Transcriptional signals of transformation in human cancer

BACKGROUND

As normal cells transform into cancers, their cell state changes, which may drive cancer cells into a stem-like or more primordial, foetal, or embryonic cell state. The transcriptomic profile of this final state may encode information about cancer's origin and how cancers relate to their normal cell counterparts.

METHODS

Here, we used single-cell atlases to study cancer transformation in transcriptional terms. We utilised bulk transcriptomes across a wide spectrum of adult and childhood cancers, using a previously established method to interrogate their relationship to normal cell states. We extend and validate these findings using single-cell cancer transcriptomes and organ-specific atlases of colorectal and liver cancer.

RESULTS

Our bulk transcriptomic data reveals that adult cancers rarely return to an embryonic state, but that a foetal state is a near-universal feature of childhood cancers. This finding was confirmed with single-cell cancer transcriptomes.

CONCLUSIONS

Our findings provide a nuanced picture of transformation in human cancer, indicating cancer-specific rather than universal patterns of transformation pervade adult epithelial cancers.

The Role of Whole Abdomen and Pelvis Radiation Therapy in Desmoplastic Small Round Cell Tumor

PURPOSE/OBJECTIVE(S)

Desmoplastic small round cell tumor (DSRCT) is a rare entity that typically presents in adolescent and young adult men with widespread abdominopelvic disease. The benefit of whole abdomen and pelvis radiation therapy (WAPRT) after chemotherapy and maximal surgical resection is unknown. Our objective was to evaluate the oncologic benefit and toxicity of WAPRT in this rare and aggressive disease.

MATERIALS/METHODS

We conducteda retrospective review of patients with DSRCT treated at our institution primarily between 2018-2021. The cumulative incidence (CI) of intra-abdominopelvic failure was compared among those who received WAPRT after chemotherapy and surgery vs those who received chemotherapy and surgery alone without WAPRT utilizing Gray's method. Progression-free survival (PFS) and overall survival (OS) were also compared among patients who did and did not receive WAPRT using the Kaplan-Meier method from the date of surgery. Toxicity was graded per CTCAE v5.0 criteria.

RESULTS

Twenty-eight patients were included (median age 17.5 years; range 6-38 years; 78% male, 22% female). All patients received chemotherapy with VDC/IE, all but one underwent extensive tumor resection, and all but two received HIPEC at time of resection. Nineteen patients (median age 13 years) received WAPRT after surgery, while 9 patients (median age 24 years) were treated with systemic therapy and surgery alone. Patients who received WAPRT were generally treated to 30 Gy in 20 fractions utilizing intensity-modulated radiation therapy (IMRT), with a boost to gross disease to a total dose of 45-50 Gy in 9 patients. Median follow up was 20 months. The CI of intra-abdominopelvic failure at 12 and 24 months was 16% and 50% with WAPRT vs 74% and 87% without WAPRT (p = 0.003), with a median time from surgery to intra-abdominopelvic failure of 15 months after WAPRT vs 5 months without. PFS was also improved with WAP-RT (94% and 83% at 12 and 24 months) vs without WAPRT (67% and 0% at 12 and 24 months), p = 0.001. Among those who received WAPRT, patients who received a boost to gross disease had similar intra-abdominopelvic control as those who had no gross disease to boost and received WAPRT only (CI at 24 months 50% without boost vs 48% with, p = 0.95). OS did not differ between those who did and did not receive WAPRT (OS at 24 months, 88% vs 83%, p = 0.89). Most toxicities after WAPRT were mild, including grade 1-2 fatigue, nausea, and vomiting, with the exception of one patient who developed veno-occlusive disease.

CONCLUSION

Although limited by selection bias and short follow up, our study shows durable intra-abdominopelvic control and an improvement in PFS after WAPRT with IMRT, without an effect on OS. Additional larger, prospective investigations evaluating the value and toxicity of WAPRT for DSRCT are warranted.

Multi-Institutional Report of Re-Irradiation for Recurrent High-Grade Glioma

PURPOSE/OBJECTIVE(S)

Significant heterogeneity exists with regards to prior published reports of re-irradiation (re-RT) in patients with recurrent high grade glioma (HGG). A multi-institutional database of 10 academic centers across the United States was created to analyze prognostic outcomes for re-RT for recurrent HGG, which included WHO Grade III and Grade IV tumors.

MATERIALS/METHODS

Patients with HGG who had initially received standard radiotherapy (RT) and were subsequently treated with a course of re-RT at recurrence were included in the study. Factors assessed to delineate a significant association with overall survival (OS) and toxicity included age, KPS, number of relapses, dose, use of bevacizumab (BEV) or temozolomide (TMZ), time from prior RT, histology, RT target, re-RT target> 5cm and extent of resection, and MGMT methylation status. The Kaplan-Meier Method was used to estimate OS. Cox proportional hazards regression models were used to identify factors associated with OS. Toxicity outcomes were assessed using logistic regression. Significance was assumed if p<0.05. Data management and decision management software were used for all analyses.

RESULTS

Between 2001 and 2022, 280 patients from 10 academic institutions were treated with re-RT for diagnosis of recurrent HGG. 133 patients (71.1%) had a histologic glioblastoma (GBM) at the time of re-RT, with the remainder having Grade 3 gliomas. Median dose delivered at re-RT was 47 Gy BED10 (IQR 47 - 53 Gy BED10), with the most common regimen being 35 Gy in 10 fractions. 83 patients (56%) had GTV greater than 5 cm treated with re-RT. 183 patients (79%) received concurrent systemic therapy, including 95 (41%) who received concurrent TMZ and 86 (45%) who received concurrent BEV. Median OS for the entire cohort was 10 months. Increasing dose at re-RT was associated with improved OS (OR 0.80 95% CI 0.67-0.95, p = 0.10 per 10 Gy BED10), as was dose greater than 47 Gy BED10, which is equivalent to 35 Gy in 10 fractions (OR 0.70, 95% CI 0.54-0.91). Concurrent TMZ was also associated with improved OS (OR 0.68, 95% CI 0.46-0.83, p < 0.01). 32/143 (22%) patients evaluable for toxicity experienced Grade 2 or greater adverse radiation effect (ARE). Use of BEV was associated with decreased toxicity (OR 0.45, 95% CI 0.21-0.98, p = 0.05). Dose at re-RT (OR 1.07 per 10 Gy BED10, p = 0.78), a GTV > 5cm (OR 1.39, p = 0.44), and the use of concurrent TMZ (OR 1.90, p = 0.10) were not associated with Grade 2 or greater ARE.

CONCLUSION

Higher dose of re-RT and use of concurrent TMZ led to improved OS in recurrent HGG patients without an associated increased rate of ARE. Use of BEV decreased the likelihood of Grade 2 or greater ARE in the re-RT setting for these recurrent HGG patients.

Targetable NOTCH1 rearrangements in reninoma

Reninomas are exceedingly rare renin-secreting kidney tumours that derive from juxtaglomerular cells, specialised smooth muscle cells that reside at the vascular inlet of glomeruli. They are the central component of the juxtaglomerular apparatus which controls systemic blood pressure through the secretion of renin. We assess somatic changes in reninoma and find structural variants that generate canonical activating rearrangements of, NOTCH1 whilst removing its negative regulator, NRARP. Accordingly, in single reninoma nuclei we observe excessive renin and NOTCH1 signalling mRNAs, with a concomitant non-excess of NRARP expression. Re-analysis of previously published reninoma bulk transcriptomes further corroborates our observation of dysregulated Notch pathway signalling in reninoma. Our findings reveal NOTCH1 rearrangements in reninoma, therapeutically targetable through existing NOTCH1 inhibitors, and indicate that unscheduled Notch signalling may be a disease-defining feature of reninoma.

An integrated single-cell analysis of human adrenal cortex development

The adrenal glands synthesize and release essential steroid hormones such as cortisol and aldosterone, but many aspects of human adrenal gland development are not well understood. Here, we combined single-cell and bulk RNA sequencing, spatial transcriptomics, IHC, and micro-focus computed tomography to investigate key aspects of adrenal development in the first 20 weeks of gestation. We demonstrate rapid adrenal growth and vascularization, with more cell division in the outer definitive zone (DZ). Steroidogenic pathways favored androgen synthesis in the central fetal zone, but DZ capacity to synthesize cortisol and aldosterone developed with time. Core transcriptional regulators were identified, with localized expression of HOPX (also known as Hop homeobox/homeobox-only protein) in the DZ. Potential ligand-receptor interactions between mesenchyme and adrenal cortex were seen (e.g., RSPO3/LGR4). Growth-promoting imprinted genes were enriched in the developing cortex (e.g., IGF2, PEG3). These findings reveal aspects of human adrenal development and have clinical implications for understanding primary adrenal insufficiency and related postnatal adrenal disorders, such as adrenal tumor development, steroid disorders, and neonatal stress.

Circulatory HMGB1 is an early predictive and prognostic biomarker of ARDS and mortality in a swine model of polytrauma

Acute respiratory distress syndrome (ARDS) is a leading cause of morbidity and mortality in polytrauma patients. Pharmacological treatments of ARDS are lacking, and ARDS patients rely on supportive care. Accurate diagnosis of ARDS is vital for early intervention and improved outcomes but is presently delayed up to days. The use of biomarkers for early identification of ARDS development is a potential solution. Inflammatory mediators high-mobility group box 1 (HMGB1), syndecan-1 (SDC-1), and C3a have been previously proposed as potential biomarkers. For this study, we analyzed these biomarkers in animals undergoing smoke inhalation and 40% total body surface area burns, followed by intensive care for 72 h post-injury (PI) to determine their association with ARDS and mortality. We found that the levels of inflammatory mediators in serum were affected, as well as the degree of HMGB1 and Toll-like receptor 4 (TLR4) signal activation in the lung. The results showed significantly increased HMGB1 expression levels in animals that developed ARDS compared with those that did not. Receiver operating characteristic (ROC) analysis showed that HMGB1 levels at 6 h PI were significantly associated with ARDS development (AUROC=0.77) and mortality (AUROC=0.82). Logistic regression analysis revealed that levels of HMGB1 ≥24.10 ng/ml are associated with a 13-fold higher incidence of ARDS [OR:13.57 (2.76-104.3)], whereas the levels of HMGB1 ≥31.39 ng/ml are associated with a 12-fold increase in mortality [OR: 12.00 (2.36-93.47)]. In addition, we found that mesenchymal stem cell (MSC) therapeutic treatment led to a significant decrease in systemic HMGB1 elevation but failed to block SDC-1 and C3a increases. Immunohistochemistry analyses showed that smoke inhalation and burn injury induced the expression of HMGB1 and TLR4 and stimulated co-localization of HMGB1 and TLR4 in the lung. Interestingly, MSC treatment reduced the presence of HMGB1, TLR4, and the HMGB1-TLR4 co-localization. These results show that serum HMGB1 is a prognostic biomarker for predicting the incidence of ARDS and mortality in swine with smoke inhalation and burn injury. Therapeutically blocking HMGB1 signal activation might be an effective approach for attenuating ARDS development in combat casualties or civilian patients.

Transcriptional signatures associated with persisting CD19 CAR-T cells in children with leukemia

In the context of relapsed and refractory childhood pre-B cell acute lymphoblastic leukemia (R/R B-ALL), CD19-targeting chimeric antigen receptor (CAR)-T cells often induce durable remissions, which requires the persistence of CAR-T cells. In this study, we systematically analyzed CD19 CAR-T cells of 10 children with R/R B-ALL enrolled in the CARPALL trial via high-throughput single-cell gene expression and T cell receptor sequencing of infusion products and serial blood and bone marrow samples up to 5 years after infusion. We show that long-lived CAR-T cells developed a CD4/CD8 double-negative phenotype with an exhausted-like memory state and distinct transcriptional signature. This persistence signature was dominant among circulating CAR-T cells in all children with a long-lived treatment response for which sequencing data were sufficient (4/4, 100%). The signature was also present across T cell subsets and clonotypes, indicating that persisting CAR-T cells converge transcriptionally. This persistence signature was also detected in two adult patients with chronic lymphocytic leukemia with decade-long remissions who received a different CD19 CAR-T cell product. Examination of single T cell transcriptomes from a wide range of healthy and diseased tissues across children and adults indicated that the persistence signature may be specific to long-lived CAR-T cells. These findings raise the possibility that a universal transcriptional signature of clinically effective, persistent CD19 CAR-T cells exists.

Spatial and molecular profiling of the mononuclear phagocyte network in classic Hodgkin lymphoma

Classic Hodgkin lymphoma (cHL) has a rich immune infiltrate, which is an intrinsic component of the neoplastic process. Malignant Hodgkin Reed-Sternberg cells (HRSCs) create an immunosuppressive microenvironment by the expression of regulatory molecules, preventing T-cell activation. It has also been demonstrated that mononuclear phagocytes (MNPs) in the vicinity of HRSCs express similar regulatory mechanisms in parallel, and their presence in tissue is associated with inferior patient outcomes. MNPs in cHL have hitherto been identified by a small number of canonical markers and are usually described as tumor-associated macrophages. The organization of MNP networks and interactions with HRSCs remains unexplored at high resolution. Here, we defined the global immune-cell composition of cHL and nonlymphoma lymph nodes, integrating data across single-cell RNA sequencing, spatial transcriptomics, and multiplexed immunofluorescence. We observed that MNPs comprise multiple subsets of monocytes, macrophages, and dendritic cells (DCs). Classical monocytes, macrophages and conventional DC2s were enriched in the vicinity of HRSCs, but plasmacytoid DCs and activated DCs were excluded. Unexpectedly, cDCs and monocytes expressed immunoregulatory checkpoints PD-L1, TIM-3, and the tryptophan-catabolizing protein IDO, at the same level as macrophages. Expression of these molecules increased with age. We also found that classical monocytes are important signaling hubs, potentially controlling the retention of cDC2 and ThExh via CCR1-, CCR4-, CCR5-, and CXCR3-dependent signaling. Enrichment of the cDC2-monocyte-macrophage network in diagnostic biopsies is associated with early treatment failure. These results reveal unanticipated complexity and spatial polarization within the MNP compartment, further demonstrating their potential roles in immune evasion by cHL.

Mapping single-cell transcriptomes in the intra-tumoral and associated territories of kidney cancer

Tumor behavior is intricately dependent on the oncogenic properties of cancer cells and their multi-cellular interactions. To understand these dependencies within the wider microenvironment, we studied over 270,000 single-cell transcriptomes and 100 microdissected whole exomes from 12 patients with kidney tumors, prior to validation using spatial transcriptomics. Tissues were sampled from multiple regions of the tumor core, the tumor-normal interface, normal surrounding tissues, and peripheral blood. We find that the tissue-type location of CD8+ T cell clonotypes largely defines their exhaustion state with intra-tumoral spatial heterogeneity that is not well explained by somatic heterogeneity. De novo mutation calling from single-cell RNA-sequencing data allows us to broadly infer the clonality of stromal cells and lineage-trace myeloid cell development. We report six conserved meta-programs that distinguish tumor cell function, and find an epithelial-mesenchymal transition meta-program highly enriched at the tumor-normal interface that co-localizes with IL1B-expressing macrophages, offering a potential therapeutic target.

The pathophysiology of bilateral and multifocal Wilms tumors: What we can learn from the study of predisposition syndromes

Approximately 5% of patients with Wilms tumor present with synchronous bilateral disease. The development of synchronous bilateral Wilms tumor (BWT) is highly suggestive of a genetic or epigenetic predisposition. Patients with known germline predisposition to Wilms tumor (WT1 variants, Beckwith Wiedemann spectrum, TRIM28 variants) have a higher incidence of BWT. This Children's Oncology Group (COG)-International Society for Pediatric Oncology (SIOP-) HARMONICA initiative review for pediatric renal tumors details germline genetic and epigenetic predisposition to BWT development, with an emphasis on alterations in 11p15.5 (ICR1 gain of methylation, paternal uniparental disomy, and postzygotic somatic mosaicism), WT1, TRIM28, and REST. Molecular mechanisms that result in BWT are often also present in multifocal Wilms tumor (multiple separate tumors in one or both kidneys). We identify priority areas for international collaborative research to better understand how predisposing genetic or epigenetic factors associate with response to neoadjuvant chemotherapy, oncologic outcomes, and long-term renal function outcomes.

Clonal diversification and histogenesis of malignant germ cell tumours

Germ cell tumours (GCTs) are a collection of benign and malignant neoplasms derived from primordial germ cells. They are uniquely able to recapitulate embryonic and extraembryonic tissues, which carries prognostic and therapeutic significance. The developmental pathways underpinning GCT initiation and histogenesis are incompletely understood. Here, we study the relationship of histogenesis and clonal diversification in GCTs by analysing the genomes and transcriptomes of 547 microdissected histological units. We find no correlation between genomic and histological heterogeneity. However, we identify unifying features including the retention of fetal developmental transcripts across tissues, expression changes on chromosome 12p, and a conserved somatic evolutionary sequence of whole genome duplication followed by clonal diversification. While this pattern is preserved across all GCTs, the developmental timing of the duplication varies between prepubertal and postpubertal cases. In addition, tumours of younger children exhibit distinct substitution signatures which may lend themselves as potential biomarkers for risk stratification. Our findings portray the extensive diversification of GCT tissues and genetic subclones as randomly distributed, while identifying overarching transcriptional and genomic features.

ATRT-10. Single-cell transcriptional profiling of ATRTs reveals heterogeneous signatures of tumor and non-malignant cell populations

Atypical Teratoid/Rhabdoid Tumors (ATRTs) are known for exhibiting high inter-tumor heterogeneity, even though they are almost all characterized by a common loss of SMARCB1 (or rarely SMARCA4). Three subgroups have been identified at bulk methylome and transcriptome level: ATRT-TYR, ATRT-SHH, and ATRT-MYC. To better understand the biology underlying each subgroup and potentially unveil their (different) cell(s) of origin, we performed single-cell transcriptomic analyses in 22 ATRTs using fresh frozen samples and both 10X and Smartseq technology. All data, grouped by technology, underwent quality control and normalization, regressing out the biases introduced by each sample. Tumor microenvironment (TME) and tumor bulk (TB) clusters were characterized by a combination of copy number variant analyses, enrichment in literature lists of marker genes for specific cell populations, and in-depth analysis of differentially enriched (DE) genes. Non-negative Matrix Factorization (NMF) was applied to TB to reveal major transcriptional profiles, which were grouped into meta-signatures. A total of 71 gene lists were retrieved from NMF (TB) and DE analyses (TME + TB), that gathered into 11 signature groups by Jaccard similarity, with one extra group accounting for unique signatures. Three groups targeted TME, accounting for either microglia, fibroblasts and endothelial cells, or OPCs, oligodendrocytes, astrocytes and neurons. These signatures are enriched in specific clusters across technologies. The remaining eight groups divide into two types, either enriched in clusters predominantly formed by cells of one or two ATRT subgroups or signatures enriched for a particular phenotype, such as cilial, cycling, axonogenesis or EM transition. While the first type is enriched across clusters in a gradient fashion, the second shows enrichment for selected clusters across technologies. Further analyses on the integrated dataset and additional samples are ongoing to validate and refine these 11 signature groups in ATRTs to see how this may lead to new treatment approaches.

Single-cell transcriptomics reveals a distinct developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia

KMT2A-rearranged infant ALL is an aggressive childhood leukemia with poor prognosis. Here, we investigated the developmental state of KMT2A-rearranged infant B-cell acute lymphoblastic leukemia (B-ALL) using bulk messenger RNA (mRNA) meta-analysis and examination of single lymphoblast transcriptomes against a developing bone marrow reference. KMT2A-rearranged infant B-ALL was uniquely dominated by an early lymphocyte precursor (ELP) state, whereas less adverse NUTM1-rearranged infant ALL demonstrated signals of later developing B cells, in line with most other childhood B-ALLs. We compared infant lymphoblasts with ELP cells and revealed that the cancer harbored hybrid myeloid-lymphoid features, including nonphysiological antigen combinations potentially targetable to achieve cancer specificity. We validated surface coexpression of exemplar combinations by flow cytometry. Through analysis of shared mutations in separate leukemias from a child with infant KMT2A-rearranged B-ALL relapsing as AML, we established that KMT2A rearrangement occurred in very early development, before hematopoietic specification, emphasizing that cell of origin cannot be inferred from the transcriptional state.

Single cell derived mRNA signals across human kidney tumors

Tumor cells may share some patterns of gene expression with their cell of origin, providing clues into the differentiation state and origin of cancer. Here, we study the differentiation state and cellular origin of 1300 childhood and adult kidney tumors. Using single cell mRNA reference maps of normal tissues, we quantify reference "cellular signals" in each tumor. Quantifying global differentiation, we find that childhood tumors exhibit fetal cellular signals, replacing the presumption of "fetalness" with a quantitative measure of immaturity. By contrast, in adult cancers our assessment refutes the suggestion of dedifferentiation towards a fetal state in most cases. We find an intimate connection between developmental mesenchymal populations and childhood renal tumors. We demonstrate the diagnostic potential of our approach with a case study of a cryptic renal tumor. Our findings provide a cellular definition of human renal tumors through an approach that is broadly applicable to human cancer.

Inherent mosaicism and extensive mutation of human placentas

Placentas can exhibit chromosomal aberrations that are absent from the fetus1. The basis of this genetic segregation, which is known as confined placental mosaicism, remains unknown. Here we investigated the phylogeny of human placental cells as reconstructed from somatic mutations, using whole-genome sequencing of 86 bulk placental samples (with a median weight of 28 mg) and of 106 microdissections of placental tissue. We found that every bulk placental sample represents a clonal expansion that is genetically distinct, and exhibits a genomic landscape akin to that of childhood cancer in terms of mutation burden and mutational imprints. To our knowledge, unlike any other healthy human tissue studied so far, the placental genomes often contained changes in copy number. We reconstructed phylogenetic relationships between tissues from the same pregnancy, which revealed that developmental bottlenecks genetically isolate placental tissues by separating trophectodermal lineages from lineages derived from the inner cell mass. Notably, there were some cases with full segregation-within a few cell divisions of the zygote-of placental lineages and lineages derived from the inner cell mass. Such early embryonic bottlenecks may enable the normalization of zygotic aneuploidy. We observed direct evidence for this in a case of mosaic trisomic rescue. Our findings reveal extensive mutagenesis in placental tissues and suggest that mosaicism is a typical feature of placental development.

Somatic mutations and single-cell transcriptomes reveal the root of malignant rhabdoid tumours

Malignant rhabdoid tumour (MRT) is an often lethal childhood cancer that, like many paediatric tumours, is thought to arise from aberrant fetal development. The embryonic root and differentiation pathways underpinning MRT are not firmly established. Here, we study the origin of MRT by combining phylogenetic analyses and single-cell mRNA studies in patient-derived organoids. Comparison of somatic mutations shared between cancer and surrounding normal tissues places MRT in a lineage with neural crest-derived Schwann cells. Single-cell mRNA readouts of MRT differentiation, which we examine by reverting the genetic driver mutation underpinning MRT, SMARCB1 loss, suggest that cells are blocked en route to differentiating into mesenchyme. Quantitative transcriptional predictions indicate that combined HDAC and mTOR inhibition mimic MRT differentiation, which we confirm experimentally. Our study defines the developmental block of MRT and reveals potential differentiation therapies.

Tumor to normal single-cell mRNA comparisons reveal a pan-neuroblastoma cancer cell

Neuroblastoma is a childhood cancer that resembles developmental stages of the neural crest. It is not established what developmental processes neuroblastoma cancer cells represent. Here, we sought to reveal the phenotype of neuroblastoma cancer cells by comparing cancer (n = 19,723) with normal fetal adrenal single-cell transcriptomes (n = 57,972). Our principal finding was that the neuroblastoma cancer cell resembled fetal sympathoblasts, but no other fetal adrenal cell type. The sympathoblastic state was a universal feature of neuroblastoma cells, transcending cell cluster diversity, individual patients, and clinical phenotypes. We substantiated our findings in 650 neuroblastoma bulk transcriptomes and by integrating canonical features of the neuroblastoma genome with transcriptional signals. Overall, our observations indicate that a pan-neuroblastoma cancer cell state exists, which may be attractive for novel immunotherapeutic and targeted avenues.

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

BACKGROUND

Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, any cell-free RNAs contained within the input solution are also captured by these assays. This sequencing of cell-free RNA constitutes a background contamination that confounds the biological interpretation of single-cell transcriptomic data.

RESULTS

We demonstrate that contamination from this "soup" of cell-free RNAs is ubiquitous, with experiment-specific variations in composition and magnitude. We present a method, SoupX, for quantifying the extent of the contamination and estimating "background-corrected" cell expression profiles that seamlessly integrate with existing downstream analysis tools. Applying this method to several datasets using multiple droplet sequencing technologies, we demonstrate that its application improves biological interpretation of otherwise misleading data, as well as improving quality control metrics.

CONCLUSIONS

We present SoupX, a tool for removing ambient RNA contamination from droplet-based single-cell RNA sequencing experiments. This tool has broad applicability, and its application can improve the biological utility of existing and future datasets.

Single-cell atlas of the first intra-mammalian developmental stage of the human parasite Schistosoma mansoni

Over 250 million people suffer from schistosomiasis, a tropical disease caused by parasitic flatworms known as schistosomes. Humans become infected by free-swimming, water-borne larvae, which penetrate the skin. The earliest intra-mammalian stage, called the schistosomulum, undergoes a series of developmental transitions. These changes are critical for the parasite to adapt to its new environment as it navigates through host tissues to reach its niche, where it will grow to reproductive maturity. Unravelling the mechanisms that drive intra-mammalian development requires knowledge of the spatial organisation and transcriptional dynamics of different cell types that comprise the schistomulum body. To fill these important knowledge gaps, we perform single-cell RNA sequencing on two-day old schistosomula of Schistosoma mansoni. We identify likely gene expression profiles for muscle, nervous system, tegument, oesophageal gland, parenchymal/primordial gut cells, and stem cells. In addition, we validate cell markers for all these clusters by in situ hybridisation in schistosomula and adult parasites. Taken together, this study provides a comprehensive cell-type atlas for the early intra-mammalian stage of this devastating metazoan parasite.

Single-cell sequencing reveals clonal expansions of pro-inflammatory synovial CD8 T cells expressing tissue-homing receptors in psoriatic arthritis

Psoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory arthritis of unknown pathogenesis commonly affecting patients with skin psoriasis. Here we use complementary single-cell approaches to study leukocytes from PsA joints. Mass cytometry demonstrates a 3-fold expansion of memory CD8 T cells in the joints of PsA patients compared to peripheral blood. Meanwhile, droplet-based and plate-based single-cell RNA sequencing of paired T cell receptor alpha and beta chain sequences show pronounced CD8 T cell clonal expansions within the joints. Transcriptome analyses find these expanded synovial CD8 T cells to express cycling, activation, tissue-homing and tissue residency markers. T cell receptor sequence comparison between patients identifies clonal convergence. Finally, chemokine receptor CXCR3 is upregulated in the expanded synovial CD8 T cells, while two CXCR3 ligands, CXCL9 and CXCL10, are elevated in PsA synovial fluid. Our data thus provide a quantitative molecular insight into the cellular immune landscape of psoriatic arthritis.

Embryonal precursors of Wilms tumor

Adult cancers often arise from premalignant clonal expansions. Whether the same is true of childhood tumors has been unclear. To investigate whether Wilms tumor (nephroblastoma; a childhood kidney cancer) develops from a premalignant background, we examined the phylogenetic relationship between tumors and corresponding normal tissues. In 14 of 23 cases studied (61%), we found premalignant clonal expansions in morphologically normal kidney tissues that preceded tumor development. These clonal expansions were defined by somatic mutations shared between tumor and normal tissues but absent from blood cells. We also found hypermethylation of the H19 locus, a known driver of Wilms tumor development, in 58% of the expansions. Phylogenetic analyses of bilateral tumors indicated that clonal expansions can evolve before the divergence of left and right kidney primordia. These findings reveal embryonal precursors from which unilateral and multifocal cancers develop.

Decoding human fetal liver haematopoiesis

Definitive haematopoiesis in the fetal liver supports self-renewal and differentiation of haematopoietic stem cells and multipotent progenitors (HSC/MPPs) but remains poorly defined in humans. Here, using single-cell transcriptome profiling of approximately 140,000 liver and 74,000 skin, kidney and yolk sac cells, we identify the repertoire of human blood and immune cells during development. We infer differentiation trajectories from HSC/MPPs and evaluate the influence of the tissue microenvironment on blood and immune cell development. We reveal physiological erythropoiesis in fetal skin and the presence of mast cells, natural killer and innate lymphoid cell precursors in the yolk sac. We demonstrate a shift in the haemopoietic composition of fetal liver during gestation away from being predominantly erythroid, accompanied by a parallel change in differentiation potential of HSC/MPPs, which we functionally validate. Our integrated map of fetal liver haematopoiesis provides a blueprint for the study of paediatric blood and immune disorders, and a reference for harnessing the therapeutic potential of HSC/MPPs.

Spatiotemporal immune zonation of the human kidney

Tissue-resident immune cells are important for organ homeostasis and defense. The epithelium may contribute to these functions directly or by cross-talk with immune cells. We used single-cell RNA sequencing to resolve the spatiotemporal immune topology of the human kidney. We reveal anatomically defined expression patterns of immune genes within the epithelial compartment, with antimicrobial peptide transcripts evident in pelvic epithelium in the mature, but not fetal, kidney. A network of tissue-resident myeloid and lymphoid immune cells was evident in both fetal and mature kidney, with postnatal acquisition of transcriptional programs that promote infection-defense capabilities. Epithelial-immune cross-talk orchestrated localization of antibacterial macrophages and neutrophils to the regions of the kidney most susceptible to infection. Overall, our study provides a global overview of how the immune landscape of the human kidney is zonated to counter the dominant immunological challenge.

BBKNN: fast batch alignment of single cell transcriptomes

MOTIVATION

Increasing numbers of large scale single cell RNA-Seq projects are leading to a data explosion, which can only be fully exploited through data integration. A number of methods have been developed to combine diverse datasets by removing technical batch effects, but most are computationally intensive. To overcome the challenge of enormous datasets, we have developed BBKNN, an extremely fast graph-based data integration algorithm. We illustrate the power of BBKNN on large scale mouse atlasing data, and favourably benchmark its run time against a number of competing methods.

AVAILABILITY AND IMPLEMENTATION

BBKNN is available at https://github.com/Teichlab/bbknn, along with documentation and multiple example notebooks, and can be installed from pip.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

BBKNN: fast batch alignment of single cell transcriptomes

Motivation

Increasing numbers of large scale single cell RNA-Seq projects are leading to a data explosion, which can only be fully exploited through data integration. A number of methods have been developed to combine diverse datasets by removing technical batch effects, but most are computationally intensive. To overcome the challenge of enormous datasets, we have developed BBKNN, an extremely fast graph-based data integration algorithm. We illustrate the power of BBKNN on large scale mouse atlasing data, and favourably benchmark its run time against a number of competing methods.

Availability and implementation

BBKNN is available at https://github.com/Teichlab/bbknn, along with documentation and multiple example notebooks, and can be installed from pip.

Supplementary information

Supplementary data are available at Bioinformatics online.

Abstract 2506: Exploring the complex etiology of oncogenic fusions in childhood cancer

Background, Rationale and Experimental Approach

Oncogenic fusions are generated via chromosomal rearrangements resulting in an exchange of coding or regulatory DNA sequences. These mutations play an important role in disease onset and subsequent cancer progression, however the exact timing and mechanisms by which they arise are unknown. Through the SickKids clinical sequencing program, KiCS, we explored how and when canonical fusions arise by studying the whole-genomes of childhood cancers with diagnostic or driver fusions. Our investigation began with the pediatric bone cancer, Ewing sarcoma, and later expanded to include other solid, blood, and brain cancers such as papillary thyroid carcinoma, myeloid leukemia, and ependymoma among others.

Results

The starting point of our investigation was ES, where we sequenced the whole-genomes of 124 cases. Ewing sarcoma (ES) represents the prototypical fusion-driven sarcoma as it is characterized and driven by the EWSR1-ETS fusion. In ~42% of cases, we found that the ES fusion gene arises by chromoplexy, a sudden burst of complex, loop-like rearrangements, rather than by simple reciprocal translocations as previously thought. We show that these rearrangements rapidly and dramatically altered the chromosomal landscape of ES tumors, producing the driver EWSR1-ETS fusion and disrupting numerous other genes in a short time. Remarkably, these complex rearrangements are enriched for genes, including those with a clear role in oncogenesis, and are associated with the earliest replicating portions of the genome. We then sequenced the genomes of 30 other childhood cancers with oncogenic fusions to study their timing and formation mechanisms. In doing so, we have identified several novel fusions in many cancer types, which have been validated by RNA sequencing and cytogenetics. In some cases, the presence of these chromoplectic fusions indicates these patients may benefit from targeted therapy due to the generation of druggable fusions. .

Conclusions

Our findings provide fundamental insights into the pathogenesis of gene fusions in human cancer. They reveal complex DNA rearrangements to be a mutational process underpinning gene fusions in cancer that influences tumorigenesis.

Citation Format: Nathaniel D. Anderson, Richard de Borja, Matthew D. Young, Fabio Fuligni, Andrej Rosic, Nicola D. Roberts, Nischalan Pillay, Jeffrey A. Toretsky, Yoshida Akihiko, Tatsuhiro Shibata, Markus Metzler, Gino Somers, Stephen W. Scherer, Adrienne M. Flanagan, Peter J. Campbell, Joshua D. Schiffman, Mary Shago, Ludmil B. Alexandrov, Jay S. Wunder, Irene L. Andrulis, David Malkin, Sam Behjati, Adam Shlien. Exploring the complex etiology of oncogenic fusions in childhood cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2506.

An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures

Anaplastic meningioma is a rare and aggressive brain tumor characterised by intractable recurrences and dismal outcomes. Here, we present an integrated analysis of the whole genome, transcriptome and methylation profiles of primary and recurrent anaplastic meningioma. A key finding was the delineation of distinct molecular subgroups that were associated with diametrically opposed survival outcomes. Relative to lower grade meningiomas, anaplastic tumors harbored frequent driver mutations in SWI/SNF complex genes, which were confined to the poor prognosis subgroup. Aggressive disease was further characterised by transcriptional evidence of increased PRC2 activity, stemness and epithelial-to-mesenchymal transition. Our analyses discern biologically distinct variants of anaplastic meningioma with prognostic and therapeutic significance.

Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors

Sarcomas are cancers of the bone and soft tissue often defined by gene fusions. Ewing sarcoma involves fusions between EWSR1, a gene encoding an RNA binding protein, and E26 transformation-specific (ETS) transcription factors. We explored how and when EWSR1-ETS fusions arise by studying the whole genomes of Ewing sarcomas. In 52 of 124 (42%) of tumors, the fusion gene arises by a sudden burst of complex, loop-like rearrangements, a process called chromoplexy, rather than by simple reciprocal translocations. These loops always contained the disease-defining fusion at the center, but they disrupted multiple additional genes. The loops occurred preferentially in early replicating and transcriptionally active genomic regions. Similar loops forming canonical fusions were found in three other sarcoma types. Chromoplexy-generated fusions appear to be associated with an aggressive form of Ewing sarcoma. These loops arise early, giving rise to both primary and relapse Ewing sarcoma tumors, which can continue to evolve in parallel.

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

Messenger RNA encodes cellular function and phenotype. In the context of human cancer, it defines the identities of malignant cells and the diversity of tumor tissue. We studied 72,501 single-cell transcriptomes of human renal tumors and normal tissue from fetal, pediatric, and adult kidneys. We matched childhood Wilms tumor with specific fetal cell types, thus providing evidence for the hypothesis that Wilms tumor cells are aberrant fetal cells. In adult renal cell carcinoma, we identified a canonical cancer transcriptome that matched a little-known subtype of proximal convoluted tubular cell. Analyses of the tumor composition defined cancer-associated normal cells and delineated a complex vascular endothelial growth factor (VEGF) signaling circuit. Our findings reveal the precise cellular identities and compositions of human kidney tumors.

Recurrent rearrangements of FOS and FOSB define osteoblastoma

The transcription factor FOS has long been implicated in the pathogenesis of bone tumours, following the discovery that the viral homologue, v-fos, caused osteosarcoma in laboratory mice. However, mutations of FOS have not been found in human bone-forming tumours. Here, we report recurrent rearrangement of FOS and its paralogue, FOSB, in the most common benign tumours of bone, osteoblastoma and osteoid osteoma. Combining whole-genome DNA and RNA sequences, we find rearrangement of FOS in five tumours and of FOSB in one tumour. Extending our findings into a cohort of 55 cases, using FISH and immunohistochemistry, provide evidence of ubiquitous mutation of FOS or FOSB in osteoblastoma and osteoid osteoma. Overall, our findings reveal a human bone tumour defined by mutations of FOS and FOSB.

The driver landscape of sporadic chordoma

Chordoma is a malignant, often incurable bone tumour showing notochordal differentiation. Here, we defined the somatic driver landscape of 104 cases of sporadic chordoma. We reveal somatic duplications of the notochordal transcription factor brachyury (T) in up to 27% of cases. These variants recapitulate the rearrangement architecture of the pathogenic germline duplications of T that underlie familial chordoma. In addition, we find potentially clinically actionable PI3K signalling mutations in 16% of cases. Intriguingly, one of the most frequently altered genes, mutated exclusively by inactivating mutation, was LYST (10%), which may represent a novel cancer gene in chordoma.Chordoma is a rare often incurable malignant bone tumour. Here, the authors investigate driver mutations of sporadic chordoma in 104 cases, revealing duplications in notochordal transcription factor brachyury (T), PI3K signalling mutations, and mutations in LYST, a potential novel cancer gene in chordoma.

Recurrent mutation of IGF signalling genes and distinct patterns of genomic rearrangement in osteosarcoma

Osteosarcoma is a primary malignancy of bone that affects children and adults. Here, we present the largest sequencing study of osteosarcoma to date, comprising 112 childhood and adult tumours encompassing all major histological subtypes. A key finding of our study is the identification of mutations in insulin-like growth factor (IGF) signalling genes in 8/112 (7%) of cases. We validate this observation using fluorescence in situ hybridization (FISH) in an additional 87 osteosarcomas, with IGF1 receptor (IGF1R) amplification observed in 14% of tumours. These findings may inform patient selection in future trials of IGF1R inhibitors in osteosarcoma. Analysing patterns of mutation, we identify distinct rearrangement profiles including a process characterized by chromothripsis and amplification. This process operates recurrently at discrete genomic regions and generates driver mutations. It may represent an age-independent mutational mechanism that contributes to the development of osteosarcoma in children and adults alike.

The interplay of long non-coding RNAs and MYC in cancer

Long non-coding RNAs (lncRNAs) are a class of RNA molecules that are changing how researchers view eukaryotic gene regulation. Once considered to be non-functional products of low-level aberrant transcription from non-coding regions of the genome, lncRNAs are now viewed as important epigenetic regulators and several lncRNAs have now been demonstrated to be critical players in the development and/or maintenance of cancer. Similarly, the emerging variety of interactions between lncRNAs and MYC, a well-known oncogenic transcription factor linked to most types of cancer, have caught the attention of many biomedical researchers. Investigations exploring the dynamic interactions between lncRNAs and MYC, referred to as the lncRNA-MYC network, have proven to be especially complex. Genome-wide studies have shown that MYC transcriptionally regulates many lncRNA genes. Conversely, recent reports identified lncRNAs that regulate MYC expression both at the transcriptional and post-transcriptional levels. These findings are of particular interest because they suggest roles of lncRNAs as regulators of MYC oncogenic functions and the possibility that targeting lncRNAs could represent a novel avenue to cancer treatment. Here, we briefly review the current understanding of how lncRNAs regulate chromatin structure and gene transcription, and then focus on the new developments in the emerging field exploring the lncRNA-MYC network in cancer.

Social cognitive theory and physical activity: a systematic review and meta-analysis

This review investigated three research questions (i) What is the utility of social cognitive theory (SCT) to explain physical activity (PA)?; (ii) Is the effectiveness of SCT moderated by sample or methodological characteristics? and (iii) What is the frequency of significant associations between the core SCT constructs and PA? Ten electronic databases were searched with no date or sample restrictions. Forty-four studies were retrieved containing 55 SCT models of PA. Methodological quality was assessed using a standardized tool. A random-effects meta-analysis revealed that SCT accounted for 31% of the variance in PA. However, methodological quality was mostly poor for these models. Methodological quality and sample age moderated the PA effect size, with increases in both associated with greater variance explained. Although self-efficacy and goals were consistently associated with PA, outcome expectations and socio-structural factors were not. This review determined that SCT is a useful framework to explain PA behaviour. Higher quality models explained more PA variance, but overall methodological quality was poor. As such, high-quality studies examining the utility of SCT to explain PA are warranted.

In vivo caprine model for osteomyelitis and evaluation of biofilm-resistant intramedullary nails

Bone infection remains a formidable challenge to the medical field. The goal of the current study is to evaluate antibacterial coatings in vitro and to develop a large animal model to assess coated bone implants. A novel coating consisting of titanium oxide and siloxane polymer doped with silver was created by metal-organic methods. The coating was tested in vitro using rapid screening techniques to determine compositions which inhibited Staphylococcus aureus growth, while not affecting osteoblast viability. The coating was then applied to intramedullary nails and evaluated in vivo in a caprine model. In this pilot study, a fracture was created in the tibia of the goat, and Staphylococcus aureus was inoculated directly into the bone canal. The fractures were fixed by either coated (treated) or non-coated intramedullary nails (control) for 5 weeks. Clinical observations as well as microbiology, mechanical, radiology, and histology testing were used to compare the animals. The treated goat was able to walk using all four limbs after 5 weeks, while the control was unwilling to bear weight on the fixed leg. These results suggest the antimicrobial potential of the hybrid coating and the feasibility of the goat model for antimicrobial coated intramedullary implant evaluation.

Predicting pulmonary embolus in orthopedic trauma patients using the Wells score

The decision to perform computed tomography pulmonary angiography (CTPA) to rule out pulmonary embolism (PE) in orthopedic trauma patients is challenging. The Wells score is a commonly used clinical probability tool developed to determine the likelihood of PE and assist in determining the need for CTPA examination. This study evaluated the usefulness of the Wells score for predicting PE in patients admitted to the orthopedic trauma service. All patients who were admitted to the orthopedic trauma service at the authors' institution between 2001 and 2011 who underwent CTPA were identified. The Wells score was calculated retrospectively for each patient, and risk categories using the traditional and alternative interpretations of the Wells score were assigned. Pulmonary embolism was diagnosed in 27 (16%) of 169 patients who underwent CTPA. In total, 27 (0.39%) of 6854 patients admitted to the orthopedic trauma service were diagnosed with PE during initial hospitalization. Mean Wells score was 3.31 (95% confidence interval, ±.28) for the entire population, 3.32 for those without PE (95% confidence interval, ±.31), and 3.28 for those with PE (95% confidence interval, ±.72) (P=.91). Average times from admission to CTPA examination for those with and without PE were 6.18 and 5.7 days, respectively (P=.94). No significant correlation existed between the Wells score and CTPA results, indicating that the Wells score is limited in predicting PE risk in orthopedic trauma patients.

Effectiveness of male-only weight loss and weight loss maintenance interventions: a systematic review with meta-analysis

The objectives of this systematic review were to investigate the effectiveness of male-only weight loss and weight loss maintenance interventions and to identify intervention characteristics associated with effectiveness. In May 2011, a systematic literature search with no date restrictions was conducted across eight databases. Twenty-four articles describing 23 studies met the eligibility criteria. All studies included a weight loss intervention and four studies included an additional weight loss maintenance intervention. Study quality was mostly poor for weight loss studies (median = 3/10, range = 1-9) and weight loss maintenance studies (median = 3.5/10, range = 1-6). Twenty-three of 31 individual weight loss interventions (74%) from the eligible studies were considered effective. Meta-analysis revealed a significant difference in weight change favouring weight loss interventions over no-intervention controls at the last reported assessment (weighted mean difference -5.66 kg [-6.35, -4.97], Z = 16.04 [P < 0.00001]). Characteristics common to effectiveness were younger sample (mean age ≤ 42.8 years), increased frequency of contact (> 2.7 contacts/month), group face-to-face contact and inclusion of a prescribed energy restriction. Preliminary evidence suggests men-only weight loss programmes may effectively engage and assist men with weight loss. However, more high-quality studies are urgently needed to improve the evidence base, particularly for maintenance studies.

Survey of high school students' perceptions about their iPod use, knowledge of hearing health, and need for education

PURPOSE

High school students' knowledge about hearing health and their perceptions of how they use personal listening devices (PLDs) including iPods were surveyed to determine the need, content, and preferred format for educational outreach to them.

METHOD

This study was a descriptive convenience survey of students at a California high school. An 83-item questionnaire was administered in December 2009 to assess students' demographics, knowledge of hearing health, perceived iPod use, and risk activities.

RESULTS

The response rate was 56%. Most of the students perceived that they used iPods safely. However, responses indicated that many of the respondents could be at risk of injury to themselves or others if they became unaware of their surroundings while listening to iPods. Some students were knowledgeable about hearing health and safe iPod use, but most needed information about hearing loss and hearing conservation.

CONCLUSION

Most of the students needed education (e.g., via health classes or the Internet) about hearing health, the warning signs of hearing loss, and how to prevent hearing loss. Resources for educational audiologists are provided.

ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity

Transcriptional control is dependent on a vast network of epigenetic modifications. One epigenetic mark of particular interest is tri-methylation of lysine 27 on histone H3 (H3K27me3), which is catalysed and maintained by Polycomb Repressive Complex 2 (PRC2). Although this histone mark is studied widely, the precise relationship between its local pattern of enrichment and regulation of gene expression is currently unclear. We have used ChIP-seq to generate genome-wide maps of H3K27me3 enrichment, and have identified three enrichment profiles with distinct regulatory consequences. First, a broad domain of H3K27me3 enrichment across the body of genes corresponds to the canonical view of H3K27me3 as inhibitory to transcription. Second, a peak of enrichment around the transcription start site (TSS) is commonly associated with ‘bivalent’ genes, where H3K4me3 also marks the TSS. Finally and most surprisingly, we identified an enrichment profile with a peak in the promoter of genes that is associated with active transcription. Genes with each of these three profiles were found in different proportions in each of the cell types studied. The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation.

From RNA-seq reads to differential expression results

Many methods and tools are available for preprocessing high-throughput RNA sequencing data and detecting differential expression.

Gene ontology analysis for RNA-seq: accounting for selection bias

We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology.

Gene ontology analysis for RNA-seq: accounting for selection bias

GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq

We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology.

Health literacy among Spanish-speaking patients in the emergency department

STUDY OBJECTIVE

Health literacy influences a patient's ability to read and understand labels on medicine containers, appointment slips, informed-consent documents and medical instructions--all of which are considered basic health documents that a patient encounters in healthcare settings. Previous research suggests Spanish-speaking patients have low levels of health literacy. This study compares the functional health literacy (FHL) of Spanish- and English-speaking adult patients in a suburban emergency department (ED).

METHODS

Through a prospective, matched cohort design, Spanish-speaking adult patients and pediatric guardians presenting to the ED were matched with English-speaking patients by age, gender and treatment area. Demographic information, including total years of school completed and self-assessed reading ability, was collected. The Test of Functional Health Literacy in Adults (TOFHLA) was administered in the subject's primary language. A score of <60 indicated inadequate FHL, 60-74 marginally adequate FHL, and >74 adequate literacy.

RESULTS

Eighty-six matched pairs were enrolled. The median age was 30.5 years, and 56% were male. Spanish speakers averaged a TOFHLA score of 59.72, and English speakers 90.78. Only 7% of English speakers had less-than-adequate FHL compared to 74% of Spanish speakers. The average years of school completed were 10.59 (7.95 Spanish; 13.19 English), and 55% of English speakers reported "excellent" reading ability compared to 13% of Spanish speakers. Last grade completed (p=0.004) and self-assessed reading ability (p=0.0007) are predictors of TOFHLA scores. Those subjects who completed less than the eighth grade had inadequate FHL.

CONCLUSIONS

The majority of Spanish-speaking subjects have less-than-adequate FHL. Self-reported reading ability and years of school completed appear to predict FHL and may be clinically useful. Due to the disproportionately low level of health literacy among Spanish-speaking patients demonstrated in this and previous studies, future efforts should focus on developing programs that improve health literacy by providing this population with oral translations and pictorial and video instructions.

Second Prize: Forced versus Minimal Intravenous Hydration in the Management of Acute Renal Colic: A Randomized Trial

BACKGROUND AND PURPOSE

The management of acute renal colic is a problem commonly encountered by both urologists and emergency medicine physicians. The classic approach to managing uncomplicated acute renal colic involves hydration, along with imaging and pain control. Previous studies have suggested that hydration has a significant impact on patient comfort, as well as spontaneous stone passage. This study evaluated the effects of maintenance v forced hydration and its effect on the pain experienced from renal colic.

PATIENTS AND METHODS

Forty male and 18 female patients with a mean age of 41 years suspected to have acute renal colic were identified in the emergency department. After screening and informed consent, the patients were enrolled in the study, and 43 patients were eventually available for analysis. Patients received intravenous (IV) analgesia, imaging with a noncontrast CT scan of abdomen and pelvis, and assignment to either forced IV hydration with 2 L of normal saline over 2 hours (N = 20) or minimal IV hydration at 20 mL of normal saline per hour (N = 23). A visual analog pain scale was completed hourly for a total of 4 hours. Demographic information, laboratory and imaging results, narcotic use in morphine equivalents (ME), and pain scores were recorded and compared. Spontaneous stone passage rates were also calculated by careful patient follow-up. Results were considered statistically significant at p < 0.05.

RESULTS

Stone size was equivalent in the two treatment groups (p > 0.05). There was no difference in the narcotic requirement in ME (p = 0.644) between the two groups. Similarly, there was no difference in hourly pain score or stone-passage rates between the groups (p > 0.05).

CONCLUSIONS

Treatment of uncomplicated renal colic has traditionally included vigorous intravenous hydration, as well as medications for the control of pain and nausea. Our data suggest that maintenance intravenous fluids are as efficacious as forced hydration with regard to patient pain perception and narcotic use. Moreover, it appears the state of hydration has little impact on stone passage.