Predicting and controlling the reactivity of immune cell populations against cancer

Heterogeneous cell populations form an interconnected network that determine their collective output. One example of such a heterogeneous immune population is tumor‐infiltrating lymphocytes (TILs), whose output can be measured in terms of its reactivity against tumors. While the degree of reactivity varies considerably between different TILs, ranging from null to a potent response, the underlying network that governs the reactivity is poorly understood. Here, we asked whether one can predict and even control this reactivity. To address this we measured the subpopulation compositions of 91 TILs surgically removed from 27 metastatic melanoma patients. Despite the large number of subpopulations compositions, we were able to computationally extract a simple set of subpopulation‐based rules that accurately predict the degree of reactivity. This raised the conjecture of whether one could control reactivity of TILs by manipulating their subpopulation composition. Remarkably, by rationally enriching and depleting selected subsets of subpopulations, we were able to restore anti‐tumor reactivity to nonreactive TILs. Altogether, this work describes a general framework for predicting and controlling the output of a cell mixture.     

Sleep/Wake Dynamics Changes during Maturation in Rats

Objectives

Conventional scoring of sleep provides little information about the process of transitioning between vigilance states. We applied the state space technique (SST) using frequency band ratios to follow normal maturation of different sleep/wake states, velocities of movements, and transitions between states of juvenile (postnatal day 34, P34) and young adult rats (P71).

Design

24-h sleep recordings of eight P34 and nine P71 were analyzed using conventional scoring criteria and SST one week following implantation of telemetric transmitter. SST is a non-categorical approach that allows novel quantitative and unbiased examination of vigilance-states dynamics and state transitions. In this approach, behavioral changes are described in a 2-dimensional state space that is derived from spectral characteristics of the electroencephalography.

Measurements and Results

With maturation sleep intensity declines, the duration of deep slow wave sleep (DSWS) and light slow wave sleep (LSWS) decreases and increases, respectively. Vigilance state determination, as a function of frequency, is not constant; there is a substantial shift to higher ratio 1 in all vigilance states except DSWS. Deep slow wave sleep decreases in adult relative to juvenile animals at all frequencies. P71 animals have 400% more trajectories from Wake to LSWS (p = 0.005) and vice versa (p = 0.005), and 100% more micro-arousals (p = 0.021), while trajectories from LSWS to DSWS (p = 0.047) and vice versa (p = 0.033) were reduced by 60%. In both juvenile and adult animals, no significant changes were found in sleep velocity at all regions of the 2-dimensional state space plot; suggesting that maturation has a partial effect on sleep stability.

Conclusions

Here, we present novel and original evidence that SST enables visualization of vigilance-state intensity, transitions, and velocities that were not evident by traditional scoring methods. These observations provide new perspectives in sleep state dynamics and highlight the usefulness of this technique in exploring the development of sleep-wake activity.     

FITNESS CONSEQUENCES OF OUTCROSSING IN A SOCIAL SPIDER WITH AN INBREEDING MATING SYSTEM

Inbreeding mating systems are uncommon because of inbreeding depression. Mating among close relatives can evolve, however, when outcrossing is constrained. Social spiders show obligatory mating among siblings. In combination with a female‐biased sex ratio, sib‐mating results in small effective populations. In such a system, high genetic homozygosity is expected, and drift may cause population divergence. We tested the effect of outcrossing in the social spider Stegodyphus dumicola. Females were mated to sib‐males, to a non‐nestmate within the population, or to a male from a distant population, and fitness traits of F1s were compared. We found reduced hatching success of broods from between‐population crosses, suggesting the presence of population divergence at a large geographical scale that may result in population incompatibility. However, a lack of a difference in offspring performance between inbred and outbred crosses indicates little genetic variation between populations, and could suggest recent colonization by a common ancestor. This is consistent with population dynamics of frequent colonizations by single sib‐mated females of common origin, and extinctions of populations after few generations. Although drift or single mutations can lead to population divergence at a relatively short time scale, it is possible that dynamic population processes homogenize these effects at longer time scales.     

Modified wind chill temperatures determined by a whole body thermoregulation model and human-based facial convective coefficients

Wind chill equivalent temperatures (WCETs) were estimated by a modified Fiala’s whole body thermoregulation model of a clothed person. Facial convective heat exchange coefficients applied in the computations concurrently with environmental radiation effects were taken from a recently derived human-based correlation. Apart from these, the analysis followed the methodology used in the derivation of the currently used wind chill charts. WCET values are summarized by the following equation: $$ \mathrm{WCET}=12.87+0.5334\ast {T}_o-\left(12.66-0.4414\ast {T}_o\right)\ast {U}_{reported}{}^{0.1228} $$ Results indicate consistently lower estimated facial skin temperatures and consequently higher WCETs than those listed in the literature and used by the North American weather services. Calculated dynamic facial skin temperatures were additionally applied in the estimation of probabilities for the occurrence of risks of frostbite. Predicted weather combinations for probabilities of “Practically no risk of frostbite for most people,” for less than 5 % risk at wind speeds above 40 km h^?1, were shown to occur at air temperatures above ?10 °C compared to the currently published air temperature of ?15 °C. At air temperatures below ?35 °C, the presently calculated weather combination of 40 km h^?1/?35 °C, at which the transition for risks to incur a frostbite in less than 2 min, is less conservative than that published: 60 km h^?1/?40 °C. The present results introduce a fundamentally improved scientific basis for estimating facial skin temperatures, wind chill temperatures and risk probabilities for frostbites over those currently practiced.     

Live-Cell Imaging in Caenorhabditis elegans Reveals the Distinct Roles of Dynamin Self-Assembly and Guanosine Triphosphate Hydrolysis in the Removal of Apoptotic Cells

Dynamins are large GTPases that oligomerize along membranes. Dynamin''s membrane fission activity is believed to underlie many of its physiological functions in membrane trafficking. Previously, we reported that DYN-1 (Caenorhabditis elegans dynamin) drove the engulfment and degradation of apoptotic cells through promoting the recruitment and fusion of intracellular vesicles to phagocytic cups and phagosomes, an activity distinct from dynamin''s well-known membrane fission activity. Here, we have detected the oligomerization of DYN-1 in living C. elegans embryos and identified DYN-1 mutations that abolish DYN-1''s oligomerization or GTPase activities. Specifically, abolishing self-assembly destroys DYN-1''s association with the surfaces of extending pseudopods and maturing phagosomes, whereas inactivating guanosine triphosphate (GTP) binding blocks the dissociation of DYN-1 from these membranes. Abolishing the self-assembly or GTPase activities of DYN-1 leads to common as well as differential phagosomal maturation defects. Whereas both types of mutations cause delays in the transient enrichment of the RAB-5 GTPase to phagosomal surfaces, only the self-assembly mutation but not GTP binding mutation causes failure in recruiting the RAB-7 GTPase to phagosomal surfaces. We propose that during cell corpse removal, dynamin''s self-assembly and GTP hydrolysis activities establish a precise dynamic control of DYN-1''s transient association to its target membranes and that this control mechanism underlies the dynamic recruitment of downstream effectors to target membranes.     

A sensitive and selective liquid chromatography/tandem mass spectrometry method for determination of MLN8237 in human plasma

We describe a selective and a highly sensitive high-performance liquid chromatography–electron spray ionization-collision induced dissociation-tandem mass spectrometry (HPLC–ESI-CID-MS/MS) assay for the Aurora A kinase inhibitor MLN8237 in human plasma. The intra-day precision based on the standard deviation of replicates of quality control samples ranged from 0.2 to 4% and with accuracy ranging from 96 to 102%. The inter-day precision ranged from 0.5 to 7% and the accuracy ranged from 93 to 105%. Stability studies showed that MLN8237 was stable both during the expected conditions for sample preparation and storage. The lower limit of quantification for MLN8237 was 5 ng/mL. The analytical method showed excellent sensitivity, precision, and accuracy. This method is robust and is being successfully employed in a Children's Oncology Group Phase 1 Consortium study of MLN8237 in children with cancer.     

Core promoter binding by histone-like TAF complexes

A major function of TFIID is core promoter recognition. TFIID consists of TATA-binding protein (TBP) and 14 TBP-associated factors (TAFs). Most of them contain a histone fold domain (HFD) that lacks the DNA-contacting residues of histones. Whether and how TAF HFDs contribute to core promoter DNA binding are yet unresolved. Here we examined the DNA binding activity of TAF9, TAF6, TAF4b, and TAF12, which are related to histones H3, H4, H2A, and H2B, respectively. Each of these TAFs has intrinsic DNA binding activity adjacent to or within the HFD. The DNA binding domains were mapped to evolutionarily conserved and essential regions. Remarkably, HFD-mediated interaction enhanced the DNA binding activity of each of the TAF6-TAF9 and TAF4b-TAF12 pairs and of a histone-like octamer complex composed of the four TAFs. Furthermore, HFD-mediated interaction stimulated sequence-specific binding by TAF6 and TAF9. These results suggest that TAF HFDs merge with other conserved domains for efficient and specific core promoter binding.