Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying complex biological systems, such as tumor heterogeneity and tissue microenvironments. However, the sources of technical and ...biological variation in primary solid tumor tissues and patient-derived mouse xenografts for scRNA-seq are not well understood.
We use low temperature (6 °C) protease and collagenase (37 °C) to identify the transcriptional signatures associated with tissue dissociation across a diverse scRNA-seq dataset comprising 155,165 cells from patient cancer tissues, patient-derived breast cancer xenografts, and cancer cell lines. We observe substantial variation in standard quality control metrics of cell viability across conditions and tissues. From the contrast between tissue protease dissociation at 37 °C or 6 °C, we observe that collagenase digestion results in a stress response. We derive a core gene set of 512 heat shock and stress response genes, including FOS and JUN, induced by collagenase (37 °C), which are minimized by dissociation with a cold active protease (6 °C). While induction of these genes was highly conserved across all cell types, cell type-specific responses to collagenase digestion were observed in patient tissues.
The method and conditions of tumor dissociation influence cell yield and transcriptome state and are both tissue- and cell-type dependent. Interpretation of stress pathway expression differences in cancer single-cell studies, including components of surface immune recognition such as MHC class I, may be especially confounded. We define a core set of 512 genes that can assist with the identification of such effects in dissociated scRNA-seq experiments.
Premise
Collecting and characterizing the genetic diversity of wild relatives of crops can contribute importantly to sustainable crop production and food security. Wild sunflower, Helianthus niveus, ...occurs in arid regions in western North America and is partially cross‐compatible with the cultivated sunflower (H. annuus). We assessed phylogenetic relationships and patterns of genetic divergence among three previously described subspecies (subsp. niveus, subsp. canescens, and subsp. tephrodes) as well as two new morphotypes of H. niveus recently discovered in extreme drought and dune habitats in Baja California, Mexico.
Methods
We measured 50 plants growing in a common garden for 27 morphological traits and conducted principal component analysis to assess patterns of phenotypic variation. Genome size of each accession was determined using flow cytometry. Pollen viability of first generation hybrids between taxa was tested to infer the strength of intrinsic postzygotic reproductive barriers. Finally, genotyping‐by‐sequencing data were used to investigate the genetic structure and phylogenetic relationships among the previously described subspecies and new morphotypes.
Results
The intraspecific genetic and phenotypic divergence of H. niveus populations closely tracks their geographical distribution. Subspecies niveus is phenotypically, genetically, and reproductively distinct from the other two subspecies and has a larger genome. Therefore, H. niveus as currently circumscribed should be considered to contain two distinct species, H. niveus and H. tephrodes. ABBA‐BABA tests revealed substantial introgression between subsp. canescens and its sympatric congener H. petiolaris, which might contribute to their morphological similarities. The two new morphotypes collected in Mexico represent local ecotypes of subsp. niveus that occur in extreme drought and dune environments. Mantel tests showed a strong positive correlation between genetic and geographic distances.
Conclusions
We conclude that geographic isolation is primarily responsible for intraspecific genomic divergence within H. niveus, while patterns of phenotypic variation appear to have been shaped by ecological selection and interspecific introgression.
Background. The persistence of protection from meningococcal disease following immunization with serogroup C meningococcal (MenC) glycoconjugate vaccines in infancy is short-lived. The duration of ...protective immunity afforded by these vaccines in other at-risk age groups (i.e., adolescents and young adults) is not known. We evaluated the persistence of bactericidal antibodies following immunization with a MenC glycoconjugate vaccine (MenCV) in adolescents and the kinetics of immune response to a meningococcal AC plain polysaccharide vaccine (MenPS) challenge or a repeat dose of MenCV. Methods. We conducted a randomized comparative trial of 274 healthy 13–15-year-olds from whom a total of 4 blood samples were obtained (prior to administration of a dose of MenPS or MenCV, again on 2 further occasions at varying times from days 2–7 after vaccination, and finally on day 28 after vaccination. The correlate of protection was a serum bactericidal assay titer ⩾8 (with a serum bactericidal assay using human complement). Results. A serum bactericidal assay using human complement titer ⩾8 was observed in 75% of participants at baseline (mean age, 14.5 years; mean time since routine MenCV vaccination, 3.7 years). No increase in serum bactericidal assay geometric mean titers was detected until day 5 after administration of MenPS. Geometric mean titers following administration of MenCV were significantly higher than those observed following administration of MenPS, at days 5, 7, and 28. Conclusions. This study showed sustained levels of bactericidal antibodies for at least 3 years after immunization of adolescents with MenCV. After challenge of immunized adolescents with MenPS, there was no increase in serum bactericidal assay observed until day 5 after vaccination, indicating that immunological memory may be too slow to generate protection against this potentially rapidly invasive organism.
Objective To determine the persistence of bactericidal antibody titres following immunisation with serogroup C meningococcal glycoconjugate vaccine at age 6-15 years in order to examine changes in ...persistence of antibodies with age.Design Observational study.Setting Secondary and tertiary educational institutions in the United Kingdom.Participants Healthy adolescents aged 11-20 years previously immunised between 6 and 15 years of age with one of the three serogroup C meningococcal vaccines.Intervention Serum obtained by venepuncture.Main outcome measures Percentage of participants with (rabbit complement) serum bactericidal antibody titres of at least 1:8; geometric mean titres of serogroup C meningococcal serum bactericidal antibody.Results Five years after immunisation, 84.1% (95% confidence interval 81.6% to 86.3%) of 987 participants had a bactericidal antibody titre of at least 1:8. Geometric mean titres of bactericidal antibody were significantly lower in 11-13 year olds (147, 95% confidence interval 115 to 188) than in 14-16 year olds (300, 237 to 380) and 17-20 year olds (360, 252 to 515) (P<0.0001 for both comparisons). Within these age bands, no significant difference in geometric mean titres of bactericidal antibody between recipients of the different serogroup C meningococcal vaccines was seen. More than 70% of participants had received a vaccine from one manufacturer; in this cohort, geometric mean titres were higher in those immunised at aged 10 years or above than in those immunised before the age of 10.Conclusions Higher concentrations of bactericidal antibody are seen five years after immunisation with serogroup C meningococcal vaccine at age 10 years or above than in younger age groups, possibly owing to immunological maturation. This provides support for adolescent immunisation programmes to generate sustained protection against serogroup C meningococcal disease not only for the vaccine recipients but also, through the maintenance of herd immunity, for younger children.
Rapid waning of anti-polysaccharide bactericidal Ab and vaccine effectiveness is observed following infant immunization with the serogroup C meningococcal (MenC) glycoconjugate vaccine. This is ...despite the demonstrable presence of immunological memory. Persistence of functional Ab, therefore, appears to be the key determinant of MenC conjugate vaccine effectiveness. Ab persistence is thought to depend in the short term on the survival of plasma cells generated during priming and in the longer term on the production of new Ab secreting cells from memory B cells. In this study, we found a strong association between the level of MenC-specific Ab and the frequency of memory B cells measured at 5 mo of age (1 mo after 3-dose primary immunization with MenC conjugate vaccine), and the persistence of functional Ab at one year of age. These findings suggest that these two parameters are good markers of B cell responses to priming and can be used as predictors of long term humoral immunity induced by glycoconjugate vaccines received in early infancy.
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