Landscape of brain myeloid cell transcriptome along the spatiotemporal progression of Alzheimer's disease reveals distinct sequential responses to Aβ and tau

Human microglia are critically involved in Alzheimer's disease (AD) progression, as shown by genetic and molecular studies. However, their role in tau pathology progression in human brain has not been well described. Here, we characterized 32 human donors along progression of AD pathology, both in time-from early to late pathology-and in space-from entorhinal cortex (EC), inferior temporal gyrus (ITG), prefrontal cortex (PFC) to visual cortex (V2 and V1)-with biochemistry, immunohistochemistry, and single nuclei-RNA-sequencing, profiling a total of 337,512 brain myeloid cells, including microglia. While the majority of microglia are similar across brain regions, we identified a specific subset unique to EC which may contribute to the early tau pathology present in this region. We calculated conversion of microglia subtypes to diseased states and compared conversion patterns to those from AD animal models. Targeting genes implicated in this conversion, or their upstream/downstream pathways, could halt gene programs initiated by early tau progression. We used expression patterns of early tau progression to identify genes whose expression is reversed along spreading of spatial tau pathology (EC > ITG > PFC > V2 > V1) and identified their potential involvement in microglia subtype conversion to a diseased state. This study provides a data resource that builds on our knowledge of myeloid cell contribution to AD by defining the heterogeneity of microglia and brain macrophages during both temporal and regional pathology aspects of AD progression at an unprecedented resolution.

Distinct transcriptomic responses to Aβ plaques, neurofibrillary tangles, and APOE in Alzheimer's disease

INTRODUCTION

Omics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimer's disease (AD) but the spatial relationships with plaques and tangles and APOE-linked differences remain unclear.

METHODS

We performed laser capture microdissection of amyloid beta (Aβ) plaques, the 50 μm halo around them, tangles with the 50 μm halo around them, and areas distant (> 50 μm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing.

RESULTS

Aβ plaques exhibited upregulated microglial (neuroinflammation/phagocytosis) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. Aβ plaques had more differentially expressed genes than tangles. We identified a gradient Aβ plaque > peri-plaque > tangle > distant for these changes. AD APOE ε4 homozygotes had greater changes than APOE ε3 across locations, especially within Aβ plaques.

DISCUSSION

Transcriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with Aβ plaques, and are exacerbated by the APOE ε4 allele.

Endothelial Cells are Heterogeneous in Different Brain Regions and are Dramatically Altered in Alzheimer's Disease

Vascular endothelial cells play an important role in maintaining brain health, but their contribution to Alzheimer's disease (AD) is obscured by limited understanding of the cellular heterogeneity in normal aged brain and in disease. To address this, we performed single nucleus RNAseq on tissue from 32 human AD and non-AD donors (19 female, 13 male) each with five cortical regions: entorhinal cortex, inferior temporal gyrus, prefrontal cortex, visual association cortex and primary visual cortex. Analysis of 51,586 endothelial cells revealed unique gene expression patterns across the five regions in non-AD donors. Alzheimer's brain endothelial cells were characterized by upregulated protein folding genes and distinct transcriptomic differences in response to amyloid beta plaques and cerebral amyloid angiopathy (CAA). This dataset demonstrates previously unrecognized regional heterogeneity in the endothelial cell transcriptome in both aged non-AD and AD brain.SIGNIFICANCE STATEMENT:In this work, we show that vascular endothelial cells collected from five different brain regions display surprising variability in gene expression. In the presence of Alzheimer's disease pathology, endothelial cell gene expression is dramatically altered with clear differences in regional and temporal changes. These findings help explain why certain brain regions appear to differ in susceptibility to disease-related vascular remodeling events that may impact blood flow.

Distinct Transcriptomic Responses to Aβ plaques, Neurofibrillary Tangles, and APOE in Alzheimer's Disease

INTRODUCTION

Omics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimer's disease (AD) but the spatial relationships with plaques and tangles and APOE -linked differences remain unclear.

METHODS

We performed laser capture microdissection of Aβ plaques, the 50μm halo around them, tangles with the 50μm halo around them, and areas distant (>50μm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing.

RESULTS

Aβ plaques exhibited upregulated microglial (neuroinflammation/phagocytosis) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. Aβ plaques had more differentially expressed genes than tangles. We identified a gradient Aβ plaque>peri-plaque>tangle>distant for these changes. AD APOE ε4 homozygotes had greater changes than APOE ε3 across locations, especially within Aβ plaques.

DISCUSSION

Transcriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with Aβ plaques, and are exacerbated by the APOE ε4 allele.

Endothelial Cells are Heterogeneous in Different Brain Regions and are Dramatically Altered in Alzheimer's Disease

Vascular endothelial cells play an important role in maintaining brain health, but their contribution to Alzheimer's disease (AD) is obscured by limited understanding of the cellular heterogeneity in normal aged brain and in disease. To address this, we performed single nucleus RNAseq on tissue from 32 AD and non-AD donors each with five cortical regions: entorhinal cortex, inferior temporal gyrus, prefrontal cortex, visual association cortex and primary visual cortex. Analysis of 51,586 endothelial cells revealed unique gene expression patterns across the five regions in non-AD donors. Alzheimer's brain endothelial cells were characterized by upregulated protein folding genes and distinct transcriptomic differences in response to amyloid beta plaques and cerebral amyloid angiopathy (CAA). This dataset demonstrates previously unrecognized regional heterogeneity in the endothelial cell transcriptome in both aged non-AD and AD brain.

Significance Statement

In this work, we show that vascular endothelial cells collected from five different brain regions display surprising variability in gene expression. In the presence of Alzheimer's disease pathology, endothelial cell gene expression is dramatically altered with clear differences in regional and temporal changes. These findings help explain why certain brain regions appear to differ in susceptibility to disease-related vascular remodeling events that may impact blood flow.

Correlation of local impedance, global impedance and contact force with resulting lesion size in RF ablation

Funding Acknowledgements

Type of funding sources: None.

Background

During clinical application of RF-energy, several parameters are constantly observed, e.g. RF time, power, global impedance and temperature. The new parameter "local impedance" is gaining importance and might be a possible real-time marker for predicting long-lasting RF-lesions and increasing safety. The aim of this study was to investigate the correlation between local and global impedance as well as RF power and contact force.

Methods

RF-lesions were created using an ex vivo model with porcine cardiac preparations. These were put in a saline-filled container with a dispersive electrode. Global impedance was held at 120 Ohm by adjusting saline and water. Additionally, a heated thermostat and a circulation pump were installed to imitate blood flow. RF-lesions were produced with different settings of energy and contact force (20, 30, 40 and 50 watts; contact force of 0-5g, 10-15g and 20-25g). While creating the lesions, global and local impedance, temperature, energy and RF time were documented, as well as the current lesion width and depth. Local and global impedance drops were calculated as the difference between baseline impedance and current impedance.

Results

In total, 1223 measurements were made during application of RF-energy. 6 steam pops occurred. Contact force, local and global impedance changes showed highly significant correlations with lesion depth and diameter. Amongst analyzed values, local impedance drop showed highest correlation with lesion diameter and depth (r = 0,391 and 0,613; p<0,001). Visualized in Figure 1 and 2, global and local impedance correlate with lesion diameter and depth.

Discussion

Local impedance was found to be a suitable real-time marker for lesion size, showing significantly higher correlations with RF lesion size than contact force and global impedance. Further investigation is necessary to find a cut off for a safe but long-lasting RF-lesion.

Electrode tissue coupling is a new main determinant of RF lesion creation, experience from a cardiac animal model

Funding Acknowledgements

Type of funding sources: None.

Background

Radiofrequency (RF) current is a classic ablation technology used in the EP lab. By now it is assumed that RF lesion size is mainly determined by RF power, duration and contact force. This ex vivo animal model study shows that a new parameter - "electrode tissue coupling" (ETC) - plays an additional major role in RF lesion creation. The ETC level describes the amount of electric contact between the RF electrode and cardiac tissue: In minor ETC levels, only the distal electrode connects to tissue. In full ETC levels, the whole RF electrode is embedded in cardiac tissue.

Methods

RF-lesions were created using an ex vivo porcine cardiac model. The experimental setup consisted of a saline-filled container, a dispersive electrode, a heated thermostat and a circulation pump to imitate in vivo conditions. Global impedance was kept at 120 Ohm as well as the temperature at 37°C. RF-lesions were created using identic values of RF duration and contact force. A RF power of 20W, 30W, 40W, and 50W was used. The ETC levels were systematically varied between minor and full coupling. All parameters (power, temperature, global and local impedance, contact force, ETC, lesion size) were measured constantly during application of RF-current, enabling real-time correlation of RF parameters and lesion size.

Results

In total, 1923 measurements during application of RF-current were analyzed. In ETC III (full tissue coupling), lesions became significantly wider and deeper. In 20W ablations, lesion diameters were significantly (1.68 fold) larger when applying ETC III instead of ETC I. This relation was found in variations of RF parameters (Table 1).

Interestingly, baseline local impedance and local impedance drop showed a high correlation with selected ETC levels. The average baseline local impedance in ETC I was 207.2 Ohm, compared to 267.3 Ohm in ETC III (p < 0.01).

Discussion

In addition to by now known parameters (power, duration, contact force), electrode tissue coupling is a main determinant of lesion size. Higher ETC levels result in higher amounts of RF current going into adjacent tissue instead of current dissipation into the blood pool. In clinical practice, the ETC level can be predicted by baseline local and global impedance. Observation of these parameters should become clinical practice during RF ablation.

Coordinated regulation of WNT/β-catenin, c-Met, and integrin signalling pathways by miR-193b controls triple negative breast cancer metastatic traits

Background

Triple negative breast cancer (TNBC) is the most aggressive subtype of breast cancer (BC). Treatment options for TNBC patients are limited and further insights into disease aetiology are needed to develop better therapeutic approaches. microRNAs’ ability to regulate multiple targets could hold a promising discovery approach to pathways relevant for TNBC aggressiveness. Thus, we address the role of miRNAs in controlling three signalling pathways relevant to the biology of TNBC, and their downstream phenotypes.

Methods

To identify miRNAs regulating WNT/β-catenin, c-Met, and integrin signalling pathways, we performed a high-throughput targeted proteomic approach, investigating the effect of 800 miRNAs on the expression of 62 proteins in the MDA-MB-231 TNBC cell line. We then developed a novel network analysis, Pathway Coregulatory (PC) score, to detect miRNAs regulating these three pathways. Using in vitro assays for cell growth, migration, apoptosis, and stem-cell content, we validated the function of candidate miRNAs. Bioinformatic analyses using BC patients’ datasets were employed to assess expression of miRNAs as well as their pathological relevance in TNBC patients.

Results

We identified six candidate miRNAs coordinately regulating the three signalling pathways. Quantifying cell growth of three TNBC cell lines upon miRNA gain-of-function experiments, we characterised miR-193b as a strong and consistent repressor of proliferation. Importantly, the effects of miR-193b were stronger than chemical inhibition of the individual pathways. We further demonstrated that miR-193b induced apoptosis, repressed migration, and regulated stem-cell markers in MDA-MB-231 cells. Furthermore, miR-193b expression was the lowest in patients classified as TNBC or Basal compared to other subtypes. Gene Set Enrichment Analysis showed that miR-193b expression was significantly associated with reduced activity of WNT/β-catenin and c-Met signalling pathways in TNBC patients.

Conclusions

Integrating miRNA-mediated effects and protein functions on networks, we show that miRNAs predominantly act in a coordinated fashion to activate or repress connected signalling pathways responsible for metastatic traits in TNBC. We further demonstrate that our top candidate, miR-193b, regulates these phenotypes to an extent stronger than individual pathway inhibition, thus emphasizing that its effect on TNBC aggressiveness is mediated by the coordinated repression of these functionally interconnected pathways.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12885-021-08955-6.

P–253 Description of a rare spontaneous monozygotic blastocyst splitting into two discrete euploid blastocysts in vitro detected with time-lapse imaging and preimplantation genetic testing (PGT)

Study question

Can spontaneous and complete blastocyst splitting into two, in vitro, be investigated using time-lapse imaging and biopsy of each trophectoderm, for inference of ploidy?

Summary answer

Time-lapse imaging combined with PGT-A gives insights into the incidence, dynamics and timing of rare blastocyst splitting and the ploidy status of each resulting blastocyst.

What is known already

It is well known that multiple births occur more often with Assisted Reproductive Technologies (ART) than spontaneous conception, even after single embryo transfer. The mechanism of Monozygotic Twinning (MZT) during ART is still unclear but cryopreservation, extended culture, PGT, maternal age and assisted hatching are reported risk factors. MZT is a rare phenomenon, with an incidence of 0.4% in natural conception compared with up to 4.9% in ART. The timing of embryo splitting dictates the type of twinning, in terms of chorionicity and amnionicty, and this is officially determined using ultrasound scanning.

Study design, size, duration

This is a case study describing the detection of the complete splitting of an IVF blastocyst at 140 hours post insemination (hpi), using time-lapse imaging.

The 40-year-old patient previously experienced biochemical pregnancy and several miscarriages; an ectopic molar pregnancy and a probable cornual ectopic. The 39-year-old male partner was normozoospermic.

Participants/materials, setting, methods

Facilitative laser breaching was performed, according to standard operating procedure, of the morula at 96hpi of embryo development, prior to PGT. Images were collected every 10 minutes and developmental events and embryos morphology annotated using the EmbryoScope+™ time lapse incubator and software.

Main results and the role of chance

Over 50,000 hatching blastocysts have been time-lapse imaged, scrutinised and annotated within this group of fertility clinics. This is the first time that such a rare blastocyst splitting event has been recorded and studied.

Following observation of two pronuclei following IVF and typical cleavage development to blastocyst, with facilitative zona breaching on, at 106.7hpi, the full blastocyst’s trophectoderm (TE) began to herniate and hatch. By 114.3hpi a second internal blastocoel cavity formed appearing to divide the inner cell mass (ICM) within the zona pellucida (ZP). This resulting blastocyst proceeded to hatch as its discrete ICM migrated out of the ZP, along with its TE. TE cells from the original blastocyst then began to hatch at 117.5hpi at the same breached site in the ZP with its ICM visibly evacuating the ZP.

By 140hpi the blastocyst had split into two discrete blastocysts while hatching from the ZP. Both resulting blastocysts had clear and separate ICMs and TEs present. Biopsy of approximately 5 cells was performed for each TE, and the blastocysts were vitrified individually. Next Generation Sequencing (NGS) reported both blastocysts to be euploid.

Limitations, reasons for caution

This case may have been detectable without time-lapse imaging, as the splitting was completed prior to biopsy. More expert scrutiny of the images may result in earlier signs of twinning in progress being detected.

Wider implications of the findings: The nature of this detectable in vitro blastocyst splitting, indicates these embryos (if they implanted) to be monozygotic, dichoriol-diamniotic ‘identical’ twins. However – as single embryo transfer is the preferred treatment plan; they may be born years apart. These observations could shed light on the debated models of monozygotic twinning.

Trial registration number

Not applicable

P–164 Mulitcentre derived time lapse algorithms developed using 6228 transferred embryos with known birth outcome incorporating novel morphological and morphokinetic markers

Study question

Can incorporation of novel markers of morphology with known temporal events successfully rank embryos to enable prediction of propensity for live birth?

Summary answer

Incorporation of variables for trophectoderm and morula grading demonstrably enhanced the model to rank embryos in order of potential for live birth.

What is known already

Models built using morphokinetic markers of development are widely used to rank embryos within a cohort. Such models include defined temporal parameters which are closely related to morphological grade. However, morphological grading by an embryologist is subjective and is not strongly correlated to outcome. Combining with defined kinetic events has been suggested to improve prediction of outcome.

Study design, size, duration

Data from 6228 known live birth outcome embryos from 8 UK clinics between 2011 – 2018 were investigated using an exploratory approach to identify novel markers of development.

Participants/materials, setting, methods

Five significant variables were defined, a derivative of time to start of blastulation; a derivative of trophectoderm grade; a kinetic variable utilising t3, t4, t5 and t8; an interval variable of tB-tSB and a variable based on novel morula classification. To maximise the output, a proxy value was derived for missing datapoints. The model was built using logistical regression and validated using fivefold cross validation with the data split as 80% training and 20% test.

Main results and the role of chance

An algorithm was developed including the five significant variables identified with an AUC of 0.685 demonstrating reliable prediction of live birth. Without morphological variables, the AUC was 0.674 demonstrating the improvement in the prediction value by including the derivative of the trophectoderm and morula grade. This resulted in ten classes of algorithm scores, 1–10, giving a live birth rate from 2% to 46%, irrespective of patient variables, for chance of live birth.

Limitations, reasons for caution

Successful application of the algorithm is reliant on stringent quality assurance for maintenance of accurate annotation and grading, and may not be transferable between laboratories with different SOPs.

Wider implications of the findings: The addition of a trophectoderm and morula grade in combination with morphokinetic parameters, increases the predictive value of the algorithm in relation to live birth outcome. Using proxy values allows maximization of data for model generation, and allows the model to be applied when missing values are present.

Trial registration number

Not applicable

Profiling Microglia From Alzheimer's Disease Donors and Non-demented Elderly in Acute Human Postmortem Cortical Tissue

Microglia are the tissue-resident macrophages of the central nervous system (CNS). Recent studies based on bulk and single-cell RNA sequencing in mice indicate high relevance of microglia with respect to risk genes and neuro-inflammation in Alzheimer's disease (AD). Here, we investigated microglia transcriptomes at bulk and single-cell levels in non-demented elderly and AD donors using acute human postmortem cortical brain samples. We identified seven human microglial subpopulations with heterogeneity in gene expression. Notably, gene expression profiles and subcluster composition of microglia did not differ between AD donors and non-demented elderly in bulk RNA sequencing nor in single-cell sequencing.

Reconstruction of Different Modes of WNT Dependent Protein Networks from Time Series Protein Quantification

Protein signaling networks are crucial cornerstones in cellular responses. Deregulation causes various diseases, including cancer. One pathway that is frequently deregulated in cancer is the WNT signaling pathway. It has been shown that WNT signaling is highly context-dependent and the availability of receptors and ligands determines downstream signaling. In order to reveal which signaling pathways are activated by a specific receptor-ligand combination, we overexpressed the non-canonical WNT receptor ROR2 in the human breast cancer cell line MCF-7 and stimulated it with its putative ligand WNT11. Based on characterization of the cells by Reverse Phase Protein Array (RPPA), we integrated the proteomic data by network reconstruction analysis with prior knowledge from a pathway database. Using this approach, we were able to identify novel edges that differed upon ROR2 overexpression and WNT11 stimulation.

The transcriptional regulator FUBP1 influences disease outcome in murine and human myeloid leukemia

The transcriptional regulator far upstream element binding protein 1 (FUBP1) acts as an oncoprotein in solid tumor entities and plays a role in the maintenance of hematopoietic stem cells. However, its potential function in leukemia is unknown. In murine models of chronic (CML) and acute myeloid leukemia (AML) induced by BCR-ABL1 and MLL-AF9, respectively, knockdown of Fubp1 resulted in prolonged survival, decreased numbers of CML progenitor cells, decreased cell cycle activity and increased apoptosis. Knockdown of FUBP1 in CML and AML cell lines recapitulated these findings and revealed enhanced DNA damage compared to leukemia cells expressing wild type FUBP1 levels. FUBP1 was more highly expressed in human CML compared to normal bone marrow cells and its expression correlated with disease progression. In AML, higher FUBP1 expression in patient leukemia cells was observed with a trend toward correlation with shorter overall survival. Treatment of mice with AML with irinotecan, known to inhibit topoisomerase I and FUBP1, significantly prolonged survival alone or in combination with cytarabine. In summary, our data suggest that FUBP1 acts as cell cycle regulator and apoptosis inhibitor in leukemia. We demonstrated that FUBP1 might play a role in DNA repair, and its inhibition may improve outcome in leukemia patients.

PI3K: A master regulator of brain metastasis-promoting macrophages/microglia

Mutations and activation of the PI3K signaling pathway in breast cancer cells have been linked to brain metastases. However, here we describe that in some breast cancer brain metastases samples the protein expression of PI3K signaling components is restricted to the metastatic microenvironment. In contrast to the therapeutic effects of PI3K inhibition on the breast cancer cells, the reaction of the brain microenvironment is less understood. Therefore we aimed to quantify the PI3K pathway activity in breast cancer brain metastasis and investigate the effects of PI3K inhibition on the central nervous system (CNS) microenvironment. First, to systematically quantify the PI3K pathway activity in breast cancer brain metastases, we performed a prospective biomarker study using a reverse phase protein array (RPPA). The majority, namely 30 out of 48 (62.5%) brain metastatic tissues examined, revealed high PI3K signaling activity that was associated with a median overall survival (OS) of 9.41 months, while that of patients, whose brain metastases showed only moderate or low PI3K activity, amounted to only 1.93 and 6.71 months, respectively. Second, we identified PI3K as a master regulator of metastasis-promoting macrophages/microglia during CNS colonization; and treatment with buparlisib (BKM120), a pan-PI3K Class I inhibitor with a good blood-brain-barrier penetrance, reduced their metastasis-promoting features. In conclusion, PI3K signaling is active in the majority of breast cancer brain metastases. Since PI3K inhibition does not only affect the metastatic cells but also re-educates the metastasis-promoting macrophages/microglia, PI3K inhibition may hold considerable promise in the treatment of brain metastasis and the respective microenvironment.

FGFR3 mRNA overexpression defines a subset of oligometastatic colorectal cancers with worse prognosis

Objectives

Metastatic colorectal cancer (CRC) remains a leading cause of cancer related deaths. Patients with oligometastatic liver disease represent a clinical subgroup with heterogeneous course. Until now, biomarkers to characterize outcome and therapeutic options have not been fully established.

Methods

We investigated the prevalence of FGFR alterations in a total of 140 primary colorectal tumors and 63 liver metastases of 55 oligometastatic CRC patients. FGF receptors (FGFR1-4) and their ligands (FGF3, 4 and 19) were analyzed for gene amplifications and rearrangements as well as for RNA overexpression in situ. Results were correlated with clinico-pathologic data and molecular subtypes.

Results

Primary tumors showed FGFR1 (6.3%) and FGF3,4,19 (2.2%) amplifications as well as FGFR1 (10.1%), FGFR2 (5.5%) and FGFR3 (16.2%) overexpression. In metastases, we observed FGFR1 amplifications (4.8%) as well as FGFR1 (8.5%) and FGFR3 (14.9%) overexpression. Neither FGFR2-4 amplifications nor gene rearrangements were observed. FGFR3 overexpression was significantly associated with shorter overall survival in metastases (mOS 19.9 vs. 47.4 months, HR=3.14, p=0.0152), but not in primary CRC (HR=1.01, p=0.985). Although rare, also FGFR1 amplification was indicative of worse outcome (mOS 12.6 vs. 47.4 months, HR=8.83, p=0.00111).

Conclusions

We provide the so far most comprehensive analysis of FGFR alterations in primary and metastatic CRC. We describe FGFR3 overexpression in 15% of CRC patients with oligometastatic liver disease as a prognosticator for poor outcome. Recently FGFR3 overexpression has been shown to be a potential therapeutic target. Therefore, we suggest focusing on this subgroup in upcoming clinical trials with FGFR-targeted therapies.

TGFβ1 regulates HGF-induced cell migration and hepatocyte growth factor receptor MET expression via C-ets-1 and miR-128-3p in basal-like breast cancer

Breast cancer is the most common cancer in women worldwide. The tumor microenvironment contributes to tumor progression by inducing cell dissemination from the primary tumor and metastasis. TGFβ signaling is involved in breast cancer progression and is specifically elevated during metastatic transformation in aggressive breast cancer. In this study, we performed genomewide correlation analysis of TGFBR2 expression in a panel of 51 breast cancer cell lines and identified that MET is coregulated with TGFBR2. This correlation was confirmed at the protein level in breast cancer cell lines and human tumor tissues. Flow cytometric analysis of luminal and basal‐like breast cancer cell lines and examination of 801 tumor specimens from a prospective cohort of breast cancer patients using reverse phase protein arrays revealed that expression of TGFBR2 and MET is increased in basal‐like breast cancer cell lines, as well as in triple‐negative breast cancer tumor tissues, compared to other subtypes. Using real‐time cell analysis technology, we demonstrated that TGFβ1 triggered hepatocyte growth factor (HGF)‐induced and MET‐dependent migration in vitro. Bioinformatic analysis predicted that TGFβ1 induces expression of C‐ets‐1 as a candidate transcription factor regulating MET expression. Indeed, TGFβ1‐induced expression of ETS1 and breast cancer cell migration was blocked by knockdown of ETS1. Further, we identified that MET is a direct target of miR‐128‐3p and that this miRNA is negatively regulated by TGFβ1. Overexpression of miR‐128‐3p reduced MET expression and abrogated HGF‐induced cell migration of invasive breast cancer cells. In conclusion, we have identified that TGFβ1 regulates HGF‐induced and MET‐mediated cell migration, through positive regulation of C‐ets‐1 and negative regulation of miR‐128‐3p expression in basal‐like breast cancer cell lines and in triple‐negative breast cancer tissue.

Do patients with diabetes type 2 or chronic heart failure understand a medication plan?

A standardized medication plan (MP) was recently enacted into German law (§ 31a SGB V). The purpose of our study was to assess if patients with chronic diseases requiring polymedication understand the standardized MP and can transfer the given information into practice. 100 patients who took at least five medicines regularly were prospectively included in a cross-sectional study: 50 patients with the primary diagnosis chronic heart failure (CHF), and 50 with diabetes mellitus type 2 (DMT2). We performed a structured test-scenario studying the handling of a provided MP then evaluated the execution of the information on the MP by filling pill boxes and requested patients' opinion. An established weighted scoring system, the "Evaluation Tool to test the handling of the Medication Plan" (ET-MP) was applied to quantitate the ability of the patients to handle the MP. In addition, signs of depression, cognitive function and self-care behavior in chronic heart failure were characterized using the PHQ-9, Mini-Cog, and G9-EHFScB-9 questionnaires, respectively. The understanding of the MP was poor and irrespective of the underlying primary diagnosis. Only 32% of all patients were able to handle the MP without difficulties (ET-MP score >90%), the median ET-MP score was 83 [(IQR) 50-98]. Comprehension of the MP was better in patients aged <70 years compared to ≥70 years (p<0.01). Patients ≥10 years of education achieved higher ET-MP results than patients with <10 years of education (p<0.01). Patients with signs of cognitive impairment exhibited significantly lower ET-MP scores than patients without cognitive impairment (p<0.001). There were no significant correlations of the ET-MP score with number of daily medications, living situation, sex, the Charlson Comorbidity Index, the PHQ-9 score, and use of a dosing aid or possession of a medication list.

Proteomic profiling of breast cancer metabolism identifies SHMT2 and ASCT2 as prognostic factors

Background

Breast cancer tumors are known to be highly heterogeneous and differences in their metabolic phenotypes, especially at protein level, are less well-understood. Profiling of metabolism-related proteins harbors the potential to establish new patient stratification regimes and biomarkers promoting individualized therapy. In our study, we aimed to examine the relationship between metabolism-associated protein expression profiles and clinicopathological characteristics in a large cohort of breast cancer patients.

Methods

Breast cancer specimens from 801 consecutive patients, diagnosed between 2009 and 2011, were investigated using reverse phase protein arrays (RPPA). Patients were treated in accordance with national guidelines in five certified German breast centers. To obtain quantitative expression data, 37 antibodies detecting proteins relevant to cancer metabolism, were applied. Hierarchical cluster analysis and individual target characterization were performed. Clustering results and individual protein expression patterns were associated with clinical data. The Kaplan-Meier method was used to estimate survival functions. Univariate and multivariate Cox regression models were applied to assess the impact of protein expression and other clinicopathological features on survival.

Results

We identified three metabolic clusters of breast cancer, which do not reflect the receptor-defined subtypes, but are significantly correlated with overall survival (OS, p ≤ 0.03) and recurrence-free survival (RFS, p ≤ 0.01). Furthermore, univariate and multivariate analysis of individual protein expression profiles demonstrated the central role of serine hydroxymethyltransferase 2 (SHMT2) and amino acid transporter ASCT2 (SLC1A5) as independent prognostic factors in breast cancer patients. High SHMT2 protein expression was significantly correlated with poor OS (hazard ratio (HR) = 1.53, 95% confidence interval (CI) = 1.10–2.12, p ≤ 0.01) and RFS (HR = 1.54, 95% CI = 1.16–2.04, p ≤ 0.01). High protein expression of ASCT2 was significantly correlated with poor RFS (HR = 1.31, 95% CI = 1.01–1.71, p ≤ 0.05).

Conclusions

Our data confirm the heterogeneity of breast tumors at a functional proteomic level and dissects the relationship between metabolism-related proteins, pathological features and patient survival. These observations highlight the importance of SHMT2 and ASCT2 as valuable individual prognostic markers and potential targets for personalized breast cancer therapy.

Trial registration

ClinicalTrials.gov, NCT01592825. Registered on 3 May 2012.

Electronic supplementary material

The online version of this article (doi:10.1186/s13058-017-0905-7) contains supplementary material, which is available to authorized users.

Characterisation of tumour-derived microvesicles in cancer patients' blood and correlation with clinical outcome

To evaluate whether tumour-derived microvesicles (T-MV), originating from the plasma membrane, represent suitable cancer biomarkers, we isolated MV from peripheral blood samples of cancer patients with locally advanced and/or metastatic solid tumours (n = 330, including 79 head & neck cancers, 74 lung cancers, 41 breast cancers, 28 colorectal cancers and 108 with other cancer forms) and controls (n = 103). Whole MV preparations were characterised using flow cytometry. While MV carrying the tumour-associated proteins MUC1, EGFR and EpCAM were found to be enhanced in a tumour-subtype-specific way in patients' blood, expression of the matrix metalloproteinase inducer EMMPRIN was increased independent of tumour type. Higher levels of EMMPRIN⁺-MV correlated significantly with poor overall survival, whereas the other markers were prognostic only in specific tumour subgroups. By combining all four tumour-associated antigens, cancer patients were separated from healthy controls with an AUC of up to 0.85. Ex vivo, whole MV preparations from cancer patients, in contrast to those of controls, induced a tumour-supporting phenotype in macrophages and increased tumour cell invasion, which was dependent on the highly glycosylated isoform of EMMPRIN. In conclusion, the detection of T-MV in whole blood, even in minor amounts, is feasible with standard techniques, proves functionally relevant and correlates with clinical outcome.

Hoxa9 and Meis1 Cooperatively Induce Addiction to Syk Signaling by Suppressing miR-146a in Acute Myeloid Leukemia

The transcription factor Meis1 drives myeloid leukemogenesis in the context of Hox gene overexpression but is currently considered undruggable. We therefore investigated whether myeloid progenitor cells transformed by Hoxa9 and Meis1 become addicted to targetable signaling pathways. A comprehensive (phospho)proteomic analysis revealed that Meis1 increased Syk protein expression and activity. Syk upregulation occurs through a Meis1-dependent feedback loop. By dissecting this loop, we show that Syk is a direct target of miR-146a, whose expression is indirectly regulated by Meis1 through the transcription factor PU.1. In the context of Hoxa9 overexpression, Syk signaling induces Meis1, recapitulating several leukemogenic features of Hoxa9/Meis1-driven leukemia. Finally, Syk inhibition disrupts the identified regulatory loop, prolonging survival of mice with Hoxa9/Meis1-driven leukemia.

Use of the Impella Device for Acute Coronary Syndrome Complicated by Cardiogenic Shock - Experience From a Single Heart Center With Analysis of Long-term Mortality

AIMS

Impella is a microaxial rotary pump that is placed across the aortic valve to expel aspirated blood from the left ventricle into the ascending aorta; it can be used in cardiogenic shock. While previous studies have evaluated the efficacy and safety of the Impella device, more clinically relevant data are necessary, especially with regard to outcomes.

METHODS AND RESULTS

We screened our database of Impella patients in our heart center and found 68 consecutive patients who underwent Impella implantation due to acute coronary syndrome (ACS) complicated by cardiogenic shock. Data were evaluated with regard to baseline and procedural characteristics and also included an assessment of the short-term and long-term outcomes. The majority of patients (74%) suffered from an ST-elevation myocardial infarction, and 59% of patients received the Impella device during the initial coronary angiography. In the remaining cases, Impella implantation was performed at a later time, most commonly after IABP implantation. Patient characteristics were not significantly different between both groups. The predominantly implanted device was an Impella 2.5. Mortality in the severely ill patient population remained high, but univariate/multivariate analyses identified significant risk factors. Interestingly, delayed initiation of Impella support was an independent predictor of higher long-term mortality (hazard ratio, 2.157; P=.04) within the Impella patient cohort.

CONCLUSION

This large series of patients with ACS complicated by cardiogenic shock who underwent Impella implantation provides information on the relevant risk factors for mortality. Early (compared with delayed) initiation of Impella support was a predictor of improved survival in this population of patients.

A computational model of a human single sinoatrial node cell

For the investigation of the spontaneous rhythmical activity response in the application of cardiac neuromodulation, we formulated a human sinoatrial node (SAN) cell model. With the aim of decreasing elevated heart rate (HR), we want to establish a hardware-in-the-loop system including this model for the analysis of optimal stimulation patterns of the neurostimulation system. Base model structures are adopted from rabbit SAN cell models available in literature and conveyed with Hodgkin-Huxley-type model equations describing the complex time and voltage dependent activation and deactivation processes of individual ion channels. The resulting model consists of 15 currents which are currently known to be responsible for the generation of the membrane action potential (AP). The model reproduces AP frequencies equivalent to those measured in isolated human SAN cells with a resulting HR of 71.8 bpm. Model validation via simulation of the inhibitory effect of ivabradine showed accordance with experimental results obtained in human studies. Furthermore, we could validate the model in regard to its HR effects upon parasympathetic stimulation with results obtained in a human trial study.

Decoding Cellular Dynamics in Epidermal Growth Factor Signaling Using a New Pathway-Based Integration Approach for Proteomics and Transcriptomics Data

Identification of dynamic signaling mechanisms on different cellular layers is now facilitated as the increased usage of various high-throughput techniques goes along with decreasing costs for individual experiments. A lot of these signaling mechanisms are known to be coordinated by their dynamics, turning time-course data sets into valuable information sources for inference of regulatory mechanisms. However, the combined analysis of parallel time-course measurements from different high-throughput platforms still constitutes a major challenge requiring sophisticated bioinformatic tools in order to ease biological interpretation. We developed a new pathway-based integration approach for the analysis of coupled omics time-series data, which we implemented in the R package pwOmics. Unlike many other approaches, our approach acknowledges the role of the different cellular layers of measurement and infers consensus profiles and time profile clusters for further biological interpretation. We investigated a time-course data set on epidermal growth factor stimulation of human mammary epithelial cells generated on the two layers of RNA and proteins. The data was analyzed using our new approach with a focus on feedback signaling and pathway crosstalk. We could confirm known regulatory patterns relevant in the physiological cellular response to epidermal growth factor stimulation as well as identify interesting new interactions in this signaling context, such as the regulatory influence of the connective tissue growth factor on transferrin receptor or the influence of growth arrest and DNA-damage-inducible alpha on the connective tissue growth factor. Thus, we show that integrated cross-platform analysis provides a deeper understanding of regulatory signaling mechanisms. Combined with time-course information it enables the characterization of dynamic signaling processes and leads to the identification of important regulatory interactions which might be dysregulated in disease with adverse effects.

Analysis of Reverse Phase Protein Array Data: From Experimental Design towards Targeted Biomarker Discovery

Mastering the systematic analysis of tumor tissues on a large scale has long been a technical challenge for proteomics. In 2001, reverse phase protein arrays (RPPA) were added to the repertoire of existing immunoassays, which, for the first time, allowed a profiling of minute amounts of tumor lysates even after microdissection. A characteristic feature of RPPA is its outstanding sample capacity permitting the analysis of thousands of samples in parallel as a routine task. Until today, the RPPA approach has matured to a robust and highly sensitive high-throughput platform, which is ideally suited for biomarker discovery. Concomitant with technical advancements, new bioinformatic tools were developed for data normalization and data analysis as outlined in detail in this review. Furthermore, biomarker signatures obtained by different RPPA screens were compared with another or with that obtained by other proteomic formats, if possible. Options for overcoming the downside of RPPA, which is the need to steadily validate new antibody batches, will be discussed. Finally, a debate on using RPPA to advance personalized medicine will conclude this article.

Abstract 50: Elucidation of B cell receptor signaling in Burkitt's lymphoma reveals novel signaling nodes with potential therapeutic relevance

B cell antigen receptors (BCR) control important cell fate decisions of the B-lineage including differentiation, proliferation and B cell survival. Recently, it was demonstrated that beside chronic lymphocytic leukemia and diffuse large B cell lymphomas of the activated B cell-type also major subgroups of Burkitt lymphomas (BL) critically depend on BCR expression. As intensive chemotherapy and anti-CD20 antibodies are the current treatment strategies, pharmacological interference with critical BCR signaling pathways might open up the possibility for targeted therapies in BL. Such targeted therapeutic approaches are needed in particular for elderly patients and patients with endemic BL in developing countries. In order to (i) identify putative drug targets in BL and (ii) to elucidate BCR induced processes, we characterized BCR signaling in BL by quantitative phosphoproteomics and transcriptome sequencing. We identified about 10.000 phospho-sites in various BL cell-types, of which more than 1000 in almost 600 proteins were regulated in a BCR-dependent manner leading to dynamic transcription of more than 100 genes. The identified BCR signaling effectors belong to various functional groups, of which kinases, transcription factors and cytoskeleton regulators are most represented and bioinformatic analyses revealed that 83% of the identified BCR effectors were not described in the context of B cells or lymphoma before.

For instance, we identified a cell surface receptor that is highly expressed in BL and whose expression is regulated by the transcription factor c-Myc which is known to be frequently dysregulated in BL. ShRNA mediated knockdown of the cell surface receptor in BL cells impaired phosphorylation of spleen tyrosine kinase (Syk) and B-cell linker protein (BLNK) upon BCR stimulation, most probably due to dysregulation of the cytoskeleton. By using stable isotope labeling with amino acids in cell culture (SILAC) we investigated in a comprehensive manner, how the newly identified BCR co-receptor influences BCR signaling. Our study is a considerable complement to recent genetic studies that elucidated the mutational landscape in BL as it reveals mechanisms of signaling addiction to non-mutated BCR effector proteins that have to be validated in the future.

Citation Format: Carmen Doebele, Jasmin Corso, Anjali Cremer, Silvia Muench, Julia Beck, Christof Lenz, Hanibal Bohnenberger, Astrid Wachter, Tim Beissbarth, Ekkehard Schütz, Hubert Serve, Henning Urlaub, Thomas Oellerich. Elucidation of B cell receptor signaling in Burkitt's lymphoma reveals novel signaling nodes with potential therapeutic relevance. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 50. doi:10.1158/1538-7445.AM2015-50

pwOmics: an R package for pathway-based integration of time-series omics data using public database knowledge

Characterization of biological processes is progressively enabled with the increased generation of omics data on different signaling levels. Here we present a straightforward approach for the integrative analysis of data from different high-throughput technologies based on pathway and interaction models from public databases. pwOmics performs pathway-based level-specific data comparison of coupled human proteomic and genomic/transcriptomic datasets based on their log fold changes. Separate downstream and upstream analyses results on the functional levels of pathways, transcription factors and genes/transcripts are performed in the cross-platform consensus analysis. These provide a basis for the combined interpretation of regulatory effects over time. Via network reconstruction and inference methods (Steiner tree, dynamic Bayesian network inference) consensus graphical networks can be generated for further analyses and visualization.

AVAILABILITY AND IMPLEMENTATION

The R package pwOmics is freely available on Bioconductor (http://www.bioconductor.org/).

CONTACT

astrid.wachter@med.uni-goettingen.de.

Novel insight into the regulation of GSH biosynthesis in higher plants

In higher plants, the redox-active tripeptide glutathione (GSH) fulfills a plethora of functions. These include its pivotal role for maintaining the cellular redox poise and its involvement in detoxification of heavy metals and xenobiotics. Intimately linked to these functions, GSH also acts as a cellular signal, mediating control of enzyme and/or regulatory protein activities, either directly or via glutaredoxins. The redox potential of the GSH/GSSG couple is not only affected by the GSH/GSSG ratio but also by changes in GSH synthesis and/or degradation. As this couple operates as redox buffer in several cellular compartments, the regulation of GSH biosynthesis and transport (both intra- and intercellularly) are fundamental to the maintenance of cellular redox homeostasis during plant development and, even more so, when plants are exposed to biotic or abiotic stress. This review highlights novel aspects of GSH biosynthesis and transport with a focus on the regulation of the GSH1 (= gamma-glutamylcysteine synthetase) enzyme. Interestingly, GSH1 appears to be exclusively confined to the plastids, whereas the second biosynthetic enzyme, GSH2, is predominantly localized in the cytosol. GSH1 expression and enzyme activity are under multiple controls, extending from transcriptional regulation to post-translational redox control. Now that the plant GSH1 protein structure has been solved, the molecular basis of GSH1 function and redox regulation can be addressed. The review concludes with a discussion of the simultaneous changes observed for GSH synthesis, transport, and metabolism during Cd-induced phytochelatin accumulation.

[Münster age- and retina study (MARS). Association between risk factors for arteriosclerosis and age-related macular degeneration]

BACKGROUND

The association between arteriosclerosis and age-related macular degeneration (AMD) has only been examined in a few studies and the data is still very inconsistent.

METHODS

A cross sectional study was initiated with 730 patients from the Münster age and retina study (MARS) which examines patients in the age range 60 to 80 years old who were referred by ophthalmologists from the Muenster area. Patients with narrow angle glaucoma were excluded. All patients underwent a standardized ophthalmoscopic examination und were classified into four groups: group 1 without AMD ( n=190), group 2 with unilateral or bilateral early forms of AMD ( n=340), group 3 with unilateral late forms of AMD ( n=139) and group 4 with bilateral late forms of AMD ( n=50). By means of these groups it was tested if there was a significant difference between the different risk factors for arteriosclerosis.

RESULTS

The mean age was 72 years and 58% were women and the sex distribution within the different groups did not differ significantly (all trend tests with p>0.1). General risk factors for arteriosclerosis such as diabetes, body-mass-index and hypertension did not differ significantly (all trend tests with p>0.1). The number of smokers increased significantly with the severity of AMD ( p=0.02). Furthermore, various lipids were examined, adjusted for age and sex and showed significant decrease of HDL ( p=0.087) and significant increases of the HDL/LDL quotient ( p=0.0007) and the non-sober triglyceride values ( p=0.0058) correlated with the severity of AMD.

CONCLUSIONS

There was a highly significant, direct association of indicators of dyslipidemia such as increasing HDL/LDL quotient and decreasing HDL with the severity of AMD. These results were underlined by increased triglyceride levels even if they were taken non-sober. The results must be interpreted with caution due to the explorative character of the evaluation.

Blood flow velocities in the basal vein after subarachnoid haemorrhage. A prospective study using transcranial duplex sonography

BACKGROUND

Early recognition of emerging delayed neurological deficits (DND) in patients after subarachnoid haemorrhage (SAH) is not always possible by transcranial Doppler sonography. Aim of this study was to investigate a) whether determination of blood flow velocities in deep cerebral basal veins can predict DND in these patients b) the correlation of venous flow velocity to cerebral blood flow (CBF).

METHODS

a) We prospectively investigated the mean flow velocity in the basal vein (VBVR), in the middle cerebral artery (VMCA) and in the extracranial internal carotid artery (VICA) in 66 patients after spontaneous SAH. Examinations were performed daily during the first 10 days, using transcranial duplex sonography. Thirty-seven patients had VMCA exceeding 120 cm/s. They were categorised in three groups: 1: no delayed neurological deficit; II: transient DND; III: permanent DND or death associated with vasospasm. b) In another group of 14 patients, interdiane variations in global cerebral blood flow (CBF) measured by the Kety-Schmidt-method were correlated with variations in VBVR, VMCA, and VICA.

FINDINGS

a) In patients without deficit, VBVR was significantly elevated above normal values the first day (p < 0.05), and days 5 and 6 (p < 0.1) after VMCA exceeding 120 cm/s. In group III (permanent deficit), flow velocities in the BVR were significantly below normal on day 5 (p < 0.05) and 9 (p < 0.1). b) The correlation between changes in VBVR to changes in CBF (r = 0.78, p < 0.001) was closer than between changes in VMCA to the changes in CBF (r = 0.54, p < 0.05).

INTERPRETATION

In case of elevated VMCA, patients with higher VBVR seem to have a better outcome. Changes in CBF correlate better with VBVR than with arterial flow velocities.

Exposure of oncologic nurses to methotrexate in the treatment of osteosarcoma

Methotrexate is a therapeutic agent used widely for osteosarcoma. We used an extremely sensitive high-performance liquid-chromatography assay to evaluate 112 urine samples obtained from 28 hospital employees during high-dose therapy with methotrexate and during routine care of patients. The highest cumulative urinary excretion was observed when methotrexate infusions were handled in a workbench from which a portion of filtered air was emitted into the room. Remarkable urine contaminations were identified for personnel, including 1 administrative employee who had "stood by" for 2 h in the room where infusions were prepared. Lower methotrexate concentrations were detected in the urine of nurses whose exclusive function was to care for patients. The urine burden in oncologic nurses decreased after a central pharmacy unit was installed. Methotrexate was excreted in the sweat of patients who were under high-dose therapy, and its elimination half-life was 11.1 h (mean maximal concentration = 1.7 micrograms/ml [n = 51). The maximal burden in spontaneous vomit from these patients was 441.5 micrograms/ml, and it declined to 0.24 micrograms/ml 19.5 h after infusion was completed. No methotrexate was detected in personnel who prepared 20-g methotrexate infusions in the central pharmacy unit. We demonstrated that occupational safety depended not only on technical precautions, but on the skills of specifically trained personnel.