Single-Cell Transcriptomic Analysis of Kaposi Sarcoma

Kaposi Sarcoma (KS) is a complex tumor caused by KS-associated herpesvirus 8 (KSHV). Histological analysis reveals a mixture of "spindle cells", vascular-like spaces, extravasated erythrocytes, and immune cells. In order to elucidate the infected and uninfected cell types in KS tumors, we examined skin and blood samples from twelve subjects by single cell RNA sequence analyses. Two populations of KSHV-infected cells were identified, one of which represented a proliferative fraction of lymphatic endothelial cells, and the second represented an angiogenic population of vascular endothelial tip cells. Both infected clusters contained cells expressing lytic and latent KSHV genes. Novel cellular biomarkers were identified in the KSHV infected cells, including the sodium channel SCN9A. The number of KSHV positive tumor cells was found to be in the 6% range in HIV-associated KS, correlated inversely with tumor-infiltrating immune cells, and was reduced in biopsies from HIV-negative individuals. T-cell receptor clones were expanded in KS tumors and blood, although in differing magnitudes. Changes in cellular composition in KS tumors were identified in subjects treated with antiretroviral therapy alone, or immunotherapy. These studies demonstrate the feasibility of single cell analyses to identify prognostic and predictive biomarkers.

Author Summary

Kaposi sarcoma (KS) is a malignancy caused by the KS-associated herpesvirus (KSHV) that causes skin lesions, and may also be found in lymph nodes, lungs, gastrointestinal tract, and other organs in immunosuppressed individuals more commonly than immunocompetent subjects. The current study examined gene expression in single cells from the tumor and blood of these subjects, and identified the characteristics of the complex mixtures of cells in the tumor. This method also identified differences in KSHV gene expression in different cell types and associated cellular genes expressed in KSHV infected cells. In addition, changes in the cellular composition could be elucidated with therapeutic interventions.

Diagnostic Accuracy of Conjunctival Rt-Pcr in Sars-Cov-2: A Systematic Review and Diagnostic Accuracy Meta-Analysis

PURPOSE

To study the positivity rate of conjunctival realtime polymerase chain reaction (RT-PCR) testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

DESIGN

Systematic review and diagnostic accuracy meta-analysis.

METHODS

MEDLINE and EMBASE were queried using medical subject headings terms. Diagnostic accuracy meta-analyses and forest plots were obtained using the RevMan software.

RESULTS

After deduplication, appraisal of abstract titles and full-text analysis of 1441 articles, 42 articles with 3351 COVID-19 patients were included in this review. Of these, 412 conjunctival swabs/Schirmer paper strips tested positive for SARS-CoV-2 by RT-PCR. The pooled sensitivity of the RT-PCR tests across the 24 studies with laboratory-confirmed COVID-19 patients was 10.3%.

CONCLUSIONS

Only 1 in 10 RT-PCR tests performed on conjunctival swabs were positive for SARS-CoV-2. Although this suggests that SARS-CoV-2 is likely present and detectable in the conjunctiva, this detection method has low diagnostic potential.

The effect of a startle-based warning, age, sex, and secondary task on takeover actions in critical autonomous driving scenarios

Introduction: In highly autonomous driving scenarios, it is critical to identify strategies to accelerate reaction times since drivers may take too long to take over control of the vehicle. Previous studies reported that an Acoustic Startling Pre-Stimulus (ASPS, i.e., a loud warning preceding an action) accelerated reaction times in simple ankle flexion exercises.

Methods: In this study, we examined if an ASPS warning leads to shorter takeover reaction times in a sled-simulated evasive swerving maneuver. Twenty-eight participants (seven male adults, seven male teenagers, seven female adults, and seven female teenagers) were instructed to align a marker on the steering wheel with a marker on a lateral post as fast as they could as soon as the lateral sled perturbation (0.75 g) started. Four conditions were examined: with and without an ASPS (105 dB, played 250 ms before sled perturbation for 40 ms), and with and without a secondary task (i.e., texting). A catch trial (ASPS only) was used to minimize anticipation. Human kinematics were captured with an 8-camera 3D motion capture system.

Results: Results showed that the drivers’ hands lifted towards the steering wheel more quickly with the ASPS (169 ± 55 ms) than without (194 ± 46 ms; p = 0.01), and that adult drivers touched the steering wheel quicker with the ASPS (435 ± 54 ms) than without (470 ± 33 ms; p = 0.01). Similar findings were not observed for the teen drivers. Additionally, female drivers were found to lift their hands towards the steering wheel faster than male drivers (166 ± 58 ms vs. 199 ± 36 ms; p = 0.009).

Discussion: Our findings suggest that the ASPS may be beneficial to accelerate driver reaction times during the initiation of a correction maneuver, and that autonomous vehicle warnings may need to be tailored to the age and sex of the driver.

Repositioning forward-leaning vehicle occupants with a pre-pretensioner belt and a startle-based warning in pre-crash scenarios

OBJECTIVE

Pre-pretensioner (PPT) seatbelts have been found to be effective in controlling vehicle occupants' motion response to disturbances in optimally positioned occupants, but it is not clear how the PPT performs when the occupant is initially forward leaning. Previous work demonstrated that an acoustic startling pre-stimulus (ASPS) reduced trunk out-of-position in sled-simulated pre-crash maneuvers. Therefore, the aim of this study was to determine if coupling the PPT with the ASPS could reduce the needed magnitude and rate of belt tension of the PPT to reposition forward leaning occupants to their optimal position within the seatbelt.

METHODS

Sixteen belt-restrained adult human volunteers (8 males and 8 females) restrained by a 3-point seatbelt on a vehicle seat in a forward leaning posture on a sled simulating pre-crash braking (approx. 1 g of maximum acceleration and 0.3 s duration) were exposed to sled perturbations with three belt configurations (low and high force PPT and no PPT), and two warning conditions (ASPS and no-ASPS). Head and trunk positions were extracted from the 3D motion-capture data. Repeated measure ANOVAs were used to understand the effect of sex, PPT, ASPS, and repetition on head and trunk positions. A survival analysis was also performed to understand the probability of the occupants moving rearward in the different conditions.

RESULTS

The probability of the head and trunk to move rearward from the initial position was greater with the PPT than without the PPT (p = 0.01) and with the high force level than the low force level (p = 0.01). The interaction effect of ASPS x PPT showed that with no PPT, there was a greater probability for the head to move rearward from the initial position with ASPS than without ASPS (p < 0.03). The trunk shows a similar trend to the head, but the ASPS vs no-ASPS differences were not statistically significant (p = 0.06). No sex differences were found.

CONCLUSIONS

The PPT, particularly the high level, may be an effective countermeasure on its own to reduce trunk and head out-of-position in forward leaning postures in pre-crash scenarios. The ASPS reduced the occupants' head forward position when the PPT was not available.

Quantitative characterization of AEB pulses across the modern fleet

OBJECTIVE

Characteristics of specific Automatic Emergency Braking (AEB) pulses can result in increased motion of the occupant, which can lead to the occupant being out-of-position such that when a crash occurs protection may be compromised. Quantifying these variations across the modern fleet is crucial to understand the loading environment to which vehicle occupants are exposed. Therefore, we categorized the AEB pulses based on acceleration pulse features such as deceleration magnitude, jerk, and ramp time.

METHODS

A total of 2278 AEB vehicle tests (years 2013-2019) were extracted from the Insurance Institute for Highway Safety (IIHS) database and analyzed. The following pulse characteristics were extracted: Jerk (g/s), Ramp-time (s), and Maximum deceleration (g). A subset of tests in which the tested vehicle did not contact the foam target (n = 1665) was analyzed further, with the following additional variables extracted: Deceleration time (s), Steady-state deceleration (g), and Duration (s). Other non-pulse related features were also considered: Test speed (20 and 40 km/h), Curb weight (Kg), and Vehicle Model Year. Using machine learning methods, the pulses were categorized into clusters. One-way ANOVAs for continuous variables and X² for categorical features were used to assess differences between clusters (p ≤ 0.05).

RESULTS

Using the entirety of the AEB vehicle tests extracted (n = 2278), a total of 3 clusters were selected. The three clusters showed significantly different Jerk, Ramp-time, and Maximum deceleration (p < 0.001). Target contact decreased in AEB tests with more recent vehicle model years (rate of contact 66% in 2014 vs 1.7% in 2019). In one cluster, Jerk and Maximum deceleration increased with vehicle model year. Using the subset of tests in which there was no contact with the foam target (n = 1665), 4 categories of pulses were selected. In both sets of clusters, Ramp-time and Jerk showed moderate inverse correlation (r = -0.7), while all other features showed a low correlation.

CONCLUSIONS

These results show that AEB technology improved over the years in obstacle avoidance. The identification of AEB pulse clusters is important in order to describe distinct approaches to achieving AEB and to be able to reproduce representative AEB pulses in the laboratory and understand the influences of those pulses on occupants' motion.

Time saving, simple and reproducible method to quantify left ventricular function in patients with atrial fibrillation

Introduction

Echocardiography is essential for the management of patients with atrial fibrillation (AF), but current methods are time consuming and lack any evidence of reproducibility.

Purpose

To compare conventional averaging of consecutive beats with an index beat approach, where systolic and diastolic measurements are taken once after two prior beats with a similar RR interval (not more than 60 ms difference).

Methods

Transthoracic echocardiography was performed using a standardized and blinded protocol in patients enrolled into the RAte control Therapy Evaluation in permanent AF randomised controlled trial (RATE-AF; NCT02391337). AF was confirmed in all patients with a preceding 12-lead ECG. A minimum of 30-beat loops were recorded. Left ventricular function was determined using the recommended averaging of 5 and 10 beats and using the index beat method, with observers blinded to clinical details. Complete loops were used to calculate the within-beat coefficient of variation (CV) and intraclass correlation coefficient (ICC) for Simpson's biplane left ventricular ejection fraction (LVEF), global longitudinal strain (GLS) and filling pressure (E/e').

Results

160 patients (median age 75 years (IQR 69–82); 46% female) were included, with median heart rate 100 beats/min (IQR 86–112). For LVEF, the index beat had the lowest CV of 32% compared to 51% for 5 consecutive beats and 53% for 10 consecutive beats (p&lt;0.001). The index beat also had the lowest CV for GLS (26% versus 43% and 42%; p&lt;0.001) and E/e' (25% versus 41% and 41%; p&lt;0.001; see Figure for ICC comparison). Intra-operator reproducibility, assessed by the same operator from two different recordings in 50 patients, was superior for the index beat with GLS bias −0.5 and narrow limits of agreement (−3.6 to 2.6), compared to −1.0 for 10 consecutive beats (−4.0 to 2.0). For inter-operator variability, assessed in 18 random patients, the index beat also showed the smallest bias with narrow confidence intervals (CI). Using a single index beat did not impact on the validity of LVEF, GLS or E/e' measurement when correlated with natriuretic peptides. Index beat analysis substantially shortened analysis time; 35 seconds (95% CI 35 to 39 seconds) for measuring E/e' with the index beat versus 98 seconds (95% CI 92 to 104 seconds) for 10 consecutive beats (see Figure).

Conclusion

Index beat determination of left ventricular function improves reproducibility, saves time and does not compromise validity compared to conventional quantification in patients with heart failure and AF. After independent validation, the index beat method should be adopted into routine clinical practice.

Comparison for measurement of E/e'

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): National Institute of Health Research UK

Neoantigen prediction and computational perspectives towards clinical benefit: recommendations from the ESMO Precision Medicine Working Group

BACKGROUND

The use of next-generation sequencing technologies has enabled the rapid identification of non-synonymous somatic mutations in cancer cells. Neoantigens are mutated peptides derived from somatic mutations not present in normal tissues that may result in the presentation of tumour-specific peptides capable of eliciting antitumour T-cell responses. Personalised neoantigen-based cancer vaccines and adoptive T-cell therapies have been shown to prime host immunity against tumour cells and are under clinical trial development. However, the optimisation and standardisation of neoantigen identification, as well as its delivery as immunotherapy are needed to increase tumour-specific T-cell responses and, thus, the clinical efficacy of current cancer immunotherapies.

METHODS

In this recommendation article, launched by the European Society for Medical Oncology (ESMO), we outline and discuss the available framework for neoantigen prediction and present a systematic review of the current scientific evidence.

RESULTS

A number of computational pipelines for neoantigen prediction are available. Most of them provide peptide major histocompatibility complex (MHC) binding affinity predictions, but more recent approaches incorporate additional features like variant allele fraction, gene expression, and clonality of mutations. Neoantigens can be predicted in all cancer types with high and low tumour mutation burden, in part by exploiting tumour-specific aberrations derived from mutational frameshifts, splice variants, gene fusions, endogenous retroelements and other tumour-specific processes that could yield more potently immunogenic tumour neoantigens. Ongoing clinical trials will highlight those cancer types and combinations of immune therapies that would derive the most benefit from neoantigen-based immunotherapies.

CONCLUSIONS

Improved identification, selection and prioritisation of tumour-specific neoantigens are needed to increase the scope of benefit from cancer vaccines and adoptive T-cell therapies. Novel pipelines are being developed to resolve the challenges posed by high-throughput sequencing and to predict immunogenic neoantigens.

Substrate Supporting Disc Method for Confirmed Detection of Total Coliforms and E. coli in all Foods: Collaborative Study

The Coli Complete® substrate supporting disc (SSD) method for simultaneous confirmed total coliform count and Escherichia coli determination in all foods was compared with AOAC most probable number (MPN) methods, 966.23 and 966.24. Twenty-nine laboratories participated in this collaborative study in which 6 food types were analyzed. Four food types, raw ground beef, pork sausage, raw liquid milk, and nut meats, were naturally contaminated with coliform bacteria. Two foods, dry egg and fresh frozen vegetables, were seeded with coliforms. Three food types, ground beef, raw liquid milk, and pork sausage, were naturally contaminated with E. coli. Although pork sausage was naturally contaminated, the level was very low (&lt;10/50 g); therefore, additional E. coli were inoculated into 1 lot of this food type. Three food types, nut meats, dry egg, and fresh frozen vegetables, were inoculated with E. coli. For naturally contaminated samples, duplicate determinations were made on 3 separate lots for each food type. For inoculated samples, low, medium, and high contamination levels plus uninoculated control samples were examined in duplicate. Data were analyzed separately for total coliform bacteria and for E. coli. Mean log MPN counts were determined by the SSD method and the appropriate AOAC MPN method. Results were then analyzed for repeatability, reproducibility, and mean log MPN statistical equivalence. Results were statistically equivalent for all total coliform levels in all food types except frozen vegetable and raw nut meat uninoculated control samples and 1 lot of pork sausage where the SSD method produced statistically significant greater numbers. For the E. coli determinations, results were statistically equivalent across all samples and all levels for each food type. The SSD method has been adopted first action by AOAC International for confirmed detection of total coliforms and E. coli in all foods.

Thermo-rheological responsive microcapsules for time-dependent controlled release of human mesenchymal stromal cells

Human mesenchymal stromal cells (hMSCs) are adult-source cells that have been extensively evaluated for cell-based therapies. hMSCs delivered by intravascular injection have been reported to accumulate at the sites of injury to promote tissue repair and can also be employed as vectors for the delivery of therapeutic genes. However, the full potential of hMSCs remains limited as the cells are lost after injection due to anoikis and the adverse pathologic environment. Encapsulation of cells has been proposed as a means of increasing cell viability. However, controlling the release of therapeutic cells over time to target tissue still remains a challenge today. Here, we report the design and development of thermo-rheological responsive hydrogels that allow for precise, time dependent controlled-release of hMSCs. The encapsulated hMSCs retained good viability from 76% to 87% dependent upon the hydrogel compositions. We demonstrated the design of different blended hydrogel composites with modulated strength (S parameter) and looseness of hydrogel networks (N parameter) to control the release of hMSCs from thermo-responsive hydrogel capsules. We further showed the feasibility for controlled-release of encapsulated hMSCs within 3D matrix scaffolds. We reported for the first time by a systematic analysis that there is a direct correlation between the thermo-rheological properties associated with the degradation of the hydrogel composite and the cell release kinetics. This work therefore provides new insights into the further development of smart carrier systems for stem cell therapy.

Genomic characterization of HER2-positive breast cancer and response to neoadjuvant trastuzumab and chemotherapy-results from the ACOSOG Z1041 (Alliance) trial

Background

HER2 (ERBB2) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference.

Patients and methods

In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483). We have extracted genomic DNA from both pre-treatment tumor biopsies and blood of these 48 cases, and performed whole genome (WGS) and exome sequencing. Coincident with these efforts, we have generated RNA-seq profiles from 42 of the tumor biopsies. Among patients in this cohort, 24 (50%) achieved a pCR.

Results

We have characterized the genomic landscape of HER2-positive breast cancer and investigated associations between genomic features and pCR. Cases assigned to the HER2-enriched subtype by RNA-seq analysis were more likely to achieve a pCR compared to the luminal, basal-like, or normal-like subtypes (19/27 versus 3/15; P = 0.0032). Mutational events led to the generation of putatively active neoantigens, but were overall not associated with pCR. ERBB2 and GRB7 were the genes most commonly observed in fusion events, and genomic copy number analysis of the ERBB2 locus indicated that cases with either no observable or low-level ERBB2 amplification were less likely to achieve a pCR (7/8 versus 17/40; P = 0.048). Moreover, among cases that achieved a pCR, tumors consistently expressed immune signatures that may contribute to therapeutic response.

Conclusion

The identification of these features suggests that it may be possible to predict, at the time of diagnosis, those HER2-positive breast cancer patients who will not respond to treatment with chemotherapy and trastuzumab.

ClinicalTrials.gov identifiers

NCT00513292, NCT00353483.

Abstract P2-02-14: Circulating tumor DNA predicts clinical outcome in early stage triple negative breast cancer

Background- Triple negative breast cancer (TNBC) is the most aggressive subtype of breast cancer as these patients have the highest risk of recurrence and death. Only 35% of TNBC patients achieve a pathologic complete response (pCR) following neoadjuvant chemotherapy. Patients who do not achieve pCR have a 27% risk of distant recurrence and ultimate death at 3 years compared to 9% for pCR. Unidentified micrometastases are responsible for ultimate overt progression and death. Developing strategies to identify patients with minimal residual disease following curative treatment is an unmet need. Circulating tumor DNA (ctDNA) can characterize and monitor advanced cancers. In this study, we sought to assess if ctDNA can predict clinical outcome in TNBC.

Methods-Biospecimens were obtained from patients with stages II and III TNBC enrolled on a neoadjuvant trial (NCT02124902). Patients have a research biopsy and plasma for ctDNA collected at baseline, cycle 1 day 3, definitive surgery for those with residual disease, and at recurrence for those who relapse. Plasma for ctDNA is also collected every 6 months for 5 years after treatment. Patients receive docetaxel and carboplatin every 3 weeks X 6 cycles. Surgery is 3-5 weeks after chemotherapy. Six patients' serial tumor samples and germline DNA were studied by whole exome sequencing. The median sequencing depth was 90.13x. Sequencing was performed on samples with high cellularity (≥50%). All 6 patients also had serial ctDNA analyzed using Swift Biosciences Accel-Amplicon™ 56G Oncology Panel v2. After identifying somatic mutations in each breast tumor series, we determined the subset of mutations that intersected with the regions targeted by the Swift 56 gene panel. We then evaluated whether corresponding mutations could be detected in ctDNA, and if ctDNA predicted clinical outcome.

Results-Four of the 6 patients were non-pCR with residual disease following chemotherapy. We identified 627 somatic variants by exome analysis that were called by at least two somatic variant callers and passed additional quality filtering steps. Of these, 10 variants overlapped with the Swift panel. TP53 variants were identified in all 6 patients' tumor tissue samples. At least one TP53 variant was identified in 4 patients' baseline pre-chemotherapy ctDNA samples. Both pCR patients had either no detectable ctDNA TP53 mutations (NTN007-ref. in baseline tumor tissue was 19.58% variant allele frequency [VAF]); or clearance of ctDNA following chemotherapy from 4.45% VAF at baseline to 0.06% following chemotherapy (NTN004-ref. in baseline tumor tissue 37.34% VAF). Three non-PCR patients had persistent TP53 mutations in ctDNA during the treatment course. One non-pCR patient did not have detectable mutations in ctDNA. The only patient with recurrent disease whose ctDNA TP53 mutation persisted during the treatment course (baseline VAF-1.65%, cycle 1 day 3-0.78%, definitive surgery-0.09%), was found to have a higher ctDNA VAF at recurrence (29.55%).

Conclusion-In this pilot study, mutation tracking by ctDNA is sensitive and distinguishes pCR from non-pCR in TNBC patients receiving neoadjuvant chemotherapy. ctDNA also identifies recurrence following curative therapy. Evaluating ctDNA as a biomarker of outcome in TNBC is warranted.

Citation Format: Ademuyiwa F, Feng Y-Y, Skidmore Z, Kunisaki J, Walker J, Fulton R, Krysiak K, Skinner T, Weilbaecher K, Ma C, Griffith O, Griffith M. Circulating tumor DNA predicts clinical outcome in early stage triple negative breast cancer [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-02-14.

Bioactive Hydrogel-Filament Scaffolds for Nerve Repair and Regeneration

The design of novel biomaterials is crucial for the advancement of tissue engineering in nerve regeneration. In this study we developed and evaluated novel biosynthetic scaffolds comprising collagen crosslinked with a terpolymer of poly(N-isopropylacrylamide) (PNiPAAm) as conduits for nerve growth. These collagen-terpolymer (collagen-TERP) scaffolds grafted with the laminin pentapeptide YIGSR were previously used as corneal substitutes in pigs and demonstrated enhanced nerve regeneration compared to allografts. The purpose of this project was to enhance neuronal growth on the collagen-TERP scaffolds through the incorporation of supporting fibers. Neuronal growth on these matrices was assessed in vitro using isolated dorsal root ganglia as a nerve source. Statistical significance was assessed using a one-way ANOVA. The incorporation of fibers into the collagen-TERP scaffolds produced a significant increase in neurite extension (p<0.05). The growth habit of the nerves varied with the type of fiber and included directional growth of the neurites along the surface of certain fiber types. Furthermore, the presence of fibers in the collagen-TERP scaffolds appeared to influence neurite morphology and function; neurites grown on fibers-incorporated collagen-TERP scaffolds expressed higher levels of Na channels compared to the scaffolds without fiber. Overall, our results suggest that incorporation of supporting fibers enhanced neurite outgrowth and that surface properties of the scaffold play an important role in promoting and guiding nerve regeneration. More importantly, this study demonstrates the potential value of tissue engineered collagen-TERP hybrid scaffolds as conduits in peripheral nerve repair.

Correction: Functionalised type-I collagen as a hydrogel building block for bio-orthogonal tissue engineering applications

Correction for 'Functionalised type-I collagen as a hydrogel building block for bio-orthogonal tissue engineering applications' by R. Ravichandran et al., J. Mater. Chem. B, 2016, 4, 318-326.

Studies on Oral Lichen Planus : I. Serum Immunoglobulins and Complement

In this preliminary study we explored the possibility of an immunologic component in oral lichen planus by assessment of serum immunoglobulins and complement levels, by skin tests for cellular immunity, and by fluorescent antibody techniques to detect immunoglobulins in the lesions. Although certain abnormalities were noted, none was consistent or of significant magnitude to clarify the cause of this disease.

Regenerative approaches for the cornea

The cornea is the transparent front part of the eye that transmits light to the back of the eye to generate vision. Loss of corneal transparency, if irreversible, leads to severe vision loss or blindness. For decades, corneal transplantation using human donor corneas has been the only option for treating corneal blindness. Despite recent improvement in surgical techniques, donor cornea transplantation remains plagued by risks of suboptimal optical results and visual acuity, immune rejection and eventually graft failure. Furthermore, the demand for suitable donor corneas is increasing faster than the number of donors, leaving thousands of curable patients untreated worldwide. Here, we critically review the state of the art of biomaterials for corneal regeneration. However, the lessons learned from the use of the cornea as a disease model will allow for extension of the biomaterials and techniques for regeneration of more complex organs such as the heart.

A genomic case study of mixed fibrolamellar hepatocellular carcinoma

We report the first comprehensive genomic analysis of a case of mixed conventional and fibrolamellar HCC (mFL-HCC). This study confirms the expression of DNAJB1:PRKACA, a fusion previously associated with pure FL-HCC but not conventional HCC, in mFL-HCC. These results indicate the DNAJB1:PRKACA fusion has diagnostic utility for both pure and mixed FL-HCC.

Background

Mixed fibrolamellar hepatocellular carcinoma (mFL-HCC) is a rare liver tumor defined by the presence of both pure FL-HCC and conventional HCC components, represents up to 25% of cases of FL-HCC, and has been associated with worse prognosis. Recent genomic characterization of pure FL-HCC identified a highly recurrent transcript fusion (DNAJB1:PRKACA) not found in conventional HCC.

Patients and Methods

We performed exome and transcriptome sequencing of a case of mFL-HCC. A novel BAC-capture approach was developed to identify a 400 kb deletion as the underlying genomic mechanism for a DNAJB1:PRKACA fusion in this case. A sensitive Nanostring Elements assay was used to screen for this transcript fusion in a second case of mFL-HCC, 112 additional HCC samples and 44 adjacent non-tumor liver samples.

Results

We report the first comprehensive genomic analysis of a case of mFL-HCC. No common HCC-associated mutations were identified. The very low mutation rate of this case, large number of mostly single-copy, long-range copy number variants, and high expression of ERBB2 were more consistent with previous reports of pure FL-HCC than conventional HCC. In particular, the DNAJB1:PRKACA fusion transcript specifically associated with pure FL-HCC was detected at very high expression levels. Subsequent analysis revealed the presence of this fusion in all primary and metastatic samples, including those with mixed or conventional HCC pathology. A second case of mFL-HCC confirmed our finding that the fusion was detectable in conventional components. An expanded screen identified a third case of fusion-positive HCC, which upon review, also had both conventional and fibrolamellar features. This screen confirmed the absence of the fusion in all conventional HCC and adjacent non-tumor liver samples.

Conclusion

These results indicate that mFL-HCC is similar to pure FL-HCC at the genomic level and the DNAJB1:PRKACA fusion can be used as a diagnostic tool for both pure and mFL-HCC.

Coloured cornea replacements with anti-infective properties: expanding the safe use of silver nanoparticles in regenerative medicine

Despite the broad anti-microbial and anti-inflammatory properties of silver nanoparticles (AgNPs), their use in bioengineered corneal replacements or bandage contact lenses has been hindered due to their intense yellow coloration. In this communication, we report the development of a new strategy to pre-stabilize and incorporate AgNPs with different colours into collagen matrices for fabrication of corneal implants and lenses, and assessed their in vitro and in vivo activity.

Abstract PD6-02: The genomics of response to neoadjuvant trastuzumab and chemotherapy in HER2-positive breast cancer – Results from the ACOSOG Z1041 (Alliance) trial

Support: Alliance U10CA180821; Alliance Statistical Center grant U10CA180882; ACOSOG grant U10CA76001

HER2 gene amplification and its corresponding overexpression are present in approximately 12% of invasive breast cancers. While HER2-targeted agents (e.g. trastuzumab, pertuzumab, and lapatinib) are effective treatments, resistance remains a major cause of death from HER2-positive breast cancer. Mechanisms of resistance are poorly understood. Without a molecular understanding of these mechanisms, therapeutic advances will be delayed. We have generated molecular profiles of primary HER2-positive breast cancers treated on a neoadjuvant clinical trial, and compared features associated with response to treatment.

The American College of Surgeons Oncology Group (ACOSOG) Z1041 trial in HER2-positive breast cancer was designed to compare the pathologic complete response (pCR) rate of a regimen of paclitaxel and trastuzumab, followed by trastuzumab administered with fluorouracil, epirubicin, and cyclophosphamide (FEC-75) to a regimen of FEC-75 alone followed by paclitaxel and trastuzumab. The trial identified no difference in pCR rates between the regimens (Buzdar et al., The Lancet Oncology 2013). In supplement to the tissues obtained from 37 of the patients enrolled in the Z1041 trial, an additional 11 cases were obtained from a single institution study (201101961) of patients treated with neoadjuvant trastuzumab that had pre-treatment core biopsies suitable for genomic studies.

We have extracted genomic DNA from both pretreatment tumor biopsies and blood samples of these 48 patients and performed whole genome (WGS) and exome sequencing. Coincident with these efforts, we have extracted high quality RNA from 42 of the 48 biopsies, and have processed RNA-seq profiles of the tumors. Among patients in this cohort, 24 (50%) achieved a pCR. Because no difference was observed between arms of the Z1041 trial, patients with or without a pCR were directly compared without adjusting for treatment regimen.

On average, each tumor and normal sample pair were sequenced to a depth of 49.4x and 32.5x by WGS respectively. In total, 15,027 candidate somatic variants were identified in known genes, including 11,606 missense, 860 nonsense, and 418 frameshift insertions or deletions. Preliminary results identified mutations in HER2 that were associated with the failure to achieve pCR in several cases. Furthermore, tumors assigned to the HER2-enriched subtype by RNA-seq analysis were more likely to achieve a pCR (19 compared to 8) than tumors with genomic features indicative of either the luminal or basal-like subtypes (3 compared to 12); a significant difference in the proportion of cases that achieve pCR (Fisher's exact test p-value = 0.0032). The identification of these features suggests that it may be possible to predict, at the time of diagnosis, those patients who will not respond to the current standard of care for HER2-positive breast cancer.

Citation Format: Lesurf R, Griffith O, Griffith M, Watson MA, Hoog J, Ellis MJ, Ota D, Suman VJ, Meric-Bernstam F, Leitch AM, Boughey JC, Unzeitig G, Buzdar AU, Hunt KK, Mardis ER. The genomics of response to neoadjuvant trastuzumab and chemotherapy in HER2-positive breast cancer – Results from the ACOSOG Z1041 (Alliance) trial. [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 PD6-02.

Self-assembled collagen-like-peptide implants as alternatives to human donor corneal transplantation

PEG-conjugated collagen-like peptides promote corneal regeneration in a pig cornea.

Functionalised type-I collagen as a hydrogel building block for bio-orthogonal tissue engineering applications

Modulating the hydrogel properties from injectable to implantable scaffolds using the bio-orthogonal thiol-Michael addition click reaction.

Controlled Delivery of Human Cells by Temperature Responsive Microcapsules

Cell therapy is one of the most promising areas within regenerative medicine. However, its full potential is limited by the rapid loss of introduced therapeutic cells before their full effects can be exploited, due in part to anoikis, and in part to the adverse environments often found within the pathologic tissues that the cells have been grafted into. Encapsulation of individual cells has been proposed as a means of increasing cell viability. In this study, we developed a facile, high throughput method for creating temperature responsive microcapsules comprising agarose, gelatin and fibrinogen for delivery and subsequent controlled release of cells. We verified the hypothesis that composite capsules combining agarose and gelatin, which possess different phase transition temperatures from solid to liquid, facilitated the destabilization of the capsules for cell release. Cell encapsulation and controlled release was demonstrated using human fibroblasts as model cells, as well as a therapeutically relevant cell line-human umbilical vein endothelial cells (HUVECs). While such temperature responsive cell microcapsules promise effective, controlled release of potential therapeutic cells at physiological temperatures, further work will be needed to augment the composition of the microcapsules and optimize the numbers of cells per capsule prior to clinical evaluation.

Novel mRNA isoforms and mutations of uridine monophosphate synthetase and 5-fluorouracil resistance in colorectal cancer

The drug fluorouracil (5-FU) is a widely used antimetabolite chemotherapy in the treatment of colorectal cancer. The gene uridine monophosphate synthetase (UMPS) is thought to be primarily responsible for conversion of 5-FU to active anticancer metabolites in tumor cells. Mutation or aberrant expression of UMPS may contribute to 5-FU resistance during treatment. We undertook a characterization of UMPS mRNA isoform expression and sequence variation in 5-FU-resistant cell lines and drug-naive or -exposed primary and metastatic tumors. We observed reciprocal differential expression of two UMPS isoforms in a colorectal cancer cell line with acquired 5-FU resistance relative to the 5-FU-sensitive cell line from which it was derived. A novel isoform arising as a consequence of exon skipping was increased in abundance in resistant cells. The underlying mechanism responsible for this shift in isoform expression was determined to be a heterozygous splice site mutation acquired in the resistant cell line. We developed sequencing and expression assays to specifically detect alternative UMPS isoforms and used these to determine that UMPS was recurrently disrupted by mutations and aberrant splicing in additional 5-FU-resistant colorectal cancer cell lines and colorectal tumors. The observed mutations, aberrant splicing and downregulation of UMPS represent novel mechanisms for acquired 5-FU resistance in colorectal cancer.

A stromal cell-derived factor-1 releasing matrix enhances the progenitor cell response and blood vessel growth in ischaemic skeletal muscle

Although many regenerative cell therapies are being developed to replace or regenerate ischaemic muscle, the lack of vasculature and poor persistence of the therapeutic cells represent major limiting factors to successful tissue restoration. In response to ischaemia, stromal cell-derived factor-1 (SDF-1) is up-regulated by the affected tissue to stimulate stem cell-mediated regenerative responses. Therefore, we encapsulated SDF-1 into alginate microspheres and further incorporated these into an injectable collagen-based matrix in order to improve local delivery. Microsphere-matrix impregnation reduced the time for matrix thermogelation, and also increased the viscosity reached. This double-incorporation prolonged the release of SDF-1, which maintained adhesive and migratory bioactivity, attributed to chemotaxis in response to SDF-1. In vivo, treatment of ischaemic hindlimb muscle with microsphere-matrix led to increased mobilisation of bone marrow-derived progenitor cells, and also improved recruitment of angiogenic cells expressing the SDF-1 receptor (CXCR4) from bone marrow and local tissues. Both matrix and SDF-1-releasing matrix were successful at restoring perfusion, but SDF-1 treatment appeared to play an earlier role, as evidenced by arterioles that are phenotypically older and by increased angiogenic cytokine production, stimulating the generation of a qualitative microenvironment for a rapid and therefore more efficient regeneration. These results support the release of implanted SDF-1 as a promising method for enhancing progenitor cell responses and restoring perfusion to ischaemic tissues via neovascularisation.

Narrow band (light) imaging of oral mucosa in routine dental patients. Part I: Assessment of value in detection of mucosal changes

The purpose of this investigation was to determine the value of adding narrow band (light) imaging (NBI) to the standard oral soft tissue examination process used to detect mucosal change. A total of 620 dental patients who came to the clinic for regular dental evaluation or for treatment of acute dental problems were given a standard oral soft tissue examination by dental students under faculty supervision. The results of the white light examination were recorded after the tissues were examined with NBI, at which point areas with a loss of fluorescence (LOF) were recorded. The nature of the tissue change was classified clinically as normal variation, inflammatory, traumatic, dysplastic, or other, and patients were categorized depending on their clinical findings: normal, need follow-up visit, or immediate biopsy. Risk factors related to oral dysplasia also were recorded. The addition of NBI added between one and two minutes to the examination process. Of the 620 examinations, an area with an LOF suggestive of pathology was detected in 69 subjects (11.1%). After a second immediate evaluation, 28 of the 69 subjects were scheduled for follow-up or biopsy. None of the lesions discovered in these 28 subjects had been detected using standard (white light) examination. Adding NBI to the routine clinical examination resulted in detection of changes not seen with white light examination in 11.1% of patients; of these, a small but important number were found to have otherwise undetected persistent changes representing inflammatory lesions or potentially dangerous oral dysplasia. Adding NBI as an adjunctive diagnostic procedure improved the quality and outcome of the examination process.

Ultrashort-pulse laser with an intracavity phase shaping element

A novel ultrashort-pulse laser cavity configuration that incorporates an intracavity deformable mirror as a phase control element is reported. A user-defined spectral phase relation of 0.7 radians relative shift could be produced at around 1035 nm. Phase shaping as well as pulse duration optimization was achieved via a computer-controlled feedback loop.

Regeneration of functional nerves within full thickness collagen-phosphorylcholine corneal substitute implants in guinea pigs

Our objective was to evaluate promotion of tissue and nerve regeneration by extracellular matrix (ECM) mimics, using corneal implantation as a model system. Porcine type I collagen and 2-methacryloyloxyethyl phosphorylcholine (MPC) were crosslinked using 1-ethyl-3-(3-dimethyl aminopropyl) carbodiimide (EDC) and N-hydroxysuccinimide (NHS) and moulded into appropriate corneal dimensions to serve as substitutes for natural corneal ECM. These were implanted as full thickness grafts by penetrating keratoplasty into the corneas of guinea pigs after removal of the host tissue, and tracked over eight months, by clinical examination, slit-lamp biomicroscopy, and esthesiometry. Histopathology and ex vivo nerve terminal impulse recordings were performed at three months and at eight months. The implants promoted regeneration of corneal cells, nerves and the tear film, while retaining optical clarity. After three months, electrophysiological recordings showed evidence of mechano-nociceptors, and polymodal units inside the implants, while cold-sensitive units were present only on the peripheral host cornea. Following eight months, the incidence of nerve activity and the frequency of spontaneous firing were higher than in control eyes as reported for regenerating fibers. Active cold nerve terminals also innervated the implant area. We show that ECM mimetic materials can promote regeneration of corneal cells and functional nerves. The simplicity in fabrication and demonstrated functionality shows potential for ECM substitutes in future clinical applications.

Optimal neural differentiation and extension of hybrid neuroblastoma cells (NDC) for nerve-target evaluations using a multifactorial approach

In vitro models of tissues, such as the cornea, represent systems for modeling cell-to-cell interactions and tissue function. The objective of this study was to develop an optimized nerve differentiation medium to incorporate into a 3D in vitro model to study innervation and cell targeting. A hybrid neuroblastoma cell line (NDC) was examined for its ability to differentiate into neurons, produce neurites, and functionally contact target cells. Neuronal differentiation of NDCs was optimized through a combinatorial approach which involved culturing cells in the presence of various extracellular matrices and soluble factors. A serum-free medium containing nerve growth factor (NGF), dimethyl sulfoxide (DMSO), or dexamethasone resulted in the greatest proportion of NDCs demonstrating a neuronal morphology. Similarly, with supplementation of cyclic AMP (cAMP) or NGF, neurite extension was optimized. Combining these factors generated an optimized differentiation and extension medium, relative to the individual components alone. In co-culture with epithelial cells, NDC neurites generated in the optimized medium formed contacts with epithelial targets and produced substance P. Similarly, NDCs seeded into a collagen matrix produced neurites that projected through the matrix to target epithelial cells, promoted epithelial stratification, and increased the rate of epithelial wound healing. As well, differentiated NDCs could target and alter acetylcholine receptor clustering in mouse C2C12 myotubes, demonstrating synaptic plasticity. Our data supports the use of NDCs, in combination with optimized medium, for generating an innervated in vitro model.

Making the most of routine data in palliative care research--a case study analysis of linked hospital and mortality data on cancer and heart failure patients in Scotland and Oxford

The research base of palliative care is growing rapidly, but despite methodological advances, some of the practical challenges of working with people at the end of life will persist. This means that analysis of routine data is arguably more important in studying palliative care than it is in other aspects of health services research. End-of-life researchers have been using the high-quality linked data from cancer registries for many years. This paper explores the value of a less well-known resource for palliative care research: linked mortality and hospital activity data. Two case studies are presented using information from Scotland (population 5.1 million) and the former Oxford region of England (population 2.5 million). The advantages and limitations of linked hospital and mortality data for research and service planning in palliative care are drawn out through analyses investigating hospital bed utilisation by people with cancer and heart failure and the influence of social deprivation on the use of hospital services in the last year of life. The use of such data deserves a higher profile.

Prevalence of gastrointestinal bacterial pathogens in a population of zoo animals

Faecal prevalence of gastrointestinal bacterial pathogens, including Campylobacter, Escherichia coli O157:H7, Salmonella, Shigella, Yersinia, as well as Arcobacter, were examined in 317 faecal specimens from 44 animal species in Belfast Zoological Gardens, during July-September 2006. Thermophilic campylobacters including Campylobacter jejuni, Campylobacter coli and Campylobacter lari, were the most frequently isolated pathogens, where members of this genus were isolated from 11 animal species (11 of 44; 25%). Yersinia spp. were isolated from seven animal species (seven of 44; 15.9%) and included, Yersinia enterocolitica (five of seven isolates; 71.4%) and one isolate each of Yersinia frederiksenii and Yersinia kristensenii. Only one isolate of Salmonella was obtained throughout the entire study, which was an isolate of Salmonella dublin (O 1,9,12: H g, p), originating from tiger faeces after enrichment. None of the animal species found in public contact areas of the zoo were positive for any gastrointestinal bacterial pathogens. Also, water from the lake in the centre of the grounds, was examined for the same bacterial pathogens and was found to contain C. jejuni. This study is the first report on the isolation of a number of important bacterial pathogens from a variety of novel host species, C. jejuni from the red kangaroo (Macropus rufus), C. lari from a maned wolf (Chrysocyon brachyurus), Y. kristensenii from a vicugna (Vicugna vicugna) and Y. enterocolitica from a maned wolf and red panda (Ailurus fulgens). In conclusion, this study demonstrated that the faeces of animals in public contact areas of the zoo were not positive for the bacterial gastrointestinal pathogens examined. This is reassuring for the public health of visitors, particularly children, who enjoy this educational and recreational resource.

Impact of whole genome amplification on analysis of copy number variants

Large-scale copy number variants (CNVs) have recently been recognized to play a role in human genome variation and disease. Approaches for analysis of CNVs in small samples such as microdissected tissues can be confounded by limited amounts of material. To facilitate analyses of such samples, whole genome amplification (WGA) techniques were developed. In this study, we explored the impact of Phi29 multiple-strand displacement amplification on detection of CNVs using oligonucleotide arrays. We extracted DNA from fresh frozen lymph node samples and used this for amplification and analysis on the Affymetrix Mapping 500k SNP array platform. We demonstrated that the WGA procedure introduces hundreds of potentially confounding CNV artifacts that can obscure detection of bona fide variants. Our analysis indicates that many artifacts are reproducible, and may correlate with proximity to chromosome ends and GC content. Pair-wise comparison of amplified products considerably reduced the number of apparent artifacts and partially restored the ability to detect real CNVs. Our results suggest WGA material may be appropriate for copy number analysis when amplified samples are compared to similarly amplified samples and that only the CNVs with the greatest significance values detected by such comparisons are likely to be representative of the unamplified samples.

Differentiation of a fibrin gel encapsulated chondrogenic cell line

Hyaline cartilage has very limited regenerative capacity following damage. Therefore engineered tissue substitutes have been the focus of much research. Our objective was to develop a fibrin-based scaffold as a cell delivery vehicle and template for hyaline cartilage regeneration, and compare its cellular properties against monolayer and pellet culture for chondrogenic cells. The chondrogenic precursor cell line, RCJ 3.1C5.18 (C5.18), was chosen as a test system for evaluating the effect of various culture conditions, including cell encapsulation, on articular chondrogenic cell differentiation. The C5.18 cells in monolayer showed elevated expression of collagen II, an articular chondrogenic marker, but also markers for fibrocartilage differentiation (collagen I and versican) when cultured with chondrogenic medium as compared to basic maintenance medium. Pellets of C5.18 cells cultured in chondrogenic medium were histologically more organized in structure than pellets cultured in control maintenance medium. The chondrogenic medium cultured pellets also secreted an extracellular matrix that was comprised of type II with very little type I collagen, indicating a trend towards a more hyaline-like cartilage. Moreover, when cultured in chondrogenic medium, fibrin-encapsulated C5.18 cells elaborated an extracellular matrix containing type II collagen, as well as aggrecan, which are both components of hyaline cartilage. This indicated a more articular-like chondrogenic differentiation for fibrin encapsulated C5.18 cells. The results of these experiments provide evidence that the C5.18 cell line can be used as a tool to evaluate potential scaffolds for articular cartilage tissue engineering.

Promotion of angiogenesis in tissue engineering: developing multicellular matrices with multiple capacities

One of the aims of tissue engineering is to be able to develop multi-tissue organs in the future. This requires the optimization of conditions for the differentiation of multiple cell types and maintenance of the differentiated phenotype within complex engineered tissues. The goal of this study was to develop prototype tissue engineered matrices to support the simultaneous growth of different cell types with a particular focus on the angiogenic process. We examined two different matrix compositions for the promotion of blood vessel and tube formation. A fibrin-based matrix with the addition of a combination of growth factors supported vascular growth and the invasion of inflammatory cells. Using this fibrin matrix, in combination with a collagen-based hydrogel, a simple in vitro model of the cornea with adjacent sclera was developed that was complete with innervation and vascular structures. In addition, we showed that collagen-based matrices were effective in delivering mononuclear endothelial progenitor cells to ischemic tissue in vivo, and allowing these cells to incorporate into vascular structures. It is anticipated that with further development, these matrices have potential for use as delivery matrices for cell transplantation and for in vitro study purposes of multiple cell types.

Introducing mechanical biological waste treatment in South Africa: a comparative study

This paper presents the results of the first pilot project on mechanical biological waste treatment (MBWT) in South Africa. The study has shown that biological waste treatment in windrows using a passive aeration system that utilises thermal convection to drive the aeration process within a windrow of waste is appropriate for South Africa, in relation to low capital costs, low energy inputs, limited plant requirements and potential for labour-intensive operations. The influence of climate, waste composition and operational facilities was evaluated to optimise the treatment technique to local conditions. The maximum temperatures reached during the intensive thermophilic stage were effectively equivalent to the German experience. The lower CO2 production experienced in the South African trials was attributed to a different waste stream (high presence of plastics) due to the absence of a proper source separated waste collection system. An accurate adjustment of the input material (structural matter in particular) to the specific ambient conditions and irrigation during composting should result in higher organic carbon degradation efficiency in equivalent timeframes. This preliminary experience suggests that the applicability of MBWT in emerging countries, such as South Africa, is directly dependant on the mechanical treatment steps, available operational facilities and nature of the input material.