Mapping the adult human esophagus in vivo and in vitro

Many esophageal diseases can arise during development or throughout life. Therefore, well-characterized in vitro models and detailed methods are essential for studying human esophageal development, homeostasis and disease. Here, we (1) create an atlas of the cell types observed in the normal adult human esophagus; (2) establish an ancestrally diverse biobank of in vitro esophagus tissue to interrogate homeostasis and injury; and (3) benchmark in vitro models using the adult human esophagus atlas. We created a single-cell RNA sequencing reference atlas using fresh adult esophagus biopsies and a continuously expanding biobank of patient-derived in vitro cultures (n=55 lines). We identify and validate several transcriptionally distinct cell classes in the native human adult esophagus, with four populations belonging to the epithelial layer, including basal, epibasal, early differentiating and terminally differentiated luminal cells. Benchmarking in vitro esophagus cultures to the in vivo reference using single-cell RNA sequencing shows that the basal stem cells are robustly maintained in vitro, and the diversity of epithelial cell types in culture is dependent on cell density. We also demonstrate that cultures can be grown in 2D or as 3D organoids, and these methods can be employed for modeling the complete epithelial layers, thereby enabling in vitro modeling of the human adult esophagus.

May the Odds Be Ever in Your Favor: Non-deterministic Mechanisms Diversifying Cell Surface Molecule Expression

How does the information in the genome program the functions of the wide variety of cells in the body? While the development of biological organisms appears to follow an explicit set of genomic instructions to generate the same outcome each time, many biological mechanisms harness molecular noise to produce variable outcomes. Non-deterministic variation is frequently observed in the diversification of cell surface molecules that give cells their functional properties, and is observed across eukaryotic clades, from single-celled protozoans to mammals. This is particularly evident in immune systems, where random recombination produces millions of antibodies from only a few genes; in nervous systems, where stochastic mechanisms vary the sensory receptors and synaptic matching molecules produced by different neurons; and in microbial antigenic variation. These systems employ overlapping molecular strategies including allelic exclusion, gene silencing by constitutive heterochromatin, targeted double-strand breaks, and competition for limiting enhancers. Here, we describe and compare five stochastic molecular mechanisms that produce variety in pathogen coat proteins and in the cell surface receptors of animal immune and neuronal cells, with an emphasis on the utility of non-deterministic variation.

UBCH5 Family Members Differentially Impact Stabilization of Mutant p53 via RNF128 Iso1 During Barrett's Progression to Esophageal Adenocarcinoma

BACKGROUND & AIMS

TP53 mutations underlie Barrett's esophagus (BE) progression to dysplasia and cancer. During BE progression, the ubiquitin ligase (E3) RNF128/GRAIL switches expression from isoform 2 (Iso2) to Iso1, stabilizing mutant p53. However, the ubiquitin-conjugating enzyme (E2) that partners with Iso1 to stabilize mutant p53 is unknown.

METHODS

Single-cell RNA sequencing of paired normal esophagus and BE tissues identified candidate E2s, further investigated in expression data from BE to esophageal adenocarcinoma (EAC) progression samples. Biochemical and cellular studies helped clarify the role of RNF128-E2 on mutant p53 stability.

RESULTS

The UBE2D family member 2D3 (UBCH5C) is the most abundant E2 in normal esophagus. However, during BE to EAC progression, loss of UBE2D3 copy number and reduced expression of RNF128 Iso2 were noted, 2 known p53 degraders. In contrast, expression of UBE2D1 (UBCH5A) and RNF128 Iso1 in dysplastic BE and EAC forms an inactive E2-E3 complex, stabilizing mutant p53. To destabilize mutant p53, we targeted RNF128 Iso1 either by mutating asparagine (N48, 59, and 101) residues to block glycosylation to facilitate β-TrCP1-mediated degradation or by mutating proline (P54 and 105) residues to restore p53 polyubiquitinating ability. In addition, either loss of UBCH5A catalytic activity, or disruption of the Iso1-UBCH5A interaction promoted Iso1 loss. Consequently, overexpression of either catalytically dead or Iso1-binding-deficient UBCH5A mutants destabilized Iso1 to degrade mutant p53, thus compromising the clonogenic survival of mutant p53-dependent BE cells.

CONCLUSIONS

Loss of RNF128 Iso2-UBCH5C and persistence of the Iso1-UBCH5A complex favors mutant p53 stability to promote BE cell survival. Therefore, targeting of Iso1-UBCH5A may provide a novel therapeutic strategy to prevent BE progression.

Developmentally regulated cell cycle dependence of swelling-activated anion channel activity in the mouse embryo

Anion channels activated by increased cell volume are a nearly ubiquitous mechanism of cell volume regulation, including in early preimplantation mouse embryos. Here, we show that the swelling-activated anion current (ICl,swell) in early mouse embryos is cell-cycle dependent, and also that this dependence is developmentally regulated. ICl,swell is present both in first meiotic prophase (germinal vesicle stage) mouse oocytes and in unfertilized mature oocytes in second meiotic metaphase, and it persists after fertilization though the 1-cell and 2-cell stages. ICl,swell was found to remain unchanged during metaphase at the end of the 1-cell stage. However, ICl,swell decreased during prophase and became nearly undetectable upon entry into metaphase at the end of the 2-cell stage. Entry into prophase/metaphase was required for the decrease in ICl,swell at the end of the 2-cell stage, since it persisted indefinitely in 2-cell embryos arrested in late G2. There is considerable evidence that the channel underlying ICl,swell is not only permeable to inorganic anions, but to organic osmolytes as well. We found a similar pattern of cell cycle and developmental dependence in the 1-cell and 2-cell stages for the swelling-induced increase in permeability to the organic osmolyte glycine. Thus, entry into metaphase deactivates ICl,swell in embryos, but only after developmental progression through the 2-cell stage.

The misclassification of blinks as saccades: implications for investigations of eye movement dysfunction in schizophrenia

It is important to have a simple. accurate method for recording eye movements. Of the two popular approaches commonly adopted, electro-oculography (EOG) and infrared oculography (IROG), IROG is often accepted as the more accurate, and it is the method that is currently used most frequently to examine eye movements in schizophrenia. This study investigated whether the misclassification of blinks as saccades affects saccade rates when the presence of a blink is determined using only IROG recordings of eye position. Both vertical electro-oculography (VEOG), which can be used to objectively identify blinks, and IROG were recorded while 17 schizophrenia patients and 19 healthy controls were presented with sinusoidal stimuli. Of the blinks identified with the VEOG for the total group of participants, a substantial number (37%) were misclassified as catch-up and anticipatory saccades when only the IROG was used. Furthermore, in the schizophrenia group, but not in the healthy control group, the use of the IROG led to a significant misclassification of blinks as anticipatory saccades. Therefore, when IROG alone is used to identify blinks, the misclassification of blinks as saccades is likely to introduce measurement error into estimates of saccade rates, particularly estimates of anticipatory saccade rates in schizophrenia patients.

Heritability of different measures of smooth pursuit eye tracking dysfunction: a study of normal twins

Research studies have found that smooth pursuit eye movement dysfunction may serve as an index of genetic liability to develop schizophrenia. The heritability of various measures of smooth pursuit eye tracking proficiency and the saccades that occur during smooth pursuit was examined in 64 monozygotic (MZ) and 48 dizygotic (DZ) twin pairs. Two age cohorts were assessed (11-12 and 17-18 years of age). Intraclass correlations indicated significant similarity in the MZ twins for almost all measures in both age cohorts, whereas few of the DZ twin correlations attained significance. Biometrical modeling indicated that genetic mechanisms influence performance on both global and specific eye tracking measures, accounting for about 40% to 60% of the variance. These findings suggest that the underlying brain systems responsible for smooth pursuit and saccade generation during pursuit are under partial genetic control.

Glycine transport by single human and mouse embryos

Mouse zygotes and early cleavage-stage embryos have previously been shown to utilize glycine as an organic osmolyte, accumulating it to oppose any decrease in cell volume. Such glycine uptake in early cleavage-stage mouse embryos is via the glycine-specific Gly transporter. Mouse embryos also possess swelling-activated channels which function to release osmotically active glycine and other osmolytes when cell volume becomes too large. In this study it was found that human cleavage-stage embryos also transported glycine via a similarly saturable, sarcosine-inhibitable transporter, implying that the Gly transporter also mediates glycine transport in human embryos. Mouse zygotes have previously been shown to accumulate more intracellular glycine when cultured at increased osmolarities for 24 h. It was found in the current study that this ability was lost as preimplantation mouse embryo development proceeded, and that early cleavage-stage human embryos may also be capable of such osmosensitive accumulation of glycine. Finally, using spare human eggs which had failed to fertilize or cleave, the presence of swelling-activated currents resembling those in mouse zygotes was demonstrated. These data indicate that osmoregulation in early human embryos occurs via similar mechanisms as in the mouse.

Fine-grained auditory discrimination: factor structures

This research tested the hypothesis that as children's language development matures, factor-analytic structural changes occur that are associated with measurements of fine-grained auditory discrimination, receptive vocabulary, receptive language, speech production, and three performance subtests of the WISC-R. Among 6- to 7-year-old children, the percent of total variance attributed to the factor defined by fine-grained auditory discrimination measures was approximately 43% for children who were intellectually impaired (Experiment 2), 27% for youngsters who had language-learning problems, and 16% for regularly progressing children (Experiment 1). The WISC-R subtest scores, generally, did not load on the auditory discrimination factor. The difference in variance explained by the auditory discrimination factor was interpreted as representing greater relative importance of auditory discrimination among children with less-well-developed language competencies than among children with more mature language skills. This interpretation was strengthened by the finding of no distinct auditory discrimination factor for 8- to 11-year-old children who were either regularly progressing or language-disabled even though the language/speech factor at this age closely resembled that found among younger children. Results were consonant with Ackerman's (1987) model, suggesting that task-specific variance associated with tasks that remain resource-dependent may diminish after practice and experience.

Discrimination of second-format-like frequency transitions

Discrimination of two types of simulated single-second-format frequency transitions was studied, transitions where members of a stimulus set shared the same onset frequency and transitions where stimuli of a set shared the same offset frequency. Experiment 1 employed an adaptive procedure to measure just-noticeable differences for transitions that increased in frequency. Experiment 2 obtained complete psychometric functions, based on a three-interval, forced-choice procedure, for transitions that either increased or decreased in frequency. In both experiments, better discrimination occurred for longer stimuli, measured in hertz/millisecond, and for transitions that shared the same onset frequency. There were no differences, in Experiment 2, between discrimination of rising and falling transitions. Results are considered from several theoretical perspectives.

Fine-grained auditory discrimination and performance on tests of receptive vocabulary and receptive language

This research investigated the relation between children's performance on two measures of receptive language and children's auditory discrimination of consonant-vowel sounds having frequency and temporal acoustic differences. The measures of fine-grained auditory discrimination produced significant multiple regression coefficients against both receptive vocabulary (Peabody Picture Vocabulary Test-Revised) and receptive language (Token Test for Children) scores. Validation analyses conducted by predicting receptive vocabulary and language scores for a new sample of children and relating them to the actual scores led to significant outcomes. It was concluded that fine-grained auditory discrimination is particularly important in the relatively early stages of language learning.

Age differences in discrimination of simulated single-formant frequency transitions

We studied auditory discrimination of simulated single-formant frequency transitions that resembled portions of certain speech consonants. Significant age differences in transition discrimination occurred; both children and older adults required larger acoustic differences between transitions for discrimination than did teenagers/young adults. Longer transitions were more easily discriminated than shorter transitions by all listeners, and there were no differences between discriminations of rising and falling transitions. Teens/young adults and older adults, but not children, required larger frequency differences to discriminate frequency transitions followed by a steady-state sound than for transitions alone. There were also age differences in discrimination of steady-state sounds. These developmental-perceptual differences may help explain why children and older adults who have good pure-tone sensitivity may experience difficulty in understanding speech.

Longitudinal changes in auditory discrimination in normal children and children with language-learning problems

Two groups of children--one progressing normally in school and the other exhibiting language-learning problems--were tested in each of 3 years on a set of fine-grained auditory discrimination tasks that required listening for small acoustic differences. Children's ages ranged from 6 to 9 years; there were 21 children per group. The children with language-learning problems, despite having normal intelligence and normal pure-tone sensitivity, showed poorer auditory discrimination than normal children for temporally based acoustic differences. This effect continued across the 3 years. Children with language-learning problems also exhibited poorer receptive vocabulary and language performance as well as more deviations from standard Midwest articulation than children making normal progress in school. All children had hearing within the normal range, but at some frequencies there was a significant association of pure-tone sensitivity with performance on the auditory discrimination, receptive language, and speech production tasks.