Tumor initiation and progression is dependent on the acquisition and accumulation of multiple driver mutations that acti­vate and fuel oncogenic pathways and deactivate tumor suppressor networks. This complex continuum of non-stochastic genetic changes in accompaniment with error-prone mitoses largely explains why tumors are a mosaic of different cells. Contrary to the long-held notion that tumors are dominated by genetically-identical cells, tumors often contain many different subsets of cells that are remarkably diverse and distinct. The extent of this intratumor heterogeneity has bewildered cancer biologists’ and clinicians alike, as this partly illuminates why most cancer treatments fail. Unsurprisingly, there is no “wonder” drug yet available which can target all the different sub-populations including rare clones, and conquer the war on cancer. Breast tumors harbor ginormous extent of intratumoral heterogeneity, both within primary and metastatic lesions. This revelation essentially calls into question mega clinical endeavors such as the Human Genome Project that have sequenced a single biopsy from a large tumor mass thus precluding realization of the fact that a single tumor mass comprises of cells that present a variety of flavors in genotypic compositions. It is also becoming recognized that intratumor clonal heterogeneity underlies therapeutic resistance. Thus to comprehend the clinical behavior and therapeutic management of tumors, it is imperative to recognize and understand how intratumor heterogeneity arises. To this end, my research proposes to study two main features/cellular traits of tumors that can be quantitatively evaluated as “surrogates” to represent tumor heterogeneity at various stages of the disease: (a) centrosome amplification and clustering, and (b) mitotic frequency. This study aims at interrogating how a collaborative interplay of these “vehicles” support the tumor’s evolutionary agenda, and how we can glean prognostic and predictive information from an accurate determination of these cellular traits.

Tetraploidy – the presence of four copies of the haploid chromosome complement – is common in cancer. There is evidence that ~40% of tumors pass through a tetraploid stage at some point during their development, and tetraploid cells injected in mice are more tumorigenic than their diploid counterparts. However, the reason for this increased tumorigenicity of tetraploid cells is not well established. Most routes by which cells may become tetraploid also confer cells with double the number of centrosomes, the small membraneless organelle that organizes the cell's microtubule cytoskeleton and mitotic spindle apparatus. Centrosome number homeostasis is crucial for health, and recent studies have shown inducing extra centrosomes in cells can induce tumor formation in mice. This has led some researchers to propose that the extra centrosomes that arise together with tetraploidy may be the reason that tetraploid cells are more tumorigenic. However, several anecdotal reports have found that tetraploid clones generated and grown in vitro appear to lose their extra centrosomes. Here, I investigate the population dynamics of the loss of extra centrosomes in newly formed tetraploid cells generated via cytokinesis failure. I uncover the mechanism driving the process and build a mathematical model that captures the experimentally observed dynamics. Next, I investigate karyotypic heterogeneity in newly formed tetraploid cells and their counterparts that are grown for 12 days under standard culture conditions and find that karyotypic heterogeneity has increased after 12 days of growth after tetraploidization. The day 12 'evolved' population with increased heterogeneity formed larger colonies in soft agar than newly formed tetraploid cells or diploid parental precursors and karyotype analysis of the largest soft agar colonies revealed recurrent aneuploidies shared by a subset of colonies. Finally, I investigate the effects of different culture conditions - meant to mimic various conditions in the tumor microenvironment - on the evolution of centrosome and chromosome number in newly formed tetraploid cells and identify a small subset of conditions that altered centrosome homeostasis or the fitness of tetraploid cells. / Doctor of Philosophy / The genetic information in cancer cells is often drastically altered compared to normal cells in the body. As one important example of this, the number and structure of chromosomes - the DNA structures that hold the genetic information - is often abnormal in cancer cells. Abnormal chromosome number is closely linked with cancer development, but the details of why this leads to more cancer are not clear. One important kind of chromosome number change is when a cell undergoes incomplete cell division, and the resulting cell acquires double the number of chromosomes compared to a normal cell (known as tetraploidy). Tetraploidy occurs in close to 40% of cancers and is linked with the most aggressive cases. The abnormal cell divisions that cause tetraploidy also lead to other cellular changes. One important change is that tetraploid cells also acquire double the number of the structures that organizes cell division (centrosomes). The centrosome organizes the mitotic spindle, the major apparatus that is responsible for equally distributing chromosomes to two daughter cells during the cell division process. Extra centrosomes in cells are closely linked with cancer and can lead to additionally chromosome number changes. Researchers have believed that the extra centrosomes that are acquired with doubled chromosome number may be the major reason that tetraploid cells are linked to more aggressive cancer. However, recent studies have suggested that tetraploid cells may lose their extra centrosomes, calling into question the details of the relationship between tetraploidy and tumor formation. Here, I use human cells grown in culture to understand how extra centrosomes are lost from tetraploid cells. I find that extra centrosomes in newly formed tetraploid cells promote abnormal 'multipolar' cell divisions, in which chromosomes are segregated unevenly to three or more partitions. Such divisions are often fatal to daughter cells. In some cases, the extra centrosomes can cluster to form bipolar spindles that segregate chromosomes into two equal partitions (as is normal). When forming bipolar spindles, extra centrosomes can cluster asymmetrically (three centrosomes at one pole, one at the other) or symmetrically (two centrosomes at each pole). Tetraploid cells with a normal number of centrosomes emerge when extra centrosomes cluster asymmetrically in a bipolar spindle, yielding one tetraploid daughter cell with a normal number of centrosomes. Such cells have a fitness advantage over cells with extra centrosomes, which over time are very likely to undergo fatal multipolar divisions. Thus, cells with a normal centrosome number 'take over' the population. Next, I investigate the cancer-like properties of tetraploid cells without their extra centrosomes and find that they display increased tumor-like behavior even in the absence of extra centrosomes. Finally, I investigate whether changing the conditions in which cells are grown (in ways meant to mimic different conditions that may be experienced in the body) affects whether tetraploid cells lose their extra centrosomes. We identify a small number of conditions that do influence loss of extra centrosomes. Together, these studies illuminate important details of the relationship between tetraploidy and tumor formation. This work lays the foundation to further explore and understand the relative roles of tetraploidy, extra centrosomes, and tissue environment in cancer.

O presente trabalho teve por objetivo avaliar alterações devido à exposição a Nanotubos de Carbono de Parede Simples (NTCPS) em duas linhagens celulares epiteliais (BBnt e HK2) e em uma linhagem celular monocítica (THP-1), enfocando os mecanismos de internalização e os efeitos sobre o ciclo celular. Foi avaliada a ação dos receptores scavenger na internalização dos NTCPS nas células HK2 e THP-1 e a interferência de duas concentrações de NTCPS sobre os elementos do citoesqueleto e no ciclo celular, nas células HK2 e BBnt. As concentrações utilizadas foram equivalentes as permitidas pelo The National Institute for Occupational Safety and Health: 2,4 e 24 mg/cm2. A análise de expressão de mRNA por RT-PCR para receptores scavenger, mostrou que a internalização do NTCPS pode ocorre por endocitose. Sendo que os receptores SCARA5 e SRA são os responsáveis pela internalização nas células THP-1, enquanto MARCO e SRA realizam o processo de internalização nas células HK2. Observou-se que em ambas as concentrações, as células BBnt apresentaram amplificação centrossômica, com a ocorrência de 25,38% e 28,46% de mitoses alteradas para cada concentração, respectivamente. Não houve interferência significativa na progressão do ciclo celular em ambas as linhagens. O estudo da interação dos NTCPS com vesículas lipídicas não apresentou evidencias de alterações ou danos na membrana das vesículas, porém as vesículas apresentaram-se associadas umas às outras após o tratamento com 24 mg/cm2. / This study aimed to assess changes due to exposure to of Single-wall Carbon Nanotubes (SWCNT) in two epithelial cell lines (BBnt and HK2) and a monocytic cell line (THP-1), focusing on the mechanisms of internalization and effects on the cell cycle. The action of scavenger receptors in the internalization of SWNTC in HK2 and THP-1 cells and the interference of two concentrations of SWNTC about elements of the cytoskeleton and the cell cycle, in BBnt and HK2 cells was evaluated. The concentrations used were equivalent to those allowed by The National Institute for Occupational Safety and Health: 2,4 to 24 mg/cm2. Analysis of mRNA expression by RT-PCR for scavenger receptors showed that the SWNTC internalization can occurs by endocytosis. Being that SCARA5 and SRA receptors are responsible for internalization in THP-1 cells, while MARCO and SRA perform the process of internalization in HK2 cells. It was observed that at both concentrations, the cells showed centrosome amplification in BBnt cells, with the occurrence of 25.38% and 28.46% of mitosis changed for each concentration, respectively. There was no significant interference with cell cycle progression in both strains. The study of the interaction of lipid vesicles with SWNTC showed no evidence of change or damage the membrane of the vesicles, but the vesicles were associated with each other after treatment with 24 mg/cm2.

O presente trabalho teve por objetivo avaliar alterações devido à exposição a Nanotubos de Carbono de Parede Simples (NTCPS) em duas linhagens celulares epiteliais (BBnt e HK2) e em uma linhagem celular monocítica (THP-1), enfocando os mecanismos de internalização e os efeitos sobre o ciclo celular. Foi avaliada a ação dos receptores scavenger na internalização dos NTCPS nas células HK2 e THP-1 e a interferência de duas concentrações de NTCPS sobre os elementos do citoesqueleto e no ciclo celular, nas células HK2 e BBnt. As concentrações utilizadas foram equivalentes as permitidas pelo The National Institute for Occupational Safety and Health: 2,4 e 24 mg/cm2. A análise de expressão de mRNA por RT-PCR para receptores scavenger, mostrou que a internalização do NTCPS pode ocorre por endocitose. Sendo que os receptores SCARA5 e SRA são os responsáveis pela internalização nas células THP-1, enquanto MARCO e SRA realizam o processo de internalização nas células HK2. Observou-se que em ambas as concentrações, as células BBnt apresentaram amplificação centrossômica, com a ocorrência de 25,38% e 28,46% de mitoses alteradas para cada concentração, respectivamente. Não houve interferência significativa na progressão do ciclo celular em ambas as linhagens. O estudo da interação dos NTCPS com vesículas lipídicas não apresentou evidencias de alterações ou danos na membrana das vesículas, porém as vesículas apresentaram-se associadas umas às outras após o tratamento com 24 mg/cm2. / This study aimed to assess changes due to exposure to of Single-wall Carbon Nanotubes (SWCNT) in two epithelial cell lines (BBnt and HK2) and a monocytic cell line (THP-1), focusing on the mechanisms of internalization and effects on the cell cycle. The action of scavenger receptors in the internalization of SWNTC in HK2 and THP-1 cells and the interference of two concentrations of SWNTC about elements of the cytoskeleton and the cell cycle, in BBnt and HK2 cells was evaluated. The concentrations used were equivalent to those allowed by The National Institute for Occupational Safety and Health: 2,4 to 24 mg/cm2. Analysis of mRNA expression by RT-PCR for scavenger receptors showed that the SWNTC internalization can occurs by endocytosis. Being that SCARA5 and SRA receptors are responsible for internalization in THP-1 cells, while MARCO and SRA perform the process of internalization in HK2 cells. It was observed that at both concentrations, the cells showed centrosome amplification in BBnt cells, with the occurrence of 25.38% and 28.46% of mitosis changed for each concentration, respectively. There was no significant interference with cell cycle progression in both strains. The study of the interaction of lipid vesicles with SWNTC showed no evidence of change or damage the membrane of the vesicles, but the vesicles were associated with each other after treatment with 24 mg/cm2.

No description available.

Centrosomes are microtubule-based organelles composed of two centrioles and peri-centriolar material, involved in the formation and organization of the mitotic spindle, serving as microtubule-organizing center and involved in ciliogenesis. Supernumerary centrosomes are detrimental for cell physiology and activate the PIDDosome, a multi-protein complex that serves as a platform for the activation of Caspase-2, composed of: PIDD1, RAIDD and Caspase-2 itself. Caspase-2’s preferred cleavage site based on peptide screening is VDVAD, however Caspase-2, when activated via the PIDDosome, cleaves its bona fide substrate MDM2 (negative p53 regulator) in the FDVPD sequence. Here, I present evidence for VDVADase activity in apoptotic cells lacking Caspase-2, which suggests that this cleavage site is not Caspase-2 specific when the Caspase-2 activation occurs via the PIDDosome. In order to investigate if the mode of activation of Caspase-2 determines its substrate specificities I performed a Caspase-2 rescue experiment and introduced several mutations affecting the Caspase-2 autoproteolytic-processing. Furthermore, I present evidence that exogenous Caspase-2 is able to form the PIDDosome and cleaves MDM2 but when key autoproteolytic sites are mutated no MDM2 cleavage is detectable. Supernumerary centrosomes also accumulate upon overexpression of PLK4 (a kinase regulator of the centriole duplication). Immunofluorescence images of cells overexpressing PLK4 were taken following the centrioles quantification over time. Consequently, a large amount of image data was accumulated, which necessitated the development of a semi-automated pipeline for centrioles counting. This pipeline was generated using the image processing and analysis tool ImageJ and the deep learning segmentation tool MitoS together with the pretrained MitoSegNet model, which was finetuned to count centrioles stained against different centrosomal epitopes, namely Centrin 1, γ-Tubulin and ANKRD26. This semi-automated method of centrioles quantification is easy to use, reproducible and faster than manual quantification. Using this pipeline to quantify centrioles in p53, SCLT1 or ANKRD26 lacking cells we demonstrate accumulation of supernumerary centrosomes in these cells similar to parental cells. / I centrosomi sono organelli cellulari a base di microtubuli, composti da due centrioli e dal materiale pericentriolare che li circonda. I centrosomi sono coinvolti nell'organizzazione dei microtubuli, nella formazione del fuso mitotico e nella ciliogenesi. I centrosomi soprannumerari sono dannosi per la fisiologia cellulare e attivano il PIDDosoma, un complesso multiproteico, composto da PIDD1, RAIDD e Caspasi-2, che funge da piattaforma per l'attivazione della caspasi stessa. Il sito preferenziale di proteolisi di Caspasi-2 è stato individuato tramite screening peptidico nella sequenza VDVAD. Nonostante ciò, quando attivata tramite il PIDDosoma, Caspasi-2 scinde il suo substrato di elezione MDM2 (regolatore negativo di p53) a livello della sequenza FDVPD. In questa tesi presento evidenze di attività VDVAD-asica in cellule apoptotiche prive di Caspasi-2, suggerendo che questo sito di taglio non sia specifico di Caspasi-2 quando la sua attivazione avviene tramite il PIDDosoma. Al fine di indagare se la modalità di attivazione della proteasi determina le sue specificità di substrato, ho eseguito esperimenti di complementazione di Caspasi-2 facendo uso di diversi mutanti che influenzano il suo processamento autoproteolitico. Inoltre, presento prove che Caspasi-2 esogena è in grado di assemblare il PIDDosoma e proteolizzare MDM2 ma quando i suoi siti chiave di autoproteolisi sono mutati non è rilevabile il taglio di MDM2. I centrosomi soprannumerari si accumulano anche in caso di sovraespressione di PLK4 (chinasi regolatrice della duplicazione dei centrioli). Immagini di immunofluorescenza di cellule che sovraesprimono PLK4 sono state acquisite seguendo la cinetica di accumulo dei centrioli nel tempo. Di conseguenza, l’ingente mole di dati generati ha reso necessario lo sviluppo di una procedura semiautomatica per la conta dei centrioli. Questa pipeline è stata generata utilizzando il programma di elaborazione e analisi di immagini ImageJ e il programma di segmentazione basato su deep learning MitoS, insieme al modello MitoSegNet, che è stato affinato per la conta dei centrioli evidenziati tramite immunofluorescenza diretta contro diversi epitopi centrosomiali, ossia: Centrin 1, γ-Tubulina e ANKRD26. Questo metodo semiautomatico di quantificazione dei centrioli è facile da usare, riproducibile e più veloce della quantificazione manuale. Utilizzando questa procedura per quantificare i centrioli nelle cellule prive di p53, SCLT1 o ANKRD26, dimostriamo che l'accumulo di centrosomi soprannumerari in queste cellule è simile a quello riscontrato nelle cellule parentali.