Leveraging Hematopoietic Cell Transplant Data and Biorepository Resources at the Center for International Blood and Marrow Transplant Research to Improve Patient Outcomes.

Hematopoietic cell transplantation (HCT) has undergone many advances over the decades. Trends in HCT utilization have been impacted by research based on the data and samples collected by the Center for International Blood and Marrow Transplant Research (CIBMTR). Here, we provide a summary report of the CIBMTR Biorepository resource and describe the biospecimen inventory along with collection and request procedures. The diversity captured in this inventory reflects transplant activity, and these samples can be leveraged for secondary analyses to generate more data and insights to advance the field. We describe how our resources have already impacted HCT practice and elaborate on possibilities for further collaboration and utilization to maximize capabilities and research opportunities. Hematopoietic cell transplant data and biorepository resources at the CIBMTR have been and continue to be leveraged to improve patient outcomes.

Midkine Attenuates Aß Fibril Assembly and AmyloidPlaque Formation.

Proteomic profiling of Alzheimer's disease (AD) brains has identified numerous understudied proteins, including midkine (MDK), that are highly upregulated and correlated with Aß since the early disease stage, but their roles in disease progression are not fully understood. Here we present that MDK attenuates Aß assembly and influences amyloid formation in the 5xFAD amyloidosis mouse model. MDK protein mitigates fibril formation of both Aß40 and Aß42 peptides in Thioflavin T fluorescence assay, circular dichroism, negative stain electron microscopy, and NMR analysis. Knockout of Mdkgene in 5xFAD increases amyloid formation and microglial activation. Further comprehensive mass spectrometry-based profiling of whole proteome and aggregated proteome in these mouse models indicates significant accumulation of Aß and Aß-correlated proteins, along with microglial components. Thus, our structural and mouse model studies reveal a protective role of MDK in counteracting amyloid pathology in Alzheimer's disease.

Improved access to better HLA-matched hematopoietic cells for allogeneic transplant: analysis of donors and cord blood units selected for Canadian patients in 2018.

BACKGROUND: Patients undergoing hematopoietic cell transplantation (HCT) often require use of an unrelated donor or cord blood unit (CBU). An understanding of evolving practices in graft selection is needed for optimization of donor recruitment and cord blood collection. STUDY DESIGN AND METHODS: Each donor workup (WU) requested in 2018 involving a Canadian (CDN) patient and unique donor product or CBU was reviewed (n = 598). Degree of HLA match; product origin (domestic or international [INT]); and non-HLA factors including donor age, sex, cytomegalovirus (CMV), and ABO compatibility were analyzed for WUs that proceeded to transplant (n = 414). We also analyzed changes compared to a similar analysis performed in 2013. RESULTS: The majority of transplants used matched unrelated donors (MUDs; n = 323; 78%) and were most often young (≤35 years), male, INT donors (n = 136). The proportion of transplants involving MUDs, as opposed to mismatched unrelated donors or CBUs, increased by 12.4% compared with 2013. When young, male, CDN MUDs were identified in patient search reports but not selected, CMV mismatching and ABO incompatibility were most likely to have influenced the decision to use an INT MUD. Consistent with global trends, CBU transplants decreased compared to 2013; however, the degree of HLA matching improved significantly, and 27% of transplanted CBUs were procured from the Canadian Blood Services Cord Blood Bank. CONCLUSIONS: Access to MUDs and better HLA-matched CBUs by CDN patients has increased since 2013. Ongoing recruitment of young registrants and cord blood donors with diverse HLA haplotypes will support selection of donors with optimal non-HLA characteristics.

Nucleome Dynamics during Retinal Development.

More than 8,000 genes are turned on or off as progenitor cells produce the 7 classes of retinal cell types during development. Thousands of enhancers are also active in the developing retinae, many having features of cell- and developmental stage-specific activity. We studied dynamic changes in the 3D chromatin landscape important for precisely orchestrated changes in gene expression during retinal development by ultra-deep in situ Hi-C analysis on murine retinae. We identified developmental-stage-specific changes in chromatin compartments and enhancer-promoter interactions. We developed a machine learning-based algorithm to map euchromatin and heterochromatin domains genome-wide and overlaid it with chromatin compartments identified by Hi-C. Single-cell ATAC-seq and RNA-seq were integrated with our Hi-C and previous ChIP-seq data to identify cell- and developmental-stage-specific super-enhancers (SEs). We identified a bipolar neuron-specific core regulatory circuit SE upstream of Vsx2, whose deletion in mice led to the loss of bipolar neurons.

Unrelated donor choices for allogeneic hematopoietic cell transplantation in Canada: an evaluation of factors influencing donor selection.

BACKGROUND: Utilization of unrelated donors and cord blood units (CBUs) for allogeneic hematopoietic cell transplantation continues to increase. Understanding the practices of donor selection by transplant centers is critical for unrelated donor registries and cord blood banks to optimize registry composition and inventory to meet patient need. STUDY DESIGN AND METHODS: Unrelated donor and CBU selection practices of Canadian transplant centers served by Canadian Blood Services' OneMatch Stem Cell & Marrow Network (OM) were reviewed, including HLA match level, locus of disparity, age, sex, and product choice (donor vs. CBU). RESULTS: HLA-matched donors within OM and/or international (INT) registries were preferentially investigated, underscoring the primary importance of HLA matching. In the case of HLA-mismatched donors, HLA-A disparities were most common while DRB1 mismatches were least common. Advanced age, sex, and lack of donor availability were the most frequent reasons that high-probability OM donors were overlooked in favor of INT donors. High-probability 10 of 10 HLA-matched female donors from OM were often avoided in favor of INT male donors. Use of female donors, however, increased in cases restricted to more HLA-disparate donor options. Caucasian patients were more likely to find 10 of 10 matched donors, whereas use of mismatched donors and CBUs were more prevalent among non-Caucasian patients. CONCLUSIONS: Recruitment and retention of young, male donors from diverse ethnic backgrounds may increase the usage of histocompatible OM donors for patients in need.

Biofilm-forming skin microflora bacteria are resistant to the bactericidal action of disinfectants used during blood donation.

BACKGROUND: A one-step skin disinfection method containing 2% chlorhexidine-gluconate (CHG) and 70% isopropyl alcohol (IPA) is currently used by blood suppliers worldwide. Reports of bacterially contaminated platelet concentrates (PCs) indicate that skin disinfection is not fully effective. Approximately 20% of skin microflora exist as surface-attached aggregates (biofilms), known for displaying increased resistance to disinfectants. This study was aimed at determining whether skin microflora biofilm-positive Staphylococcus epidermidis and Staphylococcus capitis are resistant to CHG and/or IPA. STUDY DESIGN AND METHODS: Free-floating cells and mono or dual (1 : 1 ratio) biofilms of S. epidermidis and S. capitis were exposed to CHG, IPA, or CHG/IPA for 30 seconds, simulating skin disinfection practices. Residual viable cells were quantified by colony counting. Morphology of disinfectant-treated S. epidermidis biofilms was examined by scanning electron microscopy. Treated S. epidermidis and S. capitis biofilms were inoculated into PCs and bacterial concentrations were determined on Days 0 and 5 of storage. RESULTS: Treatment of staphylococcal biofilm cells with all disinfectants caused cell damage and significant reduction in viability, with CHG/IPA being the most effective. However, biofilms were significantly more resistant to treatment than free-floating cells. Disinfectant-treated S. epidermidis proliferated better in PCs than S. capitis, especially when grown as monospecies biofilms. CONCLUSION: Although CHG/IPA is effective in reducing the viability of S. epidermidis and S. capitis biofilms, these organisms are not completely eliminated. Furthermore, disinfectant-treated staphylococcal biofilms multiply well in PCs. These results demonstrate that the biofilm-forming capability of the skin microflora reduces the bactericidal efficiency of blood donor skin disinfectants.

Characterization of the growth dynamics and biofilm formation of Staphylococcus epidermidis strains isolated from contaminated platelet units.

Bacterial contamination of platelet concentrates (PCs) poses the highest transfusion-associated infectious risk, with Staphylococcus epidermidis being a predominant contaminant. Herein, the growth dynamics of 20 S. epidermidis strains in PCs and regular media were characterized. Strains were categorized as fast (short lag phase) or slow (long lag phase) growers in PCs. All strains were evaluated for the presence of the biofilm-associated icaAD genes by PCR, their capability to produce extracellular polysaccharide (slime) on Congo red agar plates and their ability to form surface-attached aggregates (biofilms) in glucose-supplemented trypticase soy broth (TSBg) using a crystal violet staining assay. A subset of four strains (two slow growers and two fast growers) was further examined for the ability for biofilm formation in PCs. Two of these strains carried the icAD genes, formed slime and produced biofilms in TSBg and PCs, while the other two strains, which did not carry icaAD, did not produce slime or form biofilms in TSBg. Although the two ica-negative slime-negative strains did not form biofilms in media, they displayed a biofilm-positive phenotype in PCs. Although all four strains formed biofilms in PCs, the two slow growers formed significantly more biofilms than the fast growers. Furthermore, growth experiments of the two ica-positive strains in plasma-conditioned platelet bags containing TSBg revealed that a slow grower isolate was more likely to escape culture-based screening than a fast grower strain. Therefore, this study provides novel evidence that links S. epidermidis biofilm formation with slow growth in PCs and suggests that slow-growing biofilm-positive S. epidermidis would be more likely to be missed with automate culture.

Enhanced pathogenicity of biofilm-negative Staphylococcus epidermidis isolated from platelet preparations.

BACKGROUND: The platelet (PLT) storage environment triggers the formation of surface-attached aggregates known as biofilms by the common PLT contaminant Staphylococcus epidermidis. The biofilm matrix is largely composed of polysaccharide intercellular adhesin (PIA) mediated by the icaADBC operon. However, PIA-negative S. epidermidis has been reported to form biofilms in PLT concentrates (PCs). Since biofilm formation is associated with increased virulence, this study was aimed at determining if PIA-negative S. epidermidis grown in PCs presents enhanced virulence using the nematode Caenorhabditis elegans as a host model for bacterial pathogenesis. STUDY DESIGN AND METHODS: Biofilm-positive S. epidermidis ATCC 35984 and 9142, which carry the icaADBC operon, and biofilm-negative S. epidermidis ATCC 12228 and 9142 ΔicaA were grown in regular media and in PCs and biofilm formation was quantified using a crystal violet assay. The virulence of these strains after passage through PCs was tested using nematode killing assays. Nematode survival was calculated using the Kaplan-Meier method and statistical differences were determined by log-rank analysis. RESULTS: All S. epidermidis strains were able to form biofilms in PCs. Although persistence of a biofilm-positive phenotype in the biofilm-negative strains grown in PCs was not observed after passage in regular medium, the virulence of all strains was significantly increased as demonstrated by shortened life spans of the nematodes in C. elegans killing assays. CONCLUSION: Our findings highlight the potential of an increased risk of nosocomial infections caused by S. epidermidis in transfusion recipients since PC storage conditions promote biofilm formation, and possibly pathogenicity, of strains traditionally known to be attenuated for virulence.

Biofilm formation by Staphylococcus capitis strains isolated from contaminated platelet concentrates.

Bacterial contamination of platelet concentrates (PCs) poses the greatest infectious risk in modern transfusion medicine despite the implementation of measures such as improved skin disinfection and first aliquot diversion. The majority of PC contaminants are commensal skin flora introduced by venipuncture at the time of blood collection. The predominant organisms are Gram-positive coagulase-negative staphylococci such as Staphylococcus capitis. This bacterium has been implicated in numerous instances of infection and sepsis, likely for its ability to form surface-associated communities of micro-organisms encased in extracellular materials, known as biofilms. In the present study, five strains of S. capitis isolated from contaminated PCs were assessed for their ability to produce extracellular polysaccharide (slime), a canonical indicator of biofilm-formation ability, on Congo red agar plates. Biofilm formation was evaluated in both glucose-enriched trypticase soy broth (TSBg) and in PCs by using a crystal violet staining assay. The chemical nature of the biofilms was evaluated by disruption assays using sodium metaperiodate and proteinase K. In addition, biofilm architecture was observed by scanning electron microscopy. The presence of the biofilm-associated icaR and icaADBC genes was also examined by PCR. While only two out of the five S. capitis strains formed biofilms in TSBg, all strains formed biofilms in PCs. The ability of strains to produce extracellular polysaccharide and their possession of wild-type ica genes were not exclusive predictors of biofilm formation in TSBg or PCs; different profiles of biofilm markers were observed among isolates. This is likely due to the proteinaceous composition of the S. capitis biofilm matrix. Interestingly, an ica-negative, non-slime-producing isolate was capable of biofilm formation in PCs. Together, these data indicate that the platelet storage environment stimulates biofilm formation in S. capitis in the absence of extracellular polysaccharide production and that multiple bacterial factors and regulatory elements are likely involved in biofilm formation in this milieu.

Communication and the electronic health record training: a comparison of three healthcare systems.

BACKGROUND: The electronic health record (EHR) used in the examination room, is becoming the primary method of medical data storage in primary care practice in the USA. One of the challenges in using EHRs is maintaining effective patient-provider communication. Many studies have focused on communication in the examination room. PURPOSE: Scant research exists on the best methods in educating nurse practitioners and other primary care providers (clinicians). The purpose of this study was to explore various health record training programmes for clinicians. METHODS: One researcher participated in and observed three health systems' EHR training programmes for ambulatory care providers in the Pacific Northwest. A focused ethnographic approach was used, emphasising patient-provider communication. RESULTS: Only one system had formalised communication training in their class, the other two systems emphasised only the software and data aspects of the EHR. CONCLUSIONS: The fact that clinicians are expected to use EHRs in the examination room necessitates the inclusion of communication training in EHR training programmes and/or as a part of primary care nurse practitioner education programmes.

Putting a face on medical errors: a patient perspective.

Knowledge of the patient's perspective on medical error is limited. Research efforts have centered on how best to disclose error and how patients desire to have medical error disclosed. On the basis of a qualitative descriptive component of a mixed method study, a purposive sample of 30 community members told their stories of medical error. Their experiences focused on lack of communication, missed communication, or provider's poor interpersonal style of communication, greatly contrasting with the formal definition of error as failure to follow a set standard of care. For these participants, being a patient was more important than error or how an error is disclosed. The patient's understanding of error must be a key aspect of any quality improvement strategy.

Addressing in-hospital "falls" of newborn infants.

BACKGROUND: During postpartum hospitalization, close physical interactions between mother and newborn facilitate attachment, breastfeeding, and relationship competence. The challenge during this time is to support these important interactions in the hospital while ensuring the safety of the newborn. A literature review indicated that newborn "falls" and drops--collectively referred to as falls-remains largely unaddressed. Experience of a seven-hospital system in Oregon offers a template for understanding how and why infant falls occur in hospitals and how to address the issue. IDENTIFYING THE PROBLEM: For a two-year period (January 2006-December 2007), a query of a live voluntary event database yielded 9 cases of newborn falls (from 22,866 births), for a rate of 3.94 falls per 10,000 births. RESPONDING TO NEWBORN FALLS: A newborn falls committee made preliminary recommendations for interventions to reduce newborn falls, including (1) expanding thel patient safety contract, (2) monitoring mothers more closely, (3) improving equipment safety, and (4) spreading information about newborn falls within the state and throughout the hospital system. For example, staff use the patient safety contract to improve awareness and prevention of falls. The mothers and significant family members are asked to review the safety information and sign the contract. CONCLUSION: Newborns experience in-hospital falls at a rate of approximately 1.6-4.14/10,000 live births, resulting in an estimated 600-1600 falls per year in the United States. Additional reports of rates of newborn falls are urgently needed to determine the true prevalence of this historically underreported event. Standardized evaluation and management guidelines need to be developed to aid the clinician in the appropriate care of newborns experiencing this infrequent event.

Interaction of host cellular proteins with components of the hepatitis delta virus.

The hepatitis delta virus (HDV) is the smallest known RNA pathogen capable of propagation in the human host and causes substantial global morbidity and mortality. Due to its small size and limited protein coding capacity, HDV is exquisitely reliant upon host cellular proteins to facilitate its transcription and replication. Remarkably, HDV does not encode an RNA-dependent RNA polymerase which is traditionally required to catalyze RNA-templated RNA synthesis. Furthermore, HDV lacks enzymes responsible for post-transcriptional and -translational modification, processes which are integral to the HDV life cycle. This review summarizes the known HDV-interacting proteins and discusses their significance in HDV biology.

Caring for the pregnant woman presenting at periviable gestation: acknowledging the ambiguity and uncertainty.

Counseling the periviable pregnant woman presenting at the edge of viability can often be confusing for the patient and frustrating for the clinician. Although neonatal survival rates have improved dramatically over the last few decades, severe morbidity is still common. This is further complicated by the fact that the information provided to the parents regarding the outcomes may not be up to date or completely accurate. The counseling is also frequently influenced by personal beliefs and biases of the medical staff. An evidence-based approach may improve the experience for both the expectant parents and the health care team.

Counseling pregnant women who may deliver extremely premature infants: medical care guidelines, family choices, and neonatal outcomes.

OBJECTIVES: The justification of neonatal intensive care for extremely premature infants is contentious and of considerable importance. The goal of this report is to describe our experience implementing consensus medical staff guidelines used for counseling pregnant women threatening extremely premature birth between 22 and 26 weeks' postmenstrual age and to give an account of family preferences and the immediate outcome of their infants. METHODS: Retrospective chart review was performed for all women threatening premature birth between 22 and 26 weeks postmenstrual age who presented to our high-risk obstetric service between June 2003 and December 2006. Women participated in comprehensive periviability counseling, which featured our specific obstetric and neonatology care recommendations for them and their infant at each gestational week. A subset of women were approached to obtain consent for a 2-step interview process beginning 3 days after the initial periviability counseling and followed with a 6- to 18-month assessment. RESULTS: Two hundred sixty women were identified as eligible subjects. After periviability counseling, but before any birth, palliative comfort care was requested by a higher percentage of families at each decreasing week. Ninety-five of the 260 women delivered 121 infants at <27 weeks' postmenstrual age. At delivery, at the request of the families and with the agreement of the medical staff, the following proportions of these infants were provided palliative comfort care: 100% at 22 weeks, 61% at 23 weeks, 38% at 24 weeks, 17% at 25 weeks, and 0% at 26 weeks. All nonresuscitations and comfort care measures were supported by the medical and nursing staffs, and all infant deaths occurred within 171 minutes. Fifty women consented to a postcounseling interview, and 25 of them also participated in a follow-up interview 6 to 18 months later. The counseling process and the guidelines were viewed as highly understandable, useful, consistent, and done in a comfortable manner. The tone and content of the parental comments regarding the counseling process were very positive, even more so at the later interview. There were no complaints or negative comments regarding the counseling process or the infant outcomes. CONCLUSIONS: Rational, consensus periviability guidelines are well accepted and can be used by all neonatologists, obstetricians, and nurses who provide care to pregnant women and infants at extremely early gestational ages. Pregnant women see these guidelines as highly understandable, useful, consistent, and respectful. When encouraged to participate with attending staff in discussions involving morbidity and mortality outcomes of premature infants and consensus medical practice recommendations, a substantial proportion of parents will choose palliative comfort care for their extremely premature infant up through 25 weeks' postmenstrual age. We believe the choice of neonatal intensive care versus palliative comfort care in extremely premature infants rightfully belongs to medically informed parents. More research is needed to examine how these decisions are made under diverse conditions of culture, religion, and technology.

The hepatitis delta virus RNA genome interacts with eEF1A1, p54(nrb), hnRNP-L, GAPDH and ASF/SF2.

Because of its extremely limited coding capacity, the hepatitis delta virus (HDV) takes over cellular machineries for its replication and propagation. Despite the functional importance of host factors in both HDV biology and pathogenicity, little is known about proteins that associate with its RNA genome. Here, we report the identification of several host proteins interacting with an RNA corresponding to the right terminal stem-loop domain of HDV genomic RNA, using mass spectrometry on a UV crosslinked ribonucleoprotein complex, RNA affinity chromatography, and screening of a library of purified RNA-binding proteins. Co-immunoprecipitation was used to confirm the interactions of eEF1A1, p54(nrb), hnRNP-L, GAPDH and ASF/SF2 with the right terminal stem-loop domain of HDV genomic RNA in vitro, and with both polarities of HDV RNA within HeLa cells. Our discovery that HDV RNA associates with RNA-processing pathways and translation machinery during its replication provides new insights into HDV biology and its pathogenicity.

The hepatitis delta virus RNA genome interacts with the human RNA polymerases I and III.

The hepatitis delta virus (HDV) relies on human transcriptional machinery for its replication and transcription. Although the involvement of RNA polymerase II in HDV RNA biosynthesis is established, the contribution of additional polymerases remains uncertain. Here, we demonstrate the interaction of both RNA polymerase I and III with HDV RNA, both in vitro and in human cells. Binding of these polymerases occurs near the terminal stem-loop domains of both polarities of the HDV RNA genome. Based on interactions of HDV RNA with numerous host polymerases, our results suggest a higher level of complexity of HDV biology than previously envisioned.

Excess cost and length of stay associated with voluntary patient safety event reports in hospitals.

This study estimates excess cost and length of stay associated with voluntary patient safety event reports at 3 hospitals. Voluntary patient safety event reporting has proliferated in hospitals in recent years, yet little is known about the cost of events captured by this type of system. Events captured in an electronic reporting system at 3 urban community hospitals in Portland, Oregon, are evaluated. Cost and length of stay are assessed by linking event reports to risk-adjusted administrative data. Hospital stays with an event report are 17% more costly and 22% longer than stays without events. Medication and treatment errors are the most expensive and most common events, representing 77% of all event types and 77% of added costs. Ninety percent of events result in no measurable harm. Patient safety events captured by voluntary event reporting reflect significant waste and inefficiency in hospital stays.

The human RNA polymerase II interacts with the terminal stem-loop regions of the hepatitis delta virus RNA genome.

The hepatitis delta virus (HDV) is an RNA virus that depends on DNA-dependent RNA polymerase (RNAP) for its transcription and replication. While it is generally accepted that RNAP II is involved in HDV replication, its interaction with HDV RNA requires confirmation. A monoclonal antibody specific to the carboxy terminal domain of the largest subunit of RNAP II was used to establish the association of RNAP II with both polarities of HDV RNA in HeLa cells. Co-immunoprecipitations using HeLa nuclear extract revealed that RNAP II interacts with HDV-derived RNAs at sites located within the terminal stem-loop domains of both polarities of HDV RNA. Analysis of these regions revealed a strong selection to maintain a rod-like conformation and demonstrated several conserved features. These results provide the first direct evidence of an association between human RNAP II and HDV RNA and suggest two transcription start sites on both polarities of HDV RNA.