From pre-processing to advanced dynamic modeling of pupil data

The pupil of the eye provides a rich source of information for cognitive scientists, as it can index a variety of bodily states (e.g., arousal, fatigue) and cognitive processes (e.g., attention, decision-making). As pupillometry becomes a more accessible and popular methodology, researchers have proposed a variety of techniques for analyzing pupil data. Here, we focus on time series-based, signal-to-signal approaches that enable one to relate dynamic changes in pupil size over time with dynamic changes in a stimulus time series, continuous behavioral outcome measures, or other participants' pupil traces. We first introduce pupillometry, its neural underpinnings, and the relation between pupil measurements and other oculomotor behaviors (e.g., blinks, saccades), to stress the importance of understanding what is being measured and what can be inferred from changes in pupillary activity. Next, we discuss possible pre-processing steps, and the contexts in which they may be necessary. Finally, we turn to signal-to-signal analytic techniques, including regression-based approaches, dynamic time-warping, phase clustering, detrended fluctuation analysis, and recurrence quantification analysis. Assumptions of these techniques, and examples of the scientific questions each can address, are outlined, with references to key papers and software packages. Additionally, we provide a detailed code tutorial that steps through the key examples and figures in this paper. Ultimately, we contend that the insights gained from pupillometry are constrained by the analysis techniques used, and that signal-to-signal approaches offer a means to generate novel scientific insights by taking into account understudied spectro-temporal relationships between the pupil signal and other signals of interest.

Structural analysis of potato starch transformation during high-energy ball-milling: Oxygen and humidity content effects

High Energy Ball-Milling (HEBM) modifies starchs' granule morphology, physicochemical properties, and chemical structure. However, understanding how the HEBM changes the starch chemical structure is necessary to control these modifications. Therefore, this study aimed to investigate the changes in potato starch's long- and short-range molecular order during HEBM at different environmental conditions such as oxygen (Air) and humidity content. Due to the correlation between the starch modification and the energy supplied (Esupp) by the HEBM, Burgio's equation was used to calculate this energy. The starch transformation was followed by X-ray diffraction, Fourier Transform-Infrared Spectroscopy, and Raman spectroscopy. A Principal Component Analysis (PCA) was conducted to reduce the HEBM variables. PAC analysis demonstrated that the different oxygen-humidity conditions do not affect the HEBM of potato starch. Based on the starch chemical structure transformation correlated with Esupp during HEBM, four stages were observed: orientation, modification, mechanolysis, and over-destruction. It was identified for the first time that at low milling energy (<1.5 kJ/g, orientation stage), the glycosidic rings change their orientation, and starch-water interaction increases while the starch's organization reduces. Ergo, the potato starch could be more susceptible to chemical modifications during the first two stages.

Global Impact of the COVID-19 Pandemic on Stroke Volumes and Cerebrovascular Events: A 1-Year Follow-up

BACKGROUND AND OBJECTIVES

Declines in stroke admission, IV thrombolysis (IVT), and mechanical thrombectomy volumes were reported during the first wave of the COVID-19 pandemic. There is a paucity of data on the longer-term effect of the pandemic on stroke volumes over the course of a year and through the second wave of the pandemic. We sought to measure the effect of the COVID-19 pandemic on the volumes of stroke admissions, intracranial hemorrhage (ICH), IVT, and mechanical thrombectomy over a 1-year period at the onset of the pandemic (March 1, 2020, to February 28, 2021) compared with the immediately preceding year (March 1, 2019, to February 29, 2020).

METHODS

We conducted a longitudinal retrospective study across 6 continents, 56 countries, and 275 stroke centers. We collected volume data for COVID-19 admissions and 4 stroke metrics: ischemic stroke admissions, ICH admissions, IVT treatments, and mechanical thrombectomy procedures. Diagnoses were identified by their ICD-10 codes or classifications in stroke databases.

RESULTS

There were 148,895 stroke admissions in the 1 year immediately before compared with 138,453 admissions during the 1-year pandemic, representing a 7% decline (95% CI [95% CI 7.1-6.9]; p < 0.0001). ICH volumes declined from 29,585 to 28,156 (4.8% [5.1-4.6]; p < 0.0001) and IVT volume from 24,584 to 23,077 (6.1% [6.4-5.8]; p < 0.0001). Larger declines were observed at high-volume compared with low-volume centers (all p < 0.0001). There was no significant change in mechanical thrombectomy volumes (0.7% [0.6-0.9]; p = 0.49). Stroke was diagnosed in 1.3% [1.31-1.38] of 406,792 COVID-19 hospitalizations. SARS-CoV-2 infection was present in 2.9% ([2.82-2.97], 5,656/195,539) of all stroke hospitalizations.

DISCUSSION

There was a global decline and shift to lower-volume centers of stroke admission volumes, ICH volumes, and IVT volumes during the 1st year of the COVID-19 pandemic compared with the prior year. Mechanical thrombectomy volumes were preserved. These results suggest preservation in the stroke care of higher severity of disease through the first pandemic year.

TRIAL REGISTRATION INFORMATION

This study is registered under NCT04934020.

1350 “TO BE A DEMENTIA-FRIENDLY HOSPITAL, I THINK YOU NEED TO HAVE…” - THE PERSPECTIVES OF PROFESSIONAL DEMENTIA EXPERTS

Introduction

Dementia-friendly hospitals (DFH) are mentioned as one of several key initiatives in national dementia strategies. In our previous integrative review, we identified 17 descriptions of DFHs and analysed six characteristics of DFH: continuity, person-centredness, consideration of phenomena within dementia, environment, valuing relatives and knowledge and expertise within the hospital (Manietta, Purwins, Reinhard et al., BMC Geriatrics, 2022, 22, 468, 1-16). We also learned that the term DFH is based more on healthcare practice than research. To address this research gap, one step of our DEMfriendlyHospital study is to examine the perspectives of professional dementia experts working in hospitals in Germany.

Method

We used a qualitative design and conducted 14 semi-structured interviews with professional dementia experts from various healthcare professions (12 nurses, two physicians, and one physiotherapist). Data were collected between November 2021 and March 2022. Using an inductive content analysis, we furthermore analysed the interviews in a participatory way involving a group of research associates and professional dementia experts.

Results

From the professional dementia experts’ perspectives, a DFH is characterised by specific hospital processes, structures and environment which consider the needs of people with dementia, dementia-specific knowledge and the skills of hospital staff, their awareness and attitude towards people with dementia. A DFH needs the social inclusion of patients with dementia and their perception as a person as well as the involvement of relatives, who are an important support for the patients and their care.

Conclusion

There are links between our results from interviews with professional dementia experts and our integrative review. At the same time, the perspectives of patients with dementia and their relatives are underrepresented. To fill this gap, our next step is to interview people with dementia who are hospitalised and their relatives, aiming to enhance the description of a DFH and its characteristics.

Contemporary Assessment of the Economic Burden of Upper Urinary Tract Stone Disease in the United States: Analysis of 1-year Healthcare Costs, 2011-2018

Background The United States healthcare landscape has witnessed numerous changes since implementation of the Affordable Care Act coupled with rising prevalence of upper urinary tract stone disease. Data on the economic burden of stone disease during this period are lacking, providing the objective of our study. Materials and Methods Adults diagnosed with stone disease from 2011-2018 were identified from PearlDiver Mariner, a national all-payer database reporting reimbursements and prescription costs for all healthcare encounters. Patients undergoing operative and non-operative care were identified. Time trends in annual expenditures were evaluated. Multivariable analysis evaluated determinants of spending. Results A total of $10B were spent on stone disease management between 2011-2018 (median overall annual expenditure=$1.4B) among 786,756 patients. Inpatient, prescription and outpatient costs accounted for 34.7%, 20.7% and 44.6% of expenditures respectively. 78% of patients were managed non-operatively (total cost=$6.9B). Average overall cost per encounter was $13,587 ($17,102 for surgical vs. $11,174 for non-surgical care). Expenditures on inpatient care decreased significantly over time, while expenditures on prescriptions and outpatient care increased significantly. On multivariable analysis, higher Charlson Comorbidity Index was associated with higher spending, while associations for age, insurance and region varied by treatment modality. Conclusions The economic burden of stone disease management is substantial, dominated by expenditure on non-operative management and outpatient care. Expenditures for prescription and outpatient care are rising, with the only consistent predictor of higher spending being Charlson Comorbidity Index. Spending variation according to demographic, clinical, and geographic factors was evident.

Perception of Nigerian Dùndún Talking Drum Performances as Speech-Like vs. Music-Like: The Role of Familiarity and Acoustic Cues

It seems trivial to identify sound sequences as music or speech, particularly when the sequences come from different sound sources, such as an orchestra and a human voice. Can we also easily distinguish these categories when the sequence comes from the same sound source? On the basis of which acoustic features? We investigated these questions by examining listeners’ classification of sound sequences performed by an instrument intertwining both speech and music: the dùndún talking drum. The dùndún is commonly used in south-west Nigeria as a musical instrument but is also perfectly fit for linguistic usage in what has been described as speech surrogates in Africa. One hundred seven participants from diverse geographical locations (15 different mother tongues represented) took part in an online experiment. Fifty-one participants reported being familiar with the dùndún talking drum, 55% of those being speakers of Yorùbá. During the experiment, participants listened to 30 dùndún samples of about 7s long, performed either as music or Yorùbá speech surrogate (n = 15 each) by a professional musician, and were asked to classify each sample as music or speech-like. The classification task revealed the ability of the listeners to identify the samples as intended by the performer, particularly when they were familiar with the dùndún, though even unfamiliar participants performed above chance. A logistic regression predicting participants’ classification of the samples from several acoustic features confirmed the perceptual relevance of intensity, pitch, timbre, and timing measures and their interaction with listener familiarity. In all, this study provides empirical evidence supporting the discriminating role of acoustic features and the modulatory role of familiarity in teasing apart speech and music.

Acoustic and linguistic features influence talker change detection

A listening test is proposed in which human participants detect talker changes in two natural, multi-talker speech stimuli sets-a familiar language (English) and an unfamiliar language (Chinese). Miss rate, false-alarm rate, and response times (RT) showed a significant dependence on language familiarity. Linear regression modeling of RTs using diverse acoustic features derived from the stimuli showed recruitment of a pool of acoustic features for the talker change detection task. Further, benchmarking the same task against the state-of-the-art machine diarization system showed that the machine system achieves human parity for the familiar language but not for the unfamiliar language.

Demolition Activity and Elevated Blood Lead Levels among Children in Detroit, Michigan, 2014-2018

Older buildings in the United States often contain lead paint, and their demolition poses the risk of community lead exposure. We investigated associations between demolitions and elevated blood lead levels (EBLLs) among Detroit children aged <6 years, 2014-2018, and evaluated yearly variation given health and safety controls implemented during this time. Case-control analysis included incident EBLL cases (≥5 µg/dL) and non-EBLL controls from test results reported to the Michigan Department of Health and Human Services. Exposure was defined as the number of demolitions (0, 1, 2+) within 400 feet of the child's residence 45 days before the blood test. We used logistic regression to calculate odds ratios (ORs) and 95% confidence intervals (CIs), and test effect modification by year. Associations between demolition and EBLL differed yearly (p = 0.07): 2+ demolitions were associated with increased odds of EBLLs in 2014 (OR: 1.75; 95% CI: (1.17, 2.55), 2016 (2.36; 1.53, 3.55) and 2017 (2.16; 1.24, 3.60), but not in 2018 (0.94; 0.41, 1.86). This pattern remained consistent in sensitivity analyses. The null association in 2018 may be related to increased health and safety controls. Maintenance of controls and monitoring are essential, along with other interventions to minimize lead exposure, especially for susceptible populations.

Mobilizing for Community Benefits to Assess Health and Promote Environmental Justice near the Gordie Howe International Bridge

Transportation infrastructure decisions contribute to social, economic, and health inequities in the U.S. Health Impact Assessments (HIAs) may improve understanding of potential strategies to mitigate adverse effects on quality of life from planned developments. We use the Gordie Howe International Bridge (GHIB), currently under construction in southwest Detroit, MI, as a case study to examine 15 years of community mobilization, which resulted in community benefits that included an HIA. We describe community engagement processes, household survey methods, and select findings of the baseline HIA, with a focus on their application to inform recommendations to promote quality of life. Baseline HIA results indicated significantly higher self-reported asthma rates among children living within 500 feet of trucking routes. Residents reported substantial economic (e.g., decreased home values), health (e.g., adverse outcomes, lack of health care access), and environmental (e.g., air pollution) concerns related to the GHIB. We discuss specific recommendations, based on HIA results, to reduce adverse impacts of the GHIB. These recommendations will inform ongoing community benefits negotiations. This case study provides lessons for community, academic, and government partners conducting HIAs, especially during building and operation of major infrastructure, and discusses their potential role in improving community engagement opportunities towards environmental justice.

[German Guideline for Idiopathic Pulmonary Fibrosis]

Idiopathic pulmonary fibrosis (IPF) is a severe and often fatal disease. Diagnosis of IPF requires considerable expertise and experience. Since publication of the international IPF guideline in the year 2011 and Update 2018 several studies and technical advances occurred, which made a new assessment of the diagnostic process mandatory. In view of the antifibrotic drugs which have been approved for the treatment of IPF patients, the goal of this guideline is to foster early, confident and effective diagnosis of IPF. The guideline focusses on the typical clinical setting of an IPF patient and provides tools to exclude known causes of interstitial lung disease including standardised questionnaires, serologic testing and cellular analysis of bronchoalveolar lavage. High resolution computed tomography remains crucial in the diagnostic work-up. If it is necessary to obtain specimen for histology transbronchial lung cryobiopsy is the primary approach, while surgical lung biopsy is reserved for patients who are fit for it and in whom bronchoscopic diagnosis did not provide the information needed. Despite considerable progress, IPF remains a diagnosis of exclusion and multidisciplinary discussion remains the golden standard of diagnosis.

[Immunophenotyping of lung tumors : An update]

The WHO Classification of Lung Tumors (2015) established the use of immunohistochemical stainings for resection specimens, however, detailed recommendations had been missing. Now, an international expert panel has summarized key questions for daily routine practice and provided recommendations to assist the community in the appropriate use of immunohistochemistry in this context. This article provides an overview of the most important aspects.

The association between the patient and the physician genders and the likelihood of intensive care unit admission in hospital with restricted ICU bed capacity

BACKGROUND

Despite the evidence that the patient gender is an important component in the intensive care unit (ICU) admission decision, the role of physician gender and the interaction between the two remain unclear.

OBJECTIVE

To investigate the association of both the patient and the physician gender with ICU admission rate of critically ill emergency department (ED) medical patients in a hospital with restricted ICU bed capacity operates with 'closed door' policy.

METHODS

A retrospective population-based cohort analysis. We included patients above 18 admitted to an ED resuscitation room (RR) of a tertiary hospital during 2011-12. Data on medical, laboratory and clinical characteristics were obtained. We used an adjusted multivariable logistic regression to analyze the association between both the patient and the physician gender to the ICU admission decision.

RESULTS

We included 831 RR admissions, 388 (46.7%) were female patients and 188 (22.6%) were treated by a female physicians. In adjusted multivariable analysis (adjusted for age, diabetes, mode of hospital transportation, first pH and patients who were treated with definitive airway and vasso-pressors in the RR), female-female combination (patient-physician, respectively) showed the lowest likelihood to be admitted to ICU (adjusted OR: 0.21; 95% CI: 0.09-0.51) compared to male-male combination, in addition to a smaller decrease among female-male (adjusted OR: 0.53; 95% CI: 0.32-0.86) and male-female (adjusted OR: 0.43; 95% CI: 0.21-0.89) combinations.

CONCLUSION

We demonstrated the existence of the possible gender bias where female gender of the patient and treating physician diminish the likelihood of the restricted health resource use.

Sample Selection for Microarray Gene Expression Studies

Objectives: The choice of biomedical samples for microarray gene expression studies is decisive for both validity and interpretability of results. We present a consistent, comprehensive framework to deal with the typical selection problems in microarray studies.

Methods: Microarray studies are designed either as case-control studies or as comparisons of parallel groups from cohort studies, since high levels of random variation in the experimental approach thwart absolute measurements of gene expression levels. Validity and results of gene expression studies heavily rely on the appropriate choice of these study groups. Therefore, the so-called principles of comparability, which are well known from both clinical and epidemiological studies, need to be applied to microarray experiments.

Results: The principles of comparability are the study-base principle, the principle of deconfounding and the principle of comparable accuracy in measurements. We explain each of these principles, show how they apply to microarray experiments, and illustrate them with examples. The examples are chosen as to represent typical stumbling blocks of microarray experimental design, and to exemplify the benefits of implementing the principles of comparability in the setting of micro-array experiments.

Conclusions: Microarray studies are closely related to classical study designs and therefore have to obey the same principles of comparability as these. Their validity should not be compromised by selection, confounding or information bias. The so-called study-base principle, calling for comparability and thorough definition of the compared cell populations, is the key principle for the choice of biomedical samples and controls in microarray studies.

Network modeling of kinase inhibitor polypharmacology reveals pathways targeted in chemical screens

Small molecule screens are widely used to prioritize pharmaceutical development. However, determining the pathways targeted by these molecules is challenging, since the compounds are often promiscuous. We present a network strategy that takes into account the polypharmacology of small molecules in order to generate hypotheses for their broader mode of action. We report a screen for kinase inhibitors that increase the efficacy of gemcitabine, the first-line chemotherapy for pancreatic cancer. Eight kinase inhibitors emerge that are known to affect 201 kinases, of which only three kinases have been previously identified as modifiers of gemcitabine toxicity. In this work, we use the SAMNet algorithm to identify pathways linking these kinases and genetic modifiers of gemcitabine toxicity with transcriptional and epigenetic changes induced by gemcitabine that we measure using DNaseI-seq and RNA-seq. SAMNet uses a constrained optimization algorithm to connect genes from these complementary datasets through a small set of protein-protein and protein-DNA interactions. The resulting network recapitulates known pathways including DNA repair, cell proliferation and the epithelial-to-mesenchymal transition. We use the network to predict genes with important roles in the gemcitabine response, including six that have already been shown to modify gemcitabine efficacy in pancreatic cancer and ten novel candidates. Our work reveals the important role of polypharmacology in the activity of these chemosensitizing agents.

Cast wedging: a systematic review of the present evidence

PURPOSE

The objective of this systematic review was to summarise the outcome after cast wedging due to loss of angulation in conservative fracture treatment of children's fractures.

METHODS

Electronic searches were performed using MEDLINE, PubMed, OVID, CENTRAL and EMBASE without language restrictions.

RESULTS

Three studies comprising 316 patients (210 radius, 52 forearm/both bone forearm fractures and 54 tibia fractures) were included in the present analysis. Cast wedge failures occurred in 14 of 316 (4.4%) patients. Three patients (0.9%) needed surgical fixation and 11 patients (3.4%) ended up with a healed deformity. Furthermore, eight of 316 (1.8%) patients needed remanipulation and cast change.

CONCLUSION

Cast wedging reflects a reliable treatment option for secondary displaced long-bone paediatric fractures.

Physician opinions concerning legal abortion in Bogotá, Colombia

Since the decriminalisation of abortion in 2006, women in Colombia have continued to seek clandestine abortions, endangering their health and contributing to maternal mortality and morbidity. The goal of this study was to explore physicians' opinions towards and knowledge about legal abortion in Bogotá, Colombia, and key barriers to the legal abortion access. We conducted 13 key informant interviews followed by a survey with a probability sample of 49 doctors working in public hospitals in Bogotá. Interview and survey data showed lack of technical experience in the provision of abortion and nuanced opinions towards its practice. Key informants described ignorance and lack of abortion training in medical schools as key barriers to provision. In the survey, 16/49 respondents had performed an abortion, 24/49 had referred a woman for an abortion and only 33/49 showed correct knowledge of the law.

A Multinational Analysis of Mutations and Heterogeneity in PZase, RpsA, and PanD Associated with Pyrazinamide Resistance in M/XDR Mycobacterium tuberculosis

Pyrazinamide (PZA) is an important first-line drug in all existing and new tuberculosis (TB) treatment regimens. PZA-resistance in M. tuberculosis is increasing, especially among M/XDR cases. Noted issues with PZA Drug Susceptibility Testing (DST) have driven the search for alternative tests. This study provides a comprehensive assessment of PZA molecular diagnostics in M/XDR TB cases. A set of 296, mostly XDR, clinical M. tuberculosis isolates from four countries were subjected to DST for eight drugs, confirmatory Wayne's assay, and whole-genome sequencing. Three genes implicated in PZA resistance, pncA, rpsA, and panD were investigated. Assuming all non-synonymous mutations cause resistance, we report 90% sensitivity and 65% specificity for a pncA-based molecular test. The addition of rpsA and panD potentially provides 2% increase in sensitivity. Molecular heterogeneity in pncA was associated with resistance and should be evaluated as a diagnostic tool. Mutations near the N-terminus and C-terminus of PZase were associated with East-Asian and Euro-American lineages, respectively. Finally, Euro-American isolates are most likely to have a wild-type PZase and escape molecular detection. Overall, the 8-10% resistance without markers may point to alternative mechanisms of resistance. Confirmatory mutagenesis may improve the disconcertingly low specificity but reduce sensitivity since not all mutations may cause resistance.

[The new TNM classification for lung tumors : Changes and the assessment of multiple tumor foci]

Recently a new TNM classification for tumors of the lung was published, encompassing some relevant changes, for example how to deal with multiple lung tumors. This article comprehensively describes respective changes. Furthermore, background information on how the new TNM classification was built and what should be done in the future to further improve prognosis and outcome prediction is reviewed.

[Multifocal Pulmonary Neuroendocrine Tumours: Genesis, Diagnostics and Treatment]

Multifocal neuroendocrine lung tumour is a rare diagnosis. Multiple lung foci of different sizes are usually apparent on chest CT scans. It is assumed that multifocal neuroendocrine lung tumours originally develop from diffuse idiopathic pulmonary neuroendocrine cell hyperplasia (DIPNECH). This results in cell aggregations formed by proliferation of neuroendocrine cells that are already physiologically present in the bronchial system. If these cell proliferations break through the bronchial basement membrane, they are considered to constitute tumourlets if they measure ≤ 5 mm and carcinoid tumours if they are larger than 5 mm. The speed of proliferation of the cell hyperplasias appears to vary. Many of the patients are completely asymptomatic, the multifocal neuroendocrine lung tumours being diagnosed by chance. However, other patients complain of breathlessness, reduced physical capacity and cough. There may also be reduction of lung function. In these cases, chest HRCT often reveals peribronchial fibrosis or bronchiectasis in addition to the lung foci. Bronchoscopy is usually not helpful. Surgical lung biopsy is considered to be the diagnostic gold standard. Histological examination typically shows a mixture of cell hyperplasias, tumourlets and carcinoid tumours. There is no consensus on the treatment of multifocal neuroendocrine tumours. Taking the clinical situation and the chest HRCT findings as our starting point, we developed a stepwise approach that is guided by the success of the individual therapeutic procedures. The most favourable prognosis is found in affected people without clinical symptoms whose lung foci all measure less than 5 mm. In these cases the 5-year survival rate is over 90%.

Abstract A73: Metabolite profiling reveals the glutathione biosynthetic pathway as a therapeutic target in triple negative breast cancers

Identifying metabolic pathway alterations that are critical to support cancer growth is a key hurdle for developing therapeutic strategies that exploit these pathways. We have applied metabolomic and pharmacological approaches to identify targetable pathways in triple negative breast cancer (TNBC). TNBC is an aggressive and genomically heterogeneous subset of breast cancer that is resistant to existing targeted therapies.

To identify dysregulated metabolic pathways in TNBC, we conducted mass spectrometry-based metabolomics of TNBC and control cells. The relative steady-state levels of 155 intracellular metabolites distinguished TNBC from non-transformed breast epithelia, and revealed two metabolic subtypes within TNBC that, unexpectedly, correlate with markers of basal-like versus non-basal-like status. Distinguishing metabolites included amino acids, lipids and the cellular redox buffer glutathione. Levels of glutathione were generally lower in TNBC cell lines compared to controls, and markedly lower in the metabolic subtype containing non-basal-like TNBC. Further, these cell lines showed enhanced sensitivity to inhibition of glutathione biosynthesis, demonstrating a dependence on glutathione production for survival.

These findings demonstrate the potential of targeting the glutathione biosynthetic pathway as a therapeutic strategy in TNBC, and suggest that existing clinical biomarkers may provide a means for stratifying TNBC tumors to identify likely responders to anti-glutathione therapy.

Note: This abstract was not presented at the conference.

Citation Format: Alexander Beatty, Lauren Fink, Alexander Strigun, Ulrike Rennefahrt, Erik Peter, Regina Reszka, Hajo Schiewe, Jeffrey R. Peterson. Metabolite profiling reveals the glutathione biosynthetic pathway as a therapeutic target in triple negative breast cancers. [abstract]. In: Proceedings of the AACR Special Conference: Metabolism and Cancer; Jun 7-10, 2015; Bellevue, WA. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(1_Suppl):Abstract nr A73.

Identifying three-dimensional structures of autophosphorylation complexes in crystals of protein kinases

Protein kinase autophosphorylation is a common regulatory mechanism in cell signaling pathways. Crystal structures of several homomeric protein kinase complexes have a serine, threonine, or tyrosine autophosphorylation site of one kinase monomer located in the active site of another monomer, a structural complex that we call an "autophosphorylation complex." We developed and applied a structural bioinformatics method to identify all such autophosphorylation complexes in x-ray crystallographic structures in the Protein Data Bank (PDB). We identified 15 autophosphorylation complexes in the PDB, of which five complexes had not previously been described in the publications describing the crystal structures. These five complexes consist of tyrosine residues in the N-terminal juxtamembrane regions of colony-stimulating factor 1 receptor (CSF1R, Tyr(561)) and ephrin receptor A2 (EPHA2, Tyr(594)), tyrosine residues in the activation loops of the SRC kinase family member LCK (Tyr(394)) and insulin-like growth factor 1 receptor (IGF1R, Tyr(1166)), and a serine in a nuclear localization signal region of CDC-like kinase 2 (CLK2, Ser(142)). Mutations in the complex interface may alter autophosphorylation activity and contribute to disease; therefore, we mutated residues in the autophosphorylation complex interface of LCK and found that two mutations impaired autophosphorylation (T445V and N446A) and mutation of Pro(447) to Ala, Gly, or Leu increased autophosphorylation. The identified autophosphorylation sites are conserved in many kinases, suggesting that, by homology, these complexes may provide insight into autophosphorylation complex interfaces of kinases that are relevant drug targets.

Abstract 4333: Metabolite profiling reveals druggable metabolic distinctions between basal-like and non-basal-like triple-negative breast cancers

Triple-negative breast cancer (TNBC) is an aggressive form of breast cancer that represents about 15-20% of all breast cancers. Because TNBC tumors do not express the estrogen or progesterone receptor and lack HER2 amplification, the disease is not responsive to current targeted therapies. The development of therapeutic approaches specific for TNBC is hindered by genetic heterogeneity, and significant efforts are being made to subtype the disease. To this end, we performed metabolite profiling (metabolomics) to characterize metabolic fingerprints within TNBC in order to define metabolic subtypes, and identify molecular drivers for the development of targeted therapies. We profiled twelve well-characterized TNBC-derived cell lines as well as a non-transformed, immortalized breast cell line and two primary human mammary epithelial cell lines. Those cancer cell lines recapitulate all 7 genetic subtypes of TNBC which were proposed recently based on mRNA gene expression profiles (1). Our approaches used and data generated have implications for drug target discovery. Hierarchical clustering based on high quality intracellular metabolites clearly and reproducibly segregated the TNBC cell lines from the non-transformed lines. Alterations in energy utilization, lipid metabolism, and other pathways of importance to highly proliferative cells differed significantly from the control cell line MCF-10A. In addition, TNBC cell lines segregated into two discrete groups, suggesting the existence of two major metabolic subtypes of TNBC, which correlated with basal-like vs. non-basal-like gene expression. Metabolites like glutamate and glutamine, serine, glycine, trans-4-hydroxyproline, 5-oxoproline, several complex lipids (phosphatidylcholines and sphingomyelins), myo-inositol, polyamines spermidine and putrescine represented metabolites differing significantly between TNBC metabolic subtypes. Ongoing studies are evaluating whether these differences represent dependencies with therapeutic relevance. Metabolite profiling was also used to identify potential metabolic liabilities generated by treatment with clinical kinase inhibitors. Response of the metabolome to treatment with rapamycin, sorafenib, imatinib, and lapatinib in four genetically diverse TNBC cell lines and MCF-10A control cell lines revealed specific drug-induced metabolic alterations. Co-targeting kinases and metabolic targets may offer an approach to synthetic lethality with a reduced likelihood for the development of drug resistance.

(1) (Lehmann BD, Bauer JA, Chen X, Sanders ME, Chakravarthy AB, Shyr Y, et al. Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies. J Clin Invest. 2011;121)

Citation Format: Alexander Beatty, Lauren Fink, Ulrike Rennefahrt, Alexander Strigun, Erik Peter, Hajo Schiewe, Regina Reszka, Jeffrey R. Peterson. Metabolite profiling reveals druggable metabolic distinctions between basal-like and non-basal-like triple-negative breast cancers. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4333. doi:10.1158/1538-7445.AM2014-4333

Abstract 3222: Broad spectrum metabolite profiling reveals metabolic finger and footprinting which correlate to gene expression signatures of triple-negative breast cancer (TNBC)

TNBC constitutes ∼20% of all breast cancers and disproportionately affects younger women and African-American women. This genomically heterogeneous disease is defined by the lack of expression of estrogen and progesterone receptors and the lack of amplification of HER2/neu. TNBC is resistant to standard breast cancer therapies. Due to the lack of a predominant genetic lesion associated with the disease, identification of metabolic fingerprints within TNBC is a critical first step for identification of molecular drivers and development of targeted therapies. Metabolite profiling (metabolomics) of a wide range of metabolites can be used to globally profile the metabolic state of cancer cells. Nine widely used TNBC-derived cell lines already characterized by gene expression signatures were analyzed by metabolomics. Two different approaches were combined: (i) untargeted, broad profiling including LC-MS/MS and GC-MS, and (ii) targeted UPLC-MS/MS Energy platform technology which covers polar key metabolites mainly reflecting energy status and nucleotide biosynthesis. Finally, 239 high quality metabolites were statistically evaluated in cell lysates and 128 metabolites in spent media samples collected from all cell lines. Using innovative bioinformatics and data mining tools we identified metabolic alterations in energy utilization, lipid synthesis, and other pathways of importance to highly proliferative cells that differ significantly from an untransformed control cell line (MCF-10A). Major metabolic changes combining results of metabolic fingerprinting and footprinting and their biological relevance will be discussed.

Citation Format: Alexander Beatty, Lauren Fink, Alexander Strigun, Ulrike Rennefahrt, Oliver Schmitz, Hajo Schiewe, Niels Moeller, Patricia R. Noppinger, Regina Reszka, Jeffrey R. Peterson. Broad spectrum metabolite profiling reveals metabolic finger and footprinting which correlate to gene expression signatures of triple-negative breast cancer (TNBC). [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3222. doi:10.1158/1538-7445.AM2013-3222

Abstract 3266: Repurposing clinical kinase inhibitors to enhance chemosensitivity by overriding checkpoints

Many conventional chemotherapies act as DNA damaging agents. Chemotherapy activates cell cycle checkpoint signaling to prevent cells from entering mitosis with either damaged or unreplicated DNA. Based on the observations that interference with the checkpoint mechanism (checkpoint override) results in cell death via mitotic catastrophe, the development of checkpoint inhibitors is actively being pursued as an anti-cancer therapy. In a cell-based screen of clinically relevant kinase inhibitors we identified three compounds that display checkpoint override properties: isomer of bosutinib, a recently FDA-approved Abl and Src inhibitor; BEZ235, a PI3K/mTOR inhibitor; and dovitinib, a multi-receptor tyrosine kinase inhibitor. Most interestingly, all compounds display off-target activity towards DNA damage checkpoint kinases including Chk1, ATR and Wee1. We determined these kinase inhibitors potently sensitized a panel of pancreatic cancer cell lines to S-phase acting (Gemcitabine, cisplatin) or G2-phase arresting (doxorubicin) DNA-damaging agents. Using a combination of live-cell videomicroscopy and immunofluorescence, we demonstrated that the inhibitors forced drug-treated cells to override the DNA damage induced checkpoint activation and aberrantly enter mitosis. The aberrant mitoses had characteristic chromatin fragmentation and that kinetochores and centromeres appeared to be detached from the chromatin mass, in a manner reminiscent of mitosis with unreplicated genomes (MUGs). As a result, cells died either in mitosis or due to mitotic catastrophe. The efficacy of pulsatile (24h and 48h after chemotherapy) administration of these previously unsuspected checkpoint inhibitors was further validated in tumor explants and cells isolated directly from a pancreatic cancer patient who is currently undergoing treatment. Tellingly, xenograft studies showed that gemcitabine and bosutinib isomer had significant activity as single agents but the combination significantly prevented tumor growth, even after drug removal. Our findings suggest that kinase inhibitors targeting cell cycle checkpoints, albeit in an off-target manner, may be fast-tracked into the clinic to enhance the efficacy of standard chemotherapies.

Citation Format: Neil Beeharry, Lauren Fink, Eugenia Banina, Vladimir Khazak, Natalia Skobeleva, Jeffrey R. Peterson, Igor Astsaturov, Timothy J. Yen. Repurposing clinical kinase inhibitors to enhance chemosensitivity by overriding checkpoints. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3266. doi:10.1158/1538-7445.AM2013-3266

Comparative gene expression profiling of post-natal and post-pneumonectomy lung growth

Although increasing numbers of patients suffer from chronic destructive lung diseases, there are no effective therapeutic options apart from transplantation. Understanding the mechanisms of physiological and regenerative alveolar septation is prerequisite for the development of regenerative therapies for the lung. We compared lung gene expression in the phase of induction of post-natal and post-pneumonectomy alveolarisation to identify regulatory genes involved in both processes. We performed genome-wide microarray screenings of newborn and pneumonectomised mouse lungs 1 and 3 days after birth or surgery. Selected candidates were validated by real-time PCR, Western blot and in situ hybridisation. We found 58 genes to be regulated in both models with 40 candidates being changed likewise. Many of these genes participated in growth and differentiation processes. Additionally, immune system, structural molecules, respiratory chain, signal transduction and metabolism were involved. Some candidates were not yet linked to specific functions. The highest regulatory concordance was observed for various isoforms of (pro-)collagen molecules, elastin and the elastin-associated protein fibrillin1 being corporately upregulated. Our findings do not definitively support a common regulating mechanism for induction of post-natal and adult alveolarisation, but some candidates in the intersection of both models are promising for further investigations.

Effect of endotoxin on COX-2 dependent proliferation of NSCLC cells: Role of CD14, TLRs, and EGFR signaling

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Background: Bacterial infections are common in NSCLC and growing evidence indicates that inflammation is contributing to cancer growth. Against this background, we investigated the effect of the bacterial cell wall components LPS on the proliferation of the NSCLC cell line A549. Methods: Proliferation of A549 cells was quantified by MTS-assay. PGE2 production was analyzed by ELISA and COX-2 mRNA was quantified by RT-PCR. Results: Incubation of A549 cells with LPS induced a time- and dose-dependent proliferation of A549 cells. Pro-proliferative effects of endotoxin could be inhibited by neutralizing antibodies targeting CD14 and TLR4, but not by inhibition of TLR2. Interestingly, interference with COX-2 activity by the specific inhibitor NS-398 strongly attenuated the LPS-induced tumor cell proliferation. In parallel, large amounts of COX-2 dependent PGE2were released by LPS-stimulated A549 cells. Moreover, enhanced transcription of COX-2 specific mRNA was detected in LPS-stimulated A549 cells. Interestingly, EGFR signaling was obviously involved in LPS-induced tumor cell proliferation and PGE2 release, as both effects could be inhibited by the neutralizing EGFR-antibody cetuximab. Conclusions: We conclude that LPS induces COX-2 dependent proliferation of A549 cells in a CD14, TLR4, and EGFR dependant manner. These effects might contribute to pathogen induced tumor proliferation in NSCLC.

No significant financial relationships to disclose.

Catabolic properties of microdissected human endosteal bone lining cells

Bone lining cells cover > 80% of endosteal surfaces of human cancellous bone. Current research assigns to them a dual role: (1) as a biological membrane regulating exchange of substrates between the bone fluid compartment and the extracellular fluid of bone marrow and (2) as a signaling link between the osteocytic network as mechanical receptor and the osteoclastic cell pool for local induction of bone resorption. Furthermore, a catabolic role has been considered. We therefore examined the presence of matrix-metalloproteinases (MMPs) and their physiological tissue inhibitors (TIMPs) as putative proteolytic elements. Firstly, human cancellous bone from 60 patients was examined by immunofluorescence with antibodies against MMPs and TIMPs. Secondly, we applied laser-assisted microdissection (LMD) to isolate bone lining cells from frozen sections of human trabecular bone. mRNA analysis was performed using a single-cell PCR protocol. Three laser microdissection systems were tested: the new generation of Leica LMD and P.A.L.M. laser pressure catapulting (LPC) were compared to P.A.L.M. laser microdissection and micromanipulation (LMM). In a few pooled cell profiles, mRNA of MMP13, MMP14, TIMP1, and CBFA-1 was clearly detected. By immunofluorescence MMP13 and -14 as well as TIMP1 and -2 were strongly present in lining cells, while MMP2, TIMP3, and TIMP4 showed weak or negative signals. Although the functional impact of these enzymatic components remains open, there is additional evidence for a catabolic function of lining cells. The new diode-laser microdissection with LMD and LPC proved to be especially suitable to gain new insights into the properties of bone lining cells.