Carbon dioxide shapes parasite-host interactions in a human-infective nematode

Skin-penetrating nematodes infect nearly one billion people worldwide. The developmentally arrested infective larvae (iL3s) seek out hosts, invade hosts via skin penetration, and resume development inside the host in a process called activation. Activated infective larvae (iL3as) traverse the host body, ending up as parasitic adults in the small intestine. Skin-penetrating nematodes respond to many chemosensory cues, but how chemosensation contributes to host seeking, intra-host development, and intra-host navigation - three crucial steps of the parasite-host interaction - remains poorly understood. Here, we investigate the role of carbon dioxide (CO2) in promoting parasite-host interactions in the human-infective threadworm Strongyloides stercoralis. We show that S. stercoralis exhibits life-stage-specific preferences for CO2: iL3s are repelled, non-infective larvae and adults are neutral, and iL3as are attracted. CO2 repulsion in iL3s may prime them for host seeking by stimulating dispersal from host feces, while CO2 attraction in iL3as may direct worms toward high-CO2 areas of the body such as the lungs and intestine. We also identify sensory neurons that detect CO2; these neurons are depolarized by CO2 in iL3s and iL3as. In addition, we demonstrate that the receptor guanylate cyclase Ss-GCY-9 is expressed specifically in CO2-sensing neurons and is required for CO2-evoked behavior. Ss-GCY-9 also promotes activation, indicating that a single receptor can mediate both behavioral and physiological responses to CO2. Our results illuminate chemosensory mechanisms that shape the interaction between parasitic nematodes and their human hosts and may aid in the design of novel anthelmintics that target the CO2-sensing pathway.

Distinct neurogenetic mechanisms establish the same chemosensory valence state at different life stages in Caenorhabditis elegans

An animal's preference for many chemosensory cues remains constant despite dramatic changes in the animal's internal state. The mechanisms that maintain chemosensory preference across different physiological contexts remain poorly understood. We previously showed that distinct patterns of neural activity and motor output are evoked by carbon dioxide (CO2) in starved adults vs dauers of Caenorhabditis elegans, despite the two life stages displaying the same preference (attraction) for CO2. However, how the distinct CO2-evoked neural dynamics and motor patterns contribute to CO2 attraction at the two life stages remained unclear. Here, using a CO2 chemotaxis assay, we show that different interneurons are employed to drive CO2 attraction at the two life stages. We also investigate the molecular mechanisms that mediate CO2 attraction in dauers vs adults. We show that insulin signaling promotes CO2 attraction in dauers but not starved adults and that different combinations of neurotransmitters and neuropeptides are used for CO2 attraction at the two life stages. Our findings provide new insight into the distinct molecular and cellular mechanisms used by C. elegans at two different life stages to generate attractive behavioral responses to CO2.

Differential processing of a chemosensory cue across life stages sharing the same valence state in Caenorhabditis elegans

Many chemosensory cues evoke responses of the same valence under widely varying physiological conditions. It remains unclear whether similar or distinct neural mechanisms are involved in the detection and processing of such chemosensory cues across contexts. We show that in Caenorhabditis elegans, a chemosensory cue is processed by distinct neural mechanisms at two different life stages that share the same valence state. Both starved adults and dauer larvae are attracted to carbon dioxide (CO₂), but CO₂ evokes different patterns of neural activity and different motor outputs at the two life stages. Moreover, the same interneuron within the CO₂ microcircuit plays a different role in driving CO₂-evoked motor output at the two life stages. The dauer-specific patterns of CO₂-evoked activity in this interneuron require a dauer-specific gap junction complex and insulin signaling. Our results demonstrate that functionally distinct microcircuits are engaged in response to a chemosensory cue that triggers the same valence state at different life stages, revealing an unexpected complexity to chemosensory processing.

Penile Ewing's Sarcoma - A Rare Entity

Introduction/Objective

Ewing sarcoma is a cancer involving the bones or the tissue around bones. It is the second most common malignant bone tumour comprising 10-15% of all primary bone tumours, most commonly affecting children and young adults. It can also be seen in adults also. Males are more commonly affected then females. Any bone can be affected but the lower extremity, the pelvis, upper extremity, axial skeleton and ribs, and face cases. Similar histology tumours when seen in soft tissue are peripheral primitive neuroectodermal tumour (pPNET), neuroepithelioma, and Askin tumour. It is always difficult to know the primary site when soft tissues are involved as it can be infiltration from bone or from soft tissue to bone. Penis is least common site involved with Ewing’s sarcoma in young male.

Methods/Case Report

This is a case report of a 22 year old male with penile lesion. He presented with the chief complaints of mass at the shaft of penis. The partial penectomy specimen was received along with the bilateral inguinal lymph node. On gross there was a ulcero-proliferative growth.

Results (if a Case Study Enter NA)

On histopathological examination showed small blue round cell tumour and further immunohistochemistry with CD99 and NKX2.2 revealed the diagnosis of Ewing’s sarcoma, however lymph nodes showed reactive lymphoid hyperplasia.

Conclusion

The Ewing sarcoma at the penile region is rarest entity. Only 7 cases are reported worldwide. The imaging modalities like CT or MRI can be used to know the extension. The diagnosis is primarily based on morphological features, immunohistochemical analysis and translocation analysis. However it is important to find out if any other soft tissue site is involved. The important prognostic markers are presence and absence of metastasis, size of tumour, necrosis and presence of fusion transcripts.

OC-003 PORT POSITIONS IN TEP FOR SHORT PATIENTS: OUR EXPERIENCE

Introduction

Totally extraperitoneal repair (TEP) is a popular technique for repair of inguinal hernia. One common technique of TEP involves placement of one 10 mm port 1–2 cm below the umbilicus just off the midline, one 5 mm port 2–3 cm above the pubic symphysis, and a third 5 mm port between these 2 ports in the midline (Figure 1a). In case the distance from the superior border of the symphysis pubis to the inferior edge of the umbilicus is less than 15 cm, this leads to crowding of instruments and results in ergonomic problems during the operation. Daes has popularized eTEP for this indication. The aim is to shift the first 10 mm port to a position 5 cm superior and 4 cm lateral to the umbilicus (Figure 1b). eTEP has also found application in the repair of ventral hernias. However, for most inguinal hernias, we feel that eTEP is an overkill.

Methods

We place the first 10 mm port at the level of the superior border of the umbilicus and just lateral to it (Figure 1c). The two 5 mm ports are placed in the midline. Initial dissection is performed telescopically.

Results

This technique provides 2–3 cm of extra working space, which improves ergonomics while operating on patients with a short pubo-umbilical distance. Other parameters like operating time, postoperative pain and other complications remain the same.

Conclusion

We recommend placement of the 10 mm port at the superior border of the umbilicus, particularly in short patients.

Isoniazid preventive therapy among child contacts of TB patients, India

BACKGROUND: Isoniazid preventive therapy (IPT) for child contacts of TB patients, a globally accepted intervention, needs to be evaluated in diverse geographical regions.OBJECTIVES: To assess the extent of IPT coverage and adherence, to ascertain its sociodemographic and programmatic correlates and to explore existing constraints from service providers and beneficiaries´ perspectives.METHODS: A mixed-method study was conducted in January-June 2021 in Paschim Bardhaman District, West Bengal, India. Quantitative assessment was done among 280 child contacts of TB cases registered between January and December 2020 in all TB units in the district. Primary caregivers were interviewed using a pre-designed questionnaire. Two focus group discussions with all senior treatment supervisors of the district and in-depth interviews with 12 purposively selected caregivers of the children were undertaken. Qualitative data were analysed thematically.RESULTS: Only 48.9% (137/280) of child contacts were screened; 58.9% (165/280) were initiated on IPT and 40% (66/165) adhered to a full course. Coverage of the full 6-month IPT among total study participants was 23.6% (66/280). Household visits by health personnel and initial screening significantly predicted increased coverage. Programmatic inadequacies, poor understanding, social stigma and COVID situation were major constraints.CONCLUSION: Coverage of IPT remains unacceptably low and requires health system strengthening for effectively implementing current recommendations of TB preventive treatment.

A conserved neuropeptide system links head and body motor circuits to enable adaptive behavior

Neuromodulators promote adaptive behaviors that are often complex and involve concerted activity changes across circuits that are often not physically connected. It is not well understood how neuromodulatory systems accomplish these tasks. Here, we show that the Caenorhabditis elegans NLP-12 neuropeptide system shapes responses to food availability by modulating the activity of head and body wall motor neurons through alternate G-protein coupled receptor (GPCR) targets, CKR-1 and CKR-2. We show ckr-2 deletion reduces body bend depth during movement under basal conditions. We demonstrate CKR-1 is a functional NLP-12 receptor and define its expression in the nervous system. In contrast to basal locomotion, biased CKR-1 GPCR stimulation of head motor neurons promotes turning during local searching. Deletion of ckr-1 reduces head neuron activity and diminishes turning while specific ckr-1 overexpression or head neuron activation promote turning. Thus, our studies suggest locomotor responses to changing food availability are regulated through conditional NLP-12 stimulation of head or body wall motor circuits.

Genome-wide analysis in 756,646 individuals provides first genetic evidence that ACE2 expression influences COVID-19 risk and yields genetic risk scores predictive of severe disease

SARS-CoV-2 enters host cells by binding angiotensin-converting enzyme 2 (ACE2). Through a genome-wide association study, we show that a rare variant (MAF = 0.3%, odds ratio 0.60, P=4.5×10^-13) that down-regulates ACE2 expression reduces risk of COVID-19 disease, providing human genetics support for the hypothesis that ACE2 levels influence COVID-19 risk. Further, we show that common genetic variants define a risk score that predicts severe disease among COVID-19 cases.

Steroid hormone pathways coordinate developmental diapause and olfactory remodeling in Pristionchus pacificus

Developmental and behavioral plasticity allow animals to prioritize alternative genetic programs during fluctuating environments. Behavioral remodeling may be acute in animals that interact with host organisms, since reproductive adults and the developmentally arrested larvae often have different ethological needs for chemical stimuli. To understand the genes that coordinate the development and host-seeking behavior, we used the entomophilic nematode Pristionchus pacificus to characterize dauer-constitutive mutants (Daf-c) that inappropriately enter developmental diapause to become dauer larvae. We found two Daf-c loci with dauer-constitutive and cuticle exsheathment phenotypes that can be rescued by the feeding of Δ7-dafachronic acid, and that are dependent on the conserved canonical steroid hormone receptor Ppa-DAF-12. Specifically at one locus, deletions in the sole hydroxysteroid dehydrogenase (HSD) in P. pacificus resulted in Daf-c phenotypes. Ppa-hsd-2 is expressed in the canal-associated neurons (CANs) and excretory cells whose homologous cells in Caenorhabditis elegans are not known to be involved in the dauer decision. While in wildtype only dauer larvae are attracted to host odors, hsd-2 mutant adults show enhanced attraction to the host beetle pheromone, along with ectopic activation of a marker for putative olfactory neurons, Ppa-odr-3. Surprisingly, this enhanced odor attraction acts independently of the Δ7-DA/DAF-12 module, suggesting that Ppa-HSD-2 may be responsible for several steroid hormone products involved in coordinating the dauer decision and host-seeking behavior in P. pacificus.

Large distal ureteric stone with high burden urothelial cancer of the entire ureter and renal pelvis: a dual pathology

Upper-tract urothelial cancer comprises only 3% of all urothelial cancers. Risk factors include tobacco smoking, recurrent urinary infection, urolithiasis and analgesic abuse. Urolithiasis-induced chronic inflammation leads to urothelial proliferation and eventual malignant transformation. The most common association is reported with squamous cell cancer. A 54-year man under evaluation for right flank pain was diagnosed with a large distal ureteric stone and urothelial cancer of the entire right ureter and renal pelvis. The patient underwent right nephroureterectomy and stone retrieval, with urinary bladder cuff excision and pelvic lymph node dissection. On follow-up, the patient succumbed to disease recurrence with widespread metastasis. Urothelial cancer associated with stone disease is atypical. Long-standing inflammation causing metaplastic and dysplastic changes is a possible hypothesis. Careful assessment of the malignancy should be looked for in patients with long-standing obstruction due to stone disease.

A catalog of associations between rare coding variants and COVID-19 outcomes

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.

High-resolution optical microscopy for characterising microstructural deformation in microtensile testing

Imaging surface deformation of a coupon specimen in microtensile testing with an optical microscope presents challenges due to the narrow depth of field (DoF) of optical microscopes. Materials being heterogeneous at microscopic length scale, the sample surface deforms into a complex 3D surface texture, evolving continuously as the loading increases. Because of the narrow DoF, the region that is in focus within the field of view (FoV) decreases substantially in size with the increasing out-of-plane heterogeneous deformation. To address this challenge, a method based on image blending and stabilisation of the captured image frames is proposed. Image blending combines the partial regions that are in focus from a set of successive image frames captured at different working distances from the object surface plane to construct a single image that has a large part of the FoV in focus. The blended images are then obtained at different levels of macroscopic strains, that is the global homogeneous strain, in order to characterise the evolution of the heterogeneous deformation. The image stabilisation removes any misalignments of the blended images by spatially realigning them choosing a common feature as a reference point. The validation of the proposed method with conventionally and additively manufactured stainless steel 316L (SS 316L) specimens demonstrates excellent improvement in image quality. Almost 100% of the FoV is maintained in focus regardless of the amount of out-of-plane heterogeneous deformation caused during tensile testing, which is quite remarkable for optical microscopy imaging. Consequently, the blended and stabilised images enhanced the accuracy of digital image correlation (DIC). Time-lapse videos of the deformation generated using these images captured the evolution of the slip bands and their transmission through twinning boundaries in the stainless steel microstructure. Overall, this study demonstrates the feasibility of using image-processing techniques to advance optical microscopy to image complex 3D surfaces evolving with time.

Chronic respiratory morbidity in the Bhopal gas disaster cohorts: a time-trend analysis of cross-sectional data (1986-2016)

OBJECTIVES

In 1984, nearly 500,000 inhabitants of Bhopal city, India, were exposed to toxic gases that leaked from a nearby pesticide manufacturing plant. In 1985, four cohorts were established to assess the long-term health impact of exposure, namely, mild, moderate, severely exposed and unexposed groups. The self-reported morbidity data of these cohorts were collected by follow-up cross-sectional surveys at regular intervals over the last 35 years. The present study aimed to analyse the long-term trend of chronic (duration of symptoms >3 months) respiratory morbidity in the four cohorts, stratified by age groups.

STUDY DESIGN

The design of this study is a longitudinal analysis of cross-sectional respiratory morbidity data.

METHODS

Chronic respiratory morbidity data within the cohorts were analysed at 5-year intervals (first recorded data from 1986). Based on age at the time of exposure, subjects were stratified into four age groups: children (aged <10 years), teenagers (aged ≥10 to <20 years), younger adults (aged ≥20 to <40 years) and older adults (aged ≥40 years).

RESULTS

During the first decade, after exposure to the toxic gases, chronic respiratory morbidity in children and teenagers was high (up to 9.1%), which declined thereafter. Progressively increasing chronic respiratory morbidity was observed in both the younger and older adult age groups within all cohorts during the initial 5-10 years after exposure. Respiratory morbidity in both the younger and older adult age groups remained high for 15-20 years and thereafter recorded a declining trend. The highest respiratory morbidity observed during this study in the younger and older adult age groups was 38.6% and 59.5%, respectively; these values were both recorded in the severely exposed cohort.

CONCLUSIONS

Exposure to toxic gases released during the Bhopal gas disaster has resulted in chronic respiratory morbidity of the exposed population; this morbidity has continued over decades. The age of the individuals at the time of exposure and exposure severity were crucial determinants of the long-term trend of respiratory morbidity.

CBETA: First Multipass Superconducting Linear Accelerator with Energy Recovery

Energy recovery has been achieved in a multipass linear accelerator, demonstrating a technology for more compact particle accelerators operating at higher currents and reduced energy consumption. Energy delivered to the beam during the first four passes through the accelerating structure was recovered during four subsequent decelerating passes. High-energy efficiency was achieved by the use of superconducting accelerating cavities and permanent magnets. The fixed-field alternating-gradient optical system used for the return loop successfully transported electron bunches of 42, 78, 114, and 150 MeV in a common vacuum chamber. This new kind of accelerator, an eight-pass energy recovery linac, has the potential to accelerate much higher current than existing linear accelerators while maintaining small beam dimensions and consuming much less energy per electron.

0438 Automatic Nighttime Agitation and Sleep Disruption Detection Using a Wearable Ankle Device and Machine Learning

Introduction

Nighttime agitation behavior such as wandering and restlessness during awake and sleep in people with Alzheimer’s disease (AD) is expensive to manage and adversely affects sleep. Nighttime agitation is mostly noted by subjective caregiver reports. An automated process for this assessment would improve clinical management. Here we report on the RestEaZeTM system that uses an ankle band and machine learning to automatically classify sleep status and nighttime agitation behaviors in older adults with AD.

Methods

We collected data on 7 adults (mean: 81 years, SD: 10.6) with AD. They wore the RestEaZeTM ankle band with a 3-axis accelerometer, a 3-axis gyroscope, and three textile capacitive sensors. A trained Research Assistant (RA) continuously observed for wandering, restlessness, wake, and sleep between 5pm and 7am using the Cohen Mansfield Agitation Inventory (CMAI). We merged, and band-pass filtered the data and divided it into 10-second non-overlapping windows. CMAI labels and time-series features (scaled using StandardScaler) extracted from the RestEaZeTM data were used to train a Random Forest binary classifier. The significant features were extracted based on the impact on the p-value for the classifier. We used the Synthetic Minority Oversampling Technique (SMOTE) to balance the dataset and performed 5-fold cross-validation with a 67-33 train-test split.

Results

We report the sensitivity, specificity, accuracy, and Area-under-the Curve (AUC) for the ROC curve for the classifiers: (1) Sleep/Awake: sensitivity=0.95, specificity=0.87, accuracy=0.92, AUC=0.97; (2) Wandering/Non-Wandering: sensitivity=0.85, specificity=0.99, accuracy=0.98, AUC=0.99; and (3) Restless/Non-Restless: sensitivity=0.84, specificity=0.84, accuracy=0.84, AUC=0.92. The significant features were related to the intensity of movements.

Conclusion

Our preliminary results show the feasibility of using RestEaZeTM for quantitatively measuring nighttime agitation. These can provide clinically useful objective measures of agitation that can be automatically transmitted to clinical or research records with minimal staff time requirements.

Support

The authors acknowledge the funding support from the National Institute on Aging under award R01AG051588 and Arbor Pharmaceuticals for support for Horizant and the matching placebo.

Decoding Inter-individual Variability in Experience-Dependent Behavioral Plasticity

Inter-individual variability in behavioral flexibility is widespread throughout the animal kingdom, but its underlying mechanisms remain poorly understood. In this issue of Neuron, Beets et al. (2020) provide novel insights into the genetic basis of inter-individual differences in behavioral flexibility using the model nematode C. elegans.

Morbidity profile of communities in Bhopal city (India) vis-à-vis distance of residence from Union Carbide India Limited plant and drinking water usage pattern

Objective:

A cross-sectional study was undertaken to assess the prevalence of morbidities in communities residing at variable distances from the closed down insecticide manufacturing plant premises of Union Carbide India Limited (UCIL), Bhopal, India and to determine association of morbidities, if any, with their drinking water usage pattern and distance of localities from the UCIL plant.

Materials and Methods:

A total of 10,827 individuals belonging to 2,184 families, residing within 0-1 km (Stratum I) and 2.5-5.0 km (Stratum II) radial distances from UCIL plant were surveyed and 9,306 of them (86%) were clinically examined. Data were analyzed to examine the association between the groups of morbidities, likely due to biological and chemical water contamination, and the distance of locality from the UCIL plant. Multiple logistic regression was used to explore the risk factors for morbidities.

Results:

Nearly similar prevalence (25.3% in stratum I, 25.8% in stratum II) and the trend of all-cause morbidities were recorded in the two strata. While morbidities related to gastrointestinal tract system (P < 0.05), auditory system (P < 0.01), neoplasm/cancers (P < 0.01) and congenital anomalies (P < 0.01) were significantly higher in stratum I, the prevalence of hypertension (6.4% stratum II, 4.7% stratum I; P < 0.01) and diabetes mellitus (3.4% stratum II, 2.0% stratum I; P < 0.001) was found significantly higher in stratum II. No association (P > 0.05) was observed between the prevalence of morbidities, likely due to the consumption of biologically or chemically contaminated drinking water, and the distance of locality/stratum from the UCIL plant.

Discussion and Conclusion:

By and large similar pattern of morbidities were recorded in the two strata suggesting that the communities, irrespective of the distance of their residences from UCIL plant or sources of their drinking water, are equally vulnerable to various morbidities.

Sexual Dimorphisms: How Sex-Shared Neurons Generate Sex-Specific Behaviors

How sexually dimorphic behaviors are represented in the brain is a long-standing question. Two new studies in C. elegans uncover novel molecular mechanisms that allow neurons shared by opposite sexes to generate distinct sex-specific behaviors.

Excitatory neurons sculpt GABAergic neuronal connectivity in the C. elegans motor circuit

Establishing and maintaining the appropriate number of GABA synapses is key for balancing excitation and inhibition in the nervous system, though we have only a limited understanding of the mechanisms controlling GABA circuit connectivity. Here, we show that disrupting cholinergic innervation of GABAergic neurons in the C. elegans motor circuit alters GABAergic neuron synaptic connectivity. These changes are accompanied by reduced frequency and increased amplitude of GABAergic synaptic events. Acute genetic disruption in early development, during the integration of post-embryonic-born GABAergic neurons into the circuit, produces irreversible effects on GABAergic synaptic connectivity that mimic those produced by chronic manipulations. In contrast, acute genetic disruption of cholinergic signaling in the adult circuit does not reproduce these effects. Our findings reveal that GABAergic signaling is regulated by cholinergic neuronal activity, probably through distinct mechanisms in the developing and mature nervous system.

Local neuropeptide signaling modulates serotonergic transmission to shape the temporal organization of C. elegans egg-laying behavior

Animal behaviors are often composed of distinct alternating behavioral states. Neuromodulatory signals are thought to be critical for establishing stable behavioral states and for orchestrating transitions between them. However, we have only a limited understanding of how neuromodulatory systems act in vivo to alter circuit performance and shape behavior. To address these questions, we have investigated neuromodulatory signaling in the context of Caenorhabditis elegans egg-laying. Egg-laying activity cycles between discrete states-short bursts of egg deposition (active phases) that alternate with prolonged quiescent periods (inactive phases). Here using genetic, pharmacological and optogenetic approaches for cell-specific activation and inhibition, we show that a group of neurosecretory cells (uv1) located in close spatial proximity to the egg-laying neuromusculature direct the temporal organization of egg-laying by prolonging the duration of inactive phases. We demonstrate that the modulatory effects of the uv1 cells are mediated by peptides encoded by the nlp-7 and flp-11 genes that act locally to inhibit circuit activity, primarily by inhibiting vesicular release of serotonin from HSN motor neurons. This peptidergic inhibition is achieved, at least in part, by reducing synaptic vesicle abundance in the HSN motor neurons. By linking the in vivo actions of specific neuropeptide signaling systems with the generation of stable behavioral outcomes, our study reveals how cycles of neuromodulation emanating from non-neuronal cells can fundamentally shape the organization of a behavioral program.

Magnetic coupling at rare earth ferromagnet/transition metal ferromagnet interfaces: A comprehensive study of Gd/Ni

Thin film magnetic heterostructures with competing interfacial coupling and Zeeman energy provide a fertile ground to study phase transition between different equilibrium states as a function of external magnetic field and temperature. A rare-earth (RE)/transition metal (TM) ferromagnetic multilayer is a classic example where the magnetic state is determined by a competition between the Zeeman energy and antiferromagnetic interfacial exchange coupling energy. Technologically, such structures offer the possibility to engineer the macroscopic magnetic response by tuning the microscopic interactions between the layers. We have performed an exhaustive study of nickel/gadolinium as a model system for understanding RE/TM multilayers using the element-specific measurement technique x-ray magnetic circular dichroism, and determined the full magnetic state diagrams as a function of temperature and magnetic layer thickness. We compare our results to a modified Stoner-Wohlfarth-based model and provide evidence of a thickness-dependent transition to a magnetic fan state which is critical in understanding magnetoresistance effects in RE/TM systems. The results provide important insight for spintronics and superconducting spintronics where engineering tunable magnetic inhomogeneity is key for certain applications.

Abstract P6-03-08: Novel recurrent lncRNA fusions detected in breast cancer using RNA-Seq technology in a neoadjuvant setting

Background: Recent discoveries of recurrent and targetable gene fusions in breast cancer suggest the need to characterize the functional significance of such genomic aberrations within larger cohorts. We quantified fusion transcript expression in patient samples using RNASeq to identify recurrent gene fusion events in breast cancer as well as study the fusions post-brief exposure to mono-therapy.

Methods: We sequenced transcriptomes of core biopsy RNA from 130 breast tumors obtained from brief-exposure preoperative clinical trials BrUOG 211A/211B. HER2- patients were treated with brief exposure to bevacizumab (B) or nab-paclitaxel (nP) followed by treatment with B/nP/carboplatin while HER2+ patients received brief exposure to trastuzumab (T) or nP followed by T/nP/carboplatin. Paired-end sequencing on 75 baseline biopsies and 55 post-exposure biopsies using amplified total RNA yielded 55 million reads on average perlsample. Fusion transcript abundance was evaluated using 2 pipelines, TopHat-Fusion and deFuse, due to their complementary strategies in fusion detection. We eliminated gene-pseuodogene fusion pairs as likely false positives arising due to alignment artifacts. Fusions that met 1 or more of the following 3 criteria were considered high confidence:

i) Called by both deFuse and TopHat. ii) Called by deFuse with probability &gt;95% iii) Called by TopHat with &gt; 15 reads supporting the fusion.

Results: We identified high confidence gene fusions, detected by both TopHat and deFuse, in 73 of the 75 baseline biopsies with 16 fusions on average per sample. We looked for modulation of gene fusions upon brief exposure to therapy in 55 patients that had post exposure biopsy data and found that out of the 545 high confidence fusions detected across these patients, 62 (11.37%) of the fusions were found to be still present after the therapy exposure. For the recurrent fusion analyses, we considered the 75 baseline samples. We found a total of 1158 unique candidate fusions. Out of these, 116 (10%) were recurrent in more than 1 patient. After further filtering, we were able to narrow down to 9 (0.77%) fusions that were reliable since they were predicted by both the algorithms in different patients. 2 of these 9 fusions involved GAS5 as a partner gene. GAS5 have been studied to have a role in apoptosis and its down-regulation has been associated with cell proliferation, which makes it a very interesting fusion candidate.

Conclusions: We find that gene fusions in breast cancer are highly heterogeneous but are enriched with cancer-related pathway genes. This is the first study to report 2 novel gene-lincRNA fusion transcripts: MDN1-GAS5 and GABRB3-GAS5. Both these fusions are called in the baseline & post-therapy for atleast 1 patient (different patients each). GAS5 has been found as participating in a fusion in B-cell lymphoma. We are currently in the process of validating the fusion calls using qRT-PCR. The heterogeneity of detected fusions suggests that multiple mechanisms could underlie the selective advantage of tumor cells expressing fusion transcripts. The brief-exposure preoperative paradigm provides a unique opportunity to evaluate modulation of fusion transcripts that can shed light on their functional importance.

Citation Format: Agrawal V, Varadan V, Banerjee N, Miskimen K, Vadodkar A, Abu-Khalaf M, Sikov W, Harris L, Dimitrova N. Novel recurrent lncRNA fusions detected in breast cancer using RNA-Seq technology in a neoadjuvant setting. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-08.

Microballoon pressure sensors for particle imaging manometry in liquid and gaseous media

We present the fabrication and testing of engineered microballoon particles that expand and contract under external pressure changes hence serving as microscopic pressure sensors. The particles consist of 12 μm hollow flexible 0.4 μm-thick parylene-C shells with and without a coating of ultrathin Al2O3 diffusion barriers, and the changes in the particle radius are measured from the particle spectral reflectivity. The microballoons display radial pressure sensitivities of 0.64 nm psi(-1) and 0.44 nm psi(-1), respectively in agreement with theoretical estimates. The microballoon devices were used for mapping the internal pressure drop within microfluidic chips. These devices experience nearly spherical symmetry which could make them potential flow-through sensors for the augmentation of particle-based flow characterization methodologies extending today's capabilities of particle imaging velocimetry.

Flexoelectric MEMS: towards an electromechanical strain diode

Piezoelectricity and flexoelectricity are two independent but not incompatible forms of electromechanical response exhibited by nanoscale ferroelectrics. Here, we show that flexoelectricity can either enhance or suppress the piezoelectric response of the cantilever depending on the ferroelectric polarity and lead to a diode-like asymmetric (two-state) electromechanical response.

Abstract P4-04-07: Heterogeneous gene fusions detected by RNASeq show enrichment of insulin signaling pathway genes in breast cancer

Background: Recent discoveries of recurrent and targetable gene fusions in breast cancer suggest the need to characterize the functional significance of such genomic aberrations within larger cohorts. We quantify fusion transcript expression in patient samples using RNASeq and evaluate their functional significance using biological pathway enrichment analysis.

Methods: We sequenced transcriptomes of core biopsy RNA from 97 breast tumors obtained from brief-exposure preoperative clinical trials BrUOG 211A/211B. HER2- patients were treated with brief exposure to bevacizumab (B) or nab-paclitaxel (nP) followed by treatment with B/nP/carboplatin while HER2+ patients received brief exposure to trastuzumab (T) or nP followed by T/nP/carboplatin. Paired-end sequencing on 55 baseline biopsies and 42 post-exposure biopsies using amplified total RNA yielded 55 million reads on average per sample. We assigned RNASeq-based PAM50 subtypes for each of the samples using standard methodology. Fusion transcript abundance was evaluated using two independent pipelines, TopHat and deFuse, due to their complementary strategies in fusion detection. We eliminated fusions of genes with their respective pseudogenes as likely false positives arising due to alignment artifacts. TopHat fusion calls with total supporting reads ≥10 and deFuse calls with probability of fusion ≥0.7 were considered reliable.

Results: We identified high confidence gene fusions, detected by both TopHat and deFuse, in 30 of the 55 baseline biopsies (54.4%), with 3.3 fusions on average per sample and a maximum of 10. Fusions were predominantly associated with chromosomal aberrations (75%), with putative deletions responsible for 32% of fusions and translocations responsible for 43%. We find a high level of fusion transcript heterogeneity within breast cancers, detecting a total of 80 fusions across the 30 samples with only three fusions recurrent in two samples with high expression in each: MDN1-GAS5 in two basal breast cancers, KRAS-GRIP1 and ITPR2-CCDC91 in two LumB cancers. Several cancer-related genes were found to be fusion partners: AKT3-SMYD3, CREB1-PPP1R1C, FLOT2-TOP2A and FOXC1-ARID1B. Pathway analysis of the fusion genes at baseline revealed enrichment of proteasome (p = 0.000752), tight junction (p = 0.027), insulin signaling (p = 0.0284) and melanogenesis (p = 0.05) pathways after multiple testing correction (FDR≤0.25). We looked for modulation of gene fusions upon brief exposure to therapy in 18 patients and found a majority of the baseline fusion transcripts to be present post-brief exposure in 44% of the patients, irrespective of therapy regimen.

Conclusions: We find that gene fusions in breast cancer are highly heterogeneous but are enriched with cancer-related pathway genes. This is the first study to report a novel gene-lincRNA fusion transcript (MDN1-GAS5). We are currently validating the fusion calls using qRT-PCR. The heterogeneity of detected fusions suggests that multiple mechanisms could underlie the selective advantage of tumor cells expressing fusion transcripts. The brief-exposure preoperative paradigm provides a unique opportunity to evaluate modulation of fusion transcripts that can shed light on their functional importance.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-07.

Abstract P4-04-02: RNA-seq reveals functional lncRNAs associated with estrogen-receptor status in breast cancer

Background: Long non-coding RNAs (lncRNAs) are pervasively transcribed in the genome yet their role in human disease is not well understood. LncRNAs can have regulatory effects on coding mRNAs through a number of mechanisms, including repressing their sense-strand protein-coding partners. There is also emerging evidence that estrogen signaling affects the expression of a wide variety of non-coding functional RNA transcripts in addition to protein-coding transcripts. We performed an RNA-seq study to characterize changes in lncRNA expression and evaluate their association to estrogen receptor (ER) status and estrogen signaling.

Methods: We sequenced transcriptomes of core biopsy RNA from 45 breast tumors obtained from neoadjuvant clinical trials BrUOG 211A/211B. RNA was derived from biopsy samples obtained before exposure to run-in monotherapy with either nab-paclitaxel, bevacizumab or trastuzumab. Paired-end sequencing was performed using amplified total RNA with 74bp read length, yielding genome-wide transcriptomic data. Transcriptomic abundance and differential expression were estimated assuming Poisson-distributed read-counts. Paired-end sequence data was aligned to a lncRNA database containing 14,572 unique lncRNAs. Changes in relative abundance of lncRNA transcripts were tested for association with estrogen receptor status using the Wilcoxon rank-sum test. Expression levels of the ER-associated lncRNAs were investigated in RNA-seq data from ER-positive MCF7 cells in response to treatment with E2 and tamoxifen (3hr, 12 hr and a non-treated control). ER-responsive binding sites on or near the ER-associated lncRNAs were investigated in a ChIP-seq study in MCF7 cells following estrogen treatment. MCF7 cell-line RNA-seq and ChIP-seq data were obtained from publicly available Short Read Archive (ERX030990 and SRX113365) at NCBI.

Results: On average, in each patient 5000 lncRNAs were detectable. Expression of 22 lncRNAs were associated ER status (p&lt;0.05) in breast tumors. 17 of the 22 ER-associated lncRNAs were detectable in ER-positive MCF7 breast cancer cells and were all responsive to E2 (estradiol) treatment. Interestingly, all 17 lncRNAs showed significant downregulation (&gt; = 2 fold) upon tamoxifen treatment. To further evaluate the regulatory relationship between ER and the 22 lncRNAs, we identified the binding sites of ER in estrogen-treated MCF7 cells using ChIP-seq. We found that &gt;50% of the ER-associated lncRNAs had ER binding site either overlapping or neighboring the lncRNA.

Discussion: We have shown that lncRNA expression levels are associated with ER status in breast tumors. We have further established that they are estrogen-responsive with a majority being direct targets of ER using cell-line data. Further functional validation studies are ongoing. We are also exploring lncRNA-mRNA expression for coding partners of lncRNAs to identify coding/noncoding gene regulatory networks important in estrogen response. Understanding the regulatory effects of lncRNA expression opens up new opportunities for stratification and management of breast cancers.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-02.

Anomalous recovery characteristics of Pd modified ZnO nanorod based acetone sensor

Unmodified and Pd modified Zinc Oxide (ZnO) hexagonal nanorods, grown by Chemical Bath Deposition (CBD), is reported in this paper for efficient detection of acetone vapor. After details structural characterization (XRD, FESEM and AFM) the nanorod based sensors were tested in resistive mode for detection of acetone in the concentration range of - 190-3040 ppm. By Pd surface modification the optimum working temperature was brought down from 350 degrees C (unmodified) to 300 degrees C with appreciable improvement in response magnitude (90% to 99%) also. Strikingly, the recovery time, after Pd modification, became faster than the corresponding response time up to certain concentrations range (190-1530 ppm) and above this concentration (> or = 1530-3040 ppm) response time was found to be faster than recovery time which is similar to the case with unmodified nanorods (for entire concentration range). There are earlier reports on such faster recovery (compared to response), but no proper explanation was provided. In this paper we tried to explain this apparent anomaly of recovery characteristics through concentration dependent reaction rate variation following Arrhenius equations. Also a correlation between the parameters of the corresponding electrical equivalent circuit of the sensor has been established.

Abstract P5-07-03: Gallotannins and Gallic acid From Mango Fruit (Mangifera Indica L) Suppress Breast Cancer Tumor Growth by Targeting Phosphatidylinositol3-kinase (PI3K)-Akt-NF-kB Pathway and Associated microRNAs

The cytotoxic and anti-inflammatory properties of polyphenolics have been demonstrated in numerous types of cancer and the objective of this research was to understand the post-transcriptional targets involved in anti-inflammatory and pro-apoptotic pathways in the breast cancer cell line BT474, treated with a polyphenolic extract (2.5–40µg/ml) rich in gallotannins and gallic acid from mango fruit in vitro and in athymic nude mice bearing BT474 cells as xenografts.

Results show that cell proliferation as well as tumor size and weight in vivo was decreased by polyphenolics 60% and 70% in vitro and vivo, respectively. NF-kB protein and mRNA expression as well as activation were decreased in a dose-dependent manner (0.6 fold).

The extract also inhibited PI3K-dependent phosphorylation of AKT and expression and this was accompanied by down-regulation of miRNA 126 of BT474 (2.25 fold) and in vivo. NFκB-dependent genes involved in apoptosis-inhibition, metastasis and angiogenesis, such as survivin, VCAM-1, and VEGF were also decreased, in vitro and in vivo.

A microRNA-array was also used to investigate whether microRNAs with target regions within affected genes were affected by the polyphenolic extract and results show that in addition to miR-126, miR-let-7a and miR-let-7b among others were significantly increased by the extract.

In summary the anti-carcinogenic and anti-inflammatory activity of mango polyphenolics in breast cancer cells were at least in part due to targeting miR-126 -Phosphatidylinositol 3-kinase (PI3K)-Akt-NF-kB which plays an important role in the proliferative/ inflammatory phenotype exhibited in this breast cancer cell line.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-07-03.

Abstract P4-01-02: Association of DCE-MRI texture features with molecular phenotypes and neoadjuvant therapy response in breast cancer

Purpose: MRI imaging phenotype features such as volume and morphology are used to characterize tumor heterogeneity and tumor response. Texture-based imaging features are important in lesion characterization but their relationship to molecular phenotypes and response is unclear. Molecular stratification of breast cancer into luminal, basal, ERBB2, and normal-like can be made based on gene expression profiles. We investigate how texture-based imaging features relate to tumor biology, genetic subtypes and neoadjuvant therapy response using MRI, histopathological and RNA-sequencing data.

Materials and Methods: Data from 74 Stage IIA to IIIB breast cancer patients enrolled in neo-adjuvant clinical trials NCT00617942 and NCT00723125 were retrospectively reviewed. We evaluated 37 gray-level co-occurrence matrix features (GLCM) on post-contrast T1 fat-suppressed images of 38 HER2− tumors and 35 HER2+ tumors. The texture features included angular second moment, contrast, correlation, first diagonal moment, entropy, regularity, roughness, line likeness and other statistical summaries. We also performed RNA-sequencing on 23 tumors and compared RNAseq-based PAM50 clustering with texture-based clustering. Patients with pCR and RCB class=I were determined to be responders and the rest were labeled non-responders. Wilcoxon signed rank test was used to compare luminal vs. basal, ER+ vs. ER− and PR+ vs. PR- tumors and determine the discriminative power of the texture features. We then performed hierarchical clustering on our patient data set based on the significant texture features and evaluated their association with subtypes, hormone receptor status and response. Statistical significance of clusters was determined by hypergeometric test.

Results: We found five MRI texture features to be significantly associated with tumor subtypes: first diagonal moment, contrast range, correlation range and entropy range (p &lt; 0.05). These five features together differentiated basal and luminal PAM50 subtypes with p = 0.001. Our analysis also showed an association between texture features and tumor hormone status. ER− tumors clustered strongly (13 of 20 ER− cases clustered, p = 0.009) with the 23 significant ER-associated texture features. Similarly, the PR- tumors formed tight grouping (15 of 24 PR- cases clustered, p = 0.006) with 26 significant PR-associated texture features in HER2− patients. Interestingly, only two texture features, entropy range and regularity, distinguished between responders and non-responders (p = 0.04). These features will be further evaluated with DCE-MRI data capturing post brief exposure dynamics.

Conclusion: Our results indicate that certain texture features from DCE-MRI images do capture biological heterogeneity in tumors and can potentially complement standard clinical evaluations. Texture features have previously been assessed for diagnostic settings but to our knowledge this is the first study that shows association of texture features with breast cancer subtyping and neoadjuvant therapy response. We speculate that this could potentially impact clinical management decisions and therapy selection.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-01-02.

Abstract PD05-05: RNA-seq identifies unique transcriptomic changes after brief exposure to preoperative nab-paclitaxel (N), bevacizumab (B) or trastuzumab (T) and reveals down-regulation of TGF-β signaling associated with response to bevacizumab

Background: Identification of differentially expressed transcripts upon brief exposure to preoperative therapy can help determine likely response markers. We quantify and compare differential transcript expression using RNA-seq on patient samples before and after one dose of T or B or N. We also evaluate correlation of brief-exposure transcriptomic changes with response to B.

Methods: We sequenced transcriptomes of core biopsy RNA from 50 pairs of breast tumors obtained from neoadjuvant clinical trials BrUOG 211A/211B. Patients were given a run-in dose of B or N or T, followed by combination biologic/chemotherapy (HER2− with B/carboplatin/N; HER2+ with T/carboplatin/N). We sequenced biopsy pairs obtained pre/post 10 day exposure to run-in monotherapy. Paired-end sequencing was done on Illumina GAII platform using amplified total RNA with 74bp read length, yielding expression data for 22,302 genes and 35,768 transcripts. We evaluated transcriptomic changes upon brief exposure to monotherapy assuming Poisson-distributed read-counts, followed by multiple testing correction and enrichment analysis of 185 KEGG pathways. We investigated association of transcriptomic changes upon brief exposure and pathologic complete response (pCR) in the B arm. Differential expression of previously published signatures of tumor vasculature, TGF-β, β-catenin, MYC, E2F3 and RAF-MEK pathway activities were evaluated to identify associations with pCR.

Results: PAM50-based clustering showed individual samples cluster together, demonstrating that tumor subtypes do not change over the 10-day treatment. We identified unique transcripts that were significantly differentially expressed in each therapy arm (p &lt; 0.05;FDR&lt;0.1). Significant down-regulation of tumor vasculature-related genes was seen in B samples (p = 0.05). We found 1024 genes whose significant differential expression correlated with pCR in the B arm (Mann-Whitney p-val&lt;0.05; abs log2-fold change≥0.5). Only 4 KEGG pathways, TGF-β signaling, Cell Cycle, DNA Replication and Steroid Biosynthesis were found to be enriched (p ≤ 0.05) in the pCR-associated gene list, and displayed significant down-regulation of member genes within the pCR group. To further evaluate the enrichment results, we used several published pathway activity gene signatures. Interestingly, clustering of the B-treated samples using a TGF-β response signature strongly clustered pCR cases due to down-regulation of TGF-β activity in that group (p = 0.004). We found that the TGF-β signature was most informative of pCR when compared to E2F3, RAF-MEK, β-catenin and MYC signatures in the B arm.

Conclusions: This is the first study to compare differential gene expression upon brief exposure across therapies using RNA-seq technology. The association of TGF-β activity with pCR in B arm was identified using both a bottom-up statistical approach and with a previously published TGF-β activity signature. The unique aspects of transcriptional response to each treatment and the association of transcriptional changes with response underscore the value of the brief-exposure paradigm to identify markers of neo-adjuvant therapeutic response.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr PD05-05.

Pyoderma Gangrenosum and High Titer Serum Aanti-CCP2 Antibodies

Pyoderma gangrenosum is an uncommon ulcerative cutaneous neutrophilic dermatosis. In about 50 percent of cases, it is associated with systemic diseases like inflammatory bowel disease, rheumatoid arthritis, systemic lupus erythromatosus, hematological diseases and various malignancies. There is no specific laboratory finding or histological features pathognomonic of pyoderma gangrenosum and it is often a diagnosis of exclusion. Here, we report an elderly female without history of any systemic disorders, presenting to us with extensive, bilaterally symmetrical, deep leg ulcers along with multiple superficial ulcers involving the right groin which was diagnosed as pyoderma gangrenosum. The only positive rheumatologic marker was serum anti-cyclic cittrulinated peptide2 antibody, which was found to be strongly positive. Dramatic response to systemic corticosteroid followed by successful split skin grafting was observed in our patient. Keywords: Anti cyclic cittrulinated peptide2, pyoderma gangrenosum, symmetric leg ulcer.

Pyoderma gangrenosum and high titer serum anti-CCP2 antibodies

Pyoderma gangrenosum is an uncommon ulcerative cutaneous neutrophilic dermatosis. In about 50 percent of cases, it is associated with systemic diseases like inflammatory bowel disease, rheumatoid arthritis, systemic lupus erythromatosus, hematological diseases and various malignancies. There is no specific laboratory finding or histological features pathognomonic of pyoderma gangrenosum and it is often a diagnosis of exclusion. Here, we report an elderly female without history of any systemic disorders, presenting to us with extensive, bilaterally symmetrical, deep leg ulcers along with multiple superficial ulcers involving the right groin which was diagnosed as pyoderma gangrenosum. The only positive rheumatologic marker was serum anti-cyclic cittrulinated peptide2 antibody, which was found to be strongly positive. Dramatic response to systemic corticosteroid followed by successful split skin grafting was observed in our patient.

P3-06-04: Sno/miRNA Expression Via Next Generation Sequencing: Variation in Patients before and after Treatment

Background

Aberrant expression of small RNA molecules has been shown in breast cancer. It is yet unclear if variation exists in small RNA molecule expression in response to treatment. Since next generation sequencing offers more globally sensitive detection of sno and miRNAs, we performed an RNA-seq study to explore patients pre- and post- brief exposure to treatment.

Methods: We sequenced transcriptomes of frozen biopsy samples from 8 breast cancer patients enrolled in a clinical trial for neoadjuvant therapy using trastuzumab (HER2 positive) or bevacizumab (HER2 negative) with chemotherapy. Tumor core biopsies were taken before and after 10 days of either biologic or nab-paclitaxel treatment and stored in OCT compound. Total RNA was extracted and libraries were constructed for the 16 samples using TruSeq (Illumina). We performed 74bp paired-end sequencing with the Illumina GAII platform. Sequences were aligned to the sno/miRNA track (containing 928 miRNAs and 413 snoRNAs) in UCSC and read counts were determined using Bowtie. We performed differential miRNA and snoRNA expression analysis pair-wise in all pre- and post-therapy samples. Given that miRNA deregulation relies on their protein-coding gene targets, we analyzed the predicted targets of the significantly varying miRNAs for functional enrichment.

Results: Each sample had on average 46 million paired-end reads, of which on average 70% were mapped to the human genome. Overall, we detected 138 miRNAs in at least one sample, with each sample expressing 33 miRNAs on average. We detected a total of 11 miRNAs (7%) that showed significant differential expression with treatment. Interestingly, 6 of these miRNAs varied in all patients. The predicted targets of these miRNAs were enriched in DNA-dependent transcription, gene expression, cell proliferation and cell communication. Similarly, we detected 202 snoRNAs in at least one sample, with each sample expressing 87 snoRNAs on average. Of these, we found 21 snoRNAs (10%) to vary significantly upon treatment and 6 of these snoRNAs showed expression changes in all patients.

Conclusions: These results suggest that variation in sno/miRNA expression may play a role in response to treatment. The consistent variation of sno/miRNAs in response to treatment suggests shared small RNA-mediated mechanisms. If validated, these results suggest that next generation sequencing technologies will allow lead to improved methods of stratifying, subclassifying and managing breast cancer.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-04.

P3-06-01: Next Generation RNA Sequencing Reveals Changes in Gene Expression and Alternative Splicing upon Brief Exposure to Therapy in Early Breast Cancer

Background

The use of next generation RNA sequencing (RNA-seq) allows for the characterization of the transcriptome at levels of detail unachievable by array-based technologies. RNA-seq analysis can quantify expression of novel transcripts and alternatively spliced isoforms in addition to known genes. Alternative splicing allows for flexibility in production of protein isoforms and is frequently dysregulated in cancer. As splice variants may play a role in response to therapy (Solier, et al, Cancer Res., 2010), we studied differential gene and isoform expression in breast cancers after one dose of treatment, prior to a course of preoperative therapy.

Methods: We sequenced transcriptomes of core biopsy samples from 8 breast cancer patients enrolled in a preoperative clinical trial using trastuzumab (HER2 positive) or bevacizumab (HER2 negative) with chemotherapy. Tumor core biopsies were taken before and after 10 days of either biologic or nab-paclitaxel treatment and stored in OCT compound. Total RNA was extracted, amplified and libraries were constructed for the 16 samples using TruSeq (Illumina). Paired-end sequencing was performed on the Illumina GAII platform with read length of 74bp. Sequence data was mapped using TopHat and transcript abundance in FPKM units (Fragments per kilo-base of mRNA per million reads) estimated for a total of 22,160 unique genes and 34,449 unique transcripts from RefSeq. Differential expression of transcripts between baseline and 10-day samples was estimated using t-statistics with read-counts modeled as a Poisson distribution. Differentially expressed transcripts were selected at a significance level of 0.05 after multiple testing correction.

Results: Each sample had on average 46 million paired-end reads, of which on average 70% were mappable to the human reference genome (UCSC, hg19). A median of 138 (range 68–948) transcripts varied with treatment. GO analysis showed enrichment of cell-adhesion, apoptosis, differentiation and cell proliferation pathways. Interestingly, the isoforms of several known cancer genes such as TP53 were seen in all treatment types. Certain isoforms were only seen to change upon brief exposure to chemotherapy such as BCL2 whereas TNF ligand and PCDH isoforms showed significant change only with biologic agents.

Conclusions: These results suggest that recurrent changes in both canonical genes and splice variants occur over the course of treatment in early breast cancer. This underscores the value of RNA-seq to provide novel information that may be clinically useful. Brief exposure to monotherapy prior to combination treatment may provide important mechanistic insights and produce predictive biomarkers. Biologic treatments may produce unique changes that can only be discovered with novel next generation sequencing techniques.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P3-06-01.

Chronic portal vein thrombosis due to combined deficiency of protein C and protein S

Portal vein thrombosis (PVT) is a rare disorder that is associated with a variety of underlying condition of which liver cirrhosis, malignancy and myeloproliferative disorders are the most common. It is of two types, acute and chronic portal vein thrombosis. Anticoagulation therapy is recommended for all patients with acute portal vein thrombosis. Chronic portal vein thrombosis is characterised by the development o f portal hypertension. Bleeding from ruptured varices is the main complication. In the absence of bleeding, continuous anticoagulation therapy should be considered for chronic portal vein thrombosis in whom an underlying prothrombotic factor is to be identified. Here in this report a 13-year-old girl presented with haematemesis. The spleen was hugely enlarged. Her Hb was 8.38 g/dl. Grade III oesophageal varices were found in oesophagogastroduodenostomy. CT abdomen showed portal cavernoma formation with increased splenic collateral. Protein C activity was 45% and protein S activity was 40%. She was treated with beta-blocker, endoscopic variceal ligation followed by low molecular weight heparin and warfarin.

Evaluation of ER/PR and HER2 status by RNA sequencing in tissue core biopsies from preoperative clinical trial specimens

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Background: Next-generation sequencing for measuring RNA (RNASeq) offer increased sensitivity, dynamic range and provide unbiased detection of all transcripts. To evaluate the clinical utility of such methods, we sequenced entire transcriptomes from fresh-frozen biopsies in a cohort of 120 patients enrolled on a preoperative therapy trial receiving carboplatin, nab paclitaxel and either bevacizumab (HER2-) or trastuzumab (HER2+).

Methods: Total RNA was extracted and amplified from frozen breast core biopsies and libraries constructed using TruSeq (Illumina). Sequencing was performed on the Illumina GAII platform. 75bp reads were mapped using Tophat and transcript abundance in FPKM units (Fragments per kilo-base of mRNA per million reads) calculated using Cufflinks. CLIA approved assays were performed for ER, PR, HER2 (IHC+/- FISH) on patient tumors. Four tumors from each subtype (ER +ve/HER2 -ve; HER2 +ve; ER/HER2 -ve) were analyzed for correlation with clinical status. PAM50 classification will be provided for verification of molecular subtypes.

Results: RNA-Seq library construction/sequencing were successful in 12/12 samples with 50-90% reads mapped. ER +ve tumors ranged in FPKM values from 1.76-22.67 and ER -ve tumors ranged from 0.00-0.79. i.e. ER RNASeq measurements can separate clinical ER status. HER2 +ve tumors ranged in FPKM values from 2.62-21.71 and HER2 -ve tumors from 0.21-1.79. Of note, 7/8 HER2 -ve tumors ranged from 0.21-0.87 with one ‘outlier’ at 1.79±0.3. This outlier was HER2 IHC 2+, FISH ratio 1.1 with 45% of tumor cells with polysomy chromosome 17. Correspondence of ER/PR and HER2 status with molecular subtyping by PAM50 analysis will be presented.

Conclusions: RNASeq has potential to provide in depth analysis of the breast cancer transcriptome and a single analysis test for standard markers. In addition, RNASeq may uncover unexpected expression patterns in conventionally-defined HER2 -ve tumors. If reproducible in larger datasets, this technology may provide both standard and novel information previously unavailable to oncologists and their patients.

Abstract P3-04-08: Epigenetic Changes Due to DNA Methylation in CpG Islands during Breast Cancer Progression

DNA methylation has been associated with several key events of gene regulation and to human cancer. It is not yet known how the epigenome of various populations is associated with clinical manifestations during the course of the disease. In this poster we describe a method for stratifying breast cancer patients from Indian origin using CpG island microarray from the University Healthcare Network (UHN) Toronto (human CpG island 12k microarray chip, HCGI12K). DNA samples were obtained from a prospective study cohort which consisted of 51 female primary breast cancers. All patients had been undergoing treatment in a tertiary care hospital and its associated centers in the southern part of India between 2007 and 2009. We have identified and classified the DNA methylation in CpG islands of patient samples using various clinical parameters such as age of disease onset, menopausal status, hormone receptor status and Her2 status. We present the methods to analyze the data from UHN CpG island arrays used in a high throughput methylation study in order to derive decision rules of stratifying the data into basic classes such as normal and benign conditions, and infiltrating ductal carcinoma. Results will be presented pertaining to differential methylation status of patients in different categories such as age of disease onset, menopausal status, hormone receptor status and Her2 status.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P3-04-08.

Genome-Wide DNA Methylation Profiles of Breast Tumors Reveal Loci Associated with Relapse Risk

Background:Breast cancer prognosis is used in determining the course of adjuvant therapy for patients. Clinical prognostic indices like the Nottingham Prognostic Index have poor specificity, overestimate the risk of disease recurrence and necessitate more specific and robust prognostic markers. Prognostic gene expression markers are already in clinical use and show improved decision support. Methylation of CpG islands, an important regulator of gene expression, is reported to be disregulated in tumors, thus making methylation markers an important alternative to gene expression markers. We present the results of a genome-wide study that explored loci whose methylation status was significantly associated with recurrence risk.Methods:We used 108 frozen primary breast cancer specimens with ten year follow-up and extensive clinical data including histopathological measurements to identify potential epigenetic markers associated with recurrence risk. Using a previously validated array based method (Kamalakaran et. al., Nucleic Acids Research, 2009) we performed genome-wide measurements of differential CpG island methylation covering over 150,000 loci. We evaluated each locus for its ability to stratify patients into good or poor prognosis groups depending on its methylation status. Statistical significance was established using permutation analysis with appropriate multiple testing corrections. Prognostic markers independent of histopathological factors (ER, PR, HER2, tumor size, grade, node status, age) were identified using multivariate Cox regression analysis.Results:The methylation status of several loci proximal to genes significantly stratified samples independent of other clinical variables. Demethylation of several loci were associated with poor prognosis including ADAMTS4 (Hazard Ratio = 17.5, p-value&lt;&lt;0.001), a metalloproteinase previously implicated in the progression of glioma; DNA Topoisomerase I (HR = 3.81; 95% CI = 1.953-7.462; p&lt;&lt;0.001), implicated in chemotherapy resistance; and JMJD2C (HR = 3.7; 95% CI = 1.828-7.519; p&lt;&lt;0.001), which was found to be frequently amplified in esophageal cancers. The methylation of several loci also had significant association with poor prognosis, such as several members in the forkhead box family (FOXF1, FOXG1B, FOXJ1, FOXL2) and FHL1 (HR = 4.78; 95% CI = 2.38-9.62; p&lt;&lt;0.001). We selected several loci to form an ensemble classifier with statistically significant performance on our dataset. We show that this classifier achieved much higher specificity when compared to the Nottingham Prognostic Index, while maintaining high sensitivity.Discussion:Our retrospective study of genome-wide DNA methylation in breast cancer has identified several novel markers for prognosis. We found methylation deregulation of CpG islands proximal to genes implicated in metastasis and chemotherapy resistance is associated with poor prognosis. Furthermore, the potential for clinical benefit of these markers is their ability to jointly identify significantly larger number of low-risk patients compared to the Nottingham Prognostic Index.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 4046.

Subtype Dependent Alterations of the DNA Methylation Landscape in Breast Cancer

Background: The diversity of breast cancers at the clinical, histopathological and molecular level reflects variation in underlying biology and affects the clinical implications for patients. Gene expression studies have identified five breast cancer subtypes with distinct expression profiles – Luminal A, Luminal B, basal, ErbB2 enriched and Normal-Like. DNA methylation is an important regulator of gene expression that is also known to be deregulated in tumors. We set out to determine the relationship between DNA methylation and breast cancer subtypes in 108 breast cancer samples with previously determined expression subtypes.Methods: We performed high-throughput genome-wide scans of CpG methylation in 108 tumors and 11 normal tissues using our previously validated Methylation Oligonucleotide Microarray Analysis (MOMA) method [Kamalakaran, S et al. Nucleic Acids Research, 2009)]. We identified loci that were most varied across all tumors or had the most significant alterations and performed unsupervised hierarchical clustering on those loci. We then used a genetic algorithm based feature selection method to identify a subset of those loci that could cluster the sample set by expression subtype. We then characterized the loci contributing to subsetting and where possible, the relationship between methylation and gene expression.Results: Unsupervised hierarchical clustering using the 500 most differentially methylated loci across all tumors and 100 most significant altered loci between tumors and Normal tissues clustered the tumors into 3 major clusters – 82% of Cluster I belonged to Luminal Subtypes (22 Luminal A and 4 Luminal B), and 86% of Cluster II samples were of Basal or ErbB2+ subtypes. Cluster III did not show any expression subtype specific enrichment, but contained samples whose expression subtype was inconclusive with weak correlations to multiple expression subtypes. Interestingly, methylation loci that contributed to this clustering were not localized to CpG islands immediately upstream of genes, with 354 loci far from gene transcription start sites. These non-geneic loci did not show any significant regulatory potential based on cross-species conservation measures and no clear function could be assigned to these regions. The remaining 146 loci could be mapped to known genes. Gene expression microarray measurements were available for 79 of these geneic loci and 36 showed significant correlation of methylation to expression levels (p&lt;0.05), implying possible functional effects of the methylation on gene expression. Additionally, distinct subtype specific patterns of methylation could also be detected in known cancer associated genes. CpG islands in the HOXA gene cluster and many other homeobox genes were significantly more methylated in Luminal A tumors.Conclusions: Our results suggest that there are subtype dependant genome-wide alterations in the methylation landscape in breast cancers, especially near homeobox genes. Many more CpG islands with no apparent functional significance get methylated according to subtype in addition to those CpG islands associated with genes with known cancer related functions.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1144.

Analysis of T-cell proliferation and cytokine secretion in the individuals exposed to arsenic

Over six million people in nine districts of West Bengal, India are exposed to very high levels of arsenic primarily through their drinking water. More than 300,000 people showed arsenic-induced skin lesions in these districts. This is regarded as the greatest arsenic calamity in the world. Chronic arsenicosis causes varied dermatological signs ranging from pigmentation changes, hyperkeratosis to non-melanocytic cancer of skin, and also malignancies in different internal organs. Higher incidences of opportunistic infections are found in the arsenic-exposed individuals, indicating that their immune systems may be impaired somehow. We have thus investigated the effect of arsenic on T-cell proliferation and cytokine secretion in 20 individuals with arsenic-induced skin lesions and compared the results with 18 arsenic-unexposed individuals. A marked dose-dependent suppression of Concanavalin A (Con A) induced T-cell proliferation was observed in the arsenic-exposed individuals compared with the unexposed ( P < 0.001) individuals. This correlated with a significant decrease in the levels of secreted cytokines by the T cells (TNF-α, IFN-γ, IL2, IL10, IL5, and IL4) in the exposed individuals ( P < 0.001). Thus it can be inferred that arsenic exposure can cause immunosuppression in humans.

Efficacy of oxaliplatin, 5 FU and gemcitabine in advanced pancreato-biliary cancer

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Background: The treatment of advanced pancreato-biliary cancer remains an unmet need. The drugs known to be effective are oxaliplatin, gemcitabine. Method: The records of twenty patients suffering with cancers of advanced gall bladder (10), common bile duct (3), ampulle of vater (3) and pancreas (4) were analysed. Twenty patients were treated in the year 2006. Median age was 52 years. The common sites of metastatis were liver (12), lymphnodes (10), peritoneum (4), lungs (1). The patients with normal bilirubin & LFT (< 3 times upper limit of normal) were included. The chemotherapy protocol was given as: oxaliplatin 50 mg, leucovorin 30 mg, and 5FU 500 mg/m2 on day 1, 2, & 3. Gemcitabine was given 800 mg/m2 on day 2, 9, and 16. The cycle was repeated every 4 weeks. Response: The regimen was well tolerated. Pancytopenia requiring G-CSF, delays in drug administration occurred in 70% cases. The response was as follows-partial response 6/20 (30%), stable disease 5/20 (25%), progressive disease 9/20 (45%). The median survival was 5.5 months, four patients completed six cycles of chemotherapy and survival for at least 12 months. Conclusion: Oxaliplatin, 5 FU, gemcitabine and leucovorin is an effective chemo-protocol in advanced pancreato-biliary cancer. However, there is a need to improve upon the existing results.

No significant financial relationships to disclose.

Indomethacin therapy in the treatment of polyhydramnios due to placental chorioangioma

A 26-year-old primigravida presented with acute polyhydramnios at 30 weeks gestation. Ultrasonography revealed a large placental chorioangioma with severe hydramnios. No anomalies were detected in the fetus. Preterm labor started with respiratory distress and indomethacin, 25 mg was given every 6 hours. The patient showed a good response with improvement of the hydramnios and respiratory symptoms. A normal infant with no neonatal complications was delivered 3 weeks later.

Cultural requirements for in vitro seed germination, protocorm growth and seedling development of Geodorum densiflorum (Lam.) Schltr

Effects of different nutrient solutions, organic supplements and plant growth regulators on in vitro seed germination and protocorm development of Geodorum densiflorum (Lam.) Schltr. were studied. Seed germination was very high (up to 96%) in all the basal media, with Knudson's C and half-strength Murashige & Skoog being slightly more productive than Vacin & Went. Application of organic supplements and NAA had little effect on germination, but BAP proved inhibitory. After germination, protocorms exhibited a clear preference for peptone and NAA for much faster growth, while BAP resulted in stunted growth. Beside normal development, disorganisation of protocorms, followed by callusing occurred in presence of peptone and NAA. The calli were compact with limited growth and frequently regenerated protocorm like bodies. Development of seedlings was preceded by an intermediary rhizome phase. Growth of rhizomes was slow in the plant growth regulator free medium and about 15 months of culture was required for seedling formation. However, it was possible to hasten the process by 8-10 months with the employment of NAA, which also enhanced the number of seedlings per protocorm through axillary branching. Combined application of high BAP and low NAA was also useful for high rate of seedling formation.

Factors determining the occurrence of unwanted pregnancies

BACKGROUND

We aimed to identify the factors involved in the occurrence of unwanted pregnancy in women seeking medical termination of pregnancy, and to describe their contraceptive practices.

METHODS

A descriptive interview-based study of 402 women seeking abortion was done. Information was gathered regarding demographic variables, contraceptive practices and reasons for the unwanted pregnancy.

RESULTS

All the women in our sample were married and multiparous. The husband's unwillingness for contraception and the improper use of condoms was responsible for one-third of all unwanted pregnancies. Lactation was believed to be a protection against pregnancy by 11.3% of women while 6.3% were unaware of any contraceptive method.

CONCLUSION

We believe that focusing on these areas in public health programmes will help to decrease the number of unwanted pregnancies.

Gravid uterus in an incisional hernia

A case of gravid uterus in an incisional hernia is reported. The pregnancy was further complicated by intrauterine growth restriction, oligohydramnios and pregnancy induced hypertension. The management of the case is discussed.