The Ludwig Institute for Cancer Research Melbourne Melanoma Cell Line Panel

Authors


We established a range of melanoma cell lines from patient material (Table 1) termed Ludwig-Melbourne-Melanoma (LM-MEL-) followed by a unique number (method: Anaka et al., 2012). These lines have been human leucocyte antigen (HLA)-typed, their mutational status for common mutated genes in melanoma determined using the Sequenom MelCarta panel, and their transcriptomes profiled. All lines are tested for mycoplasma, and ethical approval for research purposes has been granted by the Austin Health Human Research Ethics Committee (HREC).

Table 1. The Ludwig Institute for Cancer Research Melbourne Melanoma Cell Lines
LM-MELSexBRAFaNRASOtherbHLA-A/B/C MHC class IReference
  1. a

    BRAF status based on HRM has been reported previously (Tan et al., 2012).

  2. b

    ND = None detected using the Sequenom MelCarta panel.

  3. c,d,eThese cell lines have been established from different tumors of the same patient.

-1aFWTQ61KNDA*2/*24,B*0702/*70,C*0704/*1203Ebert et al. (2008)
-2MV600KWTNDA*0201,B*5101,C*1402 
-3FV600EWT MEK A*0101/*2402,B*0702/0801,C*0701/*0702Dimopoulos et al. (2009)
-4MV600EWTNDA*6801/*1101,B*0702/*0801,C*0702/*0704 
-5aMWTQ61KNDA*0201/*0301,B*0702/*5701,C*0602/*0702 
-6FV600EWTNDA*0301/*6801,B*61/*5301,C*0202/*0401 
-8MV600EWTNDA*0101/*2902,B*0702/*0801,C*0701/*0702 
-9MWTQ61KNDA*0101/*1101,B*5101/*5701,C*0602/*1502 
-12MWTWTNDA*0101/*3303,B0801/*3503,C*0401/*0701 
-14FV600EWTNDA*2301/*2402,B1501/*4403,C*0303/*0401(Ebert et al. (2008) and Gedye et al. (2009)
-15MWTQ61QNDA*2601/*6801,B*4402/*5101,C*0501Gedye et al. (2009)
-16FV600EWTNDA*0101/*0301,B*65/*5701,C*0501/*0611 
-17MV600EWTNDA*0101/*A2,B*44/*1501,C*0304/*5Ebert et al. (2008)
-19MWTQ61KNDA*0101/*0201,B0801/*1501,C*0304/*0701 
-20MWTWT KRAS A*2/*3201,B*4402/*62,C*3/*0501Ebert et al. (2008)
-24FV600KWTNDA*1/*2,B*8/*44,C*5/*07Ebert et al. (2008)
-25MWTWTNDA*0101/*2301,B*0801/*2705,C*0102/*0701 
-26MV600EWT MET A*0201/*2402,B*0702/*2705,C*0102/*0702Ebert et al. (2008, 2009)
-27FWTWTNDA*1101/*3301,B*0801/*3501,C*0401/*0701 
-28FV600EWTNDA*0201,B*1501/*5701,C*0304/*0701Ebert et al. (2008)
-29MWTWTNDA*0101,B*0801,C*0701 
-30MV600EWTNDA*0101/*3101,B*5101/*3503,C*0401/*1203 
-31FV600EWTNDA*0201/*2402,B*4403/*4001,C*0304/*0401 
-33MV600EWTNDA*0201/*0301,B*60/*47,C*0304/*0602 
-34FWTQ61QNDA*0201/*2601,B*2703/*5601,C*0102/*0303Ebert et al. (2008) and Gedye et al. (2009)
-35MWTQ61HNDA*0101/*2601,B*0801/*2705,C*0102/*0701 
-36MV600KWTNDA*2402/*2501,B*3901/*3906,C*0702/*1203 
-38acFV600EWTNDA*0201/*0301,B*0702/*5701,C*6/*7 
-39FWTWTNDA*0301/*3201,B*1501/*4001,C*0303/*0304 
-40FG469EQ61HNDA*3201,B*0801/*5101,C*0701/*1402 
-41MV600EWTNDA*0101/*0201,B*4901/*5101,C*0602/*1402 
-42MV600KWTNDA*1101/*0201,B*55/*27,C*03Ebert et al. (2008) and Gedye et al. (2009)
-44dFWTWTNDA*0201,B*60/*4402,C*0304/*0501Ebert et al. (2008)
-45cFV600EWTNDA*0201/*0301,B*0702/*5701,C*0602/*0702 
-46MV600EWTNDA*0201/*0301,B*4501/*62,C*0304/*0602Ebert et al. (2008)
-47FV600EWTNDA*0201,B*62,C*0304Ebert et al. (2008) and Gedye et al. (2009)
-48FWTQ61QNDA*01/*32,B*08/*14,C*07/*08 
-49MV600EWTNDA*29/*32,B*65/*44,C*8/*16 
-50MV600KWTNDA*2902/*6801,B*65/*4403,C*0802/*1601 
-53dFWTWTNDA*0201,B*60/*4402,C*0304/*0501Ebert et al. (2008)
-57MWTWTNDA*0101/*0201,B*0801/*5701,C*0602/*0701Anaka et al. (2012)
-59FWTQ61QNDA*1101/*2402,B*1801/*5201,C*0701/*1202Anaka et al. (2012) and Zhao et al. (2012)
-60MV600KWTNDA*2402,B*0801/*3503,C*7/*4 
-62MG469EWTNDA*0201/*3101,B*0702/*60,C*0304/*0702Anaka et al. (2012) and Gedye et al. (2009)
-64eMV600EWTNDA*0101/*1101,B*1501/*2705,C*0102/*0303Anaka et al. (2012)
-69FWTQ61QNDA*0201,B*3901/*60,C*0304/*1203Anaka et al. (2012)
-70eMV600EWTNDA*1/*11,B*15/*27,C*1/*0303 
-71MV600KWTNDA*0201,B*0702/*4402,C*0501/*0702 
-73MV600EWT PTK2B A*0201/*0301,B*2705/*4402,C*0202/*0501 
-75MWTWTNDA*2402/*2902,B*3801/*4403,C*1203/*1601 
-77MWTWTNDA*1/*2,B*8,C*7 
-97FWTWT KIT A*02/*11,B*15/*35,C*03/*04 
-98MV600EWTNDA*2/*24,B*15/*57,C*06/*07 
-100MK601EWTNDA*02/*11,B*15/*55,C*03 
-101MV600EWTNDA*2/*30,B*13/*15,C*03/*06 

Therapeutic options for advanced stage melanoma are limited, and despite the recent success with inhibitors of mutant v-raf murine sarcoma viral oncogene homolog B1 (BRAF) activity, long-lasting responses remain rare (Chapman et al., 2011). Immunotherapy may help overcome treatment failure, and there has been some success in the clinic with immunotherapy agents (Hodi et al., 2010). Knowledge of the antigen presenting major histocompatibility complex (MHC) class I HLA-types and antigenic proteins expressed by model systems is crucial for the preclinical testing of immunological interventions such as therapeutic cancer vaccines.

Cancer-testis antigens (CTAg) and differentiation-antigens [mainly regulated by the microphtalmia-associated transcription factor (MITF)], represent two of the most studied families of potential cancer vaccine targets in melanoma (Caballero and Chen, 2009); and show various degrees of tissue-restriction and immunogenicity. The expression levels of some of these ‘immune-targetable’ genes premelanosome protein (PMEL), melan-A(MLANA), tyrosinase (TYR) and members of the melanoma antigen family (MAGE) in the LM-MEL cell lines are shown as an example in Figure 1. The complete gene-expression data and available additional clinical data of the here presented cell line panel are accessible online at ArrayExpress (http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1496/) and in Table S1. All cell lines are available upon request for a small handling fee or on a collaborative basis and slides for IHC from matched patient tumors and matched PBMCs/sera are accessible for some lines in limited quantities.

Figure 1.

Hierarchical clustering of melanoma differentiation and MAGE family cancer-testis antigen gene expression in the LM-MEL melanoma cell lines. Raw microarray data were background corrected, log transformed, and quantile normalized using limma (Smyth, 2005). Clustering used average linkage and Pearsons dissimilarity as a distance metric. Data for each gene was mean-centered and scaled to a standard deviation of one. Green represents above average expression, red below average expression.

Acknowledgements

AB is supported by a fellowship from the Cure Cancer Australia Foundation. JC and AB are supported by a grant from the Melanoma Research Alliance (MRA) and JC is supported by a practitioner fellowship from the Nation Health and Medical Research Council (NHMRC). This research was supported in part by the Cancer Council Victoria (CCV), the Austin Medical Research Foundation (AHMRF) and Operational Infrastructure Support Program Funding of the Victorian State Government.

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