Overexpression of activation-induced cytidine deaminase in B cells is associated with production of highly pathogenic autoantibodies

Defective receptor editing or defective B cell checkpoints have been associated with increased frequency of multireactive autoantibodies in autoimmune disease. However, Ig somatic hypermutation and/or class switch recombination may be mechanisms enabling the development of pathogenic multireactive autoantibodies. In this study, we report that, in the BXD2 mouse model of autoimmune disease, elevated expression of activation-induced cytidine deaminase (AID) in recirculating follicular CD86(+) subsets of B cells and increased germinal center B cell activity are associated with the production of pathogenic multireactive autoantibodies. CD4 T cells from BXD2 mice that expressed increased levels of CD28 and an increased proliferative response to anti-CD3 and anti-CD28 stimulation are required for this process. Inhibition of the CD28-CD86 interaction in BXD2 mice with AdCTLA4-Ig resulted in normalization of AID in the B cells and suppression of IgG autoantibodies. This treatment also prevented the development of germinal center autoantibody-producing B cells, suggesting that an optimal microenvironment enabling AID function is important for the formation of pathogenic autoantibodies. Taken together, our data indicate that AID expression in B cells is a promising therapeutic target for the treatment of autoimmune diseases and that suppression of this gene may be a molecular target of CTLA4-Ig therapy.     

Induction of robust diabetes resistance and prevention of recurrent type 1 diabetes following islet transplantation by gene therapy

We have previously shown that the development of type 1 diabetes (T1D) can be prevented in nonobese diabetic (NOD) mice by reconstitution with autologous hemopoietic stem cells retrovirally transduced with viruses encoding MHC class II I-A beta-chain molecules associated with protection from the disease. In this study we examined whether a blockade of the programmed death-1 (PD-1)-programmed death ligand-1 (PD-L1) pathway, a major pathway known to control diabetes occurrence, could precipitate T1D in young NOD mice following reconstitution with autologous bone marrow retrovirally transduced with viruses encoding protective MHC class II I-A beta-chain molecules. In addition, we examined whether the expression of protective MHC class II alleles in hemopoietic cells could be used to prevent the recurrence of diabetes in mice with pre-existing disease following islet transplantation. Protection from the occurrence of T1D diabetes in young NOD mice by the expression of protective MHC class II I-A beta-chain molecules in bone marrow-derived hemopoietic cells was resistant to induction by PD-1-PD-L1 blockade. Moreover, reconstitution of NOD mice with pre-existing T1D autologous hemopoietic stem cells transduced with viruses encoding protective MHC class II I-A beta-chains allowed for the successful transplantation of syngeneic islets, resulting in the long-term reversal of T1D. Reversal of diabetes was resistant to induction by PD-1-PDL-1 blockade and depletion of CD25(+) T cells. These data suggest that expression of protective MHC class II alleles in bone marrow-derived cells establishes robust self-tolerance to islet autoantigens and is sufficient to prevent the recurrence of autoimmune diabetes following islet transplantation.     

Outcomes of deliveries by family physicians or obstetricians: a population-based cohort study using an instrumental variable

Background:

Previous research has suggested that obstetric outcomes are similar for deliveries by family physicians and obstetricians, but many of these studies were small, and none of them adjusted for unmeasured selection bias. We compared obstetric outcomes between these provider types using an econometric method designed to adjust for unobserved confounding.

Methods:

We performed a retrospective population-based cohort study of all Canadian (except Quebec) hospital births with delivery by family physicians and obstetricians at more than 20 weeks gestational age, with birth weight greater than 500 g, between Apr. 1, 2006, and Mar. 31, 2009. The primary outcomes were the relative risks of in-hospital perinatal death and a composite of maternal mortality and major morbidity assessed with multivariable logistic regression and instrumental variable–adjusted multivariable regression.

Results:

After exclusions, there were 3600 perinatal deaths and 14 394 cases of maternal morbidity among 799 823 infants and 793 053 mothers at 390 hospitals. For deliveries by family physicians v. obstetricians, the relative risk of perinatal mortality was 0.98 (95% confidence interval [CI] 0.85–1.14) and of maternal morbidity was 0.81 (95% CI 0.70–0.94) according to logistic regression. The respective relative risks were 0.97 (95% CI 0.58–1.64) and 1.13 (95% CI 0.65–1.95) according to instrumental variable methods.

Interpretation:

After adjusting for both observed and unobserved confounders, we found a similar risk of perinatal mortality and adverse maternal outcome for obstetric deliveries by family physicians and obstetricians. Whether there are differences between these groups for other outcomes remains to be seen.Over the past several decades in Canada, obstetric deliveries have increasingly been attended by specialist obstetricians rather than family physicians.¹ Although specialized care is beneficial for high-risk mothers and their infants,^2–4 there are concerns that it might increase risk for women whose deliveries could be safely managed without a specialized approach. Most prior studies have concluded that obstetric outcomes between family physicians and obstetricians are similar, but many of these studies were small, and none of them adjusted for unmeasured factors that might affect both the choice of delivery provider and outcomes.^5–8Obstetric risk is typically divided between providers, with family physicians and obstetricians sharing the lowest-risk patients, obstetricians caring for moderate-risk patients, and sub-specialized perinatologists caring for the highest-risk individuals. Although traditional statistical methods can be used to adjust for observed differences between these groups, they cannot be used to adjust for unobserved differences. For example, the presence of gestational diabetes mellitus is usually noted, but its severity is often not coded in administrative databases. Women with mild diabetes mellitus are usually eligible for delivery by family physicians, but those with severe diabetes (and the attendant increased risk of adverse outcome) are not. There are many prominent examples where traditional analyses of observational data produced results that were subsequently refuted by randomized trials, presumably because of these unmeasured or unknown factors that also affect treatment decisions or outcomes.^4,9–11The instrumental variable method from the field of econometrics is a technique designed to control for unmeasured covariates in regression analyses. Results from instrumental variable–controlled observational analyses of the effect of angiography after myocardial infarction⁹ and of long-acting bronchodilators on asthma control¹² closely approximated those of randomized controlled trials, whereas analyses using traditional statistical methods differed substantially. Instrumental variable analyses of obstetric data have shown that traditional statistical approaches significantly underestimate the mortality benefit of high-volume hospitals for high-risk neonates.⁴ The objective of the current study was to compare perinatal mortality and maternal morbidity and mortality for deliveries by family physicians and obstetricians using instrumental variable methodology.     

Sample size and power for the weighted log-rank test and Kaplan-Meier based tests with allowance for nonproportional hazards

Asymptotic distributions under alternative hypotheses and their corresponding sample size and power equations are derived for nonparametric test statistics commonly used to compare two survival curves. Test statistics include the weighted log-rank test and the Wald test for difference in (or ratio of) Kaplan-Meier survival probability, percentile survival, and restricted mean survival time. Accrual, survival, and loss to follow-up are allowed to follow any arbitrary continuous distribution. We show that Schoenfeld's equation—often used by practitioners to calculate the required number of events for the unweighted log-rank test—can be inaccurate even when the proportional hazards (PH) assumption holds. In fact, it can mislead one to believe that 1:1 is the optimal randomization ratio (RR), when actually power can be gained by assigning more patients to the active arm. Meaningful improvements to Schoenfeld's equation are made. The present theory should be useful in designing clinical trials, particularly in immuno-oncology where nonproportional hazards are frequently encountered. We illustrate the application of our theory with an example exploring optimal RR under PH and a second example examining the impact of delayed treatment effect. A companion R package npsurvSS is available for download on CRAN.     

Fingerprinting facies of the Tuff IF marker,with implications for early hominin palaeoecology,Olduvai Gorge,Tanzania

The top of Tuff IF marks the upper boundary of the Plio-/Pleistocene Bed I succession exposed in Olduvai Gorge, NE Tanzania, a tephrostratigraphic interval that is well known for remarkable Oldowan archaeological and vertebrate fossil assemblages, including early hominins. Geochemically, Tuff IF is characterized by a relatively consistent silica-undersaturated trachytic to phonolitic composition that relates both in terms of numerical ages (1.79 Ma) and compositional constraints to Olmoti volcano, located 22–38 km E of Olduvai Gorge.Measured Tuff IF sections are characterized by a thick unwelded pyroclastic flow in proximal settings and a succession of surges and ashfalls that interfingers with fluvio-lacustrine deposits of the Olduvai Basin in the medial to distal settings. Only in those areas with a relatively low topographic gradient, in distal reaches and beyond the toe of an Olmoti-sourced volcaniclastic fan, did the Tuff IF marker develop a typical threefold subdivision comprising: (1) primary surges and minor fallout, (2) reworked pumice units as lateral correlatives of proximally emplaced pyroclastic flows and (3) a succession of mass flows in conjunction with aeolian and fluvially reworked units.The pyroclastic marker unit is thus highly heterogeneous with regard to its vertical and lateral facies architecture and this has immediate effects on its preservation potential and in situ burial of fossils and stone artifacts. Even though the volcanically-related environmental perturbations were probably more severe at the eastern lake margin, the evidence for at least temporary freshwater sources and trees suggests environments conducive to hominin activities, but not during emplacement of Tuff IF pyroclastic flows and surges. This inference is supported by the presence of rich Oldowan stone artifact assemblages immediately preceding and following the deposition of Tuff IF, but only extremely sparse archaeological traces from one site in Tuff IF, restricted to the upper, fluvially reworked portion of Tuff IF.Tuff IF facies record the maximum of a regressive (drying) cycle that correlates with regional marine arid indicators. An ecological crisis covering ～ 2000–3500 a of time during Tuff IF deposition resulted not only from the lethal effects of explosive volcanism but also from its coincidence with a pronounced period of climate induced drought. These combined effects appear to have made at least the eastern basin uninhabitable by hominins and other vertebrates for most of the time during which Tuff IF accumulated.     

Lack of low frequency variants masks patterns of non-neutral evolution following domestication

Detecting artificial selection in the genome of domesticated species can not only shed light on human history but can also be beneficial to future breeding strategies. Evidence for selection has been documented in domesticated species including maize and rice, but few studies have to date detected signals of artificial selection in the Sorghum bicolor genome. Based on evidence that domesticated S. bicolor and its wild relatives show significant differences in endosperm structure and quality, we sequenced three candidate seed storage protein (kafirin) loci and three candidate starch biosynthesis loci to test whether these genes show non-neutral evolution resulting from the domestication process. We found strong evidence of non-neutral selection at the starch synthase IIa gene, while both starch branching enzyme I and the beta kafirin gene showed weaker evidence of non-neutral selection. We argue that the power to detect consistent signals of non-neutral selection in our dataset is confounded by the absence of low frequency variants at four of the six candidate genes. A future challenge in the detection of positive selection associated with domestication in sorghum is to develop models that can accommodate for skewed frequency spectrums.