A survey of chromosomal instability measures across mechanistic models

Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, six-centromere FISH, bulk transcriptomics, and single-cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples significantly correlated (R = 0.72; P < 0.001) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also significantly correlate (R = 0.76; P < 0.001) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, scDNAseq detects CIN with high sensitivity, and significantly correlates with imaging methods (R = 0.82; P < 0.001). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate the comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division. This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.

The reckoning of chromosomal instability: past, present, future

Quantitative measures of CIN are crucial to our understanding of its role in cancer. Technological advances have changed the way CIN is quantified, offering increased accuracy and insight. Here, we review measures of CIN through its rise as a field, discuss considerations for its measurement, and look forward to future quantification of CIN.

A survey of CIN measures across mechanistic models

Chromosomal instability (CIN) is the persistent reshuffling of cancer karyotypes via chromosome mis-segregation during cell division. In cancer, CIN exists at varying levels that have differential effects on tumor progression. However, mis-segregation rates remain challenging to assess in human cancer despite an array of available measures. We evaluated measures of CIN by comparing quantitative methods using specific, inducible phenotypic CIN models of chromosome bridges, pseudobipolar spindles, multipolar spindles, and polar chromosomes. For each, we measured CIN fixed and timelapse fluorescence microscopy, chromosome spreads, 6-centromere FISH, bulk transcriptomics, and single cell DNA sequencing (scDNAseq). As expected, microscopy of tumor cells in live and fixed samples correlated well (R=0.77; p<0.01) and sensitively detect CIN. Cytogenetics approaches include chromosome spreads and 6-centromere FISH, which also correlate well (R=0.77; p<0.01) but had limited sensitivity for lower rates of CIN. Bulk genomic DNA signatures and bulk transcriptomic scores, CIN70 and HET70, did not detect CIN. By contrast, single-cell DNA sequencing (scDNAseq) detects CIN with high sensitivity, and correlates very well with imaging methods (R=0.83; p<0.01). In summary, single-cell methods such as imaging, cytogenetics, and scDNAseq can measure CIN, with the latter being the most comprehensive method accessible to clinical samples. To facilitate comparison of CIN rates between phenotypes and methods, we propose a standardized unit of CIN: Mis-segregations per Diploid Division (MDD). This systematic analysis of common CIN measures highlights the superiority of single-cell methods and provides guidance for measuring CIN in the clinical setting.

939 Autocrine/paracrine factors in cancer associated fibroblasts drive immunosuppression through impaired myeloid cell functions

Background

Cancer associated fibroblasts (CAFs) promote tumorigenesis by secreting immunosuppressive cytokines, stimulating angiogenesis, and supporting the growth of tumor cells. Through their interactions with immune cells, CAFs are known to directly impact the functionality of T cells and macrophages. However, CAF interaction with dendritic cells (DCs) and DC progenitor cells and its impact on DC function is relatively understudied and was the main focus of this study.

Methods

Two types of coculture systems were used in this study. For the human system, fibroblasts from lung squamous cell carcinoma (LUSC) were cocultured with MUTZ3 cells (hematopoietic progenitor cells) in the presence of DC differentiation stimuli, sometimes followed by DC maturation stimuli. For the mouse coculture system, activated (YPSC-c) and inactivated (PSC-b) pancreatic stellate cells (PSCs) were isolated from the pancreas of C57BL/6 mice by the density gradient method and co-cultured in the presence of bone marrow cells in the presence of DC differentiation and maturation stimuli. For human tumor antigen processing and cross presentation assay MART1 peptide (10mer and 20mer) was used.

Results

Co-culture of human and murine hematopoietic progenitor cells with fibroblasts (human LUSC CAFs and murine PSC results in decrease in differentiation and maturation of DCs. DCs differentiated and matured in the presence of fibroblasts have impaired ability to process and present tumor antigen to T cells. In the presence of PSC fibroblasts DC differentiation from murine bone marrow cells is skewed more towards MDSC and macrophages. In contrast to inactivated PSC-b, activated PSC-c influence DC differentiation in a contact dependent manner. Furthermore, PSC-b and PSC-c show transcriptionally distinct signatures which translate to unique secretory profiles as measured by Luminex. Analysis of the conditioned media from the coculture demonstrated that PSC-c secrete (among others) CXCL1, IL6, and CCL5 chemo/cytokines. These and other factors may play an important role in mediating fibroblast induced suppression of DC differentiation from monocytes.

Conclusions

Our study demonstrates that cancer associated fibroblasts, or their precursors directly impact DC differentiation and antigen presentation via cytokines that could be targeted therapeutically to improve DC expansion and activity in the tumor microenvironment.

A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer

Mass cytometry is a powerful tool for high-dimensional single cell characterization. Since the introduction of the first commercial CyTOF mass cytometer by DVS Sciences in 2009, mass cytometry technology has matured and become more widely utilized, with sequential platform upgrades designed to address specific limitations and to expand the capabilities of the platform. Fluidigm's third-generation Helios mass cytometer introduced a number of upgrades over the previous CyTOF2. One of these new features is a modified narrow bore sample injector that generates smaller ion clouds, which is expected to improve sensitivity and throughput. However, following rigorous testing, we find that the narrow-bore sample injector may have unintended negative consequences on data quality and result in lower median and higher coefficients of variation in many antibody-associated signal intensities. We describe an alternative Helios acquisition protocol using a wider bore injector, which largely mitigates these data quality issues. We directly compare these two protocols in a multisite study of 10 Helios instruments across 7 institutions and show that the modified protocol improves data quality and reduces interinstrument variability. These findings highlight and address an important source of technical variability in mass cytometry experiments that is of particular relevance in the setting of multicenter studies. © 2019 International Society for Advancement of Cytometry.

Bacteria transport and deposition under unsaturated conditions: the role of the matrix grain size and the bacteria surface protein

Unsaturated (80% water saturated) packed column experiments were conducted to investigate the influence of grain size distribution and bacteria surface macromolecules on bacteria (Rhodococcus rhodochrous) transport and deposition mechanisms. Three sizes of silica sands were used in these transport experiments, and their median grain sizes were 607, 567, and 330 microm. The amount of retained bacteria increased with decreasing sand size, and most of the deposited bacteria were found adjacent to the column inlet. The deposition profiles were not consistent with predictions based on classical filtration theory. The experimental data could be accurately characterized using a mathematical model that accounted for first-order attachment, detachment, and time and depth-dependent straining processes. Visual observations of the bacteria deposition as well as mathematical modelling indicated that straining was the dominant mechanism of deposition in these sands (78-99.6% of the deposited bacteria), which may have been enhanced due to the tendency of this bacterium to form aggregates. An additional unsaturated experiment was conducted to better deduce the role of bacteria surface macromolecules on attachment and straining processes. In this case, the bacteria surface was treated using a proteolitic enzyme. This technique was assessed by examining the Fourier-transform infrared spectrum and hydrophobicity of untreated and enzyme treated cells. Both of these analytical procedures demonstrated that this enzymatic treatment removed the surface proteins and/or associated macromolecules. Transport and modelling studies conducted with the enzyme treated bacteria, revealed a decrease in attachment, but that straining was not significantly affected by this treatment.

In vitro transposon mutagenesis of an equine herpesvirus 1 genome cloned as a bacterial artificial chromosome

The 150-kbp genome of the alphaherpesvirus equine herpesvirus 1 (EHV-1) strain HVS25A was cloned as a bacterial artificial chromosome (EHV-1 BAC), with mini F plasmid sequences inserted between genes 62 and 63. Transfection of EHV-1 BAC DNA purified from E. coli gave rise to progeny virus that had a similar growth rate and yield in mammalian cell culture to those of parental wild-type EHV-1. Using in vitro mutagenesis with a Mu transposon, a large library of EHV-1 BAC mutants was generated, and sequence analysis indicated that insertions were dispersed randomly across the EHV-1 genome. Following transfections of a pilot sample of mutant EHV-1 BAC DNAs into mammalian cells, no CPE was observable by light microscopy for mutants carrying insertions in genes for the major capsid protein, large tegument protein, glycoprotein K, catalytic subunit of DNA polymerase, or single-stranded DNA-binding protein. Mutants that were able to produce CPE similar to wild-type EHV-1 included those with interruptions in ORFs of several tegument proteins. Analysis of several glycoprotein gene mutants indicated that those carrying insertions near the start of genes encoding glycoproteins E and I were viable, but showed markedly diminished plaque areas. These results were supported by confocal microscopy of transfected or infected cultures. Electron microscopy of cells infected with a gE mutant revealed accumulations of particles within cytoplasmic vesicles, consistent with a partial obstruction of maturation. The transposon library is a resource for comprehensive functional analysis of the HVS25A genome, with multiple mutants available in any of the predicted genes of EHV-1.

Managing chronic headaches in the clinic

Chronic daily headache (CDH), which is often linked to a history of migraine, tension-type headache and the abuse of headache medications, and cluster headache are the best known of the chronic headaches. These headaches may not be well recognised or well treated in primary care. This article outlines the development of management algorithms for these headache subtypes, designed for use by the primary care physician with an interest in headache. Principles of care for chronic headaches include implementation of screening procedures, differential diagnosis, tailoring of management to the individual's needs, proactive follow-up and a team approach to care. These principles can be customised to the headache subtype by the selection of appropriate therapies. The optimal treatments for CDH include physical therapy to the neck if there is any stiffness there, withdrawal of abused medications and treatment of any subsequent withdrawal symptoms and headache prophylaxis, together with the provision of acute medications as rescue therapy. Optimal treatments for cluster headache include short- and long-term prophylaxis to prevent the headaches developing and acute medications for use as rescue. If treatment is ineffective, alternative medications can be provided at follow-up, with the possibility of referral for refractory patients.

Bcl-2 inhibits cell death of serum-free mouse embryo cells caused by epidermal growth factor deprivation

SFME cells are brain-derived neural precursor cells that are acutely dependent on epidermal growth factor (EGF) for survival, undergoing apoptosis within 24 h after EGF withdrawal. Because the expression of the protooncogene bcl-2 inhibits apoptosis induced by the withdrawal of interleukins or nerve growth factor in some growth factor-dependent haematopoietic or neuronal cell cultures, we examined the effect of Bcl-2 expression on cell death of SFME cells in the absence of EGF. SFME cells expressing human Bcl-2 showed prolonged survival when deprived of EGF compared to control cells not expressing Bcl-2. A significant fraction of Bcl-2-expressing cells remained viable for 4 days in the absence of EGF and resumed proliferation upon readdition of EGF to the cultures. These results suggest that apoptosis induced by EGF withdrawal in SFME cells may share common mechanisms with other growth factor-related apoptotic systems.

Familiarity Norms for the Boston Naming Test Stimuli

Forty-nine young adults (M age = 22 years) and 30 elderly adults (M age = 69 years) rated the 60 pictorial stimuli from the Boston Naming Test (BNT) on familiarity, providing the first such normative data for these stimuli along this dimension. Participants also made speeded lexical decisions about the word item representations of each BNT picture. B NT word frequency values were also examined in relation to BNT familiarity and speeded lexical decision performance. For both young and elderly adults, lexical decision reaction times to the word representations of BNT stimuli were negatively related to word frequency and familiarity of the BNT pictures. These patterns suggest that increases in word frequency and picture familiarity facilitate (i. e., speed up) the processing of BNT word representations. Furthermore, speed of processing appears to be a relevant dimension of BNT performance, at least when young and elderly adults free from clinical aphasia are involved.

Cloning, sequencing, and embryonic expression of an N-ras proto-oncogene isolated from an enriched zebrafish (Danio rerio) cDNA library

An enriched zebrafish (Danio rerio) complementary DNA library was constructed for screening of ras-related genes, and a positive clone was isolated from one plate of 3 x 10(4) plaques. This clone, Zras-B1, carried an insert of 2592 base pairs (bp) with an open reading frame encoding a ras p21 protein of 188 amino acids. The deduced amino-terminal 86 amino acid residues and the carboxy-terminal CAAX binding motif are identical to mammalian ras. The full-length Zras-B1-encoded protein is most closely related to human N-ras (91% identity), with lesser homology to Ha-ras (84%) and Ki-ras (85%). Preliminary screening data also indicate other ras genes in zebrafish, at least one of which is also transcribed in adults. A Zras-B1-related 3.1-kb transcript was found to be abundant in embryos from zygote through gastrulation, and may be maternally derived.

Graft surveillance and angioplasty prolongs dialysis graft patency

BACKGROUND

In the United States of America, vascular access complications are the most frequent cause of death among patients with end-stage renal disease on hemodialysis. The majority of American patients with end-stage renal disease have prosthetic grafts for access. The most common complication of prosthetic graft fistulas is thrombosis. To prolong graft life and decrease the frequency of operations, a university-based dialysis unit adopted a policy of graft surveillance by measuring venous resistance, followed by fistulagram and percutaneous dilatation of identified stenoses. The purpose of this retrospective study is to determine if this policy affected graft patency and graft life.

STUDY DESIGN

This retrospective review compares outcomes for two years before adoption of this policy (control group, 210 patients) with the outcomes for three years after adoption (study group, 260 patients). Fifty (24 percent) of the control group and 71 (27 percent) of the study group were defined as "complicated" patients because they underwent more than one intervention over any 12-month period.

RESULTS

The 50 complicated patients in the control group underwent 104 operations for thrombosis over two years, 1.04 thrombotic episodes and operations per patient year. Seventy new grafts were placed with a mean primary patency of 3.9 months. Mean graft survival time was 6.3 months. The 71 complicated patients in the study group underwent 111 fistulagrams, 80 angioplasties, and 110 operations over three years, for 0.52 thrombotic episodes per patient year (p < .001). Forty-five new grafts were placed with a primary patency of 11.5 months (p < .001). Mean graft survival time was 15.8 months (p < .001).

CONCLUSIONS

This retrospective study demonstrates the effectiveness of a policy of graft surveillance and percutaneous treatment of graft stenosis in prolonging primary surgical patency and graft survival.

A clinician looks at androgen resistance

Androgen resistance in genetic males occurs when gonadotropins and testosterone are normal, but the physiological androgen response in androgen target organs is absent or decreased. In androgen-dependent target tissues two main defects may be found: 1) defective testosterone metabolism (5 alpha-reductase type 2 deficiency) and 2) anomalies in androgen receptors (androgen insensitivity syndrome (AIS)). The clinical manifestations of these defects vary from subjects with female external genitalia to subjects with mild forms of impaired masculinization. In particular, in the complete form of AIS (CAIS) the phenotype is feminine, and in the partial form (PAIS) the external genitalia are ambiguous with an extremely variable phenotype. The diagnosis requires clinical, hormonal, genetic, and molecular investigation for appropriate gender assignation and treatment. In AIS, cloning of androgen receptor cDNA using the polymerase chain reaction, denaturing gradient gel electrophoresis, and nucleotide sequencing have enabled a variety of molecular defects in the androgen receptor to be identified. The complexity of phenotypic presentation of AIS probably reflects the heterogeneity of androgen receptor gene mutations, but to date a relationship between genotype/phenotype has been difficult to establish, with the same point mutation reported to be associated with different phenotypic expressions. Other factors must therefore also contribute to the clinical presentation of AIS, although none have yet been identified. Establishing the functional consequences of androgen receptor mutations in vitro systems and correlating them with clinical presentation may ultimately provide an explanation for the variable clinical presentation of AIS and perhaps enable prediction of the response to androgen therapy in infants with PAIS.

Meeting the health promotion challenge through a model of shared responsibility

AT&T's Total Life Concept (TLC) program has incorporated a multidimensional strategy for health promotion that attempts to avoid the pitfalls of a unifocal individual approach. Combining individual, organizational, and environmental health promotion efforts, TLC has adopted an "ecological" model, which is described in this chapter. The central philosophy that unifies these three dimensions is a "shared responsibility" for health care.

Peroxidase-Induced Wilting in Transgenic Tobacco Plants

Peroxidases are a family of isoenzymes found in all higher plants. However, little is known concerning their role in growth, development, or response to stress. Plant peroxidases are heme-containing monomeric glycoproteins that utilize either H2O2 or O2 to oxidize a wide variety of molecules. To obtain more information on possible in planta functions of peroxidases, we have used a cDNA clone for the primary isoenzyme form of peroxidase to synthesize high levels of this enzyme in transgenic plants. We were able to obtain Nicotiana tabacum and N. sylvestris transformed plants with peroxidase activity that is 10-fold higher than in wild-type plants by introducing a chimeric gene composed of the cauliflower mosaic virus 35S promoter and the tobacco anionic peroxidase cDNA. The elevated peroxidase activity was a result of increased levels of two anionic peroxidases in N. tabacum, which apparently differ in post-translational modification. Transformed plants of both species have the unique phenotype of chronic severe wilting through loss of turgor in leaves, which was initiated at the time of flowering. The peroxidase-induced wilting was shown not to be an effect of diminished water uptake through the roots, decreased conductance of water through the xylem, or increased water loss through the leaf surface or stomata. Possible explanations for the loss of turgor, and the significance of these types of experiments in studying isoenzyme families, are discussed.

Peroxidase-Induced Wilting in Transgenic Tobacco Plants

Peroxidases are a family of isoenzymes found in all higher plants. However, little is known concerning their role in growth, development, or response to stress. Plant peroxidases are heme-containing monomeric glycoproteins that utilize either H2O2 or O2 to oxidize a wide variety of molecules. To obtain more information on possible in planta functions of peroxidases, we have used a cDNA clone for the primary isoenzyme form of peroxidase to synthesize high levels of this enzyme in transgenic plants. We were able to obtain Nicotiana tabacum and N. sylvestris transformed plants with peroxidase activity that is 10-fold higher than in wild-type plants by introducing a chimeric gene composed of the cauliflower mosaic virus 35S promoter and the tobacco anionic peroxidase cDNA. The elevated peroxidase activity was a result of increased levels of two anionic peroxidases in N. tabacum, which apparently differ in post-translational modification. Transformed plants of both species have the unique phenotype of chronic severe wilting through loss of turgor in leaves, which was initiated at the time of flowering. The peroxidase-induced wilting was shown not to be an effect of diminished water uptake through the roots, decreased conductance of water through the xylem, or increased water loss through the leaf surface or stomata. Possible explanations for the loss of turgor, and the significance of these types of experiments in studying isoenzyme families, are discussed.

Affinity fractionation and characterization of chick brain synaptosomes

Chick brain synaptosomes were fractionated by affinity chromatography on concanavalin A-Sepharose. Three subfractions were obtained. One, designated UBF, was not bound to the affinity adsorbent and represented 36% of the total synaptosomal protein treated with the beads. A second fraction, designated BF1, adhered to concanavalin A-Sepharose exclusively through its carbohydrate recognition site. The third fraction, called BF2, bound to the beads through hydrophobic interactions and represented about 20% of the total synaptosomal protein. About 20% of the total synaptosomal protein was found to be retarded on three ligand-less gels, with potential for only hydrophobic interactions. This binding can be reversed, however, by ethylene glycol, a result indicating hydrophobic binding sites on the synaptosomes. Enzyme marker studies and electron microscopy showed differences between UBF, BF1, and BF2, mainly with respect to mitochondrial contamination. Binding studies with [3H]-Con A show the absence of Con A-specific carbohydrates from the surface of UBF or BF2. As expected strong and specific binding between [3H]-Con A and [3H] BF1 was observed. These findings are discussed in relation to a model for the interior working of the synaptosomes.

Predictors of mortality in alcoholic women: prospective follow-up study

An 11-year follow-up of 100 alcoholic women who were systematically interviewed and diagnosed during hospitalization found 31% dead, the majority as a result of alcohol-related causes. There were over 4 times as many deaths in alcoholic women as expected in the general population. The life span of alcoholic women was shortened by over 15 years. Only those women who had abstained during the interval following hospitalization had fewer than expected deaths. Five variables correctly predicted survival status for 79% of the subjects (80% of survivors and 77% of those who died): older age at index, onset of alcoholism before age 30, history of frequent benders, primary diagnosis of antisocial personality, and short-term drinking status.

Synthesis of bacterial flagella. I. Requirement for protein and ribonucleic acid synthesis during flagellar regeneration in Bacillus subtilis

A relatively simple immunochemical procedure for estimating flagellar protein was developed. This procedure involved measuring the binding of purified, radioactively labeled, antiflagellar antibodies to bacteria. The assay was used to determine the requirements for ribonucleic acid (RNA) and protein synthesis during flagellar regeneration in Bacillus subtilis. Immediate inhibition of flagella development was observed when chloramphenical or puromycin was added to cells. This inhibition indicated the absence of a large pool of flagella precursors that could be assembled in the absence of protein synthesis. When the cells were starved for uracil or treated with actinomycin D to inhibit RNA synthesis, the ability of the cells to regenerate flagella decayed with a half-life of 5.5 min. When B. subtilis auxotrophs were starved for tryptophan, they continued to synthesize flagella, although this process was also inhibited by actinomycin D. On the basis of these results, we concluded that (i) the system involved in flagellar regeneration does not have unusual metabolic stability, (ii) regeneration requires both concomitant protein and RNA syntheses, and (iii) B. subtilis continues to synthesize messenger RNA during tryptophan starvation.

Attention in the newborn: Effect on motility and skin potential

Newborn infants showed lower motility and greater reactivity of the skin potential while attending to a visual target than when equally alert but inattentive.