Aromatase inhibition remodels the clonal architecture of estrogen-receptor-positive breast cancers

Resistance to oestrogen-deprivation therapy is common in oestrogen-receptor-positive (ER+) breast cancer. To better understand the contributions of tumour heterogeneity and evolution to resistance, here we perform comprehensive genomic characterization of 22 primary tumours sampled before and after 4 months of neoadjuvant aromatase inhibitor (NAI) treatment. Comparing whole-genome sequencing of tumour/normal pairs from the two time points, with coincident tumour RNA sequencing, reveals widespread spatial and temporal heterogeneity, with marked remodelling of the clonal landscape in response to NAI. Two cases have genomic evidence of two independent tumours, most obviously an ER− ‘collision tumour', which was only detected after NAI treatment of baseline ER+ disease. Many mutations are newly detected or enriched post treatment, including two ligand-binding domain mutations in ESR1. The observed clonal complexity of the ER+ breast cancer genome suggests that precision medicine approaches based on genomic analysis of a single specimen are likely insufficient to capture all clinically significant information

Modeling and integrative analysis with applications to DNA replication, cancer, and epigenetics

Biological organisms have evolved complex epigenetic mechanisms to tailor their gene expression programs to specific needs. These adaptations allow cells, that otherwise have identical genomes, to carry out specialized functions. In this work I develop and use data-integrative techniques to examine the mechanisms and consequences of epigenetic processes. To better understand the changes in DNA methylation landscape that accompany breast cancer molecular subtypes, I integrated DNA methylation and gene expression data from 208 breast cancer samples obtained from a Polish population-based case-control study. Using a weighted correlation network approach, I identified gene co-methylation modules and asked if the genes in these modules are preferentially methylated and silenced in a breast cancer subtype-specific manner. This approach identified two non-overlapping gene co-methylation modules. The first module is silenced in Basal breast cancers, while the second is silenced in Luminal B breast cancers. Gene-set enrichment analysis suggests that epigenetic silencing of these modules interferes with processes that maintain cellular differentiation, and that the methylation status of the Luminal B module is associated with disease prognosis. To uncover the determinants of the temporal order of metazoan genome replication, I used a reductionist model of DNA replication to test the ability of hundreds of epigenetic marks to predict replication timing. My work showed that DNA replication timing can be completely predicted from locations of DNase I hypersensitive sites. I further demonstrated the robust emergent character of DNA replication that could be understood without invoking a complex regulatory mechanism. To determine the underlying cause of cell de-differentiation in osteosarcoma, I examined the relationship between microRNA expression and the bone-cell differentiation program. Focusing on the inhibitory role of miR-23a in bone differentiation, I analyzed the effect of its over-expression in osteosarcoma cells. Extensive computational analysis led me to propose that a major mechanism by which miR-23a exerts its effect is by interfering with expression of GJA1, which encodes a gap junction channel essential for intercellular communication and external stimuli sensing in bone cells. Follow-up experiments indicate that GJA1 is sharply up-regulated during bone cell differentiation and that GJA1 inhibition significantly delays the onset of differentiation. Together, this work uses data integrative techniques to provide new insights into the decisive role of epigenetic processes in cellular differentiation.2019-04-01T00:00:00

Changes in the gut microbiome associated with liver stiffness improvement in nonalcoholic steatohepatitis

BackgroundLongitudinal studies are needed to decipher mechanistic links between the gut microbiome and nonalcoholic steatohepatitis (NASH). We examined shifts in the gut microbiome in persons with NASH with improvement in liver stiffness measurement (LSM) by magnetic resonance (MR) elastography.MethodsGut microbial profiling was performed at baseline and study completion (24 weeks) using 16 S rRNA gene sequencing in 69 adults with biopsy-confirmed NASH and significant fibrosis (stages 2-3) enrolled in a multi-center randomized controlled trial evaluating selonsertib alone or in combination with simtuzumab. Differential abundance of bacterial taxa at baseline and end of study were examined in participants with and without longitudinal improvement in LSM. Gut microbial shifts that correlated with secondary outcomes, including reduction in MR imaging-derived proton density fat faction (MRI-PDFF) and histologic fibrosis regression were evaluated. Fecal samples from 32 healthy adults were profiled and genus-level multidimensional scaling was used to determine if microbial shifts in persons with NASH improvement represented a shift toward a healthy gut microbiome.ResultsShifts in abundance of 36 bacterial taxa including Lactobacillus (log2FC = -4.51, FDR < 0.001), Enterococcus (log2FC = -6.72, FDR < 0.001), and Megasphaera (log2FC = 7.74, FDR < 0.001) were associated with improvement in LSM. Improvement in LSM was associated with microbial shifts toward healthy reference (p = 0.05). Significant shifts in 10 and 12 bacterial taxa were associated with improvement in LSM in addition to MRI-PDFF and fibrosis regression, respectively, indicating consistent taxonomic changes across multiple clinical endpoints.ConclusionLongitudinal changes in the gut microbiota are observed in adults with NASH and clinical improvement and represent a shift toward a healthy microbiome

DNA Methylation and Immune Cell Markers Demonstrate Evidence of Accelerated Aging in Patients with Chronic HBV or HCV, with or without HIV Co-Infection

BACKGROUND: Several chronic diseases accelerate biological aging. We investigated age acceleration and the association between peripheral blood DNA methylation (DNAm) and immune cell markers in patients chronically infected with the hepatitis B virus (HBV) or the hepatitis C virus (HCV) with and without human immunodeficiency virus (HIV) co-infection. METHODS: Age acceleration was measured as the difference between epigenetic age (Horvath clock) and chronological age. The immune marker model of age acceleration was developed using Elastic Net regression to select both the immune markers and their associated weights in the final linear model. RESULTS: Patients with chronic HBV (n = 51) had a significantly higher median epigenetic age compared to chronological age (age accelerated) (P < .001). In patients with chronic HCV infection (n = 63), age acceleration was associated with liver fibrosis as assessed by histology (P < .05), or presence of HIV co-infection (P < .05), but not HCV mono-infection. Age acceleration defined by immune markers was concordant with age acceleration by DNA methylation (correlation coefficient = .59 in HBV; P = .0025). One-year treatment of HBV patients with nucleoside therapy was associated with a modest reduction in age acceleration, as measured using the immune marker model (-.65 years, P = .018). CONCLUSION: Our findings suggest that patients with chronic viral hepatitis have accelerated epigenetic aging, that immune markers define biological age, and have the potential to assess the effects of therapeutic intervention on age acceleratio