Andreas Leha

Common genetic variation drives molecular heterogeneity in human iPSCs

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5–46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells.

A high-content platform to characterise human induced pluripotent stem cell lines

Graphical abstract

Selected items from the Charcot-Marie-Tooth (CMT) Neuropathy Score and secondary clinical outcome measures serve as sensitive clinical markers of disease severity in CMT1A patients

This study evaluates primary and secondary clinical outcome measures in Charcot-Marie-Tooth disease type 1A (CMT1A) with regard to their contribution towards discrimination of disease severity. The nine components of the composite Charcot-Marie-Tooth disease Neuropathy Score and six additional secondary clinical outcome measures were assessed in 479 adult patients with genetically proven CMT1A and 126 healthy controls. Using hierarchical clustering, we identified four significant clusters of patients according to clinical severity. We then tested the impact of each of the CMTNS components and of the secondary clinical parameters with regard to their power to differentiate these four clusters. The CMTNS components ulnar sensory nerve action potential (SNAP), pin sensibility, vibration and strength of arms did not increase the discriminant value of the remaining five CMTNS components (Ulnar compound motor action potential [CMAP], leg motor symptoms, arm motor symptoms, leg strength and sensory symptoms). However, three of the six additional clinical outcome measures - the 10m-timed walking test (T10MW), 9 hole-peg test (9HPT), and foot dorsal flexion dynamometry - further improved discrimination between severely and mildly affected patients. From these findings, we identified three different composite measures as score hypotheses and compared their discriminant power with that of the CMTNS. A composite of eight components CMAP, Motor symptoms legs, Motor symptoms arms, Strength of Legs, Sensory symptoms), displayed the strongest power to discriminate between the clusters. As a conclusion, five items from the CMTNS and three secondary clinical outcome measures improve the clinical assessment of patients with CMT1A significantly and are beneficial for upcoming clinical and therapeutic trials.

Gender affects acute organ toxicity during radiochemotherapy for rectal cancer: Long-term results of the German CAO/ARO/AIO-94 phase III trial

INTRODUCTION The CAO/ARO/AIO-94 phase-III-trial demonstrated a significant improvement of preoperative chemoradiotherapy (CRT) versus postoperative CRT on local control for UICC stage II/III rectal cancer patients, but no effect on long-term survival. In this add-on evaluation, we investigated the association of gender and age with acute toxicity and outcome. PATIENTS AND METHODS According to actual treatment analyses, 654 of 799 patients had received pre- (n=406) or postoperative CRT (n=248); in 145 patients postoperative CRT was not applied. Gender, age and clinicopathological parameters were correlated with CRT-associated acute toxicity and survival. RESULTS The 10-year survival was higher in women than in men, with 72.4% versus 65.6% for time to recurrence (p=0.088) and 62.7% versus 58.4% for overall-survival (OS) (p=0.066), as expected. For patients receiving CRT, women showed higher hematologic (p<0.001) and acute organ toxicity (p<0.001) in the entire cohort as well as in subgroup analyses according to pre- (p=0.016) and postoperative CRT (p<0.001). Lowest OS was seen in patients without acute toxicity (p=0.0271). Multivariate analyses for OS showed that acute organ toxicity (p=0.034) was beneficial while age (p<0.001) was associated with worse OS. DISCUSSION Female gender is significantly associated with CRT-induced acute toxicity in rectal cancer. Acute toxicity during CRT may be associated with improved long-term outcome.

Integrated miRNA and mRNA profiling of tumor-educated macrophages identifies prognostic subgroups in estrogen receptor-positive breast cancer

Various studies have identified aberrantly expressed miRNAs in breast cancer and demonstrated an association between distinct miRNAs and malignant progression as well as metastasis. Even though tumor‐associated macrophages (TAM) are known mediators of these processes, little is known regarding their miRNA expression upon education by malignant cells in vivo.

Biomarkers predict outcome in Charcot-Marie-Tooth disease 1A

Background Charcot-Marie-Tooth disease type 1A (CMT1A) is the most common inherited neuropathy, a debilitating disease without known cure. Among patients with CMT1A, disease manifestation, progression and severity are strikingly variable, which poses major challenges for the development of new therapies. Hence, there is a strong need for sensitive outcome measures such as disease and progression biomarkers, which would add powerful tools to monitor therapeutic effects in CMT1A. Methods We established a pan-European and American consortium comprising nine clinical centres including 311 patients with CMT1A in total. From all patients, the CMT neuropathy score and secondary outcome measures were obtained and a skin biopsy collected. In order to assess and validate disease severity and progression biomarkers, we performed qPCR on a set of 16 animal model-derived potential biomarkers in skin biopsy mRNA extracts. Results In 266 patients with CMT1A, a cluster of eight cutaneous transcripts differentiates disease severity with a sensitivity and specificity of 90% and 76.1%, respectively. In an additional cohort of 45 patients with CMT1A, from whom a second skin biopsy was taken after 2–3 years, the cutaneous mRNA expression of GSTT2, CTSA, PPARG, CDA, ENPP1 and NRG1-Iis changing over time and correlates with disease progression. Conclusions In summary, we provide evidence that cutaneous transcripts in patients with CMT1A serve as disease severity and progression biomarkers and, if implemented into clinical trials, they could markedly accelerate the development of a therapy for CMT1A.

Treatment of prostate cancer cells with S-adenosylmethionine leads to genome-wide alterations in transcription profiles

The hypomethylation of DNA may support tumor progression; however, the mechanism underlying this relationship is not clear. Several studies have demonstrated that the in vitro application of the methyl donor S-adenosylmethionine (SAM) leads to promoter remethylation and the downregulation of proto-oncogene expression in cancer cells. It is not clear if this represents a general mechanism of SAM or is limited to selected genes. We examined this problem using new bisulfite sequencing and transcriptomic technologies. Treatment with SAM caused the downregulation of proliferation, migration, and invasion of prostate cancer (PC-3) cells. RNA sequencing revealed the genome-wide downregulation of genes involved in proliferation, migration, invasion, and angiogenesis. Real-time PCR of a subset of the genes confirmed these results. Reduced representation bisulfite sequencing (RRBS) displayed only minor differential methylation between treated cells and controls. In summary, we confirmed the anti-proliferative and anti-invasive effects of SAM. Additionally, we observed anti-migratory effects and downregulation of genes, especially those related to cancerogenesis. For some of the related genes, this is the first reported evidence of an association with prostate cancer. However, genome-wide modifications in methylation profiles were not observed by RRBS; thus, they are obviously not a major cause of alteration in transcription profiles and anti-cancer effects.

Utilization of ordinal response structures in classification with high-dimensional expression data

Molecular diagnosis or prediction of clinical treatment outcome based on high-throughput genomics data is a modern application of machine learning techniques for clinical problems. In practice, clinical parameters, such as patient health status or toxic reaction to therapy, are often measured on an ordinal scale (e.g. good, fair, poor). Commonly, the prediction of ordinal end-points is treated as a multi-class classification problem, disregarding the ordering information contained in the response. This may result in a loss of prediction accuracy. Classical approaches to model ordinal response directly, including for instance the cumulative logit model, are typically not applicable to high-dimensional data. We present hierarchical twoing (hi2), a novel algorithm for classification of high-dimensional data into ordered categories. hi2 combines the power of well-understood binary classification with ordinal response prediction. A comparison of several approaches for ordinal classification on real world data as well as simulated data shows that classification algorithms especially designed to handle ordered categories fail to improve upon state-of-the-art non-ordinal classification algorithms. In general, the classification performance of an algorithm is dominated by its ability to deal with the high-dimensionality of the data. Only hi2 outperforms its competitors in the case of moderate effects.

Parallelizing scientific code with invasive interactive parallelization: a case study with reuseware

We present a case study of parallelizing serial legacy code using Invasive Interactive Parallelization (IIP) - a compositional approach to parallelizing code refactoring rooted in the Invasive Software Composition (ISC) and the Separation of Concerns (SoC). The study focuses on scientific code, in particular, Gaussian elimination where parallelization neither requires nor incurs serious changes in the algorithmic structure. As the major contribution we show how parallelization of Gaussian elimination can be automatized with reusable parallelization recipes implemented as composers in Reuseware. We consider parallelization for both shared-and distributed-memory systems with OpenMP and MPI respectively. We present the speed-ups achieved and discuss gains in code reusability.

Corrigendum: Common genetic variation drives molecular heterogeneity in human iPSCs

This corrects the article DOI: 10.1038/nature22403.