Targeting Lysine-Specific Demethylase 1 Rescues Major Histocompatibility Complex Class I Antigen Presentation and Overcomes Programmed Death-Ligand 1 Blockade Resistance in SCLC

Authors: Nguyen, Evelyn M., Taniguchi, Hirokazu, Chan, Joseph M., Zhan, Yingqian A., Chen, Xiaoping, Qiu, Juan, de Stanchina, Elisa, Allaj, Viola, Shah, Nisargbhai S., Uddin, Fathema, Manoj, Parvathy, Liu, Michael, Cai, Sheng F., Levine, Ross, Quintanal-Villalonga, Álvaro, Sen, Triparna, Chow, Andrew, Rudin, Charles M.

Source: In Journal of Thoracic Oncology August 2022 17(8):1014-1031

WEE1 inhibition enhances the antitumor immune response to PD-L1 blockade by the concomitant activation of STING and STAT1 pathways in SCLC

Authors: Taniguchi, Hirokazu, Caeser, Rebecca, Chavan, Shweta S., Zhan, Yingqian A., Chow, Andrew, Manoj, Parvathy, Uddin, Fathema, Kitai, Hidenori, Qu, Rui, Hayatt, Omar, Shah, Nisargbhai S., Quintanal Villalonga, Álvaro, Allaj, Viola, Nguyen, Evelyn M., Chan, Joseph, Michel, Adam O., Mukae, Hiroshi, de Stanchina, Elisa, Rudin, Charles M., Sen, Triparna

Source: In Cell Reports 17 May 2022 39(7)

Complex-dependent histone acetyltransferase activity of KAT8 determines its role in transcription and cellular homeostasis

Authors: Radzisheuskaya, Aliaksandra, Shliaha, Pavel V., Grinev, Vasily V., Shlyueva, Daria, Damhofer, Helene, Koche, Richard, Gorshkov, Vladimir, Kovalchuk, Sergey, Zhan, Yingqian, Rodriguez, Keli L., Johnstone, Andrea L., Keogh, Michael-C, Hendrickson, Ronald C., Jensen, Ole N., Helin, Kristian

Source: In Molecular Cell 15 April 2021 81(8):1749-1765

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.

Authors: Gao, Vianne R., Yang, Rui, Das, Arnav, Luo, Renhe, Luo, Hanzhi, McNally, Dylan R., Karagiannidis, Ioannis, Rivas, Martin A., Wang, Zhong-Min, Barisic, Darko, Karbalayghareh, Alireza, Wong, Wilfred, Zhan, Yingqian A., Chin, Christopher R., Noble, William S., Bilmes, Jeff A., Apostolou, Effie, Kharas, Michael G., Béguelin, Wendy, Viny, Aaron D.

Source: Nature Communications; 11/1/2024, Vol. 15 Issue 1, p1-15, 15p

Subject Terms: GENETIC regulation, CHROMATIN, PREDICTION models, GENOMICS, MICE

Ageing limits stemness and tumorigenesis by reprogramming iron homeostasis

Authors: Zhuang, Xueqian, Wang, Qing, Joost, Simon, Ferrena, Alexander, Humphreys, David T., Li, Zhuxuan, Blum, Melissa, Krause, Klavdija, Ding, Selena, Landais, Yuna, Zhan, Yingqian, Zhao, Yang, Chaligne, Ronan, Lee, Joo-Hyeon, Carrasco, Sebastian E., Bhanot, Umeshkumar K., Koche, Richard P., Bott, Matthew J., Katajisto, Pekka, Soto-Feliciano, Yadira M., Pisanic, Thomas, Thomas, Tiffany, Zheng, Deyou, Wong, Emily S., Tammela, Tuomas

Source: Nature; January 2025, Vol. 637 Issue: 8044 p184-194, 11p

Correction: SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing.

Authors: Redin, Esther, Sridhar, Harsha, Zhan, Yingqian A., Pereira Mello, Barbara, Zhong, Hong, Durani, Vidushi, Sabet, Amin, Manoj, Parvathy, Linkov, Irina, Qiu, Juan, Koche, Richard P., de Stanchina, Elisa, Astorkia, Maider, Betel, Doron, Quintanal-Villalonga, Álvaro, Rudin, Charles M.

Source: Journal of Hematology & Oncology; 9/29/2024, Vol. 17 Issue 1, p1-8, 8p

Subject Terms: NOTCH genes, SMALL cell lung cancer, GENE expression, HIPPO signaling pathway, WESTERN immunoblotting

SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing.

Authors: Redin, Esther, Sridhar, Harsha, Zhan, Yingqian A., Pereira Mello, Barbara, Zhong, Hong, Durani, Vidushi, Sabet, Amin, Manoj, Parvathy, Linkov, Irina, Qiu, Juan, Koche, Richard P., de Stanchina, Elisa, Astorkia, Maider, Betel, Doron, Quintanal-Villalonga, Álvaro, Rudin, Charles M.

Source: Journal of Hematology & Oncology; 7/30/2024, Vol. 17 Issue 1, p1-19, 19p

CDC7 inhibition impairs neuroendocrine transformation in lung and prostate tumors through MYC degradation.

Authors: Quintanal-Villalonga, Alvaro, Kawasaki, Kenta, Redin, Esther, Uddin, Fathema, Rakhade, Swanand, Durani, Vidushi, Sabet, Amin, Shafer, Moniquetta, Karthaus, Wouter R., Zaidi, Samir, Zhan, Yingqian A., Manoj, Parvathy, Sridhar, Harsha, Kinyua, Dennis, Zhong, Hong, Mello, Barbara P., Ciampricotti, Metamia, Bhanot, Umesh K., Linkov, Irina, Qiu, Juan

Source: Signal Transduction & Targeted Therapy; 7/26/2024, Vol. 9 Issue 1, p1-14, 14p

The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans

Authors: Zhan, Yingqian Ada, Ytreberg, F. Marty

Source: In Archives of Biochemistry and Biophysics 1 June 2015 575:22-29

3151 – THE ALTERNATIVE NUCLEOSOME REMODELING FACTOR COMPLEX SUSTAINS ACUTE MYELOID LEUKEMIA BY REGULATING THE ACCESSIBILITY OF INSULATOR REGIONS

Authors: Roemer, Isabel Pena, Radzisheuskaya, Aliaksandra, Lorenzini, Eugenia, Koche, Richard, Zhan, Yingqian, Shliaha, Pavel V, Cooper, Alexandra, Shlyueva, Daria, Johansen, Jens, Hendrickson, Ronald, Helin, Kristian

Source: Experimental hematology. 124(S):S125-S125

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100195476748.0x000001&indx=1&recIds=ETOCvdc_100195476748.0x000001

An alternative NURF complex sustains acute myeloid leukemia by regulating the accessibility of insulator regions.

Authors: Radzisheuskaya, Aliaksandra, Peña‐Rømer, Isabel, Lorenzini, Eugenia, Koche, Richard, Zhan, Yingqian, Shliaha, Pavel V, Cooper, Alexandra J, Fan, Zheng, Shlyueva, Daria, Johansen, Jens V, Hendrickson, Ronald C, Helin, Kristian

Source: EMBO Journal; 12/11/2023, Vol. 42 Issue 24, p1-22, 22p

Subject Terms: ACUTE myeloid leukemia, CELL survival, CELL growth, CRISPRS, CHROMATIN

Exportin 1 inhibition prevents neuroendocrine transformation through SOX2 down-regulation in lung and prostate cancers.

Authors: Quintanal-Villalonga, Alvaro, Durani, Vidushi, Sabet, Amin, Redin, Esther, Kawasaki, Kenta, Shafer, Moniquetta, Karthaus, Wouter R., Zaidi, Samir, Zhan, Yingqian A., Manoj, Parvathy, Sridhar, Harsha, Shah, Nisargbhai S., Chow, Andrew, Bhanot, Umesh K., Linkov, Irina, Asher, Marina, Yu, Helena A., Qiu, Juan, de Stanchina, Elisa, Patel, Radhika A.

Source: Science Translational Medicine; 8/2/2023, Vol. 15 Issue 707, p1-14, 14p

Subject Terms: LUNG cancer, SMALL cell lung cancer, PROSTATE cancer, ANDROGEN receptors, SMALL cell carcinoma, PHENOTYPIC plasticity, ANDROGEN drugs

Fostering bioinformatics education through skill development of professors: Big Genomic Data Skills Training for Professors.

Authors: Zhan, Yingqian Ada¹, Wray, Charles Gregory² charlie.wray@jax.org, Namburi, Sandeep¹, Glantz, Spencer T.¹, Laubenbacher, Reinhard^1,3, Chuang, Jeffrey H.^1,4 jeff.chuang@jax.org

Source: PLoS Computational Biology. 6/13/2019, Vol. 15 Issue 6, p1-11. 11p. 3 Charts, 1 Graph.

Subject Terms: *LIFE science education, *UNIVERSITIES & colleges, *BIG data, *COMPUTATIONAL biology, *ART colleges

Geographic Terms: UNITED States

TET2 guards against unchecked BATF3-induced CAR T cell expansion.

Authors: Jain, Nayan, Zhao, Zeguo, Feucht, Judith, Koche, Richard, Iyer, Archana, Dobrin, Anton, Mansilla-Soto, Jorge, Yang, Julie, Zhan, Yingqian, Lopez, Michael, Gunset, Gertrude, Sadelain, Michel

Source: Nature; Mar2023, Vol. 615 Issue 7951, p315-322, 8p

Author Correction: ChromaFold predicts the 3D contact map from single-cell chromatin accessibility.

Authors: Gao, Vianne R., Yang, Rui, Das, Arnav, Luo, Renhe, Luo, Hanzhi, McNally, Dylan R., Karagiannidis, Ioannis, Rivas, Martin A., Wang, Zhong-Min, Barisic, Darko, Karbalayghareh, Alireza, Wong, Wilfred, Zhan, Yingqian A., Chin, Christopher R., Noble, William S., Bilmes, Jeff A., Apostolou, Effie, Kharas, Michael G., Béguelin, Wendy, Viny, Aaron D.

Source: Nature Communications; 1/15/2025, Vol. 16 Issue 1, p1-1, 1p

Comprehensive molecular characterization of lung tumors implicates AKT and MYC signaling in adenocarcinoma to squamous cell transdifferentiation.

Authors: Quintanal-Villalonga, Alvaro, Taniguchi, Hirokazu, Zhan, Yingqian A., Hasan, Maysun M., Chavan, Shweta S., Meng, Fanli, Uddin, Fathema, Allaj, Viola, Manoj, Parvathy, Shah, Nisargbhai S., Chan, Joseph M., Ciampricotti, Metamia, Chow, Andrew, Offin, Michael, Ray-Kirton, Jordana, Egger, Jacklynn D., Bhanot, Umesh K., Linkov, Irina, Asher, Marina, Roehrl, Michael H.

Source: Journal of Hematology & Oncology; 10/16/2021, Vol. 14 Issue 1, p1-19, 19p

Subject Terms: LUNG tumors, DRUG target, PI3K/AKT pathway, PROGNOSIS, OSIMERTINIB

HiC-DC+ enables systematic 3D interaction calls and differential analysis for Hi-C and HiChIP.

Authors: Sahin, Merve, Wong, Wilfred, Zhan, Yingqian, Van Deynze, Kinsey, Koche, Richard, Leslie, Christina S.

Source: Nature Communications; 6/7/2021, Vol. 12 Issue 1, p1-11, 11p

Subject Terms: SOFTWARE development tools, CHROMATIN, GENE expression, COHESINS, CHROMOSOMES

Loss of TET2 Uncouples Proliferative and Effector Functions in CAR T Cells

Authors: Jain, Nayan ^*, Zhao, Zeguo ^*, Iyer, Archana S. ^*, Lopez, Michael ^*, Feucht, Judith ^*, Koche, Richard P. ^*, Zhan, Yingqian ^*, Sadelain, Michel

Source: In Blood 5 November 2020 136 Supplement 1:1-1

Effect of 1-methyladenine on double-helical DNA structures

Authors: Yang, Hao, Zhan, Yingqian, Fenn, Dickson, Chi, Lai Man, Lam, Sik Lok

Source: In FEBS Letters 2008 582(11):1629-1633

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