Download Prostate cancer cell lines case study on cell cycle map

Case study for data visualiza1on using NaviCell Data Visualiza1on Web Service Prostate cancer cell lines LNCAP vs. DU145 LNCAP vs. DU145 cell lines in Cell Cycle map Mutated genes from the cell cycle map in both cell lines. There are represented using glyphs (blue dots) genes ATR CDK4 CDK7 CHEK2 CREBBP EP300 HDAC1 MGA RB1 RBL2 TP53 LNCAP_mut DU145_mut K1379N 0 P110L 0 0 G338_splice T387N 0 A110V 0 G1778W 0 E455del 0 L1902M,E20
68*,A1860V 0 0 K715* K332R P1119A 0 V274F Gene expressions are visualized on the map using map staining func1on from NaviCell 2 LNCAP DU145 Interpreta1on of the data visualiza1on For cell cycle map: If we consider the data as the mean expression of genes of a popula1on of asynchronous cells, most LNCAP cells seem to be expressing genes from the early G1 state (could be considered as the G0 state) and the G1-­‐S checkpoint. Two interpreta1ons are possible for the LNCAP cells: -­‐  most cells are expressing genes of the G1/S checkpoint. The LNCAP cells could try to overpass the checkpoint with less success than DU145 cells. They remain stuck at the checkpoint. -­‐  the cells are prolifera1ng (going through mitosis) and since G1 and S are the longest phases of the cycle, they might simply represent a higher propor1on of asynchronous cells in these phases of the cycle. For the DU145 cells, genes involved in later stages of the cell cycle seem to be more expressed compared to the LNCAP cells. It can be that if the LNCAP cells were arrested, they have advanced in the cycle by overpassing the G1/S checkpoint and got arrested at the spindle checkpoint (confirmed by the higher expression of the spindle checkpoint module in DNA repair map). They are more prone to proliferate than the LNCAP cells. We verified the expression of KI-­‐67, a marker of prolifera1on, and the expression is indeed higher in DU145 than in LNCAP cells (next page). The DU145 is more prolifera1ve than LNCAP cells. Similarly, muta1ons (blue dots) seem to be more numerous in later stages in DU145 when compared to muta1ons in LNCAP. KI67 marker of prolifera1on COMMON LNCAPCLONEFGC_PROSTATE DU145_PROSTATE MKI67 7.52189 9.060399 ⇒  Increase in prolifera1on in DU145 wrt LNCAP LNCAP vs. DU145 cell lines in DNA repair map Genes_mutated LNCAPCLONEFGC_PR
OSTATE DU145_PROSTATE ATR BRCA2 CDH1 CDK4 CDK7 K1379N CHEK2 CREBBP EP300 ERCC3 ERCC5 ERCC6 FANCB HSP90AB1 MEN1 MLH1 MSH2 MSH3 MSH6 MYC PMS2 PRKCB PRKCH PRKCQ PRKCZ PRKDC RAD50 RAD51B T387N A110V G1778W A740T,R391W L1023I RB1 RBBP8 TP53 TP53BP1 TP73 P700S,P94T P110L 0 S2284L K440_splice 0 G338_splice 0 F1437I,Q794H 0 G702W 0 D244N Y318* K381fs 0 A586V,C39_splice 0 L736I K381fs 0 S1067I N30S K489N R271* E313* L719fs R18C G354fs Q106*,R634Q Y487H 0 H189Y P616T 0 D275Y 0 N3605fs N509K 0 K715* S679G 0 V274F G1221_splice DNA repair map modules G1/S checkpoint; S phase checkpoint; G2/M
0 checkpoint
HR, FANCONI
M cell cycle phase
0 G1 cell cycle phase
G1 cell cycle phase; S cell cycle phase; NER
G1/S checkpoint; S phase checkpoint; G2/M
0 checkpoint
0 G2/M checkpoint
0 G1/S checkpoint; G2/M checkpoint
0 NER
0 BER; NER
NER
FANCONI; TLS
HR; FANCONI; G2/M checkpoint
0 M cell cycle phase
BER; MER; FANCONI; TLS
BER; MMR; SSA; FANCONI
MMR; SSA; FANCONI
BER; MMR
0 G1/S checkpoint; G1 cell cycle phase
MMR; FANCONI
REGULATORS
0 REGULATORS
0 REGULATORS
REGULATORS
REGULATORS
HR; MMEJ; S phase checkpoint; G2/M checkpoint
0 HR; G2/M checkpoint
G1 cell cycle phase; S cell cycle phase; G1/S
checkpoint
G1/S checkpoint; G2/M checkpoint
G1/S checkpoint; G2/M checkpoint
G1/S checkpoint; G2/M checkpoint
0 G2/M checkpoint
For genes mutated in DU145 cell line, we have highlighted: -­‐ DNA repair pathways (Blue) -­‐ cell cycle or checkpoints (Yellow) TO KNOW: 1.  One muta1on may appear several 1mes on the maps: proteins affected by the gene muta1ons are marked every 1me they occur on the map. Note that muta1ons are not known to be ac1va1ng or inhibi1ng muta1ons. 2.  Absolute gene expressions are mapped on the map (from 3 to 12) LNCAP DU145 Interpreta1on of the data visualiza1on For DNA repair map: The muta1ons in the DU145 cell line are more frequently affec1ng the regulators of various DNA repair pathways and G1/S, S and G2/M checkpoints, compared to the LNCAP cell line. The altera1ons of both the DNA repair pathways and the DNA damage-­‐controlling checkpoints most probably lead to accumula1on of DNA rearrangements, and the cells might divide and proliferate even with accumulated DNA damage. In par1cular, the muta1ons in DU145 cell line are affec1ng mul1func1onal key regulators of the DNA repair pathways that may alter the ac1vity of several pathways simultaneously. For example, if members of the MSH family are altered (e.g. MSH 2,3,6), single strand DNA damage repair pathways, such as BER, MMR, are affected. In addi1on, double strand DNA damage repair pathways as SSA, FANCONI seem to be altered as well. Muta1ons in the key regulators of HR pathway as BRCA2 and RAD50 responsible for the ini1a1on of the DNA repair pathway, indicate disability of the major double strand DNA damage repair pathway in the DU145 cell line. References • 
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Cancer Cell Line Encyclopedia from the Broad Ins1tute and Novar1s, containing 883 samples; raw data at the CCLE. Barre1na et al. Nature 2012. Data extracted from www.cBioPortal.org => list of genes composing the two maps: DNA repair and CellCycle from ACSN ACSN: hmp://acsn.curie.fr