Biology subjects

Schubert, M.

Publications and source records attributed to Schubert, M..

46 records · Page 3Linked to original sources

bioRxiv2020

CIS checkpoint deletion enhances the fitness of cord blood derived natural killer cells transduced with a chimeric antigen receptor

Immune checkpoint therapy has produced remarkable improvements in the outcome for certain cancers. To broaden the clinical impact of checkpoint targeting, we devised a strategy that couples targeting of the cytokine-inducible SH2-containing (CIS) protein, a key negative regulator of interleukin (IL)-15 signaling, with chimeric antigen receptor (CAR) engineering of natural killer (NK) cells. This combined strategy boosted NK cell effector function through enhancing the Akt/mTORC1 axis and c-MYC signaling, resulting in increased aerobic glycolysis. When tested in a lymphoma mouse model, this combined approach improved NK cell anti-tumor activity more than either alteration alone, eradicating lymphoma xenografts without signs of any measurable toxicity. We conclude that combining CIS checkpoint deletion with CAR engineering promotes the metabolic fitness of NK cells in an otherwise suppressive tumor microenvironment. This approach, together with the prolonged survival afforded by CAR modification, represents a promising milestone in the development of the next generation of NK cells for cancer immunotherapy.

immunology↗

bioRxiv2019

Gene networks in cancer are biased by aneuploidies and sample impurities

Gene regulatory network inference is a standard technique for obtaining structured regulatory information from, among other data sources, gene expression measurements. Methods performing this task have been extensively evaluated on synthetic, and to a lesser extent real data sets. They are often applied to gene expression of human cancers. However, in contrast to the evaluations, these data sets often contain fewer samples, more potential regulatory links, and are biased by copy number aberrations as well as cell mixtures and sample impurities. Here, we take networks inferred from TCGA cohorts as an example to show that (1) transcription factor annotations are essential to obtaining reliable networks, and (2) even when taking these into account, we should expect between 20 and 80% of edges to be caused by copy number changes and cell mixtures rather than transcription factor regulation.

bioinformatics↗

bioRxiv2019

Altering microtubule dynamics is synergistically toxic with inhibition of the spindle checkpoint

Chromosome instability (CIN) and aneuploidy are hallmarks of cancer. As the majority of cancers are aneuploid, targeting aneuploidy or CIN may be an effective way to target a broad spectrum of cancers. Here, we perform two small molecule compound screens to identify drugs that selectively target cells that are aneuploid or exhibit a CIN phenotype. We find that aneuploid cells are much more sensitive to the energy metabolism regulating drug ZLN005 than their euploid counterparts. Furthermore, cells with an ongoing CIN phenotype, induced by spindle assembly checkpoint (SAC) alleviation, are significantly more sensitive to the Src kinase inhibitor SKI606. We show that inhibiting Src kinase increases microtubule polymerization rates and, more generally, that deregulating microtubule polymerization rates is particularly toxic to cells with a defective SAC. Our findings therefore suggest that tumors with a dysfunctional SAC are particularly sensitive to microtubule poisons and, vice versa, that compounds alleviating the SAC provide a powerful means to treat tumors with deregulated microtubule dynamics.

cancer biology↗

bioRxiv2019

Monitoring contractility in single cardiomyocytes and whole hearts with bio-integrated microlasers

Cardiac regeneration and stem cell therapies depend critically on the ability to locally resolve the contractile properties of heart tissue1,2. Current regeneration approaches explore the growth of cardiac tissue in vitro and the injection of stem cell-derived cardiomyocytes3-6 (CMs) but scientists struggle with low engraftment rates and marginal mechanical improvements, leaving the estimated 26 million patients suffering from heart failure worldwide without effective therapy7-9. One impediment to further progress is the limited ability to functionally monitor injected cells as currently available techniques and probes lack speed and sensitivity as well as single cell specificity. Here, we introduce microscopic whispering gallery mode (WGM) lasers into beating cardiomyocytes to realize all-optical recording of transient cardiac contraction profiles with cellular resolution. The brilliant emission and high spectral sensitivity of microlasers to local changes in refractive index enable long-term tracking of individual cardiac cells, monitoring of drug administration, and accurate measurements of organ scale contractility in live zebrafish. Our study reveals changes in sarcomeric protein density as underlying factor to cardiac contraction which is of fundamental importance for understanding the mechano-biology of cardiac muscle activation. The ability to non-invasively assess functional properties of transplanted cells and engineered cardiac tissue will stimulate the development of novel translational approaches and the in vivo monitoring of physiological parameters more broadly. Likewise, the use of implanted microlasers as cardiac sensors is poised to inspire the adaptation of the most advanced optical tools known to the microresonator community, like quantum-enhanced single-molecule biosensing or frequency comb spectroscopy10.

biophysics↗

bioRxiv2018

The grass subfamily Pooideae: late Cretaceous origin and climate-driven Cenozoic diversification

* AimFrost is among the most dramatic stresses a plant can experience and complex physiological adaptations are needed to endure long periods of sub-zero temperatures. Due to the need for evolving these complex adaptations, transitioning from tropical to temperate climates is regarded difficult and only half of the worlds seed plant families have temperate representatives. Here, we study the transition from tropical to temperate climates in the grass subfamily Pooideae, which dominates the northern temperate grass floras. Specifically, we investigate the role of climate cooling in diversification.\n\n* LocationGlobal, temperate regions\n\n* Time periodLate Cretaceous-Cenozoic\n\n* Major taxaThe grass subfamily Pooideae\n\n* MethodsWe date a comprehensive Pooideae phylogeny and test for the impact of paleoclimates on diversification rates. Using ancestral state reconstruction, we investigate if Pooideae ancestors experienced frost and winter. To locate the area of origin of Pooideae we perform biogeographical analyses.\n\n* ResultsWe estimated a late Cretaceous origin of the Pooideae (66 million years ago (Mya)), and all major clades had already diversified at the Eocene-Oligocene transition climate cooling (34 Mya). Climate cooling was a probable driving force of Pooideae diversification. Pooideae likely evolved in mountainous regions of southwestern Eurasia in a temperate niche experiencing frost, but not long winters.\n\n* Main conclusionPooideae originated in a temperate niche and experienced cold temperatures and frost long before the expansion of temperate biomes after the Eocene-Oligocene transition. This suggests that the Pooideae ancestor had adaptations to temperate climate and that extant Pooideae grasses share responses to low temperature stress in Pooideae. Throughout the Cenozoic falling temperatures triggered diversification. However, complex mechanisms for enduring strongly seasonal climate with long, cold winters most likely evolved independently in lower taxonomic lineages. Our findings provide insight into how adaptations to historic changes in chill and frost exposure influence distribution of plant diversity today.

evolutionary biology↗

bioRxiv2017

Evolution of cold acclimation in temperate grasses (Pooideae)

In the past 50 million years climate cooling has triggered the expansion of temperate biomes. During this period, many extant plant lineages in temperate biomes evolved from tropical ancestors and adapted to seasonality and cool conditions. Among the Poaceae (grass family), one of the subfamilies that successfully shifted from tropical to temperate biomes is the Pooideae (temperate grasses). Subfamily Pooideae contains the most important crops cultivated in the temperate regions including wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the need of well-adapted cultivars, extensive research has produced a large body of knowledge about the mechanisms underlying cold adaptation in cultivated Pooideae species. Especially cold acclimation, a process which increases the frost tolerance during a period of non-freezing cold, plays an important role. Because cold adaptation is largely unexplored in lineages that diverged early in the evolution of the Pooideae, little is known about the evolutionary history of cold acclimation in the Pooideae. Here we test if several species of early diverging lineages exhibit increased frost tolerance after a period of cold acclimation. We further investigate the conservation of five well-studied gene families that are known to be involved in the cold acclimation of Pooideae crop species. Our results indicate that cold acclimation exists in early diverging lineages, but that genes involved in regulation of cold acclimation are not conserved. The investigated gene families show signs of lineage-specific evolution and support the hypothesis that gene family expansion is an important mechanism in adaptive evolution.

evolutionary biology↗

bioRxiv2017

High-throughput creation and functional profiling of eukaryotic DNA sequence variant libraries using CRISPR/Cas9

Construction of genetic variant libraries with phenotypic measurement is central to advancing todays functional genomics, and remains a grand challenge. Here, we introduce a Cas9-based approach for generating pools of mutants with defined genetic alterations (deletions, substitutions and insertions), along with methods for tracking their fitness en masse. We demonstrate the utility of our approach in performing focused analysis of hundreds of mutants of a single protein and in investigating the biological function of an entire family of poorly characterized genetic elements. Our platform allows fundamental biology questions to be investigated in a quick, easy and affordable manner.

bioengineering↗

bioRxiv2017

Comparative transcriptomics reveals lineage specific evolution of cold response in Pooideae

BackgroundUnderstanding how complex traits evolve through adaptive changes in gene regulation remains a major challenge in evolutionary biology. Over the last ~50 million years, Earth has experienced climate cooling and ancestrally tropical plants have adapted to expanding temperate environments. The grass subfamily Pooideae dominates the grass flora of the temperate regions, but the role of cold-response gene regulation in the transitioning from tropical to temperate climate remains unexplored.\n\nResultsTo establish if molecular responses to cold are conserved throughout the phylogeny, we assembled the transcriptomes of five Pooideae species spanning early to later diverging lineages, and compared short- and long-term cold responsive genes using 8633 high confidence ortholog groups with resolved gene tree topologies. We found that a majority of cold responsive genes were specific to one or two lineages, an observation that we deem incompatible with a cold adapted Pooideae ancestor. However, all five species shared short-term cold response in a small set of general stress genes as well as the ability to down-regulate the photosynthetic machinery during cold temperatures.\n\nConclusionsOur observations indicate that the different Pooideae lineages have assembled cold response programs in parallel by taking advantage of a common potential for cold adaptation.

evolutionary biology↗

bioRxiv2017

Development of a high-density, 2M SNP genotyping array and 670k SNP imputation array for the domestic horse

BackgroundTo date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.\n\nResultsUsing whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of [~]5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix, now Thermo Fisher Scientific) a set of [~]2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of [~]670 thousand SNPs (MNEc670k), was designed for genotype imputation.\n\nConclusionsHere, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.

genomics↗

bioRxiv2016

Genomic determinants of protein abundance variation in colorectal cancer cells

Assessing the extent to which genomic alterations compromise the integrity of the proteome is fundamental in identifying the mechanisms that shape cancer heterogeneity. We have used isobaric labelling and tribrid mass spectrometry to characterize the proteomic landscapes of 50 colorectal cancer cell lines and to decipher the relationships between genomic and proteomic variation. The robust quantification of 12,000 proteins and 27,000 phosphopeptides revealed how protein symbiosis translates to a co-variome which is subjected to a hierarchical order and exposes the collateral effects of somatic mutations on protein complexes. Targeted depletion of key chromatin modifiers confirmed the transmission of variation and the directionality as characteristics of protein interactions. Protein level variation was leveraged to build drug response predictive models towards a better understanding of pharmacoproteomic interactions in colorectal cancer. Overall, we provide a deep integrative view of the molecular structure underlying the variation of colorectal cancer cells.\n\nHighlightsO_LIThe cancer cell functional \"co-variome\" is a strong attribute of the proteome.\nC_LIO_LIMutations can have a direct impact on protein levels of chromatin modifiers.\nC_LIO_LITransmission of genomic variation is a characteristic of protein interactions.\nC_LIO_LIPharmacoproteomic models are strong predictors of response to DNA damaging agents.\nC_LI\n\nAbbreviations

systems biology↗