Julie Livingstone
A5061507303- Prostate Cancer Treatment and Research
- Advanced Proteomics Techniques and Applications
- Cancer Genomics and Diagnostics
- Prostate Cancer Diagnosis and Treatment
- Radiomics and Machine Learning in Medical Imaging
- Cancer, Lipids, and Metabolism
- HER2/EGFR in Cancer Research
- Cancer-related molecular mechanisms research
- Lung Cancer Treatments and Mutations
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Genetic factors in colorectal cancer
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Cancer, Hypoxia, and Metabolism
- Cancer Cells and Metastasis
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Cancer-related Molecular Pathways
- Evolution and Genetic Dynamics
- Telomeres, Telomerase, and Senescence
- Cancer-related gene regulation
- Microtubule and mitosis dynamics
- Chromosomal and Genetic Variations
University of California, Los Angeles
2020-2025
Ontario Institute for Cancer Research
2015-2024
Precision Research (United States)
2021-2024
APLA Health
2023
UCLA Health
2022
University of Colorado Denver
2022
University of Colorado Cancer Center
2022
Princess Margaret Cancer Centre
2020-2021
University Health Network
2020-2021
University of Toronto
2018-2021
Abstract Germline mutations in the BRCA2 tumour suppressor are associated with both an increased lifetime risk of developing prostate cancer (PCa) and aggressive disease. To understand this aggression, here we profile genomes methylomes localized PCa from 14 carriers deleterious germline ( -mutant PCa). We show that harbour genomic instability a mutational more closely resembles metastastic than shows epigenomic dysregulation MED12L / MED12 axis, which is frequently dysregulated metastatic...
Metastatic castration-resistant prostate cancer (mCRPC) has a highly complex genomic landscape. With the recent development of novel treatments, accurate stratification strategies are needed. Here we present whole-genome sequencing (WGS) analysis fresh-frozen metastatic biopsies from 197 mCRPC patients. Using unsupervised clustering based on features, define eight distinct clusters. We observe potentially clinically relevant genotypes, including microsatellite instability (MSI), homologous...
Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated cancers, yet molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions cancer, including 213 patients primary anaplastic carcinomas. also whole genome 9 using multi-region sequencing both and cancer components. Using these data, we demonstrate thatanaplastic carcinomas have a higher burden mutations than other distinct mutational signatures...
Abstract Newly diagnosed prostate cancers differ dramatically in mutational composition and lethality. The most accurate clinical predictor of lethality is tumor tissue architecture, quantified as grade. To interrogate the evolutionary origins cancer heterogeneity, we analyzed 666 whole genomes. We identified a compendium 223 recurrently mutated driver regions, influencing downstream processes gene expression. validated individual germline variants that predispose tumors to acquire specific...
Invasive cribriform and intraductal carcinoma (CR/IDC) is associated with adverse outcome of prostate cancer patients. The aim this study was to determine the molecular aberrations CR/IDC in primary cancer, focusing on genomic instability somatic copy number alterations (CNA). Whole-slide images Cancer Genome Atlas Project (TCGA, N = 260) Canadian Prostate Network (CPC-GENE, 199) radical prostatectomy datasets were reviewed for Gleason score (GS) presence CR/IDC. Genomic assessed by...
Abstract Single-cell RNA sequencing studies have suggested that total mRNA content correlates with tumor phenotypes. Technical and analytical challenges, however, so far impeded at-scale pan-cancer examination of content. Here we present a method to quantify tumor-specific expression (TmS) from bulk data, taking into account transcript proportion, purity ploidy, which are estimated through transcriptomic/genomic deconvolution. We estimate validate TmS in 6,590 patient tumors across 15 cancer...
Breast carcinoma (BC) has been extensively profiled by high-throughput technologies for over a decade, and broadly speaking, these studies can be grouped into those that seek to identify patient subtypes (studies of heterogeneity) or gene signatures with prognostic predictive capacity. The sheer number reported led speculation everything is in BC. Here, we show this ubiquity an apparition caused poor understanding the interrelatedness between subtype molecular determinants prognosis. Our...
Abstract Prostate cancer is the second most commonly diagnosed malignancy among men worldwide. Recurrently mutated in primary and metastatic prostate tumors, FOXA1 encodes a pioneer transcription factor involved disease onset progression through both androgen receptor-dependent receptor-independent mechanisms. Despite its oncogenic properties however, regulation of expression remains unknown. Here, we identify set six cis -regulatory elements regulatory plexus harboring somatic...
Prostate cancer is characterized by profound heterogeneity in its clinical trajectory. While genomic has been well-characterized, epigenomic remains less understood. To fill this gap, we compiled 2,149 multi-ancestric prostate methylomes spanning normal tissue through localized disease of varying grades to poly-metastatic disease, most with multi-omic DNA and/or RNA characterization. We identify four subtypes that varied stage, grade and mutational subtype. extensive interplay between ploidy...
N6-methyladenosine (m6A), the most abundant internal RNA modification in humans, regulates aspects of processing. Prostate cancer is characterized by widespread transcriptomic dysregulation; therefore, we m6A landscape 162 localized prostate tumors with matched DNA, and protein profiling. abundance varied dramatically across tumors, global patterns emerging via complex germline–somatic cooperative regulation. Individual germline polymorphisms regulated abundance, cooperating somatic mutation...
The mammary epithelium depends on specific lineages and their stem progenitor function to accommodate hormone-triggered physiological demands in the adult female. Perturbations of these underpin breast cancer risk, yet our understanding normal cell composition is incomplete. Here, we build a multimodal resource for gland through comprehensive profiling primary epigenomes, transcriptomes, proteomes. We define systems-level relationships between chromatin–DNA–RNA–protein states, identify...
Cell populations able to generate a large repertoire of genetic variants have increased potential tumor cells that survive through the multiple selection steps involved in progression. A mechanism for generation aneuploid cancer involves passage tetraploid stage. Supernumerary centrosomes, however, can lead multipolar mitosis and cell death. Using tissue culture transgenic mouse models breast cancer, we report Cut homeobox 1 (CUX1) causes chromosomal instability by activating transcriptional...
Abstract Rab coupling protein (FIP1C), an effector of the Rab11 GTPases, including Rab25, is amplified and overexpressed in 10% to 25% primary breast cancers correlates with poor clinical outcome. Rab25 also frequently silenced triple-negative cancer, suggesting its ability function as either oncogene or a tumor suppressor, depending on cancer subtype. However, pathobiologic role FIP family members, such FIP1C, tumor-specific setting remains elusive. In this study, we used ErbB2 mouse models...
Abstract Gene expression is a multi-step transformation of biological information from its storage form (DNA) into functional forms (protein and some RNAs). Regulatory activities at each step this multiply single gene myriad proteoforms. Proteogenomics the study how genomic transcriptomic variation creates proteoform diversity, limited by challenges modeling complexities gene-expression. We therefore created moPepGen, graph-based algorithm that comprehensively enumerates proteoforms in...