Uncovering regulatory pathways that affect hematopoietic stem cell function using 'genetical genomics'

We combined large-scale mRNA expression analysis and gene mapping to identify genes and loci that control hematopoietic stem cell (HSC) function. We measured mRNA expression levels in purified HSCs isolated from a panel of densely genotyped recombinant inbred mouse strains. We mapped quantitative trait loci (QTLs) associated with variation in expression of thousands of transcripts. By comparing the physical transcript position with the location of the controlling QTL, we identified polymorphic cis-acting stem cell genes. We also identified multiple trans-acting control loci that modify expression of large numbers of genes. These groups of coregulated transcripts identify pathways that specify variation in stem cells. We illustrate this concept with the identification of candidate genes involved with HSC turnover. We compared expression QTLs in HSCs and brain from the same mice and identified both shared and tissue-specific QTLs. Our data are accessible through WebQTL, a web-based interface that allows custom genetic linkage analysis and identification of coregulated transcripts.

The emergence of a stable neuronal ensemble from a wider pool of activated neurons in the dorsal medial prefrontal cortex during appetitive learning in mice

Animals selectively respond to environmental cues associated with food reward to optimize nutrient intake. Such appetitive CS-US associations are thought to be encoded in select, stable neuronal populations or neuronal ensembles, which undergo physiological modifications during appetitive conditioning. These ensembles in the medial prefrontal cortex (mPFC) control well-established, cue-evoked food seeking, but the mechanisms involved in the genesis of these ensembles are unclear. Here, we utilized male Fos-GFP mice that express the green fluorescent protein (GFP) in recently behaviorally-activated neurons, to reveal how dorsal mPFC neurons are recruited and modified to encode CS-US memory representations using an appetitive conditioning task. In the initial conditioning session, animals did not exhibit discriminated, cue-selective food seeking, but did so in later sessions indicating that a CS-US association was established. Using microprism-based in vivo 2-Photon imaging, we revealed that only a minority of neurons activated during the initial session was consistently activated throughout subsequent conditioning sessions and during cue-evoked memory recall. Notably, using ex vivo electrophysiology we found that neurons activated following the initial session exhibited transient hyper-excitability. Chemogenetically enhancing the excitability of these neurons throughout subsequent conditioning sessions interfered with the development of reliable cue-selective food seeking, indicated by persistent, non-discriminated performance. We demonstrate how appetitive learning consistently activates a subset of neurons to form a stable neuronal ensemble during the formation of a CS-US association. This ensemble may arise from a pool of hyper-excitable neurons activated during the initial conditioning session

Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaques

BACKGROUND: How a potentially diverse population of hematopoietic stem cells (HSCs) differentiates and proliferates to supply more than 10(11) mature blood cells every day in humans remains a key biological question. We investigated this process by quantitatively analyzing the clonal structure of peripheral blood that is generated by a population of transplanted lentivirus-marked HSCs in myeloablated rhesus macaques. Each transplanted HSC generates a clonal lineage of cells in the peripheral blood that is then detected and quantified through deep sequencing of the viral vector integration sites (VIS) common within each lineage. This approach allowed us to observe, over a period of 4-12 years, hundreds of distinct clonal lineages. RESULTS: While the distinct clone sizes varied by three orders of magnitude, we found that collectively, they form a steady-state clone size-distribution with a distinctive shape. Steady-state solutions of our model show that the predicted clone size-distribution is sensitive to only two combinations of parameters. By fitting the measured clone size-distributions to our mechanistic model, we estimate both the effective HSC differentiation rate and the number of active HSCs. CONCLUSIONS: Our concise mathematical model shows how slow HSC differentiation followed by fast progenitor growth can be responsible for the observed broad clone size-distribution. Although all cells are assumed to be statistically identical, analogous to a neutral theory for the different clone lineages, our mathematical approach captures the intrinsic variability in the times to HSC differentiation after transplantation. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0191-8) contains supplementary material, which is available to authorized users

Further phenotypic characterization of the primitive lineage− CD34+CD38−CD90+CD45RA− hematopoietic stem cell/progenitor cell sub-population isolated from cord blood, mobilized peripheral blood and patients with chronic myelogenous leukemia

The most primitive hematopoietic stem cell (HSC)/progenitor cell (PC) population reported to date is characterized as being Lin−CD34+CD38−CD90+CD45R. We have a long-standing interest in comparing the characteristics of hematopoietic progenitor cell populations enriched from normal subjects and patients with chronic myelogenous leukemia (CML). In order to investigate further purification of HSCs and for potential targetable differences between the very primitive normal and CML stem/PCs, we have phenotypically compared the normal and CML Lin−CD34+CD38−CD90+CD45RA− HSC/PC populations. The additional antigens analyzed were HLA-DR, the receptor tyrosine kinases c-kit and Tie2, the interleukin-3 cytokine receptor, CD33 and the activation antigen CD69, the latter of which was recently reported to be selectively elevated in cell lines expressing the Bcr-Abl tyrosine kinase. Notably, we found a strikingly low percentage of cells from the HSC/PC sub-population isolated from CML patients that were found to express the c-kit receptor (<1%) compared with the percentages of HSC/PCs expressing the c-kitR isolated from umbilical cord blood (50%) and mobilized peripheral blood (10%). Surprisingly, Tie2 receptor expression within the HSC/PC subset was extremely low from both normal and CML samples. Using in vivo transplantation studies, we provide evidence that HLA-DR, c-kitR, Tie2 and IL-3R may not be suitable markers for further partitioning of HSCs from the Lin−CD34+CD38−CD90+CD45RA− sub-population

Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis

Cellular decision-making is mediated by a complex interplay of external stimuli with the intracellular environment, in particular transcription factor regulatory networks. Here we have determined the expression of a network of 18 key haematopoietic transcription factors in 597 single primary blood stem and progenitor cells isolated from mouse bone marrow. We demonstrate that different stem/progenitor populations are characterized by distinctive transcription factor expression states, and through comprehensive bioinformatic analysis reveal positively and negatively correlated transcription factor pairings, including previously unrecognized relationships between Gata2, Gfi1 and Gfi1b. Validation using transcriptional and transgenic assays confirmed direct regulatory interactions consistent with a regulatory triad in immature blood stem cells, where Gata2 may function to modulate cross-inhibition between Gfi1 and Gfi1b. Single-cell expression profiling therefore identifies network states and allows reconstruction of network hierarchies involved in controlling stem cell fate choices, and provides a blueprint for studying both normal development and human disease

A self-renewal assay for cancer stem cells

Cancers of epithelial origin are responsible for the majority of cancer-related deaths in the USA. Unfortunately, although chemotherapy and/or radiation therapy can sometimes shrink tumors, metastatic cancers of epithelial origin are essentially incurable. It is clear that new approaches are needed to treat these diseases. Although cancer cell lines provide invaluable information, their biological properties often differ in crucial ways from de novo cancer cells. Our laboratory has developed a novel mouse model that reliably permits individual cancer cells isolated directly from patients’ tumors to be assayed. This will allow the characterization of crucial signaling pathways involved in processes such as self-renewal that are critical for tumor formation by the cancer cells within de novo tumors. These tools should lead to new insights into the cellular and molecular mechanisms that drive human breast cancer growth and invasion.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46932/1/280_2005_Article_97.pd

Characterization of fuel gases with fiber-enhanced Raman spectroscopy

Common gaseous fuels are mixtures of several components. As the properties of the fuels can vary with the composition, but combustion needs to be stable, reliable analytical methods are highly sought after. Raman spectroscopic methods have proved their suitability for the characterization of diverse gaseous mixtures. They have the potential to overcome existing limitations of established technologies, since they are fast, non-consumptive, and accurate. Here, we demonstrate a gas sensor based on fiber-enhanced Raman spectroscopy (FERS) for fuel gas monitoring. Online detection of all gas components, including alkanes, carbon dioxide (CO2), nitrogen (N2), and hydrogen sulfide (H2S), for varying concentration ranges from tens of vol% down to the ppm level enables a comprehensive characterization of the fuels. The developed sensor system features a pinhole assembly which sufficiently reduces the background signal from the fiber to enable the detection of C2–C4 alkanes occurring in low concentrations. Detection limits in the low ppm region were achieved for the minor components of fuel gases, which allow the online monitoring of necessary purification steps, e.g., for biogas. The obtained results indicate that fiber-enhanced Raman sensors have the potential for comprehensive online and onsite gas sensing for fuel gas quality control

Onsite cavity enhanced Raman spectrometry for the investigation of gas exchange processes in the Earth's critical zone

Raman gas spectrometry is introduced as a robust, versatile method for onsite, battery-powered field measurements of gases in the unsaturated and saturated critical zone. In this study, depth-profiles of the concentrations of oxygen and carbon dioxide were simultaneously monitored down to ∼70 meters depth in the subsurface via a transect of drilling holes located in the Hainich Critical Zone Exploratory in central Germany. A special multichannel monitoring system was designed to access and analyze these gases non-consumptively onsite in a closed loop measurement cycle. During the timeframe of six months, seasonal changes in groundwater levels and microbial activity were related to changes observed in gas concentrations. High oxygen concentrations were found in the depths surrounding a karstified aquifer complex, while low oxygen concentrations were found in a fractured aquifer complex. Raman gas depth-profiles complement standard dissolved oxygen measurements as they also deliver oxygen concentrations in the unsaturated zone. The measured depth-profiles of the gas concentrations indicated that regions of anoxia can exist between the aquifer complexes. Lateral transport of O2 in the deeper aquifer complex provides a local source of O2 that can influence metabolism. Correlations were found between the observed CO2 concentrations and pH-values, indicating strong control of carbonate equilibria. The concentrations of O2 and CO2 were largely decoupled, thus simultaneous measurements of O2 soil effluxes give additional insights into biotic and abiotic processes in the Hainich CZE. These results illustrate the versatility of robust onsite Raman multigas measurements of the soil atmosphere and how they can contribute to the analysis of complex processes in previous uncharacterized environments in the critical zone