The mSK-Mel Cell Line Cohort: A Model of NF1 altered Melanoma

Caelin 1,2
Foley , Alexis M. 1
Jones , David B. Solit 1

1Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY; 2Bryn Mawr College, Bryn Mawr, PA
ABSTRACT RESULTS RESULTS
The mSKMel Cell Line Cohort was created in the David B. Solit Lab to investigate the role of NF1 in
Melanoma as well as how to best treat Melanomas with NF1 driver mutations. After using the MSKCC A.
cBioPortal to confirm the clinical relevance between the murine cell lines and patient data, current
treatments at Memorial Sloan Kettering were analyzed to understand the outcome for patients and the
effect on the 5-year-survival rate. When looking at the data, current treatments like Pembrolizumab,
A.
Ipilimumab, and Nivolumab do not show strong improvements in the condition of patients. However,
western blot analysis and cell growth studies showed the combination of SHP099 and Trametinib yields
promising results for patients who have NF1/TP53 mutations. Research in the future will focus on
diminishing the pERK rebound when combining SHP099 and Trametinib to ensure elimination of
cancerous cells.

BACKGROUND
NF1 is a tumor-suppressing gene that regulates cell growth
within the MAPK pathway by negatively regulating RAS. NF1
mutations have recently been discovered as a driver of
melanoma, with 70% of melanoma cases having MAPK B.
pathway alterations and 20% of those being NF1 alterations.
NF1 is the 3rd most common molecular subtype of Melanoma. R440*
R1362

Q2239*
The mSK-Mel Cell Line Cohort consists of twenty-five murine cell
lines that were created by conditionally knocking out or in a
combination of genes common to Melanoma in all pigment
producing cells; The NF1 gene, Tp53 gene, and knocking in the B.
BRAF V600E mutation. Tumors from these mice were then
cultured in vitro. H179Y/R/L* R248W/Q/G
R342*

Using the MSKCC cBioportal, which allows for C. Gene Symbol Reference Transcript % of NF1 mutated group

the user to navigate different genetic data sets TP53 ENSG00000141510 52%
from thousands of MSKCC patients, view
TERT ENSG00000164362 28.80%
protein and gene mutations, and more, I was
able to compare the mSKMel Cell Line Cohort to KMT2D ENSG00000167548 24.70%
the MSKCC Melanoma patient population. All PIK3CA ENSG00000121879 21.40%
data utilized the MSKCC IMPACT Assay, which
ARID1A ENSG00000117713 21.20%
stands for integrated mutation profiling of
actionable cancer targets and detects mutations KMT2C ENSG00000055609 19.90%
in both rare and common tumors. Figure 2: Representation of the current treatments being given to patients at MSKCC
PTPRD ENSG00000153707 19.80%
for Melanomas caused by mutations in NF1. It is important to note this is a small sample
FAT1 ENSG00000083857 19.80% size as many patients are diagnosed at MSK and treated elsewhere. A. has an overall
KMT2B ENSG00000272333 19.20%
sample size of 38 patients, with the most popular treatment being Pembrolizumab. B. has a
smaller sample size of 14 patients, with the most popular treatment being a combination of
ZFHX3 ENSG00000140836 18.80%
Ipilimumab and Nivolumab.
By having a cell line cohort that correlates to Figure 1: MSKCC patient data concerning Melanoma caused by NF1 mutations. A. details the number of patients in
main driver mutations in the MSKCC patient the MSKCC melanoma cohort that correspond with the mSK-Mel murine cohort; 126 NF1/TP53 mutations, 21
TP53/BRAF mutations, and 12 NF1/BRAF V600E mutations. B. lollipop plots of the NF1/TP53 mutations, with significant
data, we can analyze the clinical relevance
between them and determine better treatment
hotspot protein changes on R1241 and R212 respectively. C. the top ten co-mutations found in patients at MSKCC who
were diagnosed with Melanoma as a result of an NF1 driver mutation. DISCUSSION AND FUTURE DIRECTIONS
options and actionable targets for patients based ➢ The mSKMel Cell Line Cohort is clinically relevant to the patient data in the MSKCC
on the results of the cell line.
RESULTS cBioPortal; with NF1 alterations significantly co-occurring with TP53.
➢ Current treatments for Melanoma, specifically for NF1/TP53 mutations and NF1/BRAF
B. V600E mutations, do not necessarily affect survival rate positively based off studies
OBJECTIVES A. conducted at other institutions.
➢ Trametinib may be slightly stronger as an individual treatment than SHP099 as seen in
➢ Determine the clinical relevance of the mSKMel Cell Line Cohort to see if it accurately models results section 3, however, the combination of both Trametinib and SHP099 shows
patient data within the cBioPortal. promising results for suppressing cell growth in individuals with NF1/TP53 mutations.
➢ Understand which mutations are the most common within patients. ➢ Further research will include the addition of NF1 null/BRAF V637E lines to determine the
➢ Use the mSKMel Cell Line Cohort to replicate patient’s conditions and understand what effect of TP53 loss, as well as an attempt to diminish the rebound of pERK in the other
treatments may be better to treat Melanoma in patients with NF1/TP53/BRAF mutations. genetic subtypes in the mSK-Mel cell line cohort (which adapts cancerous cells to
adverse conditions within the body, including treatment).

METHODS Figure 3: Positive responses to SHP099 and Trametinib in

➢ Analyzed the most common mutations within the patient data on cBioPortal and cross- cell line mSK-MEL 254 which is both NF1 and TP53 null. A.
shows that SHP099 and Trametinib slow cell growth individually
referenced it with the mSKMel Cell Line Cohort to verify if it was an accurate representation of to an extent, but when combined, plateau cell growth
NF1 mutations in Melanoma. completely, suppressing additional tumor growth. B. is a
➢ Utilized MSKCC cBioPortal to analyze the treatments currently being offered and their 5-year Western Blot that shows that at any hour chosen, the
combination of SHP099 and Trametinib continues to suppress
survival rates on Melanoma patients. the growth of cells more than each drug individually by looking
➢ Used Western Blot analysis and cell growth data to understand the effects of SHP099 and at pERK output signaling. Preventing pERK output halts MAPK
Trametinib on Melanomas caused by NF1 in comparison to the treatments that are currently signaling and stops cell growth.
available to MSKCC patients.
ACKNOWLEDGEMENTS AND REFERENCES
I would like to acknowledge and thank Alexis M. Jones and Dr. David Solit for their guidance and mentorship throughout this
summer, as well as Memorial Sloan Kettering Cancer Center and Vicky Baudin and Alicia Maisonet for hosting this opportunity.
References
Cerami et al. The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data. Cancer
Discovery. May 2012 2; 401. PubMed.Gao et al. Integrative analysis of complex cancer genomics and clinical profiles using the
cBioPortal. Sci. Signal. 6, pl1 (2013). PubMed.
Nissan MH, Pratilas CA, Jones AM, Ramirez R, Won H, Liu C, Tiwari S, Kong L, Hanrahan AJ, Yao Z, Merghoub T, Ribas A,
Chapman PB, Yaeger R, Taylor BS, Schultz N, Berger MF, Rosen N, Solit DB. Loss of NF1 in cutaneous melanoma is associated
with RAS activation and MEK dependence. Cancer Res. 2014 Apr 15;74(8):2340-50. doi: 10.1158/0008-5472.CAN-13-2625. Epub
2014 Feb 27. PMID: 24576830; PMCID: PMC4005042.