In cancer research, there is a need to make accurate spatial measurements in multi-layered fluorescence microscopy images. Researchers would like to measure distances in and between biological objects such as nerves and tumours, to investigate questions which includes if nerve distribution in and around tumours can have a prognostic value in cancer diagnostics. This thesis is split into two parts, the first being: given arbitrary florescent images of cancer tissue samples, investigate the feasibility of automatically identifying nerves, tumours and blood vessels using classic image analysis. The second part is: given an image with identified objects, quantify their spatial data. By analysing 58 different cancer tissue samples we found that a modified Otsu method gives the most promising results for image segmentation. We found that non-verifiable objects and verifiable objects share the same pixel intensity distributions which implies that it is in general not possible to solely use thresholding methods to separate them from each other. For the spatial analysis, two measurement methods were introduced. An object based method that provides measurements from the edges of nerves to tumour edges, and a pixel based measurement method, which provides fraction based measurements that are comparable between different tissue samples.

Single-cell sequencing techniques, such as single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq), have revolutionized our understanding of cellular diversity and function. Genetic and epigenetic factors influence phenotypic heterogeneity in ways that are just beginning to be understood. In this work, we develop methods for inferring mechanisms of biological heterogeneity in single-cell data, with particular applications to cancer biology. First, we develop a kernel archetype analysis method for overcoming noise and sparsity in single-cell data by aggregating single cells into high-resolution cell states. We show that the proposed approach captures robust and biologically meaningful cell states and enables the inference of epigenetic regulation of phenotypic heterogeneity. In the second part of this thesis, we develop methods for linking genotypic and phenotypic information, first by using aggregated single-cell RNA sequencing and a hidden Markov model to infer copy number variation. We demonstrate that aggregation improves copy number inference over existing approaches. We then integrate DNA sequencing with single-cell RNA sequencing to infer copy number profiles in a rapid autopsy of a patient with metastatic pancreatic cancer. We develop a scalable algorithm for inferring phylogenetic relationships between cells from noisy copy number profiles. We show that our approach more accurately recovers phylogenetic relationships between cells and apply it to understand the relationship between genotype and phenotype in metastatic cancer. Finally, we develop a metric for quantifying the extent to which genotype determines phenotype in lineage tracing data. We show that it more accurately quantifies phenotypic plasticity compared to existing approaches. Altogether, these methods can be used to help uncover the mechanisms underlying phenotypic heterogeneity in biological systems.

Studies reporting a high concentration of WR-2721 in mouse salivary glands led to our studies of possible radioprotection of these glands by this drug from ionizing radiation. Oral effects of radiation in the presence of WR-2721 were studied in mice and dogs. Histological evaluation of mouse salivary glands irradiated with 1000 rads of 60Co showed essentially no difference between control and experimental animals. Almost full regeneration of the serous salivary components occurred by 6 months in both groups and neither group had changes in the mucous glands. The use of higher doses of radiation in the mouse was prevented by the oral cavity death syndrome (LD50/8-10) which was reduced by a factor of 2.1 when WR-2721 was given 30 minutes before irradiation of the head. Salivary function in mongrel dogs measured at weekly intervals for one month following radiation showed no significant difference in control and experimental animals; therefore the salivary gland may be an organ capable of metabolizing or excreting of WR-2721. Marked protection from acute radiation damage of the skin and oral mucosa was observed in dogs receiving WR-2721 prior to treatment with radiation. A dose modifying factor of 1.67 was obtained for these structures. If such normal tissue sparing could be achieved clinically, higher doses of radiation could be used in treatment of head and neck malignancies, thereby increasing the probability for successful radiation therapy for such tumors.

This thesis reports the investigation of spontaneous Raman Spectroscopy (RS) for its applicability in early drug discovery. A key focus has been to develop an understanding of the applicability of RS for the quantification and localisation of compound concentration inside mammalian cells. Further investigation into the use of Surface Enhanced Raman Spectroscopy (SERS) for research on Visceral Leishmaniasis (VL) and Leishmania donovani as well as investigating applicability for cancer research are decisive parts of this work. The key work described in this thesis is the investigation of whole cell concentration of compounds inside THP-1 and Madin Darby Canine Kidney (MDCK) cells. For true quantification the Cell Silent Region (CSR) is used to measure without interference from cellular background signal. The model compound is erlotinib, an anti-cancer drug with an alkyne group expressing a peak in the CSR. The developed RS system is calibrated using the current gold standard technique Ultra Performance Liquid Chromatography tandem Mass Spectrometry (UPLC-MS/MS). However, because of the single cell nature of the RS information on inter cell variability can be extracted. The RS measurements suggest that there is a large variation of concentration within single cell populations. The RS measurements can therefore give insight in single cell behaviour within a large cell population. Findings shows that washing cycles, before fixation, alter the intra-cellular concentrations significantly. This is hypothesised to be caused by the sudden change in concentration on the outside of the cell that applies an osmotic pressure, leading to loss of substance from inside the cell wall. Localisation of erlotinib is shown within THP-1 cells and points towards an accumulation inside the cell nucleus. Later, internalised Au nano-particles in the range of 30 nm to 80 nm have been investigated for their enhancement effects and localisation inside THP-1 cells. Au nano-particles are found to be internalised easily by differentiated THP-1 cells and accumulate in lysosomes. This allows for a high local enhancement of the spontaneous Raman signal. However, no advantage for the detection of lysosomally trapped compounds (chloroquine, chlorpromazine) was achieved. The detection of substances without a signal in the CSR was achieved without enhancement. Nonetheless, compounds with intrinsic peaks in the CSR could benefit from this enhancement. Lastly the RS system is explored for alternative uses in early drug discovery. This includes the detection of toxicity as well as the discrimination of cell types. Toxicity has been detected using optically trapped THP-1 cells and doxorubicin. Utilising Principal Component Analysis (PCA) combined with Linear Discriminant Analysis (LDA) on these measured spectra, allowed for a clear discrimination of toxically influenced from healthy cells. Differences mainly show up in DNA content caused by the mode of action of doxorubicin and caused by the trapping, which generates most of the signal within the nucleus of the cell. Discriminating cancerogenic (DU145) from healthy prostate cells (PNT2) has been achieved by probing fixed cells and evaluating the acquired Raman spectra with a PCA/LDA combination. The accuracy of separation of these cells when tested with a 10-fold cross-validation technique, is above 98 %, allowing a good discrimination.

Photodynamic therapy(PDT) has recently emerged as a promising new non-invasive treatment modality for a large number of neoplastic and non-neoplastic lesions. Photoexcitation of a photosensitizing drug in the tumor tissue causes generation of reactive oxygen species which results in cell death. The current porphyrinic photosensitizers suffer a wide range of drawbacks leading to the development of the chemistry of alternative photosensitizing agents in PDT. Among them, the 4d and 5d transition metal-based photosensitizers have been explored extensively with the exception of the 3d metal complexes. The objective of this thesis work is to design and synthesize photoactive iron(III) abd cobalt(III) complexes and evalutate their photonuclease and photocytotoxic potential. Bioessential 3d metal ions provide an excellent platform for metal-based PDT drug designing as because of its varied spectral, magnetic and redox properties, with its complexes possessing rich photochemical behavior in aqueous and non-aqueous media. We have synthesized binary iron(III) complexes as netropsin mimics using amino acid Schiff bases derived from salicylaldehyde/napthaldehyde and arginine/lysine. The complexes were found to be good AT selective DNA binders and exhibited significant DNA photocleavage activity. To enhance the photodynamic potential, we further synthesized iron(III) complexes of phenolate-based ligand and planar phenanthroline bases. The DNA photocleavage activity of these complexes and their photocytotoxic potential in cancer models were studied. ROS generated by these complexes were found to induce apoptotic cell death. Ternary cobalt(III) complexes were synthesized to study the effect of the central metal atom. The diamagnetic cobalt(III) complexes were structurally dissimilar to their iron(III) analogues. Although the Co(III)/Co(II) redox couple is chemically and photochemically accessible but the Co(III)-dppz complex, unlike its iron(III)-dppz analogue, exhibited selective damage to hTSHR expressing cells but not in HeLa cells. A structure-activity relationship study on iron(III) phenolates having modified dppz ligands was carried out and it was found that electron donating group on the phenazine unit and an increase of the aromatic surface area largely improved the PDT efficiency. Finally, SMVT targeted iron(III) complexes with biotin as targeting moiety were synthesized and the in vitro efficacy of the complexes was tested in HepG2 cells over-expressing SMVTs and compared to HeLa amd HEK293 cells. The complexes exhibited higher phytocytotoxicity in HepG2 than in HeLa and cells and HEK293 cells. An endocytotic mode of uptake took place in HepG2 cells whereas in HEK293 cells, uptake is purely by diffusion. This is expected to reduce the side-effects and have less effect on cells with relatively less SMVTs. In summary, the present research work opens up novel strategies for the design and development of primarily iron-based photosensitizers for their potential applications in PDT with various targeting moieties.

Indiana University-Purdue University Indianapolis (IUPUI) / The addition and removal of phosphate groups is a key regulatory mechanism for many cellular processes. The balance between phosphorylation and dephosphorylation is delicate and must be maintained in order for proper cell functions to be carried out. Protein kinases and phosphatases are the keepers of this balance with kinases adding phosphate groups and phosphatases removing them. As such, mutation and/or altered regulation of these proteins can be the driving factor in disease. Phosphatase of Regenerating Liver (PRL) is a family novel of three dual specificity phosphatases (DSPs) first discovered in the regenerating liver tissue of rats. PRLs have also been shown to act as oncogenes in cell culture and in animal models. However, the physiological substrate and mechanisms of the PRLs are not yet known. Recently, our lab has developed a PRL 2 knockout mouse and found several striking phenotypes all of which correspond to a significant increase in PTEN. We also found that PRL 2 is targetable by small molecular inhibitors that can potentially be used to disrupt tumor growth and spermatogenesis. Furthermore, a PTEN heterozygous mouse model crossed into our PRL 2 knockout line was generated to investigate the relevance of PRL interaction with PTEN in cancer.

Indiana University-Purdue University Indianapolis (IUPUI) / The aims of this research were to evaluate the merit of a communication-based medical approach to cancer prevention in Taiwan and to give deeper understanding of whether physicians view this type of method as a possible solution to public health problems. It is also hoped that this research will be able to find out whether doctors support the use of COMBI for managing public health issues in Taiwan. The results show that Taiwanese physicians perceive communication-based approach and communication methods as a way for managing public health problems, and they also agree that COMBI can be used for cancer or other public health issues prevention. The World Health Organization has used COMBI to deal with public health issues and has made a huge impact in many countries, combating diseases such as dengue fever, leprosy, lymphatic filariasis, tuberculosis, malaria, and HIV/AIDS with successful results. There is also a large body of research indicating that there is a strong relationship between eating fruits and vegetables and cancer prevention. In Taiwan, cancer has been both the top cause of death for 18 years and one of the top ten causes of death for 30 years. However, more than 80% of people in Taiwan still do not consume enough fruits and vegetables daily. Thus, this COMBI plan is hoped to help change these people’s eating habits for cancer prevention. The plan is also evaluated by doctors from Taiwan in terms of its pros and cons in this document, and suggestions for changes are made. These doctors view communication-based strategies like COMBI as a key component for managing public health problems, and they also believe that this COMBI plan will accomplish its goal of increasing people's fruit and vegetable intake for cancer prevention in Taiwan. Up till now, only minimal research has been conducted on the use of COMBI in Taiwan. Therefore, this investigation is hoped to initiate this research and provide a guideline for future COMBI-based actions taken in Taiwan.

Indiana University-Purdue University Indianapolis (IUPUI) / Introduction: Cancer registries collect tumor-related data to monitor incident rates and support population-based research. A common concern with using population-based registry data for research is reporting timeliness. Data timeliness have been recognized as an important data characteristic by both the Centers for Disease Control and Prevention (CDC) and the Institute of Medicine (IOM). Yet, few recent studies in the United States (U.S.) have systemically measured timeliness. The goal of this research is to evaluate the quality of cancer data and examine methods by which the reporting process can be improved. The study aims are: 1- evaluate the timeliness of cancer cases at the Indiana State Department of Health (ISDH) Cancer Registry, 2- identify the perceived barriers and facilitators to timely reporting, and 3- reengineer the current reporting process to improve turnaround time. Method: For Aim 1: Using the ISDH dataset from 2000 to 2009, we evaluated the reporting timeliness and subtask within the process cycle. For Aim 2: Certified cancer registrars reporting for ISDH were invited to a semi-structured interview. The interviews were recorded and qualitatively analyzed. For Aim 3: We designed a reengineered workflow to minimize the reporting timeliness and tested it using simulation. Result: The results show variation in the mean reporting time, which ranged from 426 days in 2003 to 252 days in 2009. The barriers identified were categorized into six themes and the most common barrier was accessing medical records at external facilities. We also found that cases reside for a few months in the local hospital database while waiting for treatment data to become available. The recommended workflow focused on leveraging a health information exchange for data access and adding a notification system to inform registrars when new treatments are available.

Cancer is a very complex genetic disease driven by combinations of mutated genes. This complexity strongly complicates the identification of driver genes and puts enormous challenges to reveal how they influence cancerogenesis, prognosis or therapy response. Thousands of molecular profiles of the major human types of cancer have been measured over the last years. Apart from well-studied frequently mutated genes, still only little is known about the role of rarely mutated genes in cancer or the interplay of mutated genes in individual cancers. Gene expression and mutation profiles can be measured routinely, but computational methods for the identification of driver candidates along with the prediction of their potential impacts on downstream targets and clinically relevant characteristics only rarely exist. Instead of only focusing on frequently mutated genes, each cancer patient should better be analyzed by using the full information in its cancer-specific molecular profiles to improve the understanding of cancerogenesis and to more precisely predict prognosis and therapy response of individual patients. This requires novel computational methods for the integrative analysis of molecular cancer data. A promising way to realize this is to consider cancer as a disease of cellular networks. Therefore, I have developed a novel network-based approach for the integrative analysis of molecular cancer data over the last years. This approach directly learns gene regulatory networks form gene expression and copy number data and further enables to quantify impacts of altered genes on clinically relevant downstream targets using network propagation. This habilitation thesis summarizes the results of seven of my publications. All publications have a focus on the integrative analysis of molecular cancer data with an overarching connection to the newly developed network-based approach. In the first three publications, networks were learned to identify major regulators that distinguish characteristic gene expression signatures with applications to astrocytomas, oligodendrogliomas, and acute myeloid leukemia. Next, the central publication of this habilitation thesis, which combines network inference with network propagation, is introduced. The great value of this approach is demonstrated by quantifying potential direct and indirect impacts of rare and frequent gene copy number alterations on patient survival. Further, the publication of the corresponding user-friendly R package regNet is introduced. Finally, two additional publications that also strongly highlight the value of the developed network-based approach are presented with the aims to predict cancer gene candidates within the region of the 1p/19q co-deletion of oligodendrogliomas and to determine driver candidates associated with radioresistance and relapse of prostate cancer. All seven publications are embedded into a brief introduction that motivates the scientific background and the major objectives of this thesis. The background is briefly going from the hallmarks of cancer over the complexity of cancer genomes down to the importance of networks in cancer. This includes a short introduction of the mathematical concepts that underlie the developed network inference and network propagation algorithms. Further, I briefly motivate and summarize my studies before the original publications are presented. The habilitation thesis is completed with a general discussion of the major results with a specific focus on the utilized network-based data analysis strategies. Major biologically and clinically relevant findings of each publication are also briefly summarized.

Indiana University-Purdue University Indianapolis (IUPUI) / Internal tandem duplications in FMS-like receptor tyrosine kinase (FLT3-ITDs) are seen in approximately 25% of all acute myeloid leukemia (AML) patients. FLT3-ITDs induce FLT3 ligand (FL)-independent cellular hyperproliferation, promiscuous and aberrant activation of STAT5, and confer a poor prognosis in patients; however, the molecular mechanisms contributing to FLT3-ITD-induced malignancy remain largely unknown. The protein tyrosine phosphatase, Shp2, is important for normal hematopoiesis as well as hematopoietic stem cell (HSC) differentiation, engraftment, and self-renewal. Furthermore, FLT3-ITD- or constitutive active STAT5-expressing CD34+ cells demonstrate enhanced hematopoietic stem cell self-renewal. Together with the previous findings that Shp2 is critical for normal hematopoiesis, that dysregulated Shp2 function contributes to myeloid malignancies, and that Shp2 has been shown to interact with WT-FLT3 tyrosine 599, which is commonly duplicated in FLT3-ITDs, a positive role for Shp2 in FLT3-ITD-induced signaling and leukemogenesis is implied. I demonstrated that Shp2 is constitutively associated with the reported FLT3-ITDs, N51-FLT3 and N73-FLT3, compared to WT-FLT3; therefore, I hypothesized that increased Shp2 recruitment to N51-FLT3 or N73-FLT3 contributes to hyperproliferation and hyperactivation of STAT5. I also hypothesized that Shp2 cooperates with STAT5 to activate STAT5 transcriptional targets contributing to the up-regulation of pro-leukemic proteins. Finally, I hypothesized that reduction of Shp2 would result in diminished N51-FLT3-induced hyperproliferation and activation of STAT5 in vitro, and prevent FLT3-ITD-induced malignancy in vivo. I found that genetic disruption of Ptpn11, the gene encoding Shp2, or pharmacologic inhibition of Shp2 with the novel Shp2 inhibitor, II-B08, resulted in significantly reduced FLT3-ITD-induced hematopoietic cell hyperproliferation and STAT5 hyperphosphorylation. I also demonstrated a novel role of Shp2 in the nucleus of FLT3-ITD-expressing hematopoietic cells where Shp2 and STAT5 co-localized at the promoter region of STAT5-transcriptional target and pro-survival protein, Bcl-XL. Furthermore, using a Shp2flox/flox;Mx1Cre+ mouse model, I demonstrated that reduced Shp2 expression in hematopoietic cells resulted in an increased latency to and reduced severity of FLT3-ITD-induced malignancy. Collectively, these findings demonstrate that Shp2 plays an integral role in FLT3-ITD-induced malignancy and suggest that targeting Shp2 may be a future therapeutic option for treating FLT3-ITD-positive AML patients.