BackgroundSingle-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer.ResultsWe sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients. By comparing the cells’ DNA copy number aberration (CNA) landscapes with those of the primary tumors and lymph node metastasis, we establish that 53% of the single cells morphologically classified as tumor cells are DTCs disseminating from the observed tumor. The remaining cells represent either non-aberrant “normal” cells or “aberrant cells of unknown origin” that have CNA landscapes discordant from the tumor. Further analyses suggest that the prevalence of aberrant cells of unknown origin is age-dependent and that at least a subset is hematopoietic in origin. Evolutionary reconstruction analysis of bulk tumor and DTC genomes enables ordering of CNA events in molecular pseudo-time and traced the origin of the DTCs to either the main tumor clone, primary tumor subclones, or subclones in an axillary lymph node metastasis.ConclusionsSingle-cell sequencing of bone marrow epithelial-like cells, in parallel with intra-tumor genetic heterogeneity profiling from bulk DNA, is a powerful approach to identify and study DTCs, yielding insight into metastatic processes. A heterogeneous population of CNA-positive cells is present in the bone marrow of non-metastatic breast cancer patients, only part of which are derived from the observed tumor lineages.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1109-7) contains supplementary material, which is available to authorized users.

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JMML is a rare and often fatal leukemia of young children exhibiting unique clinical, hematopoietic and genetic features including GM-CSF hypersensitivity, and mutations of NF1, RAS, and PTPN11. Ras proteins control a number of cell signaling events becoming activated in part by the addition of a farnesyl moiety via farnesyl protein transferase (FTPase). Given that hyperactive Ras is central to JMML pathogenesis, it is intuitive that an FTPase is an appropriate therapeutic target in JMML. One FTPase inhibitor, L739,749, has previously been shown to abrogate spontaneous in vitro colony growth in 9 JMML samples (Blood 95:639, 2000). R115777 is a potent in vitro and in vivo inhibitor of FTPase, abrogating the growth of H-ras, K-ras and N-ras transformed tumors. In humans, it is well tolerated with the dose-limiting toxicities being myelosuppression and diarrhea. To assess the efficacy and toxicity of R115777 in JMML, a phase II window study was conducted as a part of COG study AAML0122 in newly diagnosed patients who were given the option of receiving this agent prior to cytosine arabinoside, fludarabine and 13-cis retinoic acid followed by stem cell transplant. R115777 was administered PO BID for 21 days with a 7 day rest for two courses in the absence of disease progression or excessive toxicity. The starting dosage in the first 11 patients was 200mg/m2 with escalation in subsequent patients to 300mg/m2 if the initial dosage was tolerated. Overall response was based upon changes in WBC and organomegaly. The impact of R115777 upon in vitro spontaneous colony growth, GM-CSF hypersensitivity and farnesylation was monitored. A total of 47 patients were accrued: M:F=30:17, median (med) age 15 mos. (1–76); med WBC 30X109/L (4–151); med monocyte count 18X109/L (1–55); med platelet count 58X109/L (2–587); elevated fetal hemoglobin 30 (65%). RAS and PTPN11 mutations were tested in 42 cases and inhibition of prenylation in 33. R115777 was well tolerated at both dosages with the most common grade 3/4 toxicities being thrombocytopenia (40%), anemia (40%), neutropenia (15%), and diarrhea (6%). There were no deaths during the trial. The table details the responses in patients receiving one course (N=47) and 2 courses (N=38) of R115777. The 9 patients not receiving two courses were removed from study due to lack of response or progressive disease. WBC ONLY 0VERALL (WBC & organomegaly) COURSE #1 CR CR PR MR SD PD Total     200mg/m2 6 0 4 4 2 1 11     300mg/m2 18 1 17 9 4 5 36 COURSE #2     200mg/m2 6 0 6 1 2 1 10     300mg/m2 17 2 14 7 2 3 28 FTPase activity was inhibited in 13/15 cases (med 71%; range 38–91%) with similar frequency and degree of inhibition at both dosages of R115777. There was no relationship between FTPase inhibition or response and the presence of RAS/PTPN11 mutations or inhibition of prenylation in an HJ2 assay. In conclusion, R115777 provides an overall CR/PR rate of 58% with no significant differences between the two dosages (p=0.7). This agent should be considered in the future management of JMML.

Nanocomposites have become a new paradigm for thermoelectric research in recent years and have resulted in the reduction of thermal conductivity via the nano-inclusion and grain boundary scattering. In this work, we report the preparation and thermoelectric study of SiGe-yttria stabilized zirconia (YSZ) nanocomposites prepared by Spark Plasma Sintering (SPS). We experimentally investigated the reduction of lattice thermal conductivity (κL) in the temperature range (30–800 K) of n-type Si80Ge20P2 alloys with the incorporation of YSZ nanoparticles (20–40 nm diameter) into the Si-Ge matrix. These samples synthesized by using the SPS technique were found to have densities > 95% of the theoretical density. The thermal conductivity, at both low and high temperatures, was measured by steady state and laser flash techniques, respectively. At room temperature, we observed approximately a 50% reduction in the lattice thermal conductivity as result of adding 10% YSZ by volume to the Si80Ge20P2 host matrix. A phenomenological model developed by Callaway was used to corroborate both the temperature dependence and reduction of κL over the measured temperature range (30–800 K) of both Si80Ge20P2 and Si80Ge20P2 + YSZ samples. The observed κL is discussed and interpreted in terms of various phonon scattering mechanisms such as alloy disorder, the Umklapp phonon scattering, and boundary scattering. In addition, a contribution from the phonon scattering by YSZ nanoparticles was further included to account for the κL of Si80Ge20P2 + YSZ sample. The theoretical calculations are in reasonably good agreement with the experimental results for both the Si80Ge20P2 and Si80Ge20P2 + YSZ alloys.