SK-MEL-28, SK-MEL-2, M14, A2058, and SK-MEL-5 are some of the most widely used cell lines for cutaneous melanoma research. Often researchers have questions on selecting the most appropriate cell line(s) for particular research uses.

TumorComparer utilizes several data types (e.g., mutation, copy number, and expression) to perform a comparison of The Cancer Genome Atlas (TCGA) tumor data to experimental cell line models from the Cancer COSMIC Cell Line Project (CCLP) for several cancer types. Please refer to Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039 for details on the methodology.

An analysis for cutaneous melanoma cell lines with differences between the cutaneous melanoma cell lines SK-MEL-28 vs SK-MEL-2; SK-MEL-28 vs M14; SK-MEL-28 vs A2058; and etc.

If you use content from this page, please cite Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.

Characteristics of Cutaneous Melanoma Cell Lines

The figure shows the presence of alterations for genes (CCND1, CDKN2A, TP53, MAP2K2, PTEN, etc.) commonly associated with cutaneous melanoma in the cell lines: SKMEL28, SKMEL5, SKMEL3, A2058, SKMEL2, etc. The gene list is retrieved from DisGeNET, and the alteration information is retrieved from cBioPortal for the Cancer Cell Line Encyclopedia (CCLE) dataset.

NOTE: Only a subset of cutaneous melanoma cell lines are shown to ensure a readable figure. Alterations for additional cutaneous melanoma cell lines and genes are available on cBioPortal using links on the table below.

Comparing cutaneous melanoma cell lines to tumor samples. Legend Abbreviations: mrna_hi = mRNA High; mrna_lo = mRNA Low; prot_hi = Protein High; prot_lo = Protein Low; mut_mis_put_pass = Missense Mutation (putative passenger); mut_mis_put_driv = Missense Mutation (putative driver); mut_inframe_put_pass = Inframe Mutation (putative passenger); mut_inframe_put_driv = Inframe Mutation (putative driver); mut_trun_put_pass = Truncating mutation (putative passenger); mut_trun_put_driv = Truncating mutation (putative driver); amp = Amplification; deep_del = Deep Deletion; homdel_rec = homdel_rec; amp_rec = amp_rec; sv = sv; sv_rec = sv_rec; splice = splice

Comparing cutaneous melanoma cell lines to tumor samples. Legend Abbreviations: mrna_hi = mRNA High; mrna_lo = mRNA Low; prot_hi = Protein High; prot_lo = Protein Low; mut_mis_put_pass = Missense Mutation (putative passenger); mut_mis_put_driv = Missense Mutation (putative driver); mut_inframe_put_pass = Inframe Mutation (putative passenger); mut_inframe_put_driv = Inframe Mutation (putative driver); mut_trun_put_pass = Truncating mutation (putative passenger); mut_trun_put_driv = Truncating mutation (putative driver); amp = Amplification; deep_del = Deep Deletion; homdel_rec = homdel_rec; amp_rec = amp_rec; sv = sv; sv_rec = sv_rec; splice = splice

List of Cutaneous Melanoma Cell Lines Compared to Pan-Cancer TCGA

The TumorComparer analysis examines the most variably expressed genes, as well as alteration information for cell lines and TCGA patient data using a weighted similarity approach; for details, read: Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.

More information for the cutaneous melanoma cell lines is available on cBioPortal using links on the table below.

The table shows cutaneous melanoma cell lines sorted by similarity to characteristics of TCGA tumors based on expression, mutation, and copy number information. Cell Lines with higher values of โ€˜% Rank by Avg % Ranksโ€™ are considered better matches.
Cell Line % Rank by Avg % Ranks More Line Info % Rank by Mutation % Rank by Copy Number % Rank by Expression
A2058 1.00 Link 0.90 0.99 0.99
COLO679 1.00 Link 0.97 0.92 0.99
GAK 1.00 NA 0.94 0.96 0.98
SKMEL24 1.00 Link 0.94 0.98 0.96
CP50MELB 0.99 NA 0.90 0.94 0.99
IGR37 0.99 Link 0.95 0.90 0.98
MZ2MEL 0.99 NA 0.91 0.98 0.96
RVH421 0.99 Link 0.92 0.92 0.97
SH4 0.99 Link 1.00 0.87 0.97
SKMEL30 0.99 Link 0.85 0.94 1.00
WM115 0.99 Link 0.95 0.95 0.95
WM1552C 0.99 NA 0.92 0.95 0.94
WM278 0.99 NA 0.96 0.90 0.96
COLO829 0.98 Link 0.96 0.76 0.98
LB2518MEL 0.98 NA 0.98 0.82 0.97
SKMEL1 0.98 Link 0.89 0.84 0.96
SKMEL3 0.98 Link 0.92 0.87 0.97
SKMEL31 0.98 Link 0.99 0.78 0.95
SKMEL5 0.98 Link 0.96 0.78 0.98
CP66MEL 0.97 NA 0.94 0.72 0.98
HT144 0.97 Link 0.97 0.66 0.97
MMACSF 0.97 NA 0.99 0.69 0.98
MZ7MEL 0.97 NA 0.88 0.78 0.99
SKMEL2 0.97 Link 0.80 0.84 0.97
UACC257 0.97 Link 0.94 0.72 1.00
UACC62 0.97 Link 0.93 0.76 0.96
A101D 0.96 Link 0.99 0.56 0.95
MEWO 0.96 Link 0.82 0.72 0.98
C32 0.95 Link 0.94 0.56 0.98
G361 0.95 Link 0.96 0.56 0.98
K2 0.95 NA 0.95 0.56 0.99
MELJUSO 0.95 Link 0.88 0.66 0.96
451LU 0.94 NA 0.90 0.56 0.99
GMEL 0.94 NA 0.96 0.52 0.96
IPC298 0.94 Link 0.86 0.56 1.00
MELHO 0.94 Link 0.98 0.46 1.00
RPMI7951 0.93 Link 0.95 0.49 0.94
LOXIMVI 0.92 Link 0.80 0.56 0.94
SKMEL28 0.92 Link 0.97 0.37 1.00
WM35 0.91 NA 0.98 0.31 0.99
IGR1 0.90 Link 0.96 0.31 0.97
ISTMEL1 0.90 NA 0.92 0.37 0.95
M14 0.89 NA 0.95 0.24 0.99
COLO800 0.88 Link 0.92 0.26 0.98
HMVII 0.88 NA 0.83 0.35 0.99
LB373MELD 0.88 NA 0.87 0.31 0.97
A375 0.84 Link 0.99 0.13 0.96
CHL1 0.84 Link 0.52 0.62 0.92
WM793B 0.80 NA 0.93 0.07 0.95
COLO792 0.78 Link 0.74 0.20 0.98
COLO783 0.74 Link 0.52 0.35 0.96

Cell Lines with Common Mutations Found in TCGA Cutaneous Melanoma

Alterations present in cell lines also present in at least two TCGA Pan-Cancer Atlas (SKCM) samples on cBioPortal.

Alterations

BRAF V600E (TCGA Altered: 35.3%; 128 out of 363 samples)

  • A101D
  • A2058
  • A375
  • C32
  • COLO679
  • COLO741
  • COLO783
  • COLO800
  • COLO818
  • COLO829
  • G361
  • HS294T
  • HS695T
  • HS939T
  • HT144
  • IGR1
  • IGR37
  • IGR39
  • K029AX
  • LOXIMVI
  • MALME3M
  • MDAMB435S
  • MELHO
  • RPMI7951
  • RVH421
  • SH4
  • SKMEL1
  • SKMEL24
  • SKMEL28
  • SKMEL3
  • SKMEL31
  • SKMEL5
  • UACC257
  • UACC62
  • WM115
  • WM1799
  • WM2664
  • WM793
  • WM88
  • WM983B

BRAF V600K (TCGA Altered: 6.6%; 24 out of 363 samples)

  • IGR1

NRAS Q61K (TCGA Altered: 9.4%; 34 out of 363 samples)

  • HS936T
  • HS944T
  • SKMEL30

NRAS Q61L (TCGA Altered: 4.1%; 15 out of 363 samples)

  • IPC298
  • MELJUSO

NRAS Q61R (TCGA Altered: 12.9%; 47 out of 363 samples)

  • SKMEL2

Customized Comparisons

Each project has unique questions. TumorComparer (tumorcomparer.org) facilities customized comparisons of cell line datasets to tumor samples directly from the browser.

Technical Information

This analysis was generated using TumorComparer: 0.99.25. If you use content from this page, please cite Sinha R et al., 2021. DOI: 10.1016/j.crmeth.2021.100039.