Publications

2024

Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correctionLi X, Liu T, Bacchiocchi A, Li M, Cheng W, Wittkop T, Mendez F, Wang Y, Tang P, Yao Q, Bosenberg M, Sznol M, Yan Q, Faham M, Weng L, Halaban R, Jin H, Hu Z. Ultra-sensitive molecular residual disease detection through whole genome sequencing with single-read error correction. EMBO Molecular Medicine 2024, 16: 2188-2209. PMID: 39164471, PMCID: PMC11393307, DOI: 10.1038/s44321-024-00115-0.
ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts.Hu B, Wiesehöfer M, de Miguel F, Liu Z, Chan L, Choi J, Melnick M, Arnal Estape A, Walther Z, Zhao D, Lopez-Giraldez F, Wurtz A, Cai G, Fan R, Gettinger S, Xiao A, Yan Q, Homer R, Nguyen D, Politi K. ASCL1 Drives Tolerance to Osimertinib in EGFR Mutant Lung Cancer in Permissive Cellular Contexts. Cancer Research 2024, 84: 1303-1319. PMID: 38359163, DOI: 10.1158/0008-5472.can-23-0438.
Combined BET and MEK Inhibition synergistically suppresses melanoma by targeting YAP1Hu R, Hou H, Li Y, Zhang M, Li X, Chen Y, Guo Y, Sun H, Zhao S, Liao M, Cao D, Yan Q, Chen X, Yin M. Combined BET and MEK Inhibition synergistically suppresses melanoma by targeting YAP1. Theranostics 2024, 14: 593-607. PMID: 38169595, PMCID: PMC10758063, DOI: 10.7150/thno.85437.

2023

Lysine Demethylation in PathogenesisCao J, Yan Q. Lysine Demethylation in Pathogenesis. Advances In Experimental Medicine And Biology 2023, 1433: 1-14. PMID: 37751133, DOI: 10.1007/978-3-031-38176-8_1.
KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the ClinicZhang S, Cao J, Yan Q. KDM5 Lysine Demethylases in Pathogenesis, from Basic Science Discovery to the Clinic. Advances In Experimental Medicine And Biology 2023, 1433: 113-137. PMID: 37751138, DOI: 10.1007/978-3-031-38176-8_6.
Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancerde Miguel F, Gentile C, Feng W, Silva S, Sankar A, Exposito F, Cai W, Melnick M, Robles-Oteiza C, Hinkley M, Tsai J, Hartley A, Wei J, Wurtz A, Li F, Toki M, Rimm D, Homer R, Wilen C, Xiao A, Qi J, Yan Q, Nguyen D, Jänne P, Kadoch C, Politi K. Mammalian SWI/SNF chromatin remodeling complexes promote tyrosine kinase inhibitor resistance in EGFR-mutant lung cancer. Cancer Cell 2023, 41: 1516-1534.e9. PMID: 37541244, PMCID: PMC10957226, DOI: 10.1016/j.ccell.2023.07.005.
The KDM6A-KMT2D-p300 axis regulates susceptibility to diverse coronaviruses by mediating viral receptor expressionWei J, Alfajaro M, Cai W, Graziano V, Strine M, Filler R, Biering S, Sarnik S, Patel S, Menasche B, Compton S, Konermann S, Hsu P, Orchard R, Yan Q, Wilen C. The KDM6A-KMT2D-p300 axis regulates susceptibility to diverse coronaviruses by mediating viral receptor expression. PLOS Pathogens 2023, 19: e1011351. PMID: 37410700, PMCID: PMC10325096, DOI: 10.1371/journal.ppat.1011351.
DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent mannerStrine M, Cai W, Wei J, Alfajaro M, Filler R, Biering S, Sarnik S, Chow R, Patil A, Cervantes K, Collings C, DeWeirdt P, Hanna R, Schofield K, Hulme C, Konermann S, Doench J, Hsu P, Kadoch C, Yan Q, Wilen C. DYRK1A promotes viral entry of highly pathogenic human coronaviruses in a kinase-independent manner. PLOS Biology 2023, 21: e3002097. PMID: 37310920, PMCID: PMC10263356, DOI: 10.1371/journal.pbio.3002097.
Epigenetic markers and therapeutic targets for metastasisKravitz C, Yan Q, Nguyen D. Epigenetic markers and therapeutic targets for metastasis. Cancer And Metastasis Reviews 2023, 42: 427-443. PMID: 37286865, PMCID: PMC10595046, DOI: 10.1007/s10555-023-10109-y.
Design of Class I/IV Bromodomain-Targeting Degraders for Chromatin Remodeling ComplexesZahid H, Costello J, Li Y, Kimbrough J, Actis M, Rankovic Z, Yan Q, Pomerantz W. Design of Class I/IV Bromodomain-Targeting Degraders for Chromatin Remodeling Complexes. ACS Chemical Biology 2023, 18: 1278-1293. PMID: 37260298, PMCID: PMC10698694, DOI: 10.1021/acschembio.2c00902.
Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infectionWei J, Patil A, Collings C, Alfajaro M, Liang Y, Cai W, Strine M, Filler R, DeWeirdt P, Hanna R, Menasche B, Ökten A, Peña-Hernández M, Klein J, McNamara A, Rosales R, McGovern B, Luis Rodriguez M, García-Sastre A, White K, Qin Y, Doench J, Yan Q, Iwasaki A, Zwaka T, Qi J, Kadoch C, Wilen C. Pharmacological disruption of mSWI/SNF complex activity restricts SARS-CoV-2 infection. Nature Genetics 2023, 55: 471-483. PMID: 36894709, PMCID: PMC10011139, DOI: 10.1038/s41588-023-01307-z.

2022

The Crossroads of Cancer Epigenetics and Immune Checkpoint Therapy.Micevic G, Bosenberg M, Yan Q. The Crossroads of Cancer Epigenetics and Immune Checkpoint Therapy. Clinical Cancer Research 2022, 29: 1173-1182. PMID: 36449280, PMCID: PMC10073242, DOI: 10.1158/1078-0432.ccr-22-0784.
Epigenetically suppressed tumor cell intrinsic STING promotes tumor immune escapeZheng H, Wu L, Xiao Q, Meng X, Hafiz A, Yan Q, Lu R, Cao J. Epigenetically suppressed tumor cell intrinsic STING promotes tumor immune escape. Biomedicine & Pharmacotherapy 2022, 157: 114033. PMID: 36436495, PMCID: PMC9826630, DOI: 10.1016/j.biopha.2022.114033.
Histone H3 proline 16 hydroxylation regulates mammalian gene expressionLiu X, Wang J, Boyer J, Gong W, Zhao S, Xie L, Wu Q, Zhang C, Jain K, Guo Y, Rodriguez J, Li M, Uryu H, Liao C, Hu L, Zhou J, Shi X, Tsai Y, Yan Q, Luo W, Chen X, Strahl B, von Kriegsheim A, Zhang Q, Wang G, Baldwin A, Zhang Q. Histone H3 proline 16 hydroxylation regulates mammalian gene expression. Nature Genetics 2022, 54: 1721-1735. PMID: 36347944, PMCID: PMC9674084, DOI: 10.1038/s41588-022-01212-x.
Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulationCai WL, Chen JF, Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. ELife 2022, 11: e78163. PMID: 36043466, PMCID: PMC9584608, DOI: 10.7554/elife.78163.
Nicotine dose-dependent epigenomic-wide DNA methylation changes in the mice with long-term electronic cigarette exposure.Peng G, Xi Y, Bellini C, Pham K, Zhuang ZW, Yan Q, Jia M, Wang G, Lu L, Tang MS, Zhao H, Wang H. Nicotine dose-dependent epigenomic-wide DNA methylation changes in the mice with long-term electronic cigarette exposure. American Journal Of Cancer Research 2022, 12: 3679-3692. PMID: 36119846, PMCID: PMC9442002.
Editorial: Epigenetic Regulation and Tumor ImmunotherapySun H, Huang B, Cao J, Yan Q, Yin M. Editorial: Epigenetic Regulation and Tumor Immunotherapy. Frontiers In Oncology 2022, 12: 893157. PMID: 35600405, PMCID: PMC9117615, DOI: 10.3389/fonc.2022.893157.
Awakening KDM5B to defeat leukemiaChan LH, Yan Q. Awakening KDM5B to defeat leukemia. Proceedings Of The National Academy Of Sciences Of The United States Of America 2022, 119: e2202245119. PMID: 35312367, PMCID: PMC9060505, DOI: 10.1073/pnas.2202245119.
Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasisFarshidfar F, Rhrissorrakrai K, Levovitz C, Peng C, Knight J, Bacchiocchi A, Su J, Yin M, Sznol M, Ariyan S, Clune J, Olino K, Parida L, Nikolaus J, Zhang M, Zhao S, Wang Y, Huang G, Wan M, Li X, Cao J, Yan Q, Chen X, Newman AM, Halaban R. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nature Communications 2022, 13: 898. PMID: 35197475, PMCID: PMC8866401, DOI: 10.1038/s41467-022-28566-4.
CECR2 drives breast cancer metastasis by promoting NF-κB signaling and macrophage-mediated immune suppressionZhang M, Liu ZZ, Aoshima K, Cai WL, Sun H, Xu T, Zhang Y, An Y, Chen JF, Chan LH, Aoshima A, Lang SM, Tang Z, Che X, Li Y, Rutter SJ, Bossuyt V, Chen X, Morrow JS, Pusztai L, Rimm DL, Yin M, Yan Q. CECR2 drives breast cancer metastasis by promoting NF-κB signaling and macrophage-mediated immune suppression. Science Translational Medicine 2022, 14: eabf5473. PMID: 35108062, PMCID: PMC9003667, DOI: 10.1126/scitranslmed.abf5473.
Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clockMinteer C, Morselli M, Meer M, Cao J, Higgins‐Chen A, Lang SM, Pellegrini M, Yan Q, Levine ME. Tick tock, tick tock: Mouse culture and tissue aging captured by an epigenetic clock. Aging Cell 2022, 21: e13553. PMID: 35104377, PMCID: PMC8844113, DOI: 10.1111/acel.13553.

2021

A DNAmCULTURE Epigenetic Fingerprint Recapitulates Physiological AgingMinteer C, Morselli M, Meer M, Cao J, Lang S, Pellegrini M, Yan Q, Levine M. A DNAmCULTURE Epigenetic Fingerprint Recapitulates Physiological Aging. Innovation In Aging 2021, 5: 5-6. PMCID: PMC8679434, DOI: 10.1093/geroni/igab046.018.
MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cellsJeong J, Shin JH, Li W, Hong JY, Lim J, Hwang JY, Chung JJ, Yan Q, Liu Y, Choi J, Wysolmerski J. MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells. Cell Reports 2021, 37: 110160. PMID: 34965434, PMCID: PMC8762588, DOI: 10.1016/j.celrep.2021.110160.
DNA methylation markers in esophageal cancer: an emerging tool for cancer surveillance and treatment.Wang H, DeFina SM, Bajpai M, Yan Q, Yang L, Zhou Z. DNA methylation markers in esophageal cancer: an emerging tool for cancer surveillance and treatment. American Journal Of Cancer Research 2021, 11: 5644-5658. PMID: 34873485, PMCID: PMC8640794.
KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelementsZhang SM, Cai WL, Liu X, Thakral D, Luo J, Chan LH, McGeary MK, Song E, Blenman KRM, Micevic G, Jessel S, Zhang Y, Yin M, Booth CJ, Jilaveanu LB, Damsky W, Sznol M, Kluger HM, Iwasaki A, Bosenberg MW, Yan Q. KDM5B promotes immune evasion by recruiting SETDB1 to silence retroelements. Nature 2021, 598: 682-687. PMID: 34671158, PMCID: PMC8555464, DOI: 10.1038/s41586-021-03994-2.
The roles of epigenetics in cancer progression and metastasisChen JF, Yan Q. The roles of epigenetics in cancer progression and metastasis. Biochemical Journal 2021, 478: 3373-3393. PMID: 34520519, PMCID: PMC8524384, DOI: 10.1042/bcj20210084.
KDM2B promotes cell viability by enhancing DNA damage response in canine hemangiosarcomaGulay KCM, Aoshima K, Shibata Y, Yasui H, Yan Q, Kobayashi A, Kimura T. KDM2B promotes cell viability by enhancing DNA damage response in canine hemangiosarcoma. Journal Of Genetics And Genomics 2021, 48: 618-630. PMID: 34023294, DOI: 10.1016/j.jgg.2021.02.005.
5‐Fluorouracil efficacy requires anti‐tumor immunity triggered by cancer‐cell‐intrinsic STINGTian J, Zhang D, Kurbatov V, Wang Q, Wang Y, Fang D, Wu L, Bosenberg M, Muzumdar MD, Khan S, Lu Q, Yan Q, Lu J. 5‐Fluorouracil efficacy requires anti‐tumor immunity triggered by cancer‐cell‐intrinsic STING. The EMBO Journal 2021, 40: embj2020106065. PMID: 33615517, PMCID: PMC8013832, DOI: 10.15252/embj.2020106065.

2020

KDM5B Is Essential for the Hyperactivation of PI3K/AKT Signaling in Prostate TumorigenesisLi G, Kanagasabai T, Lu W, Zou M, Zhang SM, Celada SI, Izban MG, Liu Q, Lu T, Ballard BR, Zhou X, Adunyah SE, Matusik RJ, Yan Q, Chen Z. KDM5B Is Essential for the Hyperactivation of PI3K/AKT Signaling in Prostate Tumorigenesis. Cancer Research 2020, 80: 4633-4643. PMID: 32868382, PMCID: PMC8034842, DOI: 10.1158/0008-5472.can-20-0505.
Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 InfectionWei J, Alfajaro MM, DeWeirdt PC, Hanna RE, Lu-Culligan WJ, Cai WL, Strine MS, Zhang SM, Graziano VR, Schmitz CO, Chen JS, Mankowski MC, Filler RB, Ravindra NG, Gasque V, de Miguel FJ, Patil A, Chen H, Oguntuyo KY, Abriola L, Surovtseva YV, Orchard RC, Lee B, Lindenbach BD, Politi K, van Dijk D, Kadoch C, Simon MD, Yan Q, Doench JG, Wilen CB. Genome-wide CRISPR Screens Reveal Host Factors Critical for SARS-CoV-2 Infection. Cell 2020, 184: 76-91.e13. PMID: 33147444, PMCID: PMC7574718, DOI: 10.1016/j.cell.2020.10.028.
Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer CellsMarczyk M, Patwardhan GA, Zhao J, Qu R, Li X, Wali VB, Gupta AK, Pillai MM, Kluger Y, Yan Q, Hatzis C, Pusztai L, Gunasekharan V. Multi-Omics Investigation of Innate Navitoclax Resistance in Triple-Negative Breast Cancer Cells. Cancers 2020, 12: 2551. PMID: 32911681, PMCID: PMC7563413, DOI: 10.3390/cancers12092551.
Potent BRD4 inhibitor suppresses cancer cell-macrophage interactionYin M, Guo Y, Hu R, Cai WL, Li Y, Pei S, Sun H, Peng C, Li J, Ye R, Yang Q, Wang N, Tao Y, Chen X, Yan Q. Potent BRD4 inhibitor suppresses cancer cell-macrophage interaction. Nature Communications 2020, 11: 1833. PMID: 32286255, PMCID: PMC7156724, DOI: 10.1038/s41467-020-15290-0.
Cancer Epigenetics, Tumor Immunity, and ImmunotherapyCao J, Yan Q. Cancer Epigenetics, Tumor Immunity, and Immunotherapy. Trends In Cancer 2020, 6: 580-592. PMID: 32610068, PMCID: PMC7330177, DOI: 10.1016/j.trecan.2020.02.003.
Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brainCai WL, Greer CB, Chen JF, Arnal-Estapé A, Cao J, Yan Q, Nguyen DX. Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain. BMC Medical Genomics 2020, 13: 33. PMID: 32143622, PMCID: PMC7060551, DOI: 10.1186/s12920-020-0695-0.
Annotation and cluster analysis of long noncoding RNA linked to male sex and estrogen in cancersLiu S, Lai W, Shi Y, Liu N, Ouyang L, Zhang Z, Chen L, Wang X, Qian B, Xiao D, Yan Q, Cao Y, Liu S, Tao Y. Annotation and cluster analysis of long noncoding RNA linked to male sex and estrogen in cancers. Npj Precision Oncology 2020, 4: 5. PMID: 32195358, PMCID: PMC7054536, DOI: 10.1038/s41698-020-0110-5.
Acquired Resistance to HER2-Targeted Therapies Creates Vulnerability to ATP Synthase InhibitionGale M, Li Y, Cao J, Liu ZZ, Holmbeck MA, Zhang M, Lang SM, Wu L, Do Carmo M, Gupta S, Aoshima K, DiGiovanna MP, Stern DF, Rimm DL, Shadel GS, Chen X, Yan Q. Acquired Resistance to HER2-Targeted Therapies Creates Vulnerability to ATP Synthase Inhibition. Cancer Research 2020, 80: 524-535. PMID: 31690671, PMCID: PMC7002225, DOI: 10.1158/0008-5472.can-18-3985.
Cancer progression is mediated by proline catabolism in non-small cell lung cancerLiu Y, Mao C, Wang M, Liu N, Ouyang L, Liu S, Tang H, Cao Y, Liu S, Wang X, Xiao D, Chen C, Shi Y, Yan Q, Tao Y. Cancer progression is mediated by proline catabolism in non-small cell lung cancer. Oncogene 2020, 39: 2358-2376. PMID: 31911619, DOI: 10.1038/s41388-019-1151-5.

2019

PBRM1 acts as a p53 lysine-acetylation reader to suppress renal tumor growthCai W, Su L, Liao L, Liu ZZ, Langbein L, Dulaimi E, Testa JR, Uzzo RG, Zhong Z, Jiang W, Yan Q, Zhang Q, Yang H. PBRM1 acts as a p53 lysine-acetylation reader to suppress renal tumor growth. Nature Communications 2019, 10: 5800. PMID: 31863007, PMCID: PMC6925188, DOI: 10.1038/s41467-019-13608-1.
Mitochondrial DNA stress signalling protects the nuclear genomeWu Z, Oeck S, West AP, Mangalhara KC, Sainz AG, Newman LE, Zhang XO, Wu L, Yan Q, Bosenberg M, Liu Y, Sulkowski PL, Tripple V, Kaech SM, Glazer PM, Shadel GS. Mitochondrial DNA stress signalling protects the nuclear genome. Nature Metabolism 2019, 1: 1209-1218. PMID: 32395698, PMCID: PMC7213273, DOI: 10.1038/s42255-019-0150-8.
Oxygen sensing and adaptability won the 2019 Nobel Prize in Physiology or medicineZhang Q, Yan Q, Yang H, Wei W. Oxygen sensing and adaptability won the 2019 Nobel Prize in Physiology or medicine. Genes & Diseases 2019, 6: 328-332. PMID: 31832511, PMCID: PMC6889041, DOI: 10.1016/j.gendis.2019.10.006.
Identification and Validation of a Novel Biologics Target in Triple Negative Breast CancerWali VB, Patwardhan GA, Pelekanou V, Karn T, Cao J, Ocana A, Yan Q, Nelson B, Hatzis C, Pusztai L. Identification and Validation of a Novel Biologics Target in Triple Negative Breast Cancer. Scientific Reports 2019, 9: 14934. PMID: 31624295, PMCID: PMC6797726, DOI: 10.1038/s41598-019-51453-w.
GIAT4RA functions as a tumor suppressor in non-small cell lung cancer by counteracting Uchl3–mediated deubiquitination of LSHYang R, Liu N, Chen L, Jiang Y, Shi Y, Mao C, Liu Y, Wang M, Lai W, Tang H, Gao M, Xiao D, Wang X, Zhou H, Tang CE, Liu W, Yu F, Cao Y, Yan Q, Liu S, Tao Y. GIAT4RA functions as a tumor suppressor in non-small cell lung cancer by counteracting Uchl3–mediated deubiquitination of LSH. Oncogene 2019, 38: 7133-7145. PMID: 31417184, DOI: 10.1038/s41388-019-0909-0.
LSH interacts with and stabilizes GINS4 transcript that promotes tumourigenesis in non-small cell lung cancerYang R, Liu N, Chen L, Jiang Y, Shi Y, Mao C, Liu Y, Wang M, Lai W, Tang H, Gao M, Xiao D, Wang X, Yu F, Cao Y, Yan Q, Liu S, Tao Y. LSH interacts with and stabilizes GINS4 transcript that promotes tumourigenesis in non-small cell lung cancer. Journal Of Experimental & Clinical Cancer Research 2019, 38: 280. PMID: 31253190, PMCID: PMC6599244, DOI: 10.1186/s13046-019-1276-y.
KDM5B Promotes Drug Resistance by Regulating Melanoma Propagating Cell SubpopulationsLiu X, Zhang SM, McGeary MK, Krykbaeva I, Lai L, Jansen DJ, Kales SC, Simeonov A, Hall MD, Kelly DP, Bosenberg MW, Yan Q. KDM5B Promotes Drug Resistance by Regulating Melanoma Propagating Cell Subpopulations. Molecular Cancer Therapeutics 2019, 18: molcanther.0395.2018. PMID: 30523048, PMCID: PMC6397704, DOI: 10.1158/1535-7163.mct-18-0395.
Long noncoding RNA LINC00336 inhibits ferroptosis in lung cancer by functioning as a competing endogenous RNAWang M, Mao C, Ouyang L, Liu Y, Lai W, Liu N, Shi Y, Chen L, Xiao D, Yu F, Wang X, Zhou H, Cao Y, Liu S, Yan Q, Tao Y, Zhang B. Long noncoding RNA LINC00336 inhibits ferroptosis in lung cancer by functioning as a competing endogenous RNA. Cell Death & Differentiation 2019, 26: 2329-2343. PMID: 30787392, PMCID: PMC6889193, DOI: 10.1038/s41418-019-0304-y.
High affinity binding of H3K14ac through collaboration of bromodomains 2, 4 and 5 is critical for the molecular and tumor suppressor functions of PBRM1Liao L, Alicea‐Velázquez N, Langbein L, Niu X, Cai W, Cho E, Zhang M, Greer CB, Yan Q, Cosgrove MS, Yang H. High affinity binding of H3K14ac through collaboration of bromodomains 2, 4 and 5 is critical for the molecular and tumor suppressor functions of PBRM1. Molecular Oncology 2019, 13: 811-828. PMID: 30585695, PMCID: PMC6441893, DOI: 10.1002/1878-0261.12434.

2018

Neuronal calcium sensor 1 (NCS1) promotes motility and metastatic spread of breast cancer cells in vitro and in vivoApasu JE, Schuette D, Laranger R, Steinle JA, Nguyen LD, Grosshans HK, Zhang M, Cai WL, Yan Q, Robert ME, Mak M, Ehrlich BE. Neuronal calcium sensor 1 (NCS1) promotes motility and metastatic spread of breast cancer cells in vitro and in vivo. The FASEB Journal 2018, 33: 4802-4813. PMID: 30592625, PMCID: PMC6436647, DOI: 10.1096/fj.201802004r.
Immunological differences between primary and metastatic breast cancerSzekely B, Bossuyt V, Li X, Wali VB, Patwardhan GA, Frederick C, Silber A, Park T, Harigopal M, Pelekanou V, Zhang M, Yan Q, Rimm DL, Bianchini G, Hatzis C, Pusztai L. Immunological differences between primary and metastatic breast cancer. Annals Of Oncology 2018, 29: 2232-2239. PMID: 30203045, DOI: 10.1093/annonc/mdy399.
Multiple tumor suppressors regulate a HIF-dependent negative feedback loop via ISGF3 in human clear cell renal cancerLiao L, Liu ZZ, Langbein L, Cai W, Cho EA, Na J, Niu X, Jiang W, Zhong Z, Cai WL, Jagannathan G, Dulaimi E, Testa JR, Uzzo RG, Wang Y, Stark GR, Sun J, Peiper S, Xu Y, Yan Q, Yang H. Multiple tumor suppressors regulate a HIF-dependent negative feedback loop via ISGF3 in human clear cell renal cancer. ELife 2018, 7: e37925. PMID: 30355451, PMCID: PMC6234029, DOI: 10.7554/elife.37925.
KDM5A Regulates a Translational Program that Controls p53 Protein ExpressionHu D, Jablonowski C, Cheng PH, AlTahan A, Li C, Wang Y, Palmer L, Lan C, Sun B, Abu-Zaid A, Fan Y, Brimble M, Gamboa N, Kumbhar RC, Yanishevski D, Miller KM, Kang G, Zambetti GP, Chen T, Yan Q, Davidoff AM, Yang J. KDM5A Regulates a Translational Program that Controls p53 Protein Expression. IScience 2018, 9: 84-100. PMID: 30388705, PMCID: PMC6214872, DOI: 10.1016/j.isci.2018.10.012.
KDM5 histone demethylases repress immune response via suppression of STINGWu L, Cao J, Cai WL, Lang SM, Horton JR, Jansen DJ, Liu ZZ, Chen JF, Zhang M, Mott BT, Pohida K, Rai G, Kales SC, Henderson MJ, Hu X, Jadhav A, Maloney DJ, Simeonov A, Zhu S, Iwasaki A, Hall MD, Cheng X, Shadel GS, Yan Q. KDM5 histone demethylases repress immune response via suppression of STING. PLOS Biology 2018, 16: e2006134. PMID: 30080846, PMCID: PMC6095604, DOI: 10.1371/journal.pbio.2006134.
Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5AHorton JR, Liu X, Wu L, Zhang K, Shanks J, Zhang X, Rai G, Mott BT, Jansen DJ, Kales SC, Henderson MJ, Pohida K, Fang Y, Hu X, Jadhav A, Maloney DJ, Hall MD, Simeonov A, Fu H, Vertino PM, Yan Q, Cheng X. Insights into the Action of Inhibitor Enantiomers against Histone Lysine Demethylase 5A. Journal Of Medicinal Chemistry 2018, 61: 3193-3208. PMID: 29537847, PMCID: PMC6322411, DOI: 10.1021/acs.jmedchem.8b00261.
The multiplexed CRISPR targeting platformsCao J, Xiao Q, Yan Q. The multiplexed CRISPR targeting platforms. Drug Discovery Today Technologies 2018, 28: 53-61. PMID: 30205881, PMCID: PMC6699180, DOI: 10.1016/j.ddtec.2018.01.001.

2017

The Molecular Basis of Histone DemethylationHorton J, Gale M, Yan Q, Cheng X. The Molecular Basis of Histone Demethylation. Cancer Drug Discovery And Development 2017, 151-219. DOI: 10.1007/978-3-319-59786-7_7.
Cell Division Cycle 42 plays a Cell type-Specific role in Lung TumorigenesisZheng C, Wang Y, Yang L, Zhou S, Gao Y, Li F, Feng Y, Wang Z, Zhan L, Yan Q, Zhu X, Wong KK, Chen Z, Ji H. Cell Division Cycle 42 plays a Cell type-Specific role in Lung Tumorigenesis. Scientific Reports 2017, 7: 10407. PMID: 28871124, PMCID: PMC5583260, DOI: 10.1038/s41598-017-10891-0.
EGLN1/c-Myc Induced Lymphoid-Specific Helicase Inhibits Ferroptosis through Lipid Metabolic Gene Expression ChangesJiang Y, Mao C, Yang R, Yan B, Shi Y, Liu X, Lai W, Liu Y, Wang X, Xiao D, Zhou H, Cheng Y, Yu F, Cao Y, Liu S, Yan Q, Tao Y. EGLN1/c-Myc Induced Lymphoid-Specific Helicase Inhibits Ferroptosis through Lipid Metabolic Gene Expression Changes. Theranostics 2017, 7: 3293-3305. PMID: 28900510, PMCID: PMC5595132, DOI: 10.7150/thno.19988.

2016

The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiationBrier AB, Loft A, Madsen JG, Rosengren T, Nielsen R, Schmidt SF, Liu Z, Yan Q, Gronemeyer H, Mandrup S. The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation. Nucleic Acids Research 2016, 45: 1743-1759. PMID: 27899593, PMCID: PMC5389521, DOI: 10.1093/nar/gkw1156.
Illumina Sequencing of Bisulfite-Converted DNA Libraries.Lizardi PM, Yan Q, Wajapeyee N. Illumina Sequencing of Bisulfite-Converted DNA Libraries. Cold Spring Harbor Protocols 2016, 2017: pdb.prot094870. PMID: 27852841, DOI: 10.1101/pdb.prot094870.
Analysis of DNA Methylation in Mammalian CellsLizardi PM, Yan Q, Wajapeyee N. Analysis of DNA Methylation in Mammalian Cells. Cold Spring Harbor Protocols 2016, 2017: pdb.top094821. PMID: 27852839, DOI: 10.1101/pdb.top094821.
Methylation-Specific Polymerase Chain Reaction (PCR) for Gene-Specific DNA Methylation Detection.Lizardi PM, Yan Q, Wajapeyee N. Methylation-Specific Polymerase Chain Reaction (PCR) for Gene-Specific DNA Methylation Detection. Cold Spring Harbor Protocols 2016, 2017: pdb.prot094847. PMID: 27852838, DOI: 10.1101/pdb.prot094847.
High-Throughput Deep Sequencing for Mapping Mammalian DNA Methylation.Lizardi PM, Yan Q, Wajapeyee N. High-Throughput Deep Sequencing for Mapping Mammalian DNA Methylation. Cold Spring Harbor Protocols 2016, 2017: pdb.prot094862. PMID: 27852842, DOI: 10.1101/pdb.prot094862.
DNA Bisulfite Sequencing for Single-Nucleotide-Resolution DNA Methylation Detection.Lizardi PM, Yan Q, Wajapeyee N. DNA Bisulfite Sequencing for Single-Nucleotide-Resolution DNA Methylation Detection. Cold Spring Harbor Protocols 2016, 2017: pdb.prot094839. PMID: 27852843, DOI: 10.1101/pdb.prot094839.
Methyl-Cytosine-Based Immunoprecipitation for DNA Methylation Analysis.Lizardi PM, Yan Q, Wajapeyee N. Methyl-Cytosine-Based Immunoprecipitation for DNA Methylation Analysis. Cold Spring Harbor Protocols 2016, 2017: pdb.prot094854. PMID: 27852840, DOI: 10.1101/pdb.prot094854.
KDM5 lysine demethylases are involved in maintenance of 3′UTR lengthBlair LP, Liu Z, Labitigan RL, Wu L, Zheng D, Xia Z, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh SG, Moore CL, Li W, Tian B, Tackett AJ, Yan Q. KDM5 lysine demethylases are involved in maintenance of 3′UTR length. Science Advances 2016, 2: e1501662. PMID: 28138513, PMCID: PMC5262454, DOI: 10.1126/sciadv.1501662.
An easy and efficient inducible CRISPR/Cas9 platform with improved specificity for multiple gene targetingCao J, Wu L, Zhang SM, Lu M, Cheung WK, Cai W, Gale M, Xu Q, Yan Q. An easy and efficient inducible CRISPR/Cas9 platform with improved specificity for multiple gene targeting. Nucleic Acids Research 2016, 44: e149-e149. PMID: 27458201, PMCID: PMC5100567, DOI: 10.1093/nar/gkw660.
Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse CompoundsHorton JR, Liu X, Gale M, Wu L, Shanks JR, Zhang X, Webber PJ, Bell JS, Kales SC, Mott BT, Rai G, Jansen DJ, Henderson MJ, Urban DJ, Hall MD, Simeonov A, Maloney DJ, Johns MA, Fu H, Jadhav A, Vertino PM, Yan Q, Cheng X. Structural Basis for KDM5A Histone Lysine Demethylase Inhibition by Diverse Compounds. Cell Chemical Biology 2016, 23: 769-781. PMID: 27427228, PMCID: PMC4958579, DOI: 10.1016/j.chembiol.2016.06.006.
Screen-identified selective inhibitor of lysine demethylase 5A blocks cancer cell growth and drug resistanceGale M, Sayegh J, Cao J, Norcia M, Gareiss P, Hoyer D, Merkel JS, Yan Q. Screen-identified selective inhibitor of lysine demethylase 5A blocks cancer cell growth and drug resistance. Oncotarget 2016, 7: 39931-39944. PMID: 27224921, PMCID: PMC5129982, DOI: 10.18632/oncotarget.9539.

2015

High-throughput screening to identify inhibitors of lysine demethylasesGale M, Yan Q. High-throughput screening to identify inhibitors of lysine demethylases. Epigenomics 2015, 7: 57-65. PMID: 25687466, PMCID: PMC4356004, DOI: 10.2217/epi.14.63.

2014

Histone Demethylase Jumonji AT-rich Interactive Domain 1B (JARID1B) Controls Mammary Gland Development by Regulating Key Developmental and Lineage Specification Genes*Zou MR, Cao J, Liu Z, Huh SJ, Polyak K, Yan Q. Histone Demethylase Jumonji AT-rich Interactive Domain 1B (JARID1B) Controls Mammary Gland Development by Regulating Key Developmental and Lineage Specification Genes*. Journal Of Biological Chemistry 2014, 289: 17620-17633. PMID: 24802759, PMCID: PMC4067197, DOI: 10.1074/jbc.m114.570853.
Histone Demethylase RBP2 Is Critical for Breast Cancer Progression and MetastasisCao J, Liu Z, Cheung WK, Zhao M, Chen SY, Chan SW, Booth CJ, Nguyen DX, Yan Q. Histone Demethylase RBP2 Is Critical for Breast Cancer Progression and Metastasis. Cell Reports 2014, 6: 868-877. PMID: 24582965, PMCID: PMC4014129, DOI: 10.1016/j.celrep.2014.02.004.
Significance of glioma-associated oncogene homolog 1 (GLI1)expression in claudin-low breast cancer and crosstalk with the nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) pathwayColavito SA, Zou MR, Yan Q, Nguyen DX, Stern DF. Significance of glioma-associated oncogene homolog 1 (GLI1)expression in claudin-low breast cancer and crosstalk with the nuclear factor kappa-light-chain-enhancer of activated B cells (NFκB) pathway. Breast Cancer Research 2014, 16: 444. PMID: 25252859, PMCID: PMC4303124, DOI: 10.1186/s13058-014-0444-4.

2013

Histone Demethylase RBP2 Promotes Lung Tumorigenesis and Cancer MetastasisTeng YC, Lee CF, Li YS, Chen YR, Hsiao PW, Chan MY, Lin FM, Huang HD, Chen YT, Jeng YM, Hsu CH, Yan Q, Tsai MD, Juan LJ. Histone Demethylase RBP2 Promotes Lung Tumorigenesis and Cancer Metastasis. Cancer Research 2013, 73: 4711-4721. PMID: 23722541, DOI: 10.1158/0008-5472.can-12-3165.
Histone Demethylases Set the Stage for Cancer MetastasisCao J, Yan Q. Histone Demethylases Set the Stage for Cancer Metastasis. Science Signaling 2013, 6: pe15, 1-2. PMID: 23633674, DOI: 10.1126/scisignal.2004188.
Identification of Small Molecule Inhibitors of Jumonji AT-rich Interactive Domain 1B (JARID1B) Histone Demethylase by a Sensitive High Throughput Screen*Sayegh J, Cao J, Zou MR, Morales A, Blair LP, Norcia M, Hoyer D, Tackett AJ, Merkel JS, Yan Q. Identification of Small Molecule Inhibitors of Jumonji AT-rich Interactive Domain 1B (JARID1B) Histone Demethylase by a Sensitive High Throughput Screen*. Journal Of Biological Chemistry 2013, 288: 9408-9417. PMID: 23408432, PMCID: PMC3611010, DOI: 10.1074/jbc.m112.419861.

2012

Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiationBeshiri ML, Holmes KB, Richter WF, Hess S, Islam AB, Yan Q, Plante L, Litovchick L, Gévry N, Lopez-Bigas N, Kaelin WG, Benevolenskaya EV. Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 18499-18504. PMID: 23093672, PMCID: PMC3494949, DOI: 10.1073/pnas.1216724109.
Epigenetic Mechanisms in Commonly Occurring CancersBlair LP, Yan Q. Epigenetic Mechanisms in Commonly Occurring Cancers. DNA And Cell Biology 2012, 31: s-49-s-61. PMID: 22519822, PMCID: PMC3460614, DOI: 10.1089/dna.2012.1654.
Histone Ubiquitination and Deubiquitination in Transcription, DNA Damage Response, and CancerCao J, Yan Q. Histone Ubiquitination and Deubiquitination in Transcription, DNA Damage Response, and Cancer. Frontiers In Oncology 2012, 2: 26. PMID: 22649782, PMCID: PMC3355875, DOI: 10.3389/fonc.2012.00026.

2011

Loss of the retinoblastoma binding protein 2 (RBP2) histone demethylase suppresses tumorigenesis in mice lacking Rb1 or Men1Lin W, Cao J, Liu J, Beshiri ML, Fujiwara Y, Francis J, Cherniack AD, Geisen C, Blair LP, Zou MR, Shen X, Kawamori D, Liu Z, Grisanzio C, Watanabe H, Minamishima YA, Zhang Q, Kulkarni RN, Signoretti S, Rodig SJ, Bronson RT, Orkin SH, Tuck DP, Benevolenskaya EV, Meyerson M, Kaelin WG, Yan Q. Loss of the retinoblastoma binding protein 2 (RBP2) histone demethylase suppresses tumorigenesis in mice lacking Rb1 or Men1. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 13379-13386. PMID: 21788502, PMCID: PMC3158206, DOI: 10.1073/pnas.1110104108.
The von Hippel–Lindau tumor suppressor protein regulates gene expression and tumor growth through histone demethylase JARID1CNiu X, Zhang T, Liao L, Zhou L, Lindner DJ, Zhou M, Rini B, Yan Q, Yang H. The von Hippel–Lindau tumor suppressor protein regulates gene expression and tumor growth through histone demethylase JARID1C. Oncogene 2011, 31: 776-786. PMID: 21725364, PMCID: PMC4238297, DOI: 10.1038/onc.2011.266.
Epigenetic Regulation by Lysine Demethylase 5 (KDM5) Enzymes in CancerBlair LP, Cao J, Zou MR, Sayegh J, Yan Q. Epigenetic Regulation by Lysine Demethylase 5 (KDM5) Enzymes in Cancer. Cancers 2011, 3: 1383-1404. PMID: 21544224, PMCID: PMC3085456, DOI: 10.3390/cancers3011383.

2010

Exploiting cellular senescence to treat cancer and circumvent drug resistanceYan Q, Wajapeyee N. Exploiting cellular senescence to treat cancer and circumvent drug resistance. Cancer Biology & Therapy 2010, 9: 166-175. PMID: 20118655, DOI: 10.4161/cbt.9.3.11166.

2008

A Role for Mammalian Sin3 in Permanent Gene Silencingvan Oevelen C, Wang J, Asp P, Yan Q, Kaelin WG, Kluger Y, Dynlacht BD. A Role for Mammalian Sin3 in Permanent Gene Silencing. Molecular Cell 2008, 32: 359-370. PMID: 18995834, PMCID: PMC3100182, DOI: 10.1016/j.molcel.2008.10.015.

2007

pVHL Acts as an Adaptor to Promote the Inhibitory Phosphorylation of the NF-κB Agonist Card9 by CK2Yang H, Minamishima YA, Yan Q, Schlisio S, Ebert BL, Zhang X, Zhang L, Kim WY, Olumi AF, Kaelin WG. pVHL Acts as an Adaptor to Promote the Inhibitory Phosphorylation of the NF-κB Agonist Card9 by CK2. Molecular Cell 2007, 28: 15-27. PMID: 17936701, PMCID: PMC2128776, DOI: 10.1016/j.molcel.2007.09.010.
Hypoxia-Inducible Factor Linked to Differential Kidney Cancer Risk Seen with Type 2A and Type 2B VHL MutationsLi L, Zhang L, Zhang X, Yan Q, Minamishima YA, Olumi AF, Mao M, Bartz S, Kaelin WG. Hypoxia-Inducible Factor Linked to Differential Kidney Cancer Risk Seen with Type 2A and Type 2B VHL Mutations. Molecular And Cellular Biology 2007, 27: 5381-5392. PMID: 17526729, PMCID: PMC1952077, DOI: 10.1128/mcb.00282-07.
The Hypoxia-Inducible Factor 2α N-Terminal and C-Terminal Transactivation Domains Cooperate To Promote Renal Tumorigenesis In VivoYan Q, Bartz S, Mao M, Li L, Kaelin WG. The Hypoxia-Inducible Factor 2α N-Terminal and C-Terminal Transactivation Domains Cooperate To Promote Renal Tumorigenesis In Vivo. Molecular And Cellular Biology 2007, 27: 2092-2102. PMID: 17220275, PMCID: PMC1820491, DOI: 10.1128/mcb.01514-06.
The Retinoblastoma Binding Protein RBP2 Is an H3K4 DemethylaseKlose RJ, Yan Q, Tothova Z, Yamane K, Erdjument-Bromage H, Tempst P, Gilliland DG, Zhang Y, Kaelin WG. The Retinoblastoma Binding Protein RBP2 Is an H3K4 Demethylase. Cell 2007, 128: 889-900. PMID: 17320163, DOI: 10.1016/j.cell.2007.02.013.

2004

Both BC-Box Motifs of Adenovirus Protein E4orf6 Are Required To Efficiently Assemble an E3 Ligase Complex That Degrades p53Blanchette P, Cheng CY, Yan Q, Ketner G, Ornelles DA, Dobner T, Conaway RC, Conaway JW, Branton PE. Both BC-Box Motifs of Adenovirus Protein E4orf6 Are Required To Efficiently Assemble an E3 Ligase Complex That Degrades p53. Molecular And Cellular Biology 2004, 24: 9619-9629. PMID: 15485928, PMCID: PMC522240, DOI: 10.1128/mcb.24.21.9619-9629.2004.
Identification of Elongin C and Skp1 Sequences That Determine Cullin Selection*Yan Q, Kamura T, Cai Y, Jin J, Ivan M, Mushegian A, Conaway RC, Conaway JW. Identification of Elongin C and Skp1 Sequences That Determine Cullin Selection*. Journal Of Biological Chemistry 2004, 279: 43019-43026. PMID: 15280393, DOI: 10.1074/jbc.m408018200.

2001

Degradation of p53 by adenovirus E4orf6 and E1B55K proteins occurs via a novel mechanism involving a Cullin-containing complexQuerido E, Blanchette P, Yan Q, Kamura T, Morrison M, Boivin D, Kaelin WG, Conaway RC, Conaway JW, Branton PE. Degradation of p53 by adenovirus E4orf6 and E1B55K proteins occurs via a novel mechanism involving a Cullin-containing complex. Genes & Development 2001, 15: 3104-3117. PMID: 11731475, PMCID: PMC312842, DOI: 10.1101/gad.926401.
MUF1, A Novel Elongin BC-interacting Leucine-rich Repeat Protein That Can Assemble with Cul5 and Rbx1 to Reconstitute a Ubiquitin Ligase*Kamura T, Burian D, Yan Q, Schmidt S, Lane W, Querido E, Branton P, Shilatifard A, Conaway R, Conaway J. MUF1, A Novel Elongin BC-interacting Leucine-rich Repeat Protein That Can Assemble with Cul5 and Rbx1 to Reconstitute a Ubiquitin Ligase*. Journal Of Biological Chemistry 2001, 276: 29748-29753. PMID: 11384984, DOI: 10.1074/jbc.m103093200.
Transcription Factors TFIIF, ELL, and Elongin Negatively Regulate SII-induced Nascent Transcript Cleavage by Non-arrested RNA Polymerase II Elongation Intermediates*Elmendorf B, Shilatifard A, Yan Q, Conaway J, Conaway R. Transcription Factors TFIIF, ELL, and Elongin Negatively Regulate SII-induced Nascent Transcript Cleavage by Non-arrested RNA Polymerase II Elongation Intermediates*. Journal Of Biological Chemistry 2001, 276: 23109-23114. PMID: 11259417, DOI: 10.1074/jbc.m101445200.

1999

Dual Roles for Transcription Factor IIF in Promoter Escape by RNA Polymerase II*Yan Q, Moreland R, Conaway J, Conaway R. Dual Roles for Transcription Factor IIF in Promoter Escape by RNA Polymerase II*. Journal Of Biological Chemistry 1999, 274: 35668-35675. PMID: 10585446, DOI: 10.1074/jbc.274.50.35668.
The Rbx1 subunit of SCF and VHL E3 ubiquitin ligase activates Rub1 modification of cullins Cdc53 and Cul2Kamura T, Conrad MN, Yan Q, Conaway RC, Conaway JW. The Rbx1 subunit of SCF and VHL E3 ubiquitin ligase activates Rub1 modification of cullins Cdc53 and Cul2. Genes & Development 1999, 13: 2928-2933. PMID: 10579999, PMCID: PMC317157, DOI: 10.1101/gad.13.22.2928.
A Role for the TFIIH XPB DNA Helicase in Promoter Escape by RNA Polymerase II*Moreland R, Tirode F, Yan Q, Conaway J, Egly J, Conaway R. A Role for the TFIIH XPB DNA Helicase in Promoter Escape by RNA Polymerase II*. Journal Of Biological Chemistry 1999, 274: 22127-22130. PMID: 10428772, DOI: 10.1074/jbc.274.32.22127.

1998

Mechanism of promoter escape by RNA polymerase II.Conaway JW, Dvir A, Moreland RJ, Yan Q, Elmendorf BJ, Tan S, Conaway RC. Mechanism of promoter escape by RNA polymerase II. Cold Spring Harbor Symposia On Quantitative Biology 1998, 63: 357-64. PMID: 10384300, DOI: 10.1101/sqb.1998.63.357.

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