14 Aug 2020-bioRxiv (Cold Spring Harbor Laboratory)-
TL;DR: MCM6 and RRM2 are involved in DNA repair whereby reduced expression may lead to increased DNA aberrations and ultimately cancer cell death, whereas ARFIP2 is involved in actin cytoskeletal regulation indicating a possible role in aspirin’s reduction of metastasis.
Abstract: Background: Evidence for aspirin9s chemopreventative properties on colorectal cancer (CRC) is substantial, but its mechanism of action is not well-understood. We combined a proteomic approach with Mendelian randomization (MR) to identify possible new aspirin targets that decrease CRC risk.
Methods: Human colorectal adenoma cells (RG/C2) were treated with aspirin (24 hours) and a stable isotope labelling with amino acids in cell culture (SILAC) based proteomics approach identified altered protein expression. Protein quantitative trait loci (pQTLs) from INTERVAL (N=3,301) and expression QTLs (eQTLs) from the eQTLGen Consortium (N=31,684) were used as genetic proxies for protein and mRNA expression levels. Two-sample MR of mRNA/protein expression on CRC risk was performed using eQTL/pQTL data combined with CRC genetic summary data from the Colon Cancer Family Registry (CCFR), Colorectal Transdisciplinary (CORECT), Genetics and Epidemiology of Colorectal Cancer (GECCO) consortia and UK Biobank (55,168 cases and 65,160 controls).
Results: Altered expression was detected for 125/5886 proteins. Of these, aspirin decreased MCM6, RRM2 and ARFIP2 expression and MR analysis showed that a standard deviation increase in mRNA/protein expression was associated with increased CRC risk (OR:1.08, 95% CI:1.03-1.13, OR:3.33, 95% CI:2.46-4.50 and OR:1.15, 95% CI:1.02-1.29, respectively).
Conclusion: MCM6 and RRM2 are involved in DNA repair whereby reduced expression may lead to increased DNA aberrations and ultimately cancer cell death, whereas ARFIP2 is involved in actin cytoskeletal regulation indicating a possible role in aspirin9s reduction of metastasis.
Impact: Our approach has shown how laboratory experiments and population-based approaches can combine to identify aspirin-targeted proteins possibly affecting CRC risk.
Several reports indicate that females have a stronger immune response, partly due to differences in hormonal profile [1, 2].
Recently, TTV has received attention as a possible endogenous biomarker for immune function, with immunocompetent individuals carrying lower levels of TTV in serum than immunocompromised, indicating a suppressing role of the immune system on the viral load [3].
The high turnover-rate of virions indicates that changes in immune status can be followed in a short time frame.
The differences in female and male immunity towards pathogens have implications for treatment and prevention of infectious diseases and may ultimately lead to a different approach depending on the sex of the patient.
2.1. Subjects
27 healthy individuals were included according to a protocol approved by the Central Ethical Review Board (Swedish Research Council, Stockholm, Dnr: €O 24–2009) and consisted of 17 premenopausal women, 6 men and 4 postmenopausal women (Table 1).
The subjects were included and sampled during 6 months (between March and September, 2010).
Informed consent was obtained from the participants.
Premenopausal women aged 20–40 years with regular menstrual cycles, without hormonal contraceptives or other hormonal, anti-inflammatory (including ASA, systemic cortisone and NSAIDs) or any morphine treatment since>3 months, and parturition no later than 12 months before inclusion, also known as The inclusion criteria were.
Men (aged 20–70) and postmenopausal women (no menstrual bleeding since >12 months) without the above stated treatment during the last 3 months.
2.2. Blood sampling and hormonal analyses
From all individuals blood was drawn at four timepoints, and for the pre-MP women Ovustick® was used to identify the LH-peak.
Simultaneously, at one or more timepoints PBMC was also sampled.
The buffycoat was transferred to new tubes and slowly frozen in 20% dimethylsulphoxide (DMSO)-albumin, using isopropanol-loaded Mr. Frosty® freezing-container overnight, before long-term storage at -80 C.
Analyses were made of WBC, differential count (including B-monocytes, Blymphocytes, B-neutrophils, B-eosinophils, B-basophils), S-TSH (thyroid stimulating hormone), S-T4, S-SHBG (sex hormone binding globulin), Sestradiol, S-testosterone, S-progesterone, S-FSH, S-LH and S-prolactin.
The participants were assessed for hypo- or hyperthyroidism, and preMP women also whether they had a normal ovulation.
2.3. TTV DNA isolation and analysis
This was performed according to QIAamp® DNA Mini and Blood Mini Handbook to increase DNA yield.
This contained pre-prepared solutions of 5, 50, 500 and 5000 copies plasmid TTV DNA per μL, as well as a sensitivity control containing 1 copy/μL.
The sample wells were run in triplicates using 10 μL of concentrated DNA solution.
According to the standard curve obtained, this corresponded to CT of 37.09, 42.09 and 39.14 respectively on the included three TTV qPCR plates.
A sample was considered positive if 2 of 3 triplicate samples were above the detection limit (i.e. below the CT-threshold mentioned above).
2.4. Statistical analyses
The average hormone levels of TSH, estradiol, LH and testosterone were calculated for each of the 17 pre-MP women.
As a logistic model with logit-link, the following was used: TTV ~ log (Mean_TSH) þ log (Mean_estradiol) þ log (Mean_LH) þ log (Mean_testosterone).
The explanatory variables are treated as covariates.
3.2. TTV prevalence and TTV levels
The detected levels of TTVwere highest among the TTV positive pre-MPwomen and lower in the post-MP women and in the men, both in terms of detected TT viral copies/mL and when adjusting for total amount of DNA in the sample (Table 2).
The differences in TTV prevalence between pre-MP and postMP women as well as between pre-MP women and men were not statistically significant (Fisher's exact test, p > 0.999 and p ¼ 0.2786) .
The raw data suggested higher prevalence in men than in preMP women, but significance testing could not rule out a chance yroid status, sex hormone levels.
For pre-MP women, day of the menstrual cycle, rone and LH, is indicated.
3.3. Hormonal status in TTV-positive pre-MP women
To determine whether sex hormones influence the risk of being TTVpositive (TTVþ) the authors compared the average sex hormone levels in TTVþ (n ¼ 3) and TTV (n¼ 14) individuals using a binomial regression including S-estradiol, S-testosterone, S-LH and S-TSH.
When comparing average TSH from TTVþ and TTV individuals in a binominal regression, there was no significant difference (p-value¼ 0.337, Table 3).
Samples from themid-luteal phase revealed (using Welch's t-test) significantly lower progesterone levels (p ¼ 0.002) in TTVþ compared to TTV pre-MP women .
Dispersion parameter for binominal family eviance: 5.5798 on 13 Df. Akaike information criterion (AIC): 15.58.
3.4. Hormonal status in men and post-MP women
All three TTV men, and two out of three TTV post-MP women hade traces of TTV, but below cut-off (Table 4B).
All men and post-MP women (TTVþ and TTV ) had normal levels of TSH.
Due to the low number of participants, it was not possible to use regression models for analyzing hormone levels in relation to TTV status in men and post-MP women.
TTV status, age and range of hormone levels are shown in Table 5.
4. Discussion
The detection of TTV in 17.6% pre-MP females, 25.0% post-MP females, and 50.0%males suggests that TTV presence in the PBMC fraction of peripheral blood may be associated with sex.
TTVþ samples from pre-MP women in their cohort were mostly found during the first half of the menstrual cycle, and pre-MP women who were positive for TTV had hormonal aberrances being either anovulatory, hypothyroid or both.
Interactions of sex hormones with the immune system are established on multiple levels (reviewed in e.g. [10, 15, 16]).
In a study by Maggi et al. (2001), TTV-levels were considerably lower in PBMC than in plasma from the same individuals [31].
Only 2.4% of the plasma samples in the study from Fern andez-Ruíz et al. [45], were below lower limit of detection, whereas in their study on PBMC, the majority of individuals (74.1%) were below cut-off.
Author contribution statement
Conceived and designed the experiments; Performed the experiments;, also known as P. Brundin.
Analyzed and interpreted the data; Wrote the paper.
B-M. Landgren, P. Fj€allstr€om and A. Johansson: Analyzed and interpreted the data.
Conceived and designed the experiments;, also known as I. Nalvarte.
Analyzed and interpreted the data; Contributed reagents, materials, analysis tools or data.
TL;DR: The authors in this article performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls.
Abstract: To further dissect the genetic architecture of colorectal cancer (CRC), we performed whole-genome sequencing of 1,439 cases and 720 controls, imputed discovered sequence variants and Haplotype Reference Consortium panel variants into genome-wide association study data, and tested for association in 34,869 cases and 29,051 controls. Findings were followed up in an additional 23,262 cases and 38,296 controls. We discovered a strongly protective 0.3% frequency variant signal at CHD1. In a combined meta-analysis of 125,478 individuals, we identified 40 new independent signals at P < 5 × 10−8, bringing the number of known independent signals for CRC to ~100. New signals implicate lower-frequency variants, Krüppel-like factors, Hedgehog signaling, Hippo-YAP signaling, long noncoding RNAs and somatic drivers, and support a role for immune function. Heritability analyses suggest that CRC risk is highly polygenic, and larger, more comprehensive studies enabling rare variant analysis will improve understanding of biology underlying this risk and influence personalized screening strategies and drug development.Genome-wide association analyses based on whole-genome sequencing and imputation identify 40 new risk variants for colorectal cancer, including a strongly protective low-frequency variant at CHD1 and loci implicating signaling and immune function in disease etiology.
TL;DR: It is important that evaluations of aspirin used as an adjunct cancer treatment are based upon all the available relevant evidence, and there appears to be a marked harmony between the effects of aspirin upon biological mechanisms and upon the clinical progress of cancer.
Abstract: Evidence on aspirin and cancer comes from two main sources: (1) the effect of aspirin upon biological mechanisms in cancer, and (2) clinical studies of patients with cancer, some of whom take aspirin. A series of systematic literature searches identified published reports relevant to these two sources. The effects of aspirin upon biological mechanisms involved in cancer initiation and growth appear to generate reasonable expectations of effects upon the progress and mortality of cancer. Clinical evidence on aspirin appears overall to be favourable to the use of aspirin, but evidence from randomized trials is limited, and inconsistent. The main body of evidence comes from meta-analyses of observational studies of patients with a wide range of cancers, about 25% of whom were taking aspirin. Heterogeneity is large but, overall, aspirin is associated with increases in survival and reductions in metastatic spread and vascular complications of different cancers. It is important that evaluations of aspirin used as an adjunct cancer treatment are based upon all the available relevant evidence, and there appears to be a marked harmony between the effects of aspirin upon biological mechanisms and upon the clinical progress of cancer.
TL;DR: In this article , the authors summarize the associations between potential causal factors and colorectal cancer (CRC) risk based on existing Mendelian randomization studies and conclude that these factors are associated with a higher risk of developing cancer.
Abstract: To summarize the associations between potential causal factors and colorectal cancer (CRC) risk based on existing Mendelian randomization studies.
TL;DR: It is shown that aspirin leads to significant metabolic reprogramming in colorectal cancer cells and raises the possibility that aspirin could significantly increase the efficacy of metabolic cancer therapies in CRC.
Abstract: To support proliferation and survival within a challenging microenvironment, cancer cells must reprogramme their metabolism. As such, targeting cancer cell metabolism is a promising therapeutic avenue. However, identifying tractable nodes of metabolic vulnerability in cancer cells is challenging due to their metabolic plasticity. Identification of effective treatment combinations to counter this is an active area of research. Aspirin has a well-established role in cancer prevention, particularly in colorectal cancer (CRC), although the mechanisms are not fully understood. Here, we comprehensively characterise the metabolic impact of long-term aspirin exposure (2-4mM for 52 weeks) on CRC cells. We show that aspirin regulates several enzymes and transporters of central carbon metabolism and results in a reduction in glutaminolysis and a concomitant increase in glucose metabolism, demonstrating reprogramming of nutrient utilisation. We show that aspirin causes likely compensatory changes that renders the cells sensitive to the glutaminase 1 (GLS1) inhibitor - CB-839. Of note given the clinical interest, treatment with CB-839 alone had little effect on CRC cell growth or survival. However, in combination with aspirin, CB-839 inhibited CRC cell proliferation and induced apoptosis in vitro, and importantly, reduced crypt proliferation in Apcfl/fl mice in vivo. Together, these results show that aspirin leads to significant metabolic reprogramming in colorectal cancer cells and raises the possibility that aspirin could significantly increase the efficacy of metabolic cancer therapies in CRC.
TL;DR: A status report on the global burden of cancer worldwide using the GLOBOCAN 2018 estimates of cancer incidence and mortality produced by the International Agency for Research on Cancer, with a focus on geographic variability across 20 world regions.
TL;DR: An adaption of Egger regression can detect some violations of the standard instrumental variable assumptions, and provide an effect estimate which is not subject to these violations, and provides a sensitivity analysis for the robustness of the findings from a Mendelian randomization investigation.
Abstract: Background: The number of Mendelian randomization analyses including large numbers of genetic variants is rapidly increasing. This is due to the proliferation of genome-wide association studies, and the desire to obtain more precise estimates of causal effects. However, some genetic variants may not be valid instrumental variables, in particular due to them having more than one proximal phenotypic correlate (pleiotropy).
Methods: We view Mendelian randomization with multiple instruments as a meta-analysis, and show that bias caused by pleiotropy can be regarded as analogous to small study bias. Causal estimates using each instrument can be displayed visually by a funnel plot to assess potential asymmetry. Egger regression, a tool to detect small study bias in meta-analysis, can be adapted to test for bias from pleiotropy, and the slope coefficient from Egger regression provides an estimate of the causal effect. Under the assumption that the association of each genetic variant with the exposure is independent of the pleiotropic effect of the variant (not via the exposure), Egger’s test gives a valid test of the null causal hypothesis and a consistent causal effect estimate even when all the genetic variants are invalid instrumental variables.
Results: We illustrate the use of this approach by re-analysing two published Mendelian randomization studies of the causal effect of height on lung function, and the causal effect of blood pressure on coronary artery disease risk. The conservative nature of this approach is illustrated with these examples.
Conclusions: An adaption of Egger regression (which we call MR-Egger) can detect some violations of the standard instrumental variable assumptions, and provide an effect estimate which is not subject to these violations. The approach provides a sensitivity analysis for the robustness of the findings from a Mendelian randomization investigation.
TL;DR: It is found that local genetic variation affects gene expression levels for the majority of genes, and inter-chromosomal genetic effects for 93 genes and 112 loci are identified, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.
Abstract: Characterization of the molecular function of the human genome and its variation across individuals is essential for identifying the cellular mechanisms that underlie human genetic traits and diseases. The Genotype-Tissue Expression (GTEx) project aims to characterize variation in gene expression levels across individuals and diverse tissues of the human body, many of which are not easily accessible. Here we describe genetic effects on gene expression levels across 44 human tissues. We find that local genetic variation affects gene expression levels for the majority of genes, and we further identify inter-chromosomal genetic effects for 93 genes and 112 loci. On the basis of the identified genetic effects, we characterize patterns of tissue specificity, compare local and distal effects, and evaluate the functional properties of the genetic effects. We also demonstrate that multi-tissue, multi-individual data can be used to identify genes and pathways affected by human disease-associated variation, enabling a mechanistic interpretation of gene regulation and the genetic basis of disease.
3,289 citations
"A combined proteomics and Mendelian..." refers methods in this paper
...As found by the Genotype-Tissue Expression 658 (GTEx) study, cis eQTLs are either shared across tissues or are specific to a small number of tissues 659 (54)....
TL;DR: A novel weighted median estimator for combining data on multiple genetic variants into a single causal estimate is presented, which is consistent even when up to 50% of the information comes from invalid instrumental variables.
Abstract: Developments in genome-wide association studies and the increasing availability of summary genetic association data have made application of Mendelian randomization relatively straightforward. However, obtaining reliable results from a Mendelian randomization investigation remains problematic, as the conventional inverse-variance weighted method only gives consistent estimates if all of the genetic variants in the analysis are valid instrumental variables. We present a novel weighted median estimator for combining data on multiple genetic variants into a single causal estimate. This estimator is consistent even when up to 50% of the information comes from invalid instrumental variables. In a simulation analysis, it is shown to have better finite-sample Type 1 error rates than the inverse-variance weighted method, and is complementary to the recently proposed MR-Egger (Mendelian randomization-Egger) regression method. In analyses of the causal effects of low-density lipoprotein cholesterol and high-density lipoprotein cholesterol on coronary artery disease risk, the inverse-variance weighted method suggests a causal effect of both lipid fractions, whereas the weighted median and MR-Egger regression methods suggest a null effect of high-density lipoprotein cholesterol that corresponds with the experimental evidence. Both median-based and MR-Egger regression methods should be considered as sensitivity analyses for Mendelian randomization investigations with multiple genetic variants.
2,959 citations
"A combined proteomics and Mendelian..." refers background or methods in this paper
...As a sensitivity analysis, 509 alternative MR methods were used when more than 2 SNPs were available as instruments for 510 mRNA/protein expression (MR Egger, simple mode, weighted mode, and weighted median) 511 (36,39,40)....
[...]
...The weighted median approach is useful as it allows a consistent estimate even if 50% of the 514 SNPs proxying protein/mRNA expression are invalid instruments (40) and the mode estimate also 515 provides a consistent causal effect estimate even if the majority of the instruments are invalid, as 516 the estimate depends on the largest number of similar instruments (39)....
TL;DR: MR-Base is a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR, and includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions.
Abstract: Results from genome-wide association studies (GWAS) can be used to infer causal relationships between phenotypes, using a strategy known as 2-sample Mendelian randomization (2SMR) and bypassing the need for individual-level data. However, 2SMR methods are evolving rapidly and GWAS results are often insufficiently curated, undermining efficient implementation of the approach. We therefore developed MR-Base ( http://www.mrbase.org ): a platform that integrates a curated database of complete GWAS results (no restrictions according to statistical significance) with an application programming interface, web app and R packages that automate 2SMR. The software includes several sensitivity analyses for assessing the impact of horizontal pleiotropy and other violations of assumptions. The database currently comprises 11 billion single nucleotide polymorphism-trait associations from 1673 GWAS and is updated on a regular basis. Integrating data with software ensures more rigorous application of hypothesis-driven analyses and allows millions of potential causal relationships to be efficiently evaluated in phenome-wide association studies.
2,520 citations
"A combined proteomics and Mendelian..." refers background or methods in this paper
...As a sensitivity analysis, 509 alternative MR methods were used when more than 2 SNPs were available as instruments for 510 mRNA/protein expression (MR Egger, simple mode, weighted mode, and weighted median) 511 (36,39,40)....
[...]
...If allele frequencies for the effect allele and the other allele were similar, thus making 499 harmonization difficult, these SNPs were dropped from the analysis (36)....
[...]
...com/MRCIEU/TwoSampleMR) (36), which allows the formatting, harmonisation and analysis 493 of summary statistics....
Q1. What have the authors contributed in "Blood hormones and torque teno virus in peripheral blood mononuclear cells" ?
In this study the authors investigated the presence and levels of TTV in peripheral blood mononuclear cells ( PBMCs ) in premenopausal ( pre-MP ) women, post-menopausal ( post-MP ) women, and men, and determined their serum sex hormone levels. Of the examined subjects ( n 1⁄4 27 ), the authors found presence of TTV in PMBC from 17. Although their study was performed on a limited number of subjects, the data suggests that TTV in PBMC is associated with an anovulatory menstrual cycle with low progesterone levels, and possibly with male sex.
Q2. What have the authors stated for future works in "Blood hormones and torque teno virus in peripheral blood mononuclear cells" ?
Preferably, future studies including sex and hormonal status ( e. g. pre- or post-menopause, contraceptives, hormonal replacement therapies and ovulation, as well as signs of hypothyroidism ), should be performed to obtain more information on the impact of the menstrual cycle on TTV load and immune response.