US 20140148354A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2014/0148354 A1 Campana et al. (43) Pub. Date: May 29, 2014 (54) METHODS AND COMPOSITIONS FOR Publication Classification IDENTIFYING MINIMIAL RESIDUAL DISEASE IN ACUTELYMPHOBLASTIC (51) Int. Cl. LEUKEMA CI2O I/68 (2006.01) (75) Inventors: Dario Campana, Kent Vale (SG); (52) U.S. Cl. Elaine Coustan-Smith, Kent Vale (SG) CPC .................................... CI2O I/6886 (2013.01) (73) Assignee: ST. JUDE CHILDREN'S RESEARCH USPC .............................................. 506/9; 435/7.21 HOSPITAL, Memphis, TN (US) (21) Appl. No.: 14/005,921 (57) ABSTRACT (22) PCT Filed: Mar. 14, 2012 (86). PCT No.: PCT/US12/28993 This invention provides methods and kits for diagnosing, ascertaining the clinical course of minimal residual disease S371 (c)(1), associated with acute lymphoblastic leukemia (ALL). Spe (2), (4) Date: Oct. 2, 2013 cifically the invention provides methods and kits useful in the Related U.S. Application Data diagnosis and determination of clinical parameters associated (60) Provisional application No. 61/470,056, filed on Mar. with diseases associated with ALL based on patterns of Sur 31, 2011. face marker expression unique to ALL. Patent Application Publication May 29, 2014 Sheet 1 of 6 US 2014/0148354 A1 PCO.0001 P40.001 1 OOO BCL2 HSPB 1 CD304 CD164 CD73 CD3OOA CD200 P&O.01 1000 N - N - N L. N. L. N. L. CD72 CD130 CD37 CD86 CD97 CD123 FIGURE 1 Patent Application Publication May 29, 2014 Sheet 2 of 6 US 2014/O148354 A1 10000 1OOO 1OOO L N. L. N. L N EPOR (CD69 CD 132 CD83 CD120 L13RA CD62L FIGURE 2 Patent Application Publication May 29, 2014 Sheet 3 of 6 US 2014/O148354 A1 O.O1 0.1 1 10 Flow Cytometry (%) FIGURE 3 Patent Application Publication May 29, 2014 Sheet 4 of 6 US 2014/0148354 A1 Pt. 2 500 BC2 O HSPB1 HSPB 400 KX CD200 CD86 300 {0 CD123 CD200 i CD97 CD102 200 : CD99 O O 19 42 O 19 42 Days from diagnosis Days from diagnosis Pt. 3 Pt. 4 300 500 CD123 {d CD123 CD300A 400 O CD97 200 300 t 200 100 100 O 19 42 O 19 42 Days from diagnosis Days from diagnosis FIGURE 4 Patent Application Publication May 29, 2014 Sheet 5 of 6 US 2014/O148354 A1 S S. S. S. O O i Hyperdiploid ETV6-RUNX1 TCF3-PBX1 BCR-ABL1. MLL Other b 20 4o 60 80 150 % of cases with differential expression FIGURE 5 Patent Application Publication May 29, 2014 Sheet 6 of 6 US 2014/O148354 A1 MRD = 0.01% CD86 CD97 CD38 CD97 CD38 CD86 CD97 CD38 FIGURE 6 US 2014/0148354 A1 May 29, 2014 METHODS AND COMPOSITIONS FOR 116:1165-1176). MRD measurements are also clinically use IDENTIFYING MINIMIAL RESIDUAL ful in patients with relapsed ALL who achieve a second DISEASE IN ACUTELYMPHOBLASTIC remission (Coustan-Smith et al. (2004) Leukemia 18:499 LEUKEMA 504; Paganinet al. (2008) Leukemia. 22:2193-2200; Raetz et al. (2008) J Clin. Oncol. 26:3971-3978), can help optimize STATEMENT REGARDING FEDERALLY the timing of hematopoietic stem cell transplantation (Bader SPONSORED RESEARCH ORDEVELOPMENT et al. (2009).J Clin Oncol. 27:377-384), and guide decisions 0001. This invention was made with support under United about donor lymphocyte infusion post-transplant (Lankester et al. (2010) Leukemia. 24: 1462-1469). States Government Grant CA60419 awarded by the National 0007. Among methods for detecting MRD in ALL, PCR Institutes of Health. The United States Government has cer amplification of antigen-receptor genes has proven to be valu tain rights in this invention. able and has been extensively standardized (Bruggemann, REFERENCE TO SEQUENCE LISTING M., et al. (2010) Leukemia. 24:521-535) but the technical SUBMITTED ELECTRONICALLY expertise and instrumentation required limit its application to specialized centers. PCR amplification of fusion transcripts 0002 The official copy of the sequence listing is submitted may also provide useful clinical information but its applica electronically via EFS-Web as an ASCII formatted sequence bility in ALL is restricted by the fact that molecular targets listing with a file named 415313SEQLIST.txt, created on currently adaptable to routine MRD studies are present in Mar. 6, 2012, and having a size of 225,858 bytes and is filed only a minority of patients. Id. Flow cytometric detection of concurrently with the specification. The sequence listing con leukemia-specific markers has been shown to predict out tained in this ASCII formatted document is part of the speci come in numerous clinical correlative studies (Coustan fication and is herein incorporated by reference in its entirety. Smithetal. (1998) Lancet. 351:550-554; Coustan-Smithetal. (2000) Blood. 96:2691-2696; Dworzak et al. (2002) Blood. FIELD OF THE INVENTION 99: 1952-1958; Borowitz, et al. (2008) Blood. 111:5477 0003. This invention relates generally to the detection of 5485; Basso et al. (2009) J Clin Oncol. 27:5168-5174; minimal residual disease in patients with acute lymphoblastic Krampera et al. (2003) BrJ Haematol 120:74-79; Vidriales et leukemia (ALL) and, more specifically, to a method to al. (2003) Blood 101:4695-4700; Hollowieckietal. (2008) Br: improve minimal residual disease monitoring for risk assign J. Haematol. 142:227-237). The method holds potential for ment and selection of therapeutic regimens. wider applicability than molecular techniques because flow cytometric methods for leukemia diagnosis are already estab BACKGROUND OF THE INVENTION lished at most cancer centers worldwide (Campana (2009) Hematol. Oncol Clin North Am. 23:1083-98, vii). 0004 Leukemia relapse is the major cause of treatment 0008 MRD studies by flow cytometry rely on panels of failure for patients with acute lymphoblastic leukemia (ALL) antibodies to define unique immunophenotypic signatures of (Pui et al. (2009) N Engl J Med. 360:2730-2741; Gokbuget leukemic cells which must distinguish leukemic blasts from and Hoelzer (2009) Semin. Hematol. 46:64-75; and Faderlet their normal counterparts, the CD19+ CD10+ lymphoid pro al. (2010) Cancer: 116:1165-1176). Relapse originates from genitors of the bone marrow (“hematogones') (Campana leukemic cells that are resistant to chemotherapy but become undetectable after initial treatment in most cases. Neverthe (2009) Hematol. Oncol Clin North Am. 23:1083-98, vii; less, methods more sensitive than microscopic examination Bruggemann et al. (2010) Leukemia. 24:521-535; McKenna can demonstrate leukemic cells in a proportion of Samples et al. (2001) Blood. 98:2498-2507; Lucio et al. (2001) Leu with no morphologic evidence of leukemia, a finding termed kemia. 15:1185-1192). “minimal residual disease (MRD)' (Campana (2009) Hema 0009 Standard four-color flow cytometry can detect one tol. Oncol Clin North Am. 23:1083-98, vii). leukemic cell in up to 10,000 normal bone marrow or periph 0005 MRD is currently the most powerful prognostic eral blood cells but this task typically requires considerable indicator in childhood ALL (Cave etal. (1998) N Engl.J.Med. interpretative expertise. Therefore, identification of new leu 339:591-598; Coustan-Smith et al. (1998) Lancet. 351:550 kemia markers that are easily detectable and are stably 554; van Dongen et al. (1998) Lancet. 352:1731-1738; Cous expressed in a large proportion of ALL cases could simplify tan-Smith et al. (2000) Blood. 96:2691-2696; Dworzak et al. the application of MRD studies, and help extend their benefit (2002) Blood. 99:1952-1958; Nyvold et al. (2002) Blood. to all patients and enhance the sensitivity of MRD detection. 99:1253-1258; Zhou et al. (2007) Blood. 110:1607-1611; BRIEF SUMMARY OF THE INVENTION Borowitz et al. (2008) Blood. 111:5477-5485. Basso et al. (2009) J Clin Oncol. 27:5168-5174; Canter et al. (2010) 0010 Methods and compositions are provided for identi Blood. 115:3206-3214; Stow et al. (2010) Blood. 115:4657 fying patients with minimal residual disease. The diagnostic 4663). There is strong evidence Supporting its prognostic methods generally comprise contacting a specimen from a significance in adult ALL (Krampera et al. (2003) Bru Hae patient with a plurality of probes, wherein each of said probes matol. 120:74-79; Vidriales, et al. (2003) Blood. 101:4695 specifically binds to a distinct marker, wherein a first probe 4700; Raffet al. (2007) Blood. 109:910-915; Hollowiecki et specifically binds to CD19, a second probe specifically binds al. (2008) Br. J. Haematol. 142:227-237; Bassan et al. (2009) to CD10, a third probe specifically binds to CD34, a fourth Blood. 113:4153-4162). probe specifically binds to CD45, and at least two additional 0006 Thus, MRD monitoring has been introduced into probes that specifically binds to any two of CD38, CD24, many contemporary treatment protocols for risk assignment CD44, CD58, CD73, CD15, CD200, CD66c, CD123, CD86, and selection of therapeutic regimens (Pui et al. (2009) N CD72, CD13, CD33, CD79b, HSPB1, BCL2, CD164, EnglJ Med. 360:2730-2741; Gokbuget and Hoelzer. (2009) CD304, CD97, CD99, CD102, or CD3.00a. The complex Semin. Hematol. 46:64-75; and Faderl et al. (2010) Cancer. formed between each of the probes and their marker is US 2014/0148354 A1 May 29, 2014 detected and a value is generated corresponding to an expres ments are provided so that this disclosure will satisfy appli sion level of each of said marker. An expression profile is cable legal requirements. Like numbers refer to like elements generated by combining the expression level values. In Such throughout. methods, the expression of CD19, CD10, CD34 and CD45 0020 Many modifications and other embodiments of the and a modulated level of at least two of CD38, CD24, CD44, inventions set forth herein will come to mind to one skilled in CD58, CD73, CD15, CD200, CD66c, CD123, CD86, CD72, the art to which these inventions pertain having the benefit of CD13, CD33, CD79b, HSPB1, BCL2, CD164, CD304, the teachings presented in the foregoing descriptions and the CD97, CD99, CD102, or CD300a relative to a normal control associated drawings.