Ash A. Alizadeh, MD/PhD

Publications

• Association of a leukemic stem cell gene expression signature with clinical outcomes in acute myeloid leukemia. Gentles AJ, Plevritis SK, Majeti R, Alizadeh AA. JAMA. 2010; 304 (24): 2706-15
• Therapeutic Antibody Targeting of CD47 Synergizes with Rituximab to Completely Eradicate Human B-Cell Lymphoma Chao MP*, Alizadeh AA* (contributed equally), Tang CZ, Mykebust JH, Varghese B, Jan M, Levy R, Weissman IL, Majeti R.. Cell. 2010; 142 (5): 699-713
• CD47 is an adverse prognostic factor and therapeutic antibody target on human acute myeloid leukemia stem cells. Majeti R, Chao MP, Alizadeh AA, Pang WW, Jaiswal S, Gibbs KD, van Rooijen N, Weissman IL. Cell. 2009; 138 (2): 286-99
• Molecular outcome prediction in diffuse large-B-cell lymphoma. Alizadeh AA, Gentles AJ, Lossos IS, Levy R. N Engl J Med. 2009; 360 (26): 2794-5
• SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. Diehn M, Sherlock G, Binkley G, Jin H, Matese JC, Hernandez-Boussard T, Rees CA, Cherry JM, Botstein D, Brown PO, Alizadeh AA. Nucleic Acids Res. 2003; 31 (1): 219-23
• Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Levy R, Wilson W, Grever MR, Byrd JC, Botstein D, Brown PO, Staudt LM. Nature. 2000; 403 (6769): 503-11
• The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Alizadeh A, Eisen M, Davis RE, Ma C, Sabet H, Tran T, Powell JI, Yang L, Marti GE, Moore DT, Hudson JR, Chan WC, Greiner T, Weisenburger D, Armitage JO, Lossos I, Levy R, Botstein D, Brown PO, Staudt LM. Cold Spring Harb Symp Quant Biol. 1999: 64 71-8
• Germinal centre protein HGAL promotes lymphoid hyperplasia and amyloidosis via BCR-mediated Syk activation. Romero-Camarero I, Jiang X, Natkunam Y, Lu X, Vicente-Dueñas C, Gonzalez-Herrero I, Flores T, Garcia JL, McNamara G, Kunder C, Zhao S, Segura V, Fontan L, Martínez-Climent JA, García-Criado FJ, Theis JD, Dogan A, Campos-Sánchez E, Green MR, Alizadeh AA, Cobaleda C, Sánchez-García I, Lossos IS. Nat Commun. 2013: 4 1338
• Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Green MR, Gentles AJ, Nair RV, Irish JM, Kihira S, Liu CL, Kela I, Hopmans ES, Myklebust JH, Ji H, Plevritis SK, Levy R, Alizadeh AA. Blood. 2013; 121 (9): 1604-11
• High PD-1 expression and suppressed cytokine signaling distinguish T cells infiltrating follicular lymphoma tumors from peripheral T cells. Myklebust JH, Irish JM, Brody J, Czerwinski DK, Houot R, Kohrt HE, Timmerman J, Said J, Green MR, Delabie J, Kolstad A, Alizadeh AA, Levy R. Blood. 2013; 121 (8): 1367-76
• Rituximab use and survival after diffuse large B-cell or follicular lymphoma: a population-based study. Keegan TH, Moy LM, Foran JM, Alizadeh AA, Chang ET, Shema SJ, Schupp CW, Clarke CA, Glaser SL. Leuk Lymphoma. 2013; 54 (4): 743-51
• Utility in prognostic value added by molecular profiles for diffuse large B-cell lymphoma. Gentles AJ, Alizadeh AA. Blood. 2013; 121 (15): 3052-4
• A retrospective study evaluating the efficacy and safety of bendamustine in the treatment of mantle cell lymphoma. Warsch S, Hosein PJ, Maeda LS, Alizadeh AA, Lossos IS. Leuk Lymphoma. 2012; 53 (7): 1299-305
• CD137 is expressed in follicular dendritic cell tumors and in classical Hodgkin and T-cell lymphomas: diagnostic and therapeutic implications. Anderson MW, Zhao S, Freud AG, Czerwinski DK, Kohrt H, Alizadeh AA, Houot R, Azambuja D, Biasoli I, Morais JC, Spector N, Molina-Kirsch HF, Warnke RA, Levy R, Natkunam Y. Am J Pathol. 2012; 181 (3): 795-803
• Correction: Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies. Liu CL, Tangsombatvisit S, Rosenberg JM, Mandelbaum G, Gillespie EC, Gozani OP, Alizadeh AA, Utz PJ. Arthritis Res Ther. 2012; 14 (4): 403
• First isolation of Cryptococcus uzbekistanensis from an immunocompromised patient with Lymphoma. Powel MS, Alizadeh AA, Budvytiene I, Schaenman JM, Banaei N. J Clin Microbiol. 2012; 50 (3): 1125-7
• Role of Smad proteins in resistance to BMP-induced growth inhibition in B-cell lymphoma. Huse K, Bakkebø M, Wälchli S, Oksvold MP, Hilden VI, Forfang L, Bredahl ML, Liestøl K, Alizadeh AA, Smeland EB, Myklebust JH. PLoS One. 2012; 7 (10): e46117
• Self-antigen recognition by follicular lymphoma B-cell receptors. Sachen KL, Strohman MJ, Singletary J, Alizadeh AA, Kattah NH, Lossos C, Mellins ED, Levy S, Levy R. Blood. 2012; 120 (20): 4182-90
• Specific post-translational histone modifications of neutrophil extracellular traps as immunogens and potential targets of lupus autoantibodies. Liu CL, Tangsombatvisit S, Rosenberg JM, Mandelbaum G, Gillespie EC, Gozani OP, Alizadeh AA, Utz PJ. Arthritis Res Ther. 2012; 14 (1): R25
• The CD47-signal regulatory protein alpha (SIRPa) interaction is a therapeutic target for human solid tumors. Willingham SB, Volkmer JP, Gentles AJ, Sahoo D, Dalerba P, Mitra SS, Wang J, Contreras-Trujillo H, Martin R, Cohen JD, Lovelace P, Scheeren FA, Chao MP, Weiskopf K, Tang C, Volkmer AK, Naik TJ, Storm TA, Mosley AR, Edris B, Schmid SM, Sun CK, Chua MS, Murillo O, Rajendran P, Cha AC, Chin RK, Kim D, Adorno M, Raveh T, Tseng D, Jaiswal S, Enger PØ, Steinberg GK, Li G, So SK, Majeti R, Harsh GR, van de Rijn M, Teng NN, Sunwoo JB, Alizadeh AA, Clarke MF, Weissman IL. Proc Natl Acad Sci U S A. 2012; 109 (17): 6662-7
• The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses. Pachynski RK, Zabel BA, Kohrt HE, Tejeda NM, Monnier J, Swanson CD, Holzer AK, Gentles AJ, Sperinde GV, Edalati A, Hadeiba HA, Alizadeh AA, Butcher EC. J Exp Med. 2012; 209 (8): 1427-35
• Three differentiation states risk-stratify bladder cancer into distinct subtypes. Volkmer JP, Sahoo D, Chin RK, Ho PL, Tang C, Kurtova AV, Willingham SB, Pazhanisamy SK, Contreras-Trujillo H, Storm TA, Lotan Y, Beck AH, Chung BI, Alizadeh AA, Godoy G, Lerner SP, van de Rijn M, Shortliffe LD, Weissman IL, Chan KS. Proc Natl Acad Sci U S A. 2012; 109 (6): 2078-83
• Treatment advances have not improved the early death rate in acute promyelocytic leukemia. McClellan JS, Kohrt HE, Coutre S, Gotlib JR, Majeti R, Alizadeh AA, Medeiros BC. Haematologica. 2012; 97 (1): 133-6
• A few good genes: simple, biologically motivated signatures for cancer prognosis. Gentles AJ, Alizadeh AA. Cell Cycle. 2011; 10 (21): 3615-6
• A proteomic approach for the identification of novel lysine methyltransferase substrates. Levy D, Liu CL, Yang Z, Newman AM, Alizadeh AA, Utz PJ, Gozani O. Epigenetics Chromatin. 2011: 4 19
• CD137 stimulation enhances the antilymphoma activity of anti-CD20 antibodies. Kohrt HE, Houot R, Goldstein MJ, Weiskopf K, Alizadeh AA, Brody J, Müller A, Pachynski R, Czerwinski D, Coutre S, Chao MP, Chen L, Tedder TF, Levy R. Blood. 2011; 117 (8): 2423-32
• Impact of TET2 mutations on mRNA expression and clinical outcomes in MDS patients treated with DNA methyltransferase inhibitors. Pollyea DA, Raval A, Kusler B, Gotlib JR, Alizadeh AA, Mitchell BS. Hematol Oncol. 2011; 29 (3): 157-60
• Prediction of survival in diffuse large B-cell lymphoma based on the expression of 2 genes reflecting tumor and microenvironment. Alizadeh AA, Gentles AJ, Alencar AJ, Liu CL, Kohrt HE, Houot R, Goldstein MJ, Zhao S, Natkunam Y, Advani RH, Gascoyne RD, Briones J, Tibshirani RJ, Myklebust JH, Plevritis SK, Lossos IS, Levy R. Blood. 2011; 118 (5): 1350-8
• Prospective separation of normal and leukemic stem cells based on differential expression of TIM3, a human acute myeloid leukemia stem cell marker. Jan M, Chao MP, Cha AC, Alizadeh AA, Gentles AJ, Weissman IL, Majeti R. Proc Natl Acad Sci U S A. 2011; 108 (12): 5009-14
• Surprise! HSC are aberrant in chronic lymphocytic leukemia. Alizadeh AA, Majeti R. Cancer Cell. 2011; 20 (2): 135-6
• Therapeutic antibody targeting of CD47 eliminates human acute lymphoblastic leukemia. Chao MP, Alizadeh AA, Tang C, Jan M, Weissman-Tsukamoto R, Zhao F, Park CY, Weissman IL, Majeti R. Cancer Res. 2011; 71 (4): 1374-84
• Utility of positron emission tomography scans in mantle cell lymphoma. Hosein PJ, Pastorini VH, Paes FM, Eber D, Chapman JR, Serafini AN, Alizadeh AA, Lossos IS. Am J Hematol. 2011; 86 (10): 841-5
• B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression. Irish JM, Myklebust JH, Alizadeh AA, Houot R, Sharman JP, Czerwinski DK, Nolan GP, Levy R. Proc Natl Acad Sci U S A. 2010; 107 (29): 12747-54
• Calreticulin is the dominant pro-phagocytic signal on multiple human cancers and is counterbalanced by CD47. Chao MP, Jaiswal S, Weissman-Tsukamoto R, Alizadeh AA, Gentles AJ, Volkmer J, Weiskopf K, Willingham SB, Raveh T, Park CY, Majeti R, Weissman IL. Sci Transl Med. 2010; 2 (63): 63ra94
• Expression profiles of adult T-cell leukemia-lymphoma and associations with clinical responses to zidovudine and interferon alpha. Alizadeh AA, Bohen SP, Lossos C, Martinez-Climent JA, Ramos JC, Cubedo-Gil E, Harrington WJ, Lossos IS. Leuk Lymphoma. 2010; 51 (7): 1200-16
• Immunophenotypic features of acute myeloid leukemia with inv(3)(q21q26.2)/t(3;3)(q21;q26.2). Medeiros BC, Kohrt HE, Arber DA, Bangs CD, Cherry AM, Majeti R, Kogel KE, Azar CA, Patel S, Alizadeh AA. Leuk Res. 2010; 34 (5): 594-7
• Is Time of the Essence in Adult Acute Myeloid Leukemia (AML)? Time to Blast Clearance and Time to Induction Therapy Fail to Predict Overall Survival (OS) Kohrt HE, Patel S, Ho M, Owen T, Majeti R, Gotlib JR, Coutre SE, Medeiros BC, Alizadeh AA.. Blood (e-Letter). 2010; 113 (1): 28-36
• Second-line mitoxantrone, etoposide, and cytarabine for acute myeloid leukemia: a single-center experience. Kohrt HE, Patel S, Ho M, Owen T, Pollyea DA, Majeti R, Gotlib J, Coutre S, Liedtke M, Berube C, Alizadeh AA, Medeiros BC. Am J Hematol. 2010; 85 (11): 877-81
• A pluripotency signature predicts histological transformation and influences survival in follicular lymphoma patients Gentles AJ**, Alizadeh AA** (contributed equally), Lee S, Myklebust JH, Shachaf CM, Shahbaba B, Levy R, Koller D, Plevritis SK.. Blood. 2009
• Therapeutic effect of CD137 immunomodulation in lymphoma and its enhancement by Treg depletion. Houot R, Goldstein MJ, Kohrt HE, Myklebust JH, Alizadeh AA, Lin JT, Irish JM, Torchia JA, Kolstad A, Chen L, Levy R. Blood. 2009; 114 (16): 3431-8
• Double trouble in follicular lymphoma: A rare and unusual synergy of oncogenes in the germinal center. Alizadeh AA, Lossos IS. Leuk Lymphoma. 2008; 49 (3): 377-80
• Evaluation and management of angioimmunoblastic T-cell lymphoma: a review of current approaches and future strategies. Alizadeh AA, Advani RH. Clin Adv Hematol Oncol. 2008; 6 (12): 899-909
• Diagnosis of a critical respiratory illness caused by human metapneumovirus by use of a pan-virus microarray. Chiu CY, Alizadeh AA, Rouskin S, Merker JD, Yeh E, Yagi S, Schnurr D, Patterson BK, Ganem D, DeRisi JL. J Clin Microbiol. 2007; 45 (7): 2340-3
• Cell-type specific gene expression profiles of leukocytes in human peripheral blood. Palmer C, Diehn M, Alizadeh AA, Brown PO. BMC Genomics. 2006: 7 115
• Distinct IL-4-induced gene expression, proliferation, and intracellular signaling in germinal center B-cell-like and activated B-cell-like diffuse large-cell lymphomas. Lu X, Nechushtan H, Ding F, Rosado MF, Singal R, Alizadeh AA, Lossos IS. Blood. 2005; 105 (7): 2924-32
• AID is expressed in germinal center B-cell-like and activated B-cell-like diffuse large-cell lymphomas and is not correlated with intraclonal heterogeneity. Lossos IS, Levy R, Alizadeh AA. Leukemia. 2004; 18 (11): 1775-9
• Fludarabine treatment of patients with chronic lymphocytic leukemia induces a p53-dependent gene expression response. Rosenwald A, Chuang EY, Davis RE, Wiestner A, Alizadeh AA, Arthur DC, Mitchell JB, Marti GE, Fowler DH, Wilson WH, Staudt LM. Blood. 2004; 104 (5): 1428-34
• Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. Chang HY, Sneddon JB, Alizadeh AA, Sood R, West RB, Montgomery K, Chi JT, van de Rijn M, Botstein D, Brown PO. PLoS Biol. 2004; 2 (2): E7
• Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. Lossos IS, Czerwinski DK, Alizadeh AA, Wechser MA, Tibshirani R, Botstein D, Levy R. N Engl J Med. 2004; 350 (18): 1828-37
• Role of interleukin 6 in myocardial dysfunction of meningococcal septic shock. Pathan N, Hemingway CA, Alizadeh AA, Stephens AC, Boldrick JC, Oragui EE, McCabe C, Welch SB, Whitney A, O'Gara P, Nadel S, Relman DA, Harding SE, Levin M. Lancet. 2004; 363 (9404): 203-9
• HGAL is a novel interleukin-4-inducible gene that strongly predicts survival in diffuse large B-cell lymphoma. Lossos IS, Alizadeh AA, Rajapaksa R, Tibshirani R, Levy R. Blood. 2003; 101 (2): 433-40
• Individuality and variation in gene expression patterns in human blood. Whitney AR, Diehn M, Popper SJ, Alizadeh AA, Boldrick JC, Relman DA, Brown PO. Proc Natl Acad Sci U S A. 2003; 100 (4): 1896-901
• Molecular heterogeneity in acute renal allograft rejection identified by DNA microarray profiling Sarwal M, Chen X, Chua MS, Kambham N, Hsieh SC, Satterwhite T, Alizadeh AA, Masek M, Diehn, M, Salvatierra O Jr, Brown PO. N Engl J Med. 2003; 349 (2): 125-38
• Rheumatoid arthritis is a heterogeneous disease: evidence for differences in the activation of the STAT-1 pathway between rheumatoid tissues. van der Pouw Kraan TC, van Gaalen FA, Kasperkovitz PV, Verbeet NL, Smeets TJ, Kraan MC, Fero M, Tak PP, Huizinga TW, Pieterman E, Breedveld FC, Alizadeh AA, Verweij CL. Arthritis Rheum. 2003; 48 (8): 2132-45
• T cell receptor-independent basal signaling via Erk and Abl kinases suppresses RAG gene expression. Roose JP, Diehn M, Tomlinson MG, Lin J, Alizadeh AA, Botstein D, Brown PO, Weiss A. PLoS Biol. 2003; 1 (2): E53
• Transformation of follicular lymphoma to diffuse large cell lymphoma is associated with a heterogeneous set of DNA copy number and gene expression alterations. Martinez-Climent JA, Alizadeh AA, Segraves R, Blesa D, Rubio-Moscardo F, Albertson DG, Garcia-Conde J, Dyer MJ, Levy R, Pinkel D, Lossos IS. Blood. 2003; 101 (8): 3109-17
• Genomic expression programs and the integration of the CD28 costimulatory signal in T cell activation. Diehn M, Alizadeh AA, Rando OJ, Liu CL, Stankunas K, Botstein D, Crabtree GR, Brown PO. Proc Natl Acad Sci U S A. 2002; 99 (18): 11796-801
• In vivo regulation of human skeletal muscle gene expression by thyroid hormone. Clément K, Viguerie N, Diehn M, Alizadeh A, Barbe P, Thalamas C, Storey JD, Brown PO, Barsh GS, Langin D. Genome Res. 2002; 12 (2): 281-91
• Software tools for high-throughput analysis and archiving of immunohistochemistry staining data obtained with tissue microarrays. Liu CL, Prapong W, Natkunam Y, Alizadeh A, Montgomery K, Gilks CB, van de Rijn M. Am J Pathol. 2002; 161 (5): 1557-65
• Stereotyped and specific gene expression programs in human innate immune responses to bacteria. Boldrick JC, Alizadeh AA, Diehn M, Dudoit S, Liu CL, Belcher CE, Botstein D, Staudt LM, Brown PO, Relman DA. Proc Natl Acad Sci U S A. 2002; 99 (2): 972-7
• The t(14;18) defines a unique subset of diffuse large B-cell lymphoma with a germinal center B-cell gene expression profile. Huang JZ, Sanger WG, Greiner TC, Staudt LM, Weisenburger DD, Pickering DL, Lynch JC, Armitage JO, Warnke RA, Alizadeh AA, Lossos IS, Levy R, Chan WC. Blood. 2002; 99 (7): 2285-90
• Transformation of follicular lymphoma to diffuse large-cell lymphoma: alternative patterns with increased or decreased expression of c-myc and its regulated genes. Lossos IS, Alizadeh AA, Diehn M, Warnke R, Thorstenson Y, Oefner PJ, Brown PO, Botstein D, Levy R. Proc Natl Acad Sci U S A. 2002; 99 (13): 8886-91
• Genomic analysis of renal allograft dysfunction using cDNA microarrays. Sarwal M, Chang S, Barry C, Chen X, Alizadeh A, Salvatierra O, Brown P. Transplant Proc. 2001 Feb-Mar; 33 (1-2): 297-8
• Relation of gene expression phenotype to immunoglobulin mutation genotype in B cell chronic lymphocytic leukemia. Rosenwald A, Alizadeh AA, Widhopf G, Simon R, Davis RE, Yu X, Yang L, Pickeral OK, Rassenti LZ, Powell J, Botstein D, Byrd JC, Grever MR, Cheson BD, Chiorazzi N, Wilson WH, Kipps TJ, Brown PO, Staudt LM. J Exp Med. 2001; 194 (11): 1639-47
• Towards a novel classification of human malignancies based on gene expression patterns. Alizadeh AA, Ross DT, Perou CM, van de Rijn M. J Pathol. 2001; 195 (1): 41-52
• 'Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns. Hastie T, Tibshirani R, Eisen MB, Alizadeh A, Levy R, Staudt L, Chan WC, Botstein D, Brown P. Genome Biol. 2000; 1 (2): RESEARCH0003
• Examining the living genome in health and disease with DNA microarrays. Diehn M, Alizadeh AA, Brown PO. JAMA. 2000; 283 (17): 2298-9
• Genomic-scale gene expression profiling of normal and malignant immune cells. Alizadeh AA, Staudt LM. Curr Opin Immunol. 2000; 12 (2): 219-25
• Ongoing immunoglobulin somatic mutation in germinal center B cell-like but not in activated B cell-like diffuse large cell lymphomas. Lossos IS, Alizadeh AA, Eisen MB, Chan WC, Brown PO, Botstein D, Staudt LM, Levy R. Proc Natl Acad Sci U S A. 2000; 97 (18): 10209-13
• Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Pollack JR, Perou CM, Alizadeh AA, Eisen MB, Pergamenschikov A, Williams CF, Jeffrey SS, Botstein D, Brown PO. Nat Genet. 1999; 23 (1): 41-6
• Probing lymphocyte biology by genomic-scale gene expression analysis. Alizadeh A, Eisen M, Botstein D, Brown PO, Staudt LM. J Clin Immunol. 1998; 18 (6): 373-9