Confidence interval methods for antimicrobial resistance surveillance data.

BACKGROUND: Antimicrobial resistance (AMR) is one of the greatest global health challenges today, but burden assessment is hindered by uncertainty of AMR prevalence estimates. Geographical representation of AMR estimates typically pools data collected from several laboratories; however, these aggregations may introduce bias by not accounting for the heterogeneity of the population that each laboratory represents. METHODS: We used AMR data from up to 381 laboratories in the United States from The Surveillance Network to evaluate methods for estimating uncertainty of AMR prevalence estimates. We constructed confidence intervals for the proportion of resistant isolates using (1) methods that account for the clustered structure of the data, and (2) standard methods that assume data independence. Using samples of the full dataset with increasing facility coverage levels, we examined how likely the estimated confidence intervals were to include the population mean. RESULTS: Methods constructing 95% confidence intervals while accounting for possible within-cluster correlations (Survey and standard methods adjusted to employ cluster-robust errors), were more likely to include the sample mean than standard methods (Logit, Wilson score and Jeffreys interval) operating under the assumption of independence. While increased geographical coverage improved the probability of encompassing the mean for all methods, large samples still did not compensate for the bias introduced from the violation of the data independence assumption. CONCLUSION: General methods for estimating the confidence intervals of AMR rates that assume data are independent, are likely to produce biased results. When feasible, the clustered structure of the data and any possible intra-cluster variation should be accounted for when calculating confidence intervals around AMR estimates, in order to better capture the uncertainty of prevalence estimates.

Modelling COVID-19 transmission in Africa: countrywise projections of total and severe infections under different lockdown scenarios.

OBJECTIVES: As of 13 January 2021, there have been 3 113 963 confirmed cases of SARS-CoV-2 and 74 619 deaths across the African continent. Despite relatively lower numbers of cases initially, many African countries are now experiencing an exponential increase in case numbers. Estimates of the progression of disease and potential impact of different interventions are needed to inform policymaking decisions. Herein, we model the possible trajectory of SARS-CoV-2 in 52 African countries under different intervention scenarios. DESIGN: We developed a compartmental model of SARS-CoV-2 transmission to estimate the COVID-19 case burden for all African countries while considering four scenarios: no intervention, moderate lockdown, hard lockdown and hard lockdown with continued restrictions once lockdown is lifted. We further analysed the potential impact of COVID-19 on vulnerable populations affected by HIV/AIDS and tuberculosis (TB). RESULTS: In the absence of an intervention, the most populous countries had the highest peaks in active projected number of infections with Nigeria having an estimated 645 081 severe infections. The scenario with a hard lockdown and continued post-lockdown interventions to reduce transmission was the most efficacious strategy for delaying the time to the peak and reducing the number of cases. In South Africa, projected peak severe infections increase from 162 977 to 2 03 261, when vulnerable populations with HIV/AIDS and TB are included in the analysis. CONCLUSION: The COVID-19 pandemic is rapidly spreading across the African continent. Estimates of the potential impact of interventions and burden of disease are essential for policymakers to make evidence-based decisions on the distribution of limited resources and to balance the economic costs of interventions with the potential for saving lives.

Immune-Modulating Effects of Conventional Therapies in Colorectal Cancer.

Biological heterogeneity and low inherent immunogenicity are two features that greatly impact therapeutic management and outcome in colorectal cancer. Despite high local control rates, systemic tumor dissemination remains the main cause of treatment failure and stresses the need for new developments in combined-modality approaches. While the role of adaptive immune responses in a small subgroup of colorectal tumors with inherent immunogenicity is indisputable, the challenge remains in identifying the optimal synergy between conventional treatment modalities and immune therapy for the majority of the less immunogenic cases. In this context, cytotoxic agents such as radiation and certain chemotherapeutics can be utilized to enhance the immunogenicity of an otherwise immunologically silent disease and enable responsiveness to immune therapy. In this review, we explore the immunological characteristics of colorectal cancer, the effects that standard-of-care treatments have on the immune system, and the opportunities arising from combining immune checkpoint-blocking therapy with immune-modulating conventional treatments.

Circulating Exosomal miR-141-3p and miR-375 in Metastatic Progression of Rectal Cancer.

As many as 30% to 40% of locally advanced rectal cancer (LARC) patients experience metastatic progression of the disease. Recognizing the potential of the genetic cargo in tumor-derived exosomes, we hypothesized that plasma exosomal microRNA (miRNA) may reflect biological aggressiveness in LARC and provide new markers for rectal cancer aggressiveness and risk stratification. In a prospective LARC cohort (NCT01816607), plasma samples were collected from 29 patients at the time of diagnosis, before neoadjuvant therapy and surgery. Exosomes, precipitated from plasma using a commercial kit, were verified by cryo-electron microscopy, nanoparticle tracking analysis, and western blotting. Expression of exosomal miRNAs was profiled using a miRCURY LNA miRNA microarray and validation of six miRNAs associated with pathological and clinical end-points was undertaken in plasma collected at the time of diagnosis from 64 patients in an independent prospective LARC cohort (NCT00278694). In both cohorts, exosomal miR-141-3p and miR-375 were higher in patients with synchronous liver metastasis than in those without (P = .010 and P = .017 respectively in the investigative cohort, and P < .001 for both in the validation cohort). Further, high exosomal miR-141-3p was associated with post-operative metastatic liver progression in the investigative cohort (P = .034). Because both miRNAs are associated with tumor angiogenesis and immune modulation, we propose that these miRNAs in circulating exosomes may reflect rectal cancer aggressiveness and accordingly be candidate biomarkers for further investigations.

Systemic immune response induced by oxaliplatin-based neoadjuvant therapy favours survival without metastatic progression in high-risk rectal cancer.

BACKGROUND: Systemic failure remains a challenge in rectal cancer. We investigated the possible systemic anti-tumour immune activity invoked within oxaliplatin-based neoadjuvant therapy. METHODS: In two high-risk patient cohorts, we assessed the circulating levels of the fms-like tyrosine kinase 3 ligand (Flt3L), a factor reflecting both therapy-induced myelosuppression and activation of tumour antigen-presenting dendritic cells, at baseline and following induction chemotherapy and sequential chemoradiotherapy, both modalities containing oxaliplatin. The primary end point was progression-free survival (PFS). RESULTS: In both cohorts, the median Flt3L level was significantly higher at completion of each sequential modality than at baseline. The 5-year PFS (most events being metastatic progression) was 68% and 71% in the two cohorts consisting of 33% and 52% T4 cases. In the principal cohort, a high Flt3L level following the induction chemotherapy was associated with low risk for a PFS event (HR: 0.15; P < 0.01). These patients also had available dose scheduling and toxicity data, revealing that oxaliplatin dose reduction during chemoradiotherapy, undertaken to maintain compliance to the radiotherapy protocol, was associated with advantageous PFS (HR: 0.47; P = 0.046). CONCLUSION: In high-risk rectal cancer, oxaliplatin-containing neoadjuvant therapy may promote an immune response that favours survival without metastatic progression.

Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.

PURPOSE: When integrating molecularly targeted compounds in radiotherapy, synergistic effects of the systemic agent and radiation may extend the limits of patient tolerance, increasing the demand for understanding the pathophysiological mechanisms of treatment toxicity. In this Pelvic Radiation and Vorinostat (PRAVO) study, we investigated mechanisms of adverse effects in response to the histone deacetylase (HDAC) inhibitor vorinostat (suberoylanilide hydroxamic acid, SAHA) when administered as a potential radiosensitiser. MATERIALS AND METHODS: This phase I study for advanced gastrointestinal carcinoma was conducted in sequential patient cohorts exposed to escalating doses of vorinostat combined with standard-fractionated palliative radiotherapy to pelvic target volumes. Gene expression microarray analysis of the study patient peripheral blood mononuclear cells (PBMC) was followed by functional validation in cultured cell lines and mice treated with SAHA. RESULTS: PBMC transcriptional responses to vorinostat, including induction of apoptosis, were confined to the patient cohort reporting dose-limiting intestinal toxicities. At relevant SAHA concentrations, apoptotic features (annexin V staining and caspase 3/7 activation, but not poly-(ADP-ribose)-polymerase cleavage) were observed in cultured intestinal epithelial cells. Moreover, SAHA-treated mice displayed significant weight loss. CONCLUSION: The PRAVO study design implemented a strategy to explore treatment toxicity caused by an HDAC inhibitor when combined with radiotherapy and enabled the identification of apoptosis as a potential mechanism responsible for the dose-limiting effects of vorinostat. To the best of our knowledge, this is the first report deciphering mechanisms of normal tissue adverse effects in response to an HDAC inhibitor within a combined-modality treatment regimen.

Circulating proteins in response to combined-modality therapy in rectal cancer identified by antibody array screening.

BACKGROUND: The increasingly complex programs of contemporary cancer therapy emphasize the need for biological indicators of both therapeutic response and adverse effects. One example is combined-modality treatment aimed at improving long-term outcome in patients with locally advanced rectal cancer, which commonly comes at the price of extended limits of patient tolerance. METHODS: In a prospective study with intensified neoadjuvant treatment of rectal cancer patients, using an antibody array, the profiling of approximately 500 proteins was performed in serial serum samples collected at different stages of the treatment course. RESULTS: The small number of proteins whose levels significantly changed after induction neoadjuvant chemotherapy (NACT) expanded substantially following the sequential chemoradiotherapy (CRT) and persisted four weeks later at treatment evaluation before pelvic surgery. Serum levels of proteins selected for validation of the experimental design, lipocalin-2 and matrix metalloproteinase-9, declined after NACT and gradually reverted to baseline values during the remaining neoadjuvant course. Of note, the greater the decline in post-NACT and post-CRT matrix metalloproteinase-9 levels, the more favorable progression-free survival. No correlation was found, however, with diarrhea scores, the clinical correlate of adverse therapeutic effects. CONCLUSIONS: Even though the findings were indicative of only tumor and not normal tissue effects, multiplex immunoassay analysis of circulating proteins in patients undergoing combined-modality therapy may in principle dissect the contribution of the individual modalities to overall systemic responses in patient outcome and tolerance. TRIAL REGISTRATION: ClinicalTrials.gov NCT00278694 ; registration date: January 16, 2006, retrospective to enrollment of the first 10 patients of the current report.

Systemic release of osteoprotegerin during oxaliplatin-containing induction chemotherapy and favorable systemic outcome of sequential radiotherapy in rectal cancer.

In colorectal cancer, immune effectors may be determinative for disease outcome. Following curatively intended combined-modality therapy in locally advanced rectal cancer metastatic disease still remains a dominant cause of failure. Here, we investigated whether circulating immune factors might correlate with outcome. An antibody array was applied to assay changes of approximately 500 proteins in serial serum samples collected from patients during oxaliplatin-containing induction chemotherapy and sequential chemoradiotherapy before final pelvic surgery. Array data was analyzed by the Significance Analysis of Microarrays software and indicated significant alterations in serum osteoprotegerin (TNFRSF11B) during the treatment course, which were confirmed by osteoprotegerin measures using a single-parameter immunoassay. Patients experiencing increase in circulating osteoprotegerin during the chemotherapy had significantly better 5-year progression-free survival than those without increase (78% versus 48%; P = 0.009 by log-rank test). Hence, systemic release of this soluble tumor necrosis factor decoy receptor following the induction phase of neoadjuvant therapy was associated with favorable long-term outcome in patients given curatively intended chemoradiotherapy and surgery but with metastatic disease as the main adverse event. This finding suggests that osteoprotegerin may mediate or reflect systemic anti-tumor immunity invoked by combined-modality therapy in locally advanced rectal cancer.

Biomarkers of treatment toxicity in combined-modality cancer therapies with radiation and systemic drugs: study design, multiplex methods, molecular networks.

Organ toxicity in cancer therapy is likely caused by an underlying disposition for given pathophysiological mechanisms in the individual patient. Mechanistic data on treatment toxicity at the patient level are scarce; hence, probabilistic and translational linkages among different layers of data information, all the way from cellular targets of the therapeutic exposure to tissues and ultimately the patient's organ systems, are required. Throughout all of these layers, untoward treatment effects may be viewed as perturbations that propagate within a hierarchically structured network from one functional level to the next, at each level causing disturbances that reach a critical threshold, which ultimately are manifested as clinical adverse reactions. Advances in bioinformatics permit compilation of information across the various levels of data organization, presumably enabling integrated systems biology-based prediction of treatment safety. In view of the complexity of biological responses to cancer therapy, this communication reports on a "top-down" strategy, starting with the systematic assessment of adverse effects within a defined therapeutic context and proceeding to transcriptomic and proteomic analysis of relevant patient tissue samples and computational exploration of the resulting data, with the ultimate aim of utilizing information from functional connectivity networks in evaluation of patient safety in multimodal cancer therapy.

Biomarkers of histone deacetylase inhibitor activity in a phase 1 combined-modality study with radiotherapy.

BACKGROUND: Following the demonstration that histone deacetylase inhibitors enhanced experimental radiation-induced clonogenic suppression, the Pelvic Radiation and Vorinostat (PRAVO) phase 1 study, combining fractionated radiotherapy with daily vorinostat for pelvic carcinoma, was designed to evaluate both clinical and novel biomarker endpoints, the latter relating to pharmacodynamic indicators of vorinostat action in clinical radiotherapy. PATIENTS AND METHODS: Potential biomarkers of vorinostat radiosensitizing action, not simultaneously manifesting molecular perturbations elicited by the radiation itself, were explored by gene expression array analysis of study patients' peripheral blood mononuclear cells (PBMC), sampled at baseline (T0) and on-treatment two and 24 hours (T2 and T24) after the patients had received vorinostat. RESULTS: This strategy revealed 1,600 array probes that were common for the comparisons T2 versus T0 and T24 versus T2 across all of the patients, and furthermore, that no significantly differential expression was observed between the T0 and T24 groups. Functional annotation analysis of the array data showed that a significant number of identified genes were implicated in gene regulation, the cell cycle, and chromatin biology. Gene expression was validated both in patients' PBMC and in vorinostat-treated human carcinoma xenograft models, and transient repression of MYC was consistently observed. CONCLUSION: Within the design of the PRAVO study, all of the identified genes showed rapid and transient induction or repression and therefore, in principle, fulfilled the requirement of being pharmacodynamic biomarkers of vorinostat action in fractionated radiotherapy, possibly underscoring the role of MYC in this therapeutic setting.

Transcriptional responses in irradiated and bystander fibroblasts after low dose α-particle radiation.

PURPOSE: The objective of this study was to demonstrate the radiation-induced bystander effect (RIBE) in human F11 fibroblasts using micronucleus (MN) formation as an end-point and to investigate transcriptional responses towards low doses of α-particle radiation in irradiated and bystander fibroblasts employing genome-wide microarray analysis. MATERIALS AND METHODS: The MN frequency was investigated in unirradiated bystander cells recipient of growth medium from α-particle irradiated (0, 0.1, 0.5 and 2 Gy) immortalized human F11 fibroblasts. The irradiated conditioned medium (ICM) was transferred from irradiated to bystander fibroblasts 2 h after irradiation. Microarray analysis was performed in 0.1 Gy α-particle irradiated cells, unirradiated bystander cells and appropriate controls at different time points after ICM transfer. Microarray data analysis was performed at the single-gene level and gene-set level. RESULTS: MN were induced in unirradiated fibroblasts recipient of ICM harvested from 0.1 Gy α-particle irradiated cultures, but not from cultures irradiated with 0.5 or 2 Gy. Fibroblasts irradiated with 0.1 Gy showed repression of 26 genes 4 h after being irradiated. However, no significantly altered genes were found in bystander fibroblasts at any of the time points used in this study. Gene-set enrichment analysis showed that pathways such as ribosome, protein export, proteasome and protein 53 (p53) signaling were enriched in irradiated cells. However, bystander cells were enriched only in the lysosome pathway 24 h after receiving ICM, indicating persistence of the signals received from the irradiated cells. CONCLUSION: MN formation was induced in bystander fibroblast receiving medium from 0.1 Gy α-particle irradiated fibroblasts, but this was accompanied with only minor transcriptional responses.

The role of serotonin and p53 status in the radiation-induced bystander effect.

PURPOSE: The aim of this study was to investigate the role of serotonin and protein 53 (p53) status of the cells in the radiation-induced bystander effects (RIBE). MATERIALS AND METHODS: The radiation-induced bystander response was investigated in human MCF-7 breast cancer cells and human HCT116 colorectal cancer cells employing medium-transfer experiments and micronuclei (MN) induction as an end-point. Irradiated cell conditioned medium (ICCM) from cells exposed to α-particle or γ-radiation was filtered and transferred to unirradiated cells 2 h following irradiation. MCF-7 cells were irradiated with 0.5 Gy α-particles, while HCT116 p53(+/+) and HCT116 p53(-/-) cells were irradiated with 0.5 Gy γ-radiation. RESULTS: Bystander MCF-7 cells, recipient of ICCM from 0.5 Gy α-particle irradiated MCF-7 cells grown in high serotonin conditions showed a modest but significant increase in MN, while MCF-7 cells receiving ICCM with low serotonin levels did not show any bystander effect. Added serotonin (100 ng/ml) led to a bystander effectin HCT116 p53(-/-) cells recipient of ICCM from 0.5 Gy γ-irradiated HCT116 p53(+/+) cells, but had no effect when the ICCM was from γ-irradiated HCT116 P53(-/-) cells. CONCLUSION: The results indicate that serotonin levels in the medium play a role in the RIBE and that there may be an interaction between the role of serotonin and the p53 status of the irradiated cells.

Genome-wide microarray analysis of human fibroblasts in response to γ radiation and the radiation-induced bystander effect.

Radiation-induced bystander effects have been studied extensively due to their potential implications for cancer therapy and radiation protection; however, a complete understanding of the molecular mechanisms remains to be elucidated. In this study, we monitored transcriptional responses to γ radiation in irradiated and bystander fibroblasts simultaneously employing a genome-wide microarray approach to determine factors that may be modulated in the generation or propagation of the bystander effect. For the microarray data we employed analysis at both the single-gene and gene-set level to place the findings in a biological context. Unirradiated bystander fibroblasts that were recipients of growth medium harvested from irradiated cultures 2 h after exposure to 2 Gy displayed transient enrichment in gene sets belonging to ribosome, oxidative phosphorylation and neurodegenerative disease pathways associated with mitochondrial dysfunctions. The response to direct irradiation was characterized by induction of signaling and apoptosis genes and the gradual formation of a cellular immune response. A set of 14 genes, many of which were regulated by p53, were found to be induced early after irradiation (prior to medium transfer) and may be important in the generation or propagation of the bystander effect.

Dosimetry of a 238Pu-based alpha-particle irradiator and its biological application in a study of the bystander effect.

A better understanding of the non-targeted (bystander) effects of radiation may have important implications with regards to radiation risk assessment, radiation protection, and targeted cancer therapy. In the present study, the direct and bystander effects of α-particle irradiation in immortalized human fibroblasts (F11hTERT) and breast cancer cells (MCF-7) was investigated. To ensure a more accurate dose delivery to these different cell lines, an existing 238Pu α-particle irradiator was improved by the addition of a collimator and the development of an analytical equation for calculation of the radiation dose to cells. The mean dose rate and α-particle fluence were calculated for each cell line by taking into consideration the size of their nuclei. Bystander effect experiments were performed by transferring medium from irradiated to unirradiated cells and by measuring micronucleus formation in the cells. Both the immortalized human fibroblasts and the breast cancer cells displayed a bystander effect. In conclusion, the broad-beam α-particle irradiator improved in this study represents a useful tool in the investigation of direct and non-targeted effects of α-particle radiation.

A (238)Pu irradiator for exposure of cultured cells with alpha-radiation: construction, calibration and dosimetry.

An alpha-particle irradiator that can facilitate investigations of alpha-radiation effects on human cells in radiation protection, carcinogenesis and radioimmunotherapy was constructed. The irradiator was based on a 1.3 GBq (238)Pu source, housed in a stainless steel tube flushed with helium. Radiation provided by (238)Pu consists mainly of alpha-particles with energy of 5.5 MeV. The alpha-particle fluence and energy spectra were measured with a silicon semiconductor detector. Monte Carlo simulations were used to estimate the mean number of alpha-particles and the mean absorbed alpha-particle dose to cells for various irradiation times and distances between cells and source. There was a linear dependence between exposure time and alpha-particle fluence for exposure times above 1s. The alpha-particle activity concentration varied with a factor 2.7 over the source area, while the variation in energy peak position was <4%. At the cell nucleus position and with a distance of 45 mm between the source and the mylar dish surface, the alpha-fluence was 4.6 x 10(4)counts/(mm(2)s), the average incident alpha-particle energy was 2.5 MeV and the average linear energy transfer was 167 keV/microm. The average dose rate to the cells, with 5 microm diameter nucleus, was 1.2 Gy/s. The (238)Pu alpha-particle irradiator is feasible for irradiation of cells and it can be used for studies of both direct effects and bystander effects of alpha-radiation.

Cytochrome c impaled: investigation of the extended lipid anchorage of a soluble protein to mitochondrial membrane models.

Cyt c (cytochrome c) has been traditionally envisioned as rapidly diffusing in two dimensions at the surface of the mitochondrial inner membrane when not engaged in redox reactions with physiological partners. However, the discovery of the extended lipid anchorage (insertion of an acyl chain of a bilayer phospholipid into the protein interior) suggests that this may not be exclusively the case. The physical and structural factors underlying the conformational changes that occur upon interaction of ferrous cyt c with phospholipid membrane models have been investigated by monitoring the extent of the spin state change that result from this interaction. Once transiently linked by electrostatic forces between basic side chains and phosphate groups, the acyl chain entry may occur between two parallel hydrophobic polypeptide stretches that are surrounded by positively charged residues. Alteration of these charges, as in the case of non-trimethylated (TML72K) yeast cyt c and Arg91Nle horse cyt c (where Nle is norleucine), led to a decline in the binding affinity for the phospholipid liposomes. The electrostatic association was sensitive to ionic strength, polyanions and pH, whereas the hydrophobic interactions were enhanced by conformational changes that contributed to the loosening of the tertiary structure of cyt c. In addition to proposing a mechanistic model for the extended lipid anchorage of cyt c, we consider what, if any, might be the physiological relevance of the phenomenon.