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Single-cell sequencing has provided a means of quantifying cellular omic phenotypes. Identifying cell-type-specific feature genes is a crucial aspect of understanding cellular heterogeneity. Over the past decade, many methods have been developed to identify feature genes; however, these methods either depend on dubious cell clustering or fail to provide subpopulation-specific markers. We introduce SifiNet, a robust and accurate approach for identifying marker gene sets based on gene co-expression network topology. The identified gene sets facilitate the calculation of cellular gene set enrichment scores and cell annotation, and can reveal potential transitional relationships between cell subpopulations. SifiNet outperforms state-of-the-art methods in marker gene set identification and cell-type annotation accuracy. It is applicable to both single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) data. We have applied SifiNet to various experimental studies, successfully identifying novel gene markers, annotating cells with complex heterogeneity, and uncovering intriguing cell developmental trajectories.

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Supplementary Figures S1 - S11

The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are enriched in the HER2 subtype of breast cancer and are associated with immunotherapy response in diverse cancer types. However, the direct consequences of APOBEC mutagenesis on the tumor immune microenvironment have not been thoroughly investigated. To address this, we developed syngeneic murine mammary tumor models with inducible expression of APOBEC3B. We found that APOBEC activity induced antitumor adaptive immune responses and CD4+ T cell–mediated, antigen-specific tumor growth inhibition. Although polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected, suggesting that APOBEC-mediated genetic heterogeneity limits antitumor adaptive immune responses. Consistent with the observed immune infiltration in APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to anti–CTLA-4 checkpoint inhibition and led to a complete response to combination anti–CTLA-4 and anti-HER2 therapy. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures and clonality as biomarkers predicting immunotherapy response in HER2-positive (HER2+) breast cancers.

Legends for Figures S1-S11 and Supplementary Tables S1-S3

The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are enriched in the HER2 subtype of breast cancer and are associated with immunotherapy response in diverse cancer types. However, the direct consequences of APOBEC mutagenesis on the tumor immune microenvironment have not been thoroughly investigated. To address this, we developed syngeneic murine mammary tumor models with inducible expression of APOBEC3B. We found that APOBEC activity induced antitumor adaptive immune responses and CD4+ T cell–mediated, antigen-specific tumor growth inhibition. Although polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected, suggesting that APOBEC-mediated genetic heterogeneity limits antitumor adaptive immune responses. Consistent with the observed immune infiltration in APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to anti–CTLA-4 checkpoint inhibition and led to a complete response to combination anti–CTLA-4 and anti-HER2 therapy. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures and clonality as biomarkers predicting immunotherapy response in HER2-positive (HER2+) breast cancers.

Rare variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggregate the effects of RVs across genomic regions to study their collective impact. Some existing methods utilize a static delineation of genomic regions, often resulting in suboptimal effect aggregation, as neutral subregions within the test region will result in an attenuation of signal. To pinpoint genomic regions enriched for disease-associated RVs, we developed a novel method, DYNATE (DYNamic Aggregation TEsting). DYNATE dynamically and hierarchically aggregates smaller genomic regions into larger ones and performs multiple testing for disease associations with controlled weighted false discovery rate. Extensive numerical simulations demonstrate the superior performance of DYNATE under various scenarios compared to existing methods. Importantly, DYNATE-identified regions have higher enrichment levels of disease-associated RVs. We applied DYNATE to an amyotrophic lateral sclerosis (ALS) study and identified a new gene,EPG5, harboringpossibly pathogenic mutations.

Alloreactivity can drive autoimmune syndromes. After allogeneic hematopoietic stem cell transplantation (allo-HCT) chronic graft-versus-host disease (cGVHD), a B cell-mediated autoimmune-like syndrome, commonly occurs. Because donor-derived B cells continually develop under selective pressure from host alloantigens, aberrant B Cell Receptor (BCR)-activation and IgG production can emerge and contribute to cGVHD pathobiology. To better understand molecular programing of B cells under selective pressure of alloantigens, we performed scRNA-Seq analysis on high numbers of purified B cells from allo-HCT patients. An unsupervised analysis revealed 10 clusters, distinguishable by signature genes for maturation, activation and memory. We found striking transcriptional differences in the memory B cell compartment after allo-HCT compared to healthy or infected individuals. To identify intrinsic properties when B-cell tolerance is lost after allo-HCT, we then assessed clusters for differentially expressed genes (DEGs) between patients with vs. without autoimmune-like manifestations (Active cGVHD vs. No cGVHD, respectively). DEGs were found in Active cGVHD in both naive and BCR-activated clusters, suggesting functional diversity. Some DEGs were also differentially expressed across most clusters, suggesting common molecular programs that may promote B cell plasticity. Our study of human allo-HCT and cGVHD provides new understanding of B-cell memory in the face of chronic alloantigen stimulation.

Cells respond to a myriad of stressors by senescing, acquiring stable growth arrest, morphologic and metabolic changes, and a senescence-associated-secretory-phenotype (SASP). The heterogeneity of senescent cells (SnCs) and their SASP is vast, yet poorly characterized. SnCs have diverse roles in health and disease and are therapeutically targetable, making characterization of SnCs and harmonization of their nomenclature a priority. The Cellular Senescence Network (SenNet), a NIH Common Fund initiative, will leverage emerging single cell and spatial-omics to identify and map SnCs in numerous organs across the lifespan of humans and mice. A common coordinate framework will integrate the data, using validated, standardized methods, creating public 4-dimensional SnC atlases. Key SenNet deliverables include development of innovative tools/technologies to detect SnCs, biomarker discovery, common annotations to describe SnCs and extensive public data sets. The goal is to comprehensively understand and map SnCs for diagnostic and therapeutic purposes to improve human health.

The factors driving therapy resistance in diffuse glioma remain poorly understood. To identify treatment-associated cellular and genetic changes, we analyzed RNA and/or DNA sequencing data from the temporally separated tumor pairs of 304 adult patients with isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant glioma. Tumors recurred in distinct manners that were dependent on IDH mutation status and attributable to changes in histological feature composition, somatic alterations, and microenvironment interactions. Hypermutation and acquired CDKN2A deletions were associated with an increase in proliferating neoplastic cells at recurrence in both glioma subtypes, reflecting active tumor growth. IDH-wild-type tumors were more invasive at recurrence, and their neoplastic cells exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. Mesenchymal transition was associated with the presence of a myeloid cell state defined by specific ligand-receptor interactions with neoplastic cells. Collectively, these recurrence-associated phenotypes represent potential targets to alter disease progression.

Rationale: Hypercapnia develops in one third of patients with advanced chronic obstructive pulmonary disease (COPD) and is associated with increased morbidity and mortality. Multiple factors in COPD are thought to contribute to the development of hypercapnia including increased carbon dioxide (CO2) production, increased dead space ventilation, and the complex interactions of deranged respiratory system mechanics, inspiratory muscle overload and the ventilatory control center in the brainstem. However, these factors have not previously been systematically analyzed in a large, well-characterized population of severe COPD patients. Methods: This is a secondary analysis of the clinical, physiologic and imaging data from the National Emphysema Treatment Trial (NETT). All patients with complete baseline data for the key predictor variables were included. An inclusive list of 32 potential predictor variables were selected a priori based on consensus of the investigators and literature review. Stepwise variable selection yielded 10 statistically significant associations in multivariate regression. Results: A total of 1419 patients with severe COPD were included in the analysis; mean age 66.4 years (standard deviation 6.3), 38% females, and 422 (29.7%) had baseline hypercapnia. Key variables associated with hypercapnia were low resting partial pressure of oxygen in blood, low minute ventilation (Ve), high volume of exhaled carbon dioxide, low forced expiratory volume in 1 second, high residual volume, lower % emphysema on chest computed tomography, use of oxygen, low ventilatory reserve (high Ve/maximal voluntary ventilation), and not being at high altitude. Low diffusing capacity for carbon monoxide showed a positive association with hypercapnia in univariate analysis but a negative correlation in multivariate analysis. Measures of dyspnea and quality of life did not associate with degree of hypercapnia in multivariable analysis. Conclusions: Hypercapnia in a well-characterized cohort with severe COPD and emphysema is chiefly related to poor lung mechanics, high CO2 production, and a reduced ventilatory capability. Hypercapnia is less impacted by gas exchange abnormalities or the presence of emphysema. (Less)

Single-cell RNA-sequencing (scRNA-seq) technology allows us to explore cellular heterogeneity in the transcriptome. Because most scRNA-seq data analyses begin with cell clustering, its accuracy considerably impacts the validity of downstream analyses. Although many clustering methods have been developed, few tools are available to evaluate the clustering "goodness-of-fit" to the scRNA-seq data. In this paper, we propose a new Clustering Deviation Index (CDI) that measures the deviation of any clustering label set from the observed single-cell data. We conduct in silico and experimental scRNA-seq studies to show that CDI can select the optimal clustering label set. Particularly, CDI also informs the optimal tuning parameters for any given clustering method and the correct number of cluster components.

OBJECTIVES: Chronic pain affects a significant number of patients following hernia repair, ranging from 11 to 54% in the literature. The aim of this study was to assess the prevalence, overall costs and health care utilization associated with chronic pain after hernia repair. MATERIALS AND METHODS: A retrospective longitudinal study was performed using the Truven MarketScan(®) database to identify patients who develop chronic neuropathic post-hernia repair pain from 2001 to 2012. Patients were grouped into Chronic Pain (CP) and No Chronic Pain (No CP) cohorts. Patients were excluded if they 1) were under 18 years of age 2) had a previous pain diagnosis 3) had chronic pain diagnosed

Although hematopoietic stem cell transplantation (HCT) is the only curative treatment for acute myeloid leukemia (AML), it is associated with significant treatment related morbidity and mortality. There is great need for predictive biomarkers associated with overall survival (OS) and clinical outcomes. We hypothesized that circulating metabolic, inflammatory, and immune molecules have potential as predictive biomarkers for AML patients who receive HCT treatment. This retrospective study was designed with an exploratory approach to comprehensively characterize immune, inflammatory, and metabolomic biomarkers. We identified patients with AML who underwent HCT and had existing baseline plasma samples. Using those samples (n = 34), we studied 65 blood based metabolomic and 61 immune/inflammatory related biomarkers, comparing patients with either long-term OS (≥ 3 years) or short-term OS (OS ≤ 1 years). We also compared the immune/inflammatory response and metabolomic biomarkers in younger vs. older AML patients (≤30 years vs. ≥ 55 years old). In addition, the biomarker profiles were analyzed for their association with clinical outcomes, namely OS, chronic graft versus host disease (cGVHD), acute graft versus host disease (aGVHD), infection and relapse. Several baseline biomarkers were elevated in older versus younger patients, and baseline levels were lower for three markers (IL13, SAA, CRP) in patients with OS ≥ 3 years. We also identified immune/inflammatory response markers associated with aGVHD (IL-9, Eotaxin-3), cGVHD (Flt-1), infection (D-dimer), or relapse (IL-17D, bFGF, Eotaxin-3). Evaluation of metabolic markers demonstrated higher baseline levels of medium- and long-chain acylcarnitines (AC) in older patients, association with aGVHD (lactate, long-chain AC), and cGVHD (medium-chain AC). These differentially expressed profiles merit further evaluation as predictive biomarkers.

Remodeling or deregulation of the calcium signaling pathway is a relevant hallmark of cancer including cutaneous melanoma (CM). In this study, using data from a published genome-wide association study (GWAS) from The University of Texas M.D. Anderson Cancer Center, we assessed the role of 41,377 common single-nucleotide polymorphisms (SNPs) of 167 calcium signaling pathway genes in CM survival. We used another GWAS from Harvard University as the validation dataset. In the single-locus analysis, 1830 SNPs were found to be significantly associated with CM-specific survival (CMSS; P ≤ 0.050 and false-positive report probability ≤ 0.2), of which 9 SNPs were validated in the Harvard study (P ≤ 0.050). Among these, three independent SNPs (i.e. PDE1A rs6750552 T>C, ITPR1 rs6785564 A>G and RYR3 rs2596191 C>A) had a predictive role in CMSS, with a meta-analysis-derived hazards ratio of 1.52 (95% confidence interval = 1.19–1.94, P = 7.21 × 10(−4)), 0.49 (0.33–0.73, 3.94 × 10(−4)) and 0.67 (0.53–0.86, 0.0017), respectively. Patients with an increasing number of protective genotypes had remarkably improved CMSS. Additional expression quantitative trait loci analysis showed that these genotypes were also significantly associated with mRNA expression levels of the genes. Taken together, these results may help us to identify prospective biomarkers in the calcium signaling pathway for CM prognosis.

The APOBEC family of cytidine deaminases is one of the most common endogenous sources of mutations in human cancer. Genomic studies of tumors have found that APOBEC mutational signatures are particularly enriched in the HER2 subtype of breast cancer and have been associated with immunotherapy response in diverse cancer types. However, the direct consequences of APOBEC mutagenesis on the tumor immune microenvironment have not been thoroughly investigated. To address this, we developed syngeneic murine mammary tumor models with inducible expression of APOBEC3B. We found that APOBEC activity induces an antitumor adaptive immune response and CD4+ T cell-mediated tumor growth inhibition. While polyclonal APOBEC tumors had a moderate growth defect, clonal APOBEC tumors were almost completely rejected by the immune system, suggesting that APOBEC-mediated genetic heterogeneity limits the antitumor adaptive immune response. Consistent with the observed immune infiltration in APOBEC tumors, APOBEC activity sensitized HER2-driven breast tumors to checkpoint inhibition. In human breast cancers, the relationship between APOBEC mutagenesis and immunogenicity varied by breast cancer subtype and the frequency of subclonal mutations. This work provides a mechanistic basis for the sensitivity of APOBEC tumors to checkpoint inhibitors and suggests a rationale for using APOBEC mutational signatures as a biomarker predicting immunotherapy response in HER2-positive breast cancers.SIGNIFICANCEAPOBEC mutational signatures are observed in many cancers, yet the consequences of these mutations on the tumor immune microenvironment are not well understood. Using a novel mouse model, we show that APOBEC activity sensitizes HER2-driven mammary tumors to checkpoint inhibition and could inform immunotherapy treatment strategies for HER2-positive breast cancer patients.

Older AML patients have low remission rates and poor survival outcomes with standard chemotherapy. Microtransplantation (MST) refers to infusion of allogeneic hematopoietic stem cells without substantial engraftment. MST has been shown to improve clinical outcomes compared with chemotherapy alone. This is the first trial reporting on broad correlative studies to define immunologic mechanisms of action of MST in older AML patients. Older patients with newly diagnosed AML were eligible for enrollment, receiving induction chemotherapy with cytarabine (100 mg/m2) on days 1-7 and idarubicin (12 mg/m2) on days 1-3 (7 + 3). MST was administered 24 hours later. Patients with complete response (CR) were eligible for consolidation with high dose cytarabine (HiDAC) and a second cycle of MST. Responses were evaluated according to standard criteria per NCCN. Immune correlative studies were performed. Sixteen patients were enrolled and received 7 + 3 and MST (median age 73 years). Nine (56%) had high-risk and seven (44%) had standard-risk cytogenetics. Ten episodes of CRS were observed. No cases of GVHD or treatment-related mortality were reported. Event-free survival (EFS) was 50% at 6 months and 19% at 1 year. Overall survival (OS) was 63% at 6 months and 44% at 1 year. Donor microchimerism was not detected. Longitudinal changes were noted in NGS, TCR sequencing, and cytokine assays. Addition of MST to induction and consolidation chemotherapy was well tolerated in older AML patients. Inferior survival outcomes in our study may be attributed to a higher proportion of very elderly patients with high-risk features. Potential immunologic mechanisms of activity of MST include attenuation of inflammatory cytokines and emergence of tumor-specific T cell clones.

PURPOSE: Previous epidemiological and cost studies of fungal meningitis have largely focused on single pathogens, leading to a poor understanding of the disease in general. We studied the largest and most diverse group of fungal meningitis patients to date, over the longest follow-up period, to examine the broad impact on resource utilization within the United States. METHODOLOGY: The Truven Health Analytics MarketScan database was used to identify patients with a fungal meningitis diagnosis in the United States between 2000 and 2012. Patients with a primary diagnosis of cryptococcal, Coccidioides, Histoplasma, or Candida meningitis were included in the analysis. Data concerning healthcare resource utilization, prevalence and length of stay were collected for up to 5 years following the original diagnosis. RESULTS: Cryptococcal meningitis was the most prevalent type of fungal meningitis (70.1 % of cases over the duration of the study), followed by coccidioidomycosis (16.4 %), histoplasmosis (6.0 %) and candidiasis (7.6 %). Cryptococcal meningitis and candidiasis patients accrued the largest average charges ($103 236 and $103 803, respectively) and spent the most time in the hospital on average (70.6 and 79 days). Coccidioidomycosis and histoplasmosis patients also accrued substantial charges and time in the hospital ($82 439, 48.1 days; $78 609, 49.8 days, respectively). CONCLUSION: Our study characterizes the largest longitudinal cohort of fungal meningitis in the United States. Importantly, the health economic impact and long-term morbidity from these infections are quantified and reviewed. The healthcare resource utilization of fungal meningitis patients in the United States is substantial.

Objectives Unplanned 30-day readmission rates contribute significantly to growing national healthcare expenditures. Drivers of unplanned 30-day readmission after spinal cord stimulator (SCS) implantation are relatively unknown. The aim of this study was to determine drivers of 30-day unplanned readmission following SCS implantation. Methods The National Readmission Database was queried to identify all patients who underwent SCS implantation for the 2013 calendar year. Patients were grouped by readmission status, “No Readmission” and “Unplanned 30-day Readmission.” Patient demographics and comorbidities were collected for each patient. The primary outcome of interest was the rate of unplanned 30-day readmissions and associated driving factors. A multivariate analysis was used to determine independent predictors of unplanned 30-day readmission after SCS implantation. Results We identified 1521 patients who underwent SCS implantation, with 113 (7.4%) experiencing an unplanned readmission within 30 days. Baseline patient demographics, comorbidities, and hospital characteristics were similar between both cohorts. The three main drivers for 30-day readmission after SCS implantation include: 1) infection (not related to SCS device), 2) infection due to device (limited to only hardware infection), and 3) mechanical complication of SCS device. Furthermore, obesity was found to be an independent predictor of 30-day readmission (OR: 1.86, p = 0.008). Conclusion Our study suggests that infectious and mechanical complications are the primary drivers of unplanned 30-day readmission after SCS implantation, with obesity as an independent predictor of unplanned readmission. Given the technological advancements in SCS, repeated studies are necessary to identify factors associated with unplanned 30-day readmission rates after SCS implantation to improve patient outcomes and reduce associated costs.

The platelet-derived growth factor (PDGF) signaling pathway plays important roles in development and progression of human cancers. In our study, we aimed to identify genetic variants of the PDGF pathway genes associated with pancreatic cancer (PC) risk in European populations using three published genome-wide association study datasets, which consisted of 9,381 cases and 7,719 controls. The expression quantitative trait loci (eQTL) analysis was also performed using data from the 1000 Genomes, TCGA and GTEx projects. As a result, we identified two potential susceptibility loci (rs5757573 and rs6001516) of PDGFB associated with PC risk [odds ratio (OR) = 1.10, 95% confidence interval (CI) = 1.05-1.16, and p = 4.70 × 10-5 for the rs5757573 C allele and 1.21, 1.11-1.32, and 2.01 × 10-5 for the rs6001516 T allele]. Haplotype analysis revealed that the C-T haplotype carriers had a significantly increased risk of PC than those carrying the T-C haplotype (OR = 1.23, 95% CI = 1.12-1.34, p =5.00 × 10-6 ). The multivariate regression model incorporating the number of unfavorable genotypes (NUGs) with age and sex showed that carriers with 1-2 NUGs, particularly among 60-70 age group or males, had an increased risk of PC, compared to those without NUG. Furthermore, the eQTL analysis revealed that both loci were correlated with a decreased mRNA expression level of PDGFB in lymphoblastoid cell lines and pancreatic tumor tissues (p = 0.015 and 0.071, respectively). Our results suggest that genetic variants in PDGFB may play a role in susceptibility to PC. Further population and functional validations of our findings are warranted.

Objectives Spinal cord stimulation (SCS) has emerged as an appropriate modality of treatment for intractable chronic pain. The present study examines variations in SCS trial-to-permanent conversion rates based on provider types performing the procedure. Materials and Methods We designed a large, retrospective analysis using the Truven MarketScan data base analyzing adult SCS patients with provider information available, with or without IPG implantation from the years 2007–2012. Patients were categorized based on provider type performing the implantation including anesthesiologists, neurosurgeons, orthopedic surgeons, and physical medicine and rehabilitation (PM&R). Univariate and multivariate models identified factors associated with successful conversion. Results A total of 7667 unique instances of SCS implants were identified across five providers. Overall, 4842 (63.2%) of those receiving trials underwent permanent SCS system implantation. Anesthesiology performed the majority of implants (62.8%), followed by neurosurgery (22.0%), orthopedic surgery (10.2%), and PMR p

Objectives Conversion rates from trial leads to permanent spinal cord stimulation (SCS) systems have important implications for healthcare resource utilization (HCRU) and pain management. We hypothesized that there is a volume-outcome effect, with chronic pain patients who visit high volume SCS implanters will have higher trial-to-permanent conversion rates. Materials and Methods We designed a large, retrospective analysis using the Truven MarketScan database analyzing adult SCS patients with provider information available, with or without IPG implantation from the years 2007 to 2012 was designed. Patients were divided into three provider-based groups: high (>25), medium (9–24), and low (3–8) volume providers. Univariate and multivariate models identified factors associated with successful conversion. Results A total of 17,850 unique trial implants were performed by 3028 providers. Of 13,879 patients with baseline data available, 8981 (64.7%) progressed to permanent SCS. Higher volume providers were associated with slightly higher conversion rates (65.9% vs. 63.3% low volume, p = 0.029), explant rates (9.2% vs. 7.7% medium volume, p = 0.026), younger age (52.0 ± 13.4 years vs. 53.0 ± 13.4 years, p = 0.0026), Medicare/Medicaid (47.8% vs. 35.0% low volume, p

Exploring resting-state brain functional connectivity of autism spectrum disorders (ASD) using functional magnetic resonance imaging (fMRI) data has become a popular topic over the past few years. The data in a standard brain template consist of over 170,000 voxel specific points in time for each human subject. Such an ultra-high dimensionality makes the voxel-level functional connectivity analysis (involving four billion voxel pairs) both statistically and computationally inefficient. In this work, we introduce a new framework to identify the functional brain network at the anatomical region level for each individual. We propose two pairwise tests to detect region dependence, and one multiple testing procedure to identify global structures of the network. The limiting null distribution of each test statistic is derived. It is also shown that the tests are rate optimal when the alternative block networks are sparse. The numerical studies show that the proposed tests are valid and powerful. We apply our method to a resting-state fMRI study on autism and identify patient-unique and control-unique hub regions. These findings are biologically meaningful and consistent with the existing literature.

Intraspinal abscesses (ISAs) are rare lesions that are often neurologically devastating. Current treatment paradigms vary widely including early surgical decompression, drainage, and systemic antibiotics, delayed surgery, and sole medical management. The National Inpatient Sample (NIS) database was queried for cases of ISA from 2003 to 2012. Early and late surgery were defined as occurring before or after 48h of admission. Outcome measures included mortality, incidence of major complications, length of stay (LOS), and inpatient costs. A total of 10,150 patients were included (6281 early surgery, 3167 delayed surgery, 702 medical management). Paralysis, the main comorbidity, was most associated with early surgery (p

Background Gastrointestinal (GI) toxicity and acute graft versus host disease (GVHD) are significant morbidities associated with allogeneic hematopoietic stem cell transplantation (HSCT). The somatostatin analogue Octreotide ameliorates mucosal injury from radiation damage in pre-clinical mouse models. We hypothesized that administration of the longer-acting synthetic somatostatin analogue, Pasireotide, in the peri-transplant period would decrease acute GI toxicity and acute GVHD related to allogeneic HSCT. Methods Adult patients who underwent matched allogeneic HSCT with myeloablative conditioning were eligible for this study. Exclusion criteria included severe cardiac and endocrine abnormalities. Pasireotide was administered at 0.9mg twice daily from the day before conditioning began to day +4. The co-primary endpoints were 1) Acute GI toxicity, defined as GI toxicity occurring from the day prior to conditioning to day +30, and 2) Acute GVHD. Results were compared with 50 historical controls matched by Transplant diagnosis, Donor, Graft, GVHD prophylaxis, and Conditioning regimen. Results 36 patients were consented for the study, 25 patients received the study drug (5 screen failures, 1 insurance denial, 3 withdrew consent, 1 switched trials, 1 enrolled at an alternate center without available follow-up). There was no difference in Acute GI toxicity, which occurred in all patients in both the Pasireotide and Control groups. Grade 3 or 4 GI toxicity was similar, occurring in 20 patients (80%) in the Pasireotide group and 35 patients (70%) in the Control group. Specific GI toxicities varied in incidence between the Control and Pasireotide study groups (Figure 1), most notable for numerically higher rates of the expected toxicities abdominal pain, bloating, and vomiting in the Pasireotide group. Other common toxicities that occurred in the Pasireotide and Control groups are listed in Figure 1. There was no significant difference in incidence of overall Acute GVHD or Acute GI GVHD (Figure 2). The subset of patients who received Total Body Irradiation (TBI) conditioning had numerically lower Acute GVHD in the Pasireotide group (5/9, 55%) compared to the Control group (16/20, 80%), however this was not statistically significant (Fisher's Exact Test, p=0.21); these patients also had a lower rate of combined upper and lower GI GVHD (3/9, 33% in the Pasireotide group versus 11/20, 55% in the Control group), though this was not statistically significant (Fisher's Exact Test, p=0.43). Conclusions In this Phase 2 study, the somatostatin analogue Pasireotide did not decrease GI toxicity in allogeneic HSCT; however, in the subset of patients who received TBI conditioning, there was a numerically (but not statistically) significant decrease in overall and GI Acute GVHD. Further study in a larger cohort of patients undergoing TBI conditioning is warranted.

Summary CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error. The algorithm uses a Trie data structure for speed and resolves ambiguous mappings by using a statistical sequencing error model based on Phred scores for each read. Availability and implementation The package source code and an accompanying tutorial are available at http://bioconductor.org/packages/bcSeq/. Supplementary information Supplementary data are available at Bioinformatics online.

Motivated by the gene co-expression pattern analysis, we propose a novel sample quantile-based contingency (squac) statistic to infer quantile associations conditioning on covariates. It features enhanced flexibility in handling variables with both arbitrary distributions and complex association patterns conditioning on covariates. We first derive its asymptotic null distribution, and then develop a multiple testing procedure based on squac to simultaneously test the independence between one pair of variables conditioning on covariates for all $p(p-1)/2$ pairs. Here, $p$ is the length of the outcomes and could exceed the sample size. The testing procedure does not require resampling or perturbation, and thus is computationally efficient. We prove by theory and numerical experiments that this testing method asymptotically controls the false discovery rate (\FDR). It outperforms all alternative methods when the complex association panterns exist. Applied to a gastric cancer data, this testing method successfully inferred the gene co-expression networks of early and late stage patients. It identified more changes in the networks which are associated with cancer survivals. We extend our method to the case that both the length of the outcomes and the length of covariates exceed the sample size, and show that the asymptotic theory still holds., Comment: 31 pages, 1 figure

APOBEC-mediated mutagenesis is one of the most common endogenous sources of mutations in human cancer. APOBEC mutations are due to the episodic activity of the APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) family of cytidine deaminases, which catalyze the deamination of cytosine to uracil on single-stranded DNA. Cytidine deamination can be repaired to result in C-to-T and C-to-G mutations throughout the somatic genome. APOBEC mutational signatures have been identified in 22 different tumor types and are particularly enriched in bladder, head and neck, cervical, and breast cancer. Importantly, APOBEC mutagenesis is the main source of hypermutation in most breast tumors. Ongoing APOBEC mutational processes introduce genetic heterogeneity in populations of cells, although the in vivo functional consequences of these mutations on neoantigen formation, immunogenicity, and tumor evolution are unknown. Here, we designed syngeneic murine mammary tumor models to induce APOBEC mutagenesis in vivo and study how APOBEC mutational signatures shape tumor cell-intrinsic evolution and interactions with the tumor-immune microenvironment. In one murine model of HER2-driven mammary tumors, APOBEC mutagenesis significantly accelerates tumor recurrence following HER2 inhibition. However, we also found that in an immunocompetent mouse model of HER2-driven primary tumors, ongoing APOBEC mutagenesis slows tumor growth and triggers an antitumor adaptive immune response. The immune response consists of increased infiltration of CD4+ and CD8+ T cells and CD103+ dendritic cells, reduced infiltration of immunosuppressive Tregs and macrophages, and upregulated proinflammatory cytokines and PD-1/PD-L1 expression. Using a catalytically inactive mutant of the APOBEC enzyme, we discovered that the tumor growth defect requires the mutagenic activity of the APOBEC enzyme. Further, the growth defect of APOBEC tumors is largely abolished in immunodeficient NOD-scid-gamma mice, suggesting that the effects on tumor growth are mediated by the immune response. Interestingly, depletion of CD4+ and CD8+ T cells does not rescue the growth defect of the APOBEC tumors, despite the robust T cell response following APOBEC mutagenesis. These data suggest that APOBEC mutagenesis has protumor and antitumor roles in shaping tumor evolution by promoting tumor recurrence and stimulating an antitumor immune response, independent of T cell-mediated cytotoxicity, and may reveal immunotherapeutic treatment strategies for breast cancer patients with APOBEC mutational signatures. Citation Format: Ashley V. DiMarco, Xiaodi Qin, Brock McKinney, Ryan Lupo, Jichun Xie, Kouros Owzar, James Alvarez. APOBEC mutagenesis as a driver of tumor evolution by promoting tumor recurrence and modulating tumor-immune system interactions in a syngeneic murine model of breast cancer [abstract]. In: Abstracts: AACR Virtual Special Conference: Tumor Immunology and Immunotherapy; 2020 Oct 19-20. Philadelphia (PA): AACR; Cancer Immunol Res 2021;9(2 Suppl):Abstract nr PO002.

Importance: Sex differences in genetic associations with human longevity remain largely unknown; investigations on this topic are important for individualized health care. Objective: To explore sex differences in genetic associations with longevity. Design, Setting, and Participants: This population-based case-control study used sex-specific genome-wide association study and polygenic risk score (PRS) analyses to examine sex differences in genetic associations with longevity. Five hundred sixty-four male and 1614 female participants older than 100 years were compared with a control group of 773 male and 1526 female individuals aged 40 to 64 years. All were Chinese Longitudinal Healthy Longevity Study participants with Han ethnicity who were recruited in 1998 and 2008 to 2014. Main Outcomes and Measures: Sex-specific loci and pathways associated with longevity and PRS measures of joint effects of sex-specific loci. Results: Eleven male-specific and 11 female-specific longevity loci (P < 10 -5) and 35 male-specific and 25 female-specific longevity loci (10 -5≤ P < 10 -4) were identified. Each of these loci's associations with longevity were replicated in north and south regions of China in one sex but were not significant in the other sex (P =.13-.97), and loci-sex interaction effects were significant (P -5) and US women (P = 4.6 × 10 -5) but not significant in Chinese and US men. The associations of the loci rs2622624 of the ABCG2 gene were replicated in Chinese women (P = 6.8 × 10 -5) and European women (P =.003) but not significant in both Chinese and European men. Eleven male-specific pathways (inflammation and immunity genes) and 34 female-specific pathways (tryptophan metabolism and PGC-1α induced) were significantly associated with longevity (P -5) and 35 male-specific and 25 female-specific loci (10 -5≤P < 10 -4) were jointly replicated across north and south discovery and target samples. Analyses using the combined data set of north and south showed that these 4 groups of sex-specific loci were jointly and significantly associated with longevity in one sex (P = 2.9 × 10 -70to 1.3 × 10 -39) but not jointly significant in the other sex (P =.11 to.70), while interaction effects between PRS and sex were significant (P = 4.8 × 10 -50to 1.2 × 10 -16). Conclusion and Relevance: The sex differences in genetic associations with longevity are remarkable, but have been overlooked by previously published genome-wide association studies on longevity. This study contributes to filling this research gap and provides a scientific basis for further investigating effects of sex-specific genetic variants and their interactions with environment on healthy aging, which may substantially contribute to more effective and targeted individualized health care for male and female elderly individuals.

Estimation of the skeleton of a directed acyclic graph (DAG) is of great importance for understanding the underlying DAG and causal effects can be assessed from the skeleton when the DAG is not identifiable. We propose a novel method named PenPC to estimate the skeleton of a high-dimensional DAG by a two-step approach. We first estimate the nonzero entries of a concentration matrix using penalized regression, and then fix the difference between the concentration matrix and the skeleton by evaluating a set of conditional independence hypotheses. For high-dimensional problems where the number of vertices p is in polynomial or exponential scale of sample size n, we study the asymptotic property of PenPC on two types of graphs: traditional random graphs where all the vertices have the same expected number of neighbors, and scale-free graphs where a few vertices may have a large number of neighbors. As illustrated by extensive simulations and applications on gene expression data of cancer patients, PenPC has higher sensitivity and specificity than the state-of-the-art method, the PC-stable algorithm.

Background Unplanned hospital readmissions contribute significantly to soaring national healthcare expenditures. To alleviate this burden, Centers for Medicare and Medicaid Services implemented initiatives to penalize hospitals for unplanned 30-d hospital readmissions. There is a paucity of data identifying patient risk factors independently associated with 30- and 90-d readmissions. Objective To investigate similarities in patient risk factors associated with 30- and 90-d unplanned readmissions following elective lumbar spine surgery. Methods The National Readmission Database (NRD) was queried to identify patients undergoing elective lumbar spine surgery between 2013 and 2014. Patients were grouped by no readmission (Non-R), unplanned readmission within 30 days (30-R), and unplanned readmission within 31 to 90 days (90-R). Multivariate analysis determined factors associated with 30- and 90-d readmissions. Results We identified 144 123 patients with 10 592 (7.3%) patients experiencing an unplanned readmission (30-R: n = 7228 [5.0%]; 90-R: n = 3364 [2.3%]; Non-R: n = 133 531). The most common inpatient complication observed in those patients readmitted was dural tear (30-R: 7.7%, 90-R: 4.6%, Non-R: 4.3%). The most prevalent 30- and 90-d complication seen among the readmitted cohort was infection (30-R: 18.5%, 90-R: 7.4%). In multivariate regression analysis, age, insurance status, chronic obstructive pulmonary disorder (COPD), depression, hypertension, diabetes, deficiency anemia, and obesity were independently associated with 30-d readmission; however, age and obesity were not independently associated with 90-d readmission. Conclusion Our study demonstrated national unplanned readmission rates after elective spinal surgery to be 7.3%. With age, insurance status, COPD, depression, hypertension, diabetes, deficiency anemia, obesity, and depression all independently associated with unplanned hospital readmission. Future solutions that focus on reducing preventable readmissions may improve patient outcomes and reduce healthcare costs.

The toll-like receptor (TLR) signaling pathway plays an important role in the innate immune responses and antigen-specific acquired immunity. Aberrant activation of the TLR pathway has a significant impact on carcinogenesis or tumor progression. Therefore, we hypothesize that genetic variants in the TLR signaling pathway genes are associated with overall survival (OS) of patients with non-small cell lung cancer (NSCLC). To test this hypothesis, we first performed Cox proportional hazards regression analysis to evaluate associations between genetic variants of 165 TLR signaling pathway genes and NSCLC OS using the genome-wide association study (GWAS) dataset from the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial (PLCO). The results were further validated by the Harvard Lung Cancer Susceptibility GWAS dataset. Specifically, we identified IRAK2 rs779901 C > T as a predictor of NSCLC OS, with a variant-allele (T) attributed hazards ratio (HR) of 0.78 [95% confidence interval (CI) = 0.67-0.91, P = 0.001] in the PLCO dataset, 0.84 (0.72-0.98, 0.031) in the Harvard dataset, and 0.81 (0.73-0.90, 1.08x10-4 ) in the meta-analysis of these two GWAS datasets. In addition, the T allele was significantly associated with an increased mRNA expression level of IRAK2. Our findings suggest that IRAK2 rs779901 C > T may be a promising prognostic biomarker for NSCLC OS.

BACKGROUND Failed back surgery syndrome (FBSS) is a cause of significant morbidity for up to 40% of patients following spine surgery, and is estimated to cost almost $20 billion. Treatment options for these patients currently include conventional medical management (CMM), repeat operation, or spinal cord stimulation (SCS). Much of the published data regarding cost effectiveness of SCS comprise smaller scale randomized controlled trials (RCTs) rather than large databases capturing practices throughout the US. SCS has been shown to have superior outcomes to CMM or repeat spinal operation in several landmark studies, yet there are few large studies examining its long-term economic impact. OBJECTIVES This study compares health care utilization for SCS compared to other management in patients with FBSS. STUDY DESIGN Retrospective. SETTING Inpatient and outpatient sample. METHODS Patients with a history of FBSS from 2000 to 2012 were selected. We compared those who received SCS to those who underwent conventional management. A longitudinal analysis was used to model the value of log(cost) in each one year interval using a generalized estimating equations (GEE) model to account for the correlation of the same patient's cost in multiple years. Similarly, a Poisson GEE model with the log link was applied to correlated count outcomes. RESULTS We identified 122,827 FBSS patients. Of these, 5,328 underwent SCS implantation (4.34%) and 117,499 underwent conventional management. Total annual costs decreased over time following implantation of the SCS system, with follow-up analysis at 1, 3, 6, and 9 years. The longitudinal GEE model demonstrated that placement of an SCS system was associated with an initial increase in total costs at the time of implantation (cost ratio [CR]: 1.74; 95% confidence interval [CI]: 1.41, 2.15, P < 0.001), however there was a significant and sustained 68% decrease in cost in the year following SCS placement (CR: 0.32; 95% CI: 0.24, 0.42, P < 0.001) compared to CMM. There was also an aggregate time trend that for each additional year after SCS, cost decreased on average 40% percent annually (CR: 0.60; 95% CI: 0.55, 0.65, P < 0.001), with follow-up up to 1, 3, 6, and 9 years post-procedure. LIMITATIONS Costs are not correlated with patient outcomes, patients are not stratified in terms of complexity of prior back surgery, as well as inherent limitations of a retrospective analysis. CONCLUSIONS We found that from 2000 to 2012, only 4.3% of patients across the United States with FBSS were treated with SCS. Long-term total annual costs for these patients were significantly reduced compared to patients with conventional management. Although implantation of an SCS system results in a short-term increase in costs at one year, the subsequent annual cumulative costs were significantly decreased long-term in the following 9 years after implantation. This study combines the largest group of FBSS patients studied to date along with the longest follow-up interval ever analyzed. Since SCS has repeatedly been shown to have superior efficacy to CMM in randomized clinical trials, the current study demonstrating improved long-term health economics at 1, 3, 6, and 9 years supports the long-term cost utility of SCS in the treatment of FBSS patients. Key words: Failed back surgery syndrome, spinal cord stimulation, back pain, leg pain, neuromodulation, FBSS, SCS.

BACKGROUND Failed back surgery syndrome (FBSS) has a high incidence following spinal surgery, is notoriously refractory to treatment, and results in high health care utilization. Spinal cord stimulation (SCS) is a well-accepted modality for pain relief in this population; however, until recently magnetic resonance imaging (MRI) was prohibited due to risk of heat conduction through the device. OBJECTIVES We examined trends in imaging use over the past decade in patients with FBSS to determine its impact on health care utilization and implications for patients receiving SCS. STUDY DESIGN Retrospective. SETTING Inpatient and outpatient sample. METHODS We identified patients from 2000 to 2012 using the Truven MarketScan database. Annual imaging rates (episodes per 1000 patient months) were determined for MRI, computed tomography (CT) scan, x-ray, and ultrasound. A multivariate Poisson regression model was used to determine imaging trends over time, and to compare imaging in SCS and non-SCS populations. RESULTS A total of 311,730 patients with FBSS were identified, of which 5.17% underwent SCS implantation (n = 16,118). The median (IQR) age was 58.0 (49.0 - 67.0) years. Significant increases in imaging rate ratios were found in all years for each of the modalities. Increases were seen in the use of CT scans (rate ratio [RR] = 3.03; 95% confidence interval [CI]: 2.79 - 3.29; P < 0.0001), MRI (RR = 1.73; 95% CI: 1.61 - 1.85; P < 0.0001), ultrasound (RR = 2.00; 95% CI: 1.84 - 2.18; P < 0.0001), and x-ray (RR = 1.10; 95% CI: 1.05 - 1.15; P < 0.0001). Despite rates of MRI in SCS patients being half that in the non-SCS group, these patients underwent 19% more imaging procedures overall (P < 0.0001). SCS patients had increased rates of x-ray (RR = 1.27; 95% CI: 1.25 - 1.29), CT scans (RR = 1.32; 95% CI: 1.30 - 1.35), and ultrasound (RR = 1.10; 95% CI: 1.07 - 1.13) (all P < 0.0001). LIMITATIONS This study is limited by a lack of clinical and historical variables including the complexity of prior surgeries and pain symptomatology. Miscoding cannot be precluded, as this sample is taken from a large nationwide database. CONCLUSIONS We found a significant trend for increased use of advanced imaging modalities between the years 2000 and 2012 in FBSS patients. Those patients treated with SCS were 50% less likely to receive an MRI (as expected, given prior incompatibility of neuromodulation devices), yet 32% and 27% more likely to receive CT and x-ray, respectively. Despite the decrease in the use of MRI in those patients treated with SCS, their overall imaging rate increased by 19% compared to patients without SCS. This underscores the utility of MR-conditional SCS systems. These findings demonstrate that imaging plays a significant role in driving health care expenditures. This is the largest analysis examining the role of imaging in the FBSS population and the impact of SCS procedures. Further studies are needed to assess the impact of MRI-conditional SCS systems on future trends in imaging in FBSS patients receiving neuromodulation therapies. Key words: Failed back surgery syndrome, spinal cord stimulation, imaging, health care utilization, MRI, chronic pain, back pain, neuromodulation.

Objective The diagnosis and treatment of complex regional pain syndrome (CRPS) is challenging and there is a paucity of data describing its overall cost burden and quantifying its impact on the US healthcare system. The aim of this study was to assess the prevalence and healthcare utilization costs associated with CRPS. Materials and Methods A retrospective longitudinal study was performed using the Truven MarketScan® database to identify patients with a new indexed diagnosis of CRPS (Type I, II, or both) from 2001 to 2012. We collected total, outpatient, and pain prescription costs three years prior to CRPS diagnosis (baseline), at year of CRPS diagnosis, and eight-year post-CRPS diagnosis. A longitudinal multivariate analysis was used to model the estimated total and pain prescription cost ratios comparing patients diagnosed before and after CRPS. Results We included 35,316 patients with a newly indexed diagnosis of CRPS (Type I: n = 18,703, Type II: n = 14,599, Unspecified: n = 2014). Baseline characteristics were similar between the CRPS cohorts. Compared to two- and three-year baseline costs, one-year prior to diagnosis for all CRPS patients yielded the highest interquartile median [IQR] costs: total costs $7904[$3469, $16,084]; outpatient costs $6706[$3119, $12,715]; and pain prescription costs $1862[$147, $7649]. At the year of CRPS diagnosis, the median [IQR] costs were significantly higher than baseline costs: total costs $8508[$3943, $16,666]; outpatient costs $7251[$3527, $13,568]; and pain prescription costs $2077[$140, $8856]. Over the eight-year period after CRPS diagnosis, costs between all the years were similar, ranging from the highest (one-year) to lowest (seven-years), $4845 to $3888. The median total cumulative cost 8-years after CRPS diagnosis was $43,026 and $12,037 for pain prescription costs. [Correction added on 06 November 2017 after first online publication: the preceding sentence has been updated to demonstrate the median cumulative cost in replacement of the additive cumulative mean costs.]. During the CRPS diagnosis period, patients are expected to have a total cost 2.17-fold and prescription cost 2.56-fold of their baseline cost annually. Conclusions Our study demonstrates that there is a significant increase in cost and healthcare resource utilization one-year prior to and around the time of CRPS diagnosis. Furthermore, there is an increased annual cost post-diagnosis compared to baseline costs prior to CRPS diagnosis.

Patients with pain conditions place significant demands on health care services globally. Health economists have reported the annual economic cost of pain in the United States as high as $635 billion. A common challenge in treating patients suffering from chronic pain conditions is accurate diagnosis and treatment.The aim of this study was to determine the modern-day prevalence of individual types of pain diagnoses in adults.Retrospective analysis of Truven MarketScan® Commercial and Medicare Supplemental database.United States patient population with a pain diagnoses from 2000 to 2012.Multivariate analysis was used to determine the individual prevalence of specific types of pain diagnoses over a 13-year period.We grouped the 6,575,999 patients with ICD-9 pain diagnoses into pain groupings.We determined the prevalence of pain groupings as back pain (74.7%), chronic pain (10.4%), complex regional pain syndrome (1.2%), degenerative spine disease (63.6%), limb pain (50.0%), neuritis/radiculitis (52.8%), and post-laminectomy syndrome (14.8%).Retrospective and non-randomized study, with a patient cohort that is weighted towards recent years and commercial insurance. Coding discrepancies that are recorded and collected for patients.The demographic differences and similarities within the subgroups highlighted the concept that pain diagnoses should be considered as separate, but related entities. The present study helps us to better understand the frequency of specific pain diagnoses, and directs future studies to appropriately focus on pain diagnoses based on prevalence. This will allow increased understanding of the variation in pain diagnoses and prevent over-generalization in studies examining pain patients to more accurately reflect the varied subtypes and their economic impact.Duke University Institutional Review Board Protocol: 00053624Key words: Pain diagnoses, CRPS, neuritis, radiculitis, limb pain, degenerative spine disease, back pain, chronic pain, post-laminectomy pain, prevalence, MarketScan.

Based on sex-stratified genome-wide association study (GWAS) of Han Chinese, 2,178 centenarians and 2,299 middle-aged controls, we identified 11 male- and 12 female-specific independent loci that are significantly associated with longevity (P-5), replicated in independent North and South regions in one sex, but are not significant (P>0.05) in the other sex. We found that the association of rs60210535 at LINC00871 with longevity replicated well between Chinese females (P=4.6x10-5) and U.S. females (P=9.0x10-5), but was not significant in both Chinese and U.S. males (P>0.05). We discovered that 11 male-specific and 34 female-specific pathways are significantly associated with longevity (PFDR) P-5 in one sex, P>0.05 in other sex), 44/58 male/female strong loci (10-5≤P-4 in one sex, P>0.4 or P>0.35 in other sex), and 191/311 male/female moderate loci (10-4≤P-3 in one sex, P>0.75 or P>0.7 in other sex) are jointly and highly associated with longevity exceeding a significance level P10-8 in one sex, but not jointly associated with longevity in the other sex (P>0.05). Our integrated PRS and novel sex-specific genetic relative benefit/loss ratio analyses indicate that females’ genetic constitution favors longevity more than males’. Further interdisciplinary collaborative efforts are warranted, such as replications from other populations, international meta-analyses with much larger sample size, lab tests, and in silico functional validations. Significance Statement: On average, women live significantly longer lives than men but they have lower physical performance and more adverse health outcomes at older ages compared to men: patterns that signify the male-female health-survival paradox (1). Research on sex differences in health and mortality has proliferated, but has yet to achieve a good understanding of the effects of genetic variants on the sex gap in longevity and health. Based on sex-stratified genome-wide association analysis (GWAS) of Han Chinese including centenarians with a sample size 2.7 times as large as other published largest single GWAS on longevity involving centenarians (2), the present study aims to contribute a better understanding of sex differences in genetic associations with longevity.

While B cells are known to contribute to the pathogenesis of chronic graft-versus-host disease (cGVHD) in mice, it has been challenging to elucidate intrinsic mechanisms of tolerance loss in patients. To identify distinct and potentially targetable B-cell subsets in cGVHD, we employed single-cell RNA-Seq along with an unsupervised hierarchical clustering analysis, targeting 10,000 single B cells from each of eight patients who were >12 months post-allogeneic hematopoietic stem cell transplantation (HCT) and either had active cGVHD manifestations (n=4) or never developed cGVHD (n=4). Bioinformatics analysis of pooled cell data (using R with Seurat extension package) identified 6 major B cell clusters common to all patients (Figure 1A). "Intra-cluster" gene comparison (using R package DESeq2, false-discovery rate 0.05) revealed numerous differentially expressed genes between patient groups. The greatest number of differentially-expressed genes occurred in a cluster referred to herein as 'Cluster 6' (Figure 1A, in yellow with asterisk). Within Cluster 6, B cells from active cGVHD patients expressed significantly increased ITGAX (CD11c, Padj =0.007), TNFRSF13B (TACI, a receptor for BAFF, Padj =0.003), IGHG1 (IgG1, Padj =9.3e-06) and IGHG3 (IgG3, Padj =1.7e-12), along with 44 additional genes (to be discussed). Thus, Cluster 6 in cGVHD patients may represent a CD11cpos, BAFF-responsive B cell subset primed to undergo isotype switching in response to alloantigen. Flow cytometry analysis on PBMCs from an independent HCT patient cohort (n=10) confirmed that CD11cpos B cells were indeed significantly expanded in cGVHD (P < 0.01, Figure 1B), and revealed these B cells were also TACIpos, CD19high, forward scatter high (FSChigh) blast-like cells (Figure 1C). We found that these CD11cpos B cells had mixed expression of CD21, CD27, IgD and CD24 (Figure 1C). Remarkably, other recent studies on bulk patient B cells have suggested that similar CD11cposCD21negCD19highT-BETpos cells are critical drivers of humoral autoimmunity in diseases including systemic lupus erythematosus (SLE; Scharer et al. 2019; Rubtsova et al. 2017; Rubtsov et al. 2011). This subset now identified by single-cell RNA-Seq is consistent with a population of TACIhigh B cells that produced IgG in response to BAFF treatment ex vivo (Sarantopoulos 2009). Data suggest we have identified functionally distinct and potentially targetable B cell subpopulations. We are employing functional assays to determine whether the additional molecular pathways now elucidated account for our previous work showing greater ex vivo B cell survival rates and hyper-responsiveness to surrogate antigen (Allen et al. 2012, 2014), certain TLR agonists (Suthers et al. 2017), and NOTCH ligand (Poe et al. 2017). In addition to more deeply characterizing B-cell subsets in cGVHD, our single-cell RNA-Seq analyses identified several genes significantly altered across multiple B cell clusters in the cGVHD group, implicating more broad alterations of some genes in this disease. Among these is CKS2, a critical cell cycle regulator, which was significantly increased in cGVHD B cells (Padj 1.0e-10 to 0.018, depending on the cluster evaluated). Increased CKS2 expression was validated by qPCR analysis on B cells from a separate HCT patient cohort with or without cGVHD (P < 0.001, Figure 1D), suggesting that the majority of cGVHD B cells are primed to enter the cell cycle at multiple stages of differentiation when exposed to the proper stimuli. In summary, we used an unbiased approach to identify and further characterize an extrafollicular CD11cposTACIposCD19high B cell population in cGVHD patients that appears to be activated and undergoing active IgG isotype switching. This plasmablast-like B cell population is potentially amenable to therapeutic intervention to prevent pathogenic antibody production. Importantly, we also identify gene alterations across the cGVHD peripheral B cell compartment that potentially underpin promotion of hyperactivated B cells in this disease. Therapeutic strategies to target these pathways will also be discussed. This work was supported by a National Institutes of Health grant, R01HL129061. Disclosures Ho: Omeros Corporation: Membership on an entity's Board of Directors or advisory committees; Jazz Pharmaceuticals: Research Funding; Jazz Pharmaceuticals: Consultancy. Horwitz:Abbvie Inc: Membership on an entity's Board of Directors or advisory committees. Rizzieri:Celgene, Gilead, Seattle Genetics, Stemline: Other: Speaker; AbbVie, Agios, AROG, Bayer, Celgene, Gilead, Jazz, Novartis, Pfizer, Sanofi, Seattle Genetics, Stemline, Teva: Other: Advisory Board; AROG, Bayer, Celgene, Celltron, Mustang, Pfizer, Seattle Genetics, Stemline: Consultancy; Stemline: Research Funding.

Objectives Certain patients ultimately undergo explantation of their spinal cord stimulation (SCS) devices. Understanding the predictors and rates of SCS explantation has important implications for healthcare resource utilization (HCRU) and pain management. The present study identifies explant predictors and discerns differences in HCRU for at-risk populations. Methods We designed a large, retrospective analysis using the Truven MarketScan Database. We included all adult patients who underwent a SCS trial from 2007 to 2012. Patients were grouped into cohorts that remained explant-free or underwent explantation over a three-year period, and multivariate models evaluated differences in healthcare resource utilization. Results A total of 8727 unique instances of trial implants between 2007 and 2012 were identified. Overall, 805 (9.2%) patients underwent device explantation. One year prior to SCS implantation, the explant cohort had significantly higher median baseline costs ($42,140.3 explant vs. $27,821.7 in non-explant groups; p

Objectives Failed back surgery syndrome (FBSS) affects 40% of patients following spine surgery with estimated costs of $20 billion to the US health care system. The aim of this study was to assess the cost differences across the different insurance providers for FBSS patients. Methods A retrospective longitudinal study was performed using the Truven MarketScan® database to identify FBSS patients from 2001 to 2012. Patients were grouped into Commercial, Medicaid, or Medicare cohorts. We collected one-year prior to FBSS diagnosis (baseline), then at year of spinal cord stimulation (SCS)-implantation and nine-year post-SCS implantation cost outcomes. Results We identified 122,827 FBSS patients, with 117,499 patients who did not undergo an SCS-implantation (Commercial: n = 49,075, Medicaid: n = 23,180, Medicare: n = 45,244) and 5328 who did undergo an SCS implantation (Commercial: n = 2279, Medicaid: n = 1003, Medicare: n = 2046). Baseline characteristics were similar between the cohorts, with the Medicare-cohort being significantly older. Over the study period, there were significant differences in overall cost metrics between the cohorts who did not undergo SCS implantation with the Medicaid-cohort had the lowest annual median (interquartile range) total cost (Medicaid: $4530.4 [$1440.6, $11,973.5], Medicare: $7292.0 [$3371.4, $13,989.4], Commercial: $4944.3 [$363.8, $13,294.0], p Conclusions Our study demonstrates a significant difference in overall costs between various insurance providers in the management of FBSS, with Medicaid-insured patients having lower overall costs compared to Commercial- and Medicare-patients. SCS is cost-effective across all insurance groups (Commercial > Medicaid > Medicare) beginning at two years and continuing through nine-year follow-up. Further studies are necessary to understand the cost differences between these insurance providers, in hopes of reducing unnecessary health care expenditures for patients with FBSS.

To examine the influence of race, gender, and socioeconomic factors on presentations and outcomes of adult Chiari I malformations.The charts of 638 adult patients with Chiari I malformations were reviewed, and 287 patients were included in the study. Race, gender, insurance status, symptoms, depth of cerebellar tonsillar herniation, and presence of syringomyelia were examined as covariates in multivariate logistic regression models to identify independent predictors of presentation and outcome.Patients with public insurance had a longer stay in the hospital (P = 0.01). A higher proportion of male patients presented with upper extremity weakness (P = 0.01), lower extremity weakness (P = 0.040), and cranial nerve findings (P = 0.02). Men had shorter onset to diagnosis times (P = 0.02), worse tonsillar herniation (P = 0.03), and more severe symptoms (P = 0.05). White patients more frequently presented with back pain (P = 0.03), and African American patients more frequently presented with lower extremity weakness (P = 0.01). African Americans had worse tonsillar herniation (P0.01) and were more likely to present with syringomyelia (P = 0.01). Multivariate regression analysis revealed that back pain (P0.01), upper extremity weakness (P ≤ 0.01), upper extremity paresthesias (P0.01), and upper with lower extremity paresthesias (P = 0.04) were significant predictors of syringomyelia. The only independent predictor of outcome was size of tonsillar herniation (P = 0.03).Significant differences in presentation of Chiari I malformation resulting from gender, race, and insurance status were quantified for the first time.