| 1. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 2. |
- Watts, Eleanor L., et al.
(författare)
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Circulating free testosterone and risk of aggressive prostate cancer : Prospective and Mendelian randomisation analyses in international consortia
- 2022
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Ingår i: International Journal of Cancer. - : John Wiley & Sons. - 0020-7136 .- 1097-0215. ; 151:7, s. 1033-1046
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Tidskriftsartikel (refereegranskat)abstract
- Previous studies had limited power to assess the associations of testosterone with aggressive disease as a primary endpoint. Further, the association of genetically predicted testosterone with aggressive disease is not known. We investigated the associations of calculated free and measured total testosterone and sex hormone-binding globulin (SHBG) with aggressive, overall and early-onset prostate cancer. In blood-based analyses, odds ratios (OR) and 95% confidence intervals (CI) for prostate cancer were estimated using conditional logistic regression from prospective analysis of biomarker concentrations in the Endogenous Hormones, Nutritional Biomarkers and Prostate Cancer Collaborative Group (up to 25 studies, 14 944 cases and 36 752 controls, including 1870 aggressive prostate cancers). In Mendelian randomisation (MR) analyses, using instruments identified using UK Biobank (up to 194 453 men) and outcome data from PRACTICAL (up to 79 148 cases and 61 106 controls, including 15 167 aggressive cancers), ORs were estimated using the inverse-variance weighted method. Free testosterone was associated with aggressive disease in MR analyses (OR per 1 SD = 1.23, 95% CI = 1.08-1.40). In blood-based analyses there was no association with aggressive disease overall, but there was heterogeneity by age at blood collection (OR for men aged <60 years 1.14, CI = 1.02-1.28; Phet =.0003: inverse association for older ages). Associations for free testosterone were positive for overall prostate cancer (MR: 1.20, 1.08-1.34; blood-based: 1.03, 1.01-1.05) and early-onset prostate cancer (MR: 1.37, 1.09-1.73; blood-based: 1.08, 0.98-1.19). SHBG and total testosterone were inversely associated with overall prostate cancer in blood-based analyses, with null associations in MR analysis. Our results support free testosterone, rather than total testosterone, in the development of prostate cancer, including aggressive subgroups.
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| 3. |
- Watts, Eleanor L., et al.
(författare)
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Circulating insulin-like growth factors and risks of overall, aggressive and early-onset prostate cancer : a collaborative analysis of 20 prospective studies and Mendelian randomization analysis
- 2023
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Ingår i: International Journal of Epidemiology. - : Oxford University Press. - 0300-5771 .- 1464-3685. ; 52:1, s. 71-86
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Tidskriftsartikel (refereegranskat)abstract
- Background: Previous studies had limited power to assess the associations of circulating insulin-like growth factors (IGFs) and IGF-binding proteins (IGFBPs) with clinically relevant prostate cancer as a primary endpoint, and the association of genetically predicted IGF-I with aggressive prostate cancer is not known. We aimed to investigate the associations of IGF-I, IGF-II, IGFBP-1, IGFBP-2 and IGFBP-3 concentrations with overall, aggressive and early-onset prostate cancer.Methods: Prospective analysis of biomarkers using the Endogenous Hormones, Nutritional Biomarkers and Prostate Cancer Collaborative Group dataset (up to 20 studies, 17 009 prostate cancer cases, including 2332 aggressive cases). Odds ratios (OR) and 95% confidence intervals (CI) for prostate cancer were estimated using conditional logistic regression. For IGF-I, two-sample Mendelian randomization (MR) analysis was undertaken using instruments identified using UK Biobank (158 444 men) and outcome data from PRACTICAL (up to 85 554 cases, including 15 167 aggressive cases). Additionally, we used colocalization to rule out confounding by linkage disequilibrium.Results: In observational analyses, IGF-I was positively associated with risks of overall (OR per 1 SD = 1.09: 95% CI 1.07, 1.11), aggressive (1.09: 1.03, 1.16) and possibly early-onset disease (1.11: 1.00, 1.24); associations were similar in MR analyses (OR per 1 SD = 1.07: 1.00, 1.15; 1.10: 1.01, 1.20; and 1.13; 0.98, 1.30, respectively). Colocalization also indicated a shared signal for IGF-I and prostate cancer (PP4: 99%). Men with higher IGF-II (1.06: 1.02, 1.11) and IGFBP-3 (1.08: 1.04, 1.11) had higher risks of overall prostate cancer, whereas higher IGFBP-1 was associated with a lower risk (0.95: 0.91, 0.99); these associations were attenuated following adjustment for IGF-I.Conclusions: These findings support the role of IGF-I in the development of prostate cancer, including for aggressive disease.
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| 4. |
- Watts, Eleanor L., et al.
(författare)
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The associations of anthropometric, behavioural and sociodemographic factors with circulating concentrations of IGF‐I, IGF‐II, IGFBP‐1, IGFBP‐2 and IGFBP‐3 in a pooled analysis of 16,024 men from 22 studies
- 2019
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Ingår i: International Journal of Cancer. - : John Wiley & Sons. - 0020-7136 .- 1097-0215. ; 145:12, s. 3244-3256
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Tidskriftsartikel (refereegranskat)abstract
- Insulin‐like growth factors (IGFs) and insulin‐like growth factor binding proteins (IGFBPs) have been implicated in the aetiology of several cancers. To better understand whether anthropometric, behavioural and sociodemographic factors may play a role in cancer risk via IGF signalling, we examined the cross‐sectional associations of these exposures with circulating concentrations of IGFs (IGF‐I and IGF‐II) and IGFBPs (IGFBP‐1, IGFBP‐2 and IGFBP‐3). The Endogenous Hormones, Nutritional Biomarkers and Prostate Cancer Collaborative Group dataset includes individual participant data from 16,024 male controls (i.e. without prostate cancer) aged 22–89 years from 22 prospective studies. Geometric means of protein concentrations were estimated using analysis of variance, adjusted for relevant covariates. Older age was associated with higher concentrations of IGFBP‐1 and IGFBP‐2 and lower concentrations of IGF‐I, IGF‐II and IGFBP‐3. Higher body mass index was associated with lower concentrations of IGFBP‐1 and IGFBP‐2. Taller height was associated with higher concentrations of IGF‐I and IGFBP‐3 and lower concentrations of IGFBP‐1. Smokers had higher concentrations of IGFBP‐1 and IGFBP‐2 and lower concentrations of IGFBP‐3 than nonsmokers. Higher alcohol consumption was associated with higher concentrations of IGF‐II and lower concentrations of IGF‐I and IGFBP‐2. African Americans had lower concentrations of IGF‐II, IGFBP‐1, IGFBP‐2 and IGFBP‐3 and Hispanics had lower IGF‐I, IGF‐II and IGFBP‐3 than non‐Hispanic whites. These findings indicate that a range of anthropometric, behavioural and sociodemographic factors are associated with circulating concentrations of IGFs and IGFBPs in men, which will lead to a greater understanding of the mechanisms through which these factors influence cancer risk.
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| 5. |
- Huang, Jiaqi
(författare)
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Epidemiology and etiology of pancreatic cancer
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Pancreatic cancer is one of the most devastating malignancies with an extremely high fatality, resulting that its mortality rate almost equals to incidence rate. Although primary prevention is of upmost importance, the underlying etiology of this cancer remains largely unknown. Pancreatic cancer is a heterogenetic disease, and the accumulated genetic alterations play an important role in pancreatic pathogenesis. Recent advances in next-generation sequencing have enabled comprehensive cancer genomic studies. However, clinical pancreatic cancer samples are characterized as having low tumor cellularity, as a result of an abundance of stroma in the tumor microenvironment, and this presents a big challenge for direct genomic sequencing for clinical pancreatic cancer samples. In this thesis, we aimed to enrich our knowledge of the etiology of pancreatic cancer with regard to several infectious agents and poor oral hygiene. Of note, we took the challenge to directly sequence clinical pancreatic cancer samples with a broad range of tumor cellularities, and attempted to depict its variant profile. In Study I, we retrieved all hepatitis C virus (HCV) and hepatitis B virus (HBV) infection notifications in Sweden from records in a national surveillance database at the Swedish Institutet for Infectious Disease Control (SMI) from 1990 to 2006, and followed them for pancreatic cancer occurrence by the end of 2008. The pancreatic cancer risk in the exposed population was compared with that in a matched reference population. Hazard ratios (HRs) were derived from Cox proportional hazards regression models. The main finding in this study is that the subjects with HCV infection had a 60% increased risk after adjustment for potential confounders. Therefore, the finding implied that HCV infection may be associated with a higher pancreatic cancer risk but further studies are warranted to confirm the observed association. The point estimate in this study also suggested an excessive risk among subjects with HBV infection, however, without statistical significance due to a lack of study power. In Study II, we took advantage of the population-based prevalence study of oral mucosal lesions conducted in Uppsala County in central Sweden during 1973-74. The study population was followed through linkages with the Swedish population and health registers. A total of 19 924 participants were included in the final analysis, with 126 pancreatic cancer ascertained during an average of 28.7 years of follow-up. Among all tested indicators of poor oral hygiene, we found that fewer teeth at baseline appeared to increase pancreatic cancer risk, although the relative risk estimates were not statistically significant. Among the subjects with more than 10 teeth, subjects with unacceptable dental plaque had a doubled risk of pancreatic cancer compared with those without dental plaque after controlling for potential confounding factors. Subjects with Candida-related or denture-related oral mucosal lesions, or tongue lesions, compared with those without any of the three lesions, showed a 70%, 30% and 80% increased pancreatic cancer risk, respectively. In Study III, we carried out a nested case-control study within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, including 448 pancreatic cancer cases and their individually matched control subjects. We measured serum antibodies against Helicobacter pylori (H. pylori) and pepsinogens I and II (markers for presence of chronic corpus atrophic gastritis) by enzyme-linked immunosorbent assays. Conditional logistic regression models were used to estimate odds ratios (ORs). Overall, our results demonstrated that pancreatic cancer risk was neither associated with H. pylori seropositivity nor CagA seropositivity. On the other hand, our findings showed that presence of chronic corpus atrophic gastritis was non-significantly associated with an increased pancreatic cancer risk. Although based on small numbers, the association was particularly prominent among individuals seronegative for both H. pylori and CagA (OR=5.66; 95% confidence interval: 1.59, 20.19; p value for interaction <0.01). In Study IV, we conducted a case-only study that sourced from a population-based case-control study of pancreatic cancer in Stockholm, Sweden. This study included patients with pancreatic ductal adenocarcinoma (PDAC) who underwent resection surgery between 2007 and 2012 (n=73). Patients were followed from diagnosis until death or the end of the study. We used an Anchored Multiplex Polymerase chain reaction (AMP)-based method for profiling variants in a panel of 65 selected genes. Our findings suggested that the AMP-based next-generation sequencing method can detect variants with allelic frequencies as low as 1% given sufficient sequencing depth. KRAS G12 mutations were completely confirmed by Sanger sequencing for high-allele-frequency samples (>5%), and also fully confirmed by allele-specific PCR and digital PCR for low-allele-frequency samples (1%-5%). The results demonstrated that KRAS mutant subtype G12V is related to a worse prognosis in PDAC patients, and transversion variants are more common among smokers. In conclusion, we found that HCV, as an infectious agent, may be associated with a higher pancreatic cancer risk. Our findings also support the hypothesis that poor oral hygiene plays a key role in the development of pancreatic cancer. On the other hand, we observed a null association between H. pylori infection and pancreatic cancer risk in the western European populations, but a suggested positive association between chronic corpus atrophic gastritis and pancreatic cancer risk based on a small sample size. Further studies are warranted to verify whether severe gastric atrophy contributes to pancreatic carcinogenesis. AMP-based next generation sequencing is a sensitive and accurate method for profiling tumor variants in PDAC. Future studies with larger sample sizes are needed to explore the role of tumor variants in PDAC prognosis and the impact of environmental risk factors on tumor mutational profile.
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| 6. |
- Huang, Jiaqi, et al.
(författare)
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Helicobacter pylori infection, chronic corpus atrophic gastritis and pancreatic cancer risk in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort : A nested case-control study
- 2017
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Ingår i: International Journal of Cancer. - : Wiley. - 0020-7136 .- 1097-0215. ; 140:8, s. 1727-1735
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Tidskriftsartikel (refereegranskat)abstract
- The association between H. pylori infection and pancreatic cancer risk remains controversial. We conducted a nested case-control study with 448 pancreatic cancer cases and their individually matched control subjects, based on the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort, to determine whether there was an altered pancreatic cancer risk associated with H. pylori infection and chronic corpus atrophic gastritis. Conditional logistic regression models were applied to calculate odds ratios (ORs) and corresponding 95% confidence intervals (CIs), adjusted for matching factors and other potential confounders. Our results showed that pancreatic cancer risk was neither associated with H. pylori seropositivity (OR = 0.96; 95% CI: 0.70, 1.31) nor CagA seropositivity (OR = 1.07; 95% CI: 0.77, 1.48). We also did not find any excess risk among individuals seropositive for H. pylori but seronegative for CagA, compared with the group seronegative for both antibodies (OR = 0.94; 95% CI: 0.63, 1.38). However, we found that chronic corpus atrophic gastritis was non-significantly associated with an increased pancreatic cancer risk (OR = 1.35; 95% CI: 0.77, 2.37), and although based on small numbers, the excess risk was particularly marked among individuals seronegative for both H. pylori and CagA (OR = 5.66; 95% CI: 1.59, 20.19, p value for interaction < 0.01). Our findings provided evidence supporting the null association between H. pylori infection and pancreatic cancer risk in western European populations. However, the suggested association between chronic corpus atrophic gastritis and pancreatic cancer risk warrants independent verification in future studies, and, if confirmed, further studies on the underlying mechanisms.
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| 7. |
- Huang, Jiaqi, et al.
(författare)
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Pancreatic cancer risk after loss of a child : a register-based study in Sweden during 1991-2009
- 2013
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Ingår i: American Journal of Epidemiology. - : Oxford University Press (OUP). - 0002-9262 .- 1476-6256. ; 178:4, s. 582-589
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Tidskriftsartikel (refereegranskat)abstract
- The potential role of psychological stress in pancreatic cancer has rarely been investigated in epidemiologic studies. During 1991-2009, we conducted a nested case-control study based on Swedish national population and health registers to investigate whether severe psychological stress induced by the death of a child was associated with subsequent risk of pancreatic cancer. The study included 16,522 cases and 82,107 controls who were matched to the cases on sex and year of birth. Conditional logistic regression was used to estimate odds ratios and 95% confidence intervals. Overall, loss of a child was associated with an odds ratio of 1.09 for pancreatic cancer (95% confidence interval (CI): 1.02, 1.17). The risk elevation was mainly seen during the first 5 years after the loss (odds ratio (OR) = 1.27, 95% CI: 1.12, 1.45) and for loss of a child due to suicide (OR = 1.23, 95% CI: 1.03, 1.46). The association was statistically significant among women but not among men, and it appeared stronger for early-onset pancreatic cancer. Persons with a history of psychiatric illness had the greatest risk increase after child loss (OR = 1.43, 95% CI: 1.17, 1.76). Although other explanations are possible, our findings provide some evidence that psychological stress may be associated with pancreatic cancer.
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| 8. |
- Huang, Jiaqi, et al.
(författare)
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Rapid Screening of Complex DNA Samples by Single-Molecule Amplification and Sequencing
- 2011
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 6:5, s. e19723-
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Tidskriftsartikel (refereegranskat)abstract
- Microbial cloning makes Sanger sequencing of complex DNA samples possible but is labor intensive. We present a simple, rapid and robust method that enables laboratories without special equipment to perform single-molecule amplicon sequencing, although in a low-throughput manner, from sub-picogram quantities of DNA. The method can also be used for quick quality control of next-generation sequencing libraries, as was demonstrated for a metagenomic sample.
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| 9. |
- Huang, Jiaqi, et al.
(författare)
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Risk of pancreatic cancer among individuals with hepatitis C or hepatitis B virus infection : a nationwide study in Sweden
- 2013
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Ingår i: British Journal of Cancer. - London, United Kingdom : Nature Publishing Group. - 0007-0920 .- 1532-1827. ; 109:11, s. 2917-2923
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Tidskriftsartikel (refereegranskat)abstract
- Background: A few studies indicated that hepatitis C and hepatitis B virus (HCV/HBV) might be associated with pancreatic cancer risk. The aim of this nationwide cohort study was to examine this possible association.Methods: Hepatitis C virus- and hepatitis B virus-infected individuals were identified from the national surveillance database from 1990 to 2006, and followed to the end of 2008. The pancreatic cancer risk in the study population was compared with the general population by calculation of Standardized Incidence Ratios (SIRs), and with a matched reference population using a Cox proportional hazards regression model to calculate hazard ratios (HRs).Results: In total 340 819 person-years in the HCV cohort and 102 295 in the HBV cohort were accumulated, with 34 and 5 pancreatic cancers identified, respectively. The SIRHCV was 2.1 (95% confidence interval, CI: 1.4, 2.9) and the SIRHBV was 1.4 (0.5, 3.3). In the Cox model analysis, the HR for HCV infection was 1.9 (95% CI: 1.3, 2.7), diminishing to 1.6 (1.04, 2.4) after adjustment for potential confounders.Conclusion: Our results indicated that HCV infection might be associated with an increased risk of pancreatic cancer but further studies are needed to verify such association. The results in the HBV cohort indicated an excess risk, however, without statistical significance due to lack of power.
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| 10. |
- Huang, Jiaqi, et al.
(författare)
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Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma.
- 2015
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Ingår i: Clinical Chemistry. - : Oxford University Press (OUP). - 0009-9147 .- 1530-8561. ; 61:11, s. 1408-16
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis. Variant profiling is crucial for developing personalized treatment and elucidating the etiology of this disease.METHODS: Patients with PDAC undergoing surgery from 2007 to 2012 (n = 73) were followed from diagnosis until death or the end of the study. We applied an anchored multiplex PCR (AMP)-based next-generation sequencing (NGS) method to a panel of 65 selected genes and assessed analytical performance by sequencing a quantitative multiplex DNA reference standard. In clinical PDAC samples, detection of low-level KRAS (Kirsten rat sarcoma viral oncogene homolog) mutations was validated by allele-specific PCR and digital PCR. We compared overall survival of patients according to KRAS mutation status by log-rank test and applied logistic regression to evaluate the association between smoking and tumor variant types.RESULTS: The AMP-based NGS method could detect variants with allele frequencies as low as 1% given sufficient sequencing depth (>1500×). Low-frequency KRAS G12 mutations (allele frequency 1%-5%) were all confirmed by allele-specific PCR and digital PCR. The most prevalent genetic alterations were in KRAS (78% of patients), TP53 (tumor protein p53) (25%), and SMAD4 (SMAD family member 4) (8%). Overall survival in T3-stage PDAC patients differed among KRAS mutation subtypes (P = 0.019). Transversion variants were more common in ever-smokers than in never-smokers (odds ratio 5.7; 95% CI 1.2-27.8).CONCLUSIONS: The AMP-based NGS method is applicable for profiling tumor variants. Using this approach, we demonstrated that in PDAC patients, KRAS mutant subtype G12V is associated with poorer survival, and that transversion variants are more common among smokers.
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