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Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma.

Schubert AD, Channah Broner E, Agrawal N, London N, Pearson A, Gupta A, Wali N, Seiwert TY, Wheelan S, Lingen M, Macleod K, Allen H, Chatterjee A, Vassiliki S, Gaykalova D, Hoque MO, Sidransky D, Suresh K, Izumchenko E.

Cancer Lett. 2020 Feb 28;471:49-60. doi: 10.1016/j.canlet.2019.12.006. Epub 2019 Dec 10.


Immune profiles in primary squamous cell carcinoma of the head and neck.

Saloura V, Izumchenko E, Zuo Z, Bao R, Korzinkin M, Ozerov I, Zhavoronkov A, Sidransky D, Bedi A, Hoque MO, Koeppen H, Keck MK, Khattri A, London N, Kotlov N, Fatima A, Vougiouklakis T, Nakamura Y, Lingen M, Agrawal N, Savage PA, Kron S, Kline J, Kowanetz M, Seiwert TY.

Oral Oncol. 2019 Sep;96:77-88. doi: 10.1016/j.oraloncology.2019.06.032. Epub 2019 Jul 12.


Targeting Cancer Stem Cells: A Strategy for Effective Eradication of Cancer.

Shibata M, Hoque MO.

Cancers (Basel). 2019 May 27;11(5). pii: E732. doi: 10.3390/cancers11050732. Review.


GSTP1 as a Potential Marker of Early Chemotherapy Response for Noninvasive Detection.

Izumchenko E, Shavit Grievink L, Rosenbaum E, Hoque MO.

Eur Urol. 2019 Sep;76(3):313-314. doi: 10.1016/j.eururo.2018.12.026. Epub 2019 Jan 12. No abstract available.


Expression of programmed cell death ligand 1 in non-small cell lung cancer: Comparison between cytologic smears, core biopsies, and whole sections using the SP263 assay.

Munari E, Zamboni G, Sighele G, Marconi M, Sommaggio M, Lunardi G, Rossi G, Cavazza A, Moretta F, Gilioli E, Caliò A, Netto GJ, Hoque MO, Martignoni G, Brunelli M, Vacca P, Moretta L, Bogina G.

Cancer Cytopathol. 2019 Feb;127(1):52-61. doi: 10.1002/cncy.22083. Epub 2018 Nov 30.


Development of biomarkers for real precision medicine.

Shibata M, Hoque MO.

Transl Lung Cancer Res. 2018 Sep;7(Suppl 3):S228-S231. doi: 10.21037/tlcr.2018.08.07. No abstract available.


CD24 regulates cancer stem cell (CSC)-like traits and a panel of CSC-related molecules serves as a non-invasive urinary biomarker for the detection of bladder cancer.

Ooki A, VandenBussche CJ, Kates M, Hahn NM, Matoso A, McConkey DJ, Bivalacqua TJ, Hoque MO.

Br J Cancer. 2018 Oct;119(8):961-970. doi: 10.1038/s41416-018-0291-7. Epub 2018 Oct 17.


PD-L1 expression comparison between primary and relapsed non-small cell lung carcinoma using whole sections and clone SP263.

Munari E, Zamboni G, Lunardi G, Marconi M, Sommaggio M, Brunelli M, Martignoni G, Netto GJ, Hoque MO, Moretta F, Mingari MC, Pegoraro MC, Mariotti FR, Vacca P, Moretta L, Bogina G.

Oncotarget. 2018 Jul 13;9(54):30465-30471. doi: 10.18632/oncotarget.25770. eCollection 2018 Jul 13.


Epigenetically regulated PAX6 drives cancer cells toward a stem-like state via GLI-SOX2 signaling axis in lung adenocarcinoma.

Ooki A, Dinalankara W, Marchionni L, Tsay JJ, Goparaju C, Maleki Z, Rom WN, Pass HI, Hoque MO.

Oncogene. 2018 Nov;37(45):5967-5981. doi: 10.1038/s41388-018-0373-2. Epub 2018 Jul 6.


Integrated transcriptomic and epigenomic analysis of ovarian cancer reveals epigenetically silenced GULP1.

Maldonado L, Brait M, Izumchenko E, Begum S, Chatterjee A, Sen T, Loyo M, Barbosa A, Poeta ML, Makarev E, Zhavoronkov A, Fazio VM, Angioli R, Rabitti C, Ongenaert M, Van Criekinge W, Noordhuis MG, de Graeff P, Wisman GBA, van der Zee AGJ, Hoque MO.

Cancer Lett. 2018 Oct 1;433:242-251. doi: 10.1016/j.canlet.2018.06.030. Epub 2018 Jun 28.


PD-L1 Assays 22C3 and SP263 are Not Interchangeable in Non-Small Cell Lung Cancer When Considering Clinically Relevant Cutoffs: An Interclone Evaluation by Differently Trained Pathologists.

Munari E, Rossi G, Zamboni G, Lunardi G, Marconi M, Sommaggio M, Netto GJ, Hoque MO, Brunelli M, Martignoni G, Haffner MC, Moretta F, Pegoraro MC, Cavazza A, Samogin G, Furlan V, Mariotti FR, Vacca P, Moretta L, Bogina G.

Am J Surg Pathol. 2018 Oct;42(10):1384-1389. doi: 10.1097/PAS.0000000000001105.


PD-L1 Expression Heterogeneity in Non-Small Cell Lung Cancer: Defining Criteria for Harmonization between Biopsy Specimens and Whole Sections.

Munari E, Zamboni G, Lunardi G, Marchionni L, Marconi M, Sommaggio M, Brunelli M, Martignoni G, Netto GJ, Hoque MO, Moretta F, Mingari MC, Pegoraro MC, Inno A, Paiano S, Terzi A, Cavazza A, Rossi G, Mariotti FR, Vacca P, Moretta L, Bogina G.

J Thorac Oncol. 2018 Aug;13(8):1113-1120. doi: 10.1016/j.jtho.2018.04.017. Epub 2018 Apr 25. Erratum in: J Thorac Oncol. 2019 Apr;14(4):744.


A time for YAP1: Tumorigenesis, immunosuppression and targeted therapy.

Shibata M, Ham K, Hoque MO.

Int J Cancer. 2018 Nov 1;143(9):2133-2144. doi: 10.1002/ijc.31561. Epub 2018 Jul 24. Review.


Arsenic promotes the COX2/PGE2-SOX2 axis to increase the malignant stemness properties of urothelial cells.

Ooki A, Begum A, Marchionni L, VandenBussche CJ, Mao S, Kates M, Hoque MO.

Int J Cancer. 2018 Jul 1;143(1):113-126. doi: 10.1002/ijc.31290. Epub 2018 Feb 14.


YAP1 and COX2 Coordinately Regulate Urothelial Cancer Stem-like Cells.

Ooki A, Del Carmen Rodriguez Pena M, Marchionni L, Dinalankara W, Begum A, Hahn NM, VandenBussche CJ, Rasheed ZA, Mao S, Netto GJ, Sidransky D, Hoque MO.

Cancer Res. 2018 Jan 1;78(1):168-181. doi: 10.1158/0008-5472.CAN-17-0836. Epub 2017 Nov 27.


Patient-derived xenografts effectively capture responses to oncology therapy in a heterogeneous cohort of patients with solid tumors.

Izumchenko E, Paz K, Ciznadija D, Sloma I, Katz A, Vasquez-Dunddel D, Ben-Zvi I, Stebbing J, McGuire W, Harris W, Maki R, Gaya A, Bedi A, Zacharoulis S, Ravi R, Wexler LH, Hoque MO, Rodriguez-Galindo C, Pass H, Peled N, Davies A, Morris R, Hidalgo M, Sidransky D.

Ann Oncol. 2017 Oct 1;28(10):2595-2605. doi: 10.1093/annonc/mdx416.


A Panel of Novel Detection and Prognostic Methylated DNA Markers in Primary Non-Small Cell Lung Cancer and Serum DNA.

Ooki A, Maleki Z, Tsay JJ, Goparaju C, Brait M, Turaga N, Nam HS, Rom WN, Pass HI, Sidransky D, Guerrero-Preston R, Hoque MO.

Clin Cancer Res. 2017 Nov 15;23(22):7141-7152. doi: 10.1158/1078-0432.CCR-17-1222. Epub 2017 Aug 29.


MicroRNAs, promising biomarkers in the diagnosis of Xp11 translocation RCC-reply.

Marchionni L, Netto GJ, Hoque MO, Argani P.

Hum Pathol. 2017 Oct;68:206-207. doi: 10.1016/j.humpath.2017.06.021. Epub 2017 Aug 12. No abstract available.


Differences in the Molecular Characteristics of Bladder Cancer between Smokers and Nonsmokers.

Hoque MO.

Eur Urol Focus. 2018 Jan;4(1):98-99. doi: 10.1016/j.euf.2016.07.005. Epub 2016 Aug 27. No abstract available.


Mitochondria in chronic obstructive pulmonary disease and lung cancer: where are we now?

Nam HS, Izumchenko E, Dasgupta S, Hoque MO.

Biomark Med. 2017 May;11(6):475-489. doi: 10.2217/bmm-2016-0373. Epub 2017 Jun 9. Review.


Intravesical BCG Induces CD4+ T-Cell Expansion in an Immune Competent Model of Bladder Cancer.

Kates M, Nirschl T, Sopko NA, Matsui H, Kochel CM, Reis LO, Netto GJ, Hoque MO, Hahn NM, McConkey DJ, Baras AS, Drake CG, Bivalacqua TJ.

Cancer Immunol Res. 2017 Jul;5(7):594-603. doi: 10.1158/2326-6066.CIR-16-0267. Epub 2017 Jun 6.


In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia.

Makarev E, Schubert AD, Kanherkar RR, London N, Teka M, Ozerov I, Lezhnina K, Bedi A, Ravi R, Mehra R, Hoque MO, Sloma I, Gaykalova DA, Csoka AB, Sidransky D, Zhavoronkov A, Izumchenko E.

Cell Death Discov. 2017 May 22;3:17022. doi: 10.1038/cddiscovery.2017.22. eCollection 2017.


MicroRNA expression profiling of Xp11 renal cell carcinoma.

Marchionni L, Hayashi M, Guida E, Ooki A, Munari E, Jabboure FJ, Dinalankara W, Raza A, Netto GJ, Hoque MO, Argani P.

Hum Pathol. 2017 Sep;67:18-29. doi: 10.1016/j.humpath.2017.03.011. Epub 2017 Apr 12.


Expression of GULP1 in bronchial epithelium is associated with the progression of emphysema in chronic obstructive pulmonary disease.

Datta S, Nam HS, Hayashi M, Maldonado L, Goldberg R, Brait M, Sidransky D, Illei P, Baras A, Vij N, Hoque MO.

Respir Med. 2017 Mar;124:72-78. doi: 10.1016/j.rmed.2017.02.011. Epub 2017 Feb 17.


Promoter methylation of MCAM, ERα and ERβ in serum of early stage prostate cancer patients.

Brait M, Banerjee M, Maldonado L, Ooki A, Loyo M, Guida E, Izumchenko E, Mangold L, Humphreys E, Rosenbaum E, Partin A, Sidransky D, Hoque MO.

Oncotarget. 2017 Feb 28;8(9):15431-15440. doi: 10.18632/oncotarget.14873.


The ratio of CD8 to Treg tumor-infiltrating lymphocytes is associated with response to cisplatin-based neoadjuvant chemotherapy in patients with muscle invasive urothelial carcinoma of the bladder.

Baras AS, Drake C, Liu JJ, Gandhi N, Kates M, Hoque MO, Meeker A, Hahn N, Taube JM, Schoenberg MP, Netto G, Bivalacqua TJ.

Oncoimmunology. 2016 Feb 18;5(5):e1134412. doi: 10.1080/2162402X.2015.1134412. eCollection 2016 May.


High-performance detection of somatic D-loop mutation in urothelial cell carcinoma patients by polymorphism ratio sequencing.

Duberow DP, Brait M, Hoque MO, Theodorescu D, Sidransky D, Dasgupta S, Mathies RA.

J Mol Med (Berl). 2016 Sep;94(9):1015-24. doi: 10.1007/s00109-016-1407-2. Epub 2016 Mar 31.


Patient-derived xenografts as tools in pharmaceutical development.

Izumchenko E, Meir J, Bedi A, Wysocki PT, Hoque MO, Sidransky D.

Clin Pharmacol Ther. 2016 Jun;99(6):612-21. doi: 10.1002/cpt.354. Epub 2016 Mar 9. Review.


Correction: Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma.

Baras AS, Gandhi N, Munari E, Faraj S, Shultz L, Marchionni L, Schoenberg M, Hahn N, Hoque MO, Berman D, Bivalacqua TJ, Netto G.

PLoS One. 2015 Nov 24;10(11):e0143990. doi: 10.1371/journal.pone.0143990. eCollection 2015. No abstract available.


Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA.

Izumchenko E, Chang X, Brait M, Fertig E, Kagohara LT, Bedi A, Marchionni L, Agrawal N, Ravi R, Jones S, Hoque MO, Westra WH, Sidransky D.

Nat Commun. 2015 Sep 16;6:8258. doi: 10.1038/ncomms9258.


An integrated genome-wide approach to discover deregulated microRNAs in non-small cell lung cancer: Clinical significance of miR-23b-3p deregulation.

Begum S, Hayashi M, Ogawa T, Jabboure FJ, Brait M, Izumchenko E, Tabak S, Ahrendt SA, Westra WH, Koch W, Sidransky D, Hoque MO.

Sci Rep. 2015 Aug 28;5:13236. doi: 10.1038/srep13236.


Identification and Validation of Protein Biomarkers of Response to Neoadjuvant Platinum Chemotherapy in Muscle Invasive Urothelial Carcinoma.

Baras AS, Gandhi N, Munari E, Faraj S, Shultz L, Marchionni L, Schoenberg M, Hahn N, Hoque MO, Berman D, Bivalacqua TJ, Netto G.

PLoS One. 2015 Jul 31;10(7):e0131245. doi: 10.1371/journal.pone.0131245. eCollection 2015. Erratum in: PLoS One. 2015;10(11):e0143990. Hoque, Mohammad [corrected to Hoque, Mohammad Obaidul].


Epigenetic silencing of S100A2 in bladder and head and neck cancers.

Lee J, Wysocki PT, Topaloglu O, Maldonado L, Brait M, Begum S, Moon D, Kim MS, Califano JA, Sidransky D, Hoque MO, Moon C.

Oncoscience. 2015 Mar 16;2(4):410-8. eCollection 2015.


Gemcitabine and cisplatin neoadjuvant chemotherapy for muscle-invasive urothelial carcinoma: Predicting response and assessing outcomes.

Gandhi NM, Baras A, Munari E, Faraj S, Reis LO, Liu JJ, Kates M, Hoque MO, Berman D, Hahn NM, Eisenberger M, Netto GJ, Schoenberg MP, Bivalacqua TJ.

Urol Oncol. 2015 May;33(5):204.e1-7. doi: 10.1016/j.urolonc.2015.02.011. Epub 2015 Mar 23.


Involvement of epigenetics and EMT-related miRNA in arsenic-induced neoplastic transformation and their potential clinical use.

Michailidi C, Hayashi M, Datta S, Sen T, Zenner K, Oladeru O, Brait M, Izumchenko E, Baras A, VandenBussche C, Argos M, Bivalacqua TJ, Ahsan H, Hahn NM, Netto GJ, Sidransky D, Hoque MO.

Cancer Prev Res (Phila). 2015 Mar;8(3):208-21. doi: 10.1158/1940-6207.CAPR-14-0251. Epub 2015 Jan 13.


Cyclin A1 expression predicts progression in pT1 urothelial carcinoma of bladder: a tissue microarray study of 149 patients treated by transurethral resection.

Munari E, Chaux A, Maldonado L, Compérat E, Varinot J, Bivalacqua TJ, Hoque MO, Netto GJ.

Histopathology. 2015 Jan;66(2):262-9. doi: 10.1111/his.12499. Epub 2015 Jan 7.


An epigenetic marker panel for recurrence risk prediction of low grade papillary urothelial cell carcinoma (LGPUCC) and its potential use for surveillance after transurethral resection using urine.

Maldonado L, Brait M, Michailidi C, Munari E, Driscoll T, Schultz L, Bivalacqua T, Schoenberg M, Sidransky D, Netto GJ, Hoque MO.

Oncotarget. 2014 Jul 30;5(14):5218-33.


Epigenetic inactivation of VGF associated with Urothelial Cell Carcinoma and its potential as a non-invasive biomarker using urine.

Hayashi M, Bernert H, Kagohara LT, Maldonado L, Brait M, Schoenberg M, Bivalacqua T, Netto GJ, Koch W, Sidransky D, Hoque MO.

Oncotarget. 2014 May 30;5(10):3350-61.


The TGFβ-miR200-MIG6 pathway orchestrates the EMT-associated kinase switch that induces resistance to EGFR inhibitors.

Izumchenko E, Chang X, Michailidi C, Kagohara L, Ravi R, Paz K, Brait M, Hoque MO, Ling S, Bedi A, Sidransky D.

Cancer Res. 2014 Jul 15;74(14):3995-4005. doi: 10.1158/0008-5472.CAN-14-0110. Epub 2014 May 15. Erratum in: Cancer Res. 2014 Sep 1;74(17):4950-1.


GSTP1 promoter methylation is associated with recurrence in early stage prostate cancer.

Maldonado L, Brait M, Loyo M, Sullenberger L, Wang K, Peskoe SB, Rosenbaum E, Howard R, Toubaji A, Albadine R, Netto GJ, Hoque MO, Platz EA, Sidransky D.

J Urol. 2014 Nov;192(5):1542-8. doi: 10.1016/j.juro.2014.04.082. Epub 2014 Apr 21.


Clear cell papillary renal cell carcinoma: micro-RNA expression profiling and comparison with clear cell renal cell carcinoma and papillary renal cell carcinoma.

Munari E, Marchionni L, Chitre A, Hayashi M, Martignoni G, Brunelli M, Gobbo S, Argani P, Allaf M, Hoque MO, Netto GJ.

Hum Pathol. 2014 Jun;45(6):1130-8. doi: 10.1016/j.humpath.2014.01.013. Epub 2014 Jan 31.


Association of promoter methylation of VGF and PGP9.5 with ovarian cancer progression.

Brait M, Maldonado L, Noordhuis MG, Begum S, Loyo M, Poeta ML, Barbosa A, Fazio VM, Angioli R, Rabitti C, Marchionni L, de Graeff P, van der Zee AG, Wisman GB, Sidransky D, Hoque MO.

PLoS One. 2013 Sep 27;8(9):e70878. doi: 10.1371/journal.pone.0070878. eCollection 2013. Erratum in: PLoS One. 2013;8(10). doi:10.1371/annotation/5d2e13d4-cb4e-44b1-a836-dff9b4144b5b. Noordhuis, Maartje [corrected to Noordhuis, Maartje G]. PLoS One. 2013;8(10). doi:10.1371/annotation/ccd51e37-fdf3-466e-b79f-2c390df9ab28.


Hypermethylation of genes detected in urine from Ghanaian adults with bladder pathology associated with Schistosoma haematobium infection.

Zhong X, Isharwal S, Naples JM, Shiff C, Veltri RW, Shao C, Bosompem KM, Sidransky D, Hoque MO.

PLoS One. 2013;8(3):e59089. doi: 10.1371/journal.pone.0059089. Epub 2013 Mar 18.


Cigarette smoke induces methylation of the tumor suppressor gene NISCH.

Ostrow KL, Michailidi C, Guerrero-Preston R, Hoque MO, Greenberg A, Rom W, Sidransky D.

Epigenetics. 2013 Apr;8(4):383-8. doi: 10.4161/epi.24195. Epub 2013 Mar 15.


Genome-wide methylation profiling and the PI3K-AKT pathway analysis associated with smoking in urothelial cell carcinoma.

Brait M, Munari E, LeBron C, Noordhuis MG, Begum S, Michailidi C, Gonzalez-Roibon N, Maldonado L, Sen T, Guerrero-Preston R, Cope L, Parrella P, Fazio VM, Ha PK, Netto GJ, Sidransky D, Hoque MO.

Cell Cycle. 2013 Apr 1;12(7):1058-70. doi: 10.4161/cc.24050. Epub 2013 Feb 22.


OGDHL is a modifier of AKT-dependent signaling and NF-κB function.

Sen T, Sen N, Noordhuis MG, Ravi R, Wu TC, Ha PK, Sidransky D, Hoque MO.

PLoS One. 2012;7(11):e48770. doi: 10.1371/journal.pone.0048770. Epub 2012 Nov 12.


SH3GL2 is frequently deleted in non-small cell lung cancer and downregulates tumor growth by modulating EGFR signaling.

Dasgupta S, Jang JS, Shao C, Mukhopadhyay ND, Sokhi UK, Das SK, Brait M, Talbot C, Yung RC, Begum S, Westra WH, Hoque MO, Yang P, Yi JE, Lam S, Gazdar AF, Fisher PB, Jen J, Sidransky D.

J Mol Med (Berl). 2013 Mar;91(3):381-93. doi: 10.1007/s00109-012-0955-3. Epub 2012 Sep 12.


A single nucleotide polymorphism in the human PIGK gene associates with low PIGK expression in colorectal cancer patients.

Dasgupta S, Pal P, Mukhopadhyay ND, Fu Y, Ratovitski EA, Moon CS, Hoque MO, Fisher PB, Trink B.

Int J Oncol. 2012 Oct;41(4):1405-10. doi: 10.3892/ijo.2012.1567. Epub 2012 Jul 23.


Correlation between BRAF mutation and promoter methylation of TIMP3, RARβ2 and RASSF1A in thyroid cancer.

Brait M, Loyo M, Rosenbaum E, Ostrow KL, Markova A, Papagerakis S, Zahurak M, Goodman SM, Zeiger M, Sidransky D, Umbricht CB, Hoque MO.

Epigenetics. 2012 Jul;7(7):710-9. doi: 10.4161/epi.20524. Epub 2012 Jul 1.


AIM1 promoter hypermethylation as a predictor of decreased risk of recurrence following radical prostatectomy.

Rosenbaum E, Begum S, Brait M, Zahurak M, Maldonado L, Mangold LA, Eisenberger MA, Epstein JI, Partin AW, Sidransky D, Hoque MO.

Prostate. 2012 Jul 1;72(10):1133-9. doi: 10.1002/pros.22461. Epub 2011 Nov 29.

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