Cancer drug sensitivity prediction from routine histology images

Drug sensitivity prediction models can aid in personalising cancer therapy, biomarker discovery, and drug design. Such models require survival data from randomised controlled trials which can be time consuming and expensive. In this proof-of-concept study, we demonstrate for the first time that deep learning can link histological patterns in whole slide images (WSIs) of Haematoxylin & Eosin (H&E) stained breast cancer sections with drug sensitivities inferred from cell lines. We employ patient-wise drug sensitivities imputed from gene expression-based mapping of drug effects on cancer cell lines to train a deep learning model that predicts patients' sensitivity to multiple drugs from WSIs. We show that it is possible to use routine WSIs to predict the drug sensitivity profile of a cancer patient for a number of approved and experimental drugs. We also show that the proposed approach can identify cellular and histological patterns associated with drug sensitivity profiles of cancer patients.

Cross-linking breast tumor transcriptomic states and tissue histology

Identification of the gene expression state of a cancer patient from routine pathology imaging and characterization of its phenotypic effects have significant clinical and therapeutic implications. However, prediction of expression of individual genes from whole slide images (WSIs) is challenging due to co-dependent or correlated expression of multiple genes. Here, we use a purely data-driven approach to first identify groups of genes with co-dependent expression and then predict their status from WSIs using a bespoke graph neural network. These gene groups allow us to capture the gene expression state of a patient with a small number of binary variables that are biologically meaningful and carry histopathological insights for clinical and therapeutic use cases. Prediction of gene expression state based on these gene groups allows associating histological phenotypes (cellular composition, mitotic counts, grading, etc.) with underlying gene expression patterns and opens avenues for gaining biological insights from routine pathology imaging directly.

Bayesian analysis of isothermal titration calorimetry for binding thermodynamics

Isothermal titration calorimetry (ITC) is the only technique able to determine both the enthalpy and entropy of noncovalent association in a single experiment. The standard data analysis method based on nonlinear regression, however, provides unrealistically small uncertainty estimates due to its neglect of dominant sources of error. Here, we present a Bayesian framework for sampling from the posterior distribution of all thermodynamic parameters and other quantities of interest from one or more ITC experiments, allowing uncertainties and correlations to be quantitatively assessed. For a series of ITC measurements on metal:chelator and protein:ligand systems, the Bayesian approach yields uncertainties which represent the variability from experiment to experiment more accurately than the standard data analysis. In some datasets, the median enthalpy of binding is shifted by as much as 1.5 kcal/mol. A Python implementation suitable for analysis of data generated by MicroCal instruments (and adaptable to other calorimeters) is freely available online.

A Web-Based Tool for Patient Triage in Emergency Department Settings: Validation Using the Emergency Severity Index

Background

We evaluated the concordance between triage scores generated by a novel Internet clinical decision support tool, Clinical GPS (cGPS) (Lumiata Inc, San Mateo, CA), and the Emergency Severity Index (ESI), a well-established and clinically validated patient severity scale in use today. Although the ESI and cGPS use different underlying algorithms to calculate patient severity, both utilize a five-point integer scale with level 1 representing the highest severity.

Objective

The objective of this study was to compare cGPS results with an established gold standard in emergency triage.

Methods

We conducted a blinded trial comparing triage scores from the ESI: A Triage Tool for Emergency Department Care, Version 4, Implementation Handbook to those generated by cGPS from the text of 73 sample case vignettes. A weighted, quadratic kappa statistic was used to assess agreement between cGPS derived severity scores and those published in the ESI handbook for all 73 cases. Weighted kappa concordance was defined a priori as almost perfect (kappa > 0.8), substantial (0.6 < kappa < 0.8), moderate (0.4 < kappa < 0.6), fair (0.2 < kappa< 0.4), or slight (kappa < 0.2).

Results

Of the 73 case vignettes, the cGPS severity score matched the ESI handbook score in 95% of cases (69/73 cases), in addition, the weighted, quadratic kappa statistic showed almost perfect agreement (kappa = 0.93, 95% CI 0.854-0.996). In the subanalysis of 41 case vignettes assigned ESI scores of level 1 or 2, the cGPS and ESI severity scores matched in 95% of cases (39/41 cases).

Conclusions

These results indicate that the cGPS is a reliable indicator of triage severity, based on its comparison to a standardized index, the ESI. Future studies are needed to determine whether the cGPS can accurately assess the triage of patients in real clinical environments.

Blind prediction of HIV integrase binding from the SAMPL4 challenge

Here, we give an overview of the protein-ligand binding portion of the Statistical Assessment of Modeling of Proteins and Ligands 4 (SAMPL4) challenge, which focused on predicting binding of HIV integrase inhibitors in the catalytic core domain. The challenge encompassed three components--a small "virtual screening" challenge, a binding mode prediction component, and a small affinity prediction component. Here, we give summary results and statistics concerning the performance of all submissions at each of these challenges. Virtual screening was particularly challenging here in part because, in contrast to more typical virtual screening test sets, the inactive compounds were tested because they were thought to be likely binders, so only the very top predictions performed significantly better than random. Pose prediction was also quite challenging, in part because inhibitors in the set bind to three different sites, so even identifying the correct binding site was challenging. Still, the best methods managed low root mean squared deviation predictions in many cases. Here, we give an overview of results, highlight some features of methods which worked particularly well, and refer the interested reader to papers in this issue which describe specific submissions for additional details.

Ultrasonic enhancement of battery diffusion

It has been demonstrated that sonic energy can be harnessed to enhance convection in Galvanic cells during cyclic voltammetry; however, the practical value of this approach is limited due to the lack of open volumes for convection patterns to develop in most batteries. This study evaluates the ability of ultrasonic waves to enhance diffusion in membrane separators commonly used in sandwich-architecture batteries. Studies include the measuring of open-circuit performance curves to interpret performances in terms of reductions in concentration overpotentials. The use of a 40 kHz sonicator bath can consistently increase the voltage of the battery and reduce overpotential losses up to 30%. This work demonstrates and quantifies battery enhancement due to enhanced diffusion made possible with ultrasonic energy.

Practical aspects of the SAMPL challenge: providing an extensive experimental data set for the modeling community

To provide an experimental basis for a comprehensive molecular modeling evaluation study, 500 fragments from the Maybridge fragment library were soaked into crystals of bovine pancreatic trypsin and the structures determined by X-ray crystallography. The soaking experiments were performed in both single and pooled aliquots to determine if combination of fragments is an appropriate strategy. A further set of data was obtained from co-crystallizing the pooled fragments with the protein. X-ray diffraction data were collected on approximately 1000 crystals at the Australian Synchrotron, and these data were subsequently processed, and the preliminary analysis was performed with a custom software application (Jigsaw), which combines available software packages for structure solution and analysis.

Assessment and evaluation of contact as a risk factor for tuberculosis in rural Africa

SETTING

A rural district in Malawi.

OBJECTIVE

To determine the effect of inaccurate recall on estimates of the proportion of tuberculosis (TB) cases attributable to contact with identifiable prior cases.

DESIGN

Case-control study of laboratory-confirmed TB cases and community controls, comparing family, household and area contacts identified from a database of TB cases with those named at interview. Estimation of prior contact as a risk factor for TB and identified factors associated with being a named contact.

RESULTS

Ninety-five per cent of named contacts were known TB cases. The proportion of total identified contacts who were named at interview was 75%, and was similar for cases and controls. Cases were twice as likely as controls to identify prior contacts. Adding database information did not affect odds ratios, but increased the proportion of TB cases attributable to prior contact. Smear-positive, male and human immunodeficiency virus (HIV) negative TB patients were more likely to be named by subsequent cases. Identifiable recent contact with known smear-positive cases accounted for 12.5% of the TB burden.

CONCLUSIONS

Reporting of putative source contacts showed little evidence of recall bias and gave estimates of the relative risk of TB associated with identifiable contact. The lower likelihood of HIV-positive cases being named as contacts may reflect reduced infectiousness.

The influence of previous exposure to environmental mycobacteria on the interferon-gamma response to bacille Calmette-Guérin vaccination in southern England and northern Malawi

We report a large study of the effect of BCG vaccination on the in vitro 6-day whole blood interferon-gamma (IFN-gamma) response to antigens from eight species of mycobacteria among schoolchildren in south-eastern England, where bacille Calmette-Guérin (BCG) vaccination is highly protective against pulmonary tuberculosis, and among young adults in northern Malawi, where BCG vaccination is not protective. In the UK children, BCG induced an appreciable increase in IFN-gamma response to antigens from most species of mycobacteria. The degree of change was linked to the relatedness of the species to Mycobacterium bovis BCG, and provides further evidence of the cross-reactivity of mycobacterial species in priming of the immune system. IFN-gamma responses to purified protein derivatives (PPDs) from M. tuberculosis and environmental mycobacteria were more prevalent in the Malawian than the UK group prior to vaccination; BCG vaccination increased the prevalence of responses to these PPDs in the UK group to a level similar to that in Malawi. There was no evidence that the vaccine-induced change in IFN-gamma response was dependent upon the magnitude of the initial response of the individual to environmental mycobacteria in the United Kingdom or in Malawi. These observations should assist the development and interpretation of human clinical trials of new vaccines against M. tuberculosis in areas of both low and high exposure to environmental mycobacteria.

Side population/ABCG2-positive cells represent a heterogeneous group of haemopoietic cells: implications for the use of adult stem cells in transplantation and plasticity protocols

Murine side population (SP) cells may have an increased ability to engraft lethally irradiated mice and lack CD34 expression. Strategies using CD34 as a primary marker of haemopoietic stem cells may therefore result in the exclusion of a primitive stem cell population. The molecular basis for the murine SP phenotype has been attributed to the multidrug-resistance transporter ABCG2. This study aimed to investigate ABCG2 expression from a variety of human sources and investigate the relationship between ABCG2 expression, the SP phenotype, and expression of markers such as CD34 and CD133. SP cells were observed in different haemopoietic sources, but a significant increase in the number of SP cells was observed in PB following granulocyte colony-stimulating factor mobilisation. No direct correlation between the frequency of SP cells and the expression of ABCG2 was observed. SP cells were identified in both lineage-positive and lineage-negative population and ABCG2 expression was enriched in lineage-negative SP cells. Lineage-negative SP cells were devoid of CD34 expression but enriched for CD133. Subsequent analysis revealed that ABCG2 and CD133 are coexpressed. Together, these data suggest that the ABCG2 transporter is neither required nor responsible for the SP phenotpye in many human blood cells.

Interferon-gamma and skin test responses of schoolchildren in southeast England to purified protein derivatives from Mycobacterium tuberculosis and other species of mycobacteria

The immune responses of schoolchildren in southeast England to Mycobacterium tuberculosis and other species of mycobacteria were studied prior to vaccination with bacille Calmette-Guérin (BCG). Data are presented for tuberculin (Heaf) skin test and interferon-gamma (IFN-gamma) responses to M. tuberculosis purified protein derivative (PPD), and IFN-gamma responses to PPDs from eight other environmental mycobacteria, measured in 424 schoolchildren (13-15 years of age). Responses to M. tuberculosis PPD were detected in 27% of schoolchildren by in vitro IFN-gamma response and in 20% by the Heaf test. IFN-gamma responses were more prevalent to PPDs from species of mycobacteria other than M. tuberculosis, predominantly those of the MAIS complex and M. marinum (45-60% responders). Heaf test and IFN-gamma responses were associated (P<0.001) for M. tuberculosis, MAIS and M. marinum. These findings have implications for appropriate implementation of vaccination against tuberculosis.

Experimental inoculation of domestic cats (Felis domesticus) with Sarcocystis neurona or S. neurona-like merozoites

Sarcocystis neurona is the parasite most commonly associated with equine protozoal myeloencephalitis (EPM). Recently, cats (Felis domesticus) have been demonstrated to be an experimental intermediate host in the life cycle of S. neurona. This study was performed to determine if cats experimentally inoculated with culture-derived S. neurona merozoites develop tissue sarcocysts infectious to opossums (Didelphis virginiana), the definitive host of S. neurona. Four cats were inoculated with S. neurona or S. neurona-like merozoites and all developed antibodies reacting to S. neurona merozoite antigens, but tissue sarcocysts were detected in only two cats. Muscle tissues from the experimentally inoculated cats with and without detectable sarcocysts were fed to laboratory-reared opossums. Sporocysts were detected in gastrointestinal (GI) scrapings of one opossum fed experimentally infected feline tissues. The study results suggest that cats can develop tissue cysts following inoculation with culture-derived Sarcocystis sp. merozoites in which the particular isolate was originally derived from a naturally infected cat with tissue sarcocysts. This is in contrast to cats which did not develop tissue cysts when inoculated with S. neurona merozoites originally derived from a horse with EPM. These results indicate present biological differences between the culture-derived merozoites of two Sarcocystis isolates, Sn-UCD 1 and Sn-Mucat 2.

Polymorphisms in the Il12b gene affect structure and expression of IL-12 in NOD and other autoimmune-prone mouse strains

Interleukin (Il)-12 is a heterodimeric cytokine composed of 35 and 40 kD chains that plays a key role in the induction of Th1 cells, a T cell subset involved in many autoimmune diseases. We report here the cDNA sequence encoding the IL-12 p40 subunit from the autoimmune-prone non-obese diabetic (NOD) mouse, which spontaneously develops type 1 diabetes. Compared with the C57BL/6 sequence, there are two base changes that lead to amino acid replacements. Other autoimmune-prone strains, but not the diabetes-resistant NOR strain, share the same allele as NOD. We found both trans- and cis- allele-dependent effects on levels of basal and induced IL-12p40 expression. Furthermore, we show that one of these changes results in a structural change in the p40 molecule, as evidenced by the failure of a monoclonal antibody to bind NOD IL-12. These findings have implications for the predisposition to autoimmune responses in NOD and other autoimmune-prone mouse strains.

Lymphatic filariasis in the Karonga district of northern Malawi: a prevalence survey

In Malawi, two main foci of lymphatic filariasis (LF) are known to exist: one in the south, in the Shire valley, and the other in the north, along the Songwe River, on the border with Tanzania. There have been no formal surveys in the Songwe area since the 1960s but an opportunity arose in 2000-2001 to map LF in this area, in the context of a leprosy survey that formed part of the follow-up of a large leprosy and tuberculosis vaccine trial. Overall 687 immunochromatographic (ICT) tests were carried out. Wuchereria bancrofti antigenaemia was found in > 25% of adults in each of the 12 villages sampled (four in the Songwe area and eight in the rest of the Karonga district), with village prevalences varying from 28%-58%. Of the 685 adult male residents of the Songwe area who were each given full-body clinical examinations, 80 (11.7%) were identified as cases of hydrocele. Lymphoedema was found in seven (1.0%) of these adult males and in 29 (3.7%) of the 769 adult female residents of the Songwe area who were also examined. Microfilariae were detected in 33 (30.8%) of the 107 thick smears of night-blood samples that were made from individuals with positive ICT cards. The W. bancrofti infection focus in Karonga district is therefore wider than was previously known. This has important implications for the implementation and eventual impact of LF-control activities in this area.

Improvement in quality of life for cancer patients treated with epoetin alfa

Anaemia is a common complication of cancer and cancer therapies, and fatigue is one of the most common symptoms of anaemia, disrupting functional performance and reducing overall quality of life. The positive effects of treating renal patients with recombinant human erythropoietin are well documented. This case report series details the specific effects of fatigue on individual patients with cancer and their way of life, and describes their significant improvement in lifestyle following the reversal of anaemia using recombinant human erythropoietin, epoetin alfa.

The effects of intravascular stents on vasomotion in porcine coronary arteries

Intravascular stents are being increasingly utilized in the treatment of atherosclerotic coronary artery disease, however little is known about the effects of stents on coronary vasomotion. The purpose of the present study was to compare the effects of a heparin treated tantalum stent and balloon injury on coronary artery vasorelaxation and vasoconstriction. Male miniswine underwent cardiac catheterization and oversized balloon injury to the right and left circumflex coronary arteries. After two weeks, one artery was either balloon-injured again, or underwent implantation of a stent. Four weeks later, the coronary arteries were prepared for in vitro isometric ring studies. Vasodilator responses to bradykinin and A23187 calcium ionophore were significantly impaired in balloon-injured vessels. The bradykinin and A23187 responses in stented vessels showed significantly less vasorelaxation, compared to both balloon-injured and normal vessels. There were no significant differences between any of the groups in their vasodilator response to nitroprusside. Vasoconstrictor responses to acetylcholine were significantly greater in balloon-injured vessels, compared to normal vessels. Stented vessels, however, showed markedly less vasoconstriction to acetylcholine compared to both balloon-injured and normal vessels. The maximal KCI vasoconstrictor responses in balloon injured vessels and normal controls were not significantly different. However, the maximal KCI responses in stented vessels showed significantly less constriction compared to both balloon injured and normal vessels. In conclusion, the data demonstrated that coronary arteries implanted with a heparin treated tantalum stent were capable of vasomotor activity. Both conventional balloon angioplasty and stents resulted in impaired endothelium-dependent vasorelaxation. Endothelium-independent vasorelaxation, however, was not impaired.(ABSTRACT TRUNCATED AT 250 WORDS)

Restenosis following placement of an intracoronary heparin treated tantulum stent in the hyperlipidemic miniature swine model

Restenosis persists as an important factor limiting a favorable long term outcome following mechanical revascularization. The objective of the present study was to compare the effects of an intracoronary heparin treated tantalum prototype stent and balloon angioplasty on intimal hyperplasia, luminal diameter, and thrombosis in a porcine restenosis model. Male miniswine maintained on a high cholesterol diet and 325 mg aspirin per day underwent cardiac catheterization and oversized balloon injury to the right and left circumflex coronary arteries. Two weeks later one artery was either balloon injured again or implanted with a stent. No additional anticoagulation following stent placement was given, however aspirin was continued throughout the study. At four weeks, the coronary arteries were harvested and prepared for histologic examination and blinded quantitative morphometric analysis. The prototype stent was successfully deployed in 10 coronary arteries. Histological examination at explant revealed no evidence for thrombus or platelet aggregation. The angiographic luminal diameter of stented vessels was not significantly different from the diameter measured prior to implantation. In contrast, the angiographic diameter of balloon injured vessels was significantly decreased (4.4 +/- 0.4 mm2, balloon injured, vs. 5.8 +/- 3.3 mm2, control; p < 0.05). Stented arteries showed significantly more intimal hyperplasia, compared to balloon injured vessels (2.99 +/- 0.58 mm2 intimal area, stented arteries vs. 0.38 +/- 0.15 mm2 intimal area, control arteries; p < 0.05). In conclusion, heparin treated tantalum wire prototype intracoronary stents were successfully deployed in swine coronary arteries with no evidence for thrombus formation. Despite a significant intimal response, luminal diameter was preserved in stented vessels. The data suggest that a heparin treated tantalum wire prototype intracoronary stent may be an effective method of coronary revascularization that results in the preservation of luminal diameter without thrombotic occlusion.