Aims
Studies in various cancer types have demonstrated discordance between results from different programmed death‐ligand 1 (PD‐L1) assays. Here, we compare the reproducibility and analytical ...concordance of four clinically developed assays for assessing PD‐L1‐positivity in tumour‐infiltrating immune cells in the tumour area (PD‐L1‐IC‐positivity) in triple‐negative breast cancer (TNBC).
Methods and results
Primary TNBC resection specimens (n = 30) were selected based on their PD‐L1‐IC‐positivity per VENTANA SP142 (<1%: 15 cases; 1–5%: seven cases; >5%: eight cases). Serial histological sections were stained for PD‐L1 using VENTANA SP142, VENTANA SP263, DAKO 22C3 and DAKO 28‐8. PD‐L1‐IC‐positivity and tumour cell expression (≥1 versus <1%) were scored by trained readers from seven sites using online virtual microscopy. The adjusted mean of PD‐L1‐IC‐positivity for SP263 (7.8%) was significantly higher than those for the other three assays (3.7–4.9%). Differences in adjusted means were statistically significant between SP263 and the other three assays (P < 0.0001) but not between the three remaining assays when excluding SP263 (P = 0.0961–0.6522). Intra‐class correlation coefficients revealed moderate‐to‐strong inter‐reader agreement for each assay (0.460–0.805) and poor‐to‐strong inter‐assay agreement for each reader (0.298–0.678) on PD‐L1‐IC‐positivity.
Conclusions
In this first multicentre study of different PD‐L1 assays in TNBC, we show that PD‐L1‐IC‐positivity for SP142, 22C3 and 28‐8 was reproducible and analytically concordant, indicating that these three assays may be analytically interchangeable. The relevance of the higher PD‐L1‐IC‐positivity for SP263 should be further investigated.
Bone marrow mononuclear cells (BMNCs) are widely used in regenerative medicine, but recent data suggests that the isolation of BMNCs by commonly used Ficoll-Paque density gradient centrifugation ...(DGC) causes significant cell loss and influences graft function. The objective of this study was to determine in an animal study whether and how Ficoll-Paque DGC affects the yield and composition of BMNCs compared to alternative isolation methods such as adjusted Percoll DGC or immunomagnetic separation of polymorphonuclear cells (PMNs). Each isolation procedure was confounded by a significant loss of BMNCs that was maximal after Ficoll-Paque DGC, moderate after adjusted Percoll DGC and least after immunomagnetic PMN depletion (25.6±5.8%, 51.5±2.3 and 72.3±6.7% recovery of total BMNCs in lysed bone marrow). Interestingly, proportions of BMNC subpopulations resembled those of lysed bone marrow indicating symmetric BMNC loss independent from the isolation protocol. Hematopoietic stem cell (HSC) content, determined by colony-forming units for granulocytes-macrophages (CFU-GM), was significantly reduced after Ficoll-Paque DGC compared to Percoll DGC and immunomagnetic PMN depletion. Finally, in a proof-of-concept study, we successfully applied the protocol for BMNC isolation by immunodepletion to fresh human bone marrow aspirates. Our findings indicate that the common method to isolate BMNCs in both preclinical and clinical research can be considerably improved by replacing Ficoll-Paque DGC with adapted Percoll DGC, or particularly by immunodepletion of PMNs.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
In this article, we propose an evolved system design approach to ultra-wideband (UWB) radar based on pseudo-random noise (PRN) sequences, the key features of which are its user-adaptability to meet ...the demands provided by desired microwave imaging applications and its multichannel scalability. In light of providing a fully synchronized multichannel radar imaging system for short-range imaging as mine detection, non-destructive testing (NDT) or medical imaging, the advanced system architecture is presented with a special focus put on the implemented synchronization mechanism and clocking scheme. The core of the targeted adaptivity is provided by means of hardware, such as variable clock generators and dividers as well as programmable PRN generators. In addition to adaptive hardware, the customization of signal processing is feasible within an extensive open-source framework using the Red Pitaya
data acquisition platform. A system benchmark in terms of signal-to-noise ratio (SNR), jitter, and synchronization stability is conducted to determine the achievable performance of the prototype system put into practice. Furthermore, an outlook on the planned future development and performance improvement is provided.
Extensive sequencing of tumor tissues has greatly improved our understanding of cancer biology over the past years. The integration of genomic and clinical data is increasingly used to select ...personalized therapies in dedicated tumor boards (Molecular Tumor Boards) or to identify patients for basket studies. Genomic alterations and clinical information can be stored, integrated and visualized in the open-access resource cBioPortal for Cancer Genomics. cBioPortal can be run as a local instance enabling storage and analysis of patient data in single institutions, in the respect of data privacy. However, uploading clinical input data and genetic aberrations requires the elaboration of multiple data files and specific data formats, which makes it difficult to integrate this system into clinical practice. To solve this problem, we developed cbpManager.
cbpManager is an R package providing a web-based interactive graphical user interface intended to facilitate the maintenance of mutations data and clinical data, including patient and sample information, as well as timeline data. cbpManager enables a large spectrum of researchers and physicians, regardless of their informatics skills to intuitively create data files ready for upload in cBioPortal for Cancer Genomics on a daily basis or in batch. Due to its modular structure based on R Shiny, further data formats such as copy number and fusion data can be covered in future versions. Further, we provide cbpManager as a containerized solution, enabling a straightforward large-scale deployment in clinical systems and secure access in combination with ShinyProxy. cbpManager is freely available via the Bioconductor project at https://bioconductor.org/packages/cbpManager/ under the AGPL-3 license. It is already used at six University Hospitals in Germany (Mainz, Gießen, Lübeck, Halle, Freiburg, and Marburg).
In summary, our package cbpManager is currently a unique software solution in the workflow with cBioPortal for Cancer Genomics, to assist the user in the interactive generation and management of study files suited for the later upload in cBioPortal.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Vacuolar myelinopathy is a fatal neurological disease that was initially discovered during a mysterious mass mortality of bald eagles in Arkansas in the United States. The cause of this wildlife ...disease has eluded scientists for decades while its occurrence has continued to spread throughout freshwater reservoirs in the southeastern United States. Recent studies have demonstrated that vacuolar myelinopathy is induced by consumption of the epiphytic cyanobacterial species
growing on aquatic vegetation, primarily the invasive
Here, we describe the identification, biosynthetic gene cluster, and biological activity of aetokthonotoxin, a pentabrominated biindole alkaloid that is produced by the cyanobacterium
We identify this cyanobacterial neurotoxin as the causal agent of vacuolar myelinopathy and discuss environmental factors-especially bromide availability-that promote toxin production.
Purpose
Hematopoietic stem cell transplantation is the only curative treatment for several hematological malignancies and immune deficiency syndromes. Nevertheless, the development of ...graft-versus-host disease (GvHD) after transplantation is a severe complication with high morbidity and mortality. The aim of this study was to image human T cells during GvHD development and their migration into GvHD-related organs. By using a radiolabeled anti-human CD3 monoclonal antibody (mAb), we were able to visualize GvHD progression in a humanized mouse model.
Methods
Human peripheral blood mononuclear cells (PBMC) were transferred into immunodeficient mice (initially
n
= 11 mice/group) to induce GvHD. One group additionally received regulatory T cells (Treg) for prevention of GvHD. T cell migration was visualized by sequential small animal PET/MRI using
89
Zr-labeled anti-human CD3 mAb. Flow cytometry and immunohistochemistry were used to measure T cell frequencies in relevant organs at different time points after engraftment.
Results
Using radiolabeled anti-CD3 mAb, we successfully visualized human T cells in inflamed organs of mice by
89
Zr-anti-CD3-PET/MRI. Upon GvHD progression, we observed increased numbers of CD3
+
T cells in the liver (22.9% on day 3; 94.2% on day 10) and the spleen (4.4% on day 3; 58.8% on day 10) which correlated with clinical symptoms. The liver showed distinct spot-like lesions representing a strong focal accumulation of T cells. Administration of Treg prior GvHD induction reduced T cell accumulation in the liver from 857 ± 177 CD3
+
cells/mm
2
to 261 ± 82 CD3
+
cells/mm
2
and thus prevented GvHD.
Conclusion
89
Zr-labeled anti-human CD3 mAb can be used as a proof of concept to detect the exact spatio-temporal distribution of GvHD-mediating T cells. In the future, radiolabeled T cell-specific mAb could be employed as a predictive early biomarker during the course of GvHD maybe even before clinical signs of the disease become evident. Furthermore, monitoring T cell migration and proliferation might improve tailored GvHD therapy.
Clear-cell renal cell carcinoma (ccRCC) is common and associated with substantial mortality. TNM stage and histopathological grading have been the sole determinants of a patient's prognosis for ...decades and there are few prognostic biomarkers used in clinical routine. Management of ccRCC involves multiple disciplines such as urology, radiology, oncology, and pathology and each of these specialties generates highly complex medical data. Here, artificial intelligence (AI) could prove extremely powerful to extract meaningful information to benefit patients.
In the study, we developed and evaluated a multimodal deep learning model (MMDLM) for prognosis prediction in ccRCC.
Two mixed cohorts of non-metastatic and metastatic ccRCC patients were used: (1) The Cancer Genome Atlas cohort including 230 patients and (2) the Mainz cohort including 18 patients with ccRCC. For each of these patients, we trained the MMDLM on multiscale histopathological images, CT/MRI scans, and genomic data from whole exome sequencing.
Outcome measurements included Harrell's concordance index (C-index) and also various performance parameters for predicting the 5-year survival status (5YSS). Different visualization techniques were used to make our model more transparent.
The MMDLM showed great performance in predicting the prognosis of ccRCC patients with a mean C-index of 0.7791 and a mean accuracy of 83.43%. Training on a combination of data from different sources yielded significantly better results compared to when only one source was used. Furthermore, the MMDLM's prediction was an independent prognostic factor outperforming other clinical parameters.
Multimodal deep learning can contribute to prognosis prediction in ccRCC and potentially help to improve the clinical management of this disease.
An AI-based computer program can analyze various medical data (microscopic images, CT/MRI scans, and genomic data) simultaneously and thereby predict the survival time of patients with renal cancer.
In ultrasound nondestructive testing (NDT), a widespread approach is to take synthetic aperture measurements from the surface of a specimen to detect and locate defects within it. Based on these ...measurements, imaging is usually performed using the synthetic aperture focusing technique (SAFT). However, SAFT is suboptimal in terms of resolution and requires oversampling in the time domain to obtain a fine grid for the delay-and-sum (DAS). On the other hand, parametric reconstruction algorithms give better resolution, but their usage for imaging becomes computationally expensive due to the size of the parameter space and a large amount of measurement data in realistic 3-D scenarios when using oversampling. In the literature, the remedies to this are twofold. First, the amount of measurement data can be reduced using state-of-the-art sub-Nyquist sampling approaches to measure Fourier coefficients instead of time-domain samples. Second, parametric reconstruction algorithms mostly rely on matrix-vector operations that can be implemented efficiently by exploiting the underlying structure of the model. In this article, we propose and compare different strategies to choose the Fourier coefficients to be measured. Their asymptotic performance is compared by numerically evaluating the Cramér-Rao bound (CRB) for the localizability of the defect coordinates. These subsampling strategies are then combined with an <inline-formula> <tex-math notation="LaTeX">\ell _{{1}} </tex-math></inline-formula>-minimization scheme to compute 3-D reconstructions from the low-rate measurements. Compared to conventional DAS, this allows us to formulate a fully physically motivated forward model matrix. To enable this, the projection operations of the forward model matrix are implemented matrix-free by exploiting the underlying two-level Toeplitz structure. Finally, we show that high-resolution reconstructions from as low as a single Fourier coefficient per A-scan are possible based on simulated data and measurements from a steel specimen.
Different immunohistochemical programmed death-ligand 1 (PD-L1) assays and scorings have been reported to yield variable results in triple-negative breast cancer (TNBC). We compared the analytical ...concordance and reproducibility of four clinically relevant PD-L1 assays assessing immune cell (IC) score, tumor proportion score (TPS), and combined positive score (CPS) in TNBC. Primary TNBC resection specimens (n = 104) were stained for PD-L1 using VENTANA SP142, VENTANA SP263, DAKO 22C3, and DAKO 28–8. PD-L1 expression was scored according to guidelines on virtual whole slide images by four trained readers.
The mean PD-L1 positivity at IC-score ≥1% and CPS ≥1 ranged between 53% and 75% with the highest positivity for SP263 and comparable levels for 22C3, 28–8, and SP142. Inter-assay agreement was good between 28–8 and 22C3 across all scores and cut-offs (kappa 0.68–0.74) and for both assays with SP142 at IC-score ≥1% and CPS ≥1 (kappa 0.61–0.67). The agreement between SP263 and all other assays was substantially lower for all scores. Inter-reader agreement for each assay was good to excellent for IC-score ≥1% (kappa 0.73–0.78) and CPS ≥1 (kappa 0.68–0.74), fair to good for CPS ≥10 (kappa 0.52–0.67) and TPS ≥1% (kappa 0.53–0.72). The percentage of overlapping cases in the positive/negative category was >90% between IC-score ≥1% and CPS ≥1 but below when comparing IC-score ≥1% with CPS ≥10. We demonstrate an overall good inter-reader agreement for all PD-L1 assays in TNBC along with assay specific differences in positivity and concordances, which may aid to select the right test strategy in routine diagnostics.
•Different PD-L1 IHC assays and scorings may show variable results in TNBC.•Overall good assay concordance between SP142, 22C3, and 28–8 at IC-score 1%.•Overall good assay concordance between SP142, 22C3, and 28–8 at CPS 1.•SP142 is less optimal for CPS assessment at higher cut-offs.•SP263 assay is not interchangeable with the other three PD-L1 assays.
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