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Background: To provide patient-centered healthcare for people with serious illness, healthcare teams must elicit needs, goals, preferences, and values from patients and care partners., Aim: Describe feasibility and acceptability of an electronic pre-visit agenda-setting questionnaire for patients and care partners to identify these topics before ambulatory palliative care visits., Design: Concurrent mixed-methods formative evaluation of questionnaire feasibility and acceptability. We extracted questionnaire responses and patient characteristics from electronic health records and sent anonymous post-visit patient experience surveys. Researchers conducted thematic analysis on semi-structured interviews with participants., Setting/participants: Patient participants had an active patient portal account and ambulatory visit at a free-standing palliative care clinic in a tertiary academic medical center in rural Northeastern United States between June 2021 and March 2023. Clinic staff included physicians, nurse practitioner, social worker, nurses, and scheduling secretary. Most visits were conducted via video or telephone., Results: Completion rate was 50% for pre-visit questionnaires (2107 of 4204 visits). Patients completing post-visit surveys (following 859 visits) reported the pre-visit questionnaire was easy to complete (75%) and helped their conversations with clinicians (79%). Patients who believed their clinician reviewed their responses rated shared decision-making higher (82%) than those who did not (59%). Semi-structured interviews with five patients, two care partners, and seven clinicians identified four themes: the questionnaire engages patients in pre-visit planning, incorporates care partners into the care team, facilitates care for the care partner, and improves perceived efficiency and care quality., Conclusions: An electronic pre-visit questionnaire was feasible and acceptable in ambulatory palliative care visits., Competing Interests: Declaration of conflicting interestsThe author(s) declared the following potential conflicts of interest with respect to the research, authorship, and/or publication of this article: Catherine H. Saunders has a program of research in clinical visit agenda setting and developed the Serious Illness Topics agenda-setting intervention. The other authors have no conflicts of interest to report related to this work.

Ku70 and Ku80 form Ku, a ring-shaped protein that initiates the non-homologous end-joining (NHEJ) DNA repair pathway. 1 Specifically, Ku binds to double-stranded DNA (dsDNA) ends and recruits other NHEJ factors ( e.g. , DNA-PKcs and LIG4). While Ku binds to double-stranded RNA (dsRNA) 2 and traps mutated-DNA-PKcs on ribosomal RNA in vivo, 3,4 the physiological significance of Ku-dsRNA interactions in otherwise wild-type cells remains elusive. Intriguingly, while dispensable for murine development, 5,6 Ku is essential in human cells. 7 Despite similar genome sizes, human cells express ∼100-fold more Ku than mouse cells, implying functions beyond NHEJ, possibly through a dose-sensitive interaction with dsRNA, which is ∼100 times weaker than with dsDNA. 2,8 While investigating the essentiality of Ku in human cells, we found that depletion of Ku - unlike LIG4 - induces profound interferon (IFN) and NF-kB responses reliant on the dsRNA-sensor MDA5/RIG-I and adaptor MAVS. Prolonged Ku-degradation also activates other dsRNA-sensors, e.g. PKR that suppresses protein translation, and OAS/RNaseL that cleaves rRNAs and eventually induces growth arrest and cell death. MAVS, RIG-I, or MDA5 knockouts suppressed IFN signaling and, together with PKR knockouts, partially rescued Ku-depleted human cells. Ku-irCLIP analyses revealed that Ku binds to diverse dsRNA, predominantly stem-loops in primate-specific Alu elements 9 at anti-sense orientation in introns and 3'-UTRs. Ku expression rose sharply in higher primates tightly correlating with Alu-expansion (r = 0.94/0.95). Together, our study identified a vital role of Ku in accommodating Alu-expansion in primates by mitigating a dsRNA-induced innate immune response, explaining the rise of Ku levels and its essentiality in human cells.

Burkitt lymphoma (BL) is the most frequent B-cell lymphoma in pediatric patients. While most patients are cured, a fraction of them are resistant to therapy. To investigate BL heterogeneity and the features distinguishing therapy responders (R) from non-responders (NR), we analyzed by single-cell (sc)-transcriptomics diagnostic EBV-negative BL specimens. Analysis of the non-tumor component revealed a predominance of immune cells and a small representation of fibroblasts, enriched in NR. Tumors displayed patient-specific features, as well as shared subpopulations that expressed transcripts related to cell cycle, signaling pathways and cell-of-origin signatures. Several transcripts were differentially expressed in R versus NR. The top candidate, Tropomyosin 2 (TPM2), a member of the tropomyosin actin filament binding protein family, was confirmed to be significantly higher in NR both at the transcript and protein level. Stratification of patients based on TPM2 expression at diagnosis significantly correlated with prognosis, independently of TP53 mutations. These results indicate that BL displays transcriptional heterogeneity and identify candidate biomarkers of therapy resistance., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

In the past decade, single-cell (sc) transcriptomics has overcome the limitations of bulk analysis by measuring gene expression in individual cells, not just a population average. This can identify diverse cell types and states within a sample with high resolution, even without prior purification. Various technologies exist, each with its own capture, barcoding, and library preparation methods. This chapter focuses on the analysis of normal and malignant mature B cells using the 10× Genomics 5' sc-gene expression in parallel with B cell immune repertoire profiling. By integrating the gene expression data from similar cells, the complete transcriptome for each population can be reconstructed, while the identification of the expressed immunoglobulin genes allows investigating clonotype evolution and the detection of tumor clones that share the same clonally rearranged B cell receptor sequence. Researchers are guided through both the experimental protocols and data analysis with a comprehensive, step-by-step walkthrough of how to use some of the more popular single-cell software tools., (© 2025. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

The myocyte enhancer factor 2B (MEF2B) transcription factor is frequently mutated in germinal center (GC)-derived B-cell lymphomas. Its ammino (N)-terminal mutations drive lymphomagenesis by escaping interaction with transcriptional repressors, while the function of carboxy (C)-terminal mutations remains to be elucidated. Here, we show that MEF2B C-tail is physiologically phosphorylated at specific residues and phosphorylation at serine (S)324 is impaired by lymphoma-associated mutations. Lack of phosphorylation at S324 enhances the interaction of MEF2B with the SWI/SNF chromatin remodeling complex, leading to higher transcriptional activity. In addition, these mutants show an increased protein stability due to impaired interaction with the CUL3/KLHL12 ubiquitin complex. Mice expressing a phosphorylation-deficient lymphoma-associated MEF2B mutant display GC enlargement and develop GC-derived lymphomas, when crossed with Bcl2 transgenic mice. These results unveil converging mechanisms of action for a diverse spectrum of MEF2B mutations, all leading to its dysregulation and GC B-cell lymphomagenesis., (© 2024. The Author(s).)

Background: Care partners of people with serious illness experience significant challenges and unmet needs during the patient's treatment period and after their death. Learning from others with shared experiences can be valuable, but opportunities are not consistently available., Objective: This study aims to design and prototype a regional, facilitated, and web-based peer support network to help active and bereaved care partners of persons with serious illness be better prepared to cope with the surprises that arise during serious illness and in bereavement., Methods: An 18-member co-design team included active care partners and those in bereavement, people who had experienced serious illness, regional health care and support partners, and clinicians. It was guided by facilitators and peer network subject-matter experts. We conducted design exercises to identify the functions and specifications of a peer support network. Co-design members independently prioritized network specifications, which were incorporated into an early iteration of the web-based network., Results: The team prioritized two functions: (1) connecting care partners to information and (2) facilitating emotional support. The design process generated 24 potential network specifications to support these functions. The highest priorities included providing a supportive and respectful community; connecting people to trusted resources; reducing barriers to asking for help; and providing frequently asked questions and responses. The network platform had to be simple and intuitive, provide technical support for users, protect member privacy, provide publicly available information and a private discussion forum, and be easily accessible. It was feasible to enroll members in the ConnectShareCare web-based network over a 3-month period., Conclusions: A co-design process supported the identification of critical features of a peer support network for care partners of people with serious illnesses in a rural setting, as well as initial testing and use. Further testing is underway to assess the long-term viability and impact of the network., (©Elizabeth A O’Donnell, Aricca D Van Citters, Inas S Khayal, Matthew M Wilson, David Gustafson, Amber E Barnato, Andrea C Buccellato, Colleen Young, Megan M Holthoff, Eugene Korsunskiy, Stephanie C Tomlin, Amelia M Cullinan, Alexandra C Steinbaugh, Jennifer J Hinson, Kristen R Johnson, Andrew Williams, Ruth M Thomson, Janet M Haines, Anne B Holmes, Ann D Bradley, Eugene C Nelson, Kathryn B Kirkland. Originally published in JMIR Human Factors (https://humanfactors.jmir.org), 08.05.2024.)

The coproduction learning health system (CLHS) model extends the definition of a learning health system to explicitly bring together patients and care partners, health care teams, administrators, and scientists to share the work of optimizing health outcomes, improving care value, and generating new knowledge. The CLHS model highlights a partnership for coproduction that is supported by data that can be used to support individual patient care, quality improvement, and research. We provide a case study that describes the application of this model to transform care within an oncology program at an academic medical center., Competing Interests: No conflicts of interest have been declared relating to the manuscript., (Copyright © 2023 The Authors. Published by Wolters Kluwer Health, Inc.)

Heterozygous inactivating mutations of the KMT2D methyltransferase and the CREBBP acetyltransferase are among the most common genetic alterations in B cell lymphoma and co-occur in 40 to 60% of follicular lymphoma (FL) and 30% of EZB/C3 diffuse large B cell lymphoma (DLBCL) cases, suggesting they may be coselected. Here, we show that combined germinal center (GC)-specific haploinsufficiency of Crebbp and Kmt2d synergizes in vivo to promote the expansion of abnormally polarized GCs, a common preneoplastic event. These enzymes form a biochemical complex on select enhancers/superenhancers that are critical for the delivery of immune signals in the GC light zone and are only corrupted upon dual Crebbp / Kmt2d loss, both in mouse GC B cells and in human DLBCL. Moreover, CREBBP directly acetylates KMT2D in GC-derived B cells, and, consistently, its inactivation by FL/DLBCL-associated mutations abrogates its ability to catalyze KMT2D acetylation. Genetic and pharmacologic loss of CREBBP and the consequent decrease in KMT2D acetylation lead to reduced levels of H3K4me1, supporting a role for this posttranslational modification in modulating KMT2D activity. Our data identify a direct biochemical and functional interaction between CREBBP and KMT2D in the GC, with implications for their role as tumor suppressors in FL/DLBCL and for the development of precision medicine approaches targeting enhancer defects induced by their combined loss.

Diffuse large B-cell lymphoma (DLBCL) is an aggressive form of non-Hodgkin lymphoma with poor response to R-CHOP therapy due to remarkable heterogeneity. Based on gene expression, DLBCL cases were divided into two subtypes, i.e. ABC and GCB, where ABC subtype is associated with poor outcomes. Due to its association with clinical outcome, this classification, also known as cell-of-origin (COO), is an efficient way to predict the response to R-CHOP therapy. Previous COO classification methods have some shortcomings, e.g. limited number of samples in the training dataset. These shortcomings challenge the robustness of methods and make it difficult to implicate these methods at clinical level. To overcome the shortcomings of previous methods, we developed a deep learning-based classifier model on a cohort of 381 DLBCL patients using expression data of 20 genes. We implemented multilayer perceptron (MLP) to train deep learning-based classifier, named MLP-COO. MLP-COO achieved accuracy of 99.70% and 94.70% on training and testing datasets, respectively, with 10-fold cross-validation. We also assessed its performance on an independent dataset of 294 DLBCL patients. On independent dataset, we achieved an accuracy of 95.90% with MCC of 0.917. To show its broader applicability, we used this classifier to predict the clinical outcome using survival data from two large cohorts of DLBCL patients. In survival analysis, MLP-COO recapitulates the survival probabilities of DLBCL patients based on their COO in both cohorts. We anticipate that MLP-COO model developed in this study will benefit in the accurate COO prediction of DLBCL patients and their clinical outcomes., (© The Author(s) 2022. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets 1-5 . However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)

Background: Despite progress in developing learning health systems (LHS) and associated metrics of success, a gap remains in identifying measures to guide the implementation and assessment of the impact of an oncology LHS. Our aim was to identify a balanced set of measures to guide a person-centered oncology LHS., Methods: A modified Delphi process and clinical value compass framework were used to prioritize measures for tracking LHS performance. A multidisciplinary group of 77 stakeholders, including people with cancer and family members, participated in 3 rounds of online voting followed by 50-minute discussions. Participants rated metrics on perceived importance to the LHS and discussed priorities., Results: Voting was completed by 94% of participants and prioritized 22 measures within 8 domains. Patient and caregiver factors included clinical health (Eastern Cooperative Oncology Group Performance Status, survival by cancer type and stage), functional health and quality of life (Patient Reported Outcomes Measurement Information System [PROMIS] Global-10, Distress Thermometer, Modified Caregiver Strain Index), experience of care (advance care planning, collaboRATE, PROMIS Self-Efficacy Scale, access to care, experience of care, end-of-life quality measures), and cost and resource use (avoidance and delay in accessing care and medications, financial hardship, total cost of care). Contextual factors included team well-being (Well-being Index; voluntary staff turnover); learning culture (Improvement Readiness, compliance with Commission on Cancer quality of care measures); scholarly engagement and productivity (institutional commitment and support for research, academic productivity index); and diversity, equity, inclusion, and belonging (screening and follow-up for social determinants of health, inclusivity of staff and patients)., Conclusions: The person-centered LHS value compass provides a balanced set of measures that oncology practices can use to monitor and evaluate improvement across multiple domains., (© The Author(s) 2022. Published by Oxford University Press.)

In response to T-cell-dependent antigens, mature B cells in the secondary lymphoid organs are stimulated to form germinal centers (GCs), which are histological structures deputed to antibody affinity maturation, a process associated with immunoglobulin gene editing by somatic hypermutation (SHM) and class switch recombination (CSR). GC B cells are heterogeneous and transition across multiple stages before being eliminated by apoptosis or committing to post-GC differentiation as memory B cells or plasma cells. In order to explore the dynamics of SHM and CSR during the GC reaction, we identified GC subpopulations by single-cell (sc) transcriptomics and analyzed the load of immunoglobulin variable (V) region mutations as well as the isotype class distribution in each subpopulation. The results showed that the large majority of GC B cells display a quantitatively similar mutational load in the V regions and analogous IGH isotype class distribution, except for the precursors of memory B cells (PreM) and plasma cells (PBL). PreM showed a bimodal pattern with about half of the cells displaying high V region germline identity and enrichment for unswitched IGH, while the rest of the cells carried a mutational load similar to the bulk of GC B cells and showed a switched isotype. PBL displayed a bias toward expression of IGHG and higher V region germline identity compared to the bulk of GC B cells. Genes implicated in SHM and CSR were significantly induced in specific GC subpopulations, consistent with the occurrence of SHM in dark zone cells and suggesting that CSR can occur within the GC., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Corinaldesi, Holmes, Shen, Grunstein, Pasqualucci, Dalla-Favera and Basso.)

Selenium contamination is a critical global issue across numerous industries. Industrial waters such as mine-impacted water (MIW) can contain toxic levels of selenate, in addition to varying concentrations of many different dissolved species from the underlying strata, such as sulfate, carbonate, nitrate, organic matter, and many dissolved metals. The removal of selenate from MIW is desired, due to selenate's acute and chronic toxicity in aquatic ecosystems at elevated concentrations. However, due to the complexity of the water matrix and the presence of many other dissolved constituents, this is often very challenging. In this study, we present for the first time the reduction of selenate in a real industrial wastewater, namely MIW, and reveal a significant advantage of photocatalytic reduction; the ability to selectively reduce selenate from >500 μg L -1 to <2 μg L -1 in the presence of the more energetically favourable electron acceptor, nitrate (250× molar concentration of selenate) and high concentrations of sulfate (1,940× molar concentration of selenate). The presence and impacts of sulfate, chloride, carbonate, and nitrate on the competitive adsorption and reduction of selenate on TiO 2 are thoroughly investigated for the first time, using formic acid as an electron hole scavenger. The electron transfer mechanism proposed follows TiO 2 conduction band electrons are responsible for the reduction of selenate to elemental Se (Se 0 ) and both carbon dioxide radicals (CO 2 ·- ) and Se conduction band electrons are responsible for the further reduction of Se 0 to hydrogen selenide (H 2 Se)., (Copyright © 2021. Published by Elsevier Ltd.)

The transcription factor forkhead box O1 (FOXO1), which instructs the dark zone program to direct germinal center (GC) polarity, is typically inactivated by phosphatidylinositol 3-kinase (PI3K) signals. Here, we investigated how FOXO1 mutations targeting this regulatory axis in GC-derived B cell non-Hodgkin lymphomas (B-NHLs) contribute to lymphomagenesis. Examination of primary B-NHL tissues revealed that FOXO1 mutations and PI3K pathway activity were not directly correlated. Human B cell lines bearing FOXO1 mutations exhibited hyperactivation of PI3K and Stress-activated protein kinase (SAPK)/Jun amino-terminal kinase (JNK) signaling, and increased cell survival under stress conditions as a result of alterations in FOXO1 transcriptional affinities and activation of transcriptional programs characteristic of GC-positive selection. When modeled in mice, FOXO1 mutations conferred competitive advantage to B cells in response to key T-dependent immune signals, disrupting GC homeostasis. FOXO1 mutant transcriptional signatures were prevalent in human B-NHL and predicted poor clinical outcomes. Thus, rather than enforcing FOXO1 constitutive activity, FOXO1 mutations enable co-option of GC-positive selection programs during the pathogenesis of GC-derived lymphomas., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 Elsevier Inc. All rights reserved.)

In response to T cell-dependent antigens, mature B cells are stimulated to form germinal centers (GCs), the sites of B cell affinity maturation and the cell of origin (COO) of most B cell lymphomas. To explore the dynamics of GC B cell development beyond the known dark zone and light zone compartments, we performed single-cell (sc) transcriptomic analysis on human GC B cells and identified multiple functionally linked subpopulations, including the distinct precursors of memory B cells and plasma cells. The gene expression signatures associated with these GC subpopulations were effective in providing a sc-COO for ∼80% of diffuse large B cell lymphomas (DLBCLs) and identified novel prognostic subgroups of DLBCL., Competing Interests: Disclosures: N. Compagno is currently employed at Novartis. No other disclosures were reported., (© 2020 Holmes et al.)

Inactivating mutations of the CREBBP and EP300 acetyltransferases are among the most common genetic alterations in diffuse large B cell lymphoma (DLBCL) and follicular lymphoma (FL). Here, we examined the relationship between these two enzymes in germinal center (GC) B cells, the normal counterpart of FL and DLBCL, and in lymphomagenesis by using conditional GC-directed deletion mouse models targeting Crebbp or Ep300. We found that CREBBP and EP300 modulate common as well as distinct transcriptional programs implicated in separate anatomic and functional GC compartments. Consistently, deletion of Ep300 but not Crebbp impaired the fitness of GC B cells in vivo. Combined loss of Crebbp and Ep300 completely abrogated GC formation, suggesting that these proteins partially compensate for each other through common transcriptional targets. This synthetic lethal interaction was retained in CREBBP-mutant DLBCL cells and could be pharmacologically targeted with selective small molecule inhibitors of CREBBP and EP300 function. These data provide proof-of-principle for the clinical development of EP300-specific inhibitors in FL and DLBCL., (Copyright © 2019 Elsevier Inc. All rights reserved.)

The study of the environmental fate of nanoscale TiO 2 (n-TiO 2 ) is a major recent research focus which requires a rapid and accurate on-site concentration determination method. Inductively coupled plasma mass spectroscopy (ICP-MS) has been the most widely used method for determining the concentration of n-TiO 2 in environmental samples; however, poses many challenges, such as hazardous hydrofluoric acid pre-treatment and clear limitations in mobile on-site measurement and monitoring. This study demonstrates that industrial wastewater containing natural organic matter (NOM) can present a major challenge to the analysis of n-TiO 2 by ICP-MS, and introduces a spectrophotometry technique that can be used as an alternative. The results suggest that spectrophotometry methods can be more accurate than slurry nebulization ICP-MS for measuring the concentrations of n-TiO 2 in wastewater containing NOM under low salt conditions. Furthermore, this study demonstrates the use of a portable flow-through spectrophotometer for use in applications of wastewater treatment and environmental monitoring with real-time feedback of n-TiO 2 concentrations. The ability to detect and monitor n-TiO 2 will greatly assist in improving the understanding of hazards and risks that emerging nanomaterials pose to the environment and the public health.

The development of nanoparticle-based soil remediation techniques is hindered by the lack of accurate in situ nanoparticle (NP) monitoring and characterization methods. Spectral induced polarization (SIP), a noninvasive geophysical technique, offers a promising approach to detect and quantify NPs in porous media. However, its successful implementation as a monitoring tool requires an understanding of the polarization mechanisms, the governing NP-associated SIP responses and their dependence on the stabilizing coatings that are typically used for NPs deployed in environmental applications. Herein, we present SIP responses (0.1-10 000 Hz) measured during injection of a poloxamer-coated superparamagnetic iron-oxide nanoparticle (SPION) suspension in flow-through columns packed with natural sand from the Borden aquifer. An advective-dispersive transport model is fitted to outflow SPION concentration measurements to compute average concentrations over the SIP spatial response domain (within the columns). The average SPION concentrations are compared with the real and imaginary components of the complex conductivity. Excellent correspondence is found between the average SPION concentrations in the columns and the imaginary conductivity values, suggesting that NP-mediated polarization (that is, charge storage) increases proportionally with increasing SPION concentration. Our results support the possibility of SIP monitoring of spatial and temporal NP distributions, which can be immediately deployed in bench-scale studies with the prospect of future real-world field applications.

The gene encoding the MEF2B transcription factor is mutated in germinal center (GC)-derived B cell lymphomas, but its role in GC development and lymphomagenesis is unknown. We demonstrate that Mef2b deletion reduces GC formation in mice and identify MEF2B transcriptional targets in GC, with roles in cell proliferation, apoptosis, GC confinement, and differentiation. The most common lymphoma-associated MEF2B mutant (MEF2B D83V ) is hypomorphic, yet escapes binding and negative regulation by components of the HUCA complex and class IIa HDACs. Mef2b D83V expression in mice leads to GC enlargement and lymphoma development, a phenotype that becomes fully penetrant in combination with BCL2 de-regulation, an event associated with human MEF2B mutations. These results identify MEF2B as a critical GC regulator and a driver oncogene in lymphomagenesis., (Copyright © 2018 Elsevier Inc. All rights reserved.)