Publications

We maintain this section to inform interested users about independent scientific studies conducted on MetaSystems products. We assume no responsibility or liability regarding the accuracy or correct use of the information or statements provided by external authors. The conclusions or statements expressed in the publications listed are those of the external authors or researchers. The publications may involve user-specific adaptations of MetaSystems products. They are not intended for diagnostic use. For publications covered by the Intended Purpose of Metafer or Ikaros, please refer to the respective instructions for use (IFU).

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Advanced Science, 11
2024

Molecular Lineages and Spatial Distributions of Subplate Neurons in the Human Fetal Cerebral Cortex

Xueyu Guo, Trevor Lee, Jason Sun, Julianne Sun, Wenjie Cai et al.

<p>The expansion of neural progenitors and production of distinct neurons are crucial for architectural assembly and formation of connectivity in human brains. Subplate neurons (SPNs) are among the firstborn neurons in the human fetal cerebral cortex, and play a critical role in establishing intra- and extracortical connections. However, little is known about SPN origin and developmental lineages. In this study, spatial landscapes and molecular trajectories of SPNs in the human fetal cortices from gestational weeks (GW) 10 to 25 are created by performing spatial transcriptomics and single-cell RNA sequencing. Genes known to be evolutionarily human-specific and genes associated with extracellular matrices (ECMs) are found to maintain stable proportions of subplate neurons among other neuronal types. Enriched ECM gene expression in SPNs varies in distinct cortical regions, with the highest level in the frontal lobe of human fetal brains. This study reveals molecular origin and lineage specification of subplate neurons in the human fetal cerebral cortices, and highlights underpinnings of SPNs to cortical neurogenesis and early structural folding.</p>

Digital object identifier (DOI): 10.1002/advs.202407137

Molecular Psychiatry, 29, 2408-2423
2024

Scanning ultrasound-mediated memory and functional improvements do not require amyloid-β reduction

Gerhard Leinenga, Xuan Vinh To, Liviu-Gabriel Bodea, Jumana Yousef, Gina Richter-Stretton et al.

<p>A prevalent view in treating age-dependent disorders including Alzheimer’s disease (AD) is that the underlying amyloid plaque pathology must be targeted for cognitive improvements. In contrast, we report here that repeated scanning ultrasound (SUS) treatment at 1 MHz frequency can ameliorate memory deficits in the APP23 mouse model of AD without reducing amyloid-β (Aβ) burden. Different from previous studies that had shown Aβ clearance as a consequence of blood-brain barrier (BBB) opening, here, the BBB was not opened as no microbubbles were used. Quantitative SWATH proteomics and functional magnetic resonance imaging revealed that ultrasound induced long-lasting functional changes that correlate with the improvement in memory. Intriguingly, the treatment was more effective at a higher frequency (1 MHz) than at a frequency within the range currently explored in clinical trials in AD patients (286 kHz). Together, our data suggest frequency-dependent bio-effects of ultrasound and a dissociation of cognitive improvement and Aβ clearance, with important implications for the design of trials for AD therapies.</p>

Digital object identifier (DOI): 10.1038/s41380-024-02509-5

Nature Communications, 15
2024

Claustrum and dorsal endopiriform cortex complex cell-identity is determined by Nurr1 and regulates hallucinogenic-like states in mice

Ioannis Mantas, Ivana Flais, Yuvarani Masarapu, Tudor Ionescu, Solène Frapard et al.

<p>The Claustrum/dorsal endopiriform cortex complex (CLA) is an enigmatic brain region with extensive glutamatergic projections to multiple cortical areas. The transcription factor Nurr1 is highly expressed in the CLA, but its role in this region is not understood. By using conditional gene-targeted mice, we show that Nurr1 is a crucial regulator of CLA neuron identity. Although CLA neurons remain intact in the absence of Nurr1, the distinctive gene expression pattern in the CLA is abolished. CLA has been hypothesized to control hallucinations, but little is known of how the CLA responds to hallucinogens. After the deletion of Nurr1 in the CLA, both hallucinogen receptor expression and signaling are lost. Furthermore, functional ultrasound and Neuropixel electrophysiological recordings revealed that the hallucinogenic-receptor agonists’ effects on functional connectivity between prefrontal and sensorimotor cortices are altered in Nurr1-ablated mice. Our findings suggest that Nurr1-targeted strategies provide additional avenues for functional studies of the CLA.</p>

Digital object identifier (DOI): 10.1038/s41467-024-52429-9

2024

Αlpha-Synuclein Induced Immune Response Triggers Parkinson’s Disease-Like Symptoms

Rebekah G. Parkinson, Tony Xu, Jacob Martin, Zizheng Xian, Ilvana Ziko et al.

<p>Increasing evidence suggests that Parkinson’s disease is an autoimmune disorder, with findings of elevated peripheral blood mononuclear cell in patients, and antigenic properties of α-synuclein driving both the innate and adaptive immunity. Yet, how the interaction of α-synuclein and a specific immune response participates to Parkinson’s disease ontogenesis has remained unanswered. Here, we reveal that autoimmune response to an α-synuclein antigen underlies Parkinson’s disease. We demonstrate that autoimmunity mediated by CD4+T cell activation with α-synuclein α-syn<sub>61-75</sub> antigen is required to lead to immune cell infiltration and localized inflammation in the substantia nigra, triggering dopaminergic cell neurodegeneration and deficits in locomotion and gait kinematics. This study offers the first immune-induced mouse model that recapitulates all features of Parkinson’s disease to study the mechanisms triggering disease onset. It provides the basis for temporally tracking symptom development, exploring preventive strategies and prodromal therapeutic interventions in Parkinson’s Disease.</p>

Digital object identifier (DOI): 10.1101/2024.05.27.596130

Cancer Discovery, 15, 83-104
2024

Chromothripsis-Mediated Small Cell Lung Carcinoma

Natasha Rekhtman, Sam E. Tischfield, Christopher A. Febres-Aldana, Jake June-Koo Lee, Jason C. Chang et al.

<p>Small cell lung carcinoma (SCLC) is a highly aggressive malignancy that is typically associated with tobacco exposure and inactivation of <em>RB1</em> and <em>TP53</em> genes. Here, we performed detailed clinicopathologic, genomic, and transcriptomic profiling of an atypical subset of SCLC that lacked <em>RB1</em> and <em>TP53</em> co-inactivation and arose in never/light smokers. We found that most cases were associated with chromothripsis—massive, localized chromosome shattering—recurrently involving chromosome 11 or 12 and resulting in extrachromosomal amplification of <em>CCND1</em> or co-amplification of <em>CCND2</em>/<em>CDK4</em>/<em>MDM2</em>, respectively. Uniquely, these clinically aggressive tumors exhibited genomic and pathologic links to pulmonary carcinoids, suggesting a previously uncharacterized mode of SCLC pathogenesis via transformation from lower-grade neuroendocrine tumors or their progenitors. Conversely, SCLC in never-smokers harboring inactivated <em>RB1</em> and <em>TP53</em> exhibited hallmarks of adenocarcinoma-to-SCLC derivation, supporting two distinct pathways of plasticity-mediated pathogenesis of SCLC in never-smokers.</p> <p><strong>Significance:</strong> Here, we provide the first detailed description of a unique SCLC subset lacking <em>RB1</em>/<em>TP53</em> alterations and identify extensive chromothripsis and pathogenetic links to pulmonary carcinoids as its hallmark features. This work defines atypical SCLC as a novel entity among lung cancers, highlighting its exceptional histogenesis, clinicopathologic characteristics, and therapeutic vulnerabilities.</p>

Digital object identifier (DOI): 10.1158/2159-8290.cd-24-0286

Neurotrauma Reports, 5, 194-202
2024

Histological Characterisation of a Sheep Model of Mild Traumatic Brain Injury: A Pilot Study

Sheryl Tan, Danica Hamlin, Eryn Kwon, Miriam Scadeng, Vickie Shim et al.

<p>Large animal models of mild traumatic brain injury (mTBI) are needed to elucidate the pathophysiology of mechanical insult to a gyrencephalic brain. Sheep (ovis aries) are an attractive model for mTBI because of their neuroanatomical similarity to humans; however, few histological studies of sheep mTBI models have been conducted. We previously developed a sheep mTBI model to pilot methods for investigating the mechanical properties of brain tissue after injury. Here, we sought to histologically characterize the cortex under the impact site in this model. Three animals received a closed skull mTBI with unconstrained head motion, delivered with an impact stunner, and 3 sham animals were anesthetized but did not receive an impact. Magnetic resonance imaging (MRI) of the brain was performed before and after the impact and revealed variable degrees of damage to the skull and brain. Fluorescent immunohistochemistry revealed regions of hemorrhage in the cortex underlying the impact site in 2 of 3 mTBI sheep, the amount of which correlated with the degree of damage observed on the post-impact MRI scans. Labeling for microtubule-associated protein 2 and neuronal nuclear protein revealed changes in cellular anatomy, but, unexpectedly, glial fibrillary acidic protein and ionized calcium-binding adaptor molecule 1 labeling were relatively unchanged compared to sham animals. Our findings provide preliminary evidence of vascular and neuronal damage with limited glial reactivity and highlight the need for further in-depth histological assessment of large animal mTBI models.</p>

Digital object identifier (DOI): 10.1089/neur.2023.0105

Brain, 147, 3547-3561
2024

Hippocampal aggregation signatures of pathogenic UBQLN2 in amyotrophic lateral sclerosis and frontotemporal dementia

Kyrah M. Thumbadoo, Birger V. Dieriks, Helen C. Murray, Molly E. V. Swanson, Ji Hun Yoo et al.

<p>Pathogenic variants in the <em>UBQLN2</em> gene cause X-linked dominant amyotrophic lateral sclerosis and/or frontotemporal dementia characterized by ubiquilin 2 aggregates in neurons of the motor cortex, hippocampus and spinal cord. However, ubiquilin 2 neuropathology is also seen in sporadic and familial amyotrophic lateral sclerosis and/or frontotemporal dementia cases not caused by <em>UBQLN2</em> pathogenic variants, particularly <em>C9orf72</em>-linked cases. This makes the mechanistic role of mutant ubiquilin 2 protein and the value of ubiquilin 2 pathology for predicting genotype unclear. Here we examine a cohort of 44 genotypically diverse amyotrophic lateral sclerosis cases with or without frontotemporal dementia, including eight cases with <em>UBQLN2</em> variants [resulting in p.S222G, p.P497H, p.P506S, p.T487I (two cases) and p.P497L (three cases)].</p> <p>Using multiplexed (five-label) fluorescent immunohistochemistry, we mapped the co-localization of ubiquilin 2 with phosphorylated TDP-43, dipeptide repeat aggregates and p62 in the hippocampus of controls (<em>n</em> = 6), or amyotrophic lateral sclerosis with or without frontotemporal dementia in sporadic (<em>n</em> = 20), unknown familial (<em>n</em> = 3), <em>SOD1</em>-linked (<em>n</em> = 1), <em>FUS</em>-linked (<em>n</em> = 1), <em>C9orf72</em>-linked (<em>n</em> = 5) and <em>UBQLN2</em>-linked (<em>n</em> = 8) cases.</p> <p>We differentiate between (i) ubiquilin 2 aggregation together with phosphorylated TDP-43 or dipeptide repeat proteins; and (ii) ubiquilin 2 self-aggregation promoted by <em>UBQLN2</em> pathogenic variants that cause amyotrophic lateral sclerosis and/or frontotemporal dementia. Overall, we describe a hippocampal protein aggregation signature that fully distinguishes mutant from wild-type ubiquilin 2 in amyotrophic lateral sclerosis with or without frontotemporal dementia, whereby mutant ubiquilin 2 is more prone than wild-type to aggregate independently of driving factors.</p> <p>This neuropathological signature can be used to assess the pathogenicity of <em>UBQLN2</em> gene variants and to understand the mechanisms of <em>UBQLN2</em>-linked disease.</p>

Digital object identifier (DOI): 10.1093/brain/awae140

Brain, Behavior, and Immunity, 117, 181-194
2024

ROCK2 regulates microglia proliferation and neuronal survival after traumatic brain injury

Emily F. Willis, Seung Jae Kim, Wei Chen, Melanie Nyuydzefe, Kelli P. A. MacDonald et al.

<p>Traumatic brain injury (TBI) results in prolonged and non-resolving activation of microglia. Forced turnover of these cells during the acute phase of <a href="https://www.sciencedirect.com/topics/neuroscience/traumatic-brain-injury" title="Learn more about TBI from ScienceDirect's AI-generated Topic Pages">TBI</a> aids recovery, but the cell-intrinsic pathways that underpin the pro-repair phenotype of these repopulating microglia remain unclear. Here, we show that selective targeting of ROCK2 with the small molecule inhibitor KD025 impairs the proliferative response of microglia after TBI as well as during genetically induced turnover of microglia. KD025 treatment abolished the substantial neuroprotective and cognitive benefits conferred by repopulating microglia, preventing these cells from replenishing the depleted niche during the early critical time window post-injury. Delaying KD025 treatment to the subacute phase of TBI allowed microglial repopulation to occur, but this did not enhance the benefits conferred by repopulating microglia. Taken together, our data indicate that ROCK2 mediates neuronal survival and microglial population dynamics after TBI, including the emergence of repopulating microglia with a pro-repair phenotype.</p>

Digital object identifier (DOI): 10.1016/j.bbi.2024.01.004

npj Parkinson’s Disease, 10
2024

Aggregate-prone brain regions in Parkinson’s disease are rich in unique N-terminus α-synuclein conformers with high proteolysis susceptibility

James A. Wiseman, Helen C. Murray, Richard L. M. F. Faull, Michael Dragunow, Clinton P. Turner et al.

<p>In Parkinson’s disease (PD), and other α-synucleinopathies, α-synuclein (α-Syn) aggregates form a myriad of conformational and truncational variants. Most antibodies used to detect and quantify α-Syn in the human brain target epitopes within the C-terminus (residues 96–140) of the 140 amino acid protein and may fail to capture the diversity of α-Syn variants present in PD. We sought to investigate the heterogeneity of α-Syn conformations and aggregation states in the PD human brain by labelling with multiple antibodies that detect epitopes along the entire length of α-Syn. We used multiplex immunohistochemistry to simultaneously immunolabel tissue sections with antibodies mapping the three structural domains of α-Syn. Discrete epitope-specific immunoreactivities were visualised and quantified in the olfactory bulb, medulla, substantia nigra, hippocampus, entorhinal cortex, middle temporal gyrus, and middle frontal gyrus of ten PD cases, and the middle temporal gyrus of 23 PD, and 24 neurologically normal cases. Distinct Lewy neurite and Lewy body aggregate morphologies were detected across all interrogated regions/cases. Lewy neurites were the most prominent in the olfactory bulb and hippocampus, while the substantia nigra, medulla and cortical regions showed a mixture of Lewy neurites and Lewy bodies. Importantly, unique N-terminus immunoreactivity revealed previously uncharacterised populations of (1) perinuclear, (2) glial (microglial and astrocytic), and (3) neuronal lysosomal α-Syn aggregates. These epitope-specific N-terminus immunoreactive aggregate populations were susceptible to proteolysis via time-dependent proteinase K digestion, suggesting a less stable oligomeric aggregation state. Our identification of unique N-terminus immunoreactive α-Syn aggregates adds to the emerging paradigm that α-Syn pathology is more abundant and complex in human brains with PD than previously realised. Our findings highlight that labelling multiple regions of the α-Syn protein is necessary to investigate the full spectrum of α-Syn pathology and prompt further investigation into the functional role of these N-terminus polymorphs.</p>

Digital object identifier (DOI): 10.1038/s41531-023-00614-w

Science advances, 9, eadh2501
August, 2023

An engineered Sox17 induces somatic to neural stem cell fate transitions independently from pluripotency reprogramming.

Weng, Mingxi, Hu, Haoqing, Graus, Matthew S., Tan, Daisylyn Senna, Gao, Ya, Ren, Shimiao, Ho, Derek Hoi Hang, Langer, Jakob, Holzner, Markus, Huang, Yuhua, Ling, Guang Sheng, Lai, Cora Sau Wan, Francois, Mathias, Jauch, Ralf

<p>Advanced strategies to interconvert cell types provide promising avenues to model cellular pathologies and to develop therapies for neurological disorders. Yet, methods to directly transdifferentiate somatic cells into multipotent induced neural stem cells (iNSCs) are slow and inefficient, and it is unclear whether cells pass through a pluripotent state with full epigenetic reset. We report iNSC reprogramming from embryonic and aged mouse fibroblasts as well as from human blood using an engineered Sox17 (eSox17 ). eSox17 efficiently drives iNSC reprogramming while Sox2 or Sox17 fail. eSox17 acquires the capacity to bind different protein partners on regulatory DNA to scan the genome more efficiently and has a more potent transactivation domain than Sox2. Lineage tracing and time-resolved transcriptomics show that emerging iNSCs do not transit through a pluripotent state. Our work distinguishes lineage from pluripotency reprogramming with the potential to generate more authentic cell models for aging-associated neurodegenerative diseases.</p>

Digital object identifier (DOI): 10.1126/sciadv.adh2501

Environmental science and pollution research international, 30, 35258--35268
March, 2023

Exudation of microplastics from commonly used face masks in COVID-19 pandemic.

Bhangare, Rahul C., Tiwari, Mahesh, Ajmal, Puthiyaveettilparambu Yousuf, Rathod, Tejas D., Sahu, Sanjay K.

<p>The COVID-19 pandemic forced use of face masks up to billions of masks per day globally. Though an important and necessary measure for control of the pandemic, use of masks also poses some inherent risks. One of those risks is inhalation of microplastics released from the mask materials. Since most of the mask materials are made from plastic/polymers, they always have the potential to expose the user to fragmented microplastics. To estimate the amount of inhalable microplastic exuded from masks, an experiment simulating real-life scenario of mask usage was performed. The study included collection of microplastics oozed out from the masks on to a filter paper followed by staining and fluorescence detection of the total number of microplastics using a microscope. Both used and new masks were studied. Based on the emission wavelength, the microplastics were found to be belonging to three different categories, namely blue, green and red emitting microplastics respectively. The number of microplastic particles emitted per mask over a period of usage of 8 h was about 5000 to 9000 for new masks and about 6500 to 15,000 for used masks respectively. The estimation of polymer type of plastic in the mask fabrics was also carried out using Raman and FTIR spectroscopy.</p>

Digital object identifier (DOI): 10.1007/s11356-022-24702-1

International journal of molecular sciences, 24
March, 2023

High Resolution and Automatable Cytogenetic Biodosimetry Using In Situ Telomere and Centromere Hybridization for the Accurate Detection of DNA Damage: An Overview.

M'Kacher, Radhia, Colicchio, Bruno, Junker, Steffen, El Maalouf, Elie, Heidingsfelder, Leonhard, Plesch, Andreas, Dieterlen, Alain, Jeandidier, Eric, Carde, Patrice, Voisin, Philippe

<p>In the event of a radiological or nuclear accident, or when physical dosimetry is not available, the scoring of radiation-induced chromosomal aberrations in lymphocytes constitutes an essential tool for the estimation of the absorbed dose of the exposed individual and for effective triage. Cytogenetic biodosimetry employs different cytogenetic assays including the scoring of dicentrics, micronuclei, and translocations as well as analyses of induced premature chromosome condensation to define the frequency of chromosome aberrations. However, inherent challenges using these techniques include the considerable time span from sampling to result, the sensitivity and specificity of the various techniques, and the requirement of highly skilled personnel. Thus, techniques that obviate these challenges are needed. The introduction of telomere and centromere (TC) staining have successfully met these challenges and, in addition, greatly improved the efficiency of cytogenetic biodosimetry through the development of automated approaches, thus reducing the need for specialized personnel. Here, we review the role of the various cytogenetic dosimeters and their recent improvements in the management of populations exposed to genotoxic agents such as ionizing radiation. Finally, we discuss the emerging potentials to exploit these techniques in a wider spectrum of medical and biological applications, e.g., in cancer biology to identify prognostic biomarkers for the optimal triage and treatment of patients.</p>

Digital object identifier (DOI): 10.3390/ijms24065699

Nature Biotechnology, 42, 1394-1403
2023

Spatial host–microbiome sequencing reveals niches in the mouse gut

Britta Lötstedt, Martin Stražar, Ramnik Xavier, Aviv Regev, Sanja Vickovic

<p>Mucosal and barrier tissues, such as the gut, lung or skin, are composed of a complex network of cells and microbes forming a tight niche that prevents pathogen colonization and supports host–microbiome symbiosis. Characterizing these networks at high molecular and cellular resolution is crucial for understanding homeostasis and disease. Here we present spatial host–microbiome sequencing (SHM-seq), an all-sequencing-based approach that captures tissue histology, polyadenylated RNAs and bacterial 16S sequences directly from a tissue by modifying spatially barcoded glass surfaces to enable simultaneous capture of host transcripts and hypervariable regions of the 16S bacterial ribosomal RNA. We applied our approach to the mouse gut as a model system, used a deep learning approach for data mapping and detected spatial niches defined by cellular composition and microbial geography. We show that subpopulations of gut cells express specific gene programs in different microenvironments characteristic of regional commensal bacteria and impact host–bacteria interactions. SHM-seq should enhance the study of native host–microbe interactions in health and disease.</p>

Digital object identifier (DOI): 10.1038/s41587-023-01988-1

Zoological Journal of the Linnean Society, 202
2023

Karyotype stasis but species-specific repetitive DNA patterns in Anguis lizards (Squamata: Anguidae), in the evolutionary framework of Anguiformes

Marie Altmanová, Marie Doležálková-Kaštánková, Daniel Jablonski, Ilias Strachinis, Vladislav Vergilov et al.

<p>Karyotype divergence may strongly affect the degree of hybridization between species. Western Palearctic slow worms (Anguis) are legless liz- ards forming different types of secondary contact zones. To identify the level of chromosomal variation in slow worms, we examined karyotype in multiple populations of all species except one and Pseudopus apodus as an outgroup. We applied conventional and molecular cytogenetic methods and whole-chromosome painting using macrochromosome probes from Varanus komodoensis to interpret results within the evolu- tionary framework of the common clade Anguiformes. All Anguis species and P. apodus have conserved karyotype structures composed of 44 chromosomes. Despite the conserved chromosome morphology, the phylogenetically oldest Anguis cephallonica living in partial sympatry with Anguis graeca, and parapatric Anguis colchica vs. Anguis fragilis exhibit distinct patterns of constitutive heterochromatin distribution and telo- meric repeat accumulation. In contrast, the sister species A. colchica and A. graeca living in allopatry display highly similar karyotype features. Our findings thus indicate karyotype stasis in Anguis and Pseudopus for &gt; 20 Myr, with fixed species-specific differences present in sympatric and parapatric species. These differences in repetitive DNA patterns may play a role as intrinsic factors co-maintaining species divergence. They may also be used as cytotaxonomic markers to identify slow worm species in practice.</p>

Digital object identifier (DOI): 10.1093/zoolinnean/zlad153

Hematology, Transfusion and Cell Therapy, 45, S837–S838
2023

Implementation of a commercial model of artificial intelligence for karyotyping.

D. Borri, R. K. Kishimoto, M. F. M. D. Santos, R. O. Safranauskas, M. G. Cordeiro et al.

<p><strong>Aims</strong><br /> Chromosomal banding analysis is the standard technique to identify cytogenetic abnormalities in both constitutional chromosomal disorders and hematological malignancies. Karyotyping is a laborious and manual technique. The development of image (metaphases) capture systems and software for karyotyping had a great impact on the routine of cytogenetic laboratories, and recently artificial intelligence (deep neural networks, DNN) has helped in the correct segmentation and chromosome classification, allowing the performance of karyotypes more quickly, with final supervision by experienced cytogeneticists. Some systems using AI are commercially available and our objective was to validate and implement one of these models in our laboratory and measure its productivity.<br /> <strong>Materials and methods</strong><br /> IA DNN –PC/GTX 1650 version 1.1.40 was configured in the automated metaphase image scanning equipment (Metafer), which uses the software for image analysis (Ikaros), all developed by Metasystems (Altlussheim, Germany). Sixteen machine learning models (classifiers) were tested for bone marrow (oncohematological karyotype) and another 16 for peripheral blood (constitutional karyotype), eight of them with the function of chromosome segmentation in metaphase (separation) and 8 of them with the function of classify chromosomes (chromosomal pairing). 55 metaphases from routine studies of bone marrow for hematological malignancies [300-400 bands, 8 with numerical (−Y, −7) or structural (20q−) chromosomal alterations] and 65 metaphases from PHA-stimulated peripheral blood [550 bands, 7 cases with multiple overlapping chromosomes and 9 with numerical (−X, +13, +21) chromosomal alterations]. The time for manual and automated analysis (time for segmentation + classification + review) was compared. The chromosomal mispairing was noted. Productivity was evaluated (percentage difference in seconds manual-automated analysis/ manual analysis in seconds ×100).<br /> <strong>Results</strong><br /> The average time for manual analysis of one metaphase in bone marrow samples was 74 ± 30 seconds (segmentation 34 seconds and classification 40 seconds) and in DNN it was 23 ± 19 seconds (segmentation 13 seconds, classification 10 seconds), with a gain of 51 ± 26 seconds and productivity gain of 68.6%, and mismatch of 1 ± 1.5 chromosomes. The average time for manual analysis of one metaphase in peripheral blood samples was 138 ± 56 seconds (segmentation 85 seconds and classification 52 seconds) and in DNN it was 29 ± 16 seconds (segmentation 15 seconds, classification 14 seconds), with a gain of 108 ± 49 seconds and productivity gain of 78.7%, and pairing error of 2.6 ± 2.<br /> <strong>Discussion</strong><br /> AI allowed a significantly gain in productivity and TAT reduction in karyotype, the constitutional from 21 days to 15 days and the oncohematological karyotype from 14 days to 7 days (5 days for acute leukemias at diagnosis).</p>

Digital object identifier (DOI): 10.1016/j.htct.2023.09.1510

Biomedicines, 10
December, 2022

The Precise Breakpoint Mapping in Paracentric Inversion 10q22.2q23.3 by Comprehensive Cytogenomic Analysis, Multicolor Banding, and Single-Copy Chromosome Sequencing.

Karamysheva, Tatyana V., Gayner, Tatyana A., Elisaphenko, Eugeny A., Trifonov, Vladimir A., Zakirova, Elvira G., Orishchenko, Konstantin E., Prokhorovich, Mariya A., Lopatkina, Maria E., Skryabin, Nikolay A., Lebedev, Igor N., Rubtsov, Nikolay B.

<p>Detection and precise genomic mapping of balanced chromosomal abnormalities in patients with impaired fertility or a clinical phenotype represent a challenge for current cytogenomics owing to difficulties with precise breakpoint localization in the regions enriched for DNA repeats and high genomic variation in such regions. Here, we present a comprehensive cytogenomic approach to breakpoint mapping in a rare paracentric inversion on 10q (in a patient with oligoasthenoteratozoospermia and necrozoospermia) that does not affect other phenotype traits. Multicolor banding, chromosomal microarray analysis, chromosome microdissection with reverse painting, and single-copy sequencing of the rearranged chromosome were performed to determine the length and position of the inverted region as well as to rule out a genetic imbalance at the breakpoints. As a result, a paracentric 19.251 Mbp inversion at 10q22.2q23.3 was described. The most probable location of the breakpoints was predicted using the hg38 assembly. The problems of genetic counseling associated with enrichment for repeats and high DNA variability of usual breakpoint regions were discussed. Possible approaches for cytogenomic assessment of couples with balanced chromosome rearrangements and problems like reproductive failures were considered and suggested as useful part of effective genetic counseling.</p>

Digital object identifier (DOI): 10.3390/biomedicines10123255

Cancer Genetics, 260, 23-29
January, 2022

Classification of fluorescent R-Band metaphase chromosomes using a convolutional neural network is precise and fast in generating karyograms of hematologic neoplastic cells

Beate Vajen, Siegfried Hänselmann, Friederike Lutterloh, Simon Käfer, Jennifer Espenkötter, Anna Beening, Jochen Bogin, Brigitte Schlegelberger, Gudrun Göhring

<p>Karyotype analysis has a great impact on the diagnosis, treatment and prognosis in hematologic neo-plasms. The identification and characterization of chromosomes is a challenging process and needs experienced personal. Artificial intelligence provides novel support tools. However, their safe and reliable application in diagnostics needs to be evaluated. Here, we present a novel laboratory approach to identify chromosomes in cancer cells using a convolutional neural network (CNN). The CNN identified the correct chromosome class for 98.8% of chromosomes, which led to a time saving of 42% for the karyotyping workflow. These results demonstrate that the CNN has potential application value in chromosome classification of hematologic neoplasms. This study contributes to the development of an automatic karyotyping platform.</p>

Digital object identifier (DOI): https://doi.org/10.1016/j.cancergen.2021.11.005

Radiation research
September, 2021

CytoRADx: A High-Throughput, Standardized Biodosimetry Diagnostic System Based on the Cytokinesis-Block Micronucleus Assay.

Capaccio, Chris, Perrier, Jay R., Cunha, Lídia, Mahnke, Ryan C., Lörch, Thomas, Porter, Michael, Smith, Chris L., Damer, Ken, Bourland, J. Daniel, Frizzell, Bart, Torelli, Jennifer, Vasquez, Marie, Brower, Jeremy B., Doyle-Eisele, Melanie, Taveras, Maria, Turner, Helen, Brenner, David J., Kowalski, Richard

<p>In a large-scale catastrophe, such as a nuclear detonation in a major city, it will be crucial to accurately diagnose large numbers of people to direct scarce medical resources to those in greatest need. Currently no FDA-cleared tests are available to diagnose radiation exposures, which can lead to complex, life-threatening injuries. To address this gap, we have achieved substantial advancements in radiation biodosimetry through refinement and adaptation of the cytokinesis-block micronucleus (CBMN) assay as a high throughput, quantitative diagnostic test. The classical CBMN approach, which quantifies micronuclei (MN) resulting from DNA damage, suffers from considerable time and expert labor requirements, in addition to a lack of universal methodology across laboratories. We have developed the CytoRADx™ System to address these drawbacks by implementing a standardized reagent kit, optimized assay protocol, fully automated microscopy and image analysis, and integrated dose prediction. These enhancements allow the CytoRADx System to obtain high-throughput, standardized results without specialized labor or laboratory-specific calibration curves. The CytoRADx System has been optimized for use with both humans and non-human primates (NHP) to quantify radiation dose-dependent formation of micronuclei in lymphocytes, observed using whole blood samples. Cell nuclei and resulting MN are fluorescently stained and preserved on durable microscope slides using materials provided in the kit. Up to 1,000 slides per day are subsequently scanned using the commercially based RADxScan™ Imager with customized software, which automatically quantifies the cellular features and calculates the radiation dose. Using less than 1 mL of blood, irradiated ex vivo, our system has demonstrated accurate and precise measurement of exposures from 0 to 8 Gy (90% of results within 1 Gy of delivered dose). These results were obtained from 636 human samples (24 distinct donors) and 445 NHP samples (30 distinct subjects). The system demonstrated comparable results during in vivo studies, including an investigation of 43 NHPs receiving single-dose total-body irradiation. System performance is repeatable across laboratories, operators, and instruments. Results are also statistically similar across diverse populations, considering various demographics, common medications, medical conditions, and acute injuries associated with radiological disasters. Dose calculations are stable over time as well, providing reproducible results for at least 28 days postirradiation, and for blood specimens collected and stored at room temperature for at least 72 h. The CytoRADx System provides significant advancements in the field of biodosimetry that will enable accurate diagnoses across diverse populations in large-scale emergency scenarios. In addition, our technological enhancements to the well-established CBMN assay provide a pathway for future diagnostic applications, such as toxicology and oncology.</p>

Digital object identifier (DOI): 10.1667/RADE-20-00030.1

The British journal of dermatology
January, 2021

COVID-19 related dermatosis in November 2019. Could this case be Italy's patient zero?

Gianotti, R., Barberis, M., Fellegara, G., Galván-Casas, C., Gianotti, E.

<p>Milan, the largest city in northern Italy, was one of the first European metropolitan areas to be affected by the COVID-19 pandemic. We analyzed skin biopsies of patients from Milan with dermatoses and positive PCR swabs for SARS-CoV-2 at different stages of the infection (1,2). The results were compared to skin biopsies of 20 COVID-19 non-diagnosed patients with dermatoses, who were at high-risk of COVID-19 infection.</p>

Digital object identifier (DOI): 10.1111/bjd.19804

Frontiers in oncology, 11, 682647
2021

The Proton-Boron Reaction Increases the Radiobiological Effectiveness of Clinical Low- and High-Energy Proton Beams: Novel Experimental Evidence and Perspectives.

Bláha, Pavel, Feoli, Chiara, Agosteo, Stefano, Calvaruso, Marco, Cammarata, Francesco Paolo, Catalano, Roberto, Ciocca, Mario, Cirrone, Giuseppe Antonio Pablo, Conte, Valeria, Cuttone, Giacomo, Facoetti, Angelica, Forte, Giusi Irma, Giuffrida, Lorenzo, Magro, Giuseppe, Margarone, Daniele, Minafra, Luigi, Petringa, Giada, Pucci, Gaia, Ricciardi, Valerio, Rosa, Enrico, Russo, Giorgio, Manti, Lorenzo

<p>Protontherapy is a rapidly expanding radiotherapy modality where accelerated proton beams are used to precisely deliver the dose to the tumor target but is generally considered ineffective against radioresistant tumors. Proton-Boron Capture Therapy (PBCT) is a novel approach aimed at enhancing proton biological effectiveness. PBCT exploits a nuclear fusion reaction between low-energy protons and B atoms, i.e. p+ B→ 3α (p-B), which is supposed to produce highly-DNA damaging α-particles exclusively across the tumor-conformed Spread-Out Bragg Peak (SOBP), without harming healthy tissues in the beam entrance channel. To confirm previous work on PBCT, here we report new in-vitro data obtained at the 62-MeV ocular melanoma-dedicated proton beamline of the INFN-Laboratori Nazionali del Sud (LNS), Catania, Italy. For the first time, we also tested PBCT at the 250-MeV proton beamline used for deep-seated cancers at the Centro Nazionale di Adroterapia Oncologica (CNAO), Pavia, Italy. We used Sodium Mercaptododecaborate (BSH) as B carrier, DU145 prostate cancer cells to assess cell killing and non-cancer epithelial breast MCF-10A cells for quantifying chromosome aberrations (CAs) by FISH painting and DNA repair pathway protein expression by western blotting. Cells were exposed at various depths along the two clinical SOBPs. Compared to exposure in the absence of boron, proton irradiation in the presence of BSH significantly reduced DU145 clonogenic survival and increased both frequency and complexity of CAs in MCF-10A cells at the mid- and distal SOBP positions, but not at the beam entrance. BSH-mediated enhancement of DNA damage response was also found at mid-SOBP. These results corroborate PBCT as a strategy to render protontherapy amenable towards radiotherapy-resilient tumor. If coupled with emerging proton FLASH radiotherapy modalities, PBCT could thus widen the protontherapy therapeutic index.</p>

Digital object identifier (DOI): 10.3389/fonc.2021.682647