1,720,985 research outputs found
Dissection of the heterogeneity of tumour microenvironment facilitates therapies of cancers
No full textTumor microenvironment (TME) has been recognized as one of the important resources of tumor heterogeneity. The dissection of the TME by taking the advantage of high throughput data such as single-cell RNA sequencing (scRNA-seq) data has facilitated cancer research and helped to identify determinants of drug response, including immunotherapy. Even though immunotherapy such as immune checkpoint blockade (ICB) has facilitated cancer therapies, most patients do not response to ICB. What determines the response to ICB and how it is affected by TME is not well-illustrated yet.
A subgroup of colorectal cancer (CRC) patients was highly immune infiltrated but had poor prognosis. I, therefore, suspected some potential factors might contribute to this phenotype. The results revealed that transposable element (TE) expression was related to immune cell infiltration and predictive of prognosis in CRC. Tumours with the highest TE expression score showed increased immune cell infiltration with upregulation of interferon (IFN) signalling pathways and downstream activation of IFN-simulated genes, which further triggered expression of PD-L1 in immune cells rather than tumour cells. This work addressed the potential immune evasion driven by TE.
Immunotherapy has revolutionized the treatment of multiple cancers. While cancer morbidity increased with age and age-associated changes in immune function have been well characterized, age-induced differences in TME and their influences on the response to immunotherapy remain unknown. The results revealed that aged individuals responded more efficiently to ICB treatment at the pan-cancer level. Further Cox regression screening on age revealed that patients above 47 years of age responded better and had longer progression-free survival than younger counterparts. scRNA-seq data analysis revealed the accumulation of immune response and chronic inflammation with increasing age in multiple cancers, including lung and gastrointestinal cancers. This work highlights sufficient ICB response in older patients.
The TME is found to be reprogrammed during cancer metastasis which also influences therapy response. Liver metastasis is commonly observed in pancreatic ductal adenocarcinoma (PDAC). To dissect the heterogeneity of PDAC upon metastasis, I analyzed integrated data of mass cytometry and scRNA-seq data and revealed that the proportion of tumor-resident CD4+/CD8+ T cells was decreased in metastasis PDAC while the proportion of CD73+ macrophage was increased, which were also validated using scRNA-seq data. This work revealed the metastasis-specific phenotypes in TME of PDAC.
Together, I linked the phenotypes of cancers such as prognosis, aging, and metastasis with TME, addressing the importance of TME during cancer progression and revealing some underlying determinants, facilitating more effective cancer therapy.published_or_final_versionBiomedical SciencesDoctoralDoctor of Philosoph
The effect of mutational processes and local determinants on cancer somatic mutation formation
No full textSomatic mutations play essential roles in cancer initiation and development. Formation of somatic mutation can be jointly caused by defect of endogenous repair mechanism like deficiency of mismatch repair and exposure of mutagens such as ultraviolet radiation, cigarette smoke and chemotherapeutic agents. Footprints left by repair and damage shape the cancer genome into unique mutational signatures, representing specific mutational processes. The distribution of mutations is uneven across the cancer genome and mutation density shows high variability at a local scale. This is largely attributed to genomic and epigenetic local determinants, including trinucleotides composition, cytosine methylation, replication timing, transcription factor binding, chromatin organization and gene expression level. By taking advantage of the vast amount of multi-omics data generated by next-generation sequencing technology, we can explore potential factors affecting cancer somatic mutation formation, thus advancing the understanding of the underlying etiology for cancer development.
In this dissertation, I leverage bioinformatic approaches on multi-omics data from samples with known mutational processes to investigate somatic mutation formation. Three projects with different perspectives were carried out during my PhD study and they are detailed in the following paragraphs.
First, we investigate the genome-wide mutation landscape of distinct polymerase epsilon (POLE) mutant cancers. We find that POLE mutants display different mutation profiles, and this can be explained by the discordant fidelities of these mutants in replicating specific DNA sequences. Significantly, these differences have important implications in cancer formation as we found that a POLE mutation is strongly associated with a specific truncating mutation of the TP53 cancer driver gene. This study furthers our understanding of the POLE mutagenic process in cancer and provides important insights into carcinogenesis in cancers with such mutations.
Second, based on mismatch repair (MMR) deficient cancer samples across multiple cohorts, we find cancer genomes with deficiency of MMR proteins MSH2/MSH6 (MutSα) exhibit mutational signature contributions distinct from those that are deficient in MLH1/PMS2 (MutLα). This disparity arises from unrepaired 5-methylcytosine (5mC) deamination, i.e. methylation damage, rather than replicative DNA polymerase errors, suggesting a non-canonical role of MMR in the protection against methylation damage in non-dividing cells and ultimately cancer development.
Third, we evaluate the influence of local determinants on panel-based tumor mutational burden (TMB) assessment. We found that cancer gene-based panels overestimate TMB calculation, potentially leading to misclassification of a subset of patients for immune checkpoint inhibitor therapy. The overestimation is largely due to increased frequency of positively selected mutations at cancer genes, which cannot simply be addressed by the removal of known hotspot mutations. We propose a cancer type and panel region-specific model that can harmonize TMB evaluation, which may have benefits for clinical practice.
In summary, interplay of DNA damage and repair, combined with local determinants, has impactful influences on cancer somatic mutation formation. These studies broaden our understanding of how certain cancers develop and provide potential support for clinical efficiency.published_or_final_versionBiomedical SciencesDoctoralDoctor of Philosoph
Predictive values of peripheral blood biomarkers for atezolizumab in combination with bevacizumab, carboplatin and pemetrexed therapy in EGFR-mutant metastatic non-small cell lung cancer patients
No full textLung cancer is the leading cause of cancer death in 2020. Non-small cell lung cancer (NSCLC), accounts for the majority of lung cancer and is very prevalent around the world. Epidermal growth factor receptor (EGFR) mutation is an important hallmark in NSCLC. As of today, 3 generations of tyrosine kinase inhibitors (TKIs) targeting EGFR have been approved by the United States Food and Drug Administration (FDA) for NSCLC treatment. However, drug resistance due to acquire EGFR mutation will develop eventually and hinder treatment efficacy. Recently, novel immunotherapy drugs such as programmed death-1 (PD-1) blockades and programmed death-ligand 1 (PD-L1) blockades have been approved by the FDA for NSCLC treatment. Despite an improved objective response rate with better safety profile, only a subset of NSCLC patients could benefit from single-agent immunotherapy. A combination of PD-L1 blockade with anti-angiogenetic agent aims to improve treatment response while maintaining a similar adverse event rate. In present study, I have quantified 8 peripheral blood biomarkers from 40 NSCLC patients treated by atezolizumab, bevacizumab, carboplatin and pemetrexed (ABCP). Peripheral blood offers a much less invasive approach to predict treatment response towards immunotherapy. Multiple studies have demonstrated the predictive value of peripheral blood biomarkers towards anti-PD-1 blockades. A significant increase in serum chemokine (C-C motif) ligand 5 (CCL5) level was detected in all patients (p < 0.01). Higher delta change of serum CCL5 level from baseline to week 10’s of treatment was associated with shorter progression-free survival (PFS) (p = 0.001), overall survival (OS) (p = 0.046) and duration of best response (p < 0.001). Furthermore, researchers revealed multiple roles of tumour-derived exosome (TEX) in cancer. Specifically, TEX could modulate anti-tumour immunity and escape immunosurveillance. Therefore, serum exosomal biomarker levels might be useful in cancer diagnosis and treatment monitoring. In present study, serum exosomal PD-L1 level and serum exosomal vascular epidermal growth factor (VEGF) level were significantly elevated after ABCP treatment (p < 0.001). However, these biomarkers were not associated with objective response rate (ORR), PFS, OS or duration of best response. Altogether, quantification of serum and serum exosomal biomarkers from peripheral blood has prognostic value towards ABCP regimen. Early identification of treatment non-responder might allow clinicians and patients to seek alternative therapeutic options and improve survival.published_or_final_versionClinical OncologyMasterMaster of Philosoph
Investigation on stem cell-associated transcription factors : artificial evolution of KLF4 and natural evolution of SOX
No full textThe generation of induced pluripotent stem cells (iPSCs) via ectopic expression of OCT4, SOX2, KLF4, and c-MYC has revolutionized the field of regenerative medicine. Among these factors, SOX2 and KLF4 are the functional core whilst OCT4 and c-MYC can be omitted. However, additional investigations are necessary for elucidating mechanisms of cell fate control, decoding the molecular basis for their ability to act as pioneer transcription factors and applying these factors for inducing next-generation stem cells for translational applications.
In the first part of this thesis, directed molecular evolution was employed to re-engineer how reprogramming factors read and write the epigenome to facilitate cell fate transitions. In the second part, the investigation was undertaken to ascertain the evolutionary origin of the transcription factor toolkit of stem cells.
Firstly, the aim was to develop new cell fate engineering paradigms by artificially evolving and enhancing the function of KLF4. From screens with three site-saturation libraries, engineered versions of KLF4 were identified, referred to as eKLF4. Two related eKLF4 variants possess correlated double mutations that enhance the affinity to DNA elements with methylated CpG sites. When combined with the other three factors, eKLF4 enables more rapid and efficient iPSC generation. Surprisingly, eKLF4 compensates for the function of the otherwise essential SOX2/OCT4 duo, allowing for reprogramming using a minimalistic two-factor cocktail alongside c-MYC. iPSCs derived from eKLF4 and c-MYC (eKM) exhibit similar characteristics to mouse embryonic stem cells in vitro and in vivo. Mechanistically, eKLF4 triggers cell-autonomous innate immunity, boosts mesenchymal to epithelial transition at the onset of reprogramming, and specifically upregulates trophectoderm genes. Chromatin accessibility profiling indicates that eKLF4 turned into a super-pioneer factor as it opens up pluripotency-associated chromatin regions otherwise requiring the presence of SOX2/OCT4. Our findings hold great promise not only for iPSC reprogramming but also for lineage reprogramming, induction of totipotency and the reprogramming of cells types and species that are challenging to turn into stem cells.
Traditionally, the Sox and POU factors have been considered specific to animals. However, we discovered that POU and Sox sequences are present in unicellular relatives of animals. Staggeringly, Sox factors from unicellular species without stem cells can replace Sox2 to induce pluripotency in mice. Likewise, resurrected Sox factors that presumably existed 700 million years ago showed that Sox genes from all the ancestral nodes leading to the Sox2 lineage have the capacity to induce pluripotency. Overall, these findings provide new insights into the evolutionary origins of stemness-associated factors and suggest that the evolution of stem cells in multicellular animals utilized a pre-existing set of transcription factors.
Taken together, in this thesis, it is demonstrated that the molecular toolkit of pluripotency predates the emergence of stem cells themselves. Through the utilization of directed molecular evolution techniques in mammalian cells, it is discovered that this toolkit can be further adapted to enable cell fate transition paradigms that were previously considered impossible.published_or_final_versionBiomedical SciencesDoctoralDoctor of Philosoph
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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