Potential impact on prevalence of obesity in the UK of a 20% price increase in high sugar snacks: modelling study

OBJECTIVE

To estimate the potential impact on body mass index (BMI) and prevalence of obesity of a 20% price increase in high sugar snacks.

DESIGN

Modelling study.

SETTING

General adult population of the United Kingdom.

PARTICIPANTS

36 324 households with data on product level household expenditure from UK Kantar FMCG (fast moving consumer goods) panel for January 2012 to December 2013. Data were used to estimate changes in energy (kcal, 1 kcal=4.18 kJ=0.00418 MJ) purchase associated with a 20% price increase in high sugar snacks. Data for 2544 adults from waves 5 to 8 of the National Diet and Nutrition Survey (2012-16) were used to estimate resulting changes in BMI and prevalence of obesity.

MAIN OUTCOME MEASURES

The effect on per person take home energy purchases of a 20% price increase for three categories of high sugar snacks: confectionery (including chocolate), biscuits, and cakes. Health outcomes resulting from the price increase were measured as changes in weight, BMI (not overweight (BMI <25), overweight (BMI ≥25 and <30), and obese (BMI ≥30)), and prevalence of obesity. Results were stratified by household income and BMI.

RESULTS

For income groups combined, the average reduction in energy consumption for a 20% price increase in high sugar snacks was estimated to be 8.9×10³ kcal (95% confidence interval -13.1×10³ to -4.2×10³ kcal). Using a static weight loss model, BMI was estimated to decrease by 0.53 (95% confidence interval -1.01 to -0.06) on average across all categories and income groups. This change could reduce the UK prevalence of obesity by 2.7 percentage points (95% confidence interval -3.7 to -1.7 percentage points) after one year. The impact of a 20% price increase in high sugar snacks on energy purchase was largest in low income households classified as obese and smallest in high income households classified as not overweight.

CONCLUSIONS

Increasing the price of high sugar snacks by 20% could reduce energy intake, BMI, and prevalence of obesity. This finding was in a UK context and was double that modelled for a similar price increase in sugar sweetened beverages.

Proteomic Insights into Phycobilisome Degradation, A Selective and Tightly Controlled Process in The Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973

Phycobilisomes (PBSs) are large (3-5 megadalton) pigment-protein complexes in cyanobacteria that associate with thylakoid membranes and harvest light primarily for photosystem II. PBSs consist of highly ordered assemblies of pigmented phycobiliproteins (PBPs) and linker proteins that can account for up to half of the soluble protein in cells. Cyanobacteria adjust to changing environmental conditions by modulating PBS size and number. In response to nutrient depletion such as nitrogen (N) deprivation, PBSs are degraded in an extensive, tightly controlled, and reversible process. In Synechococcus elongatus UTEX 2973, a fast-growing cyanobacterium with a doubling time of two hours, the process of PBS degradation is very rapid, with 80% of PBSs per cell degraded in six hours under optimal light and CO₂ conditions. Proteomic analysis during PBS degradation and re-synthesis revealed multiple proteoforms of PBPs with partially degraded phycocyanobilin (PCB) pigments. NblA, a small proteolysis adaptor essential for PBS degradation, was characterized and validated with targeted mass spectrometry. NblA levels rose from essentially 0 to 25,000 copies per cell within 30 min of N depletion, and correlated with the rate of decrease in phycocyanin (PC). Implications of this correlation on the overall mechanism of PBS degradation during N deprivation are discussed.

Evidence on the magnitude of the economic, health and population effects of palm cooking oil consumption: an integrated modelling approach with Thailand as a case study

Background

Palm oil’s high yields, consequent low cost and highly versatile properties as a cooking oil and food ingredient have resulted in its thorough infiltration of the food sector in some countries. Longitudinal studies have associated palm oil’s high saturated fatty acid content with non-communicable disease, but neither the economic or disease burdens have been assessed previously.

Methods

This novel palm oil-focussed disease burden assessment employs a fully integrated health, macroeconomic and demographic Computable General Equilibrium Model for Thailand with nine regional (urban/rural) households. Nutritional changes from food consumption are endogenously translated into health (myocardial infarction (MI) and stroke) and population outcomes and are fed back into the macroeconomic model as health and caregiver-related productive labour supply effects and healthcare costs to generate holistic 2016–2035 burden estimates. Model scenarios mirror the replacement of palm cooking oil with other dietary oils and are compared with simulated total Thai health and macroeconomic burdens for MI and stroke.

Results

Replacing consumption of palm cooking oil with other dietary oils could reduce MI/stroke incident cases by 8280/2639 and cumulative deaths by 4683/894 over 20 years, removing approximately 0.5% of the total Thai burden of MI/stroke. This palm cooking oil replacement would reduce consumption shares of saturated/monounsaturated fatty acids in Thai household consumption by 6.5%/3% and increase polyunsaturated fatty acid consumption shares by 14%, yielding a 1.74% decrease in the population-wide total-to-HDL cholesterol ratio after 20 years. The macroeconomic burden that would be removed is US$308mn, approximately 0.44% of the total burden of MI/stroke on Thailand’s economy or 0.003% of cumulative 20-year GDP. Bangkok and Central region households benefit most from removal of disease burdens.

Conclusions

Simulations indicate that consumption of palm cooking oil, rather than other dietary oils, imposes a negative health burden (MI and stroke) and associated economic burden on a high consuming country, such as Thailand. Integrated sectoral model frameworks to assess these burdens are possible, and burden estimates from our simulated direct replacement of palm cooking oil indicate that using these frameworks both for broader analyses of dietary palm oil use and total burden analyses of other diseases may also be beneficial.

Electronic supplementary material

The online version of this article (10.1186/s12963-019-0191-y) contains supplementary material, which is available to authorized users.

Recent trends in energy and nutrient content of take-home food and beverage purchases in Great Britain: an analysis of 225 million food and beverage purchases over 6 years

Introduction

In recent years, there has been an increased focus on developing a coherent obesity policy in the UK, which has led to various national policy initiatives aimed at improving population diet. We sought to determine whether there have been concurrent changes in trends in the nutrient content of take-home food and beverage purchases within this policy environment.

Methods

We used 2012–2017 data from the UK Kantar Fast-Moving Consumer Goods (FMCG) panel, a nationally representative panel study of food and beverages bought by British households and brought into the home (n≈32 000 per year). Households used hand-held barcode scanners to report over 225 million product-level purchases of food and beverages, for which nutritional information was obtained. We estimated daily per capita purchases of energy and nutrients from 32 healthier and less healthy food groups defined using the nutrient profiling model used by the UK Department of Health.

Results

From 2012 to 2017, daily purchases of energy from food and beverages taken home decreased by 35.4 kcal (95% CI 25.5 to 45.2) per capita. This is explained by moderate decreases in the purchase of products with high contents in carbohydrate (−13.1 g (−14.4 to –11.8)) and sugar (−4.4 g (−5.1 to –3.7)), despite small increases in protein (1.7 g (1.4 to 2.1)) and saturated fat (0.4 g (0.2 to 0.6)). Food and beverage purchases exceeded daily reference intake values in fat (on average +6%), saturated fat (+43%), sugar (+16%) and protein (+28%) across all years. Although substitutions between individual food groups were large in energy and nutrients purchased, the heterogeneity of these patterns resulted in modest overall changes.

Conclusion

There have been small declines in the purchase of less healthy food products, which translated to a small reduction of total energy and sugar purchases taken home. However, the rate of change needs to be accelerated in order to substantially reduce the health risks of poor diets, suggesting that more radical policies may be needed to attain larger population effects.

International trade, dietary change, and cardiovascular disease health outcomes: Import tariff reform using an integrated macroeconomic, environmental and health modelling framework for Thailand

United Nations (UN) member states have, since 2011, worked to address the emerging global NCD crisis, but progress has, so far, been insufficient. Food trade policy is recognised to have the potential to impact certain major diet-related health and environmental outcomes. We study the potential for using import tariff protection as a health and environmental policy instrument. Specifically, we apply a rigorous and consistent Macroeconomic-Environmental-Demographic-health (MED-health) simulation model framework to study fiscal food policy import tariffs and dietary change in Thailand over the future 20 year period 2016-2035. We find that the existing Thai tariff structure, by lowering imports, lowers agricultural Land Use Change (LUC)-related GHG emissions and protects against cholesterol-related cardiovascular disease (CVD). This confirms previous evidence that food trade, measured by import shares of food expenditures and caloric intakes, is correlated with unhealthy eating and adverse health outcomes among importing country populations. A continued drive towards tariff liberalization and economic efficiency in Thailand may therefore come at the expense of reduced health and environmental sustainability of food consumption and production systems. Due to large efficiency losses, the existing tariff structure is, however, not cost-effective as an environmental or health policy instrument. However, additional simulations confirm that stylized 30% food sector import tariffs generally improve nutritional, clinical health, demographic, and environmental indicators across the board. We also find that diet-related health improvements can go hand-in-hand with increased Saturated Fatty Acid (SFA) intakes. Despite limited cost-effectiveness, policy makers from Thailand and abroad, including WHO, would therefore be well advised to consider targeted fiscal food policy tariffs as a potential intervention to maintain combined health and environmental sustainability, and to reconsider the specification of WHO dietary guidelines with their focus on SFA intake (rather than composition of fatty acid intake) targets.

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Fully integrated Macroeconomic-Environmental-Demographic-health model for Thailand.

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Methodologically rigorous quantitative approach to analysing trade and health.

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Existing Thai tariff structure protects against cholesterol-related CVD illness.

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Food import tariffs generally improve nutritional, health and demographic outcomes.

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Protective import tariffs generally lead to economic-environmental trade-offs.

Automated Nanoflow Two-Dimensional Reversed-Phase Liquid Chromatography System Enables In-Depth Proteome and Phosphoproteome Profiling of Nanoscale Samples

Two-dimensional reversed-phase capillary liquid chromatography (2D RPLC) separations have enabled comprehensive proteome profiling of biological systems. However, milligram sample quantities of proteins are typically required due to significant losses during offline fractionation. Such a large sample requirement generally precludes the application samples in the nanogram to low-microgram range. To achieve in-depth proteomic analysis of such small-sized samples, we have developed the nanoFAC (nanoflow Fractionation and Automated Concatenation) 2D RPLC platform, in which the first dimension high-pH fractionation was performed on a 75-μm i.d. capillary column at a 300 nL/min flow rate with automated fraction concatenation, instead of on a typically used 2.1 mm column at a 200 μL/min flow rate with manual concatenation. Each fraction was then fully transferred to the second-dimension low-pH nanoLC separation using an autosampler equipped with a custom-machined syringe. We have found that using a polypropylene 96-well plate as collection device as well as the addition of n-Dodecyl β-d-maltoside (0.01%) in the collection buffer can significantly improve sample recovery. We have demonstrated the nanoFAC 2D RPLC platform can achieve confident identifications of ∼49,000-94,000 unique peptides, corresponding to ∼6,700-8,300 protein groups using only 100-1000 ng of HeLa tryptic digest (equivalent to ∼500-5,000 cells). Furthermore, by integrating with phosphopeptide enrichment, the nanoFAC 2D RPLC platform can identify ∼20,000 phosphopeptides from 100 μg of MCF-7 cell lysate.

Abstract 957: An essential role for Argonaute 2 in mouse models of KRAS-driven cancers

In 2016, we identified a direct interaction between RAS and Argonaute 2 (AGO2), a key mediator of RNA-mediated gene silencing, that is essential for KRAS-driven oncogenesis using pancreatic and lung cancer cell line models. Recently, we employed a genetically engineered mouse model of pancreatic cancer to define the effects of conditional loss of AGO2 in KRASG12D-driven pancreatic cancer (KC model). Genetic ablation of AGO2 did not interfere with development of the normal pancreas or KRASG12D-driven early precursor pancreatic intraepithelial neoplasia (PanIN) lesions. However, AGO2 loss prevents progression from early to late PanIN lesions, development of pancreatic ductal adenocarcinoma (PDAC), and metastatic progression. This results in a dramatic increase in the survival of KRASG12D mutant mice deficient in AGO2 expression. Mechanistically, lack of PanIN to PDAC progression was due to oncogene-induced senescence (OIS) through activation of EGFR-wild type RAS-phosphoERK signaling in the absence of AGO2.

Using validated pan-RAS and AGO2 antibodies for immunofluorescence (IF) and proximity ligation assay (PLA), we observed increased RAS and AGO2 co-localization at the plasma membrane in mouse and human pancreatic tissues associated with PDAC progression. While AGO2 ablation permits PanIN initiation driven by the EGFR-RAS axis, these lesions undergo OIS rather than progressing to PDAC. Further, we used co-IP and PLA analyses to probe the effects of EGF stimulation in cell lines expressing wild-type and mutant forms of KRAS. In wild-type RAS expressing cells, RAS-AGO2 co-localization and interaction were limited to the intracellular regions of the cells, and dramatically increased and shifted to the plasma membrane under conditions of stress (serum starvation). Interestingly, EGF stimulation disrupted this membrane RAS-AGO2 interaction and restored it to intracellular levels. Using phosphorylation-deficient AGO2 mutants, we further demonstrate that the disruption of wild-type RAS-AGO2 interaction is due to EGFR-mediated AGO2Y393 phosphorylation. Interestingly, mutant KRAS-AGO2 interaction is not subject to EGFR activation, suggesting that although both the wild type and mutant RAS bind AGO2, they are differentially regulated through growth factor receptor activation.

We will discuss our ongoing studies evaluating the effects of AGO2 ablation in the KRASG12Ddriven lung cancer mouse model and PDAC progression with p53 loss (KPC model). Our recent in vivo work supports a biphasic model of pancreatic cancer development: an AGO2-independent early phase of PanIN formation reliant on EGFR and wild-type RAS signaling, and an AGO2-dependent phase wherein the mutant KRAS-AGO2 interaction is critical for PDAC progression.

Citation Format: Sunita Shankar, Jean Ching-Yi Tien, Ronald F. Siebenaler, Vijaya L. Dommeti, Sylvia Zelenka-Wang, Jessica Waninger, Kristin M. Juckette, Alice Xu, Xiao-Ming Wang, Seema Chugh, Malay Mody, Sanjana Eyunni, Andrew Goodrum, Grace Tsaloff, Yuping Zhang, Ingrid J. Apel, Javed Siddiqui, Richard D. Smith, Heather A. Carlson, John Tesmer, Xuhong Cao, Jiaqi Shi, Chandan Kumar-Sinha, Arul M. Chinnaiyan. An essential role for Argonaute 2 in mouse models of KRAS-driven cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 957.

Abstract LB-006: Proteogenomic characterization of human colon cancer reveals new therapeutic opportunities

We prospectively collected matched tumor specimens, adjacent non-tumor tissues, and blood samples from 110 colon cancer patients and analyzed the samples using seven omics platforms, including whole-exome sequencing, copy number arrays, RNA-Seq, miRNA-Seq, label-free global proteomics, isobaric tandem mass tag (TMT) labeling-based global proteomics, and TMT-based phosphoproteomics. Comparative proteomic and phosphoproteomic analysis of paired tumor and adjacent normal samples produced the first comprehensive catalogue of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers and drug targets. These cancer-associated proteins and phosphosites had very little overlap with known cancer genes in the Cancer Gene Census, providing a novel information layer to our knowledge about colon cancer. One notable finding in differential proteome analysis is the identification of several cancer/testis antigens that were recurrently over-expressed in tumors compared to adjacent normal tissue, including IGF2BP3 (51%), SPAG1 (14%), and ATAD2 (8%). Through integrative analysis of the whole-exome sequencing, RNA-Seq, and proteomics data, we further predicted personalized neoantigens for 38% of the patients. In total, we found proteomics-supported neoantigens or cancer/testis antigens for 78% of the tumors in this cohort, demonstrating the potential of proteogenomics in identifying tumor antigens for cancer vaccine development. Proteomics data complemented somatic copy number analysis results and showed that multiple somatic copy number deletion events converge to repress the endocytosis pathway, suggesting its tumor suppressor role in colon cancer. In addition to reinforcing or complementing genomic findings, proteogenomic integration may also contradict genomics data-based inferences and lead to unexpected discoveries and therapeutic opportunities. Proteomics data identified SOX9 as an oncogene in colon cancer, whereas it was predicted to be a tumor suppressor based on somatic mutation data in the TCGA study. Phosphoproteomics data revealed a dual role of Rb phosphorylation in promoting proliferation and repressing apoptosis in colon cancer, clarifying the long-standing puzzle of colon cancer-specific amplification of this tumor suppressor and highlighting a unique opportunity for targeting Rb phosphorylation in colon cancer. Microsatellite instability status has been approved by the FDA as a biomarker for selecting patients for checkpoint inhibitor therapy in colorectal and other solid tumors. However, many MSI-high tumors fail to respond to checkpoint inhibition. Our proteogenomic analysis identified a subtype-specific association between increased glycolysis and decreased CD8 T cell infiltration in MSI-high colon tumors, suggesting glycolysis as a target for overcoming immune evasion in this MSI-H tumors. We make the primary and processed datasets available in publicly accessible data repositories and portals to allow broad use of these datasets for new biological discoveries and therapeutic hypothesis generation.

Citation Format: Bing Zhang, Suhas Vasaikar, Chen Huang, Xiaojing Wang, Vladislav A. Petyuk, Sara R. Savage, Bo Wen, Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A. Arshad, Marina A. Gritsenko, Lisa J. Zimmerman, Jason E. McDermott, Therese R. Clauss, Ronald J. Moore, Rui Zhao, Matthew E. Monroe, Yi-Ting Wang, Matthew C. Chambers, Robbert J. Slebos, Ken S. Lau, Qianxing Mo, Li Ding, Matthew Ellis, Mathangi Thiagarajan, Christopher R. Kinsinger, Henry Rodriguez, Richard D. Smith, Karin D. Rodland, Daniel C. Liebler, Tao Liu, CPTAC Investigators. Proteogenomic characterization of human colon cancer reveals new therapeutic opportunities [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-006.

Socio-economic patterning of expenditures on 'out-of-home' food and non-alcoholic beverages by product and place of purchase in Britain

While most food is consumed at home, food eaten out-of-home plays an important role in diets and it has been associated with higher energy intake and higher body weight. Beyond prepared meals, there is limited understanding of what foods people buy out-of-home and where they buy them from. This study analyses out-of-home food purchases by food groups and food outlet types, and estimates socio-economic differences in these expenditure patterns. We used a nationally representative product-level dataset of expenditures (n=2,734,987) on foods and non-alcoholic beverages for out-of-home consumption for 9,704 respondents in Great Britain (June 2015-December 2017). Population weighted estimates of per capita weekly expenditures and shares of expenditure were derived for four outlet types and eight food groups. We used linear multi-level modelling to determine differences in expenditure patterns by socio-economic status (SES) characterised via occupational social grade. Out-of-home purchases make up 25-39% of total food and beverage expenditures. Mid- and high-SES respondents spent nearly twice as much (£17.76 and £15.11 weekly), compared to low-SES respondents (£9.69) for out-ofhome food consumption. A third of expenditures across SES (36-37%) were spent in venues other than restaurants or fast-food and takeaway outlets. Meals accounted for 60% of expenditures, but a third was spent on beverages (10-12% non-alcoholic cold beverages, 17-18% hot beverages) and 9-10% on snacks. Mid- and low-SES respondents had a greater share of expenditure in takeaway and fast-food outlets, supermarkets and convenience stores, and on cold non-alcoholic beverages. Overall, low-SES respondents spent less on out-of-home foods but the share of this expenditure across different foods or outlets varied less. While restaurants, fast-food and takeaway outlets were a major source of out-of-home purchases, a significant proportion was spent in other outlets. Policies targeting out-of-home consumption should therefore consider the full range of foods as well as the diversity of places where they are sold.

Case selection for urological input in planned laparoscopic rectovaginal endometriosis surgery

BACKGROUND

Surgery for deep endometriosis often requires input from urological surgeons. This study aims to determine pre-operative and intra-operative factors that influence the need for urological input in laparoscopic resection of rectovaginal endometriosis and to assess the usefulness of a scoring system to predict this.

METHODS

We conducted a retrospective cohort study of 230 patients undergoing laparoscopic excision of deep endometriosis, at a tertiary referral centre for endometriosis in London UK, 2011 to 2015. Data from pre-operative assessment, surgery and post-operative follow up were analysed and patients were categorised according to their pre-operative and intra-operative risk factors. The primary outcome measure was the requirement of intra-operative input by urological surgeons.

RESULTS

The median age was 35 years. In addition to the excision of endometriosis, 19.6% patients (45 patients) underwent hysterectomy, 14.8% (34 patients) required JJ stent placement, 6.1% (14 patients) had bowel resections and 2.6% (6 patients) required an ileostomy. 93.9% (216 patients) were considered normal-risk pre-operatively, of whom 89.4% (193/216) did not require any intra-operative urological input. 10.6% of this normal-risk group (23/216) required JJ stents, of whom 69.6% (16/23) also required a hysterectomy or bowel resection. Post operative complications occurred in 0.9% (2/216) of normal-risk patients, with none having required intra-operative urological reconstruction.Six percent (14 patients) were deemed to be increased-risk pre-operatively, of whom 78.6% (11/14) required JJ stent insertion. Thirty-six percent of increased-risk patients (5/14) had pre-operative renal dysfunction demonstrated on MAG3/DMSA and 80.0% of these (4/5) required intra-operative ureteric reconstruction.

CONCLUSIONS

Patients considered normal-risk pre-operatively, planned for excision, without hysterectomy or bowel resection, can be safely managed without specific urology input. Patients with risk-features are highly likely to require urological input, particularly for JJ stent insertion. Patients with pre-operative renal dysfunction, demonstrated on MAG3/DMSA, have a high chance of requiring intra-operative ureteric reconstruction and are best managed with pre-planned reconstructive urologist input.

Dual Polarity Ion Confinement and Mobility Separations

Here, we present simulations and describe the initial implementation of a device capable of performing simultaneous ion mobility (IM) separations of positive and negative ions based upon the structures for lossless ion manipulations (SLIM). To achieve dual polarity ion confinement, the DC fields used for lateral confinement in previous SLIM were replaced with RF fields. Concurrent ion transport and mobility separation in the SLIM device are shown possible due to the nature of the traveling wave (TW) voltage profile which has potential minima at opposite sides of the wave for each ion polarity. We explored the potential for performing simultaneous IM separations of cations and anions over the same SLIM path and the impacts on the achievable IM resolution and resolving power. Initial results suggest comparable IM performance with previous single-polarity SLIM separations can be achieved. We also used ion trajectory simulations to investigate the capability to manipulate the spatial distributions of ion populations based on their polarities by biasing the RF fields and TW potentials on each SLIM surface so as to limit the interactions between opposite polarity ions. Graphical Abstract.

A Targeted Mass Spectrometric Assay for Reliable Sensitive Hepcidin Quantification

Hepcidin, a cysteine-rich peptide hormone, secreted mainly by the liver, plays a central role in iron metabolism regulation. Emerging evidence suggests that disordered iron metabolism is a risk factor for various types of diseases including cancers. However, it remains challenging to apply current mass spectrometry (MS)-based hepcidin assays for precise quantification due to the low fragmentation efficiency of intact hepcidin as well as synthesis difficulties for the intact hepcidin standard. To address these issues we recently developed a reliable sensitive targeted MS assay for hepcidin quantification from clinical samples that uses fully alkylated rather than intact hepcidin as the internal standard. Limits of detection and quantification were determined to be <0.5 ng/mL and 1 ng/mL, respectively. Application of the alkylated hepcidin assay to 70 clinical plasma samples (42 non-cancerous and 28 ovarian cancer patient samples) enabled reliable detection of endogenous hepcidin from the plasma samples, as well as conditioned culture media. The hepcidin concentrations ranged from 0.0 to 95.6 ng/mL across non-cancerous and cancer plasma specimens. Interestingly, cancer patients were found to have significantly higher hepcidin concentrations compared to non-cancerous patients (mean: 20.6 ng/ml for cancer; 5.94 ng/ml for non-cancerous) (p value < 0.001). Our results represent the first application of the alkylated hepcidin assay to clinical samples and demonstrate that the developed assay has better sensitivity and quantification accuracy than current MS-based hepcidin assays without the challenges in synthesis of intact hepcidin standard and accurately determining its absolute amount.

Boosting to Amplify Signal with Isobaric Labeling (BASIL) Strategy for Comprehensive Quantitative Phosphoproteomic Characterization of Small Populations of Cells

Comprehensive phosphoproteomic analysis of small populations of cells remains a daunting task due primarily to the insufficient MS signal intensity from low concentrations of enriched phosphopeptides. Isobaric labeling has a unique multiplexing feature where the "total" peptide signal from all channels (or samples) triggers MS/MS fragmentation for peptide identification, while the reporter ions provide quantitative information. In light of this feature, we tested the concept of using a "boosting" sample (e.g., a biological sample mimicking the study samples but available in a much larger quantity) in multiplexed analysis to enable sensitive and comprehensive quantitative phosphoproteomic measurements with <100 000 cells. This simple boosting to amplify signal with isobaric labeling (BASIL) strategy increased the overall number of quantifiable phosphorylation sites more than 4-fold. Good reproducibility in quantification was demonstrated with a median CV of 15.3% and Pearson correlation coefficient of 0.95 from biological replicates. A proof-of-concept experiment demonstrated the ability of BASIL to distinguish acute myeloid leukemia cells based on the phosphoproteome data. Moreover, in a pilot application, this strategy enabled quantitative analysis of over 20 000 phosphorylation sites from human pancreatic islets treated with interleukin-1β and interferon-γ. Together, this signal boosting strategy provides an attractive solution for comprehensive and quantitative phosphoproteome profiling of relatively small populations of cells where traditional phosphoproteomic workflows lack sufficient sensitivity.

Increased β-cell proliferation before immune cell invasion prevents progression of type 1 diabetes

Type 1 diabetes (T1D) is characterized by pancreatic islet infiltration by autoreactive immune cells and a near-total loss of β-cells¹. Restoration of insulin-producing β-cells coupled with immunomodulation to suppress the autoimmune attack has emerged as a potential approach to counter T1D^2-4. Here we report that enhancing β-cell mass early in life, in two models of female NOD mice, results in immunomodulation of T-cells, reduced islet infiltration and lower β-cell apoptosis, that together protect them from developing T1D. The animals displayed altered β-cell antigens, and islet transplantation studies showed prolonged graft survival in the NOD-LIRKO model. Adoptive transfer of splenocytes from the NOD-LIRKOs prevented development of diabetes in pre-diabetic NOD mice. A significant increase in the splenic CD4⁺CD25⁺FoxP3⁺ regulatory T-cell (Treg) population was observed to underlie the protected phenotype since Treg depletion rendered NOD-LIRKO mice diabetic. The increase in Tregs coupled with activation of TGF-β/SMAD3 signaling pathway in pathogenic T-cells favored reduced ability to kill β-cells. These data support a previously unidentified observation that initiating β-cell proliferation, alone, prior to islet infiltration by immune cells alters the identity of β-cells, decreases pathologic self-reactivity of effector cells and increases Tregs to prevent progression of T1D.

Opening new paths for biological applications of ion mobility - mass spectrometry using Structures for Lossless Ion Manipulations

Ion mobility separations coupled to mass spectrometry (IM-MS) have received much attention for their ability to provide complementary structural information to solution-phase-based separations, as well as to aid in the identification of unknown compounds. While IM-MS is an increasingly powerful analytical technique, significant bottlenecks related to the resolution of measurements have kept it from becoming broadly applied for biological analyses. Presently, IM-MS-based measurements also remain limited in terms of their sensitivity as compared to state of the art MS-based approaches alone. Structures for Lossless Ion Manipulations (SLIM)-based IM separations provide a basis for overcoming these bottlenecks, addressing issues associated with resolution and sensitivity in the omics, and potentially opening the door to much broader application.

Ion Mobility Spectrometry and the Omics: Distinguishing Isomers, Molecular Classes and Contaminant Ions in Complex Samples

Ion mobility spectrometry (IMS) is a widely used analytical technique providing rapid gas phase separations. IMS alone is useful, but its coupling with mass spectrometry (IMS-MS) and various front-end separation techniques has greatly increased the molecular information achievable from different omic analyses. IMS-MS analyses are specifically gaining attention for improving metabolomic, lipidomic, glycomic, proteomic and exposomic analyses by increasing measurement sensitivity (e.g. S/N ratio), reducing the detection limit, and amplifying peak capacity. Numerous studies including national security-related analyses, disease screenings and environmental evaluations are illustrating that IMS-MS is able to extract information not possible with MS alone. Furthermore, IMS-MS has shown great utility in salvaging molecular information for low abundance molecules of interest when high concentration contaminant ions are present in the sample by reducing detector suppression. This review highlights how IMS-MS is currently being used in omic analyses to distinguish structurally similar molecules, isomers, molecular classes and contaminant ions.

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

We performed the first proteogenomic study on a prospectively collected colon cancer cohort. Comparative proteomic and phosphoproteomic analysis of paired tumor and normal adjacent tissues produced a catalog of colon cancer-associated proteins and phosphosites, including known and putative new biomarkers, drug targets, and cancer/testis antigens. Proteogenomic integration not only prioritized genomically inferred targets, such as copy-number drivers and mutation-derived neoantigens, but also yielded novel findings. Phosphoproteomics data associated Rb phosphorylation with increased proliferation and decreased apoptosis in colon cancer, which explains why this classical tumor suppressor is amplified in colon tumors and suggests a rationale for targeting Rb phosphorylation in colon cancer. Proteomics identified an association between decreased CD8 T cell infiltration and increased glycolysis in microsatellite instability-high (MSI-H) tumors, suggesting glycolysis as a potential target to overcome the resistance of MSI-H tumors to immune checkpoint blockade. Proteogenomics presents new avenues for biological discoveries and therapeutic development.

The challenge of antimicrobial resistance: What economics can contribute

As antibiotic consumption grows, bacteria are becoming increasingly resistant to treatment. Antibiotic resistance undermines much of modern health care, which relies on access to effective antibiotics to prevent and treat infections associated with routine medical procedures. The resulting challenges have much in common with those posed by climate change, which economists have responded to with research that has informed and shaped public policy. Drawing on economic concepts such as externalities and the principal–agent relationship, we suggest how economics can help to solve the challenges arising from increasing resistance to antibiotics. We discuss solutions to the key economic issues, from incentivizing the development of effective new antibiotics to improving antibiotic stewardship through financial mechanisms and regulation.

Separation of β-Amyloid Tryptic Peptide Species with Isomerized and Racemized l-Aspartic Residues with Ion Mobility in Structures for Lossless Ion Manipulations

Accumulation of β-amyloid (Aβ) is one of the hallmarks of Alzheimer's disease. The deposition of β-amyloid plaques is likely to start years in advance of manifestation of clinical symptoms, although the exact timing is unknown. Over the years, Aβ peptides undergo both post-translational modification and stereoisomerization. Analysis of the resulting stereoisomers is particularly challenging because of their identical elemental composition and similar physicochemical properties. Herein, we have utilized our recently developed structures for lossless ion manipulations ion mobility-mass spectrometry platform (SLIM IM-MS), in conjunction with serpentine ultralong path with extended routing (SUPER), to baseline resolve four distinct sets of Aβ17-28 tryptic peptide epimers on a rapid (∼1 s) time scale. We discovered that sodium adduct ions, [M + H + Na]2+, allowed baseline SLIM SUPER IM resolution for all Aβ epimer sets assessed, while such baseline separations were unachievable for their [M + 2H]2+ doubly protonated ions.

Integrating Agriculture and Health Research for Development: LCIRAH as an Interdisciplinary Programme to Address a Global Challenge

The multiple burdens of persistent undernutrition and micronutrient deficiencies, along with the rapidly growing rates of overweight, obesity, and associated chronic diseases, are major challenges globally. The role of agriculture and the food system in meeting these challenges is very poorly understood. Achieving food security and addressing malnutrition in all its forms, a Sustainable Development Goal, requires an understanding of how changing food systems affect health outcomes and the development of new tools to design and evaluate interventions. An interinstitutional programme to address this interdisciplinary research challenge is described. Over the past seven years, the Leverhulme Centre for Integrative Research on Agriculture and Health has built a portfolio of successful and innovative research, trained a new cadre of interdisciplinary researchers in "Agri-Health," and built an international research community with a particular focus on strengthening research capacity in low- and middle-income countries. The evolution of this programme is described, and key factors contributing to its success are discussed that may be of general value in designing interdisciplinary research programmes directed at supporting global development goals.

Multimodal in vivo brain electrophysiology with integrated glass microelectrodes

Electrophysiology is the most used approach for the collection of functional data in basic and translational neuroscience, but it is typically limited to either intracellular or extracellular recordings. The integration of multiple physiological modalities for the routine acquisition of multimodal data with microelectrodes could be useful for biomedical applications, yet this has been challenging owing to incompatibilities of fabrication methods. Here, we present a suite of glass pipettes with integrated microelectrodes for the simultaneous acquisition of multimodal intracellular and extracellular information in vivo, electrochemistry assessments, and optogenetic perturbations of neural activity. We used the integrated devices to acquire multimodal signals from the CA1 region of the hippocampus in mice and rats, and show that these data can serve as ground-truth validation for the performance of spike-sorting algorithms. The microdevices are applicable for basic and translational neurobiology, and for the development of next-generation brain-machine interfaces.

Proximity-dependent proteomics of the Chlamydia trachomatis inclusion membrane reveals functional interactions with endoplasmic reticulum exit sites

Chlamydia trachomatis is the most common cause of bacterial sexually transmitted infection, responsible for millions of infections each year. Despite this high prevalence, the elucidation of the molecular mechanisms of Chlamydia pathogenesis has been difficult due to limitations in genetic tools and its intracellular developmental cycle. Within a host epithelial cell, chlamydiae replicate within a vacuole called the inclusion. Many Chlamydia-host interactions are thought to be mediated by the Inc family of type III secreted proteins that are anchored in the inclusion membrane, but their array of host targets are largely unknown. To investigate how the inclusion membrane proteome changes over the course of an infected cell, we have adapted the APEX2 system of proximity-dependent biotinylation. APEX2 is capable of specifically labeling proteins within a 20 nm radius in living cells. We transformed C. trachomatis to express the enzyme APEX2 fused to known inclusion membrane proteins, allowing biotinylation and purification of inclusion-associated proteins. Using quantitative mass spectrometry against APEX2 labeled samples, we identified over 400 proteins associated with the inclusion membrane at early, middle, and late stages of epithelial cell infection. This system was sensitive enough to detect inclusion interacting proteins early in the developmental cycle, at 8 hours post infection, a previously intractable time point. Mass spectrometry analysis revealed a novel, early association between C. trachomatis inclusions and endoplasmic reticulum exit sites (ERES), functional regions of the ER where COPII-coated vesicles originate. Pharmacological and genetic disruption of ERES function severely restricted early chlamydial growth and the development of infectious progeny. APEX2 is therefore a powerful in situ approach for identifying critical protein interactions on the membranes of pathogen-containing vacuoles. Furthermore, the data derived from proteomic mapping of Chlamydia inclusions has illuminated an important functional role for ERES in promoting chlamydial developmental growth.