Tho Duc Pham

All Publications

• Germline-encoded specificities and the predictability of the B cell response. PLoS pathogens C Vieira, M., Palm, A. E., Stamper, C. T., Tepora, M. E., Nguyen, K. D., Pham, T. D., Boyd, S. D., Wilson, P. C., Cobey, S. 2023; 19 (8): e1011603

  Abstract

  Antibodies result from the competition of B cell lineages evolving under selection for improved antigen recognition, a process known as affinity maturation. High-affinity antibodies to pathogens such as HIV, influenza, and SARS-CoV-2 are frequently reported to arise from B cells whose receptors, the precursors to antibodies, are encoded by particular immunoglobulin alleles. This raises the possibility that the presence of particular germline alleles in the B cell repertoire is a major determinant of the quality of the antibody response. Alternatively, initial differences in germline alleles' propensities to form high-affinity receptors might be overcome by chance events during affinity maturation. We first investigate these scenarios in simulations: when germline-encoded fitness differences are large relative to the rate and effect size variation of somatic mutations, the same germline alleles persistently dominate the response of different individuals. In contrast, if germline-encoded advantages can be easily overcome by subsequent mutations, allele usage becomes increasingly divergent over time, a pattern we then observe in mice experimentally infected with influenza virus. We investigated whether affinity maturation might nonetheless strongly select for particular amino acid motifs across diverse genetic backgrounds, but we found no evidence of convergence to similar CDR3 sequences or amino acid substitutions. These results suggest that although germline-encoded specificities can lead to similar immune responses between individuals, diverse evolutionary routes to high affinity limit the genetic predictability of responses to infection and vaccination.

  View details for DOI 10.1371/journal.ppat.1011603

  View details for PubMedID 37624867

• Blood transfusion in cardiac surgeries - Toward a personalized protocol. American journal of surgery Min, Y., Dalal, A. R., Pedroza, A. J., Pham, T. D., Panigrahi, A. K., Goldstone, A. B., MacArthur, J. W., Woo, Y. J., Baiocchi, M., Fischbein, M. P. 2023

  View details for DOI 10.1016/j.amjsurg.2023.07.035

  View details for PubMedID 37558518

• Hepatitis E virus seropositivity in an ethnically diverse community blood donor population. Vox sanguinis Mah, J. K., Keck, M., Chu, D. Y., Sooryanarain, H., Sahoo, M. K., Lau, P., Huang, C., Weber, J., Belanger, G. A., Keck, Z., Shan, H., Meng, X., Foung, S. K., Pinsky, B. A., Pham, T. D. 2023

  Abstract

  BACKGROUND AND OBJECTIVES: Hepatitis E virus (HEV) is an underrecognized and emerging infectious disease that may threaten the safety of donor blood supply in many parts of the world. We sought to elucidate whether our local community blood supply is at increased susceptibility for transmission of transfusion-associated HEV infections.MATERIALS AND METHODS: We screened 10,002 randomly selected donations over an 8-month period between 2017 and 2018 at the Stanford Blood Center for markers of HEV infection using commercial IgM/IgG serological tests and reverse transcriptase quantitative polymerase chain reaction assays (RT-qPCR). Donor demographic information, including gender, age, self-identified ethnicity, location of residence and recent travel, were obtained from the donor database and used to generate multivariate binary logistic regressions for risk factors of IgG seropositivity.RESULTS: A total of 10,002 blood donations from 7507 unique donors were screened, and there was no detectable HEV RNA by RT-qPCR. The overall seropositivity rate was 12.1% for IgG and 0.56% for IgM. Multivariate analysis of unique donors revealed a significantly higher risk of IgG seropositivity with increasing age, White/Asian ethnicities and residence in certain local counties.CONCLUSION: Although HEV IgG seroprevalence in the San Francisco Bay Area is consistent with ongoing infection, the screening of a large donor population did not identify any viraemic blood donors. While HEV is an underrecognized and emerging infection in other regions, there is no evidence to support routine blood screening for HEV in our local blood supply currently; however, periodic monitoring may still be required to assess the ongoing risk.

  View details for DOI 10.1111/vox.13487

  View details for PubMedID 37366233

• Targeting Repetitive Laboratory Testing with Electronic Health Records-Embedded Predictive Decision Support: A Pre-Implementation Study. Clinical biochemistry Rabbani, N., Ma, S. P., Li, R. C., Winget, M., Weber, S., Boosi, S., Pham, T. D., Svec, D., Shieh, L., Chen, J. H. 2023

  Abstract

  INTRODUCTION: Unnecessary laboratory testing contributes to patient morbidity and healthcare waste. Despite prior attempts at curbing such overutilization, there remains opportunity for improvement using novel data-driven approaches. This study presents the development and early evaluation of a clinical decision support tool that uses a predictive model to help providers reduce low-yield, repetitive laboratory testing in hospitalized patients.METHODS: We developed an EHR-embedded SMART on FHIR application that utilizes a laboratory test result prediction model based on historical laboratory data. A combination of semi-structured physician interviews, usability testing, and quantitative analysis on retrospective laboratory data were used to inform the tool's development and evaluate its acceptability and potential clinical impact.KEY RESULTS: Physicians identified culture and lack of awareness of repeat orders as key drivers for overuse of inpatient blood testing. Users expressed an openness to a lab prediction model and 13/15 physicians believed the tool would alter their ordering practices. The application received a median System Usability Scale score of 75, corresponding to the 75th percentile of software tools. On average, physicians desired a prediction certainty of 85% before discontinuing a routine recurring laboratory order and a higher certainty of 90% before being alerted. Simulation on historical lab data indicates that filtering based on accepted thresholds could have reduced 22% of repeat chemistry panels.CONCLUSIONS: The use of a predictive algorithm as a means to calculate the utility of a diagnostic test is a promising paradigm for curbing laboratory test overutilization. An EHR-embedded clinical decision support tool employing such a model is a novel and acceptable intervention with the potential to reduce low-yield, repetitive laboratory testing.

  View details for DOI 10.1016/j.clinbiochem.2023.01.002

  View details for PubMedID 36623759

• Implementation strategy for complete pathogen reduction technology treated apheresis platelet inventory. Transfusion Shu, E., Dela Cruz Batilo, C., Sussmann, H., Owen, B., Belanger, G. A., Pandey, S., Pham, T. D. 2022

  Abstract

  Bacterial contamination in platelets remain a major public health concern, which prompted the US Food and Drug Administration guidance for bacterial contamination mitigation. Pathogen reduction technology (PRT) is one mitigation strategy that has shown success in Europe over the last decade. Therefore, our center sought to transition from a dual system of bacterial culturing (BacT) and PRT to full PRT.A 1 month pilot study was conducted to simulate 100% PRT conditions. Our center also collected baseline data on key platelet production metrics in the 4 months prior to 100% PRT and compared it to the 4 months post-implementation.The pilot study showed no statistical differences in split rate, proportion of low-yield products, or proportion of single, double, and triple collections. The only observed difference was an 11 min increase in the average duration of double collections. Our baseline versus post-implementation monitoring showed no difference in split rate, discard rate, percentage of low-yield units, and average yield of low yield units. Statistical differences were detected in the proportion of single, double, and triple collections, as well as the average yield of full dose products. Roughly 20% of our inventory consisted of low-yield products.With suitable mitigation strategies, transitioning to a full PRT inventory may result in higher net margins while not adversely affecting overall platelet production. A pilot study is a good way to project potential effects of switching from a dual BacT and PRT inventory to full PRT, and can be adopted by other centers aiming to make the transition.

  View details for DOI 10.1111/trf.17081

  View details for PubMedID 36052676

• Transfusion Outcomes between Regular and Low Yield Pathogen Reduced Platelets across Different Patient Populations in a Single Institution Tang, M., Shu, E., Sussman, H., Virk, M., Pandey, S., Shan, H., Pham, T. WILEY. 2022: 268A

  View details for Web of Science ID 000854334900392

• Transfusion outcomes between regular and low yield pathogen reduced platelets across different patient populations in a single institution. Transfusion Tang, M. S., Shu, E., Sussman, H., Virk, M., Pandey, S., Shan, H., Pham, T. 2022

  Abstract

  Pathogen reduction technology (PRT) effectively mitigates bacterial contamination in platelets but is more likely to produce low yield units. Although low dose transfusion using conventional platelets has not been associated with increased bleeding, these findings have not been reproduced with PRT-treated platelets.Platelet transfusions in a tertiary adult hospital were retrospectively reviewed. Comparisons were made between PRT-treated regular (PRT-PR) and low (PRT-PL) yield platelets. Outcomes examined included the number of platelets and RBCs transfused, transfusion-free interval, and corrected count increment (CCI). Subgroup analyses were also performed on hematology-oncology inpatients and outpatients, as well as non-hematology-oncology patients.Platelet utilization per patient remained mostly unchanged (mean 2.9-4.3 units per patient per month) even when the frequency of PRT-PL transfusion increased. Among 1402 patients examined, the number of platelets and RBCs transfused was not significantly different between patients first transfused with PRT-PR versus PRT-PL (mean number of platelet units = 2.8 vs. 3.1, p = 0.38; mean number of RBC units = 4.8 vs. 4.3, p = 0.93). Among 10,257 platelet transfusions examined, the transfusion-free interval (hazard ratio = 1.05, 95% confidence interval 1.00-1.10) and CCI (10.2 vs. 11.0, p = 0.70) were comparable between PRT-PR and PRT-PL units. Similar findings were observed in all subgroups, except for shortened transfusion-free intervals among hematology-oncology inpatients.PRT-PR and PRT-PL units may be used in an equivalent manner to maintain an adequate platelet inventory, since there was only a minor difference in time between transfusions.

  View details for DOI 10.1111/trf.17043

  View details for PubMedID 35924914

• Hospital red blood cell and platelet supply and utilization from March to December of the first year of the COVID-19 pandemic: The BEST Collaborative Study. Transfusion Lu, W., Yazer, M., Li, N., Ziman, A., Wendel, S., Tang, H., Tsang, H., Titlestad, K., Thibodeaux, S. R., Shih, A. W., Poisson, J. L., Pham, T., Pandey, S., Pagano, M. B., Shan, H., Murphy, M., Murphy, C., Savioli, M. L., Kutner, J. M., Hess, A. S., Fontaine, M. J., Fachini, R., Dunbar, N. M., Kaufman, R. M., Biomedical Excellence for Safer Transfusions Collaborative 2022

  Abstract

  BACKGROUND: At the start of the COVID-19 pandemic, widespread blood shortages were anticipated. We sought to determine how hospital blood supply and blood utilization were affected by the first wave of COVID-19.STUDY DESIGN AND METHODS: Weekly red blood cell (RBC) and platelet (PLT) inventory, transfusion, and outdate data were collected from 13 institutions in the United States, Brazil, Canada, and Denmark from March 1st to December 31st of 2020 and 2019. Data from the sites were aligned based on each site's local 1st peak of COVID-19 cases, and data from 2020 (pandemic year) were compared with data from the corresponding period in 2019 (pre-pandemic baseline).RESULTS: RBC inventories were 3% lower in 2020 than in 2019 (680 v. 704, p <0.001) and 5% fewer RBCs were transfused per week compared to 2019 (477 v. 501, p <0.001). However, during the 1st COVID-19 peak, RBC and PLT inventories were higher than normal, as reflected by deviation from par, days on hand, and percent outdated. At this time, 16% fewer inpatient beds were occupied, and 43% fewer surgeries were performed compared to 2019 (p <0.001). In contrast to 2019 when there was no correlation, there was, in 2020, significant negative correlations between RBC and PLT days on hand and both percentage occupancy of inpatient beds and percentage of surgeries performed.CONCLUSION: During the COVID-19 pandemic in 2020, RBC and PLT inventories remained adequate. During the first wave of cases, significant decreases in patient care activities were associated with excess RBC and PLT supplies and increased product outdating.

  View details for DOI 10.1111/trf.17023

  View details for PubMedID 35808950

• Factors associated with first-time and repeat blood donation: Adverse reactions and effects on donor behavior. Transfusion Brunson, D. C., Belanger, G. A., Sussmann, H., Fine, A. M., Pandey, S., Pham, T. D. 2022

  Abstract

  BACKGROUND: Blood centers have a dual mission to protect donors and patients; donor safety is paramount to maintaining an adequate blood supply. Elucidating donor factors associated with adverse reactions (AR) is critical to this mission.STUDY DESIGN/METHODS: A retrospective cohort analysis of whole blood donors from 2003 to 2020 was conducted at a single blood center in northern California. Adjusted odds ratios (AORs) with 95% CIs for ARs were estimated via multivariable logistic regression on demographics, donation history, and physical examination data. Where appropriate, Wilcoxon-Rank Sum and chi-squared tests were used to determine significance.RESULTS: First-time blood donors (FTD) exhibited a higher AR rate than repeat donors (4.4% vs. 1.9% p<.0001). When compared with FTDs without AR, FTDs with ARs (FT-AR) were less likely to return (30.0% vs. 47.3%, p<.0001), and, of those who returned, had a higher rate of reaction 20.2% versus 2.8% (p<.001). Factors found to be associated with FT-AR (younger age, increased heart rate, and higher diastolic blood pressure) still correlated positively with AR on return donation, but to a lower degree. FTD who potentially witnessed an AR had a lower return rate (44.6% vs. 47.3%, p=<.001) and donated fewer units (2.38 vs. 3.37, p<.001) when compared to FTD who did not witness an AR.CONCLUSION: The AR on FTD increases the AR likelihood of return donation. Longitudinal analysis shows that a time-based deferral policy targeted at FT-AR young donors can reduce the number of ARs while not dramatically impacting the blood supply.

  View details for DOI 10.1111/trf.16893

  View details for PubMedID 35510783

• Differential Peripheral Blood Glycoprotein Profiles in Symptomatic and Asymptomatic COVID-19. Viruses Pickering, C., Zhou, B., Xu, G., Rice, R., Ramachandran, P., Huang, H., Pham, T. D., Schapiro, J. M., Cong, X., Chakraborty, S., Edwards, K., Reddy, S. T., Guirgis, F., Wang, T. T., Serie, D., Lindpaintner, K. 2022; 14 (3)

  Abstract

  Glycosylation is the most common form of post-translational modification of proteins, critically affecting their structure and function. Using liquid chromatography and mass spectrometry for high-resolution site-specific quantification of glycopeptides coupled with high-throughput artificial intelligence-powered data processing, we analyzed differential protein glycoisoform distributions of 597 abundant serum glycopeptides and nonglycosylated peptides in 50 individuals who had been seriously ill with COVID-19 and in 22 individuals who had recovered after an asymptomatic course of COVID-19. As additional comparison reference phenotypes, we included 12 individuals with a history of infection with a common cold coronavirus, 16 patients with bacterial sepsis, and 15 healthy subjects without history of coronavirus exposure. We found statistically significant differences, at FDR < 0.05, for normalized abundances of 374 of the 597 peptides and glycopeptides interrogated between symptomatic and asymptomatic COVID-19 patients. Similar statistically significant differences were seen when comparing symptomatic COVID-19 patients to healthy controls (350 differentially abundant peptides and glycopeptides) and common cold coronavirus seropositive subjects (353 differentially abundant peptides and glycopeptides). Among healthy controls and sepsis patients, 326 peptides and glycopeptides were found to be differentially abundant, of which 277 overlapped with biomarkers that showed differential expression between symptomatic COVID-19 cases and healthy controls. Among symptomatic COVID-19 cases and sepsis patients, 101 glycopeptide and peptide biomarkers were found to be statistically significantly abundant. Using both supervised and unsupervised machine learning techniques, we found specific glycoprotein profiles to be strongly predictive of symptomatic COVID-19 infection. LASSO-regularized multivariable logistic regression and K-means clustering yielded accuracies of 100% in an independent test set and of 96% overall, respectively. Our findings are consistent with the interpretation that a majority of glycoprotein modifications observed which are shared among symptomatic COVID-19 and sepsis patients likely represent a generic consequence of a severe systemic immune and inflammatory state. However, there are glycoisoform changes that are specific and particular to severe COVID-19 infection. These may be representative of either COVID-19-specific consequences or susceptibility to or predisposition for a severe course of the disease. Our findings support the potential value of glycoproteomic biomarkers in the biomedical understanding and, potentially, the clinical management of serious acute infectious conditions.

  View details for DOI 10.3390/v14030553

  View details for PubMedID 35336960

• Regulation of the BCR signalosome by the class II peptide editor, H2-M, affects the development and repertoire of innate-like B cells. Cell reports Ghosh, D., Pham, T. D., Nanaware, P. P., Sengupta, D., Adler, L. N., Li, C. G., He, X., O'Mara, M. E., Kantor, A. B., Nguyen, K. D., Yang, Y., Eisenlohr, L. C., Jensen, P. E., Herzenberg, L. A., Stern, L. J., Boyd, S. D., Ghosn, E. E., Mellins, E. D. 1800; 38 (4): 110200

  Abstract

  The non-classical Major Histocompatibility Complex class II (MHCII) protein, H2-M, edits peptides bound to conventional MHCII in favor of stable peptide/MHCII (p/MHCII) complexes. Here, we show that H2-M deficiency affects B-1 cell survival, reduces cell renewal capacity, and alters immunoglobulin repertoire, allowing for the selection of cells specific for highly abundant epitopes, but not low-frequency epitopes. H2-M-deficient B-1 cells have shorter CDR3 length, higher content of positively charged amino acids, shorter junctional regions, less mutation frequency, and a skewed clonal distribution. Mechanistically, H2-M loss reduces plasma membrane p/MHCII association with B cell receptors (BCR) on B-1 cells and diminishes integrated BCR signal strength, a key determinant of B-1 cell selection, maturation, and maintenance. Thus, H2-M:MHCII interaction serves as a cell-intrinsic regulator of BCR signaling and influences the selection of the B-1 cell clonal repertoire.

  View details for DOI 10.1016/j.celrep.2021.110200

  View details for PubMedID 35081339

• How do I implement pathogen-reduced platelets? Transfusion Pham, T. D., Kadi, W., Shu, E., Pandey, S., Sussmann, H., Shan, H., Virk, M. S. 2021

  Abstract

  BACKGROUND: Several risk mitigation steps have improved the safety of platelets in regard to bacterial contamination, but this continues to be a concern today. A Food and Drug Administration (FDA) Guidance issued in December 2018 aims to further limit this risk. The guidance offers multiple pathways for compliance, and hospital blood banks will have to collaborate with blood donor centers to assess various factors before deciding which method is most appropriate for them.METHODS AND MATERIALS: Our institution considered several factors before moving forward with pathogen reduction technology. This included an assessment of platelet shelf-life, bacterial testing requirements, the efficacy of low-yield platelets, and managing a mixed platelet inventory. The decision to transition to pathogen-reduced platelets was associated with complex collection and processing limitations that resulted in either an increase in platelets that were over-concentrated or products with a low platelet yield.RESULTS: Through trials of various collection settings with unique target volumes and target platelet yields, our blood donor center was able to optimize the production. At the hospital end, this transition required a thorough review of low-yield platelet products and their clinical efficacy. Additionally, this implementation necessitated collaboration with clinical colleagues, comprehensive education, and training.CONCLUSIONS: Pathogen-reduced platelets would be the most efficient way for our institution to be compliant. This summary may serve as a roadmap for other institutions that are considering which FDA prescribed method to use and provide support for those that have decided on pathogen reduction technology but need to optimize their collections to best utilize low-yield products.

  View details for DOI 10.1111/trf.16744

  View details for PubMedID 34796968

• ABO antibody titer performance characteristics and correlates between two automated platforms. Transfusion and apheresis science : official journal of the World Apheresis Association : official journal of the European Society for Haemapheresis Corean, J., Gilsdorf, J., Sauter, J., Pamukcu, P., Thorpe, S., Pham, T. 2021: 103262

  Abstract

  BACKGROUND: AABB standards require a policy for assessing transfusing ABO-incompatible plasma. After a fatal hemolytic event with incompatible plasma, our institution instituted platelet donor population titer method for ABO antibodies on the PK7300, with high-titer being defined as having isohemagglutinin titers greater than 256. We recently switched titering platforms to the Neo Iris and we seek to determine the equivalent isohemagglutinin high-titer cutoff on the Neo Iris as compared to the PK7300.METHODS: We measured the titers on 299 apheresis platelet donors and compared its performance characteristics at various cutoffs to the PK7300 reference standard. Discrepant results were manually diluted and retested on the Neo Galileo. Furthermore, since the Neo Iris is able to determine isotype and antigen specific titers, we also characterized these features in our donor population.RESULTS: IgM titer of 128 on the Neo Iris has better accuracy compared to the titer of 64 (94 % vs 93.6 %). Eleven of sixteen discordant results were in agreement with Neo Iris. Blood group O had the highest IgG antibody titers for both anti-A and anti-B (p = 8.4E-17 and 4.3E-09, respectively). Additionally, group O donors exhibited lower anti-A2 than anti-A1 IgG titers.DISCUSSION: The Neo Iris titer cut-off of 128 had the best overall accuracy and correlation with a 256 cut-off on our laboratory developed test on the PK7300 platform. Additionally, we found that group O donors had the highest titer antibodies, with typically higher IgG titers than IgM, and generally multiple dilution levels greater than other blood types.

  View details for DOI 10.1016/j.transci.2021.103262

  View details for PubMedID 34483036

• Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues. Science (New York, N.Y.) Yang, F., Nielsen, S. C., Hoh, R. A., Roltgen, K., Wirz, O. F., Haraguchi, E., Jean, G. H., Lee, J., Pham, T. D., Jackson, K. J., Roskin, K. M., Liu, Y., Nguyen, K., Ohgami, R. S., Osborne, E. M., Nadeau, K. C., Niemann, C. U., Parsonnet, J., Boyd, S. D. 2021

  Abstract

  Vaccination and infection promote the formation, tissue distribution, and clonal evolution of B cells, which encode humoral immune memory. We evaluated convergent antigen-specific antibody genes of similar sequences shared between individuals in pediatric and adult blood, and deceased organ donor tissues. B cell memory varied for different pathogens. Polysaccharide antigen-specific clones were not exclusive to the spleen. Adults had higher clone frequencies and greater class-switching in lymphoid tissues than blood, while pediatric blood had abundant class-switched convergent clones. Consistent with reported serology, pre-pandemic children had class-switched convergent clones to SARS-CoV-2 with weak cross-reactivity to other coronaviruses, while adult blood or tissues showed few such clones. The results highlight the prominence of early childhood B cell clonal expansions and cross-reactivity for future responses to novel pathogens.

  View details for DOI 10.1126/science.abf6648

  View details for PubMedID 33846272

• A Single Immunization with Spike-Functionalized Ferritin Vaccines Elicits Neutralizing Antibody Responses against SARS-CoV-2 in Mice. ACS central science Powell, A. E., Zhang, K., Sanyal, M., Tang, S., Weidenbacher, P. A., Li, S., Pham, T. D., Pak, J. E., Chiu, W., Kim, P. S. 2021; 7 (1): 183–99

  Abstract

  The development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SDeltaC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines, and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SDeltaC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SDeltaC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.

  View details for DOI 10.1021/acscentsci.0c01405

  View details for PubMedID 33527087

• Use of Outpatient-Derived COVID-19 Convalescent Plasma in COVID-19 Patients Before Seroconversion. Frontiers in immunology Wirz, O. F., Roltgen, K., Stevens, B. A., Pandey, S., Sahoo, M. K., Tolentino, L., Verghese, M., Nguyen, K., Hunter, M., Snow, T. T., Singh, A. R., Blish, C. A., Cochran, J. R., Zehnder, J. L., Nadeau, K. C., Pinsky, B. A., Pham, T. D., Boyd, S. D. 2021; 12: 739037

  Abstract

  Background: Transfusion of COVID-19 convalescent plasma (CCP) containing high titers of anti-SARS-CoV-2 antibodies serves as therapy for COVID-19 patients. Transfusions early during disease course was found to be beneficial. Lessons from the SARS-CoV-2 pandemic could inform early responses to future pandemics and may continue to be relevant in lower resource settings. We sought to identify factors correlating to high antibody titers in convalescent plasma donors and understand the magnitude and pharmacokinetic time course of both transfused antibody titers and the endogenous antibody titers in transfused recipients.Methods: Plasma samples were collected up to 174 days after convalescence from 93 CCP donors with mild disease, and from 16 COVID-19 patients before and after transfusion. Using ELISA, anti-SARS-CoV-2 Spike RBD, S1, and N-protein antibodies, as well as capacity of antibodies to block ACE2 from binding to RBD was measured in an in vitro assay. As an estimate for viral load, viral RNA and N-protein plasma levels were assessed in COVID-19 patients.Results: Anti-SARS-CoV-2 antibody levels and RBD-ACE2 blocking capacity were highest within the first 60 days after symptom resolution and markedly decreased after 120 days. Highest antibody titers were found in CCP donors that experienced fever. Effect of transfused CCP was detectable in COVID-19 patients who received high-titer CCP and had not seroconverted at the time of transfusion. Decrease in viral RNA was seen in two of these patients.Conclusion: Our results suggest that high titer CCP should be collected within 60 days after recovery from donors with past fever. The much lower titers conferred by transfused antibodies compared to endogenous production in the patient underscore the importance of providing CCP prior to endogenous seroconversion.

  View details for DOI 10.3389/fimmu.2021.739037

  View details for PubMedID 34594341

• Efficient Identification of High-Titer Anti-Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Antibody Plasma Samples by Pooling Method. Archives of pathology & laboratory medicine Nguyen, K. D., Wirz, O. F., Röltgen, K., Pandey, S., Tolentino, L., Boyd, S. D., Pham, T. D. 2021

  Abstract

  The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has elicited a surge in demand for serological testing to identify previously infected individuals. In particular, antibody testing is crucial in identifying COVID-19 convalescent plasma (CCP), which has been approved by the Food and Drug Administration (FDA) under the Emergency Use Authorization (EUA) for use as passive immune therapy for hospitalized patients infected with COVID-19. Currently, high-titer CCP can be qualified by Ortho's Vitros COVID-19 IgG antibody test (VG).To explore the use of an efficient testing method to identify high-titer CCP for use in treating COVID-19 infected patients and track COVID-19 positivity over time.We evaluated an ELISA-based method that detects antibodies specific to the SARSCoV-2 receptor binding domain (RBD) with individual and pooled plasma samples and compared its performance against VG. Using the pooled RBD-ELISA (P-RE) method, we also screened over 10,000 longitudinal healthy blood donor samples to assess seroprevalence.P-RE demonstrates 100% sensitivity in detecting FDA-defined high-titer samples when compared to VG. Overall sensitivity of P-RE when compared to VG and our individual sample RBD-ELISA (I-RE) were 83% and 56%, respectively. When screening 10,218 healthy blood donor samples by P-RE, we found the seroprevalence correlated with the local infection rates with a correlation coefficient of 0.21 (P< .001).Pooling plasma samples can be used to efficiently screen large populations for individuals with high-titer anti-RBD antibodies, important for CCP identification.

  View details for DOI 10.5858/arpa.2021-0215-SA

  View details for PubMedID 34101801

• Identifying correlations between donor demographics and isohemagglutinin titers as a potential method to screen for low-titer group O whole blood. Transfusion and apheresis science : official journal of the World Apheresis Association : official journal of the European Society for Haemapheresis Jacob, R. P., Wang, D., Hodghead, K., Pham, T. D. 2020: 102970

  Abstract

  BACKGROUND: With more hospitals using low-titer group O whole blood in trauma resuscitation, having an efficient screening method for low-titer donors is critical. Our blood center uses an automated screen for high-titer isohemagglutinins in our platelet donations while collecting detailed donor demographic information. Using this data, we can identify key demographics often associated with titer status, thereby helping develop a donor-triaging method for titering.STUDY DESIGN AND METHODS: Titer results were read with an automated microplate system as either high or low, based on agglutination, with a cutoff equivalent to 1:256 (both anti-A and anti-B). Donor demographic data analyzed included date of donation, blood group, age, gender, and ethnicity.RESULTS: 57,508 donations were collected from 2073 unique donors between 2014 and 2018. We found the following demographics to be correlated with titer status: gender, ABO blood group, age, and ethnicity. Variability in titer status was identified in 215 individuals. This represented around 10 % of the total unique donors and was split equally amongst gender. We also found that donors between the ages of 41-60had the highest likelihood of having variability in titer status, peaking at 13 %, and this proportion declined past age 60.CONCLUSION: Titer status is associated with the following donor demographics: gender, ABO type, age, and ethnicity. We also discovered that variability in titer status is correlated with age. In blood centers that do not have automated and routine titer screening procedure, these findings could be used as a method to efficiently identify low-titer donors a-priori.

  View details for DOI 10.1016/j.transci.2020.102970

  View details for PubMedID 33223473

• SARS-CoV-2 Antibody Responses Correlate with Resolution of RNAemia But Are Short-Lived in Patients with Mild Illness. medRxiv : the preprint server for health sciences Röltgen, K., Wirz, O. F., Stevens, B. A., Powell, A. E., Hogan, C. A., Najeeb, J., Hunter, M., Sahoo, M. K., Huang, C., Yamamoto, F., Manalac, J., Otrelo-Cardoso, A. R., Pham, T. D., Rustagi, A., Rogers, A. J., Shah, N. H., Blish, C. A., Cochran, J. R., Nadeau, K. C., Jardetzky, T. S., Zehnder, J. L., Wang, T. T., Kim, P. S., Gombar, S., Tibshirani, R., Pinsky, B. A., Boyd, S. D. 2020

  Abstract

  SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, could offer protective immunity, and may affect clinical outcomes of COVID-19 patients. We analyzed 625 serial plasma samples from 40 hospitalized COVID-19 patients and 170 SARS-CoV-2-infected outpatients and asymptomatic individuals. Severely ill patients developed significantly higher SARS-CoV-2-specific antibody responses than outpatients and asymptomatic individuals. The development of plasma antibodies was correlated with decreases in viral RNAemia, consistent with potential humoral immune clearance of virus. Using a novel competition ELISA, we detected antibodies blocking RBD-ACE2 interactions in 68% of inpatients and 40% of outpatients tested. Cross-reactive antibodies recognizing SARS-CoV RBD were found almost exclusively in hospitalized patients. Outpatient and asymptomatic individuals' serological responses to SARS-CoV-2 decreased within 2 months, suggesting that humoral protection may be short-lived.

  View details for DOI 10.1101/2020.08.15.20175794

  View details for PubMedID 32839786

  View details for PubMedCentralID PMC7444305

• The class II peptide editor, H2-M, affects the development and repertoire of B-1 cells Ghosh, D., Pham, T. D., He, X., O'mara, M. E., Kantor, A. B., Khoa Nguyen, Sengupta, D., Eisenlohr, L. C., Jensen, P. E., Herzenberg, L. A., Boyd, S. D., Ghosn, E. B., Mellins, E. D. AMER ASSOC IMMUNOLOGISTS. 2020

  View details for Web of Science ID 000589972401412

• Defining the features and duration of antibody responses to SARS-CoV-2 infection associated with disease severity and outcome. Science immunology Röltgen, K. n., Powell, A. E., Wirz, O. F., Stevens, B. A., Hogan, C. A., Najeeb, J. n., Hunter, M. n., Wang, H. n., Sahoo, M. K., Huang, C. n., Yamamoto, F. n., Manohar, M. n., Manalac, J. n., Otrelo-Cardoso, A. R., Pham, T. D., Rustagi, A. n., Rogers, A. J., Shah, N. H., Blish, C. A., Cochran, J. R., Jardetzky, T. S., Zehnder, J. L., Wang, T. T., Narasimhan, B. n., Gombar, S. n., Tibshirani, R. n., Nadeau, K. C., Kim, P. S., Pinsky, B. A., Boyd, S. D. 2020; 5 (54)

  Abstract

  SARS-CoV-2-specific antibodies, particularly those preventing viral spike receptor binding domain (RBD) interaction with host angiotensin-converting enzyme 2 (ACE2) receptor, can neutralize the virus. It is, however, unknown which features of the serological response may affect clinical outcomes of COVID-19 patients. We analyzed 983 longitudinal plasma samples from 79 hospitalized COVID-19 patients and 175 SARS-CoV-2-infected outpatients and asymptomatic individuals. Within this cohort, 25 patients died of their illness. Higher ratios of IgG antibodies targeting S1 or RBD domains of spike compared to nucleocapsid antigen were seen in outpatients who had mild illness versus severely ill patients. Plasma antibody increases correlated with decreases in viral RNAemia, but antibody responses in acute illness were insufficient to predict inpatient outcomes. Pseudovirus neutralization assays and a scalable ELISA measuring antibodies blocking RBD-ACE2 interaction were well correlated with patient IgG titers to RBD. Outpatient and asymptomatic individuals' SARS-CoV-2 antibodies, including IgG, progressively decreased during observation up to five months post-infection.

  View details for DOI 10.1126/sciimmunol.abe0240

  View details for PubMedID 33288645

• A single immunization with spike-functionalized ferritin vaccines elicits neutralizing antibody responses against SARS-CoV-2 in mice. bioRxiv : the preprint server for biology Powell, A. E., Zhang, K. n., Sanyal, M. n., Tang, S. n., Weidenbacher, P. A., Li, S. n., Pham, T. D., Pak, J. E., Chiu, W. n., Kim, P. S. 2020

  Abstract

  Development of a safe and effective SARS-CoV-2 vaccine is a public health priority. We designed subunit vaccine candidates using self-assembling ferritin nanoparticles displaying one of two multimerized SARS-CoV-2 spikes: full-length ectodomain (S-Fer) or a C-terminal 70 amino-acid deletion (SΔC-Fer). Ferritin is an attractive nanoparticle platform for production of vaccines and ferritin-based vaccines have been investigated in humans in two separate clinical trials. We confirmed proper folding and antigenicity of spike on the surface of ferritin by cryo-EM and binding to conformation-specific monoclonal antibodies. After a single immunization of mice with either of the two spike ferritin particles, a lentiviral SARS-CoV-2 pseudovirus assay revealed mean neutralizing antibody titers at least 2-fold greater than those in convalescent plasma from COVID-19 patients. Additionally, a single dose of SΔC-Fer elicited significantly higher neutralizing responses as compared to immunization with the spike receptor binding domain (RBD) monomer or spike ectodomain trimer alone. After a second dose, mice immunized with SΔC-Fer exhibited higher neutralizing titers than all other groups. Taken together, these results demonstrate that multivalent presentation of SARS-CoV-2 spike on ferritin can notably enhance elicitation of neutralizing antibodies, thus constituting a viable strategy for single-dose vaccination against COVID-19.

  View details for DOI 10.1101/2020.08.28.272518

  View details for PubMedID 32869030

  View details for PubMedCentralID PMC7457616

• Symptomatic SARS-CoV-2 infections display specific IgG Fc structures. medRxiv : the preprint server for health sciences Chakraborty, S. n., Edwards, K. n., Buzzanco, A. S., Memoli, M. J., Sherwood, R. n., Mallajosyula, V. n., Xie, M. M., Gonzalez, J. n., Buffone, C. n., Kathale, N. n., Providenza, S. n., Jagannathan, P. n., Andrews, J. R., Blish, C. A., Krammer, F. n., Dugan, H. n., Wilson, P. C., Pham, T. D., Boyd, S. D., Zhang, S. n., Taubenberger, J. K., Morales, T. n., Schapiro, J. M., Parsonnet, J. n., Wang, T. T. 2020

  Abstract

  The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has caused a public health crisis that is exacerbated by our poor understanding of correlates of immunity. SARS-CoV-2 infection can cause Coronavirus Disease 2019 (COVID-19), with a spectrum of symptoms ranging from asymptomatic carriage to life threatening pneumonia and cytokine dysregulation [1-3]. Although antibodies have been shown in a variety of in vitro assays to promote coronavirus infections through mechanisms requiring interactions between IgG antibodies and Fc gamma receptors (FcγRs), the relevance of these observations to coronavirus infections in humans is not known [4-7]. In light of ongoing clinical trials examining convalescent serum therapy for COVID-19 patients and expedited SARS-CoV-2 vaccine testing in humans, it is essential to clarify the role of antibodies in the pathogenesis of COVID-19. Here we show that adults with PCR-diagnosed COVID-19 produce IgG antibodies with a specific Fc domain repertoire that is characterized by reduced fucosylation, a modification that enhances interactions with the activating FcγR, FcγRIIIa. Fc fucosylation was reduced when compared with SARS-CoV-2-seropositive children and relative to adults with symptomatic influenza virus infections. These results demonstrate an antibody correlate of symptomatic SARS-CoV-2 infections in adults and have implications for novel therapeutic strategies targeting FcγRIIIa pathways.

  View details for DOI 10.1101/2020.05.15.20103341

  View details for PubMedID 32511463

  View details for PubMedCentralID PMC7252581

• SARS-CoV-2 RNAemia in a Healthy Blood Donor 40 Days After Respiratory Illness Resolution. Annals of internal medicine Pham, T. D., Huang, C. n., Wirz, O. F., Röltgen, K. n., Sahoo, M. K., Layon, A. n., Pandey, S. n., Foung, S. K., Boyd, S. D., Pinsky, B. A. 2020

  View details for DOI 10.7326/L20-0725

  View details for PubMedID 32678685

• Interferon-gamma release assay for accurate detection of SARS-CoV-2 T cell response. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Murugesan, K. n., Jagannathan, P. n., Pham, T. D., Pandey, S. n., Bonilla, H. F., Jacobson, K. n., Parsonnet, J. n., Andrews, J. R., Weiskopf, D. n., Sette, A. n., Pinsky, B. A., Singh, U. n., Banaei, N. n. 2020

  Abstract

  We investigated feasibility and accuracy of an interferon-gamma release assay (IGRA) for detection of T cell responses to SARS-CoV-2. Whole blood IGRA accurately distinguished between convalescents and uninfected healthy blood donors with a predominantly CD4+ T cell response. SARS-CoV-2 IGRA may serve as a useful diagnostic tool in managing the COVID-19 pandemic.

  View details for DOI 10.1093/cid/ciaa1537

  View details for PubMedID 33035306

• Optimizing O-negative RBC utilization using a data-driven approach. Transfusion Virk, M. S., Lancaster, D. n., Quach, T. n., Lim, A. n., Shu, E. n., Belanger, G. n., Pham, T. D. 2020

  Abstract

  O-negative red blood cells (ON-RBC) are a precious resource and the international blood banking community has become increasingly concerned with its inappropriate utilization. AABB recently made several recommendations to address the issue. Solutions must be multifaceted and involve donor centers, blood banks, and clinical departments. From the perspective of a hospital blood bank, it is difficult to rely solely on increased donor recruitment and ubiquitous blood typing of the entire in-patient population. We therefore focused on interventions within the blood bank to optimize inventory and policies to ensure appropriate ON-RBC utilization.Transfusion data over one year was examined for the rate of out-of-group/inappropriate ON-RBC. Furthermore, we assessed whether that rate was related to product life on the day of transfusion. We also examined our stock inventory levels and how excess inventory can contribute to inappropriate ON-RBC usage.The ON-RBC inventory level was decreased in order to reduce the rate of inappropriate transfusions while maintaining a safe level for optimal patient care. Compared to baseline, our intervention caused ON-RBCs to be transfused earlier in their shelf-life (9.27 vs. 11.15 days from expiration [DFE], p = 0.0012). This reduced the overall rate of inappropriate ON-RBC transfusions (67% vs. 54%, p = 0.0035), approximating 185 units of ON-RBC saved over the course of 6 months.A data-driven approach to optimize stock inventory levels is widely applicable; it can be adopted by numerous institutions to improve utilization and establish a benchmark for the broader blood banking community.

  View details for DOI 10.1111/trf.15713

  View details for PubMedID 32077488

• Proinflammatory IgG Fc structures in patients with severe COVID-19 Nature Immunology Chakraborty, S., Gonzales, J., Edwards, K., Mallajosyulla, V., Buzzanco, A. S., Sherwood, R., Buffone, C., Kathale, N., Providenza, S., Xie, M. M., Andrews, J. R., Blish, C. A., Singh, U., Dugan, H., Wilson, P. C., Pham, T. D., Boyd, S. D., Nadeau, K. C., Pinsky, B. A., Zhang, S., Memoli, M. J., Taubenberger, J. K., Morales, T., Schapiro, J. M., Tan, G. S., et al 2020

  View details for DOI 10.1038/s41590-020-00828-7

• High-Titer Isohemagglutinins in Platelet Donors Jacob, R., Wang, D., Hodghead, K., Pham, T. WILEY. 2019: 53A–54A

  View details for Web of Science ID 000502826600113

• A FLOW CYTOMETRY BASED ABO-BLOOD GROUP ANTIBODY ASSAY (FABO-AB) FOR PREDICTING HEMOLYSIS IN ABO-MISMATCHED BONE MARROW TRANSPLANTATION (BMT) Liu, H., Nguyen, K. D., Virk, M. S., Pham, T. D., Chen, G. ELSEVIER SCIENCE INC. 2019: 40

  View details for DOI 10.1016/j.humimm.2019.07.035

  View details for Web of Science ID 000489085600033

• Shaping of infant B cell receptor repertoires by environmental factors and infectious disease. Science translational medicine Nielsen, S. C., Roskin, K. M., Jackson, K. J., Joshi, S. A., Nejad, P., Lee, J., Wagar, L. E., Pham, T. D., Hoh, R. A., Nguyen, K. D., Tsunemoto, H. Y., Patel, S. B., Tibshirani, R., Ley, C., Davis, M. M., Parsonnet, J., Boyd, S. D. 2019; 11 (481)

  Abstract

  Antigenic exposures at epithelial sites in infancy and early childhood are thought to influence the maturation of humoral immunity and modulate the risk of developing immunoglobulin E (IgE)-mediated allergic disease. How different kinds of environmental exposures influence B cell isotype switching to IgE, IgG, or IgA, and the somatic mutation maturation of these antibody pools, is not fully understood. We sequenced antibody repertoires in longitudinal blood samples in a birth cohort from infancy through the first 3 years of life and found that, whereas IgG and IgA show linear increases in mutational maturation with age, IgM and IgD mutations are more closely tied to pathogen exposure. IgE mutation frequencies are primarily increased in children with impaired skin barrier conditions such as eczema, suggesting that IgE affinity maturation could provide a mechanistic link between epithelial barrier failure and allergy development.

  View details for PubMedID 30814336

• Shaping of infant B cell receptor repertoires by environmental factors and infectious disease SCIENCE TRANSLATIONAL MEDICINE Nielsen, S. A., Roskin, K. M., Jackson, K. L., Joshi, S. A., Nejad, P., Lee, J., Wagar, L. E., Pham, T. D., Hoh, R. A., Nguyen, K. D., Tsunemoto, H. Y., Patel, S. B., Tibshirani, R., Ley, C., Davis, M. M., Parsonnet, J., Boyd, S. D. 2019; 11 (481)

  View details for DOI 10.1126/scitranslmed.aat2004

  View details for Web of Science ID 000460307000001

• Molecular Characterizations of Anti-ABO Blood Group Antibodies Nguyen, K., Pham, T., Boyd, S. WILEY. 2018: 22A

  View details for Web of Science ID 000444475900034

• Streamlining a blood center and hospital transfusion service supply chain with an informatics vendor-managed inventory solution: development, implementation, and 3-month follow-up TRANSFUSION Tsang, H. C., Garcia, A., Scott, R., Lancaster, D., Geary, D., Anh-Thu Nguyen, Shankar, R., Buchanan, L., Pham, T. D. 2018; 58 (7): 1718–25

  Abstract

  The ordering process at Stanford Health Care involved twice-daily shipments predicated upon current stock levels from the blood center to the hospital transfusion service. Manual census determination is time consuming and error prone. We aimed to enhance inventory management by developing an informatics platform to streamline the ordering process and reallocate staff productivity.The general inventory accounts for more than 50 product categories based on characteristics including component, blood type, irradiation status, and cytomegalovirus serology status. Over a 5-month calibration period, inventory levels were determined algorithmically and electronically. An in-house software program was created to determine inventory levels, optimize the electronic ordering process, and reduce labor time. A 3-month pilot period was implemented using this program.This system showed noninferiority while saving labor time. The average weekly transfused:stocked ratios for cryoprecipitate, plasma, and red blood cells, respectively, were 1.03, 1.21, and 1.48 before the pilot period, compared with 0.88, 1.17, and 1.40 during (p = 0.28). There were 27 (before) and 31 (during) average STAT units ordered per week (p = 0.86). The number of monthly wasted products due to expiration was 226 (before) and 196 (during) units, respectively (p = 0.28). An estimated 7 hours per week of technologist time was reallocated to other tasks.An in-house electronic ordering system can enhance information fidelity, reallocate and optimize valuable staff productivity, and further standardize ordering. This system showed noninferiority to the labor-intensive manual system while freeing up over 360 hours of staff time per year.

  View details for PubMedID 29770454

• Big data modeling to predict platelet usage and minimize wastage in a tertiary care system PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Guan, L., Tian, X., Gombar, S., Zemek, A. J., Krishnan, G., Scott, R., Narasimhan, B., Tibshirani, R. J., Pham, T. D. 2017; 114 (43): 11368–73

  Abstract

  Maintaining a robust blood product supply is an essential requirement to guarantee optimal patient care in modern health care systems. However, daily blood product use is difficult to anticipate. Platelet products are the most variable in daily usage, have short shelf lives, and are also the most expensive to produce, test, and store. Due to the combination of absolute need, uncertain daily demand, and short shelf life, platelet products are frequently wasted due to expiration. Our aim is to build and validate a statistical model to forecast future platelet demand and thereby reduce wastage. We have investigated platelet usage patterns at our institution, and specifically interrogated the relationship between platelet usage and aggregated hospital-wide patient data over a recent consecutive 29-mo period. Using a convex statistical formulation, we have found that platelet usage is highly dependent on weekday/weekend pattern, number of patients with various abnormal complete blood count measurements, and location-specific hospital census data. We incorporated these relationships in a mathematical model to guide collection and ordering strategy. This model minimizes waste due to expiration while avoiding shortages; the number of remaining platelet units at the end of any day stays above 10 in our model during the same period. Compared with historical expiration rates during the same period, our model reduces the expiration rate from 10.5 to 3.2%. Extrapolating our results to the ∼2 million units of platelets transfused annually within the United States, if implemented successfully, our model can potentially save ∼80 million dollars in health care costs.

  View details for PubMedID 29073058

• Occult Hemolytic Anemia Due to Anti-Mur in a Patient Receiving Blood from a Region with a Prominent Asian Donor Population Oak, J., Mallari, R., de Asis, M., Shu, E., Hughes, J., Pham, T. WILEY. 2017: 178A

  View details for Web of Science ID 000409065000450

• Streamlining a Blood Center and Hospital Transfusion Service Supply-Chain with an Informatics Vendor-Managed Inventory Solution Tsang, H. C., Lancaster, D., Geary, D., Scott, R., Nguyen, A., Garcia, A., Shankar, R., Buchanan, L., Pham, T. WILEY. 2017: 211A

  View details for Web of Science ID 000409065000532

• Normalizing Microbiota-Induced Retinoic Acid Deficiency Stimulates Protective CD8(+) T Cell-Mediated Immunity in Colorectal Cancer. Immunity Bhattacharya, N., Yuan, R., Prestwood, T. R., Penny, H. L., DiMaio, M. A., Reticker-Flynn, N. E., Krois, C. R., Kenkel, J. A., Pham, T. D., Carmi, Y., Tolentino, L., Choi, O., Hulett, R., Wang, J., Winer, D. A., Napoli, J. L., Engleman, E. G. 2016; 45 (3): 641-655

  Abstract

  Although all-trans-retinoic acid (atRA) is a key regulator of intestinal immunity, its role in colorectal cancer (CRC) is unknown. We found that mice with colitis-associated CRC had a marked deficiency in colonic atRA due to alterations in atRA metabolism mediated by microbiota-induced intestinal inflammation. Human ulcerative colitis (UC), UC-associated CRC, and sporadic CRC specimens have similar alterations in atRA metabolic enzymes, consistent with reduced colonic atRA. Inhibition of atRA signaling promoted tumorigenesis, whereas atRA supplementation reduced tumor burden. The benefit of atRA treatment was mediated by cytotoxic CD8(+) T cells, which were activated due to MHCI upregulation on tumor cells. Consistent with these findings, increased colonic expression of the atRA-catabolizing enzyme, CYP26A1, correlated with reduced frequencies of tumoral cytotoxic CD8(+) T cells and with worse disease prognosis in human CRC. These results reveal a mechanism by which microbiota drive colon carcinogenesis and highlight atRA metabolism as a therapeutic target for CRC.

  View details for DOI 10.1016/j.immuni.2016.08.008

  View details for PubMedID 27590114

  View details for PubMedCentralID PMC5132405

• Human B-cell isotype switching origins of IgE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Looney, T. J., Lee, J., Roskin, K. M., Hoh, R. A., King, J., Glanville, J., Liu, Y., Pham, T. D., Dekker, C. L., Davis, M. M., Boyd, S. D. 2016; 137 (2): 579-?

  Abstract

  B cells expressing IgE contribute to immunity against parasites and venoms and are the source of antigen specificity in allergic patients, yet the developmental pathways producing these B cells in human subjects remain a subject of debate. Much of our knowledge of IgE lineage development derives from model studies in mice rather than from human subjects.We evaluate models for isotype switching to IgE in human subjects using immunoglobulin heavy chain (IGH) mutational lineage data.We analyzed IGH repertoires in 9 allergic and 24 healthy adults using high-throughput DNA sequencing of 15,843,270 IGH rearrangements to identify clonal lineages of B cells containing members expressing IgE. Somatic mutations in IGH inherited from common ancestors within the clonal lineage are used to infer the relationships between B cells.Data from 613,641 multi-isotype B-cell clonal lineages, of which 592 include an IgE member, are consistent with indirect switching to IgE from IgG- or IgA-expressing lineage members in human subjects. We also find that these inferred isotype switching frequencies are similar in healthy and allergic subjects.We found evidence that secondary isotype switching of mutated IgG1-expressing B cells is the primary source of IgE in human subjects, with lesser contributions from precursors expressing other switched isotypes and rarely IgM or IgD, suggesting that IgE is derived from previously antigen-experienced B cells rather than naive B cells that typically express low-affinity unmutated antibodies. These data provide a basis from which to evaluate allergen-specific human antibody repertoires in healthy and diseased subjects.

  View details for DOI 10.1016/j.jaci.2015.07.014

  View details for Web of Science ID 000369235500028

• Single B-cell deconvolution of peanut-specific antibody responses in allergic patients JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Hoh, R. A., Joshi, S. A., Liu, Y., Wang, C., Roskin, K. M., Lee, J., Pham, T., Looney, T. J., Jackson, K. J., Dixit, V. P., King, J., Lyu, S., Jenks, J., Hamilton, R. G., Nadeau, K. C., Boyd, S. D. 2016; 137 (1): 157-167

  Abstract

  The frequencies, cellular phenotypes, epitope specificity, and clonal diversity of allergen-specific B cells in patients with food allergy are not fully understood but are of major pathogenic and therapeutic significance.We sought to characterize peanut allergen-specific B-cell populations and the sequences and binding activities of their antibodies before and during immunotherapy.B cells binding fluorescently labeled Ara h 1 or Ara h 2 were phenotyped and isolated by means of flow cytometric sorting from 18 patients at baseline and 13 patients during therapy. Fifty-seven mAbs derived from allergen-binding single B cells were evaluated by using ELISA, Western blotting, and peptide epitope mapping. Deep sequencing of the B-cell repertoires identified additional members of the allergen-specific B-cell clones.Median allergen-binding B-cell frequencies were 0.0097% (Ara h 1) or 0.029% (Ara h 2) of B cells in baseline blood from allergic patients and approximately 3-fold higher during immunotherapy. Five of 57 allergen-specific cells belonged to clones containing IgE-expressing members. Almost all allergen-specific antibodies were mutated, and binding to both conformational and linear allergen epitopes was detected. Increasing somatic mutation of IgG4 members of a clone was seen in immunotherapy, whereas IgE mutation levels in the clone did not increase.Most peanut allergen-binding B cells isolated by means of antigen-specific flow sorting express mutated and isotype-switched antibodies. Immunotherapy increases their frequency in the blood, and even narrowly defined allergen epitopes are recognized by numerous distinct B-cell clones in a patient. The results also suggest that oral immunotherapy can stimulate somatic mutation of allergen-specific IgG4.

  View details for DOI 10.1016/j.jaci.2015.05.029

  View details for Web of Science ID 000367724300006

• Normalizing microbiota-induced retinoic acid deficiency stimulates protective CD8+ T-cell-mediated immunity in colorectal cancer Immunity Bhattacharya, N., Yuan, R., Prestwood, T., Penny, H., DiMaio, M., Reticker-Flynn, N., Krois, C., Kenkel, J., Pham, T., Carmi, Y., Tolentino, L., Choi, O., Hulett, R., Wang, J., Winer, D., Napoli, J., Engleman, E. 2016; 45: 641–55

  Abstract

  Although all-trans-retinoic acid (atRA) is a key regulator of intestinal immunity, its role in colorectal cancer (CRC) is unknown. We found that mice with colitis-associated CRC had a marked deficiency in colonic atRA due to alterations in atRA metabolism mediated by microbiota-induced intestinal inflammation. Human ulcerative colitis (UC), UC-associated CRC, and sporadic CRC specimens have similar alterations in atRA metabolic enzymes, consistent with reduced colonic atRA. Inhibition of atRA signaling promoted tumorigenesis, whereas atRA supplementation reduced tumor burden. The benefit of atRA treatment was mediated by cytotoxic CD8(+) T cells, which were activated due to MHCI upregulation on tumor cells. Consistent with these findings, increased colonic expression of the atRA-catabolizing enzyme, CYP26A1, correlated with reduced frequencies of tumoral cytotoxic CD8(+) T cells and with worse disease prognosis in human CRC. These results reveal a mechanism by which microbiota drive colon carcinogenesis and highlight atRA metabolism as a therapeutic target for CRC.

  View details for DOI 10.1016/j.immuni.2016.08.008

  View details for PubMedCentralID PMC5132405

• How do I implement an automated screen for high-titer ABO antibody as an inventory management tool for ABO plasma-incompatible platelets? TRANSFUSION Fontaine, M. J., Webster, J., Gomez, S., Pham, T. D., Goodnough, L. T., Galel, S. A. 2015; 55 (12): 2783-2789

  Abstract

  Plasma volume reduction (PVR) may reduce the risk of hemolysis associated with transfusion of plateletpheresis blood products (PLTs) containing ABO-incompatible plasma. But PVR may delay PLT issue. In collaboration with our blood donor center we evaluated an automated screen of PLT for high-titer ABO antibody and to apply PVR to high-titer PLTs.At the donor center, plasma from PLT donors was tested using an automated microplate system (PK7300, Beckman). PK settings were set for a detection cutoff equivalent to 1 in 256 using a manual tube method. The donors associated with high-titer PLTs were characterized by sex and age. In the transfusion service, the number of PVR procedures was evaluated before and after implementation of the high-titer screen.During validation, 157 of 1008 PLT units (15%) were positive by the automated method versus 121 (12%) by manual method. After implementation, 2112 of 15,240 PLT units were high-titer, with higher frequency in donations from females versus males (18% vs. 12%, p < 0.0001). The PLT PVR rate was reduced by 50%.Implementation of an automated method to screen PLTs for high-titer ABO antibody at the donor center improves the inventory management of PLTs containing ABO-incompatible plasma at the hospital transfusion service.

  View details for DOI 10.1111/trf.13374

  View details for Web of Science ID 000367950600004

• How do I implement an automated screen for high-titer ABO antibody as an inventory management tool for ABO plasma-incompatible platelets? Transfusion Fontaine, M. J., Webster, J., Gomez, S., Pham, T. D., Goodnough, L. T., Galel, S. A. 2015; 55 (12): 2783-9

  Abstract

  Plasma volume reduction (PVR) may reduce the risk of hemolysis associated with transfusion of plateletpheresis blood products (PLTs) containing ABO-incompatible plasma. But PVR may delay PLT issue. In collaboration with our blood donor center we evaluated an automated screen of PLT for high-titer ABO antibody and to apply PVR to high-titer PLTs.At the donor center, plasma from PLT donors was tested using an automated microplate system (PK7300, Beckman). PK settings were set for a detection cutoff equivalent to 1 in 256 using a manual tube method. The donors associated with high-titer PLTs were characterized by sex and age. In the transfusion service, the number of PVR procedures was evaluated before and after implementation of the high-titer screen.During validation, 157 of 1008 PLT units (15%) were positive by the automated method versus 121 (12%) by manual method. After implementation, 2112 of 15,240 PLT units were high-titer, with higher frequency in donations from females versus males (18% vs. 12%, p < 0.0001). The PLT PVR rate was reduced by 50%.Implementation of an automated method to screen PLTs for high-titer ABO antibody at the donor center improves the inventory management of PLTs containing ABO-incompatible plasma at the hospital transfusion service.

  View details for DOI 10.1111/trf.13374

  View details for PubMedID 26448376

• IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Science translational medicine Roskin, K. M., Simchoni, N., Liu, Y., Lee, J., Seo, K., Hoh, R. A., Pham, T., Park, J. H., Furman, D., Dekker, C. L., Davis, M. M., James, J. A., Nadeau, K. C., Cunningham-Rundles, C., Boyd, S. D. 2015; 7 (302): 302ra135-?

  Abstract

  Common variable immune deficiency (CVID) is the most common symptomatic primary immune deficiency, affecting ~1 in 25,000 persons. These patients suffer from impaired antibody responses, autoimmunity, and susceptibility to lymphoid cancers. To explore the cellular basis for these clinical phenotypes, we conducted high-throughput DNA sequencing of immunoglobulin heavy chain gene rearrangements from 93 CVID patients and 105 control subjects and sorted naïve and memory B cells from 13 of the CVID patients and 10 of the control subjects. The CVID patients showed abnormal VDJ rearrangement and abnormal formation of complementarity-determining region 3 (CDR3). We observed a decreased selection against antibodies with long CDR3s in memory repertoires and decreased variable gene replacement, offering possible mechanisms for increased patient autoreactivity. Our data indicate that patient immunodeficiency might derive from both decreased diversity of the naïve B cell pool and decreased somatic hypermutation in memory repertoires. The CVID patients also exhibited an abnormal clonal expansion of unmutated B cells relative to the controls. Although impaired B cell germinal center activation is commonly viewed as causative in CVID, these data indicate that CVID B cells diverge from controls as early as the pro-B stage, cell and suggest possible explanations for the increased incidence of autoimmunity, immunodeficiency, and lymphoma CVID patients.

  View details for DOI 10.1126/scitranslmed.aab1216

  View details for PubMedID 26311730

  View details for PubMedCentralID PMC4584259

• IgH sequences in common variable immune deficiency reveal altered B cell development and selection. Science translational medicine Roskin, K. M., Simchoni, N., Liu, Y., Lee, J., Seo, K., Hoh, R. A., Pham, T., Park, J. H., Furman, D., Dekker, C. L., Davis, M. M., James, J. A., Nadeau, K. C., Cunningham-Rundles, C., Boyd, S. D. 2015; 7 (302): 302ra135-?

  Abstract

  Common variable immune deficiency (CVID) is the most common symptomatic primary immune deficiency, affecting ~1 in 25,000 persons. These patients suffer from impaired antibody responses, autoimmunity, and susceptibility to lymphoid cancers. To explore the cellular basis for these clinical phenotypes, we conducted high-throughput DNA sequencing of immunoglobulin heavy chain gene rearrangements from 93 CVID patients and 105 control subjects and sorted naïve and memory B cells from 13 of the CVID patients and 10 of the control subjects. The CVID patients showed abnormal VDJ rearrangement and abnormal formation of complementarity-determining region 3 (CDR3). We observed a decreased selection against antibodies with long CDR3s in memory repertoires and decreased variable gene replacement, offering possible mechanisms for increased patient autoreactivity. Our data indicate that patient immunodeficiency might derive from both decreased diversity of the naïve B cell pool and decreased somatic hypermutation in memory repertoires. The CVID patients also exhibited an abnormal clonal expansion of unmutated B cells relative to the controls. Although impaired B cell germinal center activation is commonly viewed as causative in CVID, these data indicate that CVID B cells diverge from controls as early as the pro-B stage, cell and suggest possible explanations for the increased incidence of autoimmunity, immunodeficiency, and lymphoma CVID patients.

  View details for DOI 10.1126/scitranslmed.aab1216

  View details for PubMedID 26311730

• Human B-cell isotype switching origins of IgE. The Journal of allergy and clinical immunology Looney, T. J., Lee, J. Y., Roskin, K. M., Hoh, R. A., King, J., Glanville, J., Liu, Y., Pham, T. D., Dekker, C. L., Davis, M. M., Boyd, S. D. 2015

  Abstract

  B cells expressing IgE contribute to immunity against parasites and venoms and are the source of antigen specificity in allergic patients, yet the developmental pathways producing these B cells in human subjects remain a subject of debate. Much of our knowledge of IgE lineage development derives from model studies in mice rather than from human subjects.We evaluate models for isotype switching to IgE in human subjects using immunoglobulin heavy chain (IGH) mutational lineage data.We analyzed IGH repertoires in 9 allergic and 24 healthy adults using high-throughput DNA sequencing of 15,843,270 IGH rearrangements to identify clonal lineages of B cells containing members expressing IgE. Somatic mutations in IGH inherited from common ancestors within the clonal lineage are used to infer the relationships between B cells.Data from 613,641 multi-isotype B-cell clonal lineages, of which 592 include an IgE member, are consistent with indirect switching to IgE from IgG- or IgA-expressing lineage members in human subjects. We also find that these inferred isotype switching frequencies are similar in healthy and allergic subjects.We found evidence that secondary isotype switching of mutated IgG1-expressing B cells is the primary source of IgE in human subjects, with lesser contributions from precursors expressing other switched isotypes and rarely IgM or IgD, suggesting that IgE is derived from previously antigen-experienced B cells rather than naive B cells that typically express low-affinity unmutated antibodies. These data provide a basis from which to evaluate allergen-specific human antibody repertoires in healthy and diseased subjects.

  View details for DOI 10.1016/j.jaci.2015.07.014

  View details for PubMedID 26309181

• Single B-cell deconvolution of peanut-specific antibody responses in allergic patients. The Journal of allergy and clinical immunology Hoh, R. A., Joshi, S. A., Liu, Y., Wang, C., Roskin, K. M., Lee, J. Y., Pham, T., Looney, T. J., Jackson, K. J., Dixit, V. P., King, J., Lyu, S. C., Jenks, J., Hamilton, R. G., Nadeau, K. C., Boyd, S. D. 2015

  Abstract

  The frequencies, cellular phenotypes, epitope specificity, and clonal diversity of allergen-specific B cells in patients with food allergy are not fully understood but are of major pathogenic and therapeutic significance.We sought to characterize peanut allergen-specific B-cell populations and the sequences and binding activities of their antibodies before and during immunotherapy.B cells binding fluorescently labeled Ara h 1 or Ara h 2 were phenotyped and isolated by means of flow cytometric sorting from 18 patients at baseline and 13 patients during therapy. Fifty-seven mAbs derived from allergen-binding single B cells were evaluated by using ELISA, Western blotting, and peptide epitope mapping. Deep sequencing of the B-cell repertoires identified additional members of the allergen-specific B-cell clones.Median allergen-binding B-cell frequencies were 0.0097% (Ara h 1) or 0.029% (Ara h 2) of B cells in baseline blood from allergic patients and approximately 3-fold higher during immunotherapy. Five of 57 allergen-specific cells belonged to clones containing IgE-expressing members. Almost all allergen-specific antibodies were mutated, and binding to both conformational and linear allergen epitopes was detected. Increasing somatic mutation of IgG4 members of a clone was seen in immunotherapy, whereas IgE mutation levels in the clone did not increase.Most peanut allergen-binding B cells isolated by means of antigen-specific flow sorting express mutated and isotype-switched antibodies. Immunotherapy increases their frequency in the blood, and even narrowly defined allergen epitopes are recognized by numerous distinct B-cell clones in a patient. The results also suggest that oral immunotherapy can stimulate somatic mutation of allergen-specific IgG4.

  View details for DOI 10.1016/j.jaci.2015.05.029

  View details for PubMedID 26152318

• Effects of Aging, Cytomegalovirus Infection, and EBV Infection on Human B Cell Repertoires JOURNAL OF IMMUNOLOGY Wang, C., Liu, Y., Xu, L. T., Jackson, K. J., Roskin, K. M., Pham, T. D., Laserson, J., Marshall, E. L., Seo, K., Lee, J., Furman, D., Koller, D., Dekker, C. L., Davis, M. M., Fire, A. Z., Boyd, S. D. 2014; 192 (2): 603-611

  Abstract

  Elderly humans show decreased humoral immunity to pathogens and vaccines, yet the effects of aging on B cells are not fully known. Chronic viral infection by CMV is implicated as a driver of clonal T cell proliferations in some aging humans, but whether CMV or EBV infection contributes to alterations in the B cell repertoire with age is unclear. We have used high-throughput DNA sequencing of IGH gene rearrangements to study the BCR repertoires over two successive years in 27 individuals ranging in age from 20 to 89 y. Some features of the B cell repertoire remain stable with age, but elderly subjects show increased numbers of B cells with long CDR3 regions, a trend toward accumulation of more highly mutated IgM and IgG Ig genes, and persistent clonal B cell populations in the blood. Seropositivity for CMV or EBV infection alters B cell repertoires, regardless of the individual's age: EBV infection correlates with the presence of persistent clonal B cell expansions, whereas CMV infection correlates with the proportion of highly mutated Ab genes. These findings isolate effects of aging from those of chronic viral infection on B cell repertoires and provide a baseline for understanding human B cell responses to vaccination or infectious stimuli.

  View details for DOI 10.4049/jimmunol.1301384

  View details for Web of Science ID 000329224000006

  View details for PubMedID 24337376