Integrative Bioinformatics of Functional and Genomic Profiles for Cancer Systems Medicine

Cancer is a leading cause of death worldwide and a major public health burden. The rapid advancements in high-throughput techniques have now made it possible to molecularly characterize large number of patient tumors, and large-scale genomic and functional profiles are routinely being generated. Such datasets hold immense potential to reveal novel genes driving cancer, biomarkers with prognostic value, and also identify promising targets for drug treatment. But the ‘big data’ nature of these highly complex datasets require concurrent development of computational models and data analysis strategies to be able to mine useful knowledge and unlock the potential of the information content that is latent in such datasets. This thesis presents computational and analytical approaches to extract potentially useful information by integrating genomic and functional profiles of cancer cells.Syöpä on maailmanlaajuisesti johtava kuolinsyy sekä suuri kansanterveystaakka. Edistyneen teknologian ansiosta voimme nykyään tutkia syöpäsoluja molekyylitasolla sekä tuottaa valtavia määriä tietoa. Tällaisissa tietomäärissä piilee suuria mahdollisuuksia uusien syöpää aiheuttavien geenien löytämiseen ja lupaavien syöpähoitokohteiden tunnistamiseen. Näiden erittäin monimutkaisten tietomäärien ”Big data” -luonne vaatii kuitenkin myös laskennallisten mallien kehittämistä ja strategioita tiedon analysointiin, jotta voidaan löytää käyttökelpoista tietoa, joka voisi olla hyödyllistä terveydenhoidossa. Tämä väitöskirja esittelee laskennallisia ja analyyttisiä tapoja löytää mahdollisesti hyödyllistä tietoa yhdistämällä erilaisia syöpäsolujen molekulaarisia malleja, kuten niiden genomisia ja toiminnallisia profiileja

FORMULATION AND EVALUATION OF METFORMIN HYDROCHLORIDE LOADED FLOATING MICROSPHERES

Objective: The main objective of this study was to develop and evaluate the eudragit and HPMC coated metformin hydrochloride floating microspheres, in which HPMC helps in floating and eudragit as a coating material for a site-specific drug release in a controlled manner and the active moiety metformin used as anti-hyperglycemic agent. Methods: The floating microsphere was prepared by the solvent evaporation method incorporating metformin as a model drug. The prepared floating microsphere were characterized for particle size, %yield, drug loading and entrapment efficiency, compatibility study, %buoyancy, surface morphology and In vitro drug release and release kinetics. Results: The result metformin loaded floating microsphere was successfully prepared and the particle size range from 397±23.22 to 595±15.82 µm, the entrapment efficiency range from 83.49±1.33 to 60.02±1.65% and drug loading capacity range from 14.3±0.54 to 13.31±0.47% and %buoyancy range from 85.67±0.58 to 80.67±1.15%. The FT-IR and X-RD analysis confirmed that no any interaction between drug and excipient, and surface morphology confirmed those particles are sphere. The floating microsphere show maximum 96% drug release in pH 0.1N HCL and follow the Korsmeyer peppas model of the super case-2 transport mechanism. Conclusion: These results suggest that metformin loaded floating microspheres could be retain in stomach for long time and give site specific drug release in controlled manner

First-principles predictions of tunable half metallicity in zigzag GaN nanoribbons with possible applications in CO detection and spintronics

Based on systematic first-principles density-functional theory (DFT) simulations, we predict that the zigzag GaN nanoribbons (ZGaNNR) can be used both as highly efficient CO detectors as well as spin filters. Our calculations performed both on infinitely long nanoribbons, and also on finite strands, suggest that: (a) CO binds strongly at the edges of ZGaNNRs, and (b) that several of the resultant configurations exhibit half-metallic behavior. We considered various edge-passivation sites and found that all the resultant structures are thermodynamically stable. The metallic, half-metallic, and semiconducting configurations are observed as a function of CO passivation coverage. We also compute the current-voltage (I-V) characteristics of various structures using the Landauer formalism and find that the devices made up of half-metallic configurations act as highly-efficient spin filters. The effect of CO concentration is also investigated which suggests a viable way to not just tune the electronic band gap of ZGaNNRs, but also their half metallicity. Our simulations thus suggest a new direction of research for possible device applications of III-V heterostructures.Comment: 14 pages, 12 figures (included

Phenotypic Screening Combined with Machine Learning for Efficient Identification of Breast Cancer-Selective Therapeutic Targets

The lack of functional understanding of most mutations in cancer, combined with the non-druggability of most proteins, challenge genomics-based identification of oncology drug targets. We implemented a machine-learning-based approach (idTRAX), which relates cell-based screening of small-molecule compounds to their kinase inhibition data, to directly identify effective and readily druggable targets. We applied idTRAX to triple-negative breast cancer cell lines and efficiently identified cancer-selective targets. For example, we found that inhibiting AKT selectively kills MFM-223 and CAL148 cells, while inhibiting FGFR2 only kills MFM-223. Since the effects of catalytically inhibiting a protein can diverge from those of reducing its levels, targets identified by idTRAX frequently differ from those identified through gene knockout/knockdown methods. This is critical if the purpose is to identify targets specifically for small-molecule drug development, whereby idTRAX may produce fewer false-positives. The rapid nature of the approach suggests that it may be applicable in personalizing therapy.Peer reviewe

Kinetically-balanced Gaussian Basis Set Approach to Relativistic Compton Profiles of Atoms

Atomic Compton profiles (CPs) are a very important property which provide us information about the momentum distribution of atomic electrons. Therefore, for CPs of heavy atoms, relativistic effects are expected to be important, warranting a relativistic treatment of the problem. In this paper, we present an efficient approach aimed at ab initio calculations of atomic CPs within a Dirac-Hartree-Fock (DHF) formalism, employing kinetically-balanced Gaussian basis functions. The approach is used to compute the CPs of noble gases ranging from He to Rn, and the results have been compared to the experimental and other theoretical data, wherever possible. The influence of the quality of the basis set on the calculated CPs has also been systematically investigated.Comment: 31 pages, 12 figure

Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells

Background: Genome-wide loss-of-function profiling is widely used for systematic identification of genetic dependencies in cancer cells; however, the poor reproducibility of RNA interference (RNAi) screens has been a major concern due to frequent off-target effects. Currently, a detailed understanding of the key factors contributing to the sub-optimal consistency is still a lacking, especially on how to improve the reliability of future RNAi screens by controlling for factors that determine their off-target propensity. Methods: We performed a systematic, quantitative analysis of the consistency between two genome-wide shRNA screens conducted on a compendium of cancer cell lines, and also compared several gene summarization methods for inferring gene essentiality from shRNA level data. We then devised novel concepts of seed essentiality and shRNA family, based on seed region sequences of shRNAs, to study in-depth the contribution of seed-mediated off-target effects to the consistency of the two screens. We further investigated two seed-sequence properties, seed pairing stability, and target abundance in terms of their capability to minimize the off-target effects in post-screening data analysis. Finally, we applied this novel methodology to identify genetic interactions and synthetic lethal partners of cancer drivers, and confirmed differential essentiality phenotypes by detailed CRISPR/Cas9 experiments. Results: Using the novel concepts of seed essentiality and shRNA family, we demonstrate how genome-wide loss-of-function profiling of a common set of cancer cell lines can be actually made fairly reproducible when considering seed-mediated off-target effects. Importantly, by excluding shRNAs having higher propensity for off-target effects, based on their seed-sequence properties, one can remove noise from the genome-wide shRNA datasets. As a translational application case, we demonstrate enhanced reproducibility of genetic interaction partners of common cancer drivers, as well as identify novel synthetic lethal partners of a major oncogenic driver, PIK3CA, supported by a complementary CRISPR/Cas9 experiment. Conclusions: We provide practical guidelines for improved design and analysis of genome-wide loss-of-function profiling and demonstrate how this novel strategy can be applied towards improved mapping of genetic dependencies of cancer cells to aid development of targeted anticancer treatments.Peer reviewe

Mesio-distal crown width in permanent dentition amongst adolescent population of Province II of Nepal

Background: The purpose of this study was to gather normative data on the mesio-distal crown dimensions amongst adolescent population of Province II, Nepal, to make an accurate diagnosis and treatment planning in orthodontics. It will also be useful in various clinical disciplines of dentistry including basic dental and anthropological research. Materials and Methods: Samples were selected Full form OPD of M B Kedia Dental College, Birgunj, Nepal. Total numbers of participants were 120, out of which 60 males and 60 females were selected after initial examination aged between 11 to 23 years. Subjects with all permanent teeth erupted (except second and third molar) without any history of previous orthodontic treatment and with no dental anomalies were included in this study. The alginate impressions were made by the well trained dental surgeon. Digital vernier calliper providing measurements to ± 0.01millimeter(mm) was used to measure the mesio-distal dimension of all teeth. Results: The mean, range and standard deviation were calculated for the size of the teeth. Independent t-test was used to compare between male and female population. The significance level was set at p value <= 0.05. The population of Province II, Nepal shows greater sexual dimorphism in mesio-distal crown dimension which was exhibited by the maxillary molars (0.88 mm) followed by mandibular molars (0.38 mm). Similarly in anterior tooth segment the maxillary canines (0.29 mm) followed by the mandibular canines (0.27 mm). Conclusion: The mean mesio-distal crown dimensions of the permanent dentition of males were larger than that of females for each type of tooth except maxillary central and lateral incisor

Novel Small Molecule Hsp90/Cdc37 Interface Inhibitors Indirectly Target K-Ras-Signaling

The ATP-competitive inhibitors of Hsp90 have been tested predominantly in kinase addicted cancers; however, they have had limited success. A mechanistic connection between Hsp90 and oncogenic K-Ras is not known. Here, we show that K-Ras selectivity is enabled by the loss of the K-Ras membrane nanocluster modulator galectin-3 downstream of the Hsp90 client HIF-1α. This mechanism suggests a higher drug sensitivity in the context of KRAS mutant, HIF-1α-high and/or Gal3-high cancer cells, such as those found, in particular, in pancreatic adenocarcinoma. The low toxicity of conglobatin further indicates a beneficial on-target toxicity profile for Hsp90/Cdc37 interface inhibitors. We therefore computationally screened >7 M compounds, and identified four novel small molecules with activities of 4 μM–44 μM in vitro. All of the compounds were K-Ras selective, and potently decreased the Hsp90 client protein levels without inducing the heat shock response. Moreover, they all inhibited the 2D proliferation of breast, pancreatic, and lung cancer cell lines. The most active compounds from each scaffold, furthermore, significantly blocked 3D spheroids and the growth of K-Ras-dependent microtumors. We foresee new opportunities for improved Hsp90/Cdc37 interface inhibitors in cancer and other aging-associated diseases

Novel Small Molecule Hsp90/Cdc37 Interface Inhibitors Indirectly Target K-Ras-Signaling

The ATP-competitive inhibitors of Hsp90 have been tested predominantly in kinase addicted cancers; however, they have had limited success. A mechanistic connection between Hsp90 and oncogenic K-Ras is not known. Here, we show that K-Ras selectivity is enabled by the loss of the K-Ras membrane nanocluster modulator galectin-3 downstream of the Hsp90 client HIF-1α. This mechanism suggests a higher drug sensitivity in the context of KRAS mutant, HIF-1α-high and/or Gal3-high cancer cells, such as those found, in particular, in pancreatic adenocarcinoma. The low toxicity of conglobatin further indicates a beneficial on-target toxicity profile for Hsp90/Cdc37 interface inhibitors. We therefore computationally screened >7 M compounds, and identified four novel small molecules with activities of 4 μM–44 μM in vitro. All of the compounds were K-Ras selective, and potently decreased the Hsp90 client protein levels without inducing the heat shock response. Moreover, they all inhibited the 2D proliferation of breast, pancreatic, and lung cancer cell lines. The most active compounds from each scaffold, furthermore, significantly blocked 3D spheroids and the growth of K-Ras-dependent microtumors. We foresee new opportunities for improved Hsp90/Cdc37 interface inhibitors in cancer and other aging-associated diseases

Seed-effect modeling improves the consistency of genome-wide loss-of-function screens and identifies synthetic lethal vulnerabilities in cancer cells

Background: Genome-wide loss-of-function profiling is widely used for systematic identification of genetic dependencies in cancer cells; however, the poor reproducibility of RNA interference (RNAi) screens has been a major concern due to frequent off-target effects. Currently, a detailed understanding of the key factors contributing to the sub-optimal consistency is still a lacking, especially on how to improve the reliability of future RNAi screens by controlling for factors that determine their off-target propensity.Methods: We performed a systematic, quantitative analysis of the consistency between two genome-wide shRNA screens conducted on a compendium of cancer cell lines, and also compared several gene summarization methods for inferring gene essentiality from shRNA level data. We then devised novel concepts of seed essentiality and shRNA family, based on seed region sequences of shRNAs, to study in-depth the contribution of seed-mediated off-target effects to the consistency of the two screens. We further investigated two seed-sequence properties, seed pairing stability, and target abundance in terms of their capability to minimize the off-target effects in post-screening data analysis. Finally, we applied this novel methodology to identify genetic interactions and synthetic lethal partners of cancer drivers, and confirmed differential essentiality phenotypes by detailed CRISPR/Cas9 experiments.Results: Using the novel concepts of seed essentiality and shRNA family, we demonstrate how genome-wide loss-of-function profiling of a common set of cancer cell lines can be actually made fairly reproducible when considering seed-mediated off-target effects. Importantly, by excluding shRNAs having higher propensity for off-target effects, based on their seed-sequence properties, one can remove noise from the genome-wide shRNA datasets. As a translational application case, we demonstrate enhanced reproducibility of genetic interaction partners of common cancer drivers, as well as identify novel synthetic lethal partners of a major oncogenic driver, PIK3CA, supported by a complementary CRISPR/Cas9 experiment.Conclusions: We provide practical guidelines for improved design and analysis of genome-wide loss-of-function profiling and demonstrate how this novel strategy can be applied towards improved mapping of genetic dependencies of cancer cells to aid development of targeted anticancer treatments