Observations with KIDs Interferometer Spectrum Survey (KISS)

We describe the preliminary on-sky results of the KIDs Interferometer Spectrum Survey (KISS), a spectral imager with a 1 deg field of view (FoV). The instrument operates in the range 120–180 GHz from the 2.25m Q-U-I JOint TEnerife telescope in Teide Observatory (Tenerife, Canary Islands), at 2 395m altitude above sea level. Spectra at low resolution, up to 1.45 GHz, are obtained using a fast (3.72 Hz mechanical frequency) Fourier transform spectrometer, coupled to a continuous dilution cryostat with a stabilized temperature of 170mK that hosts two 316-pixel arrays of lumped-element kinetic inductance detectors. KISS generates more than 3 000 spectra per second during observations and represents a pathfinder to demonstrate the potential for spectral mapping with large FoV.We give an overall description of the spectral mapping paradigm and we present recent results from observations, in this paper.

CONCERTO at APEX: Installation and first phase of on-sky commissioning

CONCERTO (CarbON CII line in post-rEionisation and ReionisaTiOn) is a large field-of-view (FoV) spectro-imager that has been installed on the Cassegrain Cabin of Atacama Pathfinder EXperiment (APEX) telescope in April 2021. CONCERTO hosts 2 focal planes and a total number of 4000 Kinetic Inductance Detectors (KID), with an instantaneous FoV of 18.6 arcminutes in the range of 130-310 GHz. The spectral resolution can be easily tuned down to 1 GHz depending on the scientific target. The scientific program of CONCERTO has many objectives, with two main programs focused on mapping the fluctuations of the [CII] line intensity in the reionisation and postreionisation epoch (4.5<z<8.5), and on studying galaxy clusters via the thermal and kinetic Sunyaev-Zel’dovich (SZ) effect. CONCERTO will also measure the dust and molecular gas contents of local and intermediate-redshift galaxies, it will study the Galactic star-forming clouds and finally it will observe the CO intensity fluctuations arising from 0.3<z<2 galaxies.

The design of the instrument, installation at APEX and current status of the commissioning phase and science verification will be presented. Also we describe the deployment and first on-sky tests performed between April and June 2021.

Impact of PD-L1 and T-cell inflamed gene expression profile on survival in advanced ovarian cancer

OBJECTIVE

Programmed death ligand 1 (PD-L1) expression affects tumor evasion of immune surveillance. The prognostic value and relationship of PD-L1 expression to T-cell-inflamed immune signatures in ovarian cancer are unclear. The purpose of this study is to evaluate the impact of PD-L1 on overall survival and its correlation with an immune-mediated gene expression profile in patients with advanced ovarian cancer.

METHODS

PD-L1 expression in tumor and immune cells was assessed by immunohistochemistry, and PD-L1-positive expression was defined as a combined positive score ≥1; a T-cell-inflamed gene expression profile containing interferon γ response genes was evaluated using extracted RNA from surgical samples. Associations between PD-L1 expression, gene expression profile status, and overall survival were analyzed using the Kaplan-Meier method, log-rank test, and multivariate Cox proportional hazards regression models.

RESULTS

A total of 376 patients with advanced epithelial ovarian, primary peritoneal, or fallopian tube cancer treated by cytoreductive surgery and platinum-based therapy were included. PD-L1-positive expression was observed in 50.5% of patients and associated with more advanced stage (p=0.047), more aggressive histologic subtype (p=0.001), and platinum sensitivity defined by increasing treatment-free interval from first platinum-based chemotherapy to next systemic treatment (p=0.027). PD-L1-positive expression was associated with longer overall survival in multivariate analyses (adjusted HR 0.72, 95% CI 0.56 to 0.93). In subgroup analyses, this association was most pronounced in patients with partially platinum-sensitive disease (treatment-free interval ≥6 to <12 months). T-cell-inflamed gene expression profile status correlated with PD-L1 expression (Spearman, ρ=0.712) but was not an independent predictor of overall survival.

CONCLUSION

PD-L1 expression is associated with longer overall survival among advanced ovarian cancer patients. PD-L1 expression may be an independent prognostic biomarker.

KISS: a spectrometric imager for millimetre cosmology

Clusters of galaxies are used to map the large-scale structures in the universe and as probe of universe evolution. They can be observed through the Sunyaev-Zel’dovich (SZ) effect. In this respect the spectro-imaging at low resolution frequency is an important tool, today, for the study of cluster of galaxies. We have developed KISS (KIDs Interferometer Spectrum Survey), a spectrometric imager dedicated to the secondary anisotropies of the Cosmic Microwave Background (CMB). The multi-frequency approach permits to improve the component separation with respect to predecessor experiments. In this paper, firstly, we provide a description of the scientific context and the state of the art of SZ observations. Secondly, we describe the KISS instrument. Finally, we show preliminary results of the ongoing commissioning campaign.

Abstract 2483: An integrated bioinformatics pipeline for profiling cancer-immune interaction from whole exome sequencing of pembrolizumab clinical samples

Purpose We built an integrated analytic pipeline to robustly and comprehensively profile molecular features of pembrolizumab-treated tumors using whole exome sequencing (WES) data from clinical trials across different indications.

Experimental design We implemented a computational framework for analysis of WES data generated by different sequencing vendors for 1467 samples from 8 major tumor types. Reads were first processed by BWA-MEM, Picard, and GATK (v2) to generate analysis-ready BAM files. Quality controls (QC) before downstream analysis included Y/X reads ratio for matched normal sample as patient sex prediction and tumor/normal concordance and contamination estimation by Conpair. Key molecular features were evaluated, including tumor mutation burden (TMB) by MuTect (v1) and VEP; HLA-I typing by OptiType; neoantigen burden by NetMHC (v3.4); mutation signature by deconstructSigs; allele-specific copy number by VarScan2 and Sequenza; clonality by PyClone; presence of oncogenic viruses (eg, EBV, HBV, HPV); and LOH score indicating homologous recombination deficiency (HRD-LOH).

Results Concordance rate between predicted and clinical sex was 1446/1464 (98.8%), and 1420/1467 (96.8%) samples passed tumor-normal alignment QC. Highest TMB (median [range]) was detected in melanoma (245 [2-6246]) and urothelial carcinoma (UC) (124 [4-1579]), with lowest TMB in metastatic castration-resistant prostate cancer (52 [1-6143]) and ovarian cancer (OvCa) (49.5 [8-272]). The correlation of median TMB across 7 cancer types in our data and TCGA was Spearman R = 0.957. Within indications, there was no difference in TMB distribution for sequencing data originating from different sequencing vendors and TCGA data, which demonstrated concordance across data sets and robust TMB calling by our integrated pipeline. Neoantigen burden strongly correlated with TMB (N = 1420; Spearman R = 0.890). HPV was detected in 20/129 (15.5%) head and neck squamous cell carcinomas (HNSCC) and 4/6 (66.7%) anal cancers; EBV was detected in 8/129 (6.2%) HNSCC and 18/318 (5.7%) gastric cancers (GC). The dominant mutation signatures by disease included APOBEC for UC (135/236) and HNSCC (22/122), alcohol for HCC (19/35), HRD for OvCa (12/64) and triple-negative breast cancer (51/175), UV exposure for melanoma (145/176), and dMMR for GC (84/287) and CRPC (16/155). Samples with deleterious BRCA mutations showed significantly higher HRD-LOH score (N = 1420; AUROC = 0.61 [95% CI, 0.53-0.69]) and HRD mutational signature (N = 1316; DOR = 6.4 [95% CI, 3.7-11.1]).

Conclusion We assembled heterogeneous computational modules into an integrated pipeline to reliably profile diverse molecular features from WES data of nearly 1500 clinical samples across different tumor types. These data serve as a foundation for translational research efforts supporting pembrolizumab development.

Citation Format: Xiaoqiao Liu, Xinwei Sher, Hongchao Lu, Jun Zhuang, Weilong Zhao, Andrew Albright, Cinthia Umemoto, Christen Wudarski, Maureen Lane, Mark Ayers, Andrea L. Webber, Sandra C. Souza, Ping Qiu, Diane Levitan, Jennifer Cho, Deepti Aurora-Garg, Matthew Marton, Alexandra Snyder, Michael Morrissey, Andrey Loboda, Ronghua Chen, Razvan Cristescu. An integrated bioinformatics pipeline for profiling cancer-immune interaction from whole exome sequencing of pembrolizumab clinical samples [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2483.

Development of a PCR Assay to Detect Low Level Trypanosoma cruzi in Blood Specimens Collected with PAXgene Blood DNA Tubes for Clinical Trials Treating Chagas Disease

Chagas disease is caused by the parasitic infection of Trypanosoma cruzi (T. cruzi). The STOP CHAGAS clinical trial was initiated in 2011 to evaluate posaconazole in treating Chagas disease, with treatment success defined as negative qualitative PCR results of detecting the parasites in blood specimens collected post-treatment. PAXgene Blood DNA tubes were utilized as a simple procedure to collect and process blood specimens. However, the PAXgene blood specimens challenged published T. cruzi PCR methods, resulting in poor sensitivity and reproducibility. To accurately evaluate the treatment efficacy of the clinical study, we developed and validated a robust PCR assay for detecting low level T. cruzi in PAXgene blood specimens. The assay combines a new DNA extraction method with a custom designed qPCR assay, resulting in limit of detection of 0.005 and 0.01 fg/μl for K98 and CL Brener, two representative strains of two of T. cruzi’s discrete typing units. Reliable qPCR standard curves were established for both strains to measure parasite loads, with amplification efficiency ≥ 90% and the lower limit of linearity ≥ 0.05 fg/μl. The assay successfully analyzed the samples collected from the STOP CHAGAS study and may prove useful for future global clinical trials evaluating new therapies for asymptomatic chronic Chagas disease.

Chagas disease is caused by the infection of the protozoan parasite Trypanosoma cruzi (T. cruzi) and carries a significant tropical disease burden in the Western Hemisphere. The STOP CHAGAS study was a global clinical trial evaluating therapies for Chagas disease. PAXgene blood DNA tubes used by the study simplified and standardized the sample collection and processing procedures, but challenged published PCR assays that detect circulating T. cruzi. In this study, we report our effort of developing and validating a robust, sensitive and specific PCR assay for detecting T. cruzi in PAXgene blood specimens. The efficacy outcome results of the STOP CHAGAS study that utilized our assay further support the use of the PCR assay as a marker of therapeutic response for patients with Chagas disease.

Development and Validation of a Template-Independent Next-Generation Sequencing Assay for Detecting Low-Level Resistance-Associated Variants of Hepatitis C Virus

To develop hepatitis C virus (HCV) direct-acting antiviral (DAA) drugs that can treat most HCV genotypes and offer higher barriers for treatment-resistant mutations, it is important to study resistance-associated variants (RAVs). Current commercially available RAV detection assays rely on genotype- or subtype-specific template-dependent PCR amplification. These assays are limited to genotypes and subtypes that are often prevalent in developed countries because of availability of public sequence databases. To support global clinical trials of DAAs, we developed and validated a template-independent (TI) next-generation sequencing (NGS) assay for HCV whole genome sequencing that can perform HCV subtyping, detect HCV mixed genotype or subtype infection, and identify low-level RAVs at a 5% fraction of the viral population with sensitivity and positive predictive value ≥ 0.9. We compared TI-NGS with commercial genotype- or subtype-specific Sanger sequencing assays, and found that TI-NGS both confirmed most of variants called by Sanger sequencing and avoided biases likely caused by PCR primers used in Sanger sequencing. To confirm TI-NGS assay's variant calls at the discrepant positions with Sanger sequencing, we custom designed template-dependent NGS assays and obtained 100% concordance with the TI-NGS assay. The ability to reliably detect low-level RAVs in HCV samples of any subtype without PCR primer-related bias makes this TI-NGS assay an important tool in studying HCV DAA drug resistance.

Production of Highly Polarized Positrons Using Polarized Electrons at MeV Energies

The Polarized Electrons for Polarized Positrons experiment at the injector of the Continuous Electron Beam Accelerator Facility has demonstrated for the first time the efficient transfer of polarization from electrons to positrons produced by the polarized bremsstrahlung radiation induced by a polarized electron beam in a high-Z target. Positron polarization up to 82% have been measured for an initial electron beam momentum of 8.19  MeV/c, limited only by the electron beam polarization. This technique extends polarized positron capabilities from GeV to MeV electron beams, and opens access to polarized positron beam physics to a wide community.

Development of a microarray platform for FFPET profiling: application to the classification of human tumors

Background

mRNA profiling has become an important tool for developing and validating prognostic assays predictive of disease treatment response and outcome. Archives of annotated formalin-fixed paraffin-embedded tissues (FFPET) are available as a potential source for retrospective studies. Methods are needed to profile these FFPET samples that are linked to clinical outcomes to generate hypotheses that could lead to classifiers for clinical applications.

Methods

We developed a two-color microarray-based profiling platform by optimizing target amplification, experimental design, quality control, and microarray content and applied it to the profiling of FFPET samples. We profiled a set of 50 fresh frozen (FF) breast cancer samples and assigned class labels according to the signature and method by van 't Veer et al [1] and then profiled 50 matched FFPET samples to test how well the FFPET data predicted the class labels. We also compared the sorting power of classifiers derived from FFPET sample data with classifiers derived from data from matched FF samples.

Results

When a classifier developed with matched FF samples was applied to FFPET data to assign samples to either "good" or "poor" outcome class labels, the classifier was able to assign the FFPET samples to the correct class label with an average error rate = 12% to 16%, respectively, with an Odds Ratio = 36.4 to 60.4, respectively. A classifier derived from FFPET data was able to predict the class label in FFPET samples (leave-one-out cross validation) with an error rate of ~14% (p-value = 3.7 × 10^-7). When applied to the matched FF samples, the FFPET-derived classifier was able to assign FF samples to the correct class labels with 96% accuracy. The single misclassification was attributed to poor sample quality, as measured by qPCR on total RNA, which emphasizes the need for sample quality control before profiling.

Conclusion

We have optimized a platform for expression analyses and have shown that our profiling platform is able to accurately sort FFPET samples into class labels derived from FF classifiers. Furthermore, using this platform, a classifier derived from FFPET samples can reliably provide the same sorting power as a classifier derived from matched FF samples. We anticipate that these techniques could be used to generate hypotheses from archives of FFPET samples, and thus may lead to prognostic and predictive classifiers that could be used, for example, to segregate patients for clinical trial enrollment or to guide patient treatment.

Characterization of Globin RNA Interference in Gene Expression Profiling of Whole-Blood Samples

Background: Blood-based biomarker discovery with gene expression profiling has been hampered by interference from endogenous, highly abundant α- and β-globin transcripts. We describe a means to quantify the interference of globin transcripts on profiling and the effectiveness of globin transcript mitigation by (a) defining and characterizing globin interference, (b) reproducing globin interference with synthetic transcripts, and (c) using ROC curves to measure sensitivity and specificity for a protocol for removing α- and β-globin transcripts.

Methods: We collected blood at 2 sites and extracted total RNA in PreAnalytiX PAXgene tubes. As a reference for characterizing interference, we supplemented aliquots of total RNA with synthesized globin transcripts and total RNA from human brain. Selected aliquots were processed with Ambion GLOBINclear to remove globin transcripts. All aliquots were labeled and hybridized to Agilent DNA microarrays by means of pooling schemes designed to quantify the mitigation of globin interference and to titrate gene expression signatures. Quantitative reverse transcription–PCR data were generated for comparison with microarray results.

Results: Our supplementation and pooling strategy for comparing the microarray data among samples demonstrated that mitigation could reduce an interference signature of &gt;1000 genes to approximately 200. Analysis of samples of endogenous globin transcripts supplemented with brain RNA indicated that results obtained with the GLOBINclear treatment approach those of peripheral blood mononuclear cell preparations.

Conclusion: We confirmed that both the absolute concentrations of globin transcripts and differences in transcript concentrations within a sample set are factors that cause globin interference (Genes Immun 2005;6:588–95). The methods and transcripts we have developed may be useful for quantitatively characterizing globin mRNA interference and its mitigation.

Responses to irrelevant probes during task-induced negative and positive shifts

The functional significance of task-induced negative and positive cortical shifts were tested with the probe-stimulus method. Both shifts were induced within the same experimental situation in three variants of a CNV paradigm, where a slow positive wave (a variant of P300) appeared following S2. In Experiment I and II, S2 called for making or withholding a motor response (go/no-go); in Experiment III, S2 informed the subject about the correctness of a previous guess. Irrelevant probe-stimuli were applied in conjunction with the task during the CNV, the post-S2 positivity and the intertrial interval (ITI). The probe-evoked vertex EPs were smaller during the post-S2 positivity as compared to the CNV and the ITI. This was true not only for the motor task but also for the guessing task, where the effect is unlikely to have been contaminated by motor potentials. This indicates that positive shifts have an inhibitory effect on the processing of irrelevant probe-stimuli and possibly on information-processing in general.

Saccade-related brain potentials during reading correct and incorrect versions of proverbs

Using a reading task, the present study investigated saccade-related brain potentials (SRPs) accompanying the perception of the final words of proverbs, i.e. of sentences where the context allows a strong anticipation of the final word. The sentences were presented one at a time on a TV monitor. The proverbs appeared either in their original form or with their final word changed to be incongruous with the sentence context. SRPs to the two types of final words were recorded from 4 scalp areas. The onset of the saccade leading to the final word was used to trigger the averaging of SRPs. Incongruent and congruent brain responses were also compared by means of difference waveforms. The results showed that a difference between SRPs to congruous vs incongruous final words of proverbs already appeared simultaneously with the SRP component indicating the analysis of the visual pattern of the word. This finding supports an interactive model of word perception.

Context effects on saccade-related brain potentials to words during reading

In two experiments saccade-related brain potentials (SRPs) to sentences were investigated under conditions approximating natural reading. Our aim was to look for electrophysiological (SRP) signs of sentence context on the processing of final words that were either congruent or incongruent with the meaning of the sentence. In Experiment 1 subjects indicated by a button-press whether or not the final word was congruent with the context, while in Experiment 2 they read silently without an overt decision. In Experiment 1, SRPs to incongruent words were more negative than SRPs to congruent words between 80-310 msec (from saccade offset). In Experiment 2, however, the inconcruent SRPs became more negative than the congruent SRPs only between 280-460 msec. These results suggest that in Experiment 1, during the processing of incongruent words the early sign of registering mismatch appears simultaneously with the analysis of the visual features of the word.

The diabetic response of weanling sand rats (Psammomys obesus) to diets containing different concentrations of salt bush (Atriplex halimus)

Understanding the sand rat's metabolic responses is necessary in order to employ the animal gainfully in the study of diabetes. Weanlings are most susceptible to the effect of diabetogenic diets. In the present experiment, weanling sand rats were fed diets at 3 levels of energy intake. The diets were based on pellets composed of different ratios of salt bush (Atriplex halimus) and a standard laboratory animal chow pellet. The results showed a significant correlation between the level of energy intake, percent body fat and signs of Type 2 diabetes. Animals with 28-30.6% body fat had blood glucose levels of 260 +/- 66 mg% and plasma insulin concentrations of greater than 558 mu u/ml, and those with 17.9-24.0% body fat had a blood glucose level of 107 +/- 19.8 mg% and a plasma insulin level of 222 +/- 35 mu u/ml. Animals with approximately 10% body fat, had a blood glucose level of 60 +/- 1.9 mg% and a plasma insulin concentration of 35 +/- 10 mu u/ml. The fattest animals had the highest percentage of glycosylated hemoglobin. The animals with the highest quantity of fat receiving high caloric intake had a lower lean body mass than those of similar weight exposed to a lower caloric intake. This result could be accounted for by assuming that the extreme hyperinsulinemia promoted fat production at the expense of lean body mass.

Electrocortical signs of word categorization in saccade-related brain potentials and visual evoked potentials

Visual evoked potentials (VEPs) elicited by foveal presentation of words were compared to brain potentials evoked by the same words in a condition where subjects had to make a saccadic eye movement in order to perceive the words (saccade-related brain potentials, SRPs). Subjects had to categorize the words responding with a button press to stimuli belonging to the target (infrequent, P = 0.2) category. The VEP and SRP waveforms showed divergences in the early (up to 250 ms) components, but a marked similarity between the late components. Principal Component Analysis also revealed the same relationship between the two types of brain responses. Peak latency of the late SRP components measured from saccade offset showed an apparent processing advantage over the corresponding late components of VEPs. The N3 component, indexing semantic processing of visual patterns, peaked between 310 and 375 ms in the SRPs, while in the VEPs it appeared between 410 and 470 ms. The P4 component, associated with final stimulus evaluation, showed a similar latency benefit in favour of SRPs (420-500 ms vs 530-590 ms in VEPs). The mean reaction time was 74 ms shorter in the eye movement condition (measured from saccade offset) than in the VEP condition (703 vs 777 ms). The question of what kind of processes may contribute to the differences in mean RTs and to the latencies of the late components between the two conditions are discussed. We suggest that the late components (P3, N3 and P4) of the VEP and the SRP, respectively, index identical brain processes.

Saccade-related brain potentials in semantic categorization tasks

Saccade-related brain potentials (SRPs) were recorded in word categorization tasks in which subjects had to perform a saccade in order to perceive the stimulus. For all three conditions representing different degrees of complexity of semantic categorization, the stimuli belonged to one of two categories which appeared with the respective probabilities of either 0.20 or 0.80. The late positivity (P4) of the SRPs to infrequent stimuli appeared systematically later as the complexity of stimulus evaluation increased: The easiest categorization was accompanied by a P4 at 400 msec, in the more complex condition it peaked at 600 msec, and in the most difficult semantic categorization the P4 peaked even later, at 680 msec. This shift in peak latency with increasing complexity of categorization is in agreement with the results for traditional ERPs (e.g. Kutas and Donchin, 1978). The possible overlap of the late components was investigated by applying Principal Component-Varimax Analysis to the SRPs.

Late components of lambda responses in cognitive tasks

The effects of stimulus probability were investigated on the late components of saccade-related brain potentials (lambda responses) in two paradigms, 'counting' and 'guessing.' Subjects performed saccadic eye movements from a middle light to the target area where one of three kinds of target light stimuli appeared in a randomized sequence, each with a different probability (0.17, 0.33, and 0.50). Brain activity was recorded from six scalp areas. In the counting task subjects were instructed to count the prespecified low-probability stimuli. In the guessing experiment they had to make a guess before each trial as to which kind of target stimulus would appear. In both experiments the late positive components showed significantly greater amplitude in the lambda responses associated with infrequent stimuli than in those elicited by frequent stimuli. Principal component-Varimax analysis of the lambda responses revealed factors corresponding to the P300 and the slow wave components of traditional evoked potential studies.

Late components of saccade-related brain potentials in guessing tasks

The late positive components of lambda responses were studied in a guessing task modified in such a way that subjects had to perform a saccadic eye movement in order to perceive task-relevant information. Responses from 6 scalp areas were investigated in 9 subjects and in 2 conditions: control and guessing. In both conditions subjects performed two consecutive saccades in a given trial: the first to the middle light, the second to the target area. In the control condition the subjects knew beforehand what the 'target' would be. In the guessing condition they had to make a guess before each trial as to which of the three target stimuli would appear. The target stimuli occurred with unequal probability and were presented in a randomized sequence. Unlike the control condition, the guessing task led to the appearance of a late positive component in the lambda response. Similar to traditional ERP findings, this late positivity showed an amplitude maximum at the parietal area and a peak latency at 375 msec from saccade onset. Furthermore, Principal Component-Varimax Analysis (PCVA) of the lambda responses revealed a first factor giving the strongest loading in the latency range of the P300, and a second factor which was identified as the slow wave. These factors are quite similar to the factors found in the PCVA of ERPs. Our results suggest that the late components of lambda responses reflect the effects of information processing in cognitive tasks similarly to the way the late positive components of ERPs do.