Reconstruction of Orbital Exenteration Defects with Cross-median Forehead Flaps

The aim of this study was to examine the role of forehead flaps in the reconstruction of orbital defects after exenteration. Patients undergoing orbital exenteration and reconstruction using median forehead flaps from January 2002 to August 2019 were enrolled in this retrospective study. All the patients were evaluated for wound complications, functional results, and tumor relapse. In total, 105 patients completed the study. Twenty-nine complications in 24 of these patients were assessed. The most common complications were wound dehiscence (11%), partial necrosis of the flap (6%), and bleeding (4%). A major complication occurred in two patients (2%), necessitating surgical correction. Only one patient had a local relapse. Sixty patients received osseointegrated implants, and 58 of them were treated with facial prostheses. The follow-up periods ranged from 6 to 189 months. Thus, forehead flap reconstruction after exenteration is a reliable method with a low complication rate. This technique can be used for primary or secondary reconstruction, and excellent long-term functional results can be achieved. A relapse-oriented follow-up is certainly possible.

nf-core/nanostring: a pipeline for reproducible NanoString nCounter analysis

MOTIVATION

The NanoString™ nCounter® technology platform is a widely used targeted quantification platform for the analysis of gene expression of up to ∼800 genes. Whereas the software tools by the manufacturer can perform the analysis in an interactive and GUI driven approach, there is no portable and user-friendly workflow available that can be used to perform reproducible analysis of multiple samples simultaneously in a scalable fashion on different computing infrastructures.

RESULTS

Here, we present the nf-core/nanostring open-source pipeline to perform a comprehensive analysis including quality control and additional features such as expression visualization, annotation with additional metadata and input creation for differential gene expression analysis. The workflow features an easy installation, comprehensive documentation, open-source code with the possibility for further extensions, a strong portability across multiple computing environments and detailed quality metrics reporting covering all parts of the pipeline. nf-core/nanostring has been implemented in the Nextflow workflow language and supports Docker, Singularity, Podman container technologies as well as Conda environments, enabling easy deployment on any Nextflow supported compatible system, including most widely used cloud computing environments such as Google GCP or Amazon AWS.

AVAILABILITY AND IMPLEMENTATION

The source code, documentation and installation instructions as well as results for continuous tests are freely available at https://github.com/nf-core/nanostring and https://nf-co.re/nanostring.

Solitary Fibrous Tumours of the Orbit - Clinical Pathology, Therapy and Prognosis

BACKGROUND

Solitary fibrous tumours are rare. The aim of this study is to describe the clinical features, therapy and outcome of affected patients and to identify factors associated with recurrence.

METHODS

Retrospective study of a cohort of 20 patients who underwent surgery for orbital solitary fibrous tumour at the University Department of Oral and Maxillofacial Surgery between 2002 and 2023. Demographic, clinical, and therapeutic data as well as tumour follow-up results were collected. Tumour volume and molecular genetic mutations were retrospectively determined.

RESULTS

The median patient age was 49.5 years at initial surgery. The left orbit was affected in 65% of cases. The most common clinical symptom was proptosis (80%). This was reported with a mean lateral difference of 3.9 mm (range: 1 - 10 mm). The tumours were localised predominantly in the intra- and extraconal space, craniolateral quadrant and middle third. The median tumour volume was 7.66 cm³ (range 2.15 - 12.57 cm³). In all patients, the diagnosis was made by pathological examination. All tumours investigated showed a NAB2-STAT6 mutation. The most frequently detected mutation was the fusion NAB2 exon 4 - STAT6 exon 2. All patients were initially managed with frontolateral orbitotomy. Incomplete resection (R1-status) occurred in 35% (n = 7). The recurrence rate was 25% (n = 5), with a median disease-free interval of 45.5 months (range 23 - 130). 80% (n = 4) of recurrences were initially R1-resected.

CONCLUSION

Orbital solitary fibrous tumours are rare tumours and are clinically manifested by signs of displacement of orbital structures. Diagnosis is made by histology and immunohistochemistry and can be proven with the molecular genetic detection of the NAB2-STAT6 mutation. The therapy of choice is complete surgical resection. R1-resection is more likely in the intraconal location as well as in location in the posterior third of the orbit - due to difficult surgical accessibility. The greatest risk factor for the development of recurrence is incomplete surgical excision. Late recurrences are possible, which is why a long-term connection to a specialised clinic is necessary.

MRI-based long-term follow-up of indolent orbital lymphomas after curative radiotherapy: imaging remission criteria and volumetric regression kinetics

We systematically analyzed the kinetics of tumor regression, the impact of residual lesions on disease control and the applicability of the Lugano classification in follow-up MRI of orbital non-Hodgkin lymphomas that were irradiated with photons. We retrospectively analyzed a total of 154 pre- and post-irradiation MRI datasets of 36 patients with low-grade, Ann-Arbor stage I, orbital non-Hodgkin lymphomas. Patients with restricted conjunctival involvement were excluded. Lymphoma lesions were delineated and volumetrically analyzed on T1-weighted sequences. Tumor residues were present in 91.2% of all cases during the first six months after treatment. Volumetric partial response rates (> 50% volume reduction) were 75%, 69.2%, and 50% at 12-24 months, 36-48 months and > 48 months after the end of treatment. The corresponding complete response (CR) rates according to the Lugano classification were 20%, 23.1% and 50%. During a median clinical follow-up of 37 months no significant differences in progression free survival (PFS) rates were observed between the CR and non-CR group (p = 0.915). A residual tumor volume below 20% of the pretreatment volume should be expected at long-term follow-up beyond one year after radiotherapy.

Long-term follow-up and health-related quality of life among cancer survivors with stage IEA orbital-type lymphoma after external photon-beam radiotherapy: Results from a longitudinal study

We assessed the long-term outcomes and treatment-related adverse effects of patients with Stage I, "orbital-type" lymphomas that were uniformly treated with photons. All consecutive patients diagnosed with low-grade, Ann Arbor Stage IEA orbital lymphoma treated between 1999 and 2020 at our department were retrospectively reviewed. We excluded patients with exclusive conjunctival involvement, typically treated with en face electrons. In order to quantify radiotherapy related side effects we applied the CTCAE criteria, analyzed changes in visual acuity, quantified dry eye symptoms by use of the Ocular Surface Disease Index (OSDI) score and applied the EORTC QLQ-C30 questionnaire for quality of life (QoL) assessment. In total 66 eyes of 62 patients were irradiated with a median dose of 30.6 Gy. The median follow-up was 43.5 months. The predominant histological subtype were MALT lymphomas. No local failure occurred in this cohort. Of nine outfield relapses, six solely occurred in the contralateral eye. The 5- and 10- years distant progression free survival rates (PFS) were 81.4% and 63.5%. The 5- and 10-years overall survival rates were 85.1% and 71.9% without any tumor related death. Of the acute toxicities none was higher than CTCAE grade 1. The predominant late toxicities were dry eyes (21.2%) of CTCAE Grade <2 and radiation induced cataracts (19.7%). During long-term follow up the average visual acuity did not deteriorate. The global QoL was worst before treatment and improved significantly after 24 months (p = 0.007). External beam radiotherapy of "orbital-type" lymphomas with photons is an effective and gentle treatment option with excellent local control rates. From the high control rates the trend to use slightly lower total doses of 24-27 Gy with conventional fractionation is supported. As non-coplanar radiotherapy techniques improved and total doses can slightly be reduced, the current status of radiotherapy as first line therapy is provided.

Abstract 1991: Characterization of the exome, transcriptome, and immunopeptidome to map alterations in primary and recurrent glioblastoma

Glioblastoma is known as the most aggressive and most common malignant primary tumor in the central nervous system. Current treatment options comprise maximal surgical resection followed by radiation and/or chemotherapy with temozolomide. However, these therapies are not able to eliminate all tumor cells, which in turn inevitably leads to disease recurrence and an alteration of identified targets in the context of clonal evolution and potential hypermutation. T cell-based immunotherapy holds great promise to target malignant cells with CAR T cell and vaccination strategies, showing first promising results in glioblastoma. These therapies rely on the rejection of cancer cells through recognition of tumor antigens and T cell-mediated cytotoxicity. In previous work, we have characterized such tumor antigens in primary glioblastoma (Neidert et al., Acta Neuropathol, 2018), nonetheless, alterations in relapsed disease have not been addressed thus far. This study investigated the whole exome, transcriptome, and mass-spectrometry-based immunopeptidome of 38 primary and 24 recurrent tumors, including 22 autologous glioblastoma pairs, to determine alterations that occur during glioblastoma progression on multiple comics levels. In concordance with Neftel et al., Cell, 2019, we identified mutations that can be allocated to astrocyte- and mesenchymal-like classified genes. In addition, an increase in the mutation rate in recurrent glioblastoma was observed which is attributed to radiation and chemotherapy pretreatment of tumors. These newly arising tumor-specific mutations give rise to HLA-presented neoepitopes in the primary cohort. Moreover, we identified transcripts that are differentially expressed between the two cohorts, showing a higher expression of transcripts related to immune system responses in the recurrent cohort. Immunopeptidome analysis of the two cohorts revealed high frequent glioblastoma-exclusive HLA class I and class II ligands presented in both the primary and recurrent cohort, serving as universally applicable tumor antigens. Class I and II HLA ligands of each sample were analyzed and revealed 2,146 HLA class I- and 2,753 HLA class II presented antigens that were uniquely identified on primary glioblastoma. A total of 610 and 1,886 source proteins represent recurrence-exclusive antigens presented on HLA class I or II molecules, respectively. Together this work addressed differences in tumor antigen expression and presentation between primary and recurrent glioblastoma using these omics layers to create an overview of the alterations that occur during disease progression. Besides providing a deep insight into the glioblastoma (immuno-)biology during progression, this study yields targets for innovative immunotherapeutic approaches to eliminate residual cells and improve survival in glioblastoma patients.

Citation Format: Marissa L. Dubbelaar, Lena K. Freudenmann, Jonas Scheid, Julia Velz, Gioele Medici, Konstantina Kapolou, Malte Mohme, Leon Bichmann, Marie Gauder, Stefan Czemmel, Christopher Mohr, Daniel J. Kowalewski, Manfred Westphal, Katrin Lamszus, Luca Regli, Michael Weller, Hans-Georg Rammensee, Helmut Salih, Marian C. Neidert, Juliane S. Walz. Characterization of the exome, transcriptome, and immunopeptidome to map alterations in primary and recurrent glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1991.

1-GHz dual-comb spectrometer with high mutual coherence for fast and broadband measurements

Dual-frequency comb spectroscopy permits broadband precision spectroscopy with high acquisition rate. The combs' repetition rates as well as the mutual coherence between the combs are key to fast and broadband measurements. Here, we demonstrate a 1-GHz high-repetition-rate dual-comb system with high mutual coherence (sub-Hz heterodyne beatnotes) based on mature, digitally controlled, low-noise erbium-doped mode-locked lasers. Two spectroscopy experiments are performed with acquisition parameters not attainable in a 100-MHz system: detection of water vapor absorption around 1375 nm, illustrating the potential for fast and ambiguity-free broadband operation, as well as acquisition of narrow gas absorption features across a spectral span of 0.6 THz (600 comb lines) in only 5 μs.

Next generation Fc scaffold for multispecific antibodies

Bispecific antibodies (Bispecifics) demonstrate exceptional clinical potential to address some of the most complex diseases. However, Bispecific production in a single cell often requires the correct pairing of multiple polypeptide chains for desired assembly. This is a considerable hurdle that hinders the development of many immunoglobulin G (IgG)-like bispecific formats. Our approach focuses on the rational engineering of charged residues to facilitate the chain pairing of distinct heavy chains (HC). Here, we deploy structure-guided protein design to engineer charge pair mutations (CPMs) placed in the CH3-CH3' interface of the fragment crystallizable (Fc) region of an antibody (Ab) to correctly steer heavy chain pairing. When used in combination with our stable effector functionless 2 (SEFL2.2) technology, we observed high pairing efficiency without significant losses in expression yields. Furthermore, we investigate the relationship between CPMs and the sequence diversity in the parental antibodies, proposing a rational strategy to deploy these engineering technologies.

Abstract 1285: In vitro characterization of sotorasib and other RAS ‘His95-groove' binders and investigation of resistance mechanisms

Sotorasib (formerly known as AMG 510), the first-in-class KRASG12C inhibitor, has demonstrated promising clinical efficacy in KRAS p.G12C mutant cancers. Sotorasib binds to KRASG12C through a unique interaction with a surface groove created by side-chain rotation of histidine 95 (His95). Characterization of sotorasib and other His95-groove binders revealed enhanced potency and selectivity as compared to other KRASG12C inhibitor scaffolds, which bind in the P2 pocket via hydrogen bonding with His95. The novel binding mode of sotorasib also translated to similar biochemical and cellular potencies against both NRASG12C and HRASG12C, which encode leucine and glutamine at position 95, respectively. In contrast, other KRASG12C inhibitor scaffolds demonstrated a dramatic loss of potency against NRASG12C and HRASG12C, suggesting that the alternate residues impacted the binding of these molecules in the P2 pocket. To extend characterization of the cellular effects of RAS ‘His95-groove' binders, we analyzed the expression of major histocompatibility complex (MHC) class I proteins and other inflammatory markers in multiple human and murine KRAS p.G12C cell lines. These studies revealed a partial dependency on the cytosolic DNA-sensing (cGAS/STING) pathway for the effects observed with some markers. Finally, His95-groove binders were evaluated for potential mechanisms of resistance to this class of KRASG12C inhibitors. In the mouse syngeneic Lewis Lung Carcinoma (LL/2) cell line, which carries both KRAS p.G12C and NRAS p.Q61H mutations, intrinsic resistance to KRASG12C inhibition was observed, but combination treatment with the MEK inhibitor trametinib demonstrated synergistic improvement in the effects on viability. MIA PaCa-2 and NCI-H358 models of acquired resistance to KRASG12C inhibition were also developed through long-term exposure to high concentrations of sotorasib. Characterization of these resistant cell lines indicated a requirement for constant exposure to sotorasib and also showed that the resistance was not due to genetic alterations but involved either overexpression of KRAS or bypass signaling through alternative pathways. Taken together, these data demonstrate that His95-binders like sotorasib display superior potency and off-target selectivity, as well as unique activity against all versions of RASG12C. In addition, characterization of potential resistance mechanisms to sotorasib will inform combination strategies in the clinic.

Citation Format: Anne Y. Saiki, Deanna Mohn, Yu Li, Tao Osgood, Karen Rex, Hui-Ling Wang, Ivonne Archibeque, Christopher Mohr, Pragathi Achanta, Andres Plata Stapper, Aaron S. Rapaport, Jude Canon, Victor J. Cee, Brian A. Lanman, J. Russell Lipford. In vitro characterization of sotorasib and other RAS ‘His95-groove' binders and investigation of resistance mechanisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1285.

Molecular Insight into Recognition of the CGRPR Complex by Migraine Prevention Therapy Aimovig (Erenumab)

Calcitonin-gene-related peptide (CGRP) plays a key role in migraine pathophysiology. Aimovig (erenumab; erenumab-aooe in the United States) is the only US Food and Drug Administration (FDA)-approved monoclonal antibody (mAb) therapy against the CGRP receptor (CGRPR) for the prevention of migraine. Aimovig is also the first FDA-approved mAb against a G-protein-coupled receptor (GPCR). Here, we report the architecture and functional attributes of erenumab critical for its potent antagonism against CGRPR. The crystal structure of erenumab in complex with CGRPR reveals a direct ligand-blocking mechanism, enabled by a remarkable 21-residue-long complementary determining region (CDR)-H3 loop, which adopts a tyrosine-rich helix-turn tip and projects into the deep interface of the calcitonin receptor-like receptor (CLR) and RAMP1 subunits of CGRPR. Furthermore, erenumab engages with residues specific to CLR and RAMP1, providing the molecular basis for its exquisite selectivity. Such structural insights reveal the drug action mechanism of erenumab and shed light on developing antibody therapeutics targeting GPCRs.

Conjunctival and uveal melanoma: Survival and risk factors following orbital exenteration

PURPOSE

This study aims to analyse disease-free survival, overall survival and risk factors after orbital exenteration in patients with conjunctival and uveal melanoma.

METHODS

Patients who underwent orbital exenteration due to conjunctival and uveal melanoma were included in this retrospective study (March 2000 to March 2018).

RESULTS

A total of 76 patients were enrolled in this study: 60 patients had a conjunctival melanoma and 16 had a uveal melanoma. In conjunctival melanoma, the mean age was 68.4 years. The overall survival rate was 82% after 1 year and 52% after 5 years. Univariate analysis of overall survival found that the following parameters were predictive of a worse prognosis: gender, extent of the primary tumour, lymph node metastases, distant metastases, adjuvant chemotherapy or radiotherapy and relapse. In multivariate analysis, relapse and adjuvant radiotherapy appeared to contribute to a significantly worse prognosis. In uveal melanoma, the mean age was 63.6 years. Eleven patients died during follow-up (mean follow up 30.7 months). The overall survival and disease-free survival rates after 1 year were 62% and 57%, respectively. An analysis of risk factors was not possible due to the small number of cases.

CONCLUSION

Orbital exenterations in conjunctival and uveal melanoma are rarely necessary, but can be performed as an ultima ratio treatment with curative intent. Disease-free survival and overall survival are significantly lower for both groups due to the advanced stage of the disease compared to patients treated without exenteration in the literature. If a recurrence occurs after exenteration, the prognosis is poor in both groups.

Reconstruction of Orbital Exenteration Defects with Cheek Rotation Flaps: Indications, Technique, Complications, Rehabilitation, and Survival

The objective of this study was to examine the role of cheek rotation flaps in the reconstruction of orbital defects after exenteration. From January 2000 to August 2018, patients undergoing orbital exenteration and reconstruction with cheek rotation flaps were enrolled in this retrospective study. All patients were evaluated for wound complications, orbital rehabilitation, tumor relapse, and survival. Thirty patients completed the study. Fourteen complications allocated to 11 patients were assessed. The most common complications were seroma (13%), temporary facial nerve weakness (13%), and partial necrosis of the flap (10%). A major complication occurred in a total of two patients (7%), so that surgical correction was necessary. Eleven patients had a relapse; 15 patients died as part of the follow-up. Fifteen patients were treated with facial prostheses. The overall survival rate was 61% after 1 year and 42% after 5 years. Follow-up periods ranged from 6 to 95 months. Cheek rotation flap reconstruction after exenteration is a reliable method with a low rate of major complications. It is indicated when an approach to the parotid gland or the neck region is necessary because of suspected lymph node metastasis and in elderly patients because of their skin's laxity. It can be performed as primary or secondary reconstruction. Good esthetic results can be achieved, especially after endosseous implantation.

Periorbital, conjunctival and primary intraorbital carcinomas: Survival and risk factors after orbital exenteration

OBJECTIVES

This study aimed to analyse the disease-free survival (DFS), overall survival (OS) and risk factors after orbital exenteration in patients with periorbital, conjunctival and primary intraorbital carcinomas.

METHODS

Patients undergoing orbital exenteration due to a primary carcinoma between March 2000 and March 2018 were included in this retrospective study. Risk factors in all the patients were evaluated using univariate and multivariate analyses.

RESULTS

In total, 97 patients were enroled in this study. The most common tumours were conjunctival carcinoma (35 cases), squamous cell carcinoma of the skin (27 cases) and basal cell carcinoma (20 cases). The median follow-up period was 36 months. The average age of the patients was 67.3 years (range, 29-93 years). In all the patients, OS was 85% after 1 year and 69% after 5 years, while DFS was 71% after 1 year and 55% after 5 years. Univariate analysis of OS revealed that the following parameters were predictive of a poor prognosis: localisation, neck dissection, lymph node metastases, lymphatic invasion, perineural invasion, resection margins and immunosuppression. Multivariate analysis revealed resection margins as the only independent risk factor.

CONCLUSION

Orbital exenteration is rarely necessary in patients with periorbital, conjunctival and primary intraorbital carcinomas; however, it can be performed as an ultima ratio treatment with a curative intent. Clear margins can be achieved in most cases. OS and DFS are not significantly different in the subgroups. In most cases, recurrence occurs within the first 2 years.

ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification

Motivation

Breast cancer is the second leading cause of cancer death among women. Tumors, even of the same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and that hence must be accounted for in the treatment decision-making process.

Results

Here, we present ClinOmicsTrail^bc, a comprehensive visual analytics tool for breast cancer decision support that provides a holistic assessment of standard-of-care targeted drugs, candidates for drug repositioning and immunotherapeutic approaches. To this end, our tool analyzes and visualizes clinical markers and (epi-)genomics and transcriptomics datasets to identify and evaluate the tumor’s main driver mutations, the tumor mutational burden, activity patterns of core cancer-relevant pathways, drug-specific biomarkers, the status of molecular drug targets and pharmacogenomic influences. In order to demonstrate ClinOmicsTrail^bc’s rich functionality, we present three case studies highlighting various ways in which ClinOmicsTrail^bc can support breast cancer precision medicine. ClinOmicsTrail^bc is a powerful integrated visual analytics tool for breast cancer research in general and for therapy stratification in particular, assisting oncologists to find the best possible treatment options for their breast cancer patients based on actionable, evidence-based results.

Availability and implementation

ClinOmicsTrail^bc can be freely accessed at https://clinomicstrail.bioinf.uni-sb.de.

Supplementary information

Supplementary data are available at Bioinformatics online.

Treatment of odontogenic abscesses: comparison of primary and secondary removal of the odontogenic focus and antibiotic therapy

PURPOSE

To examine the time of removal of the odontogenic focus, antibiotic therapy and risk factors in odontogenic abscesses.

PATIENTS

From January 2012 to December 2015, inpatients undergoing incision due to odontogenic abscesses were identified in a retrospective study. All the patients were evaluated for time of removal of the odontogenic focus, antibiotic therapy, germ spectrum, complications and risk factors.

RESULTS

Two hundred ten patients completed the study. In 89 cases (42.4%), the odontogenic focus was removed as part of the abscess treatment (group A). In 121 cases (57.6%), the focus was secondarily removed (group B). On average, 2 ± 4 teeth were removed in group A, and 6 ± 5 teeth in group B (p < 0.0001). An average of 1.2 ± 0.4 surgical interventions were performed in group A, and 2 ± 0.2 operations in group B (p < 0.0001). Microbiological examination was positive in one-third of the cases (70 cases). Most commonly, streptococci (27%) were isolated. A resistance screening was possible in 57 of the detected germs (68.7%). In 89% of these patients, the combination of ampicillin-sulbactam was effective. The hospital stay was 4.8 ± 2 days for group A and 7.6 ± 3 days for group B (p < 0.0001). The clinical evaluation revealed 12 intermediate (5.7%) and three long-term (1.4%) complications. The long-term complications included a recurrence in two cases (1%) and an osteomyelitis in one case (0.5%). A logistic regression analysis identified no significant risk factor in relation to these complications.

CONCLUSION

The study shows that a primary removal of the odontogenic focus may have advantages over a secondary removal: (1) fewer operations, (2) shorter hospital stay and (3) shorter antibiotic therapy. Broad-spectrum penicillins in combination with beta-lactamase inhibitors are a possible, sufficient antibiotic regimen. Long-term complications are rare. No risk factors are identified in relation to these complications.

On the fate of oxygenated organic molecules in atmospheric aerosol particles

Highly oxygenated organic molecules (HOMs) are formed from the oxidation of biogenic and anthropogenic gases and affect Earth's climate and air quality by their key role in particle formation and growth. While the formation of these molecules in the gas phase has been extensively studied, the complexity of organic aerosol (OA) and lack of suitable measurement techniques have hindered the investigation of their fate post-condensation, although further reactions have been proposed. We report here novel real-time measurements of these species in the particle phase, achieved using our recently developed extractive electrospray ionization time-of-flight mass spectrometer (EESI-TOF). Our results reveal that condensed-phase reactions rapidly alter OA composition and the contribution of HOMs to the particle mass. In consequence, the atmospheric fate of HOMs cannot be described solely in terms of volatility, but particle-phase reactions must be considered to describe HOM effects on the overall particle life cycle and global carbon budget.

Discovery of a Covalent Inhibitor of KRASG12C (AMG 510) for the Treatment of Solid Tumors

KRAS^G12C has emerged as a promising target in the treatment of solid tumors. Covalent inhibitors targeting the mutant cysteine-12 residue have been shown to disrupt signaling by this long-"undruggable" target; however clinically viable inhibitors have yet to be identified. Here, we report efforts to exploit a cryptic pocket (H95/Y96/Q99) we identified in KRAS^G12C to identify inhibitors suitable for clinical development. Structure-based design efforts leading to the identification of a novel quinazolinone scaffold are described, along with optimization efforts that overcame a configurational stability issue arising from restricted rotation about an axially chiral biaryl bond. Biopharmaceutical optimization of the resulting leads culminated in the identification of AMG 510, a highly potent, selective, and well-tolerated KRAS^G12C inhibitor currently in phase I clinical trials (NCT03600883).

The clinical KRAS(G12C) inhibitor AMG 510 drives anti-tumour immunity

KRAS is the most frequently mutated oncogene in cancer and encodes a key signalling protein in tumours^1,2. The KRAS(G12C) mutant has a cysteine residue that has been exploited to design covalent inhibitors that have promising preclinical activity^3-5. Here we optimized a series of inhibitors, using novel binding interactions to markedly enhance their potency and selectivity. Our efforts have led to the discovery of AMG 510, which is, to our knowledge, the first KRAS(G12C) inhibitor in clinical development. In preclinical analyses, treatment with AMG 510 led to the regression of KRAS^G12C tumours and improved the anti-tumour efficacy of chemotherapy and targeted agents. In immune-competent mice, treatment with AMG 510 resulted in a pro-inflammatory tumour microenvironment and produced durable cures alone as well as in combination with immune-checkpoint inhibitors. Cured mice rejected the growth of isogenic KRAS^G12D tumours, which suggests adaptive immunity against shared antigens. Furthermore, in clinical trials, AMG 510 demonstrated anti-tumour activity in the first dosing cohorts and represents a potentially transformative therapy for patients for whom effective treatments are lacking.

Discovery of N-(1-Acryloylazetidin-3-yl)-2-(1H-indol-1-yl)acetamides as Covalent Inhibitors of KRASG12C

KRAS regulates many cellular processes including proliferation, survival, and differentiation. Point mutants of KRAS have long been known to be molecular drivers of cancer. KRAS p.G12C, which occurs in approximately 14% of lung adenocarcinomas, 3-5% of colorectal cancers, and low levels in other solid tumors, represents an attractive therapeutic target for covalent inhibitors. Herein, we disclose the discovery of a class of novel, potent, and selective covalent inhibitors of KRAS^G12C identified through a custom library synthesis and screening platform called Chemotype Evolution and structure-based design. Identification of a hidden surface groove bordered by H95/Y96/Q99 side chains was key to the optimization of this class of molecules. Best-in-series exemplars exhibit a rapid covalent reaction with cysteine 12 of GDP-KRAS^G12C with submicromolar inhibition of downstream signaling in a KRAS^G12C-specific manner.

Low mutational load in pediatric medulloblastoma still translates into neoantigens as targets for specific T-cell immunotherapy

BACKGROUND

Medulloblastoma is the most common malignant brain tumor in childhood and adolescence. Although some patients present with distinct genetic alterations, such as mutated TP53 or MYC amplification, pediatric medulloblastoma is a tumor entity with minimal mutational load and low immunogenicity.

METHODS

We identified tumor-specific mutations using next-generation sequencing of medulloblastoma DNA and RNA derived from primary tumor samples from pediatric patients. Tumor-specific mutations were confirmed using deep sequencing and in silico analyses predicted high binding affinity of the neoantigen-derived peptides to the patients' human leukocyte antigen molecules. Tumor-specific peptides were synthesized and used to induce a de novo T-cell response characterized by interferon gamma and tumor necrosis factor alpha release of CD8⁺ cytotoxic T cells in vitro.

RESULTS

Despite low mutational tumor burden, at least two immunogenic tumor-specific peptides were identified in each patient. T cells showed a balanced CD4/CD8 ratio and mostly effector memory phenotype. Induction of a CD8-specific T-cell response was achieved for the neoepitopes derived from Histidine Ammonia-Lyase (HAL), Neuraminidase 2 (NEU2), Proprotein Convertase Subtilisin (PCSK9), Programmed Cell Death 10 (PDCD10), Supervillin (SVIL) and tRNA Splicing Endonuclease Subunit 54 (TSEN54) variants.

CONCLUSION

Detection of patient-specific, tumor-derived neoantigens confirms that even in tumors with low mutational load a molecular design of targets for specific T-cell immunotherapy is possible. The identified neoantigens may guide future approaches of adoptive T-cell transfer, transgenic T-cell receptor transfer or tumor vaccination.

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

BACKGROUND

Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs.

METHODS

In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data.

RESULTS

The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations.

CONCLUSIONS

This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden.

Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma

BACKGROUND

Although mutated HLA ligands are considered ideal cancer-specific immunotherapy targets, evidence for their presentation is lacking in hepatocellular carcinomas (HCCs). Employing a unique multi-omics approach comprising a neoepitope identification pipeline, we assessed exome-derived mutations naturally presented as HLA class I ligands in HCCs.

METHODS

In-depth multi-omics analyses included whole exome and transcriptome sequencing to define individual patient-specific search spaces of neoepitope candidates. Evidence for the natural presentation of mutated HLA ligands was investigated through an in silico pipeline integrating proteome and HLA ligandome profiling data.

RESULTS

The approach was successfully validated in a state-of-the-art dataset from malignant melanoma, and despite multi-omics evidence for somatic mutations, mutated naturally presented HLA ligands remained elusive in HCCs. An analysis of extensive cancer datasets confirmed fundamental differences of tumor mutational burden in HCC and malignant melanoma, challenging the notion that exome-derived mutations contribute relevantly to the expectable neoepitope pool in malignancies with only few mutations.

CONCLUSIONS

This study suggests that exome-derived mutated HLA ligands appear to be rarely presented in HCCs, inter alia resulting from a low mutational burden as compared to other malignancies such as malignant melanoma. Our results therefore demand widening the target scope for personalized immunotherapy beyond this limited range of mutated neoepitopes, particularly for malignancies with similar or lower mutational burden.

Discovery of ( R)-8-(6-Methyl-4-oxo-1,4,5,6-tetrahydropyrrolo[3,4- b]pyrrol-2-yl)-3-(1-methylcyclopropyl)-2-((1-methylcyclopropyl)amino)quinazolin-4(3 H)-one, a Potent and Selective Pim-1/2 Kinase Inhibitor for Hematological Malignancies

Pim kinases are a family of constitutively active serine/threonine kinases that are partially redundant and regulate multiple pathways important for cell growth and survival. In human disease, high expression of the three Pim isoforms has been implicated in the progression of hematopoietic and solid tumor cancers, which suggests that Pim kinase inhibitors could provide patients with therapeutic benefit. Herein, we describe the structure-guided optimization of a series of quinazolinone-pyrrolodihydropyrrolone analogs leading to the identification of potent pan-Pim inhibitor 28 with improved potency, solubility, and drug-like properties. Compound 28 demonstrated on-target Pim activity in an in vivo pharmacodynamic assay with significant inhibition of BAD phosphorylation in KMS-12-BM multiple myeloma tumors for 16 h postdose. In a 2-week mouse xenograft model, daily dosing of compound 28 resulted in 33% tumor regression at 100 mg/kg.

Abstract CT057: Phase I trial to evaluate the feasibility and safety of an individualized peptide vaccine of unmodified cancer antigens: PepIVAC-01

Current research has entered into an unprecedented territory of analytical possibilities represented by so called “omics” technologies, allowing the examination of patients and their individual diseases on a previously unimaginable level. This development represents a serious challenge considering established trial designs and research conduct, particularly in early phase clinical trials, since novel theranostics (biomarker based allocation therapies) in principle would allow for patient selection far beyond traditional stratification approaches; further, many different therapeutic combinatorial therapies cannot be easily evaluated in a traditional way within a reasonable timeframe. The summit of this paradigm is biomarker-based selection and manufacturing of a previously undefined drug product directly adapted to patient- and disease-specific features. In our view, such an approach is ideally suited for cancer immunotherapy, since both malignancies and the human immune system require a high level of individuality. Hence, defining naturally presented HLA-Ligands specific for individual malignancies and manufacturing respective T cell targets according to current Good Manufacturing Practice (GMP) standards formulated as a multi-peptide vaccine in a clinical trial is a completely new state of the art approach. On this background, we designed a pilot clinical trial and implemented the required environment, addressing patients with particularly high unmet medical need and exceedingly high relapse rates in an adjuvant setting. The trial follows a platform design including different disease entities, encompassing non-small cell lung cancer (NSCLC), advanced colorectal cancer (CRC), triple negative breast cancer, cholangiocarcinoma, hepatocellular carcinoma (HCC) and high-risk soft tissue sarcoma. Target selection follows a five-pronged approach and is based on analyzing patient autologous tumor material on different omics levels, including the whole exome and transcriptome as well as the HLA-ligandome (comprehensive analysis of the naturally presented HLA ligands on tumor (and benign) tissue by tandem mass spectrometry) to select ideal immunological targets. Further, this trial will endorse a three tier escalation protocol featuring an individual multi-peptide vaccine with Montanide ISA 51 VG and topical imiquimod in a first step, combined with the novel lipopeptide adjuvant XS-15 (TLR7 ligand) and finally introducing a checkpoint inhibitor as a third tier. This pilot trial will primarily focus on endpoints safety and feasibility but endorse various secondary objectives including detailed immunomonitoring of induced vaccine responses and other immune markers. The HCC trial part is supported by the European Commission's 7th Framework Program (www.hepavac.eu).

Citation Format: Sebastian Haen, Markus W. Löffler, Oliver Kohlbacher, Sven Nahnsen, Christopher Mohr, Monika Stieglbaueren, Patricia Hrstic, Luigi Buonaguro, Peter Martus, Maik Häntschel, Cécile Gouttefangeas, Stefan Beckert, Alfred Königsrainer, Stefan Stevanovic, Lothar Kanz, Hans-Georg Rammensee. Phase I trial to evaluate the feasibility and safety of an individualized peptide vaccine of unmodified cancer antigens: PepIVAC-01 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr CT057.

qPortal: A platform for data-driven biomedical research

Modern biomedical research aims at drawing biological conclusions from large, highly complex biological datasets. It has become common practice to make extensive use of high-throughput technologies that produce big amounts of heterogeneous data. In addition to the ever-improving accuracy, methods are getting faster and cheaper, resulting in a steadily increasing need for scalable data management and easily accessible means of analysis.

We present qPortal, a platform providing users with an intuitive way to manage and analyze quantitative biological data. The backend leverages a variety of concepts and technologies, such as relational databases, data stores, data models and means of data transfer, as well as front-end solutions to give users access to data management and easy-to-use analysis options. Users are empowered to conduct their experiments from the experimental design to the visualization of their results through the platform. Here, we illustrate the feature-rich portal by simulating a biomedical study based on publically available data. We demonstrate the software’s strength in supporting the entire project life cycle. The software supports the project design and registration, empowers users to do all-digital project management and finally provides means to perform analysis. We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology. Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy).

qPortal, a one-stop-shop solution for biomedical projects offers up-to-date analysis pipelines, quality control workflows, and visualization tools. Through intensive user interactions, appropriate data models have been developed. These models build the foundation of our biological data management system and provide possibilities to annotate data, query metadata for statistics and future re-analysis on high-performance computing systems via coupling of workflow management systems. Integration of project and data management as well as workflow resources in one place present clear advantages over existing solutions.

Metastases from distant primary tumours on the head and neck: clinical manifestation and diagnostics of 91 cases

PURPOSE

The aim of this study was to evaluate which primary tumours metastasize on the head and neck region, identify the kind of clinical manifestation, the types of diagnostics that should be performed, and prove that the therapy appears possible and useful.

PATIENTS

As many as 91 patients with a distant metastasis on the head and neck were enrolled in this retrospective clinical study from January 2004 to September 2016. All the patients were evaluated for clinical symptoms, primary tumour, localization, diagnostics, and surgical procedure.

RESULTS

A total of 31 patients had asymptomatic swelling, 27 patients had symptomatic swelling, and nine experienced isolated pain without swelling. Most other symptoms were organ-specific. The most frequent localizations were the orbit (44 metastases), mandible (19), neck region (9), and skin (7). The most common primary tumours were breast carcinoma (44), bronchial carcinoma (12), and renal carcinoma (9). A biopsy was performed on 38 patients, a partial resection was done on 28 patients, extirpation on six patients, and a radical resection on 19 patients.

CONCLUSION

Distant metastases on the head and neck are rare and, therefore, pose a challenge for the oncologist and other involved disciplines. Most distant metastases occur within the first five years. Late metastases, especially in breast carcinoma, are still possible after 20 years. A surgical examination should be carried out if the findings are not clear due to multiple differential diagnoses. In particular, surgical options under palliative aspects should be examined.

Correction of whistle deformity using autologous free fat grafting: first results of a pilot study and review of the literature

PURPOSE

Whistle deformities are frequent sequelae after surgical correction of cleft lip, trauma, or tumor excision. The aim of this study was to examine the role of autologous free fat grafting in the reconstruction of whistle deformity.

PATIENTS

Fifteen patients with whistle deformity were enrolled in this pilot study. The mean follow-up period was 19 months. Liposuction was done followed by the replantation of an average of 2.2 ml autologous fat per patient (range 0.7-4 ml). An overcorrection was performed in all patients.

RESULTS

All the patients showed improvements in whistle deformity. The mean resorption rate was 53% (range 30-80%). Three patients (20%) were not satisfied with the postoperative result. Six complications were assessed (4× feeling of pressure [27%], one hematoma [7%], one recurrent pain [7%]), but a major complication did not occur.

REVIEW

We also present a review of the literature with different techniques that were described in the last 20 years.

CONCLUSION

Autologous free fat graftings for reconstruction of whistle deformity represent a reliable method with a low complication rate. However, the resorption rate is unpredictable. If necessary, several autologous fat transplantations should be conducted at an interval of at least 6 months.

Autologous dermis - Fat grafts as primary and secondary orbital transplants before rehabilitation with artificial eyes

OBJECTIVE

The aim of this study was to examine the role of autologous dermis-fat grafts in the reconstruction of orbital soft-tissue defects.

PATIENTS

Thirty-six patients (3-84 years) were enrolled in this retrospective study from 2002 to 2014. The dermis-fat graft was primarily transplanted in seven cases, and secondarily in 29 patients. All the patients were evaluated for complications, adequate prosthetic cavity, possibility of artificial eye supply and movement, as well as cosmetic results. Follow-up periods ranged from 25 to 144 months.

RESULTS

All the patients could be supplied with an artificial eye in the long term after dermis-fat transplantation. The clinical evaluation revealed 17 complications allocated to 11 patients. A major complication occurred in three patients (8.3%) so that a surgical correction was necessary. Thirty-three patients (91.7%) showed an aesthetically stable long-term outcome.

CONCLUSION

Dermis-fat grafts for reconstruction of anophthalmic orbit represent a reliable method with a low complication rate and good cosmetic and functional results. The graft can be used as primary and secondary transplants. The stable long-term results and high aesthetic satisfaction lead us to recommend this method as a routine operation.

ImmunoNodes - graphical development of complex immunoinformatics workflows

Background

Immunoinformatics has become a crucial part in biomedical research. Yet many immunoinformatics tools have command line interfaces only and can be difficult to install. Web-based immunoinformatics tools, on the other hand, are difficult to integrate with other tools, which is typically required for the complex analysis and prediction pipelines required for advanced applications.

Result

We present ImmunoNodes, an immunoinformatics toolbox that is fully integrated into the visual workflow environment KNIME. By dragging and dropping tools and connecting them to indicate the data flow through the pipeline, it is possible to construct very complex workflows without the need for coding.

Conclusion

ImmunoNodes allows users to build complex workflows with an easy to use and intuitive interface with a few clicks on any desktop computer.

Personalized peptide vaccine-induced immune response associated with long-term survival of a metastatic cholangiocarcinoma patient

BACKGROUND & AIMS

We report a novel experimental immunotherapeutic approach in a patient with metastatic intrahepatic cholangiocarcinoma. In the 5year course of the disease, the initial tumor mass, two local recurrences and a lung metastasis were surgically removed. Lacking alternative treatment options, aiming at the induction of anti-tumor T cells responses, we initiated a personalized multi-peptide vaccination, based on in-depth analysis of tumor antigens (immunopeptidome) and sequencing.

METHODS

Tumors were characterized by immunohistochemistry, next-generation sequencing and mass spectrometry of HLA ligands.

RESULTS

Although several tumor-specific neo-epitopes were predicted in silico, none could be validated by mass spectrometry. Instead, a personalized multi-peptide vaccine containing non-mutated tumor-associated epitopes was designed and applied. Immunomonitoring showed vaccine-induced T cell responses to three out of seven peptides administered. The pulmonary metastasis resected after start of vaccination showed strong immune cell infiltration and perforin positivity, in contrast to the previous lesions. The patient remains clinically healthy, without any radiologically detectable tumors since March 2013 and the vaccination is continued.

CONCLUSIONS

This remarkable clinical course encourages formal clinical studies on adjuvant personalized peptide vaccination in cholangiocarcinoma.

LAY SUMMARY

Metastatic cholangiocarcinomas, cancers that originate from the liver bile ducts, have very limited treatment options and a fatal prognosis. We describe a novel therapeutic approach in such a patient using a personalized multi-peptide vaccine. This vaccine, developed based on the characterization of the patient's tumor, evoked detectable anti-tumor immune responses, associating with long-term tumor-free survival.

Discovery of imidazopyridazines as potent Pim-1/2 kinase inhibitors

High levels of Pim expression have been implicated in several hematopoietic and solid tumor cancers, suggesting that inhibition of Pim signaling could provide patients with therapeutic benefit. Herein, we describe our progress towards this goal using a screening hit (rac-1) as a starting point. Modification of the indazole ring resulted in the discovery of a series of imidazopyridazine-based Pim inhibitors exemplified by compound 22m, which was found to be a subnanomolar inhibitor of the Pim-1 and Pim-2 isoforms (IC₅₀ values of 0.024nM and 0.095nM, respectively) and to potently inhibit the phosphorylation of BAD in a cell line that expresses high levels of all Pim isoforms, KMS-12-BM (IC₅₀=28nM). Profiling of Pim-1 and Pim-2 expression levels in a panel of multiple myeloma cell lines and correlation of these data with the potency of compound 22m in a proliferation assay suggests that Pim-2 inhibition would be advantageous for this indication.

Discovery and Optimization of Macrocyclic Quinoxaline-pyrrolo-dihydropiperidinones as Potent Pim-1/2 Kinase Inhibitors

The identification of Pim-1/2 kinase overexpression in B-cell malignancies suggests that Pim kinase inhibitors will have utility in the treatment of lymphoma, leukemia, and multiple myeloma. Starting from a moderately potent quinoxaline-dihydropyrrolopiperidinone lead, we recognized the potential for macrocyclization and developed a series of 13-membered macrocycles. The structure-activity relationships of the macrocyclic linker were systematically explored, leading to the identification of 9c as a potent, subnanomolar inhibitor of Pim-1 and -2. This molecule also potently inhibited Pim kinase activity in KMS-12-BM, a multiple myeloma cell line with relatively high endogenous levels of Pim-1/2, both in vitro (pBAD IC50 = 25 nM) and in vivo (pBAD EC50 = 30 nM, unbound), and a 100 mg/kg daily dose was found to completely arrest the growth of KMS-12-BM xenografts in mice.

Molecular Composition and Volatility of Organic Aerosol in the Southeastern U.S.: Implications for IEPOX Derived SOA

We present measurements as part of the Southern Oxidant and Aerosol Study (SOAS) during which atmospheric aerosol particles were comprehensively characterized. We present results utilizing a Filter Inlet for Gases and AEROsol coupled to a chemical ionization mass spectrometer (CIMS). We focus on the volatility and composition of isoprene derived organic aerosol tracers and of the bulk organic aerosol. By utilizing the online volatility and molecular composition information provided by the FIGAERO-CIMS, we show that the vast majority of commonly reported molecular tracers of isoprene epoxydiol (IEPOX) derived secondary organic aerosol (SOA) is derived from thermal decomposition of accretion products or other low volatility organics having effective saturation vapor concentrations <10(-3) μg m(-3). In addition, while accounting for up to 30% of total submicrometer organic aerosol mass, the IEPOX-derived SOA has a higher volatility than the remaining bulk. That IEPOX-SOA, and more generally bulk organic aerosol in the Southeastern U.S. is comprised of effectively nonvolatile material has important implications for modeling SOA derived from isoprene, and for mechanistic interpretations of molecular tracer measurements. Our results show that partitioning theory performs well for 2-methyltetrols, once accretion product decomposition is taken into account. No significant partitioning delays due to aerosol phase or viscosity are observed, and no partitioning to particle-phase water or other unexplained mechanisms are needed to explain our results.

FRED 2: an immunoinformatics framework for Python

Summary: Immunoinformatics approaches are widely used in a variety of applications from basic immunological to applied biomedical research. Complex data integration is inevitable in immunological research and usually requires comprehensive pipelines including multiple tools and data sources. Non-standard input and output formats of immunoinformatics tools make the development of such applications difficult. Here we present FRED 2, an open-source immunoinformatics framework offering easy and unified access to methods for epitope prediction and other immunoinformatics applications. FRED 2 is implemented in Python and designed to be extendable and flexible to allow rapid prototyping of complex applications.

Availability and implementation: FRED 2 is available at http://fred-2.github.io

Contact:schubert@informatik.uni-tuebingen.de

Supplementary information:Supplementary data are available at Bioinformatics online.

Abstract A113: iVacALL: A personalized peptide-vaccination design platform for pediatric acute lymphoblastic leukemia patients based on patient-individual tumor-specific variants

We established a platform for the design of patient-individual peptide vaccination cocktails by combination of whole exome sequencing of tumor and normal tissue with in silico epitope prediction algorithms for individual patient HLA types.

Acute lymphoblastic leukemia (ALL) is the most common pediatric malignancy. Standard chemotherapy is a successful treatment in 80% of patients, only about 20% develop a relapse, however these patients have a dismal prognosis. Prevention of relapse after first-line chemotherapy or stem cell transplantation (SCT) is therefore mandatory. Accumulation of somatic mutations is one characteristic feature of malignant cells. These single nucleotide variants (SNVs) can lead to altered amino acid sequences of the translated proteins, which in turn can be presented as antigenic peptides on HLA molecules of the malignant cells. Mutated peptides represent ideal T cell targets as they are true neoantigens, specific for the tumor, and should not have been subject to central tolerance selection mechanisms. A peptide vaccination composed of mutated T cell epitopes specific for individual patient tumors is therefore a promising approach to prevent relapse in high-risk patients. For this purpose we detect nonsynonymous mutations by whole exome and transcriptome sequencing of patient leukemic blasts and normal reference tissue. HLA binding peptides harboring the altered amino acids are subsequently predicted in silico by algorithms SYFPEITHI, NetMHC and NetMHCpan for the patients' individual HLA type.

Whole exome sequencing was performed for 17 c-ALL, 2 cortical T-ALL and 1 pro-B-ALL sample pairs. ALL-specific SNVs, as well as insertions and deletions (InDels) were identified using a comparative bioinformatics pipeline. The determined variants were further validated by deep sequencing in 9/20 patients so far, with an average of 12 (+/- 8) validated mutations per patient. For all patients with validated variants, MHC class I and MHC class II epitopes could be predicted successfully.

We applied the platform for 3 patients based on compassionate need and designed individual peptide vaccines. One patient underwent haploidentical SCT with relapsed c-ALL, a second patient received autologous SCT with ependymoma and the third patient got allogeneic SCT with pro-B ALL. In all cases validated mutations could be identified and epitope prediction was performed for MHC I & II binders. The predicted peptides were synthesized and vaccination cocktails were formulated. The vaccination schedule provides 16 vaccinations over 33 weeks using GM-CSF and Imiquimod as adjuvant. The vaccination was generally well tolerated. Response to the vaccination was monitored by detection of T cells recognizing the vaccinated peptides occurring over time in peripheral blood of the patients. Monitoring was performed for each vaccination time point by prestimulation with the peptides and subsequent intracellular cytokine staining (ICS) of T cells and FACS analysis. In all 3 patients we could detect a developing CD4+ T cell response against the vaccinated mutated MHC II binding peptides.

Whole exome sequencing of pediatric ALL patients is feasible and yields a small amount of validated mutations per patients. However, these few mutations seem sufficient to predict HLA-binding peptides that are immunogenic when vaccinated and elicit specific T cell responses in patients. Moreover, the platform is not limited to ALL/leukemia but can also be applied for solid tumor patients.

Citation Format: Armin Rabsteyn, Christina Kyzirakos, Christopher Schröder, Marc Sturm, Christopher Mohr, Mathias Walzer, Ulrike Pflückhahn, Michael Walter, Magdalena Feldhahn, Karoline Laske, Michael Bonin, Martin Ebinger, Stefan Stevanovic, Peter Bauer, Oliver Kohlbacher, Cecile Gouttefangeas, Hans-Georg Rammensee, Rupert Handgretinger, Peter Lang. iVacALL: A personalized peptide-vaccination design platform for pediatric acute lymphoblastic leukemia patients based on patient-individual tumor-specific variants. [abstract]. In: Proceedings of the CRI-CIMT-EATI-AACR Inaugural International Cancer Immunotherapy Conference: Translating Science into Survival; September 16-19, 2015; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(1 Suppl):Abstract nr A113.

Midinfrared frequency comb from self-stable degenerate GaAs optical parametric oscillator

We pump a degenerate frequency-divide-by-two optical parametric oscillator (OPO) based on orientation-patterned GaAs with a stable Tm frequency comb at 2 micrometer wavelength and measure the OPO comb offset frequency and linewidth. We show frequency division by two with sub-Hz relative linewidth of the comb teeth. The OPO thermally self-stabilizes and oscillates for nearly an hour without any active control.

The measurement invariance of schizotypy in Europe

The short version of the Oxford-Liverpool Inventory of Feelings and Experiences (sO-LIFE) is a widely used measure assessing schizotypy. There is limited information, however, on how sO-LIFE scores compare across different countries. The main goal of the present study is to test the measurement invariance of the sO-LIFE scores in a large sample of non-clinical adolescents and young adults from four European countries (UK, Switzerland, Italy, and Spain). The scores were obtained from validated versions of the sO-LIFE in their respective languages. The sample comprised 4190 participants (M=20.87 years; SD=3.71 years). The study of the internal structure, using confirmatory factor analysis, revealed that both three (i.e., positive schizotypy, cognitive disorganisation, and introvertive anhedonia) and four-factor (i.e., positive schizotypy, cognitive disorganisation, introvertive anhedonia, and impulsive nonconformity) models fitted the data moderately well. Multi-group confirmatory factor analysis showed that the three-factor model had partial strong measurement invariance across countries. Eight items were non-invariant across samples. Significant statistical differences in the mean scores of the s-OLIFE were found by country. Reliability scores, estimated with Ordinal alpha ranged from 0.75 to 0.87. Using the Item Response Theory framework, the sO-LIFE provides more accuracy information at the medium and high end of the latent trait. The current results show further evidence in support of the psychometric proprieties of the sO-LIFE, provide new information about the cross-cultural equivalence of schizotypy and support the use of this measure to screen for psychotic-like features and liability to psychosis in general population samples from different European countries.

Ultra-low noise all polarization-maintaining Er fiber-based optical frequency combs facilitated with a graphene modulator

High bandwidth carrier phase and repetition rate control are critical for the construction of low phase noise optical frequency combs. Here we demonstrate the use of a graphene modulator for the former and a bulk electro-optic modulator for the latter enabling record low phase noise operation of an Er fiber frequency comb. For applications that do not require carrier phase control, we show that the form factor of a fiber comb can be reduced by adapting a graphene modulator for rapid repetition rate control. Moreover, the whole system demonstration is performed with all-polarization maintaining Er fiber frequency combs, highly suitable for applications in the field.

Association between adaptive behaviour and age in adults with Down syndrome without dementia: examining the range and severity of adaptive behaviour problems

BACKGROUND

Studies on adaptive behaviour and ageing in adults with Down syndrome (DS) (without dementia) have typically analysed age-related change in terms of the total item scores on questionnaires. This research extends the literature by investigating whether the age-related changes in adaptive abilities could be differentially attributed to changes in the number or severity (intensity) of behavioural questionnaire items endorsed.

METHODS

The Adaptive Behaviour Assessment System-II Adult (ABAS-II Adult) was completed by parents and caregivers of 53 adults with DS aged between 16 and 56 years. Twenty adults with DS and their parents/caregivers were a part of a longitudinal study, which provided two time points of data. In addition 33 adults with DS and their parents/caregivers from a cross-sectional study were included. Random effects regression analyses were used to examine the patterns in item scores associated with ageing.

RESULTS

Increasing age was found to be significantly associated with lower adaptive behaviour abilities for all the adaptive behaviour composite scores, expect for the practical composite. These associations were entirely related to fewer ABAS-II Adult items being selected as present for the older participants, as opposed to the scores being attributable to lower item severity.

CONCLUSIONS

This study provides evidence for a differential pattern of age-related change for various adaptive behaviour skills in terms of range, but not severity. Possible reasons for this pattern will be discussed. Overall, these findings suggest that adults with DS may benefit from additional support in terms of their social and conceptual abilities as they age.

Nasal Entrance Correction in Unilateral Cleft Lip Repair

PURPOSE

Correction of cleft nose deformity in patients with unilateral cleft lip is challenging and involves primarily the nasal cartilage and the nasal entrance. No consensus on the most effective surgical technique has been reached. This article describes a surgical procedure for nasal entrance correction.

PATIENTS AND METHODS

In this retrospective study, 30 adult patients underwent secondary nasal entrance corrections. According to a modified Van der Meulen technique, a nasal alar rim flap with anatomic repositioning of the alar cartilage was applied. Symmetry and esthetic results were evaluated by semiquantitative photographic analysis.

RESULTS

In all patients, the nasal tip was narrowed considerably, and a lifting of the nasal tip was achieved. Columellar elongation averaged 40%, and the form of the nostril was changed from horizontally oval to longitudinally oval.

CONCLUSION

The described technique is well suited for a sustainable correction of complex cleft-induced deformities without visible scars in adult patients.