Single-cell RNA sequencing can reveal valuable insights into cellular heterogeneity within tumour microenvironments (TMEs), paving the way for a deep understanding of cellular mechanisms contributing ...to cancer. However, high heterogeneity among the same cancer types and low transcriptomic variation in immune cell subsets present challenges for accurate, high-resolution confirmation of cells' identities. Here we present scATOMIC; a modular annotation tool for malignant and non-malignant cells. We trained scATOMIC on >300,000 cancer, immune, and stromal cells defining a pan-cancer reference across 19 common cancers and employ a hierarchical approach, outperforming current classification methods. We extensively confirm scATOMIC's accuracy on 225 tumour biopsies encompassing >350,000 cancer and a variety of TME cells. Lastly, we demonstrate scATOMIC's practical significance to accurately subset breast cancers into clinically relevant subtypes and predict tumours' primary origin across metastatic cancers. Our approach represents a broadly applicable strategy to analyse multicellular cancer TMEs.
Uncovering the interaction between genomes and the environment is a principal challenge of modern genomics and preventive medicine. While theoretical models are well defined, little is known of the G ...× E interactions in humans. We used an integrative approach to comprehensively assess the interactions between 1.6 million data points, encompassing a range of environmental exposures, health, and gene expression levels, coupled with whole-genome genetic variation. From ∼1000 individuals of a founder population in Quebec, we reveal a substantial impact of the environment on the transcriptome and clinical endophenotypes, overpowering that of genetic ancestry. Air pollution impacts gene expression and pathways affecting cardio-metabolic and respiratory traits, when controlling for genetic ancestry. Finally, we capture four expression quantitative trait loci that interact with the environment (air pollution). Our findings demonstrate how the local environment directly affects disease risk phenotypes and that genetic variation, including less common variants, can modulate individual's response to environmental challenges.
Age-related clonal hematopoiesis (ARCH) is characterized by age-associated accumulation of somatic mutations in hematopoietic stem cells (HSCs) or their pluripotent descendants. HSCs harboring driver ...mutations will be positively selected and cells carrying these mutations will rise in frequency. While ARCH is a known risk factor for blood malignancies, such as Acute Myeloid Leukemia (AML), why some people who harbor ARCH driver mutations do not progress to AML remains unclear. Here, we model the interaction of positive and negative selection in deeply sequenced blood samples from individuals who subsequently progressed to AML, compared to healthy controls, using deep learning and population genetics. Our modeling allows us to discriminate amongst evolutionary classes with high accuracy and captures signatures of purifying selection in most individuals. Purifying selection, acting on benign or mildly damaging passenger mutations, appears to play a critical role in preventing disease-predisposing clones from rising to dominance and is associated with longer disease-free survival. Through exploring a range of evolutionary models, we show how different classes of selection shape clonal dynamics and health outcomes thus enabling us to better identify individuals at a high risk of malignancy.
Cystic Fibrosis (CF) exhibits morbidity in several organs, including progressive lung disease in all patients and intestinal obstruction at birth (meconium ileus) in ~15%. Individuals with the same ...causal CFTR mutations show variable disease presentation which is partly attributed to modifier genes. With >6,500 participants from the International CF Gene Modifier Consortium, genome-wide association investigation identified a new modifier locus for meconium ileus encompassing ATP12A on chromosome 13 (min p = 3.83x10(-10)); replicated loci encompassing SLC6A14 on chromosome X and SLC26A9 on chromosome 1, (min p<2.2x10(-16), 2.81x10(-11), respectively); and replicated a suggestive locus on chromosome 7 near PRSS1 (min p = 2.55x10(-7)). PRSS1 is exclusively expressed in the exocrine pancreas and was previously associated with non-CF pancreatitis with functional characterization demonstrating impact on PRSS1 gene expression. We thus asked whether the other meconium ileus modifier loci impact gene expression and in which organ. We developed and applied a colocalization framework called the Simple Sum (SS) that integrates regulatory and genetic association information, and also contrasts colocalization evidence across tissues or genes. The associated modifier loci colocalized with expression quantitative trait loci (eQTLs) for ATP12A (p = 3.35x10(-8)), SLC6A14 (p = 1.12x10(-10)) and SLC26A9 (p = 4.48x10(-5)) in the pancreas, even though meconium ileus manifests in the intestine. The meconium ileus susceptibility locus on chromosome X appeared shifted in location from a previously identified locus for CF lung disease severity. Using the SS we integrated the lung disease association locus with eQTLs from nasal epithelia of 63 CF participants and demonstrated evidence of colocalization with airway-specific regulation of SLC6A14 (p = 2.3x10(-4)). Cystic Fibrosis is realizing the promise of personalized medicine, and identification of the contributing organ and understanding of tissue specificity for a gene modifier is essential for the next phase of personalizing therapeutic strategies.
Risk prediction models can translate genetic association findings for clinical decision-making. Most models are evaluated on their ability to discriminate, and the calibration of risk-prediction ...models is largely overlooked in applications. Models that demonstrate good discrimination in training datasets, if not properly calibrated to produce unbiased estimates of risk, can perform poorly in new patient populations. Poorly calibrated models arise due to missing covariates, such as genetic interactions that may be unknown or not measured. We demonstrate that models omitting interactions can lead to increased bias in predicted risk for patients at the tails of the risk distribution; i.e., those patients who are most likely to be affected by clinical decision making. We propose a new calibration test for Cox risk-prediction models that aggregates martingale residuals for subjects from extreme high and low risk groups with a test statistic maximum chosen by varying which risk groups are included in the extremes. To estimate the empirical significance of our test statistic, we simulate from a Gaussian distribution using the covariance matrix for the grouped sums of martingale residuals. Simulation shows the new test maintains control of type 1 error with improved power over a conventional goodness-of-fit test when risk prediction deviates at the tails of the risk distribution. We apply our method in the development of a prediction model for risk of cystic fibrosis-related diabetes. Our study highlights the importance of assessing calibration and discrimination in predictive modeling, and provides a complementary tool in the assessment of risk model calibration.
Abstract Background context No clinical trial of spinal manipulation for chronic neck pain (NP), for either single or multiple intervention session(s), has used an effective manual sham-manipulation ...control group. Purpose Validate a practical sham cervical high-velocity low-amplitude spinal manipulation. Study design/setting Randomized experimental validation study in an institutional clinical research laboratory. Patient sample Eligible subjects were males and females, 18 to 60 years of age with mechanical NP (as defined by the International Association for the Study of Pain Classification) of at least 3 months' duration. Subjects with arm pain, any pathologic cause of NP, or any contraindication to spinal manipulation were excluded. Outcome measures The primary outcome was the patient's self-report or registration of group allocation after treatment. Secondary outcomes were numerical rating scale-101 for NP, range of motion (ROM; by goniometer), and tenderness (by pressure algometry). Methods Eligible subjects were randomly allocated to one of two groups: real cervical manipulation (RM) or sham cervical manipulation (SM). All subjects were given two procedures in sequence, either RM+SM or SM+SM. Immediately after the two procedures, subjects were asked to register any pain experienced during the procedures and to identify their treatment group allocation. Force-time profiles were recorded during all procedures. Secondary clinical outcome measures were obtained at baseline, 5 and 15 minutes after the intervention, including ROM, self-report of pain, and local spinous process tenderness. Data for each variable were summarized and tested for normality in distribution. Summary statistics were obtained for each variable and statistically tested. Results Sixty-seven subjects were randomized. Data from 64 subjects (32 per group) were available for analysis. There were no significant differences between the groups at baseline. One adverse event occurred in the “real” group, which was a mild posttreatment pain reaction lasting less than 24 hours. In the RM group, 50% of subjects incorrectly registered their treatment allocation; in the sham group, 53% did so. For the SM group, none of the procedures resulted in cavitation, whereas in the RM group, 87% of procedures resulted in cavitation. There were no significant changes between groups on pain, tenderness, or ROM. Force-time profiles of the RM and SM procedures demonstrated fidelity with significant differences between components as intended. Conclusions The novel sham procedure has been shown to be effective in masking subjects to group allocation and to be clinically inert with respect to common outcomes in the immediate posttreatment stage. Further research on serial applications and for multiple operators is warranted.
Circulating immunoreactive trypsinogen (IRT), a biomarker of exocrine pancreatic disease in cystic fibrosis (CF), is elevated in most CF newborns. In those with severe CF transmembrane conductance ...regulator (CFTR) genotypes, IRT declines rapidly in the first years of life, reflecting progressive pancreatic damage. Consistent with this progression, a less elevated newborn IRT measure would reflect more severe pancreatic disease, including compromised islet compartments, and potentially increased risk of CF-related diabetes (CFRD). We show in two independent CF populations that a lower newborn IRT estimate is associated with higher CFRD risk among individuals with severe CFTR genotypes, and we provide evidence to support a causal relationship. Increased loge(IRT) at birth was associated with decreased CFRD risk in Canadian and Colorado samples (hazard ratio 0.30 95% CI 0.15-0.61 and 0.39 0.18-0.81, respectively). Using Mendelian randomization with the SLC26A9 rs7512462 genotype as an instrumental variable since it is known to be associated with IRT birth levels in the CF population, we provide evidence to support a causal contribution of exocrine pancreatic status on CFRD risk. Our findings suggest CFRD risk could be predicted in early life and that maintained ductal fluid flow in the exocrine pancreas could delay the onset of CFRD.
Abstract Objective Sitting has been identified as a cause of mechanical low back pain. The purpose of this study was to use plain film x-rays to measure lumbar spine and pelvic posture differences ...between standing and sitting. Methods Eight male subjects were radiographed standing and sitting in an automobile seat. Measures of lumbar lordosis, intervertebral disk angles, lumbosacral angle, lumbosacral lordosis, and sacral tilt were completed. One-way analysis of variance ( α = .05) was conducted on the variables stated above. A Bland-Altman analysis was conducted to assess agreement and repeatability of the lumbar lordosis angle using 2 raters. Results Lumbar lordosis values in standing (average, 63° ± 15°) and sacral inclination (average, 43° ± 10°) decreased by 43° and 44°, respectively, in sitting. Intervertebral joint angles in sitting underwent substantial flexion (L1/L2—5° ±3°, L2/L3—7° ±3°, L3/L4—8° ±3°, L4/L5—13° ±3°, and L5/S1—4° ±10°). Measures of lumbar lordosis; intervertebral disk angles between L2/L3, L3/L4, and L4/L5; lumbosacral lordosis; lumbosacral angle; and sacral tilt were significantly decreased between standing and sitting ( P < .001). Intervertebral disk angle between L5/S1 was not significantly different. Analysis using the Bland-Altman technique found good agreement and stable repeatability of measures with no statistical significant differences between or within raters (R1, P = .8474; R2, P = .4402; and R-R2, P = .8691). Conclusion The significant differences in lumbar and pelvic measures from standing to sitting further emphasize the range of motion experienced at vertebral levels in sitting. Based on the results of this study, interventions to return motion segments to a less flexed posture should be investigated because they may play a role in preventing injury and low back pain.
We generalize Levene's test for variance (scale) heterogeneity between k groups for more complex data, when there are sample correlation and group membership uncertainty. Following a two-stage ...regression framework, we show that least absolute deviation regression must be used in the stage 1 analysis to ensure a correct asymptotic $X_{k - 1}^2/(k\, - \,\,1)$ distribution of the generalized scale (gS) test statistic. We then show that the proposed gS test is independent of the generalized location test, under the joint null hypothesis of no mean and no variance heterogeneity. Consequently, we generalize the recently proposed joint location-scale (gJLS) test, valuable in settings where there is an interaction effect but one interacting variable is not available. We evaluate the proposed method via an extensive simulation study and two genetic association application studies.
Objectives To test the hypothesis that multiple constituents of the apical plasma membrane residing alongside the causal cystic fibrosis (CF) transmembrane conductance regulator protein, including ...known CF modifiers SLC26A9 , SLC6A14 , and SLC9A3 , would be associated with prenatal exocrine pancreatic damage as measured by newborn screened (NBS) immunoreactive trypsinogen (IRT) levels. Study design NBS IRT measures and genome-wide genotype data were available on 111 subjects from Colorado, 37 subjects from Wisconsin, and 80 subjects from France. Multiple linear regression was used to determine whether any of 8 single nucleotide polymorphisms (SNPs) in SLC26A9 , SLC6A14 , and SLC9A3 were associated with IRT and whether other constituents of the apical plasma membrane contributed to IRT. Results In the Colorado sample, 3 SLC26A9 SNPs were associated with NBS IRT (min P = 1.16 × 10−3 ; rs7512462), but no SLC6A14 or SLC9A3 SNPs were associated ( P > .05). The rs7512462 association replicated in the Wisconsin sample ( P = .03) but not in the French sample ( P = .76). Furthermore, rs7512462 was the top-ranked apical membrane constituent in the combined Colorado and Wisconsin sample. Conclusions NBS IRT is a biomarker of prenatal exocrine pancreatic disease in patients with CF, and a SNP in SLC26A9 accounts for significant IRT variability. This work suggests SLC26A9 as a potential therapeutic target to ameliorate exocrine pancreatic disease.
PDF
