A multiplexed assay for quantifying immunomodulatory proteins supports correlative studies in immunotherapy clinical trials

Introduction

Immunotherapy is an effective treatment for a subset of cancer patients, and expanding the benefits of immunotherapy to all cancer patients will require predictive biomarkers of response and immune-related adverse events (irAEs). To support correlative studies in immunotherapy clinical trials, we are developing highly validated assays for quantifying immunomodulatory proteins in human biospecimens.

Methods

Here, we developed a panel of novel monoclonal antibodies and incorporated them into a novel, multiplexed, immuno-multiple reaction monitoring mass spectrometry (MRM-MS)-based proteomic assay targeting 49 proteotypic peptides representing 43 immunomodulatory proteins.

Results and discussion

The multiplex assay was validated in human tissue and plasma matrices, where the linearity of quantification was >3 orders of magnitude with median interday CVs of 8.7% (tissue) and 10.1% (plasma). Proof-of-principle demonstration of the assay was conducted in plasma samples collected in clinical trials from lymphoma patients receiving an immune checkpoint inhibitor. We provide the assays and novel monoclonal antibodies as a publicly available resource for the biomedical community.

Metapopulation dynamics and the quality of the matrix

In both strictly theoretical and more applied contexts it has been historically assumed that metapopulations exist within a featureless, uninhabitable matrix and that dynamics within the matrix are unimportant. In this article, we explore the range of theoretical consequences that result from relaxing this assumption. We show, with a variety of modeling techniques, that matrix quality can be extremely important in determining metapopulation dynamics. A higher-quality matrix generally buffers against extinction. However, in some situations, an increase in matrix quality can generate chaotic subpopulation dynamics, where stability had been the rule in a lower-quality matrix. Furthermore, subpopulations acting as source populations in a low-quality matrix may develop metapopulation dynamics as the quality of the matrix increases. By forcing metapopulation dynamics on a formerly heterogeneous (but stable within subpopulations) population, the probability of simultaneous extinction of all subpopulations actually increases. Thus, it cannot be automatically assumed that increasing matrix quality will lower the probability of global extinction of a population.

Effects of predatory ants on lower trophic levels across a gradient of coffee management complexity

1. Ants are important predators in agricultural systems, and have complex and often strong effects on lower trophic levels. Agricultural intensification reduces habitat complexity, food web diversity and structure, and affects predator communities. Theory predicts that strong top-down cascades are less likely to occur as habitat and food web complexity decrease. 2. To examine relationships between habitat complexity and predator effects, we excluded ants from coffee plants in coffee agroecosystems varying in vegetation complexity. Specifically, we studied the effects of eliminating ants on arthropod assemblages, herbivory, damage by the coffee berry borer and coffee yields in four sites differing in management intensification. We also sampled ant assemblages in each management type to see whether changes in ant assemblages relate to any observed changes in top-down effects. 3. Removing ants did not change total arthropod densities, herbivory, coffee berry borer damage or coffee yields. Ants did affect densities of some arthropod orders, but did not affect densities of different feeding groups. The effects of ants on lower trophic levels did not change with coffee management intensity. 4. Diversity and activity of ants on experimental plants did not change with coffee intensification, but the ant species composition differed. 5. Although variation in habitat complexity may affect trophic cascades, manipulating predatory ants across a range of coffee agroecosystems varying in management intensity did not result in differing effects on arthropod assemblages, herbivory, coffee berry borer attack or coffee yields. Thus, there is no clear pattern that top-down effects of ants in coffee agroecosystems intensify or dampen with decreased habitat complexity.

Increased competition may promote species coexistence

It is a mainstay of community ecology that local exclusion of species will result if competitive pressures become too large. The pattern of exclusion may be complicated, but the qualitative orthodoxy has changed little since the pioneering work of Lotka, Volterra, and Gause--no two species can occupy the same niche. Stated in a more precise form, the higher the intensity of interspecific competition in an assemblage of species, the fewer the number of species that can coexist in perpetuity. We suggest that this orthodoxy results from "linear" thinking, and that if the classical equations are formulated more realistically with attendant nonlinearities, the orthodoxy breaks down and higher levels of competition may actually increase the likelihood that species will avoid competitive exclusion. Furthermore, this increased probability of coexistence at higher levels of competition is accompanied by characteristic dynamic patterns: (i) at lower levels of competition, after all extinction events have occurred, remaining species follow irregular chaotic patterns; (ii) at higher levels of competition, when most species coexist, all species are entrained in a single large limit cycle; (iii) the transient behavior appears to correspond to a special case of chaos, uniform phase chaotic amplitude.

Hurricane disturbance and tropical tree species diversity

The debate over the maintenance of high diversity of tree species in tropical forests centers on the role of tree-fall gaps as a primary source of disturbance. Using a 10-year data series accumulated since Hurricane Joan struck the Caribbean coast of Nicaragua in 1988, we examined the pattern of species accumulation over time and with increased sampling of individuals. Our analysis shows that the pattern after a hurricane differs from the pattern after a simple tree-fall disturbance, and we conclude that pioneers are limited in large disturbances and thus do not suppress other species the way they do in smaller disturbances.

Follow-up of rape victims in a family practice setting

Health care for rape victims traditionally has been crisis oriented, focused solely upon the victim, and provided either by a gynecologist or psychiatrist. A family practice health team, working in a county hospital, offered rape victims and their families crisis counseling in the emergency room, and follow-up care in a family practice clinic. Follow-up of victims markedly increased from 8% before initiation of the program to 86% afterward. Family members of more than half of the victims seen on follow-up received treatment. A wide range of health needs of both victims and their families, not identified in the emergency room, was identified on follow-up visits. In this way emergency care of the rape victim often became an entry point into the health care system. Rape must be viewed as a family's as well as victim's health problem, often demanding a broader service than can be offered by a gynecologist or psychiatrist alone.

Mechanism of protein chain termination: further characterization of a mutant defective in a new protein synthesis factor

Mutant N4316 is conditionally lethal at 43 degrees . At 36 degrees it suppresses the termination codons UGA and UAA, but not the UAG codon or a missense mutant of T4 bacteriophage. In vitro, a factor rescues protein synthesis from a temperature-dependent arrest when N4316 extracts are used with RNA from bacteriophage f2. Analyses of the substrate in the arrested synthesis and of the product of the rescue reaction indicate that the factor works at the level of coat protein termination, and that it also affects the synthesis of noncoat protein products. The rescue factor is different from the release factors RF-1, RF-2, and RF-3. Model systems previously used to study release fail to score for at least one vital function in protein chain termination.