The gene regulatory basis of bystander activation in CD8+ T cells

CD8+ T cells are classically recognized as adaptive lymphocytes based on their ability to recognize specific foreign antigens and mount memory responses. However, recent studies indicate that some antigen-inexperienced CD8+ T cells can respond to innate cytokines alone in the absence of cognate T cell receptor stimulation, a phenomenon referred to as bystander activation. Here, we demonstrate that neonatal CD8+ T cells undergo a robust and diverse program of bystander activation, which corresponds to enhanced innate-like protection against unrelated pathogens. Using a multi-omics approach, we found that the ability of neonatal CD8+ T cells to respond to innate cytokines derives from their capacity to undergo rapid chromatin remodeling, resulting in the usage of a distinct set of enhancers and transcription factors typically found in innate-like T cells. We observed that the switch between innate and adaptive functions in the CD8+ T cell compartment is mediated by changes in the abundance of distinct subsets of cells. The innate CD8+ T cell subset that predominates in early life was also present in adult mice and humans. Our findings provide support for the layered immune hypothesis and indicate that the CD8+ T cell compartment is more functionally diverse than previously thought.

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we perform single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.

Single-cell and spatial multi-omics highlight effects of anti-integrin therapy across cellular compartments in ulcerative colitis

Ulcerative colitis (UC) is driven by immune and stromal subsets, culminating in epithelial injury. Vedolizumab (VDZ) is an anti-integrin antibody that is effective for treating UC. VDZ is known to inhibit lymphocyte trafficking to the intestine, but its broader effects on other cell subsets are less defined. To identify the inflammatory cells that contribute to colitis and are affected by VDZ, we performed single-cell transcriptomic and proteomic analyses of peripheral blood and colonic biopsies in healthy controls and patients with UC on VDZ or other therapies. Here we show that VDZ treatment is associated with alterations in circulating and tissue mononuclear phagocyte (MNP) subsets, along with modest shifts in lymphocytes. Spatial multi-omics of formalin-fixed biopsies demonstrates trends towards increased abundance and proximity of MNP and fibroblast subsets in active colitis. Spatial transcriptomics of archived specimens pre-treatment identifies epithelial-, MNP-, and fibroblast-enriched genes related to VDZ responsiveness, highlighting important roles for these subsets in UC.

Integrated longitudinal multi-omics study identifies immune programs associated with COVID-19 severity and mortality in 1152 hospitalized participants

Hospitalized COVID-19 patients exhibit diverse clinical outcomes, with some individuals diverging over time even though their initial disease severity appears similar. A systematic evaluation of molecular and cellular profiles over the full disease course can link immune programs and their coordination with progression heterogeneity. In this study, we carried out deep immunophenotyping and conducted longitudinal multi-omics modeling integrating ten distinct assays on a total of 1,152 IMPACC participants and identified several immune cascades that were significant drivers of differential clinical outcomes. Increasing disease severity was driven by a temporal pattern that began with the early upregulation of immunosuppressive metabolites and then elevated levels of inflammatory cytokines, signatures of coagulation, NETosis, and T-cell functional dysregulation. A second immune cascade, predictive of 28-day mortality among critically ill patients, was characterized by reduced total plasma immunoglobulins and B cells, as well as dysregulated IFN responsiveness. We demonstrated that the balance disruption between IFN-stimulated genes and IFN inhibitors is a crucial biomarker of COVID-19 mortality, potentially contributing to the failure of viral clearance in patients with fatal illness. Our longitudinal multi-omics profiling study revealed novel temporal coordination across diverse omics that potentially explain disease progression, providing insights that inform the targeted development of therapies for hospitalized COVID-19 patients, especially those critically ill.

Cyclone: an accessible pipeline to analyze, evaluate, and optimize multiparametric cytometry data

In the past decade, high-dimensional single-cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation, which are computationally intense and difficult to evaluate and optimize. Here, we present Cytometry Clustering Optimization and Evaluation (Cyclone), an analysis pipeline integrating dimensionality reduction, clustering, evaluation, and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full-spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification but also enables the unsupervised identification of lymphocytes and mononuclear phagocyte subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on a variety of cytometry datasets, which will further power immunology research and provide a scaffold for biological discovery.

Distinct pulmonary and systemic effects of dexamethasone in severe COVID-19

Dexamethasone is the standard of care for critically ill patients with COVID-19, but the mechanisms by which it decreases mortality and its immunological effects in this setting are not understood. We performed bulk and single-cell RNA sequencing of the lower respiratory tract and blood, and plasma cytokine profiling to study the effect of dexamethasone on systemic and pulmonary immune cells. We find decreased signatures of antigen presentation, T cell recruitment, and viral injury in patients treated with dexamethasone. We identify compartment- and cell- specific differences in the effect of dexamethasone in patients with severe COVID-19 that are reproducible in publicly available datasets. Our results highlight the importance of studying compartmentalized inflammation in critically ill patients.

A pilot study for development of a pulmonary function test induction jacket to automate effort in performing the forced vital capacity manoeuvre

The pulmonary function test (PFT) induction jacket was invented to make the process of performing the forced vital capacity (FVC) manoeuvre with a computerized spirometer effortless and productive for both the patient and the medical practitioner. The jacket is composed of three layers of PVC material sealed together to form a single jacket with two chambers. The inner chamber is formed between the inner layer and the middle layer, in which cold water at a temperature of 10 °C is circulated using a connected water unit when triggered. Similarly, the outer chamber is formed between the middle layer and the outer layer, in which air is pressurized using a connected air unit. Thirty volunteers performed the FVC manoeuvre with and without wearing the jacket. There was no difference between the results in spirometry parameters in the participants without a jacket and those with a jacket. However, use of the jacket significantly reduced the number of trials the participants had to undergo to perform spirometry. The jacket automated the FVC manoeuvre by triggering a physiological inspiratory gasp using cold water and circumscribing pressurized air for expiration. Additionally, subsequent advancements in the jacket have been suggested.

Astroglial toxicity promotes synaptic degeneration in the thalamocortical circuit in frontotemporal dementia with GRN mutations

Mutations in the human progranulin (GRN) gene are a leading cause of frontotemporal lobar degeneration (FTLD). While previous studies implicate aberrant microglial activation as a disease-driving factor in neurodegeneration in the thalamocortical circuit in Grn-/- mice, the exact mechanism for neurodegeneration in FTLD-GRN remains unclear. By performing comparative single-cell transcriptomics in the thalamus and frontal cortex of Grn-/- mice and patients with FTLD-GRN, we have uncovered a highly conserved astroglial pathology characterized by upregulation of gap junction protein GJA1, water channel AQP4, and lipid-binding protein APOE, and downregulation of glutamate transporter SLC1A2 that promoted profound synaptic degeneration across the two species. This astroglial toxicity could be recapitulated in mouse astrocyte-neuron cocultures and by transplanting induced pluripotent stem cell-derived astrocytes to cortical organoids, where progranulin-deficient astrocytes promoted synaptic degeneration, neuronal stress, and TDP-43 proteinopathy. Together, these results reveal a previously unappreciated astroglial pathology as a potential key mechanism in neurodegeneration in FTLD-GRN.

Cyclone: an accessible pipeline to analyze, evaluate and optimize multiparametric cytometry data

In the past decade, high-dimensional single cell technologies have revolutionized basic and translational immunology research and are now a key element of the toolbox used by scientists to study the immune system. However, analysis of the data generated by these approaches often requires clustering algorithms and dimensionality reduction representation which are computationally intense and difficult to evaluate and optimize. Here we present Cyclone, an analysis pipeline integrating dimensionality reduction, clustering, evaluation and optimization of clustering resolution, and downstream visualization tools facilitating the analysis of a wide range of cytometry data. We benchmarked and validated Cyclone on mass cytometry (CyTOF), full spectrum fluorescence-based cytometry, and multiplexed immunofluorescence (IF) in a variety of biological contexts, including infectious diseases and cancer. In each instance, Cyclone not only recapitulates gold standard immune cell identification, but also enables the unsupervised identification of lymphocytes and mononuclear phagocytes subsets that are associated with distinct biological features. Altogether, the Cyclone pipeline is a versatile and accessible pipeline for performing, optimizing, and evaluating clustering on variety of cytometry datasets which will further power immunology research and provide a scaffold for biological discovery.

Prognostic implications of clinical phenotype and severity of cardiac involvement in patients presenting with immunoglobulin light chain amyloidosis

Background

Patients with systemic immunoglobulin light chain (AL) amyloidosis may present with a wide array of signs and symptoms due to the multi-systemic organ involved. The presence of cardiac involvement is the key determinant of survival. Cardiac magnetic resonance (CMR) has the unique ability to measure the continuum of cardiac amyloidosis (CA) infiltration providing a deep characterisation from early CA involvement to severe degree of CA burden.

Purpose

The aim of this study was to characterise the clinical profiles and the severity of organ involvement in patients presenting with AL amyloidosis and to investigate implications for long-term outcome.

Methods

Patients newly diagnosed with AL amyloidosis at the National Amyloidosis Centre underwent comprehensive clinical, laboratory and instrumental work up, including CMR imaging with left ventricular (LV) mass, late gadolinium enhancement (LGE) and extracellular volume (ECV). The clinical phenotypes were classified in cardiac, renal and other according to the symptoms at presentation. The degree of CA was investigated by CMR: 0= no features of CA (normal LV mass, no LGE and normal ECV); 1=early cardiac amyloid infiltration (normal LV mass, raised ECV no LGE); 2= characteristic of CA with normal mass (diffuse subendocardial or transmural LGE, altered gadolinium kinetics and raised ECV); 3= characteristic of CA with elevated mass (diffuse subendocardial or transmural LGE and raised ECV). The study outcome was all-cause mortality.

Results

The study population included 241 AL patients presenting with cardiac and renal (22.8%, n=55), cardiac (28.2%, n=68), renal (33.2%, n=80) and other (15.8% n=38) phenotypes. During a median follow up of 33 (IQR 7–52) months, cardiac phenotype either in isolation or in combination with renal phenotype was associated with a higher rate of all-cause mortality compared to the others (p<0.001) (Figure). On CMR imaging, 43.2% of patients without cardiac phenotype (49%, n=118/241) had characteristic scans of CA (CMR grade 2 and 3) whilst 13.8% of patients with cardiac phenotype (51%, n=123/241) had no features of CA on CMR images (CMR grade 0) in (p<0.001). With Kaplan Meier analysis, the risk of all-cause death increased in patients with characteristic features of CA on CMR scan (Figure 1) and in patients with cardiac phenotype and features of CA on CMR scans compared to the others (both p<0.001) (Figure). At multivariable analysis, age at diagnosis (hazard ratio [HR] 1.03, p=0.009), clinical phenotype at presentation (HR 1.35, p=0.014) and ECV measured by CMR (HR 56, p<0.001) emerged as independent prognostic parameters.

Conclusions

Patients with newly diagnosed AL amyloidosis present most frequently with renal and cardiac phenotypes. CMR detects CA in >40% of patients with non-cardiac phenotype. ECV is an independent predictor of all-cause mortality across the full clinical spectrum of AL amyloidosis.

Funding Acknowledgement

Type of funding sources: None.

Myocardial ischaemia in cardiac amyloidosis: a change of perspective

Introduction

Cardiac involvement is the main driver of clinical outcomes in systemic amyloidosis; however many clinical observations are not explained by the concept of replacement of the interstitium by amyloid material. Preliminary studies support the hypothesis that myocardial ischaemia contributes to cellular damage.

Purpose

This study assesses the presence and mechanisms of myocardial ischaemia using cardiovascular magnetic resonance (CMR) with multiparametric mapping and histopathological assessment.

Methods

Ninety-two patients with cardiac amyloidosis (CA) (AL = 41, ATTR = 51) and 97 without CA (3-vessel coronary disease (3VD) = 47, unobstructed coronary arteries = 26, healthy volunteers (HV) = 24) underwent quantitative stress perfusion CMR with myocardial blood flow (MBF) mapping. Twenty-six myocardial biopsies and 3 explanted hearts with CA were analysed histopathologically.

Results

Stress MBF was severely reduced in patients with CA with lower values than patients with 3VD, unobstructed coronary arteries and HV (CA = 1.03±0.51 ml/min/g, 3VD = 1.35±0.50 ml/min/g, Unobstructed coronaries = 2.92±0.52 ml/min/g, HV = 3.14±0.69 ml/min/g; CA vs 3VD p=0.008, CA vs Unobstructed coronaries p<0.001, CA vs HV p<0.001). After adjustment for intracellular volume the MBF in patients with CA remained significantly lower than in HV (stress MBF/ICV: AL = 2.24±1.12, ATTR = 2.22±0.93, HV = 4.38±1.06; AL vs. ATTR p=1.000, AL vs HV p<0.001, ATTR vs. HV p<0.001). Myocardial perfusion reserve (MPR) was severely reduced in CA patients, compared to HV and patients with unobstructed coronary arteries, with the degree of reduction being comparable only to patients with 3VD (CA = 1.55±0.60, 3VD = 1.54±0.51, unobstructed coronaries = 2.78±0.70, HV = 4.08±0.86; CA vs 3VD p=1.000, CA vs unobstructed coronary arteries p<0.001, CA vs. HV p<0.001). Myocardial perfusion abnormalities correlated with amyloid burden, systolic and diastolic function, structural parameters and blood biomarkers (p<0.05). Biopsies demonstrated diffuse hypoxia with abnormal VEGF staining in cardiomyocytes and endothelial cells. Amyloid infiltration in intramural arteries was associated with severe lumen reduction in 20% of vessels, and severe reduction in capillary density.

Conclusion

CA is associated with severe myocardial ischaemia demonstrable by histology and CMR stress perfusion mapping. Histological evaluation indicates a complex pathophysiology, where systolic and diastolic dysfunction, amyloid infiltration of the epicardial arteries and disruption and rarefaction of the capillaries play a role in contributing to myocardial ischaemia.

Funding Acknowledgement

Type of funding sources: None.

Changes in referral pathway and phenotypic status of patients diagnosed with ATTR cardiac amyloidosis during the past 20 years

Background

Diagnostic and therapeutic advances have led to much increased awareness of transthyretin (ATTR) cardiac amyloidosis (CA).

Purpose

We sought to characterise the impact of this on referral practice, cardiac phenotype at diagnosis and specifically to determine whether patients are now being diagnosed at an earlier stage in their disease process.

Methods

We studied 1845 patients diagnosed with ATTR-CA at the National Amyloidosis Centre (NAC) from 2002–2021, all of whom underwent deep clinical phenotyping and follow-up.

Results

Analysis by 5-year quartiles revealed a substantial incremental increase in patients diagnosed with ATTR-CA (35 vs 260 vs 704 vs 846), which was associated with greater proportions of patients referred following advanced cardiac imaging (referrals following cardiac magnetic resonance and bone scintigraphy: 3% vs 44% vs 67% vs 76%; P<0.001). Over time, median duration of symptoms prior to diagnosis diminished from 36-months between 2002–2006 to 12-months between 2017–2021 (P<0.001) and a greater proportion of patients presented with milder disease across the 5-yearly quartiles (NAC stage 1: 40% vs 43% vs 44% vs 57%; P<0.001). The latter was associated with more favourable echocardiographic parameters of structure and function, including an incremental reduction in maximal left ventricular wall thickness (18.26mm vs 17.41mm vs 17.09mm vs 16.68mm; P=0.017). This was associated with improved survival in the overall population (2007–2011 vs 2012–2016: HR=1.65, 95% CI [1.33–2.06]; P<0.001 and 2012–2016 vs 2017–2021: HR =1.83, 95% CI [1.45–2.31]; P<0.001) and in each genotype (wtATTR, T60A and V122I). Despite a significant increase in the proportion of patients enrolled into clinical trials (0.0% vs 0.0% vs 2.6% vs 23.9%; P<0.001) and prescribed disease modifying therapy (5.7% vs 0.4% vs 4.8% vs 13.5%; P<0.001); the improved survival remained significant even after adjusting for clinical trials and disease modifying therapy (2012–2016 vs. 2017–2021: HR=1.65 95% CI [1.29–2.11], P<0.001).

Conclusion

Increased awareness and advances in cardiac imaging have been associated with a substantial increase in the diagnosis of ATTR-CA and at a progressively earlier stage of the disease, which has contributed to improved survival in recent years. These changes may have important implications for initiation and outcome of therapy. Given that ATTR-CA is now being diagnosed earlier, more data are needed to guide decisions on in whom and when to initiate treatment, and which treatments should be used at each disease stage. Furthermore, the changes in ATTR-CA phenotype at diagnosis urgently need to be factored into clinical trial design, given that pre-determined end-points based on trials performed in the past may no longer be appropriate, or at least sufficiently powered, or of adequate duration to evaluate efficacy of novel agents.

Funding Acknowledgement

Type of funding sources: None.

Multi-imaging characterisation of cardiac phenotype in different types of amyloidosis

Background

Bone scintigraphy is extremely valuable when assessing patients with suspected cardiac amyloidosis (CA), but the clinical significance and associated phenotype of different degrees of myocardial tracer uptake across different types of amyloidosis is yet to be defined.

Purpose

We sought to define the phenotypes of patients with varying degrees of cardiac uptake on bone scintigraphy, across multiple types of systemic amyloidosis using extensive characterisation comprising of biomarkers, echocardiographic and cardiac magnetic resonance (CMR) imaging.

Methods

A total of 296 patients (117 immunoglobulin light-chain [AL] amyloidosis, 165 transthyretin [ATTR] amyloidosis, 7 apolipoprotein-A1-amyloidosis [AApoAI],and 7 apolipoprotein-A4-amyloidosis [AApoA4]) underwent deep characterisation of their cardiac phenotype.

Results

AL-amyloidosis patients with grade 0 myocardial radiotracer uptake spanned the spectrum of CMR findings from no evidence of CA to characteristic features of CA, while AL-amyloidosis patients with grade 1–3 always produced characteristic CMR features. In ATTR-amyloidosis the CA burden strongly correlated with myocardial tracer uptake (correlation between bone scintigraphy cardiac uptake and CMR derived extracellular volume: R=0.88, 95% CI [0.84–0.91], P<0.001), except in patients with the Ser77Tyr variant. AApoAI-amyloidosis presented with grade 0–1 myocardial tracer uptake, and unique features of disproportionate right sided involvement such as disproportionate right ventricular (RV) and right atrial uptake on bone scintigraphy, RV free wall thickening, and tricuspid valve thickening and dysfunction. Within our cohort, AApoAIV-amyloidosis always presented with grade 0 myocardial tracer uptake, and characteristic features of CA on CMR. All AL-amyloidosis patients with grade 1 myocardial tracer uptake had characteristic CMR features of CA (n=48, 100%), while only ATTR-amyloidosis grade 1 patients with the Ser77Tyr variant had characteristic features of CA on CMR (n=5, 11.4%). Following the exclusion of Ser77Tyr and AApoAI, a CMR showing characteristic features of CA or an extracellular volume >0.40 in a patient with grade 1 myocardial tracer uptake had a sensitivity and specificity of 100% for diagnosing AL-amyloidosis.

Conclusion

Deep characterisation of the cardiac phenotype in different types of amyloidosis, across a range of bone scintigraphy cardiac uptake grades has identified clear differences between each amyloidosis type. The distinctive characteristics in each cohort has allowed the development of a diagnostic pathway to help define the diagnostic differentials and the clinical phenotype in each individual patient, following comprehensive assessment with bone scintigraphy and CMR.

Funding Acknowledgement

Type of funding sources: None.

Inhibition of MET Signaling with Ficlatuzumab in Combination with Chemotherapy in Refractory AML: Clinical Outcomes and High-Dimensional Analysis

Acute myeloid leukemia patients refractory to induction therapy or relapsed within one year have poor outcomes. Autocrine production of hepatocyte growth factor by myeloid blasts drives leukemogenesis in pre-clinical models. A phase Ib trial evaluated ficlatuzumab, a first-in-class anti-HGF antibody, in combination with cytarabine in this high-risk population. Dose-limiting toxicities were not observed, and 20 mg/kg was established as the recommended phase II dose. The most frequent treatment-related adverse event was febrile neutropenia. Among 17 evaluable patients, the overall response rate was 53%, all complete remissions. Phospho-proteomic mass cytometry showed potent on-target suppression of p-MET after ficlatuzumab treatment and that attenuation of p-S6 was associated with clinical response. Multiplexed single cell RNA sequencing using prospectively acquired patient specimens identified interferon response genes as adverse predictive factors. The ficlatuzumab and cytarabine combination is well-tolerated with favorable efficacy. High-dimensional analyses at single-cell resolution represent promising approaches for identifying biomarkers of response and mechanisms of resistance in prospective clinical studies.

Lin28b promotes innate functions in CD8+ T cells through rapid chromatin remodeling

Lin28b serves as a master regulator of fetal lymphopoiesis and promotes the development of more innate-like lymphocytes in early life. However, it is still unclear how Lin28b alters the function of CD8+ T cells and protects the host against infection. In this report we examined how Lin28b transcriptionally and epigenetically programs neonatal CD8+ T cells for innate immune defense. We found that murine neonatal CD8+ T cells possess innate-like transcriptomes, are more responsive to innate cytokines in the absence of antigen and produce a broader spectrum of cytokines compared to their adult counterparts. This unique program of bystander activation in early life corresponded with enhanced innate-like protection against irrelevant strains of bacterial, helminth and virus infections. To understand how this diversity of immune function is mediated, we used flow cytometry and scRNAseq and discovered that the neonatal CD8+ T cell pool is composed of many subsets of cells expressing distinct cytokines. ATACseq analysis revealed that neonatal CD8+ T cells are programmed to display innate-like properties and produce a diverse array of cytokines, which may be due to their ability to undergo extensive chromatin remodeling upon cytokine stimulation. These unique properties may be driven by high Lin28b expression in fetal progenitor cells, as adult cells expressing Lin28b initiated a program of bystander activation and immune protection that was analogous to neonates. Collectively, our data suggests that Lin28b enables neonatal CD8+ T cells to undergo a more diverse program of bystander activation, allowing them to deploy a bet-hedging immune strategy and protect the host against a rapidly changing pathogenic environment.

Robust partitioning of microRNA targets from downstream regulatory changes

The biological impact of microRNAs (miRNAs) is determined by their targets, and robustly identifying direct miRNA targets remains challenging. Existing methods suffer from high false-positive rates and are unable to effectively differentiate direct miRNA targets from downstream regulatory changes. Here, we present an experimental and computational framework to deconvolute post-transcriptional and transcriptional changes using a combination of RNA-seq and PRO-seq. This novel approach allows us to systematically profile the regulatory impact of a miRNA. We refer to this approach as CARP: Combined Analysis of RNA-seq and PRO-seq. We apply CARP to multiple miRNAs and show that it robustly distinguishes direct targets from downstream changes, while greatly reducing false positives. We validate our approach using Argonaute eCLIP-seq and ribosome profiling, demonstrating that CARP defines a comprehensive repertoire of targets. Using this approach, we identify miRNA-specific activity of target sites within the open reading frame. Additionally, we show that CARP facilitates the dissection of complex changes in gene regulatory networks triggered by miRNAs and identification of transcription factors that mediate downstream regulatory changes. Given the robustness of the approach, CARP would be particularly suitable for dissecting miRNA regulatory networks in vivo.

In Vitro Evolution Reveals a Single Mutation as Sole Source of Src-Family Kinase C-Helix-out Inhibitor Resistance

Understanding cancer cell drug resistance to protein-tyrosine kinase inhibitors, which often arises from acquired mutations in the target kinase, is central to the development of more durable therapies. Experimental systems that reveal potential paths to resistance for a given inhibitor and kinase target have an important role in preclinical development of kinase inhibitor drugs. Here, we employed a codon mutagenesis strategy to define the mutational landscape of acquired resistance in HCK, a member of the SRC tyrosine kinase family and therapeutic target in acute myeloid leukemia (AML). Using PCR-based saturation mutagenesis, we created a cDNA library designed to replace each codon in the HCK open reading frame with all possible codons. This HCK mutant library was used to transform Rat-2 fibroblasts, followed by selection for resistant colonies with A-419259, a pyrrolopyrimidine HCK inhibitor and drug lead for AML. X-ray crystallography has shown that A-419259 binding induces outward rotation of the kinase domain αC-helix, a conformation incompatible with phosphotransfer. Remarkably, only a single resistance mutation evolved during A-419259 selection: histidine substitution for threonine at the gatekeeper position in the kinase domain. Deep sequencing confirmed representation of nearly all other missense mutations across the entire HCK open reading frame. This observation suggests that A-419259 and other C-helix-out Src-family kinase inhibitors may have a narrow path to acquired resistance in the context of AML cases where Hck is an oncogenic driver.

0816 Sleep Correlates Of Nightmares Among Veterans

Introduction

There is an increased prevalence of Nightmare disorder (ND) among patients with obstructive sleep apnea (OSA). A further investigation of objectively measured sleep parameters among patients with and without ND could inform on potential comorbidities. We hypothesize ND correlates with Epworth sleepiness scale (ESS), apnea hypopnea index (AHI), Trough 02% (Sp02 nadir), and periodic limb movement (PLM) index.

Methods

Data presented herein are interim results from an IRB approved study to determine correlates and sequelae of nightmares. A cohort of all patients with ND visiting James A Haley Veterans Hospital between 2007 and 2011 was defined along with a random cohort of control patients. Demographic and outpatient visit data between January 2006 and April 2016 was pulled from VISTA for both the ND and control cohorts, and patients who had undergone a sleep study were identified. To date, sleep summary data has been individually extracted for 111 ND patients and 835 control patients. Logistic regression (SAS 9.4) was used to compare ESS, AHI, Sp02 nadir, and PLM Index.

Results

Mean age for ND was significantly lower at 49.7 ± 14, compared to 58.4 ± 12 for controls. Other demographic measures were similar including gender, race, and marital status. PLM index was significantly lower in ND compared to controls, however this relationship disappeared after adjusting for age. There were neither significant differences between other polysomnographic (PSG) variables, specifically AHI and Sp02 nadir, nor did OSA severity significantly different between ND and controls.

Conclusion

Among veterans undergoing a PSG, there were no significant differences between measured sleep parameters. Our results contradict our hypothesis that ND correlates with ESS, AHI, Sp02 nadir, and PLM index.

Support

This material is the result of work supported with resources and the use of facilities at the James A. Haley Veterans’ Hospital.

Expression of myeloid Src-family kinases is associated with poor prognosis in AML and influences Flt3-ITD kinase inhibitor acquired resistance

Unregulated protein-tyrosine kinase signaling is a common feature of AML, often involving mutations in Flt3 and overexpression of myeloid Src-family kinases (Hck, Fgr, Lyn). Here we show that high-level expression of these Src kinases predicts poor survival in a large cohort of AML patients. To test the therapeutic benefit of Flt3 and Src-family kinase inhibition, we used the pyrrolopyrimidine kinase inhibitor A-419259. This compound potently inhibits Hck, Fgr, and Lyn as well as Flt3 bearing an activating internal tandem duplication (ITD). Flt3-ITD expression sensitized human TF-1 myeloid cells to growth arrest by A-419259, supporting direct action on the Flt3-ITD kinase domain. Cells transformed with the Flt3-ITD mutants D835Y and F691L were resistant to A-419259, while co-expression of Hck or Fgr restored inhibitor sensitivity to Flt3-ITD D835Y. Conversely, Hck and Fgr mutants with engineered A-419259 resistance mutations decreased sensitivity of TF-1/Flt3-ITD cells. To investigate de novo resistance mechanisms, A-419259-resistant Flt3-ITD+ AML cell populations were derived via long-term dose escalation. Whole exome sequencing identified a distinct Flt3-ITD kinase domain mutation (N676S/T) among all A-419259 target kinases in each of six independent resistant cell populations. These studies show that Hck and Fgr expression influences inhibitor sensitivity and the pathway to acquired resistance in Flt3-ITD+ AML.

CDK2 kinase activity is a regulator of male germ cell fate

The ability of men to remain fertile throughout their lives depends upon establishment of a spermatogonial stem cell (SSC) pool from gonocyte progenitors, and thereafter balancing SSC renewal versus terminal differentiation. Here, we report that precise regulation of the cell cycle is crucial for this balance. Whereas cyclin-dependent kinase 2 (Cdk2) is not necessary for mouse viability or gametogenesis stages prior to meiotic prophase I, mice bearing a deregulated allele (Cdk2Y15S ) are severely deficient in spermatogonial differentiation. This allele disrupts an inhibitory phosphorylation site (Tyr15) for the kinase WEE1. Remarkably, Cdk2Y15S/Y15S mice possess abnormal clusters of mitotically active SSC-like cells, but these are eventually removed by apoptosis after failing to differentiate properly. Analyses of lineage markers, germ cell proliferation over time, and single cell RNA-seq data revealed delayed and defective differentiation of gonocytes into SSCs. Biochemical and genetic data demonstrated that Cdk2Y15S is a gain-of-function allele causing elevated kinase activity, which underlies these differentiation defects. Our results demonstrate that precise regulation of CDK2 kinase activity in male germ cell development is crucial for the gonocyte-to-spermatogonia transition and long-term spermatogenic homeostasis.

Evaluation of variation of interfraction doses to organs at risk during brachytherapy of cervical cancer

Background

Two-dimensional treatment planning using radiographs or simulator films was the standard in planning brachytherapy for patients with cervical cancer. Three-dimensional (3D) treatment planning has improved treatment efficacy. This retrospective study compares conventional and 3D treatment planning of brachytherapy in patients with cervical cancer and interfraction dose variation to bladder and rectum (D2cc).

Methods

The mean doses to bladder and rectum (D2cc) were computed by computed tomography (CT)-based planning during 100 sessions of intracavitary brachytherapy for carcinoma cervix with the same source configuration as generated for conventional planning, and these estimates were compared with the doses at International Commission on Radiation Units and measurements (ICRU) rectal, bladder points and point A. Interfraction variation of doses to bladder and rectum during various sessions was also analysed.

Result

The mean ICRU bladder dose and D2cc of the bladder for all patients was 3.7 Gy and 7.4 Gy, respectively (p < 0.001). The mean ICRU rectal dose from conventional plan was 4.3Gy and with CT planning, 4.45 Gy (p = 0.04). Interfraction dose variations for D2cc of the bladder were min -5.3 Gy and max 4.8 Gy and those of the rectum were min -1.8 Gy and max 1.72Gy.

Conclusion

Dosimetric evaluation of conventional and 3D CT-based treatment planning for the same brachytherapy sessions demonstrated underestimation of ICRU bladder dose points (p < 0.001) and the rectal ICRU point dose and D2cc (p=0.04). The doses to organs at risk did not show a statistically significant variation between the fractions. However, large variation was noted between the interfractional maximum and minimum doses to bladder and rectum.

The Notch signaling pathway promotes basophil responses during helminth-induced type 2 inflammation

Basophils promote type 2 inflammation that mediates worm clearance during murine infection with the gastrointestinal helminth parasite Trichuris muris. Webb et al. show for the first time that basophil–intrinsic Notch signaling is required for basophil gene expression and a functional program that support helminth expulsion.

Type 2 inflammation drives the clearance of gastrointestinal helminth parasites, which infect over two billion people worldwide. Basophils are innate immune cells that support host-protective type 2 inflammation during murine infection with the helminth Trichuris muris. However, the mechanisms required for basophil function and gene expression regulation in this context remain unclear. We show that during T. muris infection, basophils localized to the intestine and up-regulated Notch receptor expression, rendering them sensitive to Notch signals that rapidly regulate gene expression programs. In vitro, Notch inhibition limited basophil cytokine production in response to cytokine stimulation. Basophil-intrinsic Notch signaling was required for T. muris–elicited changes in genome-wide basophil transcriptional programs. Mice lacking basophil-intrinsic functional Notch signaling had impaired worm clearance, decreased intestinal type 2 inflammation, altered basophil localization in the intestine, and decreased CD4⁺ T helper 2 cell responses following infection. These findings demonstrate that Notch is required for basophil gene expression and effector function associated with helminth expulsion during type 2 inflammation.

MiR-146a wild-type 3' sequence identity is dispensable for proper innate immune function in vivo

The prevailing model of microRNA function is that the "seed region" (nt 2-8) is sufficient to mediate target recognition and repression. However, numerous recent studies have challenged this model, either by demonstrating extensive 3' pairing between physically defined miRNA-mRNA pairs or by showing in Caenorhabditis elegans that disrupted 3' pairing can result in impaired function in vivo. To test the importance of miRNA 3' pairing in a mammalian system in vivo, we engineered a mutant murine mir-146a allele in which the 5' half of the mature microRNA retains its wild-type sequence, but the 3' half's sequence has been altered to robustly disrupt predicted pairing to this latter region. Mice homozygous or hemizygous for this mutant allele are phenotypically indistinguishable from wild-type controls and do not recapitulate any of the immunopathology previously described for mir-146a-null mice. Our results indicate that 3' pairing is dispensable for the established myeloid function of this key mammalian microRNA.

The Src family kinase Fgr is a transforming oncoprotein that functions independently of SH3-SH2 domain regulation

Fgr is a member of the Src family of nonreceptor tyrosine kinases, which are overexpressed and constitutively active in many human cancers. Fgr expression is restricted to myeloid hematopoietic cells and is markedly increased in a subset of bone marrow samples from patients with acute myeloid leukemia (AML). Here, we investigated the oncogenic potential of Fgr using Rat-2 fibroblasts that do not express the kinase. Expression of either wild-type or regulatory tail-mutant constructs of Fgr promoted cellular transformation (inferred from colony formation in soft agar), which was accompanied by phosphorylation of the Fgr activation loop, suggesting that the kinase domain of Fgr functions independently of regulation by its noncatalytic SH3-SH2 region. Unlike other family members, recombinant Fgr was not activated by SH3-SH2 domain ligands. However, hydrogen-deuterium exchange mass spectrometry data suggested that the regulatory SH3 and SH2 domains packed against the back of the kinase domain in a Src-like manner. Sequence alignment showed that the activation loop of Fgr was distinct from that of all other Src family members, with proline rather than alanine at the +2 position relative to the activation loop tyrosine. Substitution of the activation loop of Fgr with the sequence from Src partially inhibited kinase activity and suppressed colony formation. Last, Fgr expression enhanced the sensitivity of human myeloid progenitor cells to the cytokine GM-CSF. Because its kinase domain is not sensitive to SH3-SH2–mediated control, simple overexpression of Fgr without mutation may contribute to oncogenic transformation in AML and other blood cancers.

Selective Inhibition of the Myeloid Src-Family Kinase Fgr Potently Suppresses AML Cell Growth in Vitro and in Vivo

Acute myelogenous leukemia (AML) is the most common hematologic malignancy in adults and is often associated with constitutive tyrosine kinase signaling. These pathways involve the nonreceptor tyrosine kinases Fes, Syk, and the three Src-family kinases expressed in myeloid cells (Fgr, Hck, and Lyn). In this study, we report remarkable anti-AML efficacy of an N-phenylbenzamide kinase inhibitor, TL02-59. This compound potently suppressed the proliferation of bone marrow samples from 20 of 26 AML patients, with a striking correlation between inhibitor sensitivity and expression levels of the myeloid Src family kinases Fgr, Hck, and Lyn. No correlation was observed with Flt3 expression or mutational status, with the four most sensitive patient samples being wild-type for Flt3. Kinome-wide target specificity profiling coupled with in vitro kinase assays demonstrated a narrow overall target specificity profile for TL02-59, with picomolar potency against the myeloid Src-family member Fgr. In a mouse xenograft model of AML, oral administration of TL02-59 for 3 weeks at 10 mg/kg completely eliminated leukemic cells from the spleen and peripheral blood while significantly reducing bone marrow engraftment. These results identify Fgr as a previously unrecognized kinase inhibitor target in AML and TL02-59 as a possible lead compound for clinical development in AML cases that overexpress this kinase independent of Flt3 mutations.

Developmental Origin Governs CD8+ T Cell Fate Decisions during Infection

Heterogeneity is a hallmark feature of the adaptive immune system in vertebrates. Following infection, naive T cells differentiate into various subsets of effector and memory T cells, which help to eliminate pathogens and maintain long-term immunity. The current model suggests there is a single lineage of naive T cells that give rise to different populations of effector and memory T cells depending on the type and amounts of stimulation they encounter during infection. Here, we have discovered that multiple sub-populations of cells exist in the naive CD8⁺ T cell pool that are distinguished by their developmental origin, unique transcriptional profiles, distinct chromatin landscapes, and different kinetics and phenotypes after microbial challenge. These data demonstrate that the naive CD8⁺ T cell pool is not as homogeneous as previously thought and offers a new framework for explaining the remarkable heterogeneity in the effector and memory T cell subsets that arise after infection.

The perils of inhibiting deficient factors

Essentials Anticoagulation in patients with factor X deficiency is an evidence-poor area. A patient with factor X deficiency was anticoagulated with warfarin followed by rivaroxaban. Warfarin may be a safer anticoagulant option than rivaroxaban in hereditary factor X deficiency. A baseline coagulation screen should be performed prior to commencement of anticoagulation.

SUMMARY

We report a case of a previously undiagnosed factor X deficiency in an 83-year-old man who had no previous bleeding history despite multiple hemostatic challenges. He was anticoagulated with warfarin for atrial fibrillation without bleeding complications; however, major hemorrhage occurred soon after a switch to rivaroxaban.

Abstract 2363: Targeting Src-family kinases to combat acquired inhibitor resistance in FLT3-ITD+ AML

Activating internal tandem duplication (ITD) mutations in the FMS-like receptor tyrosine kinase 3 (Flt3) are found in approximately 30% of acute myeloid leukemia (AML) patients. Flt3-ITD expression is associated with aggressive, chemotherapy-resistant disease and decreased overall survival. Multiple selective Flt3 kinase inhibitors have been developed as targeted therapy for Flt3-ITD+ AML. However, the clinical utility of these kinase inhibitors has been limited by the rapid recurrence of drug-resistant disease that often results from Flt3 kinase domain mutations that prevent inhibitor action. Recent studies revealed that multiple non-receptor tyrosine kinases are over-expressed in AML, including the myeloid Src-family kinases Hck, Lyn and Fgr, and may cooperate with Flt3 to drive disease. These observations suggest that kinase inhibitors with specificity profiles targeting Flt3 and these AML-associated cytoplasmic kinases may be less prone to acquired resistance. In the present study, we determined the contributions of Hck and Fgr kinase activities to Flt3-ITD+ AML cell growth using a chemical genetics approach. While RNAi-mediated knockdown of each of these kinases reduces proliferation and increases apoptosis in primary AML cells, the impact of pharmacologic inhibition of their kinase activities on AML cell growth is not known. Because no selective Hck or Fgr inhibitors exist, we developed kinase domain mutants that desensitize each kinase to the broad-spectrum SRC-family kinase inhibitor, A-419259. Examination of a previous crystal structure of Hck with A-419259 bound to the active site suggested a role for the ‘gatekeeper’ residue in compound binding. Substitution of the gatekeeper threonine of Hck and Fgr with methionine conferred 3-fold resistance to A-419259 in vitro without diminishing kinase activity. When expressed in human TF-1 myeloid cells transformed with Flt3-ITD, these inhibitor-resistant Hck and Fgr mutants conferred resistance to growth inhibition by A-419259 to a similar extent, while expression of the corresponding wild-type kinases was without effect. The sensitivity of the TF-1/Flt3-ITD cell lines to A-419259 correlated with inhibition of mutant Hck and Fgr kinase activity in the cells. Our findings suggest that suppression of AML cell growth by A-419259 is due in part to inhibition of Hck and Fgr, and identify these AML-associated kinases as therapeutic targets. Ongoing studies are addressing the role of Hck and Fgr as inhibitor targets in Flt3-ITD+ AML cell lines and patient samples as well as the propensity of A-419259 and other multi-targeted inhibitors of AML-associated kinases for acquired drug resistance.

Citation Format: Ravi K. Patel, Mark Weir, Sabine Hellwig, Heather Dorman, Thomas E. Smithgall. Targeting Src-family kinases to combat acquired inhibitor resistance in FLT3-ITD+ AML [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2363. doi:10.1158/1538-7445.AM2017-2363

Abstract 2377: The AML linked Src family kinase Fgr is uncoupled from SH2 and SH3 domain regulation and drives oncogenic transformation

Fgr is a member of the Src family of non-receptor protein-tyrosine kinases, which are over-expressed and constitutively active in many human cancers. Fgr expression is restricted to myeloid hematopoietic cells and strongly upregulated in a subset of primary human AML bone marrow samples, suggesting that Fgr kinase activity may contribute to AML pathogenesis. To investigate the oncogenic potential of Fgr, we expressed the wild-type kinase in Rat-2 fibroblasts and scored transformation in soft-agar colony-forming assays. Remarkably, Fgr expression resulted in strong transforming activity, suggesting that over-expression of the kinase is sufficient to overcome regulatory control by its SH2 and SH3 domains. To test this idea, we mutated the negative regulatory tail tyrosine of Fgr. Phosphorylation of the homologous tyrosines in c-Src, Hck and other Src-family members by the regulatory kinase Csk causes intramolecular engagement of the SH2 domain to suppress kinase activity. Substitution of the Fgr tail tyrosine with phenylalanine did not further enhance the transforming or kinase activity of Fgr in Rat-2 cells, suggesting that its kinase domain is uncoupled from regulation by its non-catalytic SH3-SH2 region. To explore the regulatory mechanism further, we expressed near-full-length Fgr in insect cells, purified it to homogeneity, and confirmed that it was singly phosphorylated on its negative regulatory tail (and not the activation loop). Hydrogen-deuterium exchange mass spectrometry demonstrated that the SH3 and SH2 domains are protected from deuterium uptake as observed previously for recombinant, downregulated Hck, suggesting that they are packed against the back of the kinase domain. We then tested recombinant Fgr for sensitivity to activation in vitro using peptide ligands for the SH3 and SH2 domains, as well as a peptide that engages both domains simultaneously. Fgr kinase activity was unaffected by these peptides, providing further evidence that the kinase domain is not allosterically coupled to SH3 and SH2 control. In contrast, Hck and c-Src were both stimulated by these peptides, consistent with a domain displacement mechanism of activation described previously. Control experiments using surface plasmon resonance spectroscopy confirmed that the SH3 and SH2 domains of both Hck and Fgr bind to each of the peptide ligands with similar kinetics and affinity. Taken together, our data show that Fgr is a unique Src family member in that its kinase domain is not subject to regulatory domain control despite evidence for intramolecular interactions with the SH3 and SH2 domains. As a consequence, simple over-expression of Fgr is sufficient to induce transformation of rodent fibroblasts, unlike Hck or other Src family members. By extension, over-expression of Fgr may contribute to AML development and selective targeting of its kinase activity may be of therapeutic benefit.

Citation Format: Kexin Shen, Heather R. Dorman, Haibin Shi, Ravi K. Patel, Jamie A. Moroco, John R. Engen, Thomas E. Smithgall. The AML linked Src family kinase Fgr is uncoupled from SH2 and SH3 domain regulation and drives oncogenic transformation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2377. doi:10.1158/1538-7445.AM2017-2377

Neonatal CD8+ T cells provide innate immune protection against unrelated pathogens

We previously found that neonatal and adult CD8+ T cells adopt different fates after infection with specific pathogens because they are derived from a distinct progenitor cell that is distinguished by expression of Lin28b. In this report, we investigated if CD8+ T cells respond differently to unrelated pathogens in early life. To start, we compared gene expression profiles of neonatal and adult CD8+ T cells after stimulation with innate cytokines (IL-12 + IL-18). Interestingly, we found that neonatal CD8+ T cells are more responsive and express a distinct cytokine profile compared to their adult counterparts. To examine the biological significance of these age-related differences, we next adoptively transferred monoclonal populations of neonatal or adult CD8+ T cells into T cell-deficient recipients and compared their ability to mediate immune protection against an irrelevant strain of Listeria monocytogenes. Surprisingly, we found that neonatal donor cell displayed increased proliferation and effector functions, and the pathogen burden was significantly reduced when compared to recipients containing adult donor cells. We also found that Lin28b may be responsible for the enhanced responsiveness to innate cytokines in early life, as ectopic expression of Lin28b in adult cells enabled them to initiate a program of bystander activation that was analogous to neonates. Collectively, these findings indicate that neonatal CD8+ T cells possess innate-like functions during infections at the cost of generating memory, and these unique behaviors may be driven by high levels of Lin28b. We currently are employing ATAC-seq to determine whether Lin28b changes the program of bystander activation by altering the chromatin landscape.

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

We provide a protocol for precision nuclear run-on sequencing (PRO-seq) and its variant, PRO-cap, which map the location of active RNA polymerases (PRO-seq) or transcription start sites (TSSs) (PRO-cap) genome-wide at high resolution. The density of RNA polymerases at a particular genomic locus directly reflects the level of nascent transcription at that region. Nuclei are isolated from cells and, under nuclear run-on conditions, transcriptionally engaged RNA polymerases incorporate one or, at most, a few biotin-labeled nucleotide triphosphates (biotin-NTPs) into the 3' end of nascent RNA. The biotin-labeled nascent RNA is used to prepare sequencing libraries, which are sequenced from the 3' end to provide high-resolution positional information for the RNA polymerases. PRO-seq provides much higher sensitivity than ChIP-seq, and it generates a much larger fraction of usable sequence reads than ChIP-seq or NET-seq (native elongating transcript sequencing). Similarly to NET-seq, PRO-seq maps the RNA polymerase at up to base-pair resolution with strand specificity, but unlike NET-seq it does not require immunoprecipitation. With the protocol provided here, PRO-seq (or PRO-cap) libraries for high-throughput sequencing can be generated in 4-5 working days. The method has been applied to human, mouse, Drosophila melanogaster and Caenorhabditis elegans cells and, with slight modifications, to yeast.

CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics

Chickpea is an important grain legume used as a rich source of protein in human diet. The narrow genetic diversity and limited availability of genomic resources are the major constraints in implementing breeding strategies and biotechnological interventions for genetic enhancement of chickpea. We developed an integrated Chickpea Transcriptome Database (CTDB), which provides the comprehensive web interface for visualization and easy retrieval of transcriptome data in chickpea. The database features many tools for similarity search, functional annotation (putative function, PFAM domain and gene ontology) search and comparative gene expression analysis. The current release of CTDB (v2.0) hosts transcriptome datasets with high quality functional annotation from cultivated (desi and kabuli types) and wild chickpea. A catalog of transcription factor families and their expression profiles in chickpea are available in the database. The gene expression data have been integrated to study the expression profiles of chickpea transcripts in major tissues/organs and various stages of flower development. The utilities, such as similarity search, ortholog identification and comparative gene expression have also been implemented in the database to facilitate comparative genomic studies among different legumes and Arabidopsis. Furthermore, the CTDB represents a resource for the discovery of functional molecular markers (microsatellites and single nucleotide polymorphisms) between different chickpea types. We anticipate that integrated information content of this database will accelerate the functional and applied genomic research for improvement of chickpea. The CTDB web service is freely available at http://nipgr.res.in/ctdb.html.

Perineal hernia formation following extralevator abdominoperineal excision

AIM

Extralevator abdominoperineal excision (ELAPE) has become increasingly used because of some evidence of improved oncological outcome. It is, however, thought to be associated with a higher incidence of perineal hernia formation, although the exact incidence is not known. The aim of this study was to identify the incidence of perineal hernia after ELAPE.

METHOD

The case notes of patients over a 54-month period were reviewed. The perineal closure technique, perineal complications and management plan were recorded.

RESULTS

During the study period, 56 patients underwent ELAPE, of whom 24 (44%) developed a perineal wound complication. Primary perineal closure was performed with (eight patients) and without (32 patients) insertion of a biological mesh or myocutaneous flap. Perineal hernia was the commonest complication (26%) and occurred in nine (45%) of 20 patients who had a laparoscopic ELAPE.

CONCLUSION

Perineal hernia formation was the commonest perineal complication of ELAPE and occurred in nearly half of patients having a laparoscopic ELAPE.

Does intentional support of degree programs in general surgery residency affect research productivity or pursuit of academic surgery?

OBJECTIVE

Many residents supplement general surgery training with years of dedicated research, and an increasing number at our institution pursue additional degrees. We sought to determine whether it was worth the financial cost for residency programs to support degrees.

DESIGN

We reviewed graduating chief residents (n = 69) in general surgery at Vanderbilt University from 2001 to 2010 and collected the data including research time and additional degrees obtained. We then compared this information with the following parameters: (1) total papers, (2) first-author papers, (3) Journal Citation Reports impact factors of journals in which papers were published, and (4) first job after residency or fellowship training.

SETTING

The general surgery resident training program at Vanderbilt University is an academic program, approved to finish training 7 chief residents yearly during the time period studied.

PARTICIPANTS

Chief residents in general surgery at Vanderbilt who finished their training 2001 through 2010.

RESULTS

We found that completion of a degree during residency was significantly associated with more total and first-author publications as compared with those by residents with only dedicated research time (p = 0.001 and p = 0.017). Residents completing a degree also produced publications of a higher caliber and level of authorship as determined by an adjusted resident impact factor score as compared with those by residents with laboratory research time only (p = 0.005). Degree completion also was significantly correlated with a first job in academia if compared to those with dedicated research time only (p = 0.046).

CONCLUSIONS

Our data support the utility of degree completion when economically feasible and use of dedicated research time as an effective way to significantly increase research productivity and retain graduates in academic surgery. Aggregating data from other academic surgery programs would allow us to further determine association of funding of additional degrees as a means to encourage academic productivity and retention.

Simultaneous analysis and quantification of markers of manjisthadi churna using high performance thin layer chromatography

Manjisthadi churna has been traditionally used in the Ayurvedic system of medicine and by traditional medical practices of India to treat hyperlipidemia. A rapid, simple and accurate method with high performance thin layer chromatography has been developed to standardised Manjisthadi churna using rubiadin, sennoside and ellagic acid as markers. Methanol extract of Manjisthadi churna were used for high performance thin layer chromatography on silica gel plates. The Rf of rubiadin, sennoside-A and ellagic acid were found to 0.48, 0.23 and 0.72, respectively with densitometric scanning at 280 nm and the calibration plot were linear in the range of 100-600 ng of markers. The correlation coefficients were higher than 0.99 were indicative of good linear dependence of peaks area on concentration. The rubiadin, sennoside-A and ellagic acid contents in Manjisthadi churna were found to be 0.014, 0.038 and 0.534% w/w, respectively. This method permits reliable quantification of rubiadin, sennoside-A and ellagic acid with good resolution and separation of the same from other constitutes of the extract of Manjisthadi churna. Recovery value from 95.66-102.33% showed the reliability and reproducibility of the method. The proposed high performance thin layer chromatography method for simultaneous quantification of markers in Manjisthadi churna can be used for routine quality testing.

A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)

Cicer arietinum L. (chickpea) is the third most important food legume crop. We have generated the draft sequence of a desi-type chickpea genome using next-generation sequencing platforms, bacterial artificial chromosome end sequences and a genetic map. The 520-Mb assembly covers 70% of the predicted 740-Mb genome length, and more than 80% of the gene space. Genome analysis predicts the presence of 27,571 genes and 210 Mb as repeat elements. The gene expression analysis performed using 274 million RNA-Seq reads identified several tissue-specific and stress-responsive genes. Although segmental duplicated blocks are observed, the chickpea genome does not exhibit any indication of recent whole-genome duplication. Nucleotide diversity analysis provides an assessment of a narrow genetic base within the chickpea cultivars. We have developed a resource for genetic markers by comparing the genome sequences of one wild and three cultivated chickpea genotypes. The draft genome sequence is expected to facilitate genetic enhancement and breeding to develop improved chickpea varieties.

Biosorption of arsenic (III) from aqueous solution by living cells of Bacillus cereus

In this work, removal of arsenic (III) from aqueous solution by living cells (Bacillus cereus), biosorption mechanism, and characterization studies have been reported. B. cereus cell surface was characterized using SEM-EDX and FTIR. Dependence of biosorption on pH of the solution, biosorbent dose, initial arsenic (III) concentration, contact time, and temperature had been studied to achieve optimum condition. The maximum biosorption capacity of living cells of B. cereus for arsenic (III) was found to be 32.42 mg/g at pH 7.5, at optimum conditions of contact time of 30 min, biomass dosage of 6 g/L, and temperature of 30 ± 2 °C. Biosorption data of arsenic (III) are fitted to linearly transformed Langmuir isotherm with R (2) (correlation coefficient) >0.99. The pseudo-second-order model description of the kinetics of arsenic (III) is successfully applied to predict the rate constant of biosorption. Thermodynamic parameters reveal the endothermic, spontaneous, and feasible nature of sorption process of arsenic (III) onto B. cereus biomass. The arsenic (III) ions are desorbed from B. cereus using both 1 M HCl and 1 M HNO(3).

Women's views on and adherence to low-molecular-weight heparin therapy during pregnancy and the puerperium

BACKGROUND

Non-adherence to prescribed medication represents a significant factor associated with treatment failure. Pregnant women identified at risk of venous thromboembolism are increasingly being prescribed low-molecular-weight heparin (LMWH) during pregnancy and the puerperium. It is important to understand women's views on and adherence to LMWH during pregnancy and the puerperium, so that women gain maximum benefit from the treatment.

OBJECTIVES

To monitor women's adherence to enoxaparin, when prescribed during pregnancy and the puerperium, and explore their beliefs about the enoxaparin therapy prescribed.

PATIENTS/METHODS

A prospective cohort study involving 95 nullparous and multiparous women prescribed enoxaparin for recognized antenatal indications. Adherence to enoxaparin was assessed through self-completion of a diary, additionally verified through laboratory tests. An adapted beliefs about medication questionnaire was administered to women during their pregnancy.

RESULTS

Women were highly adherent to enoxaparin: antenatally, mean percentage adherence 97.92%; postnatally, mean percentage adherence 93.37% (paired t-test, P = 0.000). In the cohort of women we followed, their perceived necessity for enoxaparin therapy outweighed any concerns they had regarding enoxaparin antenatally, necessity-concerns differential 2.20. In some women, however, this perceived necessity does decrease postnatally.

CONCLUSIONS

Our results suggest that most women prescribed enoxaparin are highly adherent to their therapy during the antenatal period and that women's antenatal beliefs about enoxaparin are able to predict a decrease in postnatal adherence. Our results have important clinical implications, particularly when women are initiated on LMWH just during the postnatal period.

Hydrogeochemical processes controlling the high fluoride concentration in groundwater: a case study at the Boden block area, Orissa, India

The present investigation reports the assessment of hydrochemical/geochemical processes controlling the concentration of fluoride in groundwater of a village in India (Boden block, Orissa). Boden block is one of the severely affected fluoride-contaminated areas in the state of Orissa (India). The sampling and subsequent analysis of water samples of the study area was carried out following standard prescribed methods. The results of the analysis indicate that 36.60% groundwater F(-) concentration exceeds the limit prescribed by the World Health Organization for drinking water. The rock interaction with groundwater containing high concentration of HCO(3)(-) and Na(+) at a higher pH value of the medium could be one of the important reasons for the release of F(-) from the aquatic matrix into groundwater. Geochemical classification of groundwater based on Chadha rectangular diagram shows that most of the groundwater samples having fluoride concentration more than 1.5 mg L(-1) belongs to the Na-K-HCO(3) type. The saturation index values evaluated for the groundwater of the study area indicated that it is oversaturated with respect to calcite, whereas the same is undersaturated with respect to fluorite content. The deficiency of calcium ion concentration in the groundwater from calcite precipitation favors fluorite dissolution leading to excess of fluoride concentration. The risk index was calculated as a function of fluoride level in drinking water and morbidity of fluorosis categorizes high risk for villages of Amera and Karlakote panchayat of Boden block.

NGS QC Toolkit: a toolkit for quality control of next generation sequencing data

Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.

Biosorption of As(V) from aqueous solutions by living cells of Bacillus cereus

In this work, the biosorption of As(V) from aqueous solutions by living cells of Bacillus cereus has been reported. The batch biosorption experiments were conducted with respect to biosorbent dosage 0.5 to 15 g/L, pH 2 to 9, contact time 5 to 90 min, initial concentration 1 to 10 mg/L and temperature 10 to 40 °C. The maximum biosorption capacity of B. cereus for As(V) was found to be 30.04 at pH 7.0, at optimum conditions of contact time of 30 min, biomass dosage of 6 g/L, and temperature of 30 ± 2 °C. Biosorption data were fitted to linearly transformed Langmuir isotherms with R(2) (correlation coefficient) >0.99. Bacillus cereus cell surface was characterized using AFM and FTIR. The metal ions were desorbed from B. cereus using both 1 M HCl and 1 M HNO(3). The pseudo-second-order model was successfully applied to predict the rate constant of biosorption.

NGS QC Toolkit: a toolkit for quality control of next generation sequencing data

Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.

NGS QC Toolkit: a toolkit for quality control of next generation sequencing data

Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.

P3-07-22: Combined Approach for Staging the Axilla in Breast Cancer Patients with Clinically (−)Nodes Versus Sentinel Node Biopsy Alone

Background

Prognostic information and local control for managing the majority of clinically node (−) breast cancer patients may be achieved by sentinel node biopsy (SNB) alone and/or limited axillary dissections (LAD). Currently, 20 - 30% of clinically node (−) patients have unnecessary surgery. This study compares the results from staging the axilla using SNB alone versus using the combined approach shown below.

Methods: Clinically node (−) patients (n=176) were subclassified according to their primary tumor histology, axillary ultrasound (US) data, and US guided Fine Needle Aspiration (US-FNA) results, as follows: Low Risk (LR) for axillary metastasis (n = 62); High Risk (HR) with normal axillary US (n = 17); HR with US suggesting minimal N1a disease (n = 23); HR with US suggesting N1a disease (n = 52); HR with US suggesting N2-3 disease (n = 22). All patients with (+) SNB or (+) US-FNA had Axillary Lymph Node Dissections (ALND). The number of (+) Sentinel Nodes (SN), Non Sentinel Nodes (NSN) and (+) LN after a (+) US-FNA from each patient category was correlated with corresponding preoperative data. HR patients were defined as having grade II tumors ≥ 1.5 cm and grade III tumors &gt; 1.0 cm. US abnormalities in the axilla were interpreted as follows: minimal N1a disease equivalent to cortical defects &lt; 5mm in 1–3 LN; N1a disease, cortical defects &gt; 5mm in 1–3 LN and N2-3 disease, complete nodal replacement in ≥ 1 LN. LAD refers to level I dissections (1-5 LN).

Results: Three subgroups of patients were identified: Group A, patients not requiring ALND (128/176 = 72%); Group B, patients requiring ALND bypassing SNB (22/176 =13%) and Group C, patients requiring LAD (26/176 = 15%). Preoperatively these 3 groups were categorized as follows: Group A included patients at LR for axillary metastasis, HR patients with normal axillary US, HR patients with axillary US suggesting minimal N1a disease and HR patients with axillary US suggesting N1a disease with (−) US-FNA; Group B included HR patients with axillary US suggesting N2-3 disease and (+) US-FNA; Group C included HR patients with axillary US suggesting N1a disease and (+) US-FNA. The post ALND characteristics for these 3 groups are summarized as follows: all Group A patients had N1a disease represented by ≤ 2 (+) LN, 94% (17/18) were SN (+) only, 85% (15/18) with 1 (+) LN and 15% with 2 (+) LN; in Group B, 20 patients had N2-3 disease and 2 patients had N1a disease, all Group B patients had &gt; 2 (+) LN; in group C, 20 patients had N1a disease and 2 patients had N2 disease, and 77% had single (+) node disease.

Conclusion: By following this approach a more patient oriented method for staging the axilla can be implemented as follows: 1. SNB alone for LR patients and for HR patients with axillary US findings suggesting no axillary disease, minimal N1a disease and/or N1a disease with (−) US-FNA; 2. ALND for HR patients with axillary findings suggesting N2-3 disease and a (+) US-FNA; 3. LAD for HR patients with US findings suggesting N1a disease and (+) US-FNA. This approach would result in a 38% (48/176) reduction in the number of SNB and a 30% (22/66) reduction in the number of ALND. This translates in to $200,000 (30-40%) in procedure-associated savings.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-07-22.

PlantRGS: a web server for the identification of most suitable candidate reference genes for quantitative gene expression studies in plants

Normalization of quantitative gene expression data with a suitable reference gene is essential for accurate and reliable results. However, the availability and choice of most suitable reference gene(s) showing uniform expression across all the experimental conditions remain a drawback. We have developed a web server, PlantRGS (http://www.nipgr.res.in/PlantRGS), for the identification of most suitable candidate reference gene(s) at the whole-genome level using microarray data for quantitative gene expression studies in plants. Microarray data from more than 11 000 tissue samples for nine plant species have been included in the PlantRGS for meta-analysis. The web server provides a user-friendly graphical user interface-based analysis tool for the identification of most suitable reference genes in the selected plant species under user-defined experimental conditions. Various parameter options and output formats will help users to investigate desired number of most suitable reference genes with wide range of expression levels. Validation of results revealed that novel reference genes identified by the PlantRGS outperforms the traditionally used reference genes in terms of expression stability. We anticipate that the PlantRGS will provide a platform for the identification of most suitable reference gene(s) under given experimental conditions and facilitate quantitative gene expression studies in plants.