Browsing by author "Baker, Ann-Marie Clare"

Now showing items 1-12 of 12

    • Cancer associated fibroblast FAK regulates malignant cell metabolism. 

      Demircioglu, F; Wang, J; Candido, J; Costa, ASH; Casado, P; et al. (NATURE PUBLISHING GROUP, 2020-03-10)
      Emerging evidence suggests that cancer cell metabolism can be regulated by cancer-associated fibroblasts (CAFs), but the mechanisms are poorly defined. Here we show that CAFs regulate malignant cell metabolism through ...

    • Crypt fusion as a homeostatic mechanism in the human colon. 

      Baker, A-M; Gabbutt, C; Williams, MJ; Cereser, B; Jawad, N; et al. (BMJ PUBLISHING GROUP, 2019-11-01)
      OBJECTIVE: The crypt population in the human intestine is dynamic: crypts can divide to produce two new daughter crypts through a process termed crypt fission, but whether this is balanced by a second process to remove ...

    • First passage time analysis of spatial mutation patterns reveals sub-clonal evolutionary dynamics in colorectal cancer. 

      Haughey, MJ; Bassolas, A; Sousa, S; Baker, A-M; Graham, TA; et al. (PUBLIC LIBRARY SCIENCE, 2023-03-01)
      The signature of early cancer dynamics on the spatial arrangement of tumour cells is poorly understood, and yet could encode information about how sub-clones grew within the expanding tumour. Novel methods of quantifying ...

    • FUME-TCRseq enables sensitive and accurate sequencing of the T-cell receptor from limited input of degraded RNA. 

      Baker, A-M; Nageswaran, G; Nenclares, P; Ronel, T; Smith, K; et al. (American Association for Cancer Research (AACR), 2024-03-14)
      Genomic analysis of the T-cell receptor (TCR) reveals the strength, breadth, and clonal dynamics of the adaptive immune response to pathogens or cancer. The diversity of the TCR repertoire, however, means that sequencing ...

    • Immunosuppressive niche engineering at the onset of human colorectal cancer. 

      Gatenbee, CD; Baker, A-M; Schenck, RO; Strobl, M; West, J; et al. (NATURE PORTFOLIO, 2022-04-04)
      The evolutionary dynamics of tumor initiation remain undetermined, and the interplay between neoplastic cells and the immune system is hypothesized to be critical in transformation. Colorectal cancer (CRC) presents a unique ...

    • Lineage tracing in human tissues. 

      Gabbutt, C; Wright, NA; Baker, A-M; Shibata, D; Graham, TA (WILEY, 2022-05-05)
      The dynamical process of cell division that underpins homeostasis in the human body cannot be directly observed in vivo, but instead is measurable from the pattern of somatic genetic or epigenetic mutations that accrue in ...

    • Phenotypic plasticity and genetic control in colorectal cancer evolution. 

      Househam, J; Heide, T; Cresswell, GD; Spiteri, I; Kimberley, C; et al. (NATURE PORTFOLIO, 2022-11-24)
      Genetic and epigenetic variation, together with transcriptional plasticity, contribute to intratumour heterogeneity1. The interplay of these biological processes and their respective contributions to tumour evolution remain ...

    • Robust RNA-based in situ mutation detection delineates colorectal cancer subclonal evolution. 

      Baker, A-M; Huang, W; Wang, X-MM; Jansen, M; Ma, X-J; et al. (NATURE PUBLISHING GROUP, 2017-12-08)
      Intra-tumor heterogeneity (ITH) is a major underlying cause of therapy resistance and disease recurrence, and is a read-out of tumor growth. Current genetic ITH analysis methods do not preserve spatial context and may not ...

    • The co-evolution of the genome and epigenome in colorectal cancer 

      Sottoriva, A; Heide, T; Cresswell, G; Spiteri, I; Lynn, C; et al. (2021-07-12)
      Colorectal malignancies are a leading cause of cancer death. Despite large-scale genomic efforts, DNA mutations do not fully explain malignant evolution. Here we study the co-evolution of the genome and epigenome of ...

    • The co-evolution of the genome and epigenome in colorectal cancer. 

      Heide, T; Househam, J; Cresswell, GD; Spiteri, I; Lynn, C; et al. (NATURE PORTFOLIO, 2022-11-24)
      Colorectal malignancies are a leading cause of cancer-related death1 and have undergone extensive genomic study2,3. However, DNA mutations alone do not fully explain malignant transformation4-7. Here we investigate the ...

    • The evolutionary landscape of colorectal tumorigenesis. 

      Cross, W; Kovac, M; Mustonen, V; Temko, D; Davis, H; et al. (NATURE PORTFOLIO, 2018-10-01)
      The evolutionary events that cause colorectal adenomas (benign) to progress to carcinomas (malignant) remain largely undetermined. Using multi-region genome and exome sequencing of 24 benign and malignant colorectal tumours, ...

    • Virtual alignment of pathology image series for multi-gigapixel whole slide images. 

      Gatenbee, CD; Baker, A-M; Prabhakaran, S; Swinyard, O; Slebos, RJC; et al. (NATURE PORTFOLIO, 2023-07-26)
      Interest in spatial omics is on the rise, but generation of highly multiplexed images remains challenging, due to cost, expertise, methodical constraints, and access to technology. An alternative approach is to register ...