Single-cell eQTL mapping in yeast reveals a tradeoff between growth and reproduction

Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved in the mating response. We showed that the effects of this locus arise from a common variant (W82R) in the gene GPA1, which encodes a signaling protein that negatively regulates the mating pathway. The 82R allele increases mating efficiency at the cost of slower cell-cycle progression and is associated with a higher rate of outcrossing in nature. Our results provide a more granular picture of the effects of genetic variants on gene expression and downstream traits.

Abstract 3851: Microenvironmental alterations co-occur with mosaic somatic clonal expansions in normal tissues

Clonal hematopoiesis confers an increased risk for myeloid neoplasia, but progression to cancer requires additional alterations. Recently described clonal expansion (CE) of mutant skin and esophagus suggests CE is pervasive across tissues. Immune evasion and angiogenesis, reliant on the microenvironment (ME), are cancer hallmarks, yet ME changes in the setting of CE have not been systematically studied. Using GTEX RNA-Seq data (25 normal tissues, n = 6,511), previously reported somatic variants (Yizhak K, Science 2019) and normalized gene expression values were downloaded. Samples were grouped by the presence of: non-synonymous mutation (NSM) in a COSMIC Cancer Gene Census gene (CGC-m), NSM in a non-cancer gene or no NSM (non-m). ME scores, i.e. stromal and immune cell abundances for all samples, were estimated using Xcell and CIBERSORTx. Our analyses focused on tissues with at least 10 CGC-m, especially skin and esophagus which had the most CGC-m cases (77/600, 12% and 166/512, 32% respectively; median :4.6%). We also compared ME scores from skin and esophagus with corresponding cancer data from TCGA. Differential gene expression (DEG) testing between CGC-m and non-m samples, Gene Set Enrichment Analysis (GSEA), and hypoxia scores (Bhandari V, Nature Comm 2020) based on findings (below) were generated. ME scores significantly differed in the CGC-m vs. non-m cohorts, with increased epithelial and lymphatic endothelial cells (skin, esophagus), megakaryocytes (skin, prostate) and neutrophils (prostate, lung) (Wilcoxon FDR p-value < 0.01). Skin showed reduced fibroblasts and esophagus, increased endothelial cells and melanocytes and lower pericytes and erythrocytes. Comparing TCGA and GTEX data, melanoma showed similar but more marked epithelial cell increase and fibroblast reduction. Esophageal carcinoma showed similar but more pronounced reductions in pericytes and erythrocytes. DEG testing between CGC-m and non-m identified: in esophagus, overexpression of genes aberrant in carcinomas (ERBB2, CDH1, SOX2 and TP63; p-adjusted < 0.01), downregulation of pro-angiogenic factors and those involved in pericyte recruitment (FGF2, ANGPT1 and PDGFB); in skin, extracellular matrix protein, ELN was overexpressed. GSEA analysis of differentially expressed genes identified dysregulation of mesenchymal-epithelial transition and myogenesis pathways in both tissues and angiogenesis-related pathway in esophagus. Hypoxia scores were markedly higher in CGC-m vs. non-m esophagus samples (Wilcoxon FDR p-value < 0.01). These results suggest ME alterations participate in initial stages of cancer progression and are tissue-specific. High hypoxia scores support a hypothesis of its early initiating role in CE-related angiogenesis in esophagus. Studying these changes may reveal novel avenues for early cancer intervention, immune or other targeted therapies and enhancement of conventional therapies.

Citation Format: Chetan Munugala, Jieting Hu, Eirini Christodoulou, Venkata Yellapantula. Microenvironmental alterations co-occur with mosaic somatic clonal expansions in normal tissues [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3851.

Genomic epidemiology of the Los Angeles COVID-19 outbreak and the early history of the B.1.43 strain in the USA

Background

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused global disruption of human health and activity. Being able to trace the early outbreak of SARS-CoV-2 within a locality can inform public health measures and provide insights to contain or prevent viral transmission. Investigation of the transmission history requires efficient sequencing methods and analytic strategies, which can be generally useful in the study of viral outbreaks.

Methods

The County of Los Angeles (hereafter, LA County) sustained a large outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To learn about the transmission history, we carried out surveillance viral genome sequencing to determine 142 viral genomes from unique patients seeking care at the University of California, Los Angeles (UCLA) Health System. 86 of these genomes were from samples collected before April 19, 2020.

Results

We found that the early outbreak in LA County, as in other international air travel hubs, was seeded by multiple introductions of strains from Asia and Europe. We identified a USA-specific strain, B.1.43, which was found predominantly in California and Washington State. While samples from LA County carried the ancestral B.1.43 genome, viral genomes from neighboring counties in California and from counties in Washington State carried additional mutations, suggesting a potential origin of B.1.43 in Southern California. We quantified the transmission rate of SARS-CoV-2 over time, and found evidence that the public health measures put in place in LA County to control the virus were effective at preventing transmission, but might have been undermined by the many introductions of SARS-CoV-2 into the region.

Conclusion

Our work demonstrates that genome sequencing can be a powerful tool for investigating outbreaks and informing the public health response. Our results reinforce the critical need for the USA to have coordinated inter-state responses to the pandemic.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08488-7.

Massively scaled-up testing for SARS-CoV-2 RNA via next-generation sequencing of pooled and barcoded nasal and saliva samples

Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens.

Swab-Seq: A high-throughput platform for massively scaled up SARS-CoV-2 testing

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is due to the high rates of transmission by individuals who are asymptomatic at the time of transmission^1,2. Frequent, widespread testing of the asymptomatic population for SARS-CoV-2 is essential to suppress viral transmission. Despite increases in testing capacity, multiple challenges remain in deploying traditional reverse transcription and quantitative PCR (RT-qPCR) tests at the scale required for population screening of asymptomatic individuals. We have developed SwabSeq, a high-throughput testing platform for SARS-CoV-2 that uses next-generation sequencing as a readout. SwabSeq employs sample-specific molecular barcodes to enable thousands of samples to be combined and simultaneously analyzed for the presence or absence of SARS-CoV-2 in a single run. Importantly, SwabSeq incorporates an in vitro RNA standard that mimics the viral amplicon, but can be distinguished by sequencing. This standard allows for end-point rather than quantitative PCR, improves quantitation, reduces requirements for automation and sample-to-sample normalization, enables purification-free detection, and gives better ability to call true negatives. After setting up SwabSeq in a high-complexity CLIA laboratory, we performed more than 80,000 tests for COVID-19 in less than two months, confirming in a real world setting that SwabSeq inexpensively delivers highly sensitive and specific results at scale, with a turn-around of less than 24 hours. Our clinical laboratory uses SwabSeq to test both nasal and saliva samples without RNA extraction, while maintaining analytical sensitivity comparable to or better than traditional RT-qPCR tests. Moving forward, SwabSeq can rapidly scale up testing to mitigate devastating spread of novel pathogens.