Baseline Immune State and T-cell Clonal Kinetics are Associated with Durable Response to CAR-T Therapy in Large B-cell Lymphoma.

Engineered cellular therapy with CD19-targeting chimeric antigen receptor T-cells (CAR-T) has revolutionized outcomes for patients with relapsed/refractory Large B-Cell Lymphoma (LBCL), but the cellular and molecular features associated with response remain largely unresolved. We analyzed serial peripheral blood samples ranging from day of apheresis (day -28/baseline) to 28 days after CAR-T infusion from 50 patients with LBCL treated with axicabtagene ciloleucel (axi-cel) by integrating single cell RNA and TCR sequencing (scRNA-seq/scTCR-seq), flow cytometry, and mass cytometry (CyTOF) to characterize features associated with response to CAR-T. Pretreatment patient characteristics associated with response included presence of B cells and increased lymphocyte-to-monocyte ratio (ALC/AMC). Infusion products from responders were enriched for clonally expanded, highly activated CD8+ T cells. We expanded these observations to 99 patients from the ZUMA-1 cohort and identified a subset of patients with elevated baseline B cells, 80% of whom were complete responders. We integrated B cell proportion 0.5% and ALC/AMC 1.2 into a two-factor predictive model and applied this model to the ZUMA-1 cohort. Estimated progression free survival (PFS) at 1 year in patients meeting one or both criteria was 65% versus 31% for patients meeting neither criterion. Our results suggest that patients' immunologic state at baseline affects likelihood of response to CAR-T through both modulation of the T cell apheresis product composition and promoting a more favorable circulating immune compartment prior to therapy. These baseline immunologic features, measured readily in the clinical setting prior to CAR-T, can be applied to predict response to therapy.

A Single Center Exploratory Survey of Patients and Nurses on post-Surgical Oral Opioid Delivery Through Patient-Controlled Analgesia.

Background: The most common route of opioid delivery is nurse-administered pills. However, there are numerous challenges such as nursing burden, opioid diversion, medication delay, and patient dissatisfaction. In this study, we conducted two surveys, first to assess patients' and nurses' opinions on the current administration of opioids in pill form, followed by their attitudes towards an innovative concept of oral medication delivery based on a medical device currently undergoing research and development within the University, patient-controlled dispenser and deactivator (PCDD) that allows patients to self-administer liquid oral opioids on demand based on physician prescription. Methods: Questionnaires were developed, verified and deployed to assess nurse and post-surgical patient opinions on the current administration of opioids in pill form, as well as the proposed new concept of patient -controlled administration of oral liquid medication via an illustration of PCDD, from September 2022 through July 2023 at a major academic tertiary care center. Quantitative and qualitative data were collected from postoperative patients and nurses from surgical specialties including General Surgery, Surgical Oncology, Trauma Surgery, Orthopedics, and Neurosurgery. Results: Forty-three patients and 53 nurses were interviewed. Seventy percent of patients frequently called nurses for pain medication post-surgery 1-4 times daily, and 32% of patients were told each day by nurses that they could not receive medication because they were not due yet. Medication delay caused 24% of patients to worry about nursing availability for medication delivery. Likewise, nurses reported that half of patients receive delayed medication (22 minutes median delay time) and half of nursing time was spent administering pain medication. Nurses expressed moderate satisfaction with their current delivery of medication (median satisfaction score 6.5 out of 10). When being introduced to the concept of PCDD via a product illustration, 15% of patients said that they prefer liquid medication and 51% said they prefer PCDD or were interested in trying it. Conclusion: Nurse-administered pills are a common but suboptimal method for postoperative pain management. Based on patient and nurse feedback, patient controlled self-administered liquid oral opioid delivery is conceptually innovative, practically viable and potentially a preferred alternative for timely and less nurse-exhaustive pain management.

Engineered Lipids for Intracellular Reactive Oxygen Species Scavenging in Steatotic Hepatocytes.

Intracellular reactive oxygen species (ROS) in steatotic cells pose a problem due to their potential to cause oxidative stress and cellular damage. Delivering engineered phospholipids to intracellular lipid droplets in steatotic hepatic cells, using the cell's inherent intracellular lipid transport mechanisms are investigated. Initially, it is shown that tail-labeled fluorescent lipids assembled into liposomes are able to be transported to intracellular lipid droplets in steatotic HepG2 cells and HHL-5 cells. Further, an antioxidant, an EUK salen-manganese derivative, which has superoxide dismutase-like and catalase-like activity, is covalently conjugated to the tail of a phospholipid and formulated as liposomes for administration. Steatotic HepG2 cells and HHL-5 cells incubated with these antioxidant liposomes have lower intracellular ROS levels compared to untreated controls and non-covalently formulated antioxidants. This first proof-of-concept study illustrates an alternative strategy to equip native organelles in mammalian cells with engineered enzyme activity.

Preeclampsia in pregnant women with COVID-19: a prospective cohort study from two tertiary hospitals in Southern Brazil.

Background: COVID-19 is an infectious pathology that shows vascular changes during pregnancy, as well as in the placentas. The main objectives of this study were to estimate the prevalence and the risk factors for preeclampsia in hospitalized pregnant women with COVID-19. As well as comparing maternal and perinatal outcomes in hospitalized pregnant women with COVID-19 and preeclampsia with those without preeclampsia. Methods: Prospective cohort study of 100 hospitalized pregnant women from two tertiary hospitals, diagnosed with COVID-19, and divided into two groups: PE+ group (pregnant women with COVID-19 and preeclampsia) and PE- group (pregnant women with COVID-19 without preeclampsia). These pregnant women had prevalence, risk factors, maternal and perinatal data analyzed. Results: The prevalence of preeclampsia was 11%. Severe COVID-19 was the main risk factor for preeclampsia (OR = 8.18 [CI 1.53-43.52]), as well as fetal growth restriction was the main perinatal outcome (OR = 8.90 [CI 1.52-38.4]). Comorbidities were more frequent in the PE+ group (63.6% vs 31.5%, p = 0.03), as well as prematurity (81.8% vs 41.6%, p = 0.02), low birth weight (63.6% vs 24.7%, p = 0.01), and the need for neonatal intensive care admission of the newborn (63.6% vs 27.0%, p = 0.03). Pregnant women with PE had twice as long a length of stay in the intensive care unit (RR = 2.35 [CI 1.34-4.14]). Although maternal mortality was more frequent among pregnant women with PE, it was not statistically significant. Conclusions: Prevalence of preeclampsia in hospitalized pregnant women with COVID-19 was 11%. Severe COVID-19 was the main risk factor for preeclampsia and associated comorbidities increased the risk for developing preeclampsia. Long length of stay in the intensive care unit was the main maternal outcome and fetal growth restriction was the main perinatal outcome of preeclampsia.

Tryptophan fuels MYC-dependent liver tumorigenesis through indole 3-pyruvate synthesis.

Cancer cells exhibit distinct metabolic activities and nutritional dependencies compared to normal cells. Thus, characterization of nutrient demands by individual tumor types may identify specific vulnerabilities that can be manipulated to target the destruction of cancer cells. We find that MYC-driven liver tumors rely on augmented tryptophan (Trp) uptake, yet Trp utilization to generate metabolites in the kynurenine (Kyn) pathway is reduced. Depriving MYC-driven tumors of Trp through a No-Trp diet not only prevents tumor growth but also restores the transcriptional profile of normal liver cells. Despite Trp starvation, protein synthesis remains unhindered in liver cancer cells. We define a crucial role for the Trp-derived metabolite indole 3-pyruvate (I3P) in liver tumor growth. I3P supplementation effectively restores the growth of liver cancer cells starved of Trp. These findings suggest that I3P is a potential therapeutic target in MYC-driven cancers. Developing methods to target this metabolite represents a potential avenue for liver cancer treatment.

A thematic analysis of how men and women post 56 years unwind from work during their free time.

BACKGROUND: Recent research indicates that as men age, their tendency to ruminate about work decreases, while ruminating remains high in women, which poses an increased risk for impaired health among older women. OBJECTIVE: This study explored gender differences/similarities in the process of unwinding from work in men and women aged between 56-65 years. METHODS: Semi-structured qualitative interviews were conducted online with eight men and eight women, recruited from a UK leading organization that provides health care solutions between May and June 2022. Participants were asked about their job role and responsibilities, their leisure time activities, how they unwind post work, and their experiences of thinking about work related thoughts outside of work. Transcripts were analyzed using an inductive analysis. RESULTS: Three superordinate themes were identified that underpinned their ability to unwind: 'Work style', 'Creating work-life balance' and 'Switching off from one's responsibilities'. Women reported a more perfectionist approach, they set high standards for themselves, were worried about making mistakes, and demonstrated, if in a supervisory role, a more nurturing and holistic approach to their colleagues/subordinates, while men, were more focused on task completion. Most women, but not men, also described difficulties in psychologically switching off from work, and stated they could only truly relax outside the home, when they are away from household activities. CONCLUSION: The study provides nuanced insights into the experiences of unwinding from work, and the findings suggest the need for person-centric approaches in developing interventions to help workers over 56 years to psychologically disengage from work.

Accuracy of linear measurements for implant planning based on low-dose cone beam CT protocols: a systematic review and meta-analysis.

OBJECTIVES: The aim of this systematic review was to verify the accuracy of linear measurements performed on low-dose CBCT protocols for implant planning, in comparison with those performed on standard and high-resolution CBCT protocols. METHODS: The literature search included four databases (Pubmed, Web of Science, Embase, and Scopus). Two reviewers independently screened titles/abstracts and full texts according to eligibility criteria, extracted the data, and examined the methodological quality. Risk of bias assessment was performed using the Quality Assessment Tool For In Vitro Studies. Random-effects meta-analysis was used for pooling measurement error data. RESULTS: The initial search yielded 4684 titles. In total, 13 studies were included in the systematic review, representing a total of 81 samples, while 9 studies were included in the meta-analysis. The risk of bias ranged from medium to low. The main results across the studies indicate a strong consistency in linear measurements performed on low-dose images in relation to the reference methods. The overall pooled planning measurement error from low-dose CBCT protocols was -0.24 mm (95% CI, -0.52 to 0.04) with a high level of heterogeneity, showing a tendency for underestimation of real values. Various studies found no significant differences in measurements across different protocols (eg, voxel sizes, mA settings, or dose levels), regions (incisor, premolar, molar) and types (height vs. width). Some studies, however, noted exceptions in measurements performed on the posterior mandible. CONCLUSION: Low-dose CBCT protocols offer adequate precision and accuracy of linear measurements for implant planning. Nevertheless, diagnostic image quality needs must be taken into consideration when choosing a low-dose CBCT protocol.

ZNF692 regulates nucleolar morphology by interacting with NPM1 and modifying its self-assembly properties.

The nucleolus, a membrane-less organelle, is responsible for ribosomal RNA transcription, ribosomal RNA processing, and ribosome assembly. Nucleolar size and number are indicative of a cell's protein synthesis rate and proliferative capacity, and abnormalities in the nucleolus have been linked to neurodegenerative diseases and cancer. In this study, we demonstrated that the nucleolar protein ZNF692 directly interacts with nucleophosmin 1 (NPM1). Knocking down ZNF692 resulted in the nucleolar redistribution of NPM1 in ring-like structures and reduced protein synthesis. Purified NPM1 forms spherical condensates in vitro but mixing it with ZNF692 produces irregular condensates more closely resembling living cell nucleoli. Our findings indicate that ZNF692, by interacting with NPM1, plays a critical role in regulating nucleolar architecture and function in living cells.

Relationship of household composition with sedentary behavior and eating habits of 102,072 adolescents: A representative sample of Brazil (PeNSE Study).

PURPOSE: The household composition is important for adolescents and understanding its relationship with their lifestyle habits is essential. This study aimed to analyze the relationship of household composition with sedentary behavior and eating habits of adolescents. METHODS: This study analyzed data from the Brazilian National Scholar Health Survey-PeNSE 2015. The sample was composed by 102,072 adolescents (11-17 years). The independent variable of the study was the household composition (living with both parents versus living with only one parent or none of them), whereas outcome variables were eating habits and sedentary behavior patterns. Logistic regression models were used to analyze the association between variables. RESULTS: Adolescents living with both parents were less likely to have high sedentary behavior (≥2 h OR = 0.89; ≥4 h OR = 0.86), eat while watching TV for ≥5 days/week (OR = 0.88), frequent fried foods (OR = 0.89), sweets (OR = 0.92), soft drinks (OR = 0.86) and ultra processed foods (OR = 0.97) consumption, as were more likely to have lunch with parents (OR = 1.87), frequent vegetables (OR = 1.12), beans (OR = 1.14) and fruits (OR = 1.11) consumption than those who live with one parent or none of them. CONCLUSION: Households composed by both father and mother was associated with lower sedentary behavior and healthy eating habits in Brazilian adolescents.

Artificial Cells and HepG2 Cells in 3D-Bioprinted Arrangements.

Artificial cells are engineered units with cell-like functions for different purposes including acting as supportive elements for mammalian cells. Artificial cells with minimal liver-like function are made of alginate and equipped with metalloporphyrins that mimic the enzyme activity of a member of the cytochrome P450 family namely CYP1A2. The artificial cells are employed to enhance the dealkylation activity within 3D bioprinted structures composed of HepG2 cells and these artificial cells. This enhancement is monitored through the conversion of resorufin ethyl ether to resorufin. HepG2 cell aggregates are 3D bioprinted using an alginate/gelatin methacryloyl ink, resulting in the successful proliferation of the HepG2 cells. The composite ink made of an alginate/gelatin liquid phase with an increasing amount of artificial cells is characterized. The CYP1A2-like activity of artificial cells is preserved over at least 35 days, where 6 nM resorufin is produced in 8 h. Composite inks made of artificial cells and HepG2 cell aggregates in a liquid phase are used for 3D bioprinting. The HepG2 cells proliferate over 35 days, and the structure has boosted CYP1A2 activity. The integration of artificial cells and their living counterparts into larger 3D semi-synthetic tissues is a step towards exploring bottom-up synthetic biology in tissue engineering.

Effects of KRAS Genetic Interactions on Outcomes in Cancers of the Lung, Pancreas, and Colorectum.

BACKGROUND: KRAS is among the most commonly mutated oncogenes in cancer, and previous studies have shown associations with survival in many cancer contexts. Evidence from both clinical observations and mouse experiments further suggests that these associations are allele- and tissue-specific. These findings motivate using clinical data to understand gene interactions and clinical covariates within different alleles and tissues. METHODS: We analyze genomic and clinical data from the AACR Project GENIE Biopharma Collaborative for samples from lung, colorectal, and pancreatic cancers. For each of these cancer types, we report epidemiological associations for different KRAS alleles, apply principal component analysis (PCA) to discover groups of genes co-mutated with KRAS, and identify distinct clusters of patient profiles with implications for survival. RESULTS: KRAS mutations were associated with inferior survival in lung, colon, and pancreas, although the specific mutations implicated varied by disease. Tissue- and allele-specific associations with smoking, sex, age, and race were found. Tissue-specific genetic interactions with KRAS were identified by PCA, which were clustered to produce five, four, and two patient profiles in lung, colon, and pancreas. Membership in these profiles was associated with survival in all three cancer types. CONCLUSIONS: KRAS mutations have tissue- and allele-specific associations with inferior survival, clinical covariates, and genetic interactions. IMPACT: Our results provide greater insight into the tissue- and allele-specific associations with KRAS mutations and identify clusters of patients that are associated with survival and clinical attributes from combinations of genetic interactions with KRAS mutations.

Bayesian combinatorial MultiStudy factor analysis.

Mutations in the BRCA1 and BRCA2 genes are known to be highly associated with breast cancer. Identifying both shared and unique transcript expression patterns in blood samples from these groups can shed insight into if and how the disease mechanisms differ among individuals by mutation status, but this is challenging in the high-dimensional setting. A recent method, Bayesian Multi-Study Factor Analysis (BMSFA), identifies latent factors common to all studies (or equivalently, groups) and latent factors specific to individual studies. However, BMSFA does not allow for factors shared by more than one but less than all studies. This is critical in our context, as we may expect some but not all signals to be shared by BRCA1-and BRCA2-mutation carriers but not necessarily other high-risk groups. We extend BMSFA by introducing a new method, Tetris, for Bayesian combinatorial multi-study factor analysis, which identifies latent factors that any combination of studies or groups can share. We model the subsets of studies that share latent factors with an Indian Buffet Process, and offer a way to summarize uncertainty in the sharing patterns using credible balls. We test our method with an extensive range of simulations, and showcase its utility not only in dimension reduction but also in covariance estimation. When applied to transcript expression data from high-risk families grouped by mutation status, Tetris reveals the features and pathways characterizing each group and the sharing patterns among them. Finally, we further extend Tetris to discover groupings of samples when group labels are not provided, which can elucidate additional structure in these data.

ZNF692 organizes a hub specialized in 40S ribosomal subunit maturation enhancing translation in rapidly proliferating cells.

Increased nucleolar size and activity correlate with aberrant ribosome biogenesis and enhanced translation in cancer cells. One of the first and rate-limiting steps in translation is the interaction of the 40S small ribosome subunit with mRNAs. Here, we report the identification of the zinc finger protein 692 (ZNF692), a MYC-induced nucleolar scaffold that coordinates the final steps in the biogenesis of the small ribosome subunit. ZNF692 forms a hub containing the exosome complex and ribosome biogenesis factors specialized in the final steps of 18S rRNA processing and 40S ribosome maturation in the granular component of the nucleolus. Highly proliferative cells are more reliant on ZNF692 than normal cells; thus, we conclude that effective production of small ribosome subunits is critical for translation efficiency in cancer cells.

Significance analysis for clustering with single-cell RNA-sequencing data.

Unsupervised clustering of single-cell RNA-sequencing data enables the identification of distinct cell populations. However, the most widely used clustering algorithms are heuristic and do not formally account for statistical uncertainty. We find that not addressing known sources of variability in a statistically rigorous manner can lead to overconfidence in the discovery of novel cell types. Here we extend a previous method, significance of hierarchical clustering, to propose a model-based hypothesis testing approach that incorporates significance analysis into the clustering algorithm and permits statistical evaluation of clusters as distinct cell populations. We also adapt this approach to permit statistical assessment on the clusters reported by any algorithm. Finally, we extend these approaches to account for batch structure. We benchmarked our approach against popular clustering workflows, demonstrating improved performance. To show practical utility, we applied our approach to the Human Lung Cell Atlas and an atlas of the mouse cerebellar cortex, identifying several cases of over-clustering and recapitulating experimentally validated cell type definitions.

Ethical and Moral Conflicts in the Nursing Care of Pediatric Patients With Cancer and Their Families.

BACKGROUND: Pediatric oncology nurses encounter ethical and moral dilemmas when providing comprehensive care to pediatric patients with cancer and their families. OBJECTIVE: The aim of this study was to explore ethical and moral conflicts arising in the field of pediatric oncology from the perspective of nursing professionals. METHOD: This qualitative secondary analysis was conducted with 10 nursing professionals from a pediatric cancer hospital through semistructured interviews and analyzed using thematic data analysis. RESULTS: Two themes emerged: (1) living with conflicts intrinsic to the relationships , which describes multiple sources of conflict in the relationships of nursing professionals with the team, with the family, and with seriously ill children, summarizing trigger-sensitive topics to be addressed for its mediation; (2) developing moral resilience , which represents how nurses reframe the conflicts and make use of strategies to avoid being personally harmful. CONCLUSIONS: The results highlight the challenging work environment of pediatric oncology, recognizing the multiple natures of sensitive topics to nursing professionals during clinical decision making and the incipient strategies in dealing with ethical and moral conflicts. IMPLICATIONS FOR PRACTICE: This study reveals self-reflection and intuitive strategies as protective factors, which could be applied as a step to support nurses encountering ethical and moral conflicts in pediatric oncology daily practice. Furthermore, because of the limited support services for nursing professionals, it is necessary to foresee institutional policies to embrace the development of moral resilience.

Astrocytes in Paper Chips and Their Interaction with Hybrid Vesicles.

The role of astrocytes in brain function has received increased attention lately due to their critical role in brain development and function under physiological and pathophysiological conditions. However, the biological evaluation of soft material nanoparticles in astrocytes remains unexplored. Here, the interaction of crosslinked hybrid vesicles (HVs) and either C8-D1A astrocytes or primary astrocytes cultured in polystyrene tissue culture or floatable paper-based chips is investigated. The amphiphilic block copolymer poly(cholesteryl methacrylate)-block-poly(2-carboxyethyl acrylate) (P1) and 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine lipids are used for the assembly of HVs with crosslinked membranes. The assemblies show no short-term toxicity towards the C8-D1A astrocytes and the primary astrocytes, and both cell types internalize the HVs when cultured in 2D cell culture. Further, it is demonstrated that both the C8-D1A astrocytes and the primary astrocytes could mature in paper-based chips with preserved calcium signaling and glial fibrillary acidic protein expression. Last, it is confirmed that both types of astrocytes could internalize the HVs when cultured in paper-based chips. These findings lay out a fundamental understanding of the interaction between soft material nanoparticles and astrocytes, even when primary astrocytes are cultured in paper-based chips offering a 3D environment.

Ras-mediated activation of mTORC2 promotes breast epithelial cell migration and invasion.

We previously identified the mechanistic target of rapamycin complex 2 (mTORC2) as an effector of Ras for the control of directed cell migration in Dictyostelium. Recently, the Ras-mediated regulation of mTORC2 was found to be conserved in mammalian cells, and mTORC2 was shown to be an effector of oncogenic Ras. Interestingly, mTORC2 has been linked to cancer cell migration, and particularly in breast cancer. Here, we investigated the role of Ras in promoting the migration and invasion of breast cancer cells through mTORC2. We observed that both Ras and mTORC2 promote the migration of different breast cancer cells and breast cancer cell models. Using HER2 and oncogenic Ras-transformed breast epithelial MCF10A cells, we found that both wild-type Ras and oncogenic Ras promote mTORC2 activation and an mTORC2-dependent migration and invasion in these breast cancer models. We further observed that, whereas oncogenic Ras-transformed MCF10A cells display uncontrolled cell proliferation and invasion, disruption of mTORC2 leads to loss of invasiveness only. Together, our findings suggest that, whereas the Ras-mediated activation of mTORC2 is expected to play a minor role in breast tumor formation, the Ras-mTORC2 pathway plays an important role in promoting the migration and invasion of breast cancer cells.

Chronic loss of muscarinic M5 receptor function manifests disparate impairments in exploratory behavior in male and female mice despite common dopamine regulation.

There are five cloned muscarinic acetylcholine receptors (M1-M5). Of these, the muscarinic type 5 receptor (M5) is the only one localized to dopamine neurons in the ventral tegmental area and substantia nigra. Unlike M1-M4, the M5 receptor has relatively restricted expression in the brain, making it an attractive therapeutic target. Here we performed an in-depth characterization of M5-dependent potentiation of dopamine transmission in the nucleus accumbens and accompanying exploratory behaviors in male and female mice. We show that M5 receptors potentiate dopamine transmission by acting directly on the terminals within the nucleus accumbens. Using the muscarinic agonist oxotremorine, we revealed a unique concentration-response curve and a sensitivity to repeated forced swim stress or restraint stress exposure. We found that constitutive deletion of M5 receptors reduced exploration of the center of an open field while at the same time impairing normal habituation only in male mice. In addition, M5 deletion reduced exploration of salient stimuli, especially under conditions of high novelty, yet had no effect on hedonia assayed using the sucrose preference test or on stress coping strategy assayed using the forced swim test. We conclude that M5 receptors are critical for both engaging with the environment and updating behavioral output in response to environment cues, specifically in male mice. A cardinal feature of mood and anxiety disorders is withdrawal from the environment. These data indicate that boosting M5 receptor activity may be a useful therapeutic target for ameliorating these symptoms of depression and anxiety.Significance Statement:The basic physiological and behavioral functions of the muscarinic M5 receptor remain understudied. Furthermore, its presence on dopamine neurons, relatively restricted expression in the brain, and recent crystallization make it an attractive target for therapeutic development. Yet, most preclinical studies of M5 receptor function have primarily focused on substance use disorders in male rodents. Here we characterized the role of M5 receptors in potentiating dopamine transmission in the nucleus accumbens, finding impaired functioning after stress exposure. Furthermore, we show that M5 receptors can modulate exploratory behavior in a sex-specific manner, without impacting hedonic behavior. These findings further illustrate the therapeutic potential of the M5 receptor, warranting further research in the context of treating mood disorders.

A probabilistic gene expression barcode for annotation of cell types from single-cell RNA-seq data.

Single-cell RNA sequencing (scRNA-seq) quantifies gene expression for individual cells in a sample, which allows distinct cell-type populations to be identified and characterized. An important step in many scRNA-seq analysis pipelines is the annotation of cells into known cell types. While this can be achieved using experimental techniques, such as fluorescence-activated cell sorting, these approaches are impractical for large numbers of cells. This motivates the development of data-driven cell-type annotation methods. We find limitations with current approaches due to the reliance on known marker genes or from overfitting because of systematic differences, or batch effects, between studies. Here, we present a statistical approach that leverages public data sets to combine information across thousands of genes, uses a latent variable model to define cell-type-specific barcodes and account for batch effect variation, and probabilistically annotates cell-type identity from a reference of known cell types. The barcoding approach also provides a new way to discover marker genes. Using a range of data sets, including those generated to represent imperfect real-world reference data, we demonstrate that our approach substantially outperforms current reference-based methods, particularly when predicting across studies.