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Abstract Background Experimental studies of gene expression have identified some of the individual molecular components and elementary reactions that comprise and control cellular behavior. Given our current understanding of gene expression, and the goals of biotechnology research, both scientists and engineers would benefit from detailed simulators that can explicitly compute genome-wide expression levels as a function of individual molecular events, including the activities and interactions of molecules on DNA at single base pair resolution. However, for practical reasons including computational tractability, available simulators have not been able to represent genome-scale models of gene expression at this level of detail. Results Here we develop a simulator, TABASCO http://openwetware.org/wiki/TABASCO, which enables the precise representation of individual molecules and events in gene expression for genome-scale systems. We use a single molecule computational engine to track individual molecules interacting with and along nucleic acid polymers at single base resolution. Tabasco uses logical rules to automatically update and delimit the set of species and reactions that comprise a system during simulation, thereby avoiding the need for a priori specification of all possible combinations of molecules and reaction events. We confirm that single molecule, base-pair resolved simulation using TABASCO (Tabasco) can accurately compute gene expression dynamics and, moving beyond previous simulators, provide for the direct representation of intermolecular events such as polymerase collisions and promoter occlusion. We demonstrate the computational capacity of Tabasco by simulating the entirety of gene expression during bacteriophage T7 infection; for reference, the 39,937 base pair T7 genome encodes 56 genes that are transcribed by two types of RNA polymerases active across 22 promoters. Conclusion Tabasco enables genome-scale simulation of transcription and translation at individual molecule and single base-pair resolution. By directly representing the position and activity of individual molecules on DNA, Tabasco can directly test the effects of detailed molecular processes on system-wide gene expression. Tabasco would also be useful for studying the complex regulatory mechanisms controlling eukaryotic gene expression. The computational engine underlying Tabasco could also be adapted to represent other types of processive systems in which individual reaction events are organized across a single spatial dimension (e.g., polysaccharide synthesis).

The combination of cord blood transplant with progenitor cells from partially HLA-matched adult donors (haplo-cord transplant) has been used over the past two decades. In Europe and the US the adult donor graft is CD34 selected and provides early hematopoiesis, but durable engraftment derives from the cord blood graft (CD34 selected haplo-cord) . Neutrophil recovery is prompt and rates of acute and chronic GVHD are low. Recent Chinese studies combine cord blood grafts with T-replete haplo-identical grafts (unmodified haplo-cord) . The haplo graft usually establishes dominance and UCB chimerism is rarely detected. Comparison studies suggest considerably decreased rates of relapse and improved outcomes, compared with either haplo-identical transplant or CBU transplant, particularly in patients with advanced leukemia. A recent prospective randomized study confirms this. Haplo-cord mitigates the engraftment delay of UCB transplant. The unique biology of UCB grafts results in low GVHD and improved GVL especially beneficial in high-risk disease.

Abstract: The optimal means of assessing candidacy of older adults (≥65 years) for chimeric antigen receptor T-cell (CAR-T) therapy are unknown. We explored the role of a geriatric assessment (GA)-guided multidisciplinary clinic (GA-MDC) in selecting and optimizing older adults for CAR-T. Sixty-one patients were evaluated in a GA-MDC (median age, 73 years; range, 58-83). A nonbinding recommendation ("proceed" or "decline") regarding suitability for CAR-T was provided for each patient based on GA results. Fifty-three patients ultimately received CAR-T (proceed, n = 47; decline, n = 6). Among patients who received B-cell maturation antigen (BCMA)-directed (n = 11) and CD19-directed CAR-T (n = 42), the median overall survival (OS) was 14.2 months and 16.6 months, respectively. GA uncovered high rates of geriatric impairment among patients proceeding to CAR-T therapy, with fewer impairments in those recommended "proceed." Patients recommended "proceed" had shorter median length of stay (17 vs 31 days; P = .05) and lower rates of intensive care unit admission (6% vs 50%; P = .01) than those recommended "decline." In patients receiving CD19- and BCMA-directed CAR-T therapy, a "proceed" recommendation was associated with superior OS compared with "decline" (median, 16.6 vs 11.4 months [P = .02]; and median, 16.4 vs 4.2 months [P = .03], respectively). When controlling for Karnofsky performance status, C-reactive protein, and lactate dehydrogenase at time of lymphodepletion, the GA-MDC treatment recommendation remained prognostic for OS (hazard ratio, 3.26; P = .04). Patients optimized via the GA-MDC without serious vulnerabilities achieved promising outcomes, whereas patients with high vulnerability experienced high toxicity and poor outcomes after CAR-T therapy., (© 2024 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)

Background: The somatic mutation of fms-like tyrosine kinase 3 ( FLT3 ) in acute myeloid leukemia (AML) is associated with increased risk of relapse and lower survival rates. FLT3i as maintenance after allogeneic hematopoietic stem cell transplant (allo-HSCT) are under study to prevent disease relapse, but real-world data are lacking., Methods: We performed a single center, retrospective cohort study and analyzed patients who had FLT3 -mutated AML and underwent allogeneic-HSCT between January 2011 to June 2022 at the University of Chicago. We identified 23 patients who received FLT3i maintenance therapy post-allo-HSCT and compared their outcomes against 57 patients who did not. Primary outcome was disease-free survival (DFS). Secondary outcomes include overall survival (OS) and relapse rate., Results: FLT3i maintenance therapy was started at a median 59 days (range, 29-216 days) after allo-HSCT with median duration of 287 days (range, 15-1,194 days). Maintenance therapy was well tolerated. Overall, the improvement in DFS rates for patients after they were placed on FLT3i maintenance therapy was not significant [hazard ratio (HR) for relapse or death =0.65, 95% confidence interval (CI): 0.32-1.31, P=0.23]. However, when adjusted for the conditioning regimen and donor status, the differences were statistically significant with improvement in DFS and OS for patients on FLT3i maintenance (HR for OS =0.42, 95% CI: 0.18-0.95, P=0.04)., Conclusions: When adjusting for conditioning regimen and donor status, there was a significant improvement in DFS and OS for patients who received FLT3i maintenance therapy compared to those who did not. Randomized prospective studies may provide more insight., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://atm.amegroups.com/article/view/10.21037/atm-23-1941/coif). The authors have no conflicts of interest to declare., (2024 Annals of Translational Medicine. All rights reserved.)

Understanding the function of rare non-coding variants represents a significant challenge. Using MapUTR, a screening method, we studied the function of rare 3' UTR variants affecting mRNA abundance post-transcriptionally. Among 17,301 rare gnomAD variants, an average of 24.5% were functional, with 70% in cancer-related genes, many in critical cancer pathways. This observation motivated an interrogation of 11,929 somatic mutations, uncovering 3928 (33%) functional mutations in 155 cancer driver genes. Functional MapUTR variants were enriched in microRNA- or protein-binding sites and may underlie outlier gene expression in tumors. Further, we introduce untranslated tumor mutational burden (uTMB), a metric reflecting the amount of somatic functional MapUTR variants of a tumor and show its potential in predicting patient survival. Through prime editing, we characterized three variants in cancer-relevant genes (MFN2, FOSL2, and IRAK1), demonstrating their cancer-driving potential. Our study elucidates the function of tens of thousands of non-coding variants, nominates non-coding cancer driver mutations, and demonstrates their potential contributions to cancer., (© 2024. The Author(s).)

Abstract: TP 53-mutated myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML) are among the most lethal malignancies, characterized by dismal outcomes with currently available therapies. Allogeneic hematopoietic cell transplantation (allo-HCT) is widely thought to be the only treatment option to offer durable disease control. However, outcomes with allo-HCT in this context are quite poor, calling into question the utility of transplantation. In this review, we summarize the latest data on allo-HCT outcomes in this subgroup, evaluating the limitations of available evidence; we review the molecular heterogeneity of this disease, delineating outcomes based on distinct biological features to aid in patient selection; and we critically examine whether allo-HCT should be routinely applied in this disease on the basis of currently available data. We propose that the exceptionally poor outcomes of patients with TP53-mutated MDS/AML with biallelic loss and/or adverse-risk cytogenetics should motivate randomized-controlled trials of HCT vs non-HCT to determine whether transplantation can prolong survival and/or positively impact other clinically relevant outcomes such as patient-reported outcomes or healthcare resource utilization in this disease subset. Without dedicated prospective randomized trials, selecting who may actually derive benefit from allo-HCT for TP53-mutated MDS/AML can be described as ambiguous guesswork and must be carefully contemplated., (© 2024 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)

Background: CD19-targeted chimeric antigen receptor (CAR) T-cell therapy has become a standard of care in relapsed/refractory (R/R) aggressive large B-cell non-Hodgkin lymphomas (B-NHL) though the majority of recipients do not receive durable disease benefit, prompting the need to better define risk factors for relapse/progression., Objectives: We performed a single-center, retrospective analysis of patients treated with commercial CAR T-cell therapy to evaluate the impact of tumor burden, as measured by whole-body metabolic tumor volume (MTV) from 18 F fluorodeoxyglucose PET imaging, on treatment outcomes., Study Design: Sixty-one patients treated with CAR T-cell therapy for R/R B-NHL between May 2016 and November 2021 were included., Results: Using a receiver operating characteristic curve-based MTV optimization cutoff of 450 mL, 1-year progression-free survival (PFS) was 22% for high MTV versus 54% for low MTV (P < .01), and 1-year overall survival (OS) was 37% and 73%, respectively (P = .01). In a subset of 46 patients, residual MTV of less than 106 mL at the day 30 (D30) disease assessment was associated with significantly improved outcomes (1-year OS 85% vs. 13%, P < .01). Incorporation of pretreatment MTV to the International Prognostic Index (IPI) scoring system significantly distinguished 2-year PFS and OS outcomes by 3 risk groups., Conclusions: Our findings suggest that both pretreatment and D30 MTV are predictive of outcomes among R/R B-NHL patients treated with CAR T-cell therapy. These data indicate that efforts to reduce pretreatment tumor burden may improve longitudinal clinical outcomes. Furthermore, D30 postinfusion MTV quantification may aid clinicians in optimally identifying patients at high-risk for progression, and in whom closer disease monitoring should be considered. MTV also adds prognostic value to patients with high-risk IPI and holds promise for incorporation in novel risk scoring systems which can identify patients prior to CAR T-cell therapy at highest risk of adverse outcomes., Competing Interests: Disclosure A.E.R., D.E.A., Y.P., N.F., S.K., M.T.N., and S.M.S. report no relevant COI. J.P.K. receives research support from Merck, iTeos, and Verastem Oncology; advisory boards for Merck, Kite Pharma, Inc./Gilead, Seattle Genetics, and Verastem Oncology; speaker for Kite Pharma, Inc./Gilead. B.A.D. has received advisory board fees from Janssen, Sanofi, and consulting fees from COTA Healthcare. A.J. receives consulting and advisory boards for AbbVie, Amgen, BMS, GSK, Janssen, and Karyopharm Therapeutics Inc. H.L. received research support from BMS and Karyopharm, has served on advisory board meeting for Agios. M.R.B. is a consultant and/or advisor for Celgene, Kite Pharma, Inc./Gilead, CRISPR Therapeutics, Takeda, and Novartis Pharmaceuticals Corporation; speaker for Kite Pharma, Inc./Gilead, BMS, Incyte, Agios, and Celgene. Other financial interest/relationship for Novartis Pharmaceuticals Corporation as a part of steering committees. P.A.R. has served as a consultant and/or advisory board member for AbbVie, Genmab, ADC Therapeutics, Pharmacyclics, Novartis, BMS, Kite/Gilead, Nurix Therapeutics, Nektar Therapeutics, Takeda, Intellia Therapeutics, Sana Biotechnology, BeiGene, Janssen, CVS Caremark. He has served as a speaker for Kite Pharma and has received honoraria from Novartis. Research support from BMS, Kite/Gilead, Novartis, MorphoSys, CRISPR Therapeutics, Calibr, Xencor, Fate Therapeutics, and Tessa Therapeutics., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Genome-wide association studies (GWASs) have successfully identified 145 genomic regions that contribute to schizophrenia risk, but linkage disequilibrium makes it challenging to discern causal variants. We performed a massively parallel reporter assay (MPRA) on 5,173 fine-mapped schizophrenia GWAS variants in primary human neural progenitors and identified 439 variants with allelic regulatory effects (MPRA-positive variants). Transcription factor binding had modest predictive power, while fine-map posterior probability, enhancer overlap, and evolutionary conservation failed to predict MPRA-positive variants. Furthermore, 64% of MPRA-positive variants did not exhibit expressive quantitative trait loci signature, suggesting that MPRA could identify yet unexplored variants with regulatory potentials. To predict the combinatorial effect of MPRA-positive variants on gene regulation, we propose an accessibility-by-contact model that combines MPRA-measured allelic activity with neuronal chromatin architecture., Competing Interests: The authors declare no competing interests., (© 2023 The Author(s).)

Protein-protein interactions (PPIs) are crucial for biological functions and have applications ranging from drug design to synthetic cell circuits. Coiled-coils have been used as a model to study the sequence determinants of specificity. However, building well-behaved sets of orthogonal pairs of coiled-coils remains challenging due to inaccurate predictions of orthogonality and difficulties in testing at scale. To address this, we develop the next-generation bacterial two-hybrid (NGB2H) method, which allows for the rapid exploration of interactions of programmed protein libraries in a quantitative and scalable way using next-generation sequencing readout. We design, build, and test large sets of orthogonal synthetic coiled-coils, assayed over 8,000 PPIs, and used the dataset to train a more accurate coiled-coil scoring algorithm (iCipa). After characterizing nearly 18,000 new PPIs, we identify to the best of our knowledge the largest set of orthogonal coiled-coils to date, with fifteen on-target interactions. Our approach provides a powerful tool for the design of orthogonal PPIs., (© 2023. The Author(s).)

Polymer-protein hybrids can be deployed to improve protein solubility and stability in denaturing environments. While previous work used robotics and active machine learning to inform new designs, further biophysical information is required to ascertain structure-function behavior. Here, we show the value of tandem small-angle x-ray scattering (SAXS) and quartz crystal microbalance with dissipation (QCMD) experiments to reveal detailed polymer-protein interactions with horseradish peroxidase (HRP) as a test case. Of particular interest was the process of polymer-protein complex formation under thermal stress whereby SAXS monitors formation in solution while QCMD follows these dynamics at an interface. The radius of gyration (R g ) of the protein as measured by SAXS does not change significantly in the presence of polymer under denaturing conditions, but thickness and dissipation changes were observed in QCMD data. SAXS data with and without thermal stress were utilized to create bead models of the potential complexes and denatured enzyme, and each model fit provided insight into the degree of interactions. Additionally, QCMD data demonstrated that HRP deforms by spreading upon surface adsorption at low concentration as shown by longer adsorption times and smaller frequency shifts. In contrast, thermally stressed and highly inactive HRP had faster adsorption kinetics. The combination of SAXS and QCMD serves as a framework for biophysical characterization of interactions between proteins and polymers which could be useful in designing polymer-protein hybrids., (© 2022 The Authors. Journal of Biomedical Materials Research Part A published by Wiley Periodicals LLC.)

There is increasing recognition that pathogenic germ line variants drive the development of hematopoietic cancers in many individuals. Currently, patients with hereditary hematologic malignancies (HHMs) receive similar standard therapies and hematopoietic stem cell transplant (HSCT) approaches as those with sporadic disease. We hypothesize that patients with myeloid malignancies and deleterious germ line predisposition variants have different posttransplant outcomes than those without such alleles. We studied 472 patients with myeloid neoplasms, of whom 26% had deleterious germ line variants and 34% underwent HSCT. Deleterious germ line variants in CHEK2 and DDX41 were most commonly seen in American and Australian cohorts, respectively. Patients with deleterious germ line DDX41 variants had a higher incidence of severe (stage 3-4) acute graft-versus-host disease (GVHD) (38%) than recipients with deleterious CHEK2 variants (0%), other HHM variants (12%), or patients without such germ line variants (9%) (P = .002). Importantly, the use of posttransplant cyclophosphamide reduced the risk of severe acute GVHD in patients receiving HSCT for deleterious germ line DDX41-associated myeloid neoplasms (0% vs 53%, P = .03). Based on these results, we advocate the use of posttransplant cyclophosphamide when individuals with deleterious germ line DDX41 variants undergo allogeneic HSCT for myeloid malignancies, even when transplantation has been performed using wild-type donors., (© 2023 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)

Relapse after allogeneic stem cell transplantation (allo-SCT) remains the primary cause of treatment failure. A second SCT can result in long-term survival in a subset of patients, but the relapse rate remains high. We conducted a single-center, phase 1, modified 3 + 3 dose-escalation study of the feasibility of combining intensity-modulated total marrow irradiation (IM-TMI) with fludarabine and melphalan for conditioning. Between December 2015 and May 2020, 21 patients with relapsed hematologic disease undergoing second or greater allo-SCT were treated with IM-TMI doses of 6 Gy, 9 Gy, or 12 Gy. Dose-limiting toxicity was defined as a grade 3 or higher treatment-related adverse event; mucositis was the primary dose-limiting toxicity. The median times to neutrophil and platelet engraftment were 10 and 18 days, respectively. The 1-year cumulative incidence of graft-versus-host disease was 65% (95% confidence interval CI, 38-83). The nonrelapse mortality at 2 years was 17% (95% CI, 4-39). Cumulative incidence of relapse at 2 years was 35% (95% CI, 13-58). Two-year progression-free survival and overall survival were 48% and 50%. We conclude that combining IM-TMI with fludarabine-melphalan is feasible. We recommend 12 Gy of IM-TMI with fludarabine-melphalan for second SCT, although 9 Gy may be used for older or underweight patients., (© 2023 by The American Society of Hematology. Licensed under Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0), permitting only noncommercial, nonderivative use with attribution. All other rights reserved.)

Predicting the function of noncoding variation is a major challenge in modern genetics. In this study, we used massively parallel reporter assays to screen 5706 variants identified from genome-wide association studies for both Alzheimer's disease (AD) and progressive supranuclear palsy (PSP), identifying 320 functional regulatory variants (frVars) across 27 loci, including the complex 17q21.31 region. We identified and validated multiple risk loci using CRISPR interference or excision, including complement 4 ( C4A ) and APOC1 in AD and PLEKHM1 and KANSL1 in PSP. Functional variants disrupt transcription factor binding sites converging on enhancers with cell type-specific activity in PSP and AD, implicating a neuronal SP1-driven regulatory network in PSP pathogenesis. These analyses suggest that noncoding genetic risk is driven by common genetic variants through their aggregate activity on specific transcriptional programs.

Objective This study was aimed at analyzing the validity and reliability of the Papanicolaou (Pap) test and visual inspection with acetic acid (VIAA) tests for cervical dysplasia screenings during the COVID-19 pandemic. Material and methods This was a retrospective study of patients 21 years or older seen at the Luis Negreiros Primary Care Center in Lima, Peru between 2020 and 2021, who underwent cervical dysplasia screening (Pap or VIAA). Relevant information regarding patient age, date of service, and Pap and VIAA results were collected. Parallel form reliability was analyzed with chi-square tests, and phi, contingency and Cramer's V coefficients. The validity of these tests was analyzed through the calculation of the sensitivity, specificity, and positive and negative predictive values with confidence intervals. A p-value less than 0.05 indicated statistical significance. Results From 4,503 records, the sensitivity, specificity, and positive and negative predictive values for Pap were 0.87 (0.81-0.92), 1.0 (1.0-1.0), 1.0 (1.0-1.0) and 0.99 (0.98-0.99), respectively, and those for VIAA were 0.22 (0.14-0.31), 0.10 (0.10-0.10), 0.53 (0.38-0.69) and 0.10 (0.10-0.10), respectively. Test validity varied slightly according to patient age and the year of testing. The correlation, although significant, was inverse; chi-square = 39.18, p <0.001, phi = -0.60, contingency = 0.51 and Cramer's V = -0.59. Conclusion The validity and reliability of Pap testing and VIAA for cervical dysplasia screening significantly decreased during the COVID-19 pandemic. The correlation between these tests, although significant, was inverse. More larger-scale studies are needed to confirm these findings and understand the reasons underlying the decreased effectiveness of these tests., Competing Interests: The authors have declared that no competing interests exist., (Copyright © 2022, Lagos-Castillo et al.)

Polymer-protein hybrids are intriguing materials that can bolster protein stability in non-native environments, thereby enhancing their utility in diverse medicinal, commercial, and industrial applications. One stabilization strategy involves designing synthetic random copolymers with compositions attuned to the protein surface, but rational design is complicated by the vast chemical and composition space. Here, a strategy is reported to design protein-stabilizing copolymers based on active machine learning, facilitated by automated material synthesis and characterization platforms. The versatility and robustness of the approach is demonstrated by the successful identification of copolymers that preserve, or even enhance, the activity of three chemically distinct enzymes following exposure to thermal denaturing conditions. Although systematic screening results in mixed success, active learning appropriately identifies unique and effective copolymer chemistries for the stabilization of each enzyme. Overall, this work broadens the capabilities to design fit-for-purpose synthetic copolymers that promote or otherwise manipulate protein activity, with extensions toward the design of robust polymer-protein hybrid materials., (© 2022 The Authors. Advanced Materials published by Wiley-VCH GmbH.)

Among the many molecules that contribute to glial scarring, chondroitin sulfate proteoglycans (CSPGs) are known to be potent inhibitors of neuronal regeneration. Chondroitinase ABC (ChABC), a bacterial lyase, degrades the glycosaminoglycan (GAG) side chains of CSPGs and promotes tissue regeneration. However, ChABC is thermally unstable and loses all activity within a few hours at 37 °C under dilute conditions. To overcome this limitation, the discovery of a diverse set of tailor-made random copolymers that complex and stabilize ChABC at physiological temperature is reported. The copolymer designs, which are based on chain length and composition of the copolymers, are identified using an active machine learning paradigm, which involves iterative copolymer synthesis, testing for ChABC thermostability upon copolymer complexation, Gaussian process regression modeling, and Bayesian optimization. Copolymers are synthesized by automated PET-RAFT and thermostability of ChABC is assessed by retained enzyme activity (REA) after 24 h at 37 °C. Significant improvements in REA in three iterations of active learning are demonstrated while identifying exceptionally high-performing copolymers. Most remarkably, one designed copolymer promotes residual ChABC activity near 30%, even after one week and notably outperforms other common stabilization methods for ChABC. Together, these results highlight a promising pathway toward sustained tissue regeneration., (© 2022 Wiley-VCH GmbH.)

High risk multiple myeloma (HRMM) continues to portend worse outcomes despite the many advances in anti-myeloma therapeutics. The optimal approach to treatment is not clearly defined on account of the variable definitions of HRMM and the paucity of studies dedicated to the treatment of HRMM. In this review, we use a case-based approach to review the definitions of HRMM, and evaluate the evidence for induction, stem cell transplantation, and post-transplant therapy approaches for HRMM., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: The urgent need for massively scaled clinical testing for SARS-CoV-2, along with global shortages of critical reagents and supplies, has necessitated development of streamlined laboratory testing protocols. Conventional nucleic acid testing for SARS-CoV-2 involves collection of a clinical specimen with a nasopharyngeal swab in transport medium, nucleic acid extraction, and quantitative reverse-transcription PCR (RT-qPCR). As testing has scaled across the world, the global supply chain has buckled, rendering testing reagents and materials scarce. To address shortages, we developed SwabExpress, an end-to-end protocol developed to employ mass produced anterior nares swabs and bypass the requirement for transport media and nucleic acid extraction., Methods: We evaluated anterior nares swabs, transported dry and eluted in low-TE buffer as a direct-to-RT-qPCR alternative to extraction-dependent viral transport media. We validated our protocol of using heat treatment for viral inactivation and added a proteinase K digestion step to reduce amplification interference. We tested this protocol across archived and prospectively collected swab specimens to fine-tune test performance., Results: After optimization, SwabExpress has a low limit of detection at 2-4 molecules/µL, 100% sensitivity, and 99.4% specificity when compared side by side with a traditional RT-qPCR protocol employing extraction. On real-world specimens, SwabExpress outperforms an automated extraction system while simultaneously reducing cost and hands-on time., Conclusion: SwabExpress is a simplified workflow that facilitates scaled testing for COVID-19 without sacrificing test performance. It may serve as a template for the simplification of PCR-based clinical laboratory tests, particularly in times of critical shortages during pandemics., (© American Association for Clinical Chemistry 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Allogeneic hematopoietic cell transplantation (HCT) offers a potentially curative therapy in patients with hematologic malignancies; however, nonrelapse mortality (NRM) remains a concern. Strategies to improve neutrophil recovery and immune reconstitution are needed to decrease NRM. Murine models of allogeneic HCT suggest that fractionated hematopoietic progenitor cell (HPC) infusion may improve engraftment through improved access of HPCs to a viable hematopoietic niche. The primary objective of the present study was to determine the impact of fractionated infusion versus unfractionated (bulk) infusion of HPCs on the time to achieve neutrophil engraftment. Secondary objectives included the effect of fractionated versus bulk infusion of HPCs on platelet engraftment, immune reconstitution, the incidence of acute graft-versus-host disease (GVHD) grade II-IV, NRM, and overall survival (OS). In this randomized phase 2 study, patients with hematologic malignancies undergoing allogeneic HCT were randomized to receive HPC infusion as a bulk (bulk arm) or in fractions (fractionated arm): 4 × 10 6 CD34 + cells/kg recipient weight infused on day 0, with the remaining HPCs CD34 + cell-selected then infused in equally distributed aliquots on days 2, 4, and 6 post-HCT. Randomization was stratified by type of transplant, unmodified (i.e. T cell-replete graft) versus CD34 + cell-selected (T cell-depleted graft). Patients whose donor failed to collect at least 7 × 10 6 CD34 + cells/kg of recipient weight received bulk HPC infusions regardless of randomization, for safety. These patients continued the HCT process on study but were replaced until each arm reached the prespecified accrual target. Per protocol, these patients were not included in this modified intention-to-treat analysis. A total of 116 patients were enrolled. Donors of 42 patients failed to mobilize the minimum CD34 + cell dose (7 × 10 6 cells/kg recipient weight) and were excluded from the analysis. The 74 evaluable patients included 38 randomized to the bulk arm and 36 randomized to the fractionated arm. All patients engrafted. The median time to an absolute neutrophil count of ≥0.5 × 10 9 /L was 11 days on both arms. The day +180 median CD4 + cell count was 179 cells/µL in the bulk arm and 111 cells/µL in the fractionated arm (P = .779). The cumulative incidence of grade II-IV acute GVHD on post-transplant day +100 was 32% in the bulk arm and 17% in the fractionated arm (P = .131). Two patients in the bulk arm, but none in the fractionated arm, experienced grade III-IV GVHD. The 4-year OS was 60% in the bulk arm and 62% in the fractionated arm (P = .414), whereas the 4-year cumulative incidences of NRM and relapse were similar in the 2 arms. Fractionated infusion of HPCs in allogeneic HCT recipients did not impact neutrophil or CD4 + cell recovery, NRM, relapse, or OS when compared with bulk HPC infusion. We also observed that with current mobilization techniques, it was unlikely that more than 60% of healthy donors would be able to collect >7 × 10 6 CD34 + cells/kg recipient weight for adult recipients. © 2021 American Society for Transplantation and Cellular Therapy. Published by Elsevier Inc., Competing Interests: Conflict of interest statement D.M.P. has served on advisory boards for Generon, Kadmon, CareDx, and Ceramedix and as a paid consultant for Guidepoint Global Advisors and Gerson Lehrman Group. M.A.P. reports honoraria from AbbVie, Astellas, Bristol-Myers Squibb, Celgene, Incyte, Karyopharm, Kite/Gilead, Merck, Miltenyi Biotec, MorphoSys, Novartis, Nektar Therapeutics, Omeros, and Takeda; serves on data safety and monitoring boards for Cidara Therapeutics, Servier, and Medigene and the scientific advisory board of NexImmune; has received research support for clinical trials from Incyte, Kite/Gilead, Miltenyi Biotec, and Novartis; and serves in a volunteer capacity as a member of the Board of Directors of Be The Match (National Marrow Donor Program), as well as on the CIBMTR Cellular Immunotherapy Data Resource Executive Committee. S.A.G. has received research funding from Actinium Pharma, Celgene, Bristol-Myers Squibb, Sanofi, Amgen, Pfizer, Jensen, and Takeda and serves as a research consultant for Kite Pharma and on advisory boards of Actinium, Celgene, Bristol-Myers Squibb, Sanofi, Amgen, Pfizer, GSK, Jazz, Jensen, and Omeros. B.G. reports research funding for a clinical trial from Actinium Pharma. The other authors have no conflicts of interest to report., (Copyright © 2021 The American Society for Transplantation and Cellular Therapy. Published by Elsevier Inc. All rights reserved.)

Aim: Emergency intensive care of the elderly is often complicated and multifaceted. Understanding the clinical profile of elderly patients admitted in an emergency department-intensive care unit (ED-ICU) is crucial in planning health policies in geriatric emergency medicine. Thus, the aim of the study was to create a local registry of elderly people utilizing the ED-ICU services and to understand the rate and predictors of mortality., Methods: A retrospective chart analysis was performed including all patients aged ≥60 years who had an ED-ICU admission during a 6-month period (August 2018-January 2019). A structured case record form was used to capture information such as basic demography, clinical profile, and outcomes., Results: Total number of records considered for final analysis were 503. Mortality was seen in 21.07% (n = 106/503). The most common presenting complaint and cause of death was breathing difficulty (n = 48/503; 29.42%) and pneumonia (n = 41/106; 38.67%), repectively. The significant predictors of mortality [adjusted odds ratio; 95% confidence intervals; P value] were hypertension (2.195; 1.255, 3.840; 0.006), chronic liver disease (CLD) (4.324; 1.170, 15.979; 0.028), malignancy (2.854; 1.045, 7.796; 0.041), requiring noninvasive ventilation (NIV) (2.618; 1.449, 4.730; 0.001), requiring intubation (6.638; 3.705, 11.894; <0.001), and requiring vasopressors (3.583; 1.985, 6.465; <0.001)., Conlusion: Approximately one in every five elderly patients getting admitted in ED-ICU died, and respiratory illness was the common diagnosis leading to death. Those with comorbidities such as hypertension, CLD, or malignancy and those requiring NIV, intubation, or vasopressors had higher mortality., Competing Interests: There are no conflicts of interest., (Copyright: © 2021 Journal of Family Medicine and Primary Care.)

Background: Atrial arrhythmias following hematopoietic stem cell transplantation (HSCT) have been associated with increased length of stay, need for intensive care, and increased mortality within one-year post-transplant. We sought to identify echocardiographic parameters that may predict the development of new atrial arrhythmias post-HSCT., Methods: We performed a retrospective chart review of 753 consecutive patients who underwent HSCT at the University of Chicago from January 2015 through December 2019. Patients with baseline echocardiogram within 6 months prior to transplantation were included. Those with prior transplants, history of atrial arrhythmias, or unavailable echocardiographic images were excluded, resulting in 187 patients included for final analysis. Baseline clinical and demographic variables, as well as echocardiographic parameters, were compared between patients who developed new atrial arrhythmias post-HSCT versus those who did not., Results: Of the 187 patients included for analysis, 25 (13%) developed new atrial arrhythmias, with 13 of these occurring within 30 days of transplantation. Despite no significant difference in left atrial (LA) end-systolic volume between those with and without new arrhythmia following HSCT (OR 1.04; 95% CI 0.91-1.09, p = 0.233), univariable analysis demonstrated that patients who developed atrial arrhythmias had reduced LA function, as reflected by lower LA emptying fraction (OR 0.94; 95% CI 0.91-0.98, p = 0.003) and lower LA reservoir strain (OR 0.95; 95% CI 0.92-0.99, p = 0.009)., Conclusions: Echocardiographic indices of LA function, namely LA emptying fraction and LA reservoir strain, can identify patients at risk for developing new atrial arrhythmias post-HSCT, prior to the development of morphologic changes in the LA., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Frequent and widespread testing of members of the population who are asymptomatic for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for the mitigation of the transmission of the virus. Despite the recent increases in testing capacity, tests based on quantitative polymerase chain reaction (qPCR) assays cannot be easily deployed at the scale required for population-wide screening. Here, we show that next-generation sequencing of pooled samples tagged with sample-specific molecular barcodes enables the testing of thousands of nasal or saliva samples for SARS-CoV-2 RNA in a single run without the need for RNA extraction. The assay, which we named SwabSeq, incorporates a synthetic RNA standard that facilitates end-point quantification and the calling of true negatives, and that reduces the requirements for automation, purification and sample-to-sample normalization. We used SwabSeq to perform 80,000 tests, with an analytical sensitivity and specificity comparable to or better than traditional qPCR tests, in less than two months with turnaround times of less than 24 h. SwabSeq could be rapidly adapted for the detection of other pathogens., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Although acute lymphoblastic leukemia (ALL) is most common in pediatric and adolescent and young adult (AYA) patients, 20% of cases are diagnosed in patients ≥ 55 years old. Use of intensive pediatric regimens in AYA populations has demonstrated excellent tolerability and significant improvements in event-free survival (EFS) and overall survival (OS). The backbone of pediatric regimens includes asparaginase and corticosteroids, both of which are associated with more toxicity in older patients and those with body mass index (BMI) ≥ 30 kg/m which leads to poor tolerance of these regimens. We tested the safety and efficacy of a dose-modified The Cancer and Leukemia Group B 10403 regimen using reduced doses of pegylated (PEG)-asparaginase (ASP) and corticosteroids (RD-10403) in 30 patients with Philadelphia-chromosome negative ALL who were ≥50-year-old and younger adults with significant metabolic or hepatic co-morbidities. The complete remission rate on day 28 was 77%, 3-year EFS was 54%, and estimated 3-year OS was 55%. Grade 3+ toxicity was noted in 40% of patients during induction, and induction-related mortality was 3%. Additional prospective evaluation of RD-10403 is merited to determine efficacy and safety of this regimen and to serve as a framework for chemoimmunotherapy combination therapy., Competing Interests: Anand Ashwin Patel, Sarah Monick, Adam S. DuVall, Sandeep Gurbuxani, and Satyajit Kosuri have no conflict of interest. Joseph Heng is honoraria from OncLive, while Emily Dworkin is honoraria from Abbvie. Benjamin A. Derman is in advisory board from Sanofi. Hongtao Liu did research funding from BMS and Karyopharm; is honoraria from Agios. Michael Thirman did research funding from Gilead Sciences, Pharmacyclics, Janssen, AbbVie, Merck, Syndax, TG Therapeutics, Tolero; is in advisory board from AstraZeneca, Celgene, Roche/Genentech, Pharmacyclics, Janssen, Abbvie. Lucy A. Godley is advisory board from Invitae, Inc; royalties from UpToDate. Olatoyosi Odenike did research funding from AstraZeneca, ABBVIE, astex, agios, incyte, janssen, NS‐Pharma, Oncotherapy Sciences, BMS; is honoraria/has ad board membership‐ ABBVIE, BMS, Celgene, Novartis, Taiho, PRA. Richard A. Larson has acted as a consultant or advisor to Amgen, Ariad/Takeda, Celgene/Bristol Myers Squibb, CVS/Caremark, Epizyme, MorphoSys, and Novartis, and has received clinical research support to his institution from Astellas, Celgene, Cellectis, Daiichi Sankyo, Forty Seven/Gilead, Novartis, Rafael Pharmaceuticals, and royalties from UpToDate. Wendy Stock is Honoraria from Abbvie, Jazz, Kite, Morphosys, Pfizer, Servier., (© 2021 The Authors. eJHaem published by British Society for Haematology and John Wiley & Sons Ltd.)

Background: Autologous hematopoietic stem cell transplant (autoHCT) is a mainstay of treatment for multiple myeloma and non-Hodgkin lymphoma but is underutilized in older adults. We investigated the association of vulnerabilities identified by a geriatric assessment (GA)-guided multidisciplinary clinic (MDC) on the receipt of autoHCT and evaluated its ability to predict outcomes in older autoHCT candidates., Methods: Patients 50+ years received GA-informed optimization recommendations: 'decline' if unlikely to realize benefits of autoHCT, 'defer' if optimization necessary before autoHCT, and 'proceed' if autoHCT could proceed without delay. We compared characteristics and outcomes of autoHCT recipients (n = 62) to non-autoHCT patients (n = 29) and evaluated GA deficits on outcomes., Results: 91 patients were evaluated; the MDC recommendation was 'decline' for 5 (6%), 'defer' for 25 (27%), and 'proceed' for 61 (67%). AutoHCT recipients had fewer GA-rated impairments relative to non-autoHCT patients, as did patients with a 'proceed' recommendation relative to 'defer'. Among autoHCT recipients, 1-year and 3-year non-relapse morality (NRM) was 0% and 5%, and there was no difference in length of hospitalization, readmission rate, or mortality after transplant by MDC recommendation. Frail grip strength and poor performance status were associated with inferior post-autoHCT progression-free survival and overall survival., Conclusions: Patients pursuing autoHCT after MDC-directed optimization achieved excellent outcomes, including patients deferred but ultimately receiving autoHCT. GA-identified functional deficits, especially frail grip strength, may improve risk stratification in older autoHCT candidates. Employing a GA earlier in the disease trajectory to inform early referral to an MDC may increase autoHCT safety and utilization in older patients., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Polymers are uniquely suited for drug delivery and biomaterial applications due to tunable structural parameters such as length, composition, architecture, and valency. To facilitate designs, researchers may explore combinatorial libraries in a high throughput fashion to correlate structure to function. However, traditional polymerization reactions including controlled living radical polymerization (CLRP) and ring-opening polymerization (ROP) require inert reaction conditions and extensive expertise to implement. With the advent of air-tolerance and automation, several polymerization techniques are now compatible with well plates and can be carried out at the benchtop, making high throughput synthesis and high throughput screening (HTS) possible. To avoid HTS pitfalls often described as "fishing expeditions," it is crucial to employ intelligent and big data approaches to maximize experimental efficiency. This is where the disruptive technologies of machine learning (ML) and artificial intelligence (AI) will likely play a role. In fact, ML and AI are already impacting small molecule drug discovery and showing signs of emerging in drug delivery. In this review, we present state-of-the-art research in drug delivery, gene delivery, antimicrobial polymers, and bioactive polymers alongside data-driven developments in drug design and organic synthesis. From this insight, important lessons are revealed for the polymer therapeutics community including the value of a closed loop design-build-test-learn workflow. This is an exciting time as researchers will gain the ability to fully explore the polymer structural landscape and establish quantitative structure-property relationships (QSPRs) with biological significance., (Copyright © 2020 Elsevier B.V. All rights reserved.)

A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.