若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 報告書

Name: Ahmed Mohamed Mohamed
Title: Network-based analysis of cancer pathways
Institute: Bioinformatics Center (Mamitsuka Laboratory), Kyoto University Institute for Chemical
Research; Kyoto, Uji, Gokasho 611-0011, Japan
Partner institute of your choice：Bioinformatics Program, Boston University (Prof. Charles DeLisi)
Duration of your choice: January 24th – April 20th , 2013
Report:Introduction to the host laboratory and general lifestyle in Boston:During my international training program, I was staying at Professor Charles DeLisi’s laboratory
in faculty of Engineering and Life Sciences at Boston University (BU). The laboratory focuses onanalysis of biological networks, with particular emphasis on applications to cancer. Professor
DeLisi was one of the initiators of the human genome project, for which he received thePresidential Citizens medal. In the laboratory, I shared a room with 2 PhD students, as well as 3
postdoctoral researchers, which facilitated constructive discussion in research and life activities.
During my first month of my stay, I lived with a host family on the suburbs of Boston. My hostfamily helped me significantly in getting accustomed to the new lifestyle. After that, I moved closer
to BU with an American friend of mine, who is also a graduate student in BU.

Research Objectives:
Cancer develops as a result of pathway dysregulations, that is, in turn, caused by mutations in its
participating genes. The successful detection of genetic mutations causing cancer (drivermutations) has been hampered by three main issues. First, complete knowledge of signaling
pathways in the cancerous tissues are still lacking. Second, the high proliferative activity of thecancerous tissue cause many additional DNA aberrations (passenger mutations). Third, the small
number of patients tested is very small, which prevents identification of gene mutation based on
their frequency.
Recent sequencing initiative for different tumor types revealed certain trends in genetic
mutations. One of these trends is Mutual exclusivity (ME), where driver mutations in the same
biological pathways tend not to occur ina1

the same patient.
illustrate

a3

a4
c1

b1

To

a2

the

biological

b2

b3

c2

b4

Figure 1 Biological Pathway Illustrationinterpretation for ME set, we consider the following example: Suppose that C2 gene need to bedysregulated for cancer development. C2 is downstream of C1, which in turn, is regulated by 2
pathways a&b. To successfully dysregulate C1, a & b pathways needs to be non-functioning.

若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 報告書

Report (Continued)：
According to the representation in Figure 1, any mutation in genes (a1~a4) is sufficient forpathways “a” de-functioning, and similarly pathway “b”. Assuming a perfect tumor evolution
process, each tumor sample will have exactly one mutation in each pathway “a” & “b”, or amutated C1 gene. Therefore, mutation network will look like the figure on the right, where blueedges indicate ME, and red edge indicate co-occurrence.
After extensive discussions with researchers in the host laboratory, we have come to theconclusion that protein complexes (multiple genes bound together to form a single functioningunit) can be treated similarly. I started a study aimed to identify ME-mutated protein complexes
that highlight commonly perturbed sub-pathways in cancer.
All human protein complexes were fetched from Reactome Database. Data for 27 recent tumor
sequencing project data were downloaded from cbioportal.org. To assess the ME of Reactome
complexes, the following steps were performed to calculate a P value:
1. For each study, get all mutations from CbioPortal.org
2. Convert Mutations to a Mutation Matrix (Pateint Gene matrix). I used UniProt IDs toindex genes because Reactome is curated on Unitpot IDs. Multiple mutations in the samegene were counted as a single mutation.
3. Calculate the hypergeometric probability for all pairwise genes in the mutation matrix.
4. Take Reactome complexes that have at least 2 genes mutated in the current study.
5. For each n-sized complex, calculate Complex “score” by summing up all pairwise
probabilities.
6. Estimate the empirical distribution of scores for n-sized random genes.
7. Calculate the P value of the complex using ECDF.

Results:
To find common complexes between studies, I plotted complexes (P<0.001), the colored them bycoverage, to see if there are common, and high-coverage complexes. Out of the 27 studies, 24
showed significant ME mutation signature in PI3K-inhibitor complex. The complex is implicatedin cancer pathways and the impairment of PI3K signaling pathway has been tightly linked withcancerdevelopment.

Othercomplexes

showing

frequentMEsignature

belongedtoimmune-regulation, mRNA splicing and cell cycle pathways, all of which are linked to cancer. Thisassured us of the potential applicability of our method is detecting driver mutations.

若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 報告書

Plan (Continued)

Figure 2 Study-Complex Plot. Complexes are coloredaccording to their coverage. The numbers above the plot
indicate complexes passing the filter in each study.

Other Activities:
Aside from wandering in Boston, I exploited my stay in the USA to visit New York City andPhiladelphia. In NYC, I visited the landmarks of Times Square, Central Park, and the Empire
State Building, while enjoying the magnificent street shows there. In Philadelphia, I visited theIndependence Hall, a historic landmark were the American constitution was written.

Boston covered in snow

Parades in NYC

In front of Independence Hall若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 報告書Acknowledgements:
I would like to express my sincere gratitude to Professor DeLisi and Dr. Zhenjun Hu for theirrelentless help during my stay. Similar thanks are also extended to the lab members for their
hospitality and help in both life and research.

若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム 報告書