CD19-specific CAR T cells were produced centrally for a global study in young people with relapsed B-cell ALL. The overall remission rate was 81%, and patients with a response were negative for ...minimal residual disease. High-grade toxic effects were frequent but treatable.
Global quantitative analysis of genetic interactions is a powerful approach for deciphering the roles of genes and mapping functional relationships among pathways. Using colony size as a proxy for ...fitness, we developed a method for measuring fitness-based genetic interactions from high-density arrays of yeast double mutants generated by synthetic genetic array (SGA) analysis. We identified several experimental sources of systematic variation and developed normalization strategies to obtain accurate single- and double-mutant fitness measurements, which rival the accuracy of other high-resolution studies. We applied the SGA score to examine the relationship between physical and genetic interaction networks, and we found that positive genetic interactions connect across functionally distinct protein complexes revealing a network of genetic suppression among loss-of-function alleles.
Background
The Safe Passage Study is a large, prospective, multidisciplinary study designed to (1) investigate the association between prenatal alcohol exposure, sudden infant death syndrome (SIDS), ...and stillbirth, and (2) determine the biological basis of the spectrum of phenotypic outcomes from exposure, as modified by environmental and genetic factors that increase the risk of stillbirth, SIDS, and in surviving children, fetal alcohol spectrum disorders.
Methods
The results provided are based on an interim assessment of 6004 women enrolled, out of the 12 000 projected, from the Northern Plains, US, and Cape Town, South Africa, areas known to be of high risk for maternal drinking during pregnancy. Research objectives, study design, and descriptive statistics, including consent, recruitment, and retention information, are provided.
Results
Overall visit compliance is 87%, and includes prenatal, delivery/newborn, and postnatal contacts through 1 year post‐delivery. Pregnancy outcome ascertainment is 98% prior to medical chart review; less than 2% of women withdraw. Consent for the use of DNA and placental tissue exceed 94%, and consent to participate in the autopsy portion of the study is 71%.
Conclusions
The Safe Passage Study is the first multi‐site study of SIDS and stillbirth to integrate prospectively collected exposure information with multidisciplinary biological information in the same maternal and fetal/infant dyad using a common protocol. Essential components of the study design and its success are close ties to the community and rigorous systems and processes to ensure compliance with the study protocol and procedures.
Intrinsically disordered regions are widespread, especially in proteomes of higher eukaryotes. Recently, protein disorder has been associated with a wide variety of cellular processes and has been ...implicated in several human diseases. Despite its apparent functional importance, the sheer range of different roles played by protein disorder often makes its exact contribution difficult to interpret.
We attempt to better understand the different roles of disorder using a novel analysis that leverages both comparative genomics and genetic interactions. Strikingly, we find that disorder can be partitioned into three biologically distinct phenomena: regions where disorder is conserved but with quickly evolving amino acid sequences (flexible disorder); regions of conserved disorder with also highly conserved amino acid sequences (constrained disorder); and, lastly, non-conserved disorder. Flexible disorder bears many of the characteristics commonly attributed to disorder and is associated with signaling pathways and multi-functionality. Conversely, constrained disorder has markedly different functional attributes and is involved in RNA binding and protein chaperones. Finally, non-conserved disorder lacks clear functional hallmarks based on our analysis.
Our new perspective on protein disorder clarifies a variety of previous results by putting them into a systematic framework. Moreover, the clear and distinct functional association of flexible and constrained disorder will allow for new approaches and more specific algorithms for disorder detection in a functional context. Finally, in flexible disordered regions, we demonstrate clear evolutionary selection of protein disorder with little selection on primary structure, which has important implications for sequence-based studies of protein structure and evolution.
Viral infection or reactivation remains a major cause of morbidity and mortality after allogeneic stem cell transplantation. We now show that infusions of single cytotoxic T lymphocyte (CTL) lines (5 ...× 106-1.35 × 108 cells/m2) with specificity for 2 commonly detected viruses, Epstein-Barr virus (EBV) and adenovirus, can be safely administered to pediatric transplantation recipients receiving partially human leukocyte antigen–matched and haploidentical stem cell grafts (n = 13), without inducing graft-versus-host disease. The EBV-specific component of the CTLs expanded in vivo and persisted for more than 12 weeks, but the adenovirus-specific component only expanded in vivo in the presence of concomitant adenoviral infection. Nevertheless, adenovirus-specific T cells could be detected for at least 8 weeks in peripheral blood, even in CTL recipients without viral infection, provided the adenovirus-specific component of their circulating lymphocytes was first expanded by exposure to adenoviral antigens ex vivo. After infusion, none of these 13 high-risk recipients developed EBV-associated lymphoproliferative disease, while 2 of the subjects had resolution of their adenoviral disease. Hence, bispecific CTLs containing both EBV- and adenovirus-specific T cells can safely reconstitute an antigen responsive “memory” population of CTLs after human leukocyte antigen–mismatched stem cell transplantation and may provide antiviral activity. This trial was registered at www.clinicaltrials.gov as #NCT00590083.
The objective of this randomized clinical trial was to investigate the effects of perfusion modalities on cerebral hemodynamics, vital organ injury, quantified by the Pediatric Logistic Organ ...Dysfunction-2 (PELOD-2) Score, and clinical outcomes in risk-stratified congenital cardiac surgery patients.
This randomized clinical trial included 159 consecutive congenital cardiac surgery patients in whom pulsatile (n = 83) or nonpulsatile (n = 76) perfusion was used. Cerebral hemodynamics were assessed using transcranial Doppler ultrasound. Multiple organ injury was quantified using the PELOD-2 score at 24, 48, and 72 hours. Clinical outcomes, including intubation time, intensive care unit length of stay (LOS), hospital LOS, and mortality, were also evaluated.
The Pulsatility Index at the middle cerebral artery and in the arterial line during aortic cross-clamping was consistently better maintained in the pulsatile group. Demographics and cardiopulmonary bypass characteristics were similar between the 2 groups. While risk stratification with The Society of Thoracic Surgeons-European Association for Cardio-Thoracic Surgery (STAT) Mortality Categories was similar between the groups, Mortality Categories 1 to 3 demonstrated more patients than Mortality Categories 4 and 5. There were no differences in clinical outcomes between the groups. The PELOD-2 scores showed a progressive improvement from 24 hours to 72 hours, but the results were not statistically different between the groups.
The Pulsatillity Index for the pulsatile group demonstrated a more physiologic pattern compared with the nonpulsatile group. While pulsatile perfusion did not increase plasma-free hemoglobin levels or microemboli delivery, it also did not demonstrate any improvements in clinical outcomes or PELOD-2 scores, suggesting that while pulsatile perfusion is a safe method, it not a “magic bullet” for congenital cardiac operations.
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Genetic interactions are highly informative for deciphering the underlying functional principles that govern how genes control cell processes. Recent developments in Synthetic Genetic Array (SGA) ...analysis enable the mapping of quantitative genetic interactions on a genome-wide scale. To facilitate access to this resource, which will ultimately represent a complete genetic interaction network for a eukaryotic cell, we developed DRYGIN (Data Repository of Yeast Genetic Interactions)--a web database system that aims at providing a central platform for yeast genetic network analysis and visualization. In addition to providing an interface for searching the SGA genetic interactions, DRYGIN also integrates other data sources, in order to associate the genetic interactions with pathway information, protein complexes, other binary genetic and physical interactions, and Gene Ontology functional annotation. DRYGIN version 1.0 currently holds more than 5.4 million measurements of genetic interacting pairs involving ~4500 genes, and is available at http://drygin.ccbr.utoronto.ca
If perturbing two genes together has a stronger or weaker effect than expected, they are said to genetically interact. Genetic interactions are important because they help map gene function, and ...functionally related genes have similar genetic interaction patterns. Mapping quantitative (positive and negative) genetic interactions on a global scale has recently become possible. This data clearly shows groups of genes connected by predominantly positive or negative interactions, termed monochromatic groups. These groups often correspond to functional modules, like biological processes or complexes, or connections between modules. However it is not yet known how these patterns globally relate to known functional modules. Here we systematically study the monochromatic nature of known biological processes using the largest quantitative genetic interaction data set available, which includes fitness measurements for ∼5.4 million gene pairs in the yeast Saccharomyces cerevisiae. We find that only 10% of biological processes, as defined by Gene Ontology annotations, and less than 1% of inter-process connections are monochromatic. Further, we show that protein complexes are responsible for a surprisingly large fraction of these patterns. This suggests that complexes play a central role in shaping the monochromatic landscape of biological processes. Altogether this work shows that both positive and negative monochromatic patterns are found in known biological processes and in their connections and that protein complexes play an important role in these patterns. The monochromatic processes, complexes and connections we find chart a hierarchical and modular map of sensitive and redundant biological systems in the yeast cell that will be useful for gene function prediction and comparison across phenotypes and organisms. Furthermore the analysis methods we develop are applicable to other species for which genetic interactions will progressively become more available.
Collecting a sufficient number of T-cells is a critical first step in the production of chimeric antigen receptor (CAR)-T cells. Herein, we report a successful implementation of anticoagulation with ...combined heparin and acid citrate dextrose solution A (ACD-A) for the continuous mononuclear cell (CMNC) protocol on the Spectra Optia in a 20-month-old, 7.5 kg patient with refractory acute lymphoblastic leukemia for manufacture of tisagenlecleucel, a CAR-T cell therapy. Combined heparin/ACD-A was used following clotting issues when ACD-A was used alone during initial CMNC collections. To our knowledge, this is the first reported case in pediatrics of combined heparin/ACD-A anticoagulation with the Spectra Optia CMNC protocol.
As part of the fetal assessment for the Safe Passage Study, we recorded raw data of the fetal ECG via five maternal abdominal wall electrodes from 20 weeks to 23 weeks 6 days' gestation.
For this ...study were extracted and analyzed the FHR patterns from the stored raw data in 16 stillbirths where the fetus weighed less than 1000 g and where autopsy was performed.
Birth weights ranged from 190 to 970 g. The proportion FHR signal loss ranged from 0.3% to 21.1%. In the smallest fetus the heart weighed 1.3 g, yet the FHR signal loss was only 0.9%.
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