Extent Of Spatial Heterogeneity Research Articles

PhyliCS: a Python library to explore scCNA data and quantify spatial tumor heterogeneity

BackgroundTumors are composed by a number of cancer cell subpopulations (subclones), characterized by a distinguishable set of mutations. This phenomenon, known as intra-tumor heterogeneity (ITH), may be studied using Copy Number Aberrations (CNAs). Nowadays ITH can be assessed at the highest possible resolution using single-cell DNA (scDNA) sequencing technology. Additionally, single-cell CNA (scCNA) profiles from multiple samples of the same tumor can in principle be exploited to study the spatial distribution of subclones within a tumor mass. However, since the technology required to generate large scDNA sequencing datasets is relatively recent, dedicated analytical approaches are still lacking.ResultsWe present PhyliCS, the first tool which exploits scCNA data from multiple samples from the same tumor to estimate whether the different clones of a tumor are well mixed or spatially separated. Starting from the CNA data produced with third party instruments, it computes a score, the Spatial Heterogeneity score, aimed at distinguishing spatially intermixed cell populations from spatially segregated ones. Additionally, it provides functionalities to facilitate scDNA analysis, such as feature selection and dimensionality reduction methods, visualization tools and a flexible clustering module.ConclusionsPhyliCS represents a valuable instrument to explore the extent of spatial heterogeneity in multi-regional tumour sampling, exploiting the potential of scCNA data.

Causes and Consequences of Spatial Within-Host Viral Spread.

The spread of viral pathogens both between and within hosts is inherently a spatial process. While the spatial aspects of viral spread at the epidemiological level have been increasingly well characterized, the spatial aspects of viral spread within infected hosts are still understudied. Here, with a focus on influenza A viruses (IAVs), we first review experimental studies that have shed light on the mechanisms and spatial dynamics of viral spread within hosts. These studies provide strong empirical evidence for highly localized IAV spread within hosts. Since mathematical and computational within-host models have been increasingly used to gain a quantitative understanding of observed viral dynamic patterns, we then review the (relatively few) computational modeling studies that have shed light on possible factors that structure the dynamics of spatial within-host IAV spread. These factors include the dispersal distance of virions, the localization of the immune response, and heterogeneity in host cell phenotypes across the respiratory tract. While informative, we find in these studies a striking absence of theoretical expectations of how spatial dynamics may impact the dynamics of viral populations. To mitigate this, we turn to the extensive ecological and evolutionary literature on range expansions to provide informed theoretical expectations. We find that factors such as the type of density dependence, the frequency of long-distance dispersal, specific life history characteristics, and the extent of spatial heterogeneity are critical factors affecting the speed of population spread and the genetic composition of spatially expanding populations. For each factor that we identified in the theoretical literature, we draw parallels to its analog in viral populations. We end by discussing current knowledge gaps related to the spatial component of within-host IAV spread and the potential for within-host spatial considerations to inform the development of disease control strategies.

Abstract P6-01-02: Spatial heterogeneity of response on whole-body MRI to first line hormonal therapy predicts progression-free survival in metastatic breast cancer

Abstract Background Whole-body magnetic resonance imaging (WB-MRI) reliably identifies types of response to systemic therapy in metastatic breast cancer (MBC) through analysis of changes in water diffusivity, cellularity and cell variability. We adapted a novel methodology that uses WB-MRI to capture spatial response heterogeneity data via the METastasis Response Assessment Diagnostic System (MET-RADS). This study evaluates whether the extent of spatial heterogeneity seen at initial response assessment is predictive of progression-free survival (PFS) in patients on first line hormonal therapy for MBC. Methods Patients on first line hormonal therapy for MBC who had undergone baseline and on-treatment response assessment WB-MRI scans were identified. All scans were performed using a published WB-MRI protocol. Patients with disease progression at their first WB-MRI response assessment were excluded from further analysis. Criteria for response assessment utilised the methodology described by MET-RADS. A Likert five-point Response Assessment Category (RAC) score (1=response highly likely; 2=response likely; 3=no change; 4=progression likely; 5=progression highly likely) was applied separately to 14 defined anatomic regions. Within each region, two RAC scores were recorded to reflect both the dominant and the next most common pattern of response behaviour. Data were therefore captured on inter- and intra-regional response heterogeneity. A novel Response Heterogeneity Index (RHI) was calculated from the regional RAC scores. The RHI value summarised the overall response heterogeneity seen across all involved regions, with higher scores indicative of greater heterogeneity of response. Depth of overall response to treatment was defined as the mean RAC score for all involved regions, with lower scores indicative of a greater depth of treatment response. RHI and mean RAC score data were separated by median values into two groups for analysis. Results Thirty-three patients were suitable for analysis. Patients with higher levels of response heterogeneity (defined as RHI≥4; n=16) had significantly shorter PFS than those with RHI <4 (n=17; median PFS: 12 vs 24 months; log rank test p=0.006). Depth of initial response, as defined by mean RAC score, and PFS were unrelated (mean RAC ≤2.5 (n=17) vs mean RAC >2.5 (n=16); median PFS: 27 vs 23 months; log rank test p=0.699). There was no correlation between RHI score and mean RAC score (r2=0.002). Conclusions Lower variability of response behaviour at first treatment assessment is predictive of longer treatment duration in patients receiving first line hormonal therapy for MBC. The spatial heterogeneity of response evident on WB-MRI may represent the genetic heterogeneity and clonal evolution of MBC, which are key factors in the development of treatment resistance. Citation Format: Kosmin M, Makris A, Sokhi H, Thijssen T, Padhani A. Spatial heterogeneity of response on whole-body MRI to first line hormonal therapy predicts progression-free survival in metastatic breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P6-01-02.

Spatial genomic heterogeneity in multiple myeloma revealed by multi-region sequencing

In multiple myeloma malignant plasma cells expand within the bone marrow. Since this site is well-perfused, a rapid dissemination of “fitter” clones may be anticipated. However, an imbalanced distribution of multiple myeloma is frequently observed in medical imaging. Here, we perform multi-region sequencing, including iliac crest and radiology-guided focal lesion specimens from 51 patients to gain insight into the spatial clonal architecture. We demonstrate spatial genomic heterogeneity in more than 75% of patients, including inactivation of CDKN2C and TP53, and mutations affecting mitogen-activated protein kinase genes. We show that the extent of spatial heterogeneity is positively associated with the size of biopsied focal lesions consistent with regional outgrowth of advanced clones. The results support a model for multiple myeloma progression with clonal sweeps in the early phase and regional evolution in advanced disease. We suggest that multi-region investigations are critical to understanding intra-patient heterogeneity and the evolutionary processes in multiple myeloma.

Evolution in spatially mixed host environments increases divergence for evolved fitness and intrapopulation genetic diversity in RNA viruses.

Virus populations may be challenged to evolve in spatially heterogeneous environments, such as mixtures of host cells that pose differing selection pressures. Spatial heterogeneity may select for evolved polymorphisms, where multiple virus subpopulations coexist by specializing on a narrow subset of the available hosts. Alternatively, spatial heterogeneity may select for evolved generalism, where a single genotype dominates the virus population by occupying a relatively broader host niche. In addition, the extent of spatial heterogeneity should influence the degree of divergence among virus populations encountering identical environmental challenges. Spatial heterogeneity creates environmental complexity that should increase the probability of differing adaptive phenotypic solutions, thus producing greater divergence among replicate virus populations, relative to counterparts evolving in strictly homogeneous host environments. Here, we tested these ideas using experimental evolution of RNA virus populations grown in laboratory tissue culture. We allowed vesicular stomatitis virus (VSV) lineages to evolve in replicated environments containing BHK-21 (baby hamster kidney) cells, HeLa (human epithelial) cells, or spatially heterogeneous host cell mixtures. Results showed that generalist phenotypes dominated in evolved virus populations across all treatments. Also, we observed greater variance in host-use performance (fitness) among VSV lineages evolved under spatial heterogeneity, relative to lineages evolved in homogeneous environments. Despite measurable differences in fitness, consensus Sanger sequencing revealed no fixed genetic differences separating the evolved lineages from their common ancestor. In contrast, deep sequencing of evolved VSV populations confirmed that the degree of divergence among replicate lineages was correlated with a larger number of minority variants. This correlation between divergence and the number of minority variants was significant only when we considered variants with a frequency of at least 10 per cent in the population. The number of lower-frequency minority variants per population did not significantly correlate with divergence.

Generating Heterogeneity Spectra from Spatially Resolved Measurements

A new method is presented for describing spatial heterogeneity in materials that simultaneously present heterogeneity on a broad distribution of length scales. The method involves fitting the experimental variogram to a nested structure consisting of many model functions, each with a single range. Experimental regularization is rigorously considered, resulting in a description of the data on point-support. The output of this method is a plot called the heterogeneity spectrum. The heterogeneity spectrum shows the extent of spatial heterogeneity as a function of length scale, without bias from finite experimental resolution and sample size, covering all length scales to which the measurement is sensitive. As an example, the heterogeneity spectra of carbonate rocks measured by magnetic resonance imaging are shown. These experiments are sensitive to heterogeneity at length scales in the range 10−0.5–102 mm, and the heterogeneity spectra reveal relevant and otherwise unavailable information about the structure of these carbonate rocks. The geostatistical methodology behind constructing the heterogeneity spectra is described here, while full details on the magnetic resonance imaging aspects are provided in a companion paper (Pomerantz, Tilke and Song in J. Magn. Reson. 193:243–250, 2008).

Rabbit Grazing, Plant Competition and Seedling Recruitment in Acid Grassland

(1) Two experiments were done to determine the effect of grazing by rabbits on plant recruitment in mature grassland and on cultivated soil. The first was a factorial experiment, with and without rabbit fencing, and with and without soil cultivation, carried out between 1986 and 1989 in acid grassland with a long history of rabbit grazing. In the second, carried out between 1982 and 1985 in two contrasting arable fields, rabbits grazed crops of winter wheat, with fencing enclosures erected at different times and for different durations. (2) Rabbit grazing affected the stature and composition of the grassland throughout the year. Species that increased in cover in rabbit-grazed grassland included the grass Anthoxanthum odoratum and the forb Rumex acetosella. Species that decreased included the grasses Festuca rubra and Agrostis capillaris and the forbs Vicia sativa and Trifolium repens. There was negligible change in the total number of plant species with grazing. (3) The cultivated treatments showed that the seed bank under the acid grassland was extremely heterogeneous. (4) Eight of the twenty-three commonest ruderal species beneath acid grassland decreased in cover significantly (e.g. Capsella bursa-pastoris and Papaver dubium), and none increased significantly. In contrast, most of the ruderal species in the seed bank of nearby arable soils increased under grazing. (5) Most plant species on cultivated grassland soils regenerated from vegetative fragments (e.g. Holcus mollis, Stellaria graminea, Rumex acetosa and R. acetosella), rather than by germination of seed. Regrowth shoots outnumbered seedlings by a factor of between 3 and 23 3. (6) The extent of spatial heterogeneity within and between plots in both the composition of the buried seed bank, and in recruitment by vegetative regrowth, highlights the need for large sample sizes in this kind of study. (7) The mechanisms that determine whether a plant species increases or decreases under grazing are discussed.

Spatial heterogeneity of local blood flow and metabolite content in dog hearts

Spatial variation (heterogeneity) of myocardial blood flow was studied under basal conditions in relation to four biochemical markers: creatine kinase (CK), lactate dehydrogenase (LDH), ATP, and glycogen. A total of 508 individual 0.5-g samples from the left ventricular free wall was studied in 12 dogs. Myocardial blood flow was measured by radioactive microspheres (15 micron diam) injected via a pigtail catheter into the left ventricle during light sedation (closed-chest flow measurements); following thoracotomy, a second set of microspheres was injected via a catheter into the left atrium (open-chest flow measurements, n = 5). In 27-54 samples/heart, myocardial blood flow, CK, LDH, protein, ATP, and glycogen were determined, permitting a direct correspondence between local blood flow and metabolic markers in each sample and an assessment of the spatial heterogeneity of flow and metabolite content. Correlations between myocardial blood flow per gram tissue and metabolite concentration per gram tissue in pooled data were weak but significant: partial correlation coefficients were 0.137 for CK (P = 0.024), 0.167 for LDH (P = 0.006), 0.341 for ATP (P less than 0.001), 0.123 for glycogen (P = 0.053), but not significant for protein vs. myocardial blood flow. The coefficient of variation, which defines the extent of spatial heterogeneity, averaged 20% for closed-chest flow measurements, 19% for open-chest flow measurements, 22% for CK, 17% for LDH, 15% for protein, 8% for ATP, and 18% for glycogen; these values are over and above the variability due to the technique error, indicating a definite physiological spatial variability. The correlation between local blood flow and the studied metabolites can only explain a minor portion of the spatial heterogeneity of myocardial blood flow. Although a physiological link between blood flow and metabolite content for small regions of the heart is demonstrated, the true local variability of blood flow may be modulated predominantly by other factors.