Human cancer cell lines are the workhorse of cancer research. Although cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here we use genomic analyses of 106 human cell lines grown in two laboratories to show extensive clonal diversity. Further comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Notably, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single-cell-derived clones demonstrated that continuous instability quickly translates into heterogeneity of the cell line. When the 27 MCF7 strains were tested against 321 anti-cancer compounds, we uncovered considerably different drug responses: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origins and consequences of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.

Natural killer (NK) cells are critical to both innate and adaptive immunity. However, the development and heterogeneity of human NK cells are yet to be fully defined. Using single-cell RNA-sequencing technology, here we identify distinct NK populations in human bone marrow and blood, including one population expressing higher levels of immediate early genes indicative of a homeostatic activation. Functionally matured NK cells with high expression of CX3CR1 , HAVCR2 (TIM-3), and ZEB2 represents terminally differentiated status with the unique transcriptional profile. Transcriptomic and pseudotime analyses identify a transitional population between CD56 bright and CD56 dim NK cells. Finally, a donor with GATA2 T354M mutation exhibits reduced percentage of CD56 bright NK cells with altered transcriptome and elevated cell death. These data expand our understanding of the heterogeneity and development of human NK cells.

BackgroundSample index cross-talk can result in false positive calls when massively parallel sequencing (MPS) is used for sensitive applications such as low-frequency somatic variant discovery, ancient DNA investigations, microbial detection in human samples, or circulating cell-free tumor DNA (ctDNA) variant detection. Therefore, the limit-of-detection of an MPS assay is directly related to the degree of index cross-talk.ResultsCross-talk rates up to 0.29% were observed when using standard, combinatorial adapters, resulting in 110,180 (0.1% cross-talk rate) or 1,121,074 (0.29% cross-talk rate) misassigned reads per lane in non-patterned and patterned Illumina flow cells, respectively. Here, we demonstrate that using unique, dual-matched indexed adapters dramatically reduces index cross-talk to ≤1 misassigned reads per flow cell lane. While the current study was performed using dual-matched indices, using unique, dual-unrelated indices would also be an effective alternative.ConclusionsFor sensitive downstream analyses, the use of combinatorial indices for multiplexed hybrid capture and sequencing is inappropriate, as it results in an unacceptable number of misassigned reads. Cross-talk can be virtually eliminated using dual-matched indexed adapters. These results suggest that use of such adapters is critical to reduce false positive rates in assays that aim to identify low allele frequency events, and strongly indicate that dual-matched adapters be implemented for all sensitive MPS applications.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4428-5) contains supplementary material, which is available to authorized users.

Naturally occurring estrogens in animal wastes may cause negative environmental impacts, yet their abundance in animal waste treatment and storage structures is poorly documented. To better quantify estrogen concentrations in animal wastes, multiple waste samples were collected from treatment and storage structures at dairy and swine facilities and analyzed for concentrations of 17beta-estradiol (E2), estrone (E1), and 17alpha-estradiol by gas chromatography-mass spectroscopy and by enzyme linked immunosorbent assay (E2 only). Mass ratios of each estrogen to the macronutrients nitrogen, phosphorus, and potassium were also determined. Because manure application rates are typically macronutrient-based, estrogen to macronutrient ratios are proportional to areal mass application rates of estrogen to fields. Swine farrowing waste (from farrowing sows and piglets) had the highest ratios of E2 to macronutrients. Mean ratios in swine farrowing waste were roughly twice those in swine finishing waste (from growing male and nonpregnant female animals) and more than four times higher than those in dairy waste (from lactating cows in various stages of their reproductive cycles); these differences were statistically significant (alpha = 0.05). Estrone followed a similar trend. In contrast, ratios of 17alpha-estradiol to macronutrients were highest in dairy operations. These results can be used to better predict estrogen loading rates on fields receiving swine and dairy wastes.

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Background: Merkel cell carcinoma (MCC) is a highly aggressive neuroendocrine carcinoma of the skin caused by either the integration of Merkel cell polyomavirus (MCPyV) and expression of viral T antigens or by ultravioletinduced damage to the tumor genome from excessive sunlight exposure. An increasing number of deep sequencing studies of MCC have identified significant differences between the number and types of point mutations, copy number alterations, and structural variants between virus-positive and virus-negative tumors. However, it has been challenging to reliably distinguish between virus positive and UV damaged MCC. Methods: In this study, we assembled a cohort of 71 MCC patients and performed deep sequencing with OncoPanel, a clinically implemented, next-generation sequencing assay targeting over 400 cancer-associated genes. To improve the accuracy and sensitivity for virus detection compared to traditional PCR and IHC methods, we developed a hybrid capture baitset against the entire MCPyV genome and software to detect integration sites and structure. Results: Sequencing from this approach revealed distinct integration junctions in the tumor genome and generated assemblies that strongly support a model of microhomology-initiated hybrid, virus-host, circular DNA intermediate that promotes focal amplification of host and viral DNA. Using the clear delineation between virus-positive and virusnegative tumors from this method, we identified recurrent somatic alterations common across MCC and alterations specific to each class of tumor, associated with differences in overall survival. Finally, comparing the molecular and clinical data from these patients revealed a surprising association of immunosuppression with virus-negative MCC and significantly shortened overall survival. Conclusions: These results demonstrate the value of high-confidence virus detection for identifying molecular mechanisms of UV and viral oncogenesis in MCC. Furthermore, integrating these data with clinical data revealed features that could impact patient outcome and improve our understanding of MCC risk factors.

Tracking how individual naive T cells from a natural TCR repertoire clonally expand, differentiate, and make lineage choices in response to an infection has not previously been possible. Here, using single-cell sequencing technology to identify clones by their unique TCR sequences, we were able to trace the clonal expansion, differentiation trajectory, and lineage commitment of individual virus-specific CD4 T cells during an acute lymphocytic choriomeningitis virus (LCMV) infection. Notably, we found previously unappreciated clonal diversity and cellular heterogeneity among virus-specific helper T cells. Interestingly, although most naive CD4 T cells gave rise to multiple lineages at the clonal level, ∼28% of naive cells exhibited a preferred lineage choice toward either Th1 or TFH cells. Mechanistically, we found that TCR structure, in particular the CDR3 motif of the TCR α chain, skewed lineage decisions toward the TFH cell fate.

Volatile sulfur compounds (VSCs) are a major class of chemicals associated with odor from animal feeding operations (AFOs). Identifying and quantifying VSCs in air is challenging due to their volatility, reactivity, and low concentrations. In the present study, a canister-based method collected whole air in fused silica-lined (FSL) mini-canister (1.4 L) following passage through a calcium chloride drying tube. Sampled air from the canisters was removed (10-600 mL), dried, pre-concentrated, and cryofocused into a GC system with parallel detectors (mass spectrometer (MS) and pulsed flame photometric detector (PFPD)). The column effluent was split 20:1 between the MS and PFPD. The PFPD equimolar sulfur response enhanced quantitation and the location of sulfur peaks for mass spectral identity and quantitation. Limit of quantitation for the PFPD and MSD was set at the least sensitive VSC (hydrogen sulfide) and determined to be 177 and 28 pg S, respectively, or 0.300 and 0.048 μg m −3 air, respectively. Storage stability of hydrogen sulfide and methanethiol was problematic in warm humid air (25 °C, 96% relative humidity (RH)) without being dried first, however, stability in canisters dried was still only 65% after 24 h of storage. Storage stability of hydrogen sulfide sampled in the field at a swine facility was over 2 days. The greater stability of field samples compared to laboratory samples was due to the lower temperature and RH of field samples compared to laboratory generated samples. Hydrogen sulfide was the dominant odorous VSCs detected at all swine facilities with methanethiol and dimethyl sulfide detected notably above their odor threshold values. The main odorous VSC detected in aged poultry litter was dimethyl trisulfide. Other VSCs above odor threshold values for poultry facilities were methanethiol and dimethyl sulfide. RightsWorks produced by employees of the U.S. Government as part of their official duties are not copyrighted within the U.S. The content of this document is not copyrighted. AbstractVolatile sulfur compounds (VSCs) are a major class of chemicals associated with odor from animal feeding operations (AFOs). Identifying and quantifying VSCs in air is challenging due to their volatility, reactivity, and low concentrations. In the present study, a canister-based method collected whole air in fused silica-lined (FSL) mini-canister (1.4 L) following passage through a calcium chloride drying tube. Sampled air from the canisters was removed (10-600 mL), dried, preconcentrated, and cryofocused into a GC system with parallel detectors (mass spectrometer (MS) and pulsed flame photometric detector (PFPD)). The column effluent was split 20:1 between the MS and PFPD. The PFPD equimolar sulfur response enhanced quantitation and the location of sulfur peaks for mass spectral identity and quantitation. Limit of quantitation for the PFPD and MSD was set at the least sensitive VSC (hydrogen sulfide) and determined to be 177 and 28 pg S, respectively, or 0.300 and 0.048 mg m À3 air, respectively. S...