderma formosanumwere screened for inhibition of DU145 cells, an androgen-independent prostate cancer cell line. Results demonstrated that both hexane (GF-EH) and butanol (GF-EB) fraction of G. formosanumethanol extract inhibited DU145 cell viability in a dose-dependent manner. GF-EH induced cell-cycle arrest in G1 phase of DU145 cells viadownregulation of cyclin E2 protein expression. In addition, GF-EB triggered extrinsic apoptosis of DU145 cells by activating caspase 3gene expression resulting in programed cell death. Above all, both GF-EH and GF-EB show lower toxicity to normal human fibroblast cell line compared to DU145 cell, implying that they possess specific drug action on cancer cells. This study provides a molecular basis of G. formosanumextract as a potential ingredient for treatment of androgen-independent prostate cancer.

Published
2020
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50. Computational identification of micro-structural variations and their proteogenomic consequences in cancer.

Author

Lin, Yen-Yi, Gawronski, Alexander, Hach, Faraz, Li, Sujun, Numanagić, Ibrahim, Sarrafi, Iman, Mishra, Swati, McPherson, Andrew, Collins, Colin C, and Radovich, Milan

Subjects
*NUCLEOTIDE sequencing, *TRANSCRIPTOMES, *PROTEOMICS, *GENE fusion, *PEPTIDES
Abstract

Motivation: Rapid advancement in high throughput genome and transcriptome sequencing (HTS) and mass spectrometry (MS) technologies has enabled the acquisition of the genomic, transcriptomic and proteomic data from the same tissue sample. We introduce a computational framework, ProTIE, to integratively analyze all three types of omics data for a complete molecular profile of a tissue sample. Our framework features MiStrVar, a novel algorithmic method to identify micro structural variants (microSVs) on genomic HTS data. Coupled with deFuse, a popular gene fusion detection method we developed earlier, MiStrVar can accurately profile structurally aberrant transcripts in tumors. Given the breakpoints obtained by MiStrVar and deFuse, our framework can then identify all relevant peptides that span the breakpoint junctions and match them with unique proteomic signatures. Observing structural aberrations in all three types of omics data validates their presence in the tumor samples. Results: We have applied our framework to all The Cancer Genome Atlas (TCGA) breast cancer Whole Genome Sequencing (WGS) and/or RNA-Seq datasets, spanning all four major subtypes, for which proteomics data from Clinical Proteomic Tumor Analysis Consortium (CPTAC) have been released. A recent study on this dataset focusing on SNVs has reported many that lead to novel peptides. Complementing and significantly broadening this study, we detected 244 novel peptides from 432 candidate genomic or transcriptomic sequence aberrations. Many of the fusions and microSVs we discovered have not been reported in the literature. Interestingly, the vast majority of these translated aberrations, fusions in particular, were private, demonstrating the extensive intergenomic heterogeneity present in breast cancer. Many of these aberrations also have matching out-of-frame downstream peptides, potentially indicating novel protein sequence and structure. Availability and implementation: MiStrVar is available for download at https://bitbucket.org/comp bio/mistrvar, and ProTIE is available at https://bitbucket.org/compbio/protie. [ABSTRACT FROM AUTHOR]

Published
2018
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