designing personalized treatments and improving clinical outcomes of cancers. Such
investigations require accurate delineation of the subclonal composition of a tumor, which
to date can only be reliably inferred from deep-sequencing data (>300x depth). The
resulting algorithm from the work presented here, incorporates an adaptive error model
into statistical decomposition of mixed populations, which corrects the mean-variance
dependency of sequencing data at the subclonal level and enables accurate subclonal
discovery in tumors sequenced at standard depths (30-50x). Tested on extensive computer
simulations and real-world data, this new method, named model-based adaptive grouping
of subclones (MAGOS), consistently outperforms existing methods on minimum
sequencing depth, decomposition accuracy and computation efficiency. MAGOS supports
subclone analysis using single nucleotide variants and copy number variants from one or
more samples of an individual tumor. GUST algorithm, on the other hand is a novel method
in detecting the cancer type specific driver genes. Combination of MAGOS and GUST
results can provide insights into cancer progression. Applications of MAGOS and GUST
to whole-exome sequencing data of 33 different cancer types’ samples discovered a
significant association between subclonal diversity and their drivers and patient overall
survival.
cellular processes of life. The last decade has witnessed dramatic advances in the
field of proteomics, which broadly include characterizing the composition, structure,
functions, interactions, and modifications of numerous proteins in biological systems,
and elucidating how the miscellaneous components collectively contribute to the
phenotypes associated with various disorders. Such large-scale proteomics studies
have steadily gained momentum with the evolution of diverse high-throughput
technologies. This work illustrates the development of novel high-throughput
proteomics platforms and their applications in translational and structural biology. In
Chapter 1, nucleic acid programmable protein arrays displaying the human
proteomes were applied to immunoprofiling of paired serum and cerebrospinal fluid
samples from patients with Alzheimer’s disease. This high-throughput
immunoproteomic approach allows us to investigate the global antibody responses
associated with Alzheimer’s disease and potentially identify the diagnostic
autoantibody biomarkers. In Chapter 2, a versatile proteomic pipeline based on the
baculovirus-insect cell expression system was established to enable high-throughput
gene cloning, protein production, in vivo crystallization and sample preparation for Xray diffraction. In conjunction with the advanced crystallography methods, this endto-end pipeline promises to substantially facilitate the protein structural
determination. In Chapter 3, modified nucleic acid programmable protein arrays
were developed and used for probing protein-protein interactions at the proteome
level. From the perspective of biomarker discovery, structural proteomics, and
protein interaction networks, this work demonstrated the power of high-throughput
proteomics technologies in myriad applications for proteome-scale structural,
functional, and biomedical research.
Human papillomavirus (HPV) 16 proteins of interest, E7, E6 and CE2 were expressed and purified in E. coli for detection of specific antibodies using lateral flow assay because viral and host factors impact the serologic responses to HPV early antigens in HPV-positive oropharyngeal cancer. 17 samples and 5 controls with already known antibody reactivity from ELISA analysis were selected for HPV serologic responses. The lateral flow strip was evaluated for its color band intensity using Image J software. Peak area was used to quantify the color intensity of the lateral flow strip. Out of the 17 samples, 11 (64.7%) showed high antibody levels to E7, 12 (70.6%) showed high Ab levels to E6 and 6 (35.3%) showed high Ab levels to CE2. Correlation coefficient between antibody detection by sight and ELISA for E7, CE2 and E6 were 0.6614, 0.4845 and 0.2372 respectively and correlation coefficient between lateral flow assay and ELISA for E7, CE2 and E6 were 0.3480, 0.1716 and 0.1644 respectively. This further proves patients or samples with HPV 16 oropharyngeal cancer have detectable antibodies to early E7, E6 and E2 proteins, which are potential biomarkers for HPV-associated oropharyngeal cancer.
Cooperative cellular phenotypes are universal across multicellular life. Division of labor, regulated proliferation, and controlled cell death are essential in the maintenance of a multicellular body. Breakdowns in these cooperative phenotypes are foundational in understanding the initiation and progression of neoplastic diseases, such as cancer. Cooperative cellular phenotypes are straightforward to characterize in extant species but the selective pressures that drove their emergence at the transition(s) to multicellularity have yet to be fully characterized. Here we seek to understand how a dynamic environment shaped the emergence of two mechanisms of regulated cell survival: apoptosis and senescence. We developed an agent-based model to test the time to extinction or stability in each of these phenotypes across three levels of stochastic environments.