Insights into the role of JAK2-I724T variant in myeloproliferative neoplasms from a unique cohort of New Zealand patients

OBJECTIVES

This study aimed to compile bioinformatic and experimental information for JAK2 missense variants previously reported in myeloproliferative neoplasms (MPN) and determine if germline JAK2-I724T, recently found to be common in New Zealand Polynesians, associates with MPN.

METHODS

For all JAK2 variants found in the literature, gnomAD_exome allele frequencies were extracted and REVEL scores were calculated using the dbNSFP database. We investigated the prevalence of JAK2-I724T in a cohort of 111 New Zealand MPN patients using a TaqMan assay, examined its allelic co-occurrence with JAK2-V617F using Oxford Nanopore sequencing, and modelled the impact of I724T on JAK2 using I-Mutant and ChimeraX software.

RESULTS

Several non-V617F JAK2 variants previously reported in MPN had REVEL scores greater than 0.5, suggesting pathogenicity. JAK2-I724T (REVEL score 0.753) was more common in New Zealand Polynesian MPN patients (n = 2/27; 7.4%) than in other New Zealand patients (n = 0/84; 0%) but less common than expected for healthy Polynesians (n = 56/377; 14.9%). Patients carrying I724T (n = 2), one with polycythaemia vera and one with essential thrombocythaemia, had high-risk MPN. Both patients with JAK2-I724T were also positive for JAK2-V617F, found on the same allele as I724T, as well as separately. In silico modelling did not identify noticeable structural changes that would give JAK2-I724T a gain-of-function.

CONCLUSION

Several non-canonical JAK2 variants with high REVEL scores have been reported in MPN, highlighting the need to further understand their relationship with disease. The JAK2-I724T variant does not drive MPN, but additional investigations are required to exclude any potential modulatory effect on the MPN phenotype.

Consensus Paper: Cerebellum and Reward

Cerebellum is a key-structure for the modulation of motor, cognitive, social and affective functions, contributing to automatic behaviours through interactions with the cerebral cortex, basal ganglia and spinal cord. The predictive mechanisms used by the cerebellum cover not only sensorimotor functions but also reward-related tasks. Cerebellar circuits appear to encode temporal difference error and reward prediction error. From a chemical standpoint, cerebellar catecholamines modulate the rate of cerebellar-based cognitive learning, and mediate cerebellar contributions during complex behaviours. Reward processing and its associated emotions are tuned by the cerebellum which operates as a controller of adaptive homeostatic processes based on interoceptive and exteroceptive inputs. Lobules VI-VII/areas of the vermis are candidate regions for the cortico-subcortical signaling pathways associated with loss aversion and reward sensitivity, together with other nodes of the limbic circuitry. There is growing evidence that the cerebellum works as a hub of regional dysconnectivity across all mood states and that mental disorders involve the cerebellar circuitry, including mood and addiction disorders, and impaired eating behaviors where the cerebellum might be involved in longer time scales of prediction as compared to motor operations. Cerebellar patients exhibit aberrant social behaviour, showing aberrant impulsivity/compulsivity. The cerebellum is a master-piece of reward mechanisms, together with the striatum, ventral tegmental area (VTA) and prefrontal cortex (PFC). Critically, studies on reward processing reinforce our view that a fundamental role of the cerebellum is to construct internal models, perform predictions on the impact of future behaviour and compare what is predicted and what actually occurs.

Elevated Electron Temperature Coincident with Observed Fusion Reactions in a Sheared-Flow-Stabilized Z Pinch

The sheared-flow-stabilized Z pinch concept has been studied extensively and is able to produce fusion-relevant plasma parameters along with neutron production over several microseconds. We present here elevated electron temperature results spatially and temporally coincident with the plasma neutron source. An optical Thomson scattering apparatus designed for the FuZE device measures temperatures in the range of 1-3 keV on the axis of the device, 20 cm downstream of the nose cone. The 17-fiber system measures the radial profiles of the electron temperature. Scanning the laser time with respect to the neutron pulse time over a series of discharges allows the reconstruction of the T_{e} temporal response, confirming that the electron temperature peaks simultaneously with the neutron output, as well as the pinch current and inductive voltage generated within the plasma. Comparison to spectroscopic ion temperature measurements suggests a plasma in thermal equilibrium. The elevated T_{e} confirms the presence of a plasma assembled on axis, and indicates limited radiative losses, demonstrating a basis for scaling this device toward net gain fusion conditions.

Myofascial trigger point (MTrP) size and elasticity properties can be used to differentiate characteristics of MTrPs in lower back skeletal muscle

Myofascial trigger points (MTrPs) are localized contraction knots that develop after muscle overuse or an acute trauma. Significant work has been done to understand, diagnose, and treat MTrPs in order to improve patients suffering from their effects. However, effective non-invasive diagnostic tools are still a missing gap in both understanding and treating MTrPs. Effective treatments for patients suffering from MTrP mediated pain require a means to measure MTrP properties quantitatively and diagnostically both prior to and during intervention. Further, quantitative measurements of MTrPs are often limited by the availability of equipment and training. Here we develop ultrasound (US) based diagnostic metrics that can be used to distinguish the biophysical properties of MTrPs, and show how those metrics can be used by clinicians during patient diagnosis and treatment. We highlight the advantages and limitations of previous US-based approaches that utilize elasticity theory. To overcome these previous limitations, we use a hierarchical approach to distinguish MTrP properties by patients' reported pain and clinician measured palpation. We show how US-based measurements can characterize MTrPs with this approach. We demonstrate that MTrPs tend to be smaller, stiffer, and deeper in the muscle tissue for patients with pain compared to patients without pain. We provide evidence that more than one MTrP within a single US-image field increases the stiffness of neighboring MTrPs. Finally, we highlight a combination of metrics (depth, thickness, and stiffness) that can be used by clinicians to evaluate individual MTrPs in combination with standard clinical assessments.

Clonal dynamics limits detection of selection in tumour xenograft CRISPR/Cas9 screens

Transplantable in vivo CRISPR/Cas9 knockout screens, in which cells are edited in vitro and inoculated into mice to form tumours, allow evaluation of gene function in a cancer model that incorporates the multicellular interactions of the tumour microenvironment. To improve our understanding of the key parameters for success with this method, we investigated the choice of cell line, mouse host, tumour harvesting timepoint and guide RNA (gRNA) library size. We found that high gRNA (80-95%) representation was maintained in a HCT116 subline transduced with the GeCKOv2 whole-genome gRNA library and transplanted into NSG mice when tumours were harvested at early (14 d) but not late time points (38-43 d). The decreased representation in older tumours was accompanied by large increases in variance in gRNA read counts, with notable expansion of a small number of random clones in each sample. The variable clonal dynamics resulted in a high level of 'noise' that limited the detection of gRNA-based selection. Using simulated datasets derived from our experimental data, we show that considerable reductions in count variance would be achieved with smaller library sizes. Based on our findings, we suggest a pathway to rationally design adequately powered in vivo CRISPR screens for successful evaluation of gene function.

Pencil Beam Scanning Proton Stereotactic Body Radiation Therapy (SBRT): A Robust Single Institution Experience

PURPOSE/OBJECTIVE(S)

To describe the feasibility of treating a complex and diverse group of patients using pencil beam scanning (PBS) proton stereotactic body radiation therapy (SBRT: 5 or fewer fractions, with a fraction size of at least 5 Gy).

MATERIALS/METHODS

Our center treats on average 105-120 PBS proton treatments daily, of which 9.5% of treatment courses are proton SBRT. Statistics of disease sites, treatment planning parameters (target volume, prescriptions, number of fields, SFO vs. MFO), and treatment efficiencies (scheduled time slots, actual treatment time) are presented for 305 consecutive SBRT patients receiving 1507 fractions in the past three years. Thermoplastic masks or Vacuum-lock bags are used to immobilize SBRT patients and index the patients' treatment position. Imaging guidance of orthogonal kV images and volumetric cone-beam CT is routinely used for patient setup.

RESULTS

SBRT patients are grouped based on the target locations: pelvis (31%), liver (17%), thoracic (13%), spine (8%), abdominal (8%), brain (7%), non-spine bone (7%), ocular (6%), and head and neck (2%). Only 112 patients (37%) were receiving their 1st RT course, whereas 113 (37%) had one prior in-field RT course, and 80 (26%) had multiple prior in-field RT courses. The median [IQR] target volume was 65.4 [29.3, 168] cc (range: 0.3-2475 cc). 72% of cases were planned with SFO and 28% with MFO. On average, 3.76 fields (range: 2 to 12) were planned for each treatment. 44% of the treatments were planned with three or fewer fields, and 10% received more than five fields, most of which involved repainting for moving targets. Over 97% of treatments were delivered in 5 fractions, with ∼3% delivered in 3 fractions. The median [IQR] prescription per treatment was 8 [7, 10] Gy (range: 5-18 Gy per treatment). 85% (84%) of the SBRT treatments were scheduled (delivered) in a 45-minute or shorter slot, and 6% (7%) of treatments were scheduled (delivered) in over a one-hour slot, most commonly for multiple isocenter treatments. 93% of treatments were delivered within 15 minutes of the planned treatment time or shorter. Deep-inspiration breath-hold (DIBH) was applied to 45% of liver SBRT cases, with the remaining 55% planned on 4D CT with (14%) or without (86%) abdominal compression. DIBH was applied in 13% of lung SBRT cases. The application of other motion mitigation approaches, such as volumetric repainting, was determined by the target motion amplitude and whether the patient could tolerate DIBH.

CONCLUSION

In the most diverse and largest proton SBRT experience delivered in the world over the past 3 years, over 300 patients were treated, demonstrating the feasibility and efficiency of delivering proton SBRT in a very busy center. The planning and treatment parameter statistics reported serve as a helpful reference for the proton community.

Chromosomal Aberrations Accumulate during Metastasis of Virus-Negative Merkel Cell Carcinoma

Merkel cell carcinoma is a rare, aggressive skin tumor initiated by polyomavirus integration or UV light DNA damage. In New Zealand, there is a propensity toward the UV-driven form (31 of 107, 29% virus positive). Using archival formalin-fixed, paraffin-embedded tissues, we report targeted DNA sequencing covering 246 cancer genes on 71 tumor tissues and 38 nonmalignant tissues from 37 individuals, with 33 of 37 being negative for the virus. Somatic variants of New Zealand virus-negative Merkel cell carcinomas partially overlapped with those reported overseas, including TP53 variants in all tumors and RB1, LRP1B, NOTCH1, and EPHA3/7 variants each found in over half of the cohort. Variants in genes not analyzed or reported in previous studies were also found. Cataloging variants in TP53 and RB1 from published datasets revealed a broad distribution across these genes. Chr 1p gain and Chr 3p loss were identified in around 50% of New Zealand virus-negative Merkel cell carcinomas, and RB1 loss of heterozygosity was found in 90% of cases. Copy number variants accumulate in most metastases. Virus-negative Merkel cell carcinomas have complex combinations of somatic DNA-sequence variants and copy number variants. They likely carry the small genomic changes permissive for metastasis from early tumor development; however, chromosomal alterations may contribute to driving metastatic progression.

Electroencephalographic (EEG) Biomarkers in Genetic Neurodevelopmental Disorders

Collectively, neurodevelopmental disorders are highly prevalent, but more than a third of neurodevelopmental disorders have an identifiable genetic etiology, each of which is individually rare. The genes associated with neurodevelopmental disorders are often involved in early brain development, neuronal signaling, or synaptic plasticity. Novel treatments for many genetic neurodevelopmental disorders are being developed, but disease-relevant clinical outcome assessments and biomarkers are limited. Electroencephalography (EEG) is a promising noninvasive potential biomarker of brain function. It has been used extensively in epileptic disorders, but its application in neurodevelopmental disorders needs further investigation. In this review, we explore the use of EEG in 3 of the most prevalent genetic neurodevelopmental disorders-Angelman syndrome, Rett syndrome, and fragile X syndrome. Quantitative analyses of EEGs, such as power spectral analysis or measures of connectivity, can quantify EEG signatures seen on qualitative review and potentially correlate with phenotypes. In both Angelman syndrome and Rett syndrome, increased delta power on spectral analysis has correlated with clinical markers of disease severity including developmental disability and seizure burden, whereas spectral power analysis on EEG in fragile X syndrome tends to demonstrate abnormalities in gamma power. Further studies are needed to establish reliable relationships between quantitative EEG biomarkers and clinical phenotypes in rare genetic neurodevelopmental disorders.

A Case of Multivessel Coronary Artery Disease and Anomalous Origin of the Right Coronary Artery With a Malignant Course Presenting With Non-exertional Chest Discomfort and Brugada Phenocopy

Coronary artery anomalies (CAAs) are an uncommon cause of chest pain in the younger population. Misdiagnosis can be detrimental and lead to sudden cardiac deaths. We present a 62-year-old male with a past medical history significant for chest pain history with a workup in 2001 presumed to be non-cardiac in origin from bronchial asthma. He presented from a Micronesian Island for the evaluation of non-exertional chest discomfort. Further workup showed a Brugada type I pattern on ECG and ST wave depressions on anterolateral and inferior leads with associated AVR elevation on exercise stress testing. Further ischemic workup with coronary angiography revealed right dominant circulation with three-vessel coronary artery disease (CAD), including mid-left anterior descending (LAD) artery chronic total occlusion (CTO) with the right to left collaterals, left circumflex, and right coronary artery (RCA) with the accompanied anomalous origin of RCA. The patient underwent surgical correction of the anomalous RCA and coronary artery bypass grafting for the multi-vessel CAD. CAAs are usually found incidentally during ischemic workups similar to this case. Patients with CAAs can be managed conservatively with caution regarding physical activity. However, high-risk patients will warrant surgical treatment to avoid sudden cardiac death. The diagnosis of CAAs can be challenging and prone to misdiagnosis and maltreatment. It may be beneficial to pursue this in younger patients with ischemia-like symptoms. Further studies should be performed to identify the true incidence and guide medical practitioners regarding the risks, costs, and benefits of diagnosing and surgically treating CAAs in the general population.

Complex patterns of genomic heterogeneity identified in 42 tumor samples and ctDNA of a pulmonary atypical carcinoid patient

Tumor evolution underlies many challenges facing precision oncology, and improving our understanding has the potential to improve clinical care. This study represents a rare opportunity to study tumor heterogeneity and evolution in a patient with an understudied cancer type. A patient with pulmonary atypical carcinoid, a neuroendocrine tumor, metastatic to 90 sites, requested and consented to donate tissues for research. 42 tumor samples collected at rapid autopsy from 14 anatomically distinct sites were analyzed through DNA whole-exome sequencing and RNA-Seq, and five analyzed through linked-read sequencing. Targeted DNA sequencing was completed on two clinical tissue biopsies and one blood plasma sample. Chromosomal alterations and gene variants accumulated over time, and specific chromosomal alterations preceded the single predicted gene driver variant (ARID1A). At the time of autopsy, all sites shared the gain of one copy of Chr 5, loss of one copy of Chr 6 and 21, chromothripsis of one copy of Chr 11, and 39 small variants. Two tumor clones (carrying additional variants) were detected at metastatic sites, and occasionally in different regions of the same organ (e.g., within the pancreas). Circulating tumor DNA (ctDNA) sequencing detected shared tumor variants in the blood plasma and captured marked genomic heterogeneity, including all metastatic clones but few private tumor variants. This study describes genomic tumor evolution and dissemination of a pulmonary atypical carcinoid donated by a single generous patient. It highlights the critical role of chromosomal alterations in tumor initiation and explores the potential of ctDNA analysis to represent genomically heterogeneous disease.

Performance of Society of Thoracic Surgeons and EuroSCORE II pre-surgical mortality risk score for cardiac surgery in a large majority-minority population

Background

Pre-surgical mortality risk scores are important tools for pre-operative assessment. The Society of Thoracic Surgeons (STS) and EuroSCORE II (ES) scores were derived from predominantly white populations; their utility in minority populations is understudied.

Purpose

To compare the performance of STS and ES in a large majority-majority population.

Methods

We used cardiac surgery registry data from a tertiary care, 500-bed, university-affiliated hospital. For each patient, STS and ES risk of mortality were calculated. We measured model performance by discrimination (ROC-AUC) and calibration (O/E ratios). We compared performance by racial subgroups, and explored differences in risk stratification by race and risk category by measuring risk reclassification if ES were used instead of STS.

Results

From 2009–20, 4061 patients underwent CABG (68%), valve (18%), or CABG/valve (7%) surgery. Of these, 51% were Asian (n=2076), 24% Native Hawaiian and other Pacific Islander (NHPI) (n=977), 23% White (n=919) and 3% Other (n=79). Overall, STS underestimated (O/E: 1.09) and ES overestimated (O/E: 0.55) mortality risk. STS had better discrimination (ROC-AUC: 0.83 vs 0.77). STS model calibration was better among Asians (O/E: 1.03) than NHPI (O/E: 1.22) and Whites (O/E: 1.14). ES calibration was poor overall (Asian O/E: 0.58, NHPI O/E: 0.54, White O/E: 0.50). Discrimination was similar in STS (Asian AUC: 0.83, NHPI AUC: 0.85, White AUC: 0.86) and ES (Asian AUC: 0.77, NHPI AUC: 0.77, White AUC: 0.81), although it did perform better for White patients. Of patients defined as Low Risk by STS, 31% were reclassified as Intermediate or High Risk by ES. Of patients defined as High Risk by STS, 27% were downgraded to Intermediate or Low Risk by ES. This differed by race. For Asians, 28% at Low Risk and 31% at High Risk by STS were reclassified when using ES. For NHPI, 36% at Low Risk and 22% of High Risk by STS were reclassified by ES. For Whites, 31% at Low Risk and 19% of High Risk by STS were reclassified by ES.

Conclusion

The choice of pre-surgical risk score can impact estimates of pre-cardiac surgery risk of mortality. While STS performs better than ES in our majority minority population, there are significant differences by race.

Funding Acknowledgement

Type of funding sources: None.

Innate immune checkpoint inhibitor resistance is associated with melanoma sub-types exhibiting invasive and de-differentiated gene expression signatures

Melanoma is a highly aggressive skin cancer, which, although highly immunogenic, frequently escapes the body’s immune defences. Immune checkpoint inhibitors (ICI), such as anti-PD1, anti-PDL1, and anti-CTLA4 antibodies lead to reactivation of immune pathways, promoting rejection of melanoma. However, the benefits of ICI therapy remain limited to a relatively small proportion of patients who do not exhibit ICI resistance. Moreover, the precise mechanisms underlying innate and acquired ICI resistance remain unclear. Here, we have investigated differences in melanoma tissues in responder and non-responder patients to anti-PD1 therapy in terms of tumour and immune cell gene-associated signatures. We performed multi-omics investigations on melanoma tumour tissues, which were collected from patients before starting treatment with anti-PD1 immune checkpoint inhibitors. Patients were subsequently categorized into responders and non-responders to anti-PD1 therapy based on RECIST criteria. Multi-omics analyses included RNA-Seq and NanoString analysis. From RNA-Seq data we carried out HLA phenotyping as well as gene enrichment analysis, pathway enrichment analysis and immune cell deconvolution studies. Consistent with previous studies, our data showed that responders to anti-PD1 therapy had higher immune scores (median immune score for responders = 0.1335, median immune score for non-responders = 0.05426, p-value = 0.01, Mann-Whitney U two-tailed exact test) compared to the non-responders. Responder melanomas were more highly enriched with a combination of CD8+ T cells, dendritic cells (p-value = 0.03) and an M1 subtype of macrophages (p-value = 0.001). In addition, melanomas from responder patients exhibited a more differentiated gene expression pattern, with high proliferative- and low invasive-associated gene expression signatures, whereas tumours from non-responders exhibited high invasive- and frequently neural crest-like cell type gene expression signatures. Our findings suggest that non-responder melanomas to anti-PD1 therapy exhibit a de-differentiated gene expression signature, associated with poorer immune cell infiltration, which establishes a gene expression pattern characteristic of innate resistance to anti-PD1 therapy. Improved understanding of tumour-intrinsic gene expression patterns associated with response to anti-PD1 therapy will help to identify predictive biomarkers of ICI response and may help to identify new targets for anticancer treatment, especially with a capacity to function as adjuvants to improve ICI outcomes.

The Utility of Acid-Fast Bacillus (AFB) and Fungal Cultures in Orthopaedic Infections

Introduction

When diagnosing suspected orthopaedic-related infections, fungal and acid-fast bacilli (AFB) cultures are often obtained intraoperatively. These cultures are difficult and time-consuming to grow and increase healthcare costs. This study aimed to quantify the rate of positive AFB and fungal cultures in orthopaedic infections and to compare potential risk factors for a positive result. 

Methods

Orthopaedic surgical cases for suspected infection at one institution from March 2013 through December 2019 were included. Data were collected on patient demographics and procedure characteristics for patients with surgical AFB or fungal lab tests ordered on the day of surgery.

Results

Of the 813 patients for whom intraoperative AFB or fungal cultures were ordered, 3.8% (N=31) had a positive result. Of the 31 positive results, 30 were from fungal cultures and one was from AFB cultures. Patients with a positive versus negative culture result did not differ significantly by age, sex, American Society of Anesthesiologists (ASA) score, diabetes, obesity, or HIV/AIDS. In both unadjusted and adjusted analyses, peripheral vascular disease (PVD) was associated with higher odds of a positive fungal culture result (adjusted OR (aOR)=3.5, 95%CI=1.3-8.4). Likewise, in both unadjusted and adjusted models, a hand/foot operating region was associated with higher odds of a positive fungal culture result compared with all other regions (aOR=4.2, 95%CI=1.9-9.8).

Conclusion

Intraoperative fungal and AFB cultures may not need to be obtained except in orthopaedic surgical cases for hand or foot infections or in patients with PVD.

A large beam high efficiency radio frequency neutron spin flipper

A design for a radio frequency (RF) neutron spin flipper obtained from magneto-static and neutron spin transport simulations is presented. The RF flipper constructed from this design provides a flipping probability of 0.999 or better for a beam size 6 cm wide and 15 cm high and a wavelength band between 0.4 and 0.6 nm. Three permanent magnet guide field sections with air gaps provide a linear field gradient along the beam propagation direction over a large cross-sectional area. An RF oscillator based on coupling the resonant coil of a Hartley oscillator to the excitation coil was developed, which provides a higher current and, thereby, a larger RF amplitude, as compared to a conventional RF power amplifier. Two opaque He3 neutron spin filters were employed to measure the flipping probability of the flipper with very high precision. A spatially uniform flipping probability of 0.9995(2) or higher was measured over the large cross-sectional area neutron guide. This RF neutron spin flipper will be employed in a polychromatic beam reflectometer at the National Institute of Standards and Technology Center for Neutron Research. This design can be applied to other polarized neutron instruments or applications requiring a very high continuous flipping probability of the neutron spin for a large cross-sectional area beam.

Genomic and signalling pathway characterization of the NZM panel of melanoma cell lines: A valuable model for studying the impact of genetic diversity in melanoma

Melanoma is a disease associated with a very high mutation burden and thus the possibility of a diverse range of oncogenic mechanisms that allow it to evade therapeutic interventions and the immune system. Here, we describe the characterization of a panel of 102 cell lines from metastatic melanomas (the NZM lines), including using whole‐exome and RNA sequencing to analyse genetic variants and gene expression changes in a subset of this panel. Lines possessing all major melanoma genotypes were identified, and hierarchical clustering of gene expression profiles revealed four broad subgroups of cell lines. Immunogenotyping identified a range of HLA haplotypes as well as expression of neoantigens and cancer–testis antigens in the lines. Together, these characteristics make the NZM panel a valuable resource for cell‐based, immunological and xenograft studies to better understand the diversity of melanoma biology and the responses of melanoma to therapeutic interventions.

Sub-millisecond time-resolved small-angle neutron scattering measurements at NIST

Instrumentation for time-resolved small-angle neutron scattering measurements with sub-millisecond time resolution, based on Gähler's TISANE (time-involved small-angle neutron experiments) concept, is in operation at NIST's Center for Neutron Research. This implementation of the technique includes novel electronics for synchronizing the neutron pulses from high-speed counter-rotating choppers with a periodic stimulus applied to a sample. Instrumentation details are described along with measurements demonstrating the utility of the technique for elucidating the reorientation dynamics of anisometric magnetic particles.

Accessing a New Dimension in TP53 Biology: Multiplex Long Amplicon Digital PCR to Specifically Detect and Quantitate Individual TP53 Transcripts

TP53, the most commonly-mutated gene in cancer, undergoes complex alternative splicing. Different TP53 transcripts play different biological roles, both in normal function and in the progression of diseases such as cancer. The study of TP53’s alternative RNA splice forms and their use as clinical biomarkers has been hampered by limited specificity and quantitative accuracy of current methods. TP53 RNA splice variants differ at both 5’ and 3’ ends, but because they have a common central region of 618 bp, the individual TP53 transcripts are impossible to specifically detect and precisely quantitate using standard PCR-based methods or short-read RNA sequencing. Therefore, we devised multiplex probe-based long amplicon droplet digital PCR (ddPCR) assays, which for the first time allow precise end-to-end quantitation of the seven major TP53 transcripts, with amplicons ranging from 0.85 to 1.85 kb. Multiple modifications to standard ddPCR assay procedures were required to enable specific co-amplification of these long transcripts and to overcome issues with secondary structure. Using these assays, we show that several TP53 transcripts are co-expressed in breast cancers, and illustrate the potential for this method to identify novel TP53 transcripts in tumour cells. This capability will facilitate a new level of biological and clinical understanding of the alternatively-spliced TP53 isoforms.

6LiF:ZnS(Ag) Neutron Detector Performance Optimized Using Waveform Recordings and ROC Curves

We used Gaussian separation and receiver operating characteristic (ROC) curves to optimize the neutron sensitivity and gamma rejection of an ultra-thin ⁶LiF:ZnS(Ag)-scintillator-based neutron detector paired with a silicon photomultiplier (SiPM). We recorded the waveforms while operating the detector in a monochromatic cold neutron beam and in the presence of isotopic ¹³⁷Cs and ⁶⁰Co gamma sources. We used a two-window charge comparison (CC) pulse-shape discrimination (PSD) technique to distinguish the neutron capture events from other types of signals. By feeding the recorded waveforms through variants of this algorithm, it was possible to optimize the duration of the integration windows [(0-100 ns) for the prompt window and (100-2300 ns)] for the delayed window. We then computed the detector's ROC curve from waveform recordings and compared that with the experimental performance. We also used this procedure to compare a series of detector configurations to select the optimal bias voltage for the SiPM photosensor.

Osteoid Osteoma in the Thumb of an Adolescent Patient

Osteoid osteoma is a relatively common benign tumor of bone, typically presenting in the diaphysis of long bones during the second or third decades of life. This tumor is rarely reported in the hand and wrist, making up only approximately 10% of cases. When reported in the hand, osteoid osteoma tends to occur more frequently in the proximal phalanx of the index and middle fingers. We present the case of an osteoid osteoma in an adolescent male in the distal phalanx of the thumb. The presentation of this osteoid osteoma was atypical owing to its location and lack of characteristic clinical features, making the initial work-up and final diagnosis challenging and pointing to the importance of considering this diagnosis on a differential for painful bony tumors in the hand.

Functional CRISPR and shRNA Screens Identify Involvement of Mitochondrial Electron Transport in the Activation of Evofosfamide

Evofosfamide (TH-302) is a hypoxia-activated DNA-crosslinking prodrug currently in clinical development for cancer therapy. Oxygen-sensitive activation of evofosfamide depends on one-electron reduction, yet the reductases that catalyze this process in tumors are unknown. We used RNA sequencing, whole-genome CRISPR knockout, and reductase-focused short hairpin RNA screens to interrogate modifiers of evofosfamide activation in cancer cell lines. Involvement of mitochondrial electron transport in the activation of evofosfamide and the related nitroaromatic compounds EF5 and FSL-61 was investigated using 143B ρ ⁰ (ρ zero) cells devoid of mitochondrial DNA and biochemical assays in UT-SCC-74B cells. The potency of evofosfamide in 30 genetically diverse cancer cell lines correlated with the expression of genes involved in mitochondrial electron transfer. A whole-genome CRISPR screen in KBM-7 cells identified the DNA damage-response factors SLX4IP, C10orf90 (FATS), and SLFN11, in addition to the key regulator of mitochondrial function, YME1L1, and several complex I constituents as modifiers of evofosfamide sensitivity. A reductase-focused shRNA screen in UT-SCC-74B cells similarly identified mitochondrial respiratory chain factors. Surprisingly, 143B ρ ⁰ cells showed enhanced evofosfamide activation and sensitivity but had global transcriptional changes, including increased expression of nonmitochondrial flavoreductases. In UT-SCC-74B cells, evofosfamide oxidized cytochromes a, b, and c and inhibited respiration at complexes I, II, and IV without quenching reactive oxygen species production. Our results suggest that the mitochondrial electron transport chain contributes to evofosfamide activation and that predicting evofosfamide sensitivity in patients by measuring the expression of canonical bioreductive enzymes such as cytochrome P450 oxidoreductase is likely to be futile.

Extracellular RNA Profile in Mesenteric Lymph from Exemplar Rat Models of Acute and Critical Illness

Background: Mesenteric lymph (ML) has been implicated in the development of multiple organ dysfunction syndrome in critical illness. Extracellular RNAs play a role in cell-to-cell communication during physiological and disease processes but they are rarely studied in ML. We aimed at examining the RNA profiles of peripheral plasma, ML, and ML's extracellular vesicle (ML-EV) and triglyceride-rich lipoprotein (ML-TRL) fractions, obtained from rodent models of critical illness. Methods and Results: We collected ML for 5 hours from rodent models of critical illness [Acute Pancreatitis, Cecal Ligation and Incision (CLI), Gut Ischemia-Reperfusion (IR)] and matching Sham control rats. ML-EV and ML-TRL fractions were also isolated. RNA sequencing was performed on the RNA extracted from ML, ML-EV, ML-TRL, and plasma by using the Ion Torrent Personal Genome Machine platform. RNA sequences were searched using the Basic Local Alignment Search Tool against rat genome and RefSeq, microRNA (miRNA), genomic tRNA, functional RNA, and Genbank nucleotide databases, and the read counts were analyzed. Each sample type had a distinct RNA profile. ML contained more RNA per volume and a larger proportion of tRNA fragments than plasma. ML-EVs were enriched with miRNA, whereas ML-TRLs contained low absolute amounts of RNA. The RNA size profiles for CLI and Gut IR were different from Sham. ML carried intestinal RNAs and in a CLI model it was significantly enriched with bacterial RNA sequences. Conclusions: We found the distinct but diverse RNA profiles of ML and its compartments, and their different profiles in critical illness. Intestinal-derived small RNAs in ML may have a direct role in critical illness and utility as potential biomarkers.

Cooperative Charging Effects of Fibers from Electrospinning of Electrically Dissimilar Polymers

Electrical charging and residual charge decay of electro-spun nonwoven webs comprised of two electrically dissimilar polymers were studied in an effort to investigate their filtration properties. Polystyrene (PS) and polyacrylonitrile (PAN) were electrospun separately, in a layer-by-layer configuration and simultaneously in a side-by-side bi-component apparatus into thin webs on a polypropylene spunbond substrate. During electrospinning of the PS and PAN polymer solutions, the fibers became positively charged when positive voltage was applied to the solution-filled spinning nozzle and became negatively charged when negative voltage was applied. This study was undertaken to examine the effect of cooperative charging from electrospinning of the two polymers, the effect of the three types of web constructions on charge retention, and filtration properties of the fibers. It was found that single, multilayered, and bi-component webs retained surface charges in the thousands of volts that diminished very little over a 20-hour period, but eventually bled off while resting for three months. Filtration properties were found to be exceptionally high for some, but not all, electrospun samples; filtration was found to have a weak dependence on both surface charge and web geometrical factors, particularly the fiber diameter, that influence pressure drop of the aerosol test.

The role of DNA methylation in human trophoblast differentiation

The placenta is a vital fetal exchange organ connecting mother and baby. Specialised placental epithelial cells, called trophoblasts, are essential for adequate placental function. Trophoblasts transform the maternal vasculature to allow efficient blood flow to the placenta and facilitate adequate nutrient uptake. Placental development is in part regulated by epigenetic mechanisms. However, our understanding of how DNA methylation contributes to human trophoblast differentiation is limited. To better understand how genome-wide methylation differences affect trophoblast differentiation, reduced representation bisulfite sequencing (RRBS) was conducted on four matched sets of trophoblasts; side-population trophoblasts (a candidate human trophoblast stem cell population), cytotrophoblasts (an intermediate progenitor population), and extravillous trophoblasts (EVT, a terminally differentiated population) each isolated from the same first trimester placenta. Each trophoblast population had a distinct methylome. In line with their close differentiation relationship, the methylation profile of side-population trophoblasts was most similar to cytotrophoblasts, whilst EVT had the most distinct methylome. In comparison to mature trophoblast populations, side-population trophoblasts exhibited differential methylation of genes and miRNAs involved in cell cycle regulation, differentiation, and regulation of pluripotency. A combined methylomic and transcriptomic approach was taken to better understand cytotrophoblast differentiation to EVT. This revealed methylation of 41 genes involved in epithelial to mesenchymal transition and metastatic cancer pathways, which likely contributes to the acquisition of an invasive EVT phenotype. However, the methylation status of a gene did not always predict gene expression. Therefore, while CpG methylation plays a role in trophoblast differentiation, it is likely not the only regulatory mechanism involved in this process.

TLR3 agonism re-establishes CNS immune competence during α4-integrin deficiency

OBJECTIVE

Natalizumab blocks α4-integrin-mediated leukocyte migration into the central nervous system (CNS). It diminishes disease activity in multiple sclerosis (MS), but carries a high risk of progressive multifocal encephalopathy (PML), an opportunistic infection with JV virus that may be prompted by diminished CNS immune surveillance. The initial host response to viral infections entails the synthesis of type I interferons (IFN) upon engagement of TLR3 receptors. We hypothesized that TLR3 agonism reestablishes CNS immune competence in the setting of α4-integrin deficiency.

METHOD

We generated the conditional knock out mouse strain Mx1.Cre+ α4-integrinfl/fl, in which the α4-integrin gene is ablated upon treatment with the TLR3 agonist poly I:C. Adoptive transfer of purified lymphocytes from poly I:C-treated Mx1.Cre+ α4-integrinfl/fl donors into naive recipients recapitulates immunosuppression under natalizumab. Active experimental autoimmune encephalomyelitis (EAE) in Mx1.Cre+ α4-integrinfl/fl mice treated with poly I:C represents immune-reconstitution.

RESULTS

Adoptive transfer of T cells from poly I:C treated Mx1.Cre+ α4-integrinfl/fl mice causes minimal EAE. The in vitro migratory capability of CD45+ splenocytes from these mice is reduced. In contrast, actively-induced EAE after poly I:C treatment results in full disease susceptibility of Mx1.Cre+ α4-integrinfl/fl mice, and the number and composition of CNS leukocytes is similar to controls. Extravasation of Evans Blue indicates a compromised blood-brain barrier. Poly I:C treatment results in a 2-fold increase in IFN β transcription in the spinal cord.

INTERPRETATION

Our data suggest that TLR3 agonism in the setting of relative α4-integrin deficiency can reestablish CNS immune surveillance in an experimental model. This pathway may present a feasible treatment strategy to treat and prevent PML under natalizumab therapy and should be considered for further experimental evaluation in a controlled setting.

Reply to 'Dissimilarity measures affected by richness differences yield biased delimitations of biogeographic realms'

Recently, we classified the oceans into 30 biogeographic realms based on species' endemicity. Castro-Insua et al. criticize the choices of dissimilarity coefficients and clustering approaches used in our paper, and reanalyse the data using alternative techniques. Here, we explain how the approaches used in our original paper yield results in line with existing biogeographical knowledge and are robust to alternative methods of analysis. We also repeat the analysis using several similarity coefficients and clustering algorithms, and a neural network theory method. Although each combination of methods produces outputs differing in detail, the overall pattern of realms is similar. The coarse nature of the present boundaries of the realms reflects the limited field data but may be improved with additional data and mapping to environmental variables.

Evofosfamide for the treatment of human papillomavirus-negative head and neck squamous cell carcinoma

Evofosfamide (TH-302) is a clinical-stage hypoxia-activated prodrug of a DNA-crosslinking nitrogen mustard that has potential utility for human papillomavirus (HPV) negative head and neck squamous cell carcinoma (HNSCC), in which tumor hypoxia limits treatment outcome. We report the preclinical efficacy, target engagement, preliminary predictive biomarkers and initial clinical activity of evofosfamide for HPV-negative HNSCC. Evofosfamide was assessed in 22 genomically characterized cell lines and 7 cell line-derived xenograft (CDX), patient-derived xenograft (PDX), orthotopic, and syngeneic tumor models. Biomarker analysis used RNA sequencing, whole-exome sequencing, and whole-genome CRISPR knockout screens. Five advanced/metastatic HNSCC patients received evofosfamide monotherapy (480 mg/m2 qw × 3 each month) in a phase 2 study. Evofosfamide was potent and highly selective for hypoxic HNSCC cells. Proliferative rate was a predominant evofosfamide sensitivity determinant and a proliferation metagene correlated with activity in CDX models. Evofosfamide showed efficacy as monotherapy and with radiotherapy in PDX models, augmented CTLA-4 blockade in syngeneic tumors, and reduced hypoxia in nodes disseminated from an orthotopic model. Of 5 advanced HNSCC patients treated with evofosfamide, 2 showed partial responses while 3 had stable disease. In conclusion, evofosfamide shows promising efficacy in aggressive HPV-negative HNSCC, with predictive biomarkers in development to support further clinical evaluation in this indication.

Human trophoblasts are primarily distinguished from somatic cells by differences in the pattern rather than the degree of global CpG methylation

The placenta is a fetal exchange organ connecting mother and baby that facilitates fetal growth in utero. DNA methylation is thought to impact placental development and function. Global DNA methylation studies using human placental lysates suggest that the placenta is uniquely hypomethylated compared to somatic tissue lysates, and this hypomethylation is thought to be important in conserving the unique placental gene expression patterns required for successful function. In the placental field, methylation has frequently been examined in tissue lysates, which contain mixed cell types that can confound results. To better understand how DNA methylation influences placentation, DNA from isolated first trimester trophoblast populations underwent reduced representation bisulfite sequencing and was compared to publicly available data of blastocyst-derived and somatic cell populations. First, this revealed that, unlike murine blastocysts, human trophectoderm and inner cell mass samples did not have significantly different levels of global methylation. Second, our work suggests that differences in global CpG methylation between trophoblasts and somatic cells are much smaller than previously reported. Rather, our findings suggest that different patterns of CpG methylation may be more important in epigenetically distinguishing the placenta from somatic cell populations, and these patterns of methylation may contribute to successful placental/trophoblast function.

Summary: The placenta may not be as uniquely hypomethylated as previously reported, rather differences in the pattern of CpG methylation are what make it epigenetically distinct.

Differential Changes in Gut Microbiota After Gastric Bypass and Sleeve Gastrectomy Bariatric Surgery Vary According to Diabetes Remission

BACKGROUND

It is unclear whether specific gut microbiota is associated with remission of type 2 diabetes (T2D) after distinct types of bariatric surgery.

AIMS

The aim of this study is to examine gut microbiota changes after laparoscopic Roux-en-Y gastric bypass (RYGB) or sleeve gastrectomy (SG) surgery in obese patients with T2D.

METHODS

Whole-metagenome shotgun sequencing of DNA fragments using Illumina HiSeq2000 was obtained from stool samples collected from 14 obese T2D patients pre-operatively (while on very low calorie diet) and 1 year after randomisation to laparoscopic SG (n = 7) or RYGB (n = 7). Resulting shotgun reads were annotated with Kyoto Encyclopedia of Genes and Genomes (KEGG).

RESULTS

Body weight reduction and dietary change was similar 1 year after both surgery types. Identical proportions (n = 5/7) achieved diabetes remission (HbA1c < 48 mmol/mol without medications) 1 year after RYGB and SG. RYGB resulted in increased Firmicutes and Actinobacteria phyla but decreased Bacteroidetes phyla. SG resulted in increased Bacteroidetes phyla. Only an increase in Roseburia species was observed among those achieving diabetes remission, common to both surgery types. KEGG Orthology and pathway analysis predicted contrasting and greater gut microbiota metabolism changes after diabetes remission following RYGB than after SG. Those with persistent diabetes post-operatively had higher Desulfovibrio species pre-operatively.

CONCLUSIONS

Overall, RYGB produces greater and more predicted favourable changes in gut microbiota functional capacity than SG. An increase in Roseburia species was the only compositional change common to both types of surgery among those achieving diabetes remission.

Placental trophoblast debris mediated feto-maternal signalling via small RNA delivery: implications for preeclampsia

To profile the small RNA cargo carried by trophoblast debris derived from the placenta during normal and preeclamptic pregnancies and to determine whether trophoblast debris can deliver its small RNAs to endothelial cells with functional consequences. We confirmed that trophoblast debris can deliver its small RNAs contents to recipient endothelial cells during the co-culture. Next generation sequencing was employed to profile the small RNA contents in both normotensive and preeclamptic trophoblast debris. We identified 1278 mature miRNAs and 2646 non-miRNA small RNA fragments contained. Differential expression analysis identified 16 miRNAs (including miR-145), 5 tRNA fragments from 3 different tRNAs, 13 snRNA fragments and 85 rRNA fragments that were present in different levels between preeclamptic and normotensive trophoblast debris. We loaded a miR-145 mimic into normotensive trophoblast debris via transfection of placental explants from which the debris was derived and found the miR-145 loaded debris induced transcriptomic changes in endothelial cells similar to those induced by preeclamptic trophoblast debris. Trophoblast debris deported into maternal circulation can deliver its small RNA contents to maternal cells thereby contributing to feto-maternal communication. Small RNAs that are dysregulated in preeclamptic trophoblast debris might contribute to the endothelial cell activation which is a hallmark of preeclampsia.

Abstract 169: Preclinical efficacy and sensitivity determinants of evofosfamide in molecularly defined models of head and neck squamous cell carcinoma

Tumor hypoxia is prevalent in head and neck squamous cell carcinoma (HNSCC), where it limits radiotherapy outcomes. Hypoxia-activated prodrugs (HAPs) have been developed to target hypoxic regions of tumors. These agents undergo oxygen-sensitive reductive activation, thereby delivering cytotoxic species within hypoxic cells. This study investigated the efficacy and sensitivity determinants of the clinical-stage HAP evofosfamide (TH-302) using molecularly-characterized models of HNSCC. We deployed a collection of 27 HPV-negative HNSCC cell lines derived from lesions of varying TNM stages and primary, nodal or recurrent sites. The collection was characterized for gene expression by RNA-seq, from which somatic variants were also called. Their transcriptomic features were investigated in the context of pan-cancer TCGA data by hierarchical clustering. The potency and hypoxic selectivity of 3 HAPs - evofosfamide, PR-104A and SN30000 - were assessed by antiproliferative assay in 22 lines and compared to bromo-isophosphoramide mustard (Br-IPM), cisplatin and 5-FU. The antitumor activity of evofosfamide (50 mg/kg qdx5 for 2-3 cycles with or without a single 10 Gy dose of radiation on day 5 of cycle 1) was evaluated in HNSCC xenografts in addition to a PDX isolated from an SCC of the glottic larynx. The hypoxic fraction at baseline and after 5 days of treatment was quantified by pimonidazole staining. Genetic modifiers of sensitivity to evofosfamide and its cytotoxic metabolite Br-IPM were explored through whole-genome CRISPR-Cas9 screens using the GeCKO v2 library. High-throughput screens with a custom shRNA pool were performed in one HNSCC and two pancreatic ductal adenocarcinoma cell lines to identify reductases responsible for the activation of evofosfamide in hypoxic cells. Evofosfamide was more potent and more selective for hypoxic HNSCC cells in vitro than PR-104A or SN30000. Cell line sensitivity to evofosfamide was correlated with Br-IPM and cisplatin but not with PR-104A, SN30000 or 5-FU, indicating distinct sensitivity determinants. Evidence of antitumor activity with evofosfamide was observed in vivo. CRISPR screens identified potential evofosfamide sensitivity genes that were reproducibly enriched following drug exposure. Reductase-focused RNA interference screens defined a cluster of sensitivity genes that mapped to mitochondrial electron transport, whereas shRNA’s targeted against presumed activating enzymes such as POR were not enriched. Concentration-dependent oxidation of cytochrome a and decreased respiration was observed in cells exposed to evofosfamide, suggesting reduction by mitochondrial complexes. This study provides a rationale for the clinical evaluation of evofosfamide with radiotherapy in genetically defined subsets of HNSCC patients.

Citation Format: Francis W. Hunter, Avik Shome, Dan Li, Way W. Wong, Peter Tsai, Nooriyah Poonawala, Purvi M. Kakadiya, Troy M. Ketelä, Maria K. Kondratyev, Courtney R. Lynch, Tet-Woo Lee, Khanh B. Tran, Jules B. Devaux, Rachel Zussman, Cho R. Hong, Dennis Kee, Andrew M. Macann, Anthony J. Hickey, Stefan K. Bohlander, Cristin G. Print, William R. Wilson, Bradly G. Wouters, Stephen M. Jamieson. Preclinical efficacy and sensitivity determinants of evofosfamide in molecularly defined models of head and neck squamous cell carcinoma [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 169. doi:10.1158/1538-7445.AM2017-169

A Study of TP53 RNA Splicing Illustrates Pitfalls of RNA-seq Methodology

TP53 undergoes multiple RNA-splicing events, resulting in at least nine mRNA transcripts encoding at least 12 functionally different protein isoforms. Antibodies specific to p53 protein isoforms have proven difficult to develop, thus researchers must rely on the transcript information to infer isoform abundance. In this study, we used deep RNA-seq, droplet digital PCR (ddPCR), and real-time quantitative reverse transcriptase PCR (RT-qPCR) from nine human cell lines and RNA-seq data available for tumors in The Cancer Genome Atlas to analyze TP53 splice variant expression. All three methods detected expression of the FL/40TP53α_T1 variant in most human tumors and cell lines. However, other less abundant variants were only detected with PCR-based methods. Using RNA-seq simulation analysis, we determined why RNA-seq is unable to detect less abundant TP53 transcripts and discuss the implications of these findings for the general interpretation of RNA-seq data. Cancer Res; 76(24); 7151-9. ©2016 AACR.

The in vitro and in vivo effects of constitutive light expression on a bioluminescent strain of the mouse enteropathogen Citrobacter rodentium

Bioluminescent reporter genes, such as those from fireflies and bacteria, let researchers use light production as a non-invasive and non-destructive surrogate measure of microbial numbers in a wide variety of environments. As bioluminescence needs microbial metabolites, tagging microorganisms with luciferases means only live metabolically active cells are detected. Despite the wide use of bioluminescent reporter genes, very little is known about the impact of continuous (also called constitutive) light expression on tagged bacteria. We have previously made a bioluminescent strain of Citrobacter rodentium, a bacterium which infects laboratory mice in a similar way to how enteropathogenic Escherichia coli (EPEC) and enterohaemorrhagic E. coli (EHEC) infect humans. In this study, we compared the growth of the bioluminescent C. rodentium strain ICC180 with its non-bioluminescent parent (strain ICC169) in a wide variety of environments. To understand more about the metabolic burden of expressing light, we also compared the growth profiles of the two strains under approximately 2,000 different conditions. We found that constitutive light expression in ICC180 was near-neutral in almost every non-toxic environment tested. However, we also found that the non-bioluminescent parent strain has a competitive advantage over ICC180 during infection of adult mice, although this was not enough for ICC180 to be completely outcompeted. In conclusion, our data suggest that constitutive light expression is not metabolically costly to C. rodentium and supports the view that bioluminescent versions of microbes can be used as a substitute for their non-bioluminescent parents to study bacterial behaviour in a wide variety of environments.