A druggable copper-signalling pathway that drives inflammation.

Inflammation is a complex physiological process triggered in response to harmful stimuli1. It involves cells of the immune system capable of clearing sources of injury and damaged tissues. Excessive inflammation can occur as a result of infection and is a hallmark of several diseases2-4. The molecular bases underlying inflammatory responses are not fully understood. Here we show that the cell surface glycoprotein CD44, which marks the acquisition of distinct cell phenotypes in the context of development, immunity and cancer progression, mediates the uptake of metals including copper. We identify a pool of chemically reactive copper(II) in mitochondria of inflammatory macrophages that catalyses NAD(H) redox cycling by activating hydrogen peroxide. Maintenance of NAD+ enables metabolic and epigenetic programming towards the inflammatory state. Targeting mitochondrial copper(II) with supformin (LCC-12), a rationally designed dimer of metformin, induces a reduction of the NAD(H) pool, leading to metabolic and epigenetic states that oppose macrophage activation. LCC-12 interferes with cell plasticity in other settings and reduces inflammation in mouse models of bacterial and viral infections. Our work highlights the central role of copper as a regulator of cell plasticity and unveils a therapeutic strategy based on metabolic reprogramming and the control of epigenetic cell states.

Histone H3 variants and their chaperones during development and disease: contributing to epigenetic control.

Within the nucleus, the interplay between lineage-specific transcription factors and chromatin dynamics defines cellular identity. Control of this interplay is necessary to properly balance stability and plasticity during the development and entire life span of multicellular organisms. Here, we present our current knowledge of the contribution of histone H3 variants to chromatin dynamics during development. We review the network of histone chaperones that governs their deposition timing and sites of incorporation and highlight how their distinct distribution impacts genome organization and function. We integrate the importance of H3 variants in the context of nuclear reprogramming and cell differentiation, and, using the centromere as a paradigm, we describe a case in which the identity of a given genomic locus is propagated across different cell types. Finally, we compare development to changes in stress and disease. Both physiological and pathological settings underline the importance of H3 dynamics for genome and chromatin integrity.

CHROMOMETHYLTRANSFERASE3/KRYPTONITE maintains the sulfurea paramutation in Solanum lycopersicum.

SignificanceParamutation involves the transfer of a repressive epigenetic mark between silent and active alleles. It is best known from exceptional non-Mendelian inheritance of conspicuous phenotypes in maize but also in other plants and animals. Recent genomic studies, however, indicate that paramutation may be less exceptional. It may be a consequence of wide-cross hybridization and may contribute to quantitative trait variation or unstable phenotypes in crops. Using the sulfurea (sulf) locus in tomato, we demonstrate that a self-reinforcing feedback loop involving DNA- and histone-methyl transferases CHROMOMETHYLTRANSFERASE3 (CMT3) and KRYPTONITE (KYP) is required for paramutation of sulf and that there is a change in chromatin organization. These findings advance the understanding of non-Mendelian inheritance in plants.

PSL Chemical Biology Symposia: Recent Progress in Ferroptosis.

This symposium is the 5th PSL (Paris Sciences & Lettres) Chemical Biology meeting (2015, 2016, 2019, 2023, 2024) held at Institut Curie. This initiative originally started at Institut de Chimie des Substances Naturelles (ICSN) in Gif-sur-Yvette, with a strong focus on chemistry. It was then continued at the Institut Curie (2015) covering a larger scope, before becoming the official PSL Chemical Biology meeting. This latest edition hosted around 150 participants and was focused on the burgeoning field of ferroptosis, its mechanism and implications in health and disease. While not initially planned, it was felt that the next large Ferroptosis venue (CSHA, China) would not happen before late 2024. A discussion involving Conrad, Birsoy, Ubellacker, Brabletz and Rodriguez next to lake Como in Italy sponsored by the DKFZ, prompted us to fill in this gap and to organize a Ferroptosis meeting in Paris beforehand.

A 19-color single-tube full spectrum flow cytometry assay for the detection of measurable residual disease in acute myeloid leukemia.

Multiparameter flow cytometry (MFC) has emerged as a standard method for quantifying measurable residual disease (MRD) in acute myeloid leukemia. However, the limited number of available channels on conventional flow cytometers requires the division of a diagnostic sample into several tubes, restricting the number of cells and the complexity of immunophenotypes that can be analyzed. Full spectrum flow cytometers overcome this limitation by enabling the simultaneous use of up to 40 fluorescent markers. Here, we used this approach to develop a good laboratory practice-conform single-tube 19-color MRD detection assay that complies with recommendations of the European LeukemiaNet Flow-MRD Working Party. We based our assay on clinically-validated antibody clones and evaluated its performance on an IVD-certified full spectrum flow cytometer. We measured MRD and normal bone marrow samples and compared the MRD data to a widely used reference MRD-MFC panel generating highly concordant results. Using our newly developed single-tube panel, we established reference values in healthy bone marrow for 28 consensus leukemia-associated immunophenotypes and introduced a semi-automated dimensionality-reduction, clustering and cell type identification approach that aids the unbiased detection of aberrant cells. In summary, we provide a comprehensive full spectrum MRD-MFC workflow with the potential for rapid implementation for routine diagnostics due to reduced cell requirements and ease of data analysis with increased reproducibility in comparison to conventional FlowMRD routines.

MRI Treatment Response Assessment Maps (TRAMs) for differentiating recurrent glioblastoma from radiation necrosis.

BACKGROUND: MRI treatment response assessment maps (TRAMs) were introduced to distinguish recurrent malignant glioma from therapy related changes. TRAMs are calculated with two contrast-enhanced T1-weighted sequences and reflect the "late" wash-out (or contrast clearance) and wash-in of gadolinium. Vital tumor cells are assumed to produce a wash-out because of their high turnover rate and the associated hypervascularization, whereas contrast medium slowly accumulates in scar tissue. To examine the real value of this method, we compared TRAMs with the pathology findings obtained after a second biopsy or surgery when recurrence was suspected. METHODS: We retrospectively evaluated TRAMs in adult patients with histologically demonstrated glioblastoma, contrast-enhancing tissue and a pre-operative MRI between January 1, 2017, and December 31, 2022. Only patients with a second biopsy or surgery were evaluated. Volumes of the residual tumor, contrast clearance and contrast accumulation before the second surgery were analyzed. RESULTS: Among 339 patients with mGBM who underwent MRI, we identified 29 repeated surgeries/biopsies in 27 patients 59 ± 12 (mean ± standard deviation) years of age. Twenty-eight biopsies were from patients with recurrent glioblastoma histology, and only one was from a patient with radiation necrosis. We volumetrically evaluated the 29 pre-surgery TRAMs. In recurrent glioblastoma, the ratio of wash-out volume to tumor volume was 36 ± 17% (range 1-73%), and the ratio of the wash-out volume to the sum of wash-out and wash-in volumes was 48 ± 21% (range 22-92%). For the one biopsy with radiation necrosis, the ratios were 42% and 54%, respectively. CONCLUSIONS: Typical recurrent glioblastoma shows a > 20%ratio of the wash-out volume to the sum of wash-out and wash-in volumes. The one biopsy with radiation necrosis indicated that such necrosis can also produce high wash-out in individual cases. Nevertheless, the additional information provided by TRAMs increases the reliability of diagnosis.

Differentiation of multiple brain metastases and glioblastoma with multiple foci using MRI criteria.

OBJECTIVE: Glioblastoma with multiple foci (mGBM) and multiple brain metastases share several common features on magnetic resonance imaging (MRI). A reliable preoperative diagnosis would be of clinical relevance. The aim of this study was to explore the differences and similarities between mGBM and multiple brain metastases on MRI. METHODS: We performed a retrospective analysis of 50 patients with mGBM and compared them with a cohort of 50 patients with multiple brain metastases (2-10 lesions) histologically confirmed and treated at our department between 2015 and 2020. The following imaging characteristics were analyzed: lesion location, distribution, morphology, (T2-/FLAIR-weighted) connections between the lesions, patterns of contrast agent uptake, apparent diffusion coefficient (ADC)-values within the lesion, the surrounding T2-hyperintensity, and edema distribution. RESULTS: A total of 210 brain metastases and 181 mGBM lesions were analyzed. An infratentorial localization was found significantly more often in patients with multiple brain metastases compared to mGBM patients (28 vs. 1.5%, p < 0.001). A T2-connection between the lesions was detected in 63% of mGBM lesions compared to 1% of brain metastases. Cortical edema was only present in mGBM. Perifocal edema with larger areas of diffusion restriction was detected in 31% of mGBM patients, but not in patients with metastases. CONCLUSION: We identified a set of imaging features which improve preoperative diagnosis. The presence of T2-weighted imaging hyperintensity connection between the lesions and cortical edema with varying ADC-values was typical for mGBM.

The CENP-T/-W complex is a binding partner of the histone chaperone FACT.

The CENP-T/-W histone fold complex, as an integral part of the inner kinetochore, is essential for building a proper kinetochore at the centromere in order to direct chromosome segregation during mitosis. Notably, CENP-T/-W is not inherited at centromeres, and new deposition is absolutely required at each cell cycle for kinetochore function. However, the mechanisms underlying this new deposition of CENP-T/-W at centromeres are unclear. Here, we found that CENP-T deposition at centromeres is uncoupled from DNA synthesis. We identified Spt16 and SSRP1, subunits of the H2A-H2B histone chaperone facilitates chromatin transcription (FACT), as CENP-W binding partners through a proteomic screen. We found that the C-terminal region of Spt16 binds specifically to the histone fold region of CENP-T/-W. Furthermore, depletion of Spt16 impairs CENP-T and CENP-W deposition at endogenous centromeres, and site-directed targeting of Spt16 alone is sufficient to ensure local de novo CENP-T accumulation. We propose a model in which the FACT chaperone stabilizes the soluble CENP-T/-W complex in the cell and promotes dynamics of exchange, enabling CENP-T/-W deposition at centromeres.

PSL Chemical Biology Symposia Third Edition: A Branch of Science in its Explosive Phase.

This symposium is the third PSL (Paris Sciences & Lettres) Chemical Biology meeting (2016, 2019, 2023) held at Institut Curie. This initiative originally started at Institut de Chimie des Substances Naturelles (ICSN) in Gif-sur-Yvette (2013, 2014), under the directorship of Professor Max Malacria, with a strong focus on chemistry. It was then continued at the Institut Curie (2015) covering a larger scope, before becoming the official PSL Chemical Biology meeting. This latest edition was postponed twice for the reasons that we know. This has given us the opportunity to invite additional speakers of great standing. This year, Institut Curie hosted around 300 participants, including 220 on site and over 80 online. The pandemic has had, at least, the virtue of promoting online meetings, which we came to realize is not perfect but has its own merits. In particular, it enables those with restricted time and resources to take part in events and meetings, which can now accommodate unlimited participants. We apologize to all those who could not attend in person this time due to space limitation at Institut Curie.

CovidGraph: a graph to fight COVID-19.

SUMMARY: Reliable and integrated data are prerequisites for effective research on the recent coronavirus disease 2019 (COVID-19) pandemic. The CovidGraph project integrates and connects heterogeneous COVID-19 data in a knowledge graph, referred to as 'CovidGraph'. It provides easy access to multiple data sources through a single point of entry and enables flexible data exploration. AVAILABILITY AND IMPLEMENTATION: More information on CovidGraph is available from the project website: https://healthecco.org/covidgraph/. Source code and documentation are provided on GitHub: https://github.com/covidgraph. SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.

Chromatin dynamics during the cell cycle at centromeres.

Centromeric chromatin undergoes major changes in composition and architecture during each cell cycle. These changes in specialized chromatin facilitate kinetochore formation in mitosis to ensure proper chromosome segregation. Thus, proper orchestration of centromeric chromatin dynamics during interphase, including replication in S phase, is crucial. We provide the current view concerning the centromeric architecture associated with satellite repeat sequences in mammals and its dynamics during the cell cycle. We summarize the contributions of deposited histone variants and their chaperones, other centromeric components - including proteins and their post-translational modifications, and RNAs - and we link the expression and deposition timing of each component during the cell cycle. Because neocentromeres occur at ectopic sites, we highlight how cell cycle processes can go wrong, leading to neocentromere formation and potentially disease.

Brainstem atrophy in dementia with Lewy bodies compared with progressive supranuclear palsy and Parkinson's disease on MRI.

BACKGROUND: Although Dementia with Lewy bodies (DLB) is the second most common form of dementia in elderly patients, it remains underdiagnosed compared with Alzheimer's (AD) and Parkinson's diseases (PD). This may be explained by overlapping clinical symptoms, e.g. Parkinsonism. While current MRI research focuses primarily on atrophy patterns of the frontal and temporal lobes, we focus on brainstem characteristics of DLB. In particular, we focused on brainstem atrophy patterns distinguishing DLB from Progressive Supranuclear Palsy (PSP) and PD based as the most common differential diagnoses. METHODS: We identified patients diagnosed with DLB, PD, PSP, and a control group (CTRL) in our psychiatric and neurological archives. All patients with competing diagnoses and without a high-quality T1 MPRAGE 3D dataset were excluded. We assessed atrophy patterns in all patients (1) manually and (2) using FastSurfer's segmentation algorithm in combination with FreeSurfer's brainstem volumetric calculations. We compared classical measurement methods and ratios with automated volumetric approaches. RESULTS: One hundred two patients were enrolled and evaluated in this study. Patients with DLB (n = 37) showed on average less atrophy of the brainstem than patients with PSP (n = 21), but a significantly more pronounced atrophy than patients with PD (n = 36) and the control group (CTRL, n = 8). The mean measured sagittal diameters of the midbrain were 8.17 ± 1.06 mm (mean ± standard deviation) for PSP, 9.45 ± 0.95 mm for DLB, 10.37 ± 0.99 mm for PD and 10.74 ± 0.70 for CTRL. The mean measured areas of the midbrain were 81 ± 18 mm2 for PSP, 105 ± 17 mm2 for DLB, 130 ± 26 mm2 for PD and 135 ± 23 mm2 for CTRL. The mean segmented volumes of the midbrain were 5595 ± 680 mm3 for PSP, 6051 ± 566 mm3 for DLB, 6646 ± 802 mm3 for PD and 6882 ± 844 mm3 for CTRL. The calculated midbrain pons ratios did not show superiority over the absolute measurements of the midbrain for distinguishing PSP from DLB. Because of the relatively uniform atrophy throughout the brainstem, the ratios were not suitable for distinguishing DLB from PD. CONCLUSIONS: DLB patients exhibit homogenous atrophy of the brainstem and can be distinguished from patients with PSP and PD by both manual measurement methods and automated volume segmentation using absolute values or ratios.

Ambulatory knee biomechanics and muscle activity 2 years after ACL surgery: InternalBraceTM-augmented ACL repair versus ACL reconstruction versus healthy controls.

BACKGROUND: Little is known about knee mechanics and muscle control after augmented ACL repair. Our aim was to compare knee biomechanics and leg muscle activity during walking between the legs of patients 2 years after InternalBraceTM-augmented anterior cruciate ligament repair (ACL-IB) and between patients after ACL-IB and ACL reconstruction (ACL-R), and controls. METHODS: Twenty-nine ACL-IB, 27 sex- and age-matched ACL-R (hamstring tendon autograft) and 29 matched controls completed an instrumented gait analysis. Knee joint angles, moments, power, and leg muscle activity were compared between the involved and uninvolved leg in ACL-IB (paired t-tests), and between the involved legs in ACL patients and the non-dominant leg in controls (analysis of variance and posthoc Bonferroni tests) using statistical parametric mapping (SPM, P < 0.05). Means and 95% confidence intervals (CI) of differences in discrete parameters (DP; i.e., maximum/minimum) were calculated. RESULTS: Significant differences were observed in ACL-IB only in minimum knee flexion angle (DP: 2.4°, CI [-4.4;-0.5]; involved > uninvolved) and maximum knee flexion moment during stance (-0.07Nm/kg, CI [-0.13;-0.00]; involved < uninvolved), and differences between ACL-IB and ACL-R only in maximum knee flexion during swing (DP: 3.6°, CI [0.5;7.0]; ACL-IB > ACL-R). Compared to controls, ACL-IB (SPM: 0-3%GC, P = 0.015; 98-100%, P = 0.016; DP: -6.3 mm, CI [-11.7;-0.8]) and ACL-R (DP: -6.0 mm, CI [-11.4;-0.2]) had lower (maximum) anterior tibia position around heel strike. ACL-R also had lower maximum knee extension moment (DP: -0.13Nm/kg, CI [-0.23;-0.02]) and internal knee rotation moment (SPM: 34-41%GC, P < 0.001; DP: -0.03Nm/kg, CI [-0.06;-0.00]) during stance, and greater maximum semitendinosus activity before heel strike (DP: 11.2%maximum voluntary contraction, CI [0.1;21.3]) than controls. CONCLUSION: Our results suggest comparable ambulatory knee function 2 years after ACL-IB and ACL-R, with ACL-IB showing only small differences between legs. However, the differences between both ACL groups and controls suggest that function in the involved leg is not fully recovered and that ACL tear is not only a mechanical disruption but also affects the sensorimotor integrity, which may not be restored after surgery. The trend toward fewer abnormalities in knee moments and semitendinosus muscle function during walking after ACL-IB warrants further investigation and may underscore the importance of preserving the hamstring muscles as ACL agonists. LEVEL OF EVIDENCE: Level III, case-control study. TRIAL REGISTRATION: clinicaltrials.gov, NCT04429165 (12/06/2020).

Arthrofibrosis is a common but poorly defined complication in multiligament knee injuries: a systematic review.

PURPOSE: The purpose of this study is to systematically review multiligament knee injury (MLKI) outcome studies to determine definitions of arthrofibrosis (AF) and provide information about incidence, management as well as potential risk factors. METHODS: A systematic literature search was performed (PubMed and Cochrane library) following the PRISMA guidelines of operatively treated MLKI (Schenck II-IV) studies reporting the incidence of AF. Twenty-five studies met the inclusion criteria. Injury pattern, timing of surgery, surgical technique, treatment of AF, rehabilitation programs and PROMS were inquired. Risk of bias and quality of evidence were assessed using the Coleman methodological score. RESULTS: Twenty-five studies with a total of 709 patients with a mean age of 33.6 ± 4.8 years were included and followed 47.2 ± 32.0 months. The majority of studies (22/25) used imprecise and subjective definitions of AF. A total of 86 patients were treated for AF, resulting in an overall prevalence of 12.1% (range 2.8-57.1). Higher-grade injuries (Schenck III-IV), acute treatment and ROM (range of motion) limiting rehabilitation programs were potential risk factors for AF. The time from index surgery to manipulation anesthesia (MUA) and arthroscopic lysis of adhesions (LOA) averaged at 14.3 ± 8.8 and 27.7 ± 12.8 weeks. Prior to MUA and LOA, the ROM was 51.7° ± 23.5 and 80.2° ± 17.0, resulting in a total ROM gain after intervention of 65.0° ± 19.7 and 48.0° ± 10.6, respectively; with no reports of any complication within the follow-up. The overall methodological quality of the studies was poor as measured by the Coleman score with average 56.3 ± 12.5 (range 31-84) points. CONCLUSIONS: AF is a common but poorly defined complication particularly in high-grade MLKI. Early postoperative and intensified physiotherapy is important to reduce the risk of AF. MUA and LOA are very effective treatment options and result in good clinical outcome. Prospective studies with bigger study population are needed to optimize treatment algorithms of further patients after MLKI. The protocol of this systematic review has been prospectively registered with PROSPERO (CRD42021229187, January 4th, 2021).

Functional leg performance 2 years after ACL surgery: a comparison between InternalBrace™-augmented repair versus reconstruction versus healthy controls.

BACKGROUND: While clinical and patient-reported outcomes have been investigated in patients after InternalBrace™-augmented anterior cruciate ligament repair (ACL-IB), less is known regarding restoration of functional performance. We aimed to determine differences in functional performance within and between patients 2 years after ACL-IB, patients 2 years after ACL reconstruction (ACL-R), and healthy controls. MATERIALS AND METHODS: A total of 29 ACL-IB, 27 ACL-R (hamstring autograft), and 29 controls performed single-leg hop (maximum forward distance hop, SLH; side hop > 40 cm in 30 s, SH), proprioception (knee joint position sense at 30° and 60° flexion), and dynamic postural balance (Y Balance) tests. Differences were calculated within groups (side-to-side difference) and between the involved leg of patients and the non-dominant leg of controls, and were evaluated to predefined statistical (P < 0.05), clinically relevant, and methodological (smallest detectable change) thresholds. The number of exceeded thresholds represented no (0), small (1), moderate (2), or strong (3) differences. In addition, the relative number of participants achieving leg symmetry (≥ 90%) and normal performance (≥ 90% of the average performance of the non-dominant leg of controls) were compared between groups (chi-squared tests, P < 0.05). RESULTS: We observed no-to-moderate leg differences within ACL-IB (moderate difference in hops) and within ACL-R (moderate difference in knee proprioception), no leg differences between patient groups, no-to-small leg differences between ACL-IB and controls, and no leg differences between ACL-R and controls in functional performance. However, two patients in ACL-IB and ACL-R, respectively, passed the hop pretest only with their uninvolved leg, and fewer patients after ACL-IB and ACL-R than controls reached a leg symmetry and normal leg performance of controls in SLH (P < 0.001). CONCLUSIONS: Functional performance seems to be comparable 2 years postoperatively between ACL-IB and ACL-R for a specific subgroup of patients (i.e., proximal ACL tears, moderate activity level). However, the presumed advantage of comparable functional outcome with preserved knee structures after augmented ACL repair compared with ACL-R, and the tendency of both patient groups toward leg asymmetry and compromised single-leg hop performance in the involved legs, warrants further investigation. Level of Evidence Level III, case-control study. Trial registration clinicaltrials.gov, NCT04429165 (12/09/2020). Prospectively registered, https://clinicaltrials.gov/ct2/show/NCT04429165 .

Biomarker Candidates for Tumors Identified from Deep-Profiled Plasma Stem Predominantly from the Low Abundant Area.

The plasma proteome has the potential to enable a holistic analysis of the health state of an individual. However, plasma biomarker discovery is difficult due to its high dynamic range and variability. Here, we present a novel automated analytical approach for deep plasma profiling and applied it to a 180-sample cohort of human plasma from lung, breast, colorectal, pancreatic, and prostate cancers. Using a controlled quantitative experiment, we demonstrate a 257% increase in protein identification and a 263% increase in significantly differentially abundant proteins over neat plasma. In the cohort, we identified 2732 proteins. Using machine learning, we discovered biomarker candidates such as STAT3 in colorectal cancer and developed models that classify the diseased state. For pancreatic cancer, a separation by stage was achieved. Importantly, biomarker candidates came predominantly from the low abundance region, demonstrating the necessity to deeply profile because they would have been missed by shallow profiling.

Iron-Sensitive Prodrugs That Trigger Active Ferroptosis in Drug-Tolerant Pancreatic Cancer Cells.

Persister cancer cells represent rare populations of cells resistant to therapy. Cancer cells can exploit epithelial-mesenchymal plasticity to adopt a drug-tolerant state that does not depend on genetic alterations. Small molecules that can interfere with cell plasticity or kill cells in a cell state-dependent manner are highly sought after. Salinomycin has been shown to kill cancer cells in the mesenchymal state by sequestering iron in lysosomes, taking advantage of the iron addiction of this cell state. Here, we report the chemo- and stereoselective synthesis of a series of structurally complex small molecule chimeras of salinomycin derivatives and the iron-reactive dihydroartemisinin. We show that these chimeras accumulate in lysosomes and can react with iron to release bioactive species, thereby inducing ferroptosis in drug-tolerant pancreatic cancer cells and biopsy-derived organoids of pancreatic ductal adenocarcinoma. This work paves the way toward the development of new cancer medicines acting through active ferroptosis.

The DNA methylation landscape of the root-knot nematode-induced pseudo-organ, the gall, in Arabidopsis, is dynamic, contrasting over time, and critically important for successful parasitism.

Root-knot nematodes (RKNs) induce giant cells (GCs) within galls which are characterized by large-scale gene repression at early stages. However, the epigenetic mechanism(s) underlying gene silencing is (are) still poorly characterized. DNA methylation in Arabidopsis galls induced by Meloidogyne javanica was studied at crucial infection stages (3 d post-infection (dpi) and 14 dpi) using enzymatic, cytological, and sequencing approaches. DNA methyltransferase mutants (met1, cmt2, cmt3, cmt2/3, drm1/2, ddc) and a DNA demethylase mutant (ros1), were analyzed for RKN resistance/tolerance, and galls were characterized by confocal microscopy and RNA-seq. Early galls were hypermethylated, and the GCs were found to be the major contributors to this hypermethylation, consistent with the very high degree of gene repression they exhibit. By contrast, medium/late galls showed no global increase in DNA methylation compared to uninfected roots, but exhibited large-scale redistribution of differentially methylated regions (DMRs). In line with these findings, it was also shown that DNA methylation and demethylation mutants showed impaired nematode reproduction and gall/GC-development. Moreover, siRNAs that were exclusively present in early galls accumulated at hypermethylated DMRs, overlapping mostly with retrotransposons in the CHG/CG contexts that might be involved in their repression, contributing to their stability/genome integrity. Promoter/gene methylation correlated with differentially expressed genes encoding proteins with basic cell functions. Both mechanisms are consistent with reprogramming host tissues for gall/GC formation. In conclusion, RNA-directed DNA methylation (RdDM; DRM2/1) pathways, maintenance methyltransferases (MET1/CMT3) and demethylation (ROS1) appear to be prominent mechanisms driving a dynamic regulation of the epigenetic landscape during RKN infection.

Manual and automated analysis of atrophy patterns in dementia with Lewy bodies on MRI.

BACKGROUND: Dementia with Lewy bodies (DLB) is the second most common dementia type in patients older than 65 years. Its atrophy patterns remain unknown. Its similarities to Parkinson's disease and differences from Alzheimer's disease are subjects of current research. METHODS: The aim of our study was (i) to form a group of patients with DLB (and a control group) and create a 3D MRI data set (ii) to volumetrically analyze the entire brain in these groups, (iii) to evaluate visual and manual metric measurements of the innominate substance for real-time diagnosis, and (iv) to compare our groups and results with the latest literature. We identified 102 patients with diagnosed DLB in our psychiatric and neurophysiological archives. After exclusion, 63 patients with valid 3D data sets remained. We compared them with a control group of 25 patients of equal age and sex distribution. We evaluated the atrophy patterns in both (1) manually and (2) via Fast Surfers segmentation and volumetric calculations. Subgroup analyses were done of the CSF data and quality of 3D T1 data sets. RESULTS: Concordant with the literature, we detected moderate, symmetric atrophy of the hippocampus, entorhinal cortex and amygdala, as well as asymmetric atrophy of the right parahippocampal gyrus in DLB. The caudate nucleus was unaffected in patients with DLB, while all the other measured territories were slightly too moderately atrophied. The area under the curve analysis of the left hippocampus volume ratio (< 3646mm3) revealed optimal 76% sensitivity and 100% specificity (followed by the right hippocampus and left amygdala). The substantia innominata's visual score attained a 51% optimal sensitivity and 84% specificity, and the measured distance 51% optimal sensitivity and 68% specificity in differentiating DLB from our control group. CONCLUSIONS: In contrast to other studies, we observed a caudate nucleus sparing atrophy of the whole brain in patients with DLB. As the caudate nucleus is known to be the last survivor in dopamine-uptake, this could be the result of an overstimulation or compensation mechanism deserving further investigation. Its relative hypertrophy compared to all other brain regions could enable an imaging based identification of patients with DLB via automated segmentation and combined volumetric analysis of the hippocampus and amygdala.

Prediction of midline shift after media ischemia using computed tomography perfusion.

BACKGROUND: Decision-making about the indication for decompressive hemicraniectomy in cases with malignant infarction in the territory of the middle cerebral artery (MCA) is still a matter of debate. Some scores have been introduced and tested, most of them are midline-shift dependent. We introduce the Kinematics of malignant MCA infarction (KM) index, which can be calculated based on an initial computed tomography perfusion scan and the chosen therapy (lysis/thrombectomy/conservative) in order to estimate the maximum midline-shift in the subsequent 6 days. METHODS: We retrospectively analyzed patients with middle cerebral artery infarction who had a non-enhanced computed tomography (CT) scan, CT angiography and a CT perfusion scan in the acute setting and who presented in our emergency room between 2015 and 2019. 186 patients were included. Midline shift was measured on follow-up imaging between days 0 and 6 after stroke. We evaluated Pearson's correlation between the KM index and the amount of midline shift. RESULTS: The mean KM index of all patients was 1.01 ± 0.09 (decompressive hemicraniectomy subgroup 1.13 ± 0.13; midline shift subgroup 1.18 ± 0.13). The correlation coefficient between the KM index and substantial midline-shift was 0.61, p < 0.01 and between KM index and decompressive hemicraniectomy or death 0.47; p < 0.05. KM index > 1.02 shows a sensitivity of 92% (22/24) and a specificity of 78% (126/162) for detecting midline shifts. The area under curve of the receiver operator characteristics was 91% for midline shifts and 86% for the occurrence of decompressive hemicraniectomy or death. CONCLUSION: In this retrospective study, KM index shows a strong correlation with significant midline-shift. The KM index can be used for risk classification regarding herniation and the need of decompressive hemicraniectomy.