Cell-type-specific consequences of mosaic structural variants in hematopoietic stem and progenitor cells.

The functional impact and cellular context of mosaic structural variants (mSVs) in normal tissues is understudied. Utilizing Strand-seq, we sequenced 1,133 single-cell genomes from 19 human donors of increasing age, and discovered the heterogeneous mSV landscapes of hematopoietic stem and progenitor cells. While mSVs are continuously acquired throughout life, expanded subclones in our cohort are confined to individuals >60. Cells already harboring mSVs are more likely to acquire additional somatic structural variants, including megabase-scale segmental aneuploidies. Capitalizing on comprehensive single-cell micrococcal nuclease digestion with sequencing reference data, we conducted high-resolution cell-typing for eight hematopoietic stem and progenitor cells. Clonally expanded mSVs disrupt normal cellular function by dysregulating diverse cellular pathways, and enriching for myeloid progenitors. Our findings underscore the contribution of mSVs to the cellular and molecular phenotypes associated with the aging hematopoietic system, and establish a foundation for deciphering the molecular links between mSVs, aging and disease susceptibility in normal tissues.

Treatment with the apoptosis inhibitor Asunercept reduces clone sizes in patients with lower risk Myelodysplastic Neoplasms.

In low-risk Myelodysplastic Neoplasms (MDS), increased activity of apoptosis-promoting factors such as tumor necrosis factor (TNFα) and pro-apoptotic Fas ligand (CD95L) have been described as possible pathomechanisms leading to impaired erythropoiesis. Asunercept (APG101) is a novel therapeutic fusion protein blocking CD95, which has previously shown partial efficacy in reducing transfusion requirement in a clinical phase I trial for low-risk MDS patients (NCT01736436; 2012-11-26). In the current study we aimed to evaluate the effect of Asunercept therapy on the clonal bone marrow composition to identify potential biomarkers to predict response. Bone marrow samples of n = 12 low-risk MDS patients from the above referenced clinical trial were analyzed by serial deep whole exome sequencing in a total of n = 58 time points. We could distinguish a mean of 3.5 molecularly defined subclones per patient (range 2-6). We observed a molecular response defined as reductions of dominant clone sizes by a variant allele frequency (VAF) decrease of at least 10% (mean 20%, range: 10.5-39.2%) in dependency of Asunercept treatment in 9 of 12 (75%) patients. Most of this decline in clonal populations was observed after completion of 12 weeks treatment. Particularly early and pronounced reductions of clone sizes were found in subclones driven by mutations in genes involved in regulation of methylation (n = 1 DNMT3A, n = 1 IDH2, n = 1 TET2). Our results suggest that APG101 could be efficacious in reducing clone sizes of mutated hematopoietic cells in the bone marrow of Myelodysplastic Neoplasms, which warrants further investigation.

Exhaled Breath Analysis Detects the Clearance of Staphylococcus aureus from the Airways of Children with Cystic Fibrosis.

BACKGROUND: Electronic nose (eNose) technology can be used to characterize volatile organic compound (VOC) mixes in breath. While previous reports have shown that eNose can detect lung infections with pathogens such as Staphylococcus aureus (SA) in people with cystic fibrosis (CF), the clinical utility of eNose for longitudinally monitoring SA infection status is unknown. METHODS: In this longitudinal study, a cloud-connected eNose, the SpiroNose, was used for the breath profile analysis of children with CF at two stable visits and compared based on changes in SA infection status between visits. Data analysis involved advanced sensor signal processing, ambient correction, and statistics based on the comparison of breath profiles between baseline and follow-up visits. RESULTS: Seventy-two children with CF, with a mean (IQR) age of 13.8 (9.8-16.4) years, were studied. In those with SA-positive airway cultures at baseline but SA-negative cultures at follow-up (n = 19), significant signal differences were detected between Baseline and Follow-up at three distinct eNose sensors, i.e., S4 (p = 0.047), S6 (p = 0.014), and S7 (p = 0.014). Sensor signal changes with the clearance of SA from airways were unrelated to antibiotic treatment. No changes in sensor signals were seen in patients with unchanged infection status between visits. CONCLUSIONS: Our results demonstrate the potential applicability of the eNose as a non-invasive clinical tool to longitudinally monitor pulmonary SA infection status in children with CF.

Pulsed-field ablation does not induce esophageal and periesophageal injury-A new esophageal safety paradigm in catheter ablation of atrial fibrillation.

INTRODUCTION: Esophageal injury is one of the most serious complications of pulmonary vein isolation (PVI) with thermic energy sources. Better tissue selectivity of primarily non-thermic pulsed field ablation (PFA) may eliminate collateral injury, particularly the risk of atrio-esophageal fistula (AEF). OBJECTIVE: To compare the incidence of any (peri)-esophageal injury following PVI using PFA to thermic energy sources. METHODS: Using endoscopy, endoscopic ultrasound, and electrogastrography before and after PVI, esophageal and periesophageal injury (mucosal lesions, food retention, periesophageal edema, or vagal nerve injury) were assessed following PFA and radiofrequency (RF)- or cryoballoon (CB)-PVI. RESULTS: Between December 2022 and February 2023, 20 patients (67 ± 10 years, 53% male) undergoing PFA (Farapulse, Boston Scientific) for atrial fibrillation (AF) were studied and compared with a previous cohort of 57 patients who underwent thermic PVI (CB: n = 33; RF: n = 24). Following PFA-PVI, none of the patients had mucosal lesions, food retention, or ablation-induced vagal nerve injury; four patients showed periesophageal edema. Following thermic ablation, 33/57 patients (58%) showed esophageal and/or periesophageal injury (CB: 21/33 [64%], RF: 12/24 [50%]), in detail 4/57 mucosal lesions, 18/57 food retention, 17/57 vagal nerve injury, and 20/52 edema. Midterm success rates were similar for all energy sources. CONCLUSION: In contrast to thermic ablation tools, PFA is not associated with relevant esophageal and periesophageal injury, and might, therefore, reduce or eliminate the risk of potentially lethal AEF in interventional treatment of AF. The etiology of ablation-induced periesophageal edema is unknown but has not been shown to be related to lesion progression.

ASXL1 mutations are associated with a response to alvocidib and 5-azacytidine combination in myelodysplastic neoplasms.

Inhibitors of anti-apoptotic BCL-2 family proteins in combination with chemotherapy and hypomethylating agents (HMAs) are promising therapeutic approaches in acute myeloid leukemia (AML) and high-risk myelodysplastic syndromes (MDS). Alvocidib, a cyclin-dependent kinase 9 (CDK9) inhibitor and indirect transcriptional repressor of the anti-apoptotic factor MCL-1, has previously shown clinical activity in AML. Availability of biomarkers for response to the alvocidib + 5- AZA could also extend the rationale of this treatment concept to high-risk MDS. In this study, we performed a comprehensive in vitro assessment of alvocidib and 5-AZA effects in n=45 high-risk MDS patients. Our data revealed additive cytotoxic effects of the combination treatment. Mutational profiling of MDS samples identified ASXL1 mutations as predictors of response. Further, increased response rates were associated with higher gene-expression of the pro-apoptotic factor NOXA in ASXL1 mutated samples. The higher sensitivity of ASXL1 mutant cells to the combination treatment was confirmed in vivo in ASXL1Y588X transgenic mice. Overall, our study demonstrated augmented activity for the alvocidib + 5-AZA combination in higher-risk MDS and identified ASXL1 mutations as a biomarker of response for potential stratification studies.

Significant improvement of bone marrow-derived MSC expansion from MDS patients by defined xeno-free medium.

BACKGROUND: Robust and reliable in vitro and in vivo models of primary cells are necessary to study the pathomechanisms of Myelodysplastic Neoplasms (MDS) and identify novel therapeutic strategies. MDS-derived hematopoietic stem and progenitor cells (HSPCs) are reliant on the support of bone marrow (BM) derived mesenchymal stroma cells (MSCs). Therefore, isolation and expansion of MCSs are essential for successfully modeling this disease. For the clinical use of healthy MSCs isolated from human BM, umbilical cord blood or adipose tissue, several studies showed that xeno-free (XF) culture conditions resulted in superior growth kinetics compared to MSCs cultured in the presence of fetal bovine serum (FBS). In this present study, we investigate, whether the replacement of a commercially available MSC expansion medium containing FBS with a XF medium is beneficial for the expansion of MSCs derived from BM of MDS patients which are often difficult to cultivate. METHODS: MSCs isolated from BM of MDS patients were cultured and expanded in MSC expansion medium with FBS or XF supplement. Subsequently, the impact of culture media on growth kinetics, morphology, immunophenotype, clonogenic potential, differentiation capacity, gene expression profiles and ability to engraft in immunodeficient mouse models was evaluated. RESULTS: Significant higher cell numbers with an increase in clonogenic potential were observed during culture of MDS MSCs with XF medium compared to medium containing FBS. Differential gene expression showed an increase in transcripts associated with MSC stemness after expansion with XF. Furthermore, immunophenotypes of the MSCs and their ability to differentiate into osteoblasts, adipocytes or chondroblasts remained stable. MSCs expanded with XF media were similarly supportive for creating MDS xenografts in vivo as MSCs expanded with FBS. CONCLUSION: Our data indicate that with XF media, higher cell numbers of MDS MSCs can be obtained with overall improved characteristics in in vitro and in vivo experimental models.

Inhibition of lysyl oxidases synergizes with 5-azacytidine to restore erythropoiesis in myelodysplastic and myeloid malignancies.

Limited response rates and frequent relapses during standard of care with hypomethylating agents in myelodysplastic neoplasms (MN) require urgent improvement of this treatment indication. Here, by combining 5-azacytidine (5-AZA) with the pan-lysyl oxidase inhibitor PXS-5505, we demonstrate superior restoration of erythroid differentiation in hematopoietic stem and progenitor cells (HSPCs) of MN patients in 20/31 cases (65%) versus 9/31 cases (29%) treated with 5-AZA alone. This effect requires direct contact of HSPCs with bone marrow stroma components and is dependent on integrin signaling. We further confirm these results in vivo using a bone marrow niche-dependent MN xenograft model in female NSG mice, in which we additionally demonstrate an enforced reduction of dominant clones as well as significant attenuation of disease expansion and normalization of spleen sizes. Overall, these results lay out a strong pre-clinical rationale for efficacy of combination treatment of 5-AZA with PXS-5505 especially for anemic MN.

Exhaled breath profiles to detect lung infection with Staphylococcus aureus in children with cystic fibrosis.

BACKGROUND: An electronic nose (eNose) can be used to detect volatile organic compounds (VOCs). Exhaled breath contains numerous VOCs and individuals' VOCs mixtures create distinct breath profiles. Previous reports have shown that eNose can detect lung infections. Whether eNose can detect Staphylococcus aureus airway infections in breath of children with cystic fibrosis (CF) is currently unclear. METHODS: In this cross-sectional observational study, a cloud-connected eNose was used for breath profile analysis of clinically stable paediatric CF patients with airway microbiology cultures positive or negative for CF pathogens. Data-analysis involved advanced signal processing, ambient correction and statistics based on linear discriminant and receiver operating characteristics (ROC) analyses. RESULTS: Breath profiles from 100 children with CF (median predicted FEV1 91%) were obtained and analysed. CF patients with positive airway cultures for any CF pathogen were distinguishable from no CF pathogens (no growth or usual respiratory flora) with accuracy of 79.0% (AUC-ROC 0.791; 95% CI: 0.669-0.913) and between patients positive for Staphylococcus aureus (SA) only and no CF pathogen with accuracy of 74.0% (AUC-ROC 0.797; 95% CI: 0.698-0.896). Similar differences were seen for Pseudomonas aeruginosa (PA) infection vs no CF pathogens (78.0% accuracy, AUC-ROC 0.876, 95% CI: 0.794-0.958). SA- and PA-specific signatures were driven by different sensors in the SpiroNose suggesting pathogen-specific breath signatures. CONCLUSIONS: Breath profiles of CF patients with SA in airway cultures are distinct from those with no infection or PA infection, suggesting the utility of eNose technology in the detection of this early CF pathogen in children with CF.

Pulmonary vein isolation-induced vagal nerve injury and gastric motility disorders detected by electrogastrography: The side effects of pulmonary vein isolation in atrial fibrillation (SEPIA) study.

INTRODUCTION: Safety of pulmonary vein isolation (PVI) has been established in clinical studies. However, despite prevention efforts the incidence of damage to (peri)-esophageal tissue has not decreased, and the pathophysiology is incompletely understood. Damage to vagal nerve branches may be involved in lesion progression to atrio-esophageal fistula. Using electrogastrography, we assessed the incidence of periesophageal vagal nerve injury (VNI) following atrial fibrillation ablation and its association with procedural parameters and endoscopic results. METHODS: Patients were studied using electrogastrography, endoscopy, and endoscopic ultrasound before and after cryoballoon (CB) or radiofrequency (RF) PVI. The incidence of ablation-induced neuropathic pattern (indicating VNI) in pre- and postprocedural electrogastrography was assessed and correlated with endoscopic results and ablation data. RESULTS: Between February 2021 und January 2022, 85 patients (67 ± 10 years, 53% male) were included, 33 were treated with CB and 52 with RF (38 with moderate power moderate duration [25-30 W] and 14 with high power short duration [50 W]). Ablation-induced VNI was detected in 27/85 patients independent of the energy form. Patients with VNI more frequently had postprocedural endoscopically detected pathology (8% mucosal esophageal lesions, 36% periesophageal edema, 33% food retention) but there was incomplete overlap. Pre-existing esophagitis increased the likelihood of VNI. Ablation data and esophageal temperature data did not predict VNI. CONCLUSION: PVI-induced VNI is quite common and independent of ablation energy source. VNI is part of (peri)-esophageal damage and only partially overlaps with endoscopic findings. VNI-associated acidic reflux may be involved in the complex pathophysiology of esophageal lesion progression to fistula.

The Continuous Matching Task (CMT) - real-time procedural stimulus generation for adaptive testing of attention.

The Continuous Matching Task (CMT) is a novel paradigm designed to measure sustained attention and alertness. It is a special type of Continuous Performance Task (CPT) that utilizes truly continuous stimulus material. Stimuli are generated in real-time by a procedural algorithm which also enables adaptive testing. The task is highly flexible and can be used in either single or dual-task configurations that also allow for task mixing. The functionality of the algorithm and applications are presented. The viability of the CMT is tested and results are compared with similar tasks, i.e. Stroop-Task and Conner's CPT (CCPT), as well as self-reports of ADHD in adults in a Multi-Trait-Multi-Method approach in a sample of N = 122 participants. Self-reports and measurements of heart rate variability during testing are analyzed to infer and compare mental workload during tasks. Overall, variants of the CMT induce a higher mental workload than the other tasks, and employing the dual-task CMT with adaptive difficulty resulted in the highest reliability and validity. Results indicate that the CMT is primarily a measure of alertness and processing speed and benefits from adaptive testing.

Functional analysis of structural variants in single cells using Strand-seq.

Somatic structural variants (SVs) are widespread in cancer, but their impact on disease evolution is understudied due to a lack of methods to directly characterize their functional consequences. We present a computational method, scNOVA, which uses Strand-seq to perform haplotype-aware integration of SV discovery and molecular phenotyping in single cells by using nucleosome occupancy to infer gene expression as a readout. Application to leukemias and cell lines identifies local effects of copy-balanced rearrangements on gene deregulation, and consequences of SVs on aberrant signaling pathways in subclones. We discovered distinct SV subclones with dysregulated Wnt signaling in a chronic lymphocytic leukemia patient. We further uncovered the consequences of subclonal chromothripsis in T cell acute lymphoblastic leukemia, which revealed c-Myb activation, enrichment of a primitive cell state and informed successful targeting of the subclone in cell culture, using a Notch inhibitor. By directly linking SVs to their functional effects, scNOVA enables systematic single-cell multiomic studies of structural variation in heterogeneous cell populations.

Artificial Nesting Hills Promote Wild Bees in Agricultural Landscapes.

The availability of nesting resources influences the persistence and survival of bee communities. Although a positive effect of artificial nesting structures has frequently been shown for aboveground cavity-nesting wild bees, studies on below ground-nesting bees are rare. Artificial nesting hills designed to provide nesting habitats for ground-nesting bees were therefore established within the BienABest project in 20 regions across Germany. Wild bee communities were monitored for two consecutive years, accompanied by recordings of landscape and abiotic nest site variables. Bee activity and species richness increased from the first to the second year after establishment; this was particularly pronounced in landscapes with a low cover of semi-natural habitat. The nesting hills were successively colonized, indicating that they should exist for many years, thereby promoting a species-rich bee community. We recommend the construction of nesting hills on sun-exposed sites with a high thermal gain of the substrate because the bees prefer south-facing sites with high soil temperatures. Although the soil composition of the nesting hills plays a minor role, we suggest using local soil to match the needs of the local bee community. We conclude that artificial nesting structures for ground-nesting bees act as a valuable nesting resource for various bee species, particularly in highly degraded landscapes. We offer a construction and maintenance guide for the successful establishment of nesting hills for bee conservation.

Design of a novel switchable antibody display system in Pichia pastoris.

Yeast surface display (YSD) has been shown to represent a powerful tool in the field of antibody discovery and engineering as well as for selection of high producer clones. However, YSD is predominantly applied in Saccharomyces cerevisiae, whereas expression of heterologous proteins is generally favored in the non-canonical yeast Pichia pastoris (Komagataella phaffii). Establishment of surface display in P. pastoris would therefore enable antibody selection and expression in a single host. Here we describe the generation of a Pichia surface display (PSD) system based on antibody expression from episomal plasmids. By screening a diverse set of expression vectors using Design of Experiments (DoE), the effect of different genetic elements on the surface expression of antibody fragments was analyzed. Among the tested genetic elements, we found that the combination of P. pastoris formaldehyde dehydrogenase (FLD1) promoter, S. cerevisiae invertase 2 signal peptide (SUC2), and α-agglutinin cell wall protein (SAG1) including an autonomously replicating sequence of Kluyveromyces lactis (panARS) were contributing most strongly to higher display levels of three tested antibody fragments. Employing this combination resulted in the display of antibody fragments for up to 25% of cells. Despite significantly reduced expression levels in PSD compared to well-established YSD in S. cerevisiae, similar fractions of antigen binding single-chain variable fragments (scFvs) were observed (80% vs. 84%). In addition, plasmid stability assays and flow cytometric analysis demonstrated the efficient plasmid clearance of cells and associated loss of antibody fragment display after removal of selective pressure. KEY POINTS: • First report of antibody display in P. pastoris using episomal plasmids. • Identification of genetic elements conferring highest levels of antibody display. • Comparable antigen binding capacity of displayed scFvs for PSD compared to YSD.

The validation of the English Impostor-Profile 30 and the exploratory formulation of the learned helplessness model of the impostor phenomenon.

The learned helplessness model of the Impostor Phenomenon is an exploratory approach to explain the Impostor Phenomenon by linking the constructs of growth mindset, learned helplessness, grit, thought-action fusion, and defensive pessimism. In this study, we (a) confirmatorily tested the factor structure of the English IPP30, (b) examined the instrument's nomological validity, and (c) exploratorily formulated a path model to explain the effects of learned helplessness on the Impostor Phenomenon. The sample consisted of n = 376 persons (46% female). The CFI indicated the bifactorial model of the English IPP30 as best-fitting, while the subscale correlations suggested the instrument's nomological validity. The exploratory path model showed sufficient goodness of fit. It proclaims a labeling as talented that decreases the growth mindset expression, which negatively correlates with learned helplessness. In addition, the model states learned helplessness as a central model component associated with grit, thought-action fusion, and finally, the Impostor Phenomenon.

Preclinical evaluation of eltrombopag in a PDX model of myelodysplastic syndromes.

Preclinical research of myelodysplastic syndromes (MDSs) is hampered by a lack of feasible disease models. Previously, we have established a robust patient-derived xenograft (PDX) model for MDS. Here we demonstrate for the first time that this model is applicable as a preclinical platform to address pending clinical questions by interrogating the efficacy and safety of the thrombopoietin receptor agonist eltrombopag. Our preclinical study included n = 49 xenografts generated from n = 9 MDS patient samples. Substance efficacy was evidenced by FACS-based human platelet quantification and clonal bone marrow evolution was reconstructed by serial whole-exome sequencing of the PDX samples. In contrast to clinical trials in humans, this experimental setup allowed vehicle- and replicate-controlled analyses on a patient-individual level deciphering substance-specific effects from natural disease progression. We found that eltrombopag effectively stimulated thrombopoiesis in MDS PDX without adversely affecting the patients' clonal composition. In conclusion, our MDS PDX model is a useful tool for testing new therapeutic concepts in MDS preceding clinical trials.

Humanized three-dimensional scaffold xenotransplantation models for myelodysplastic syndromes.

Patient-derived xenograft (PDX) models have emerged as versatile preclinical platforms for investigation of functional pathomechanisms in myelodysplastic syndromes (MDS) and other myeloid neoplasms. However, despite increasingly improved methodology, engraftment efficiencies frequently remain low. Humanized three-dimensional scaffold models (ossicle xenotransplantation models) in immunocompromised mice have recently been found to enable improved engraftment rates of healthy and malignant human hematopoiesis. We therefore interrogated the feasibility of using four different three-dimensional ossicle-based PDX models for application with primary MDS samples. In a fully standardized comparison, we evaluated scaffold materials such as Gelfoam, extracellular matrix (ECM), and human or xenogenous bone substance in comparison to intrafemoral (IF) co-injection of bone marrow (BM)-derived mesenchymal stromal cells (MSCs) and CD34+ hematopoietic stem and progenitor cells (HSPCs). Our study included13 primary MDS patient samples transplanted in parallel according to these five different conditions. Engraftment of MDS samples was assessed by flow cytometry, immunohistological staining, and molecular validation. We determined that three-dimensional ossicle-based methods achieved higher relative rates of engraftment and enabled long-term retrievability of patient-derived MSCs from implanted ossicles. In summary, HSPCs and MSCs derived from MDS BM, which did not significantly engraft in NSG mice after intrafemoral injection, were able to colonize humanized scaffold models. Therefore, these models are promising new xenotransplantation techniques for addressing preclinical and functional questions of the interaction between hematopoiesis and the BM niche in MDS.

Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states.

Single-cell genomics technology has transformed our understanding of complex cellular systems. However, excessive cost and a lack of strategies for the purification of newly identified cell types impede their functional characterization and large-scale profiling. Here, we have generated high-content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all main hematopoietic cell types in healthy aging and leukemia. These reference maps enable the automatic design of cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems and permit the purification of precisely defined cell states. The systematic integration of cytometry and proteo-genomic data enables the functional capacities of precisely mapped cell states to be measured at the single-cell level. Our study serves as an accessible resource and paves the way for a data-driven era in cytometry.

Bone marrow derived stromal cells from myelodysplastic syndromes are altered but not clonally mutated in vivo.

The bone marrow (BM) stroma in myeloid neoplasms is altered and it is hypothesized that this cell compartment may also harbor clonal somatically acquired mutations. By exome sequencing of in vitro expanded mesenchymal stromal cells (MSCs) from n = 98 patients with myelodysplastic syndrome (MDS) and n = 28 healthy controls we show that these cells accumulate recurrent mutations in genes such as ZFX (n = 8/98), RANK (n = 5/98), and others. MDS derived MSCs display higher mutational burdens, increased replicative stress, senescence, inflammatory gene expression, and distinct mutational signatures as compared to healthy MSCs. However, validation experiments in serial culture passages, chronological BM aspirations and backtracking of high confidence mutations by re-sequencing primary sorted MDS MSCs indicate that the discovered mutations are secondary to in vitro expansion but not present in primary BM. Thus, we here report that there is no evidence for clonal mutations in the BM stroma of MDS patients.