Assessing the Phenotype of a Homologous Recombination Deficiency Using High Resolution Array-Based Comparative Genome Hybridization in Ovarian Cancer

Ovarian cancer (OC) cells with homologous recombination deficiency (HRD) accumulate genomic scars (LST, TAI, and LOH) over a value of 42 in sum. PARP inhibitors can treat OC with HRD. The detection of HRD can be done directly by imaging these genomic scars, or indirectly by detecting mutations in the genes involved in HR. We show that HRD detection is also possible using high-resolution aCGH. A total of 30 OCs were analyzed retrospectively with high-resolution arrays as a test set and 19 OCs prospectively as a validation set. Mutation analysis was performed by HBOC TruRisk V2 panel to detect HR-relevant mutations. CNVs were clustered with respect to the involved HR genes versus the OC cases. In prospective validation, the HRD status determined by aCGH was compared with external HRD assessments. Two BRCA mutation carriers did not have HRD. OC could approximately differentiate into two groups with characteristic CNV patterns with different survival rates. Mutation frequencies have a linear regression on the HRD score. Mutations in individual HR-relevant genes do not always indicate HRD. This may depend on the mutation frequency in tumor cells. The aCGH shows the genomic scars of an HRD inexpensively and directly.

Coordination of Tetracyanoquinodimethane-Derivatives with Tris(pentafluorophenyl)borane Provides Stronger p-Dopants with Enhanced Stability

Strong molecular dopants for organic semiconductors that are stable against diffusion are in demand, enhancing the performance of organic optoelectronic devices. The conventionally used p-dopants based on 7,7,8,8-tetracyanoquinodimethane (TCNQ) and its derivatives "FxTCN(N)Q", such as 2,3,4,6-tetrafluoro-7,7,8,8-tetracyanoquinodimethane (F4TCNQ) and 1,3,4,5,7,8-hexafluorotetracyano-naphthoquinodimethane (F6TCNNQ), feature limited oxidation strength, especially for modern polymer semiconductors with high ionization energy (IE). These small molecular dopants also exhibit pronounced diffusion in the polymer hosts. Here, we demonstrate a facile approach to increase the oxidation strength of FxTCN(N)Q by coordination with four tris(pentafluorophenyl)borane (BCF) molecules using a single-step solution mixing process, resulting in bulky dopant complexes "FxTCN(N)Q-4(BCF)". Using a series of polymer semiconductors with IE up to 5.9 eV, we show by optical absorption spectroscopy of solutions and thin films that the efficiency of doping using FxTCN(N)Q-4(BCF) is significantly higher compared to that using FxTCN(N)Q or BCF alone. Electrical transport measurements with the prototypical poly(3-hexylthiophene-2,5-diyl) (P3HT) confirm the higher doping efficiency of F4TCNQ-4(BCF) compared to F4TCNQ. Additionally, the bulkier structure of F4TCNQ-4(BCF) is shown to result in higher stability against drift in P3HT under an applied electric field as compared to F4TCNQ. The simple approach of solution-mixing of readily accessible molecules thus offers access to enhanced molecular p-dopants for the community.

Influence of Backbone Ladderization and Side Chain Variation on the Orientation of Diketopyrrolopyrrole-Based Donor-Acceptor Copolymers

Ladder polymers with poly(diketopyrrolopyrrole) (DPP) moieties have recently attracted enormous interest for a large variety of opto-electronic applications. Since the rigidity of the backbone increases with ladderization, a strong influence on the self-organization of thin films is expected. We study the molecular orientation of DPP-based ladder polymers in about 50 nm thin films using polarization modulation-infrared reflection-absorption spectroscopy (PM-IRRAS). Exemplarily, for one polymer, the orientation in thicker films is qualitatively investigated by infrared spectroscopy in transmission. Further, this method allows us to rule out the effects of a possible azimuthal ordering, which would affect the analysis of the orientation by PM-IRRAS. For all polymers, the long axis of the polymer backbone is preferentially oriented parallel to the substrate surface, pointing to a high degree of ordering. It is suggested that the choice of the side chains might be a promising way to tune for face-on and edge-on orientations. The exemplarily performed investigation of interface properties on substrates with different work functions suggests that the choice of the side chains has a minor effect on the interfacial electronic interface structure.

GSK3α Regulates Temporally Dynamic Changes in Ribosomal Proteins upon Amino Acid Starvation in Cancer Cells

Amino acid availability is crucial for cancer cells' survivability. Leukemia and colorectal cancer cells have been shown to resist asparagine depletion by utilizing GSK3-dependent proteasomal degradation, termed the Wnt-dependent stabilization of proteins (Wnt/STOP), to replenish their amino acid pool. The inhibition of GSK3α halts the sourcing of amino acids, which subsequently leads to cancer cell vulnerability toward asparaginase therapy. However, resistance toward GSK3α-mediated protein breakdown can occur, whose underlying mechanism is poorly understood. Here, we set out to define the mechanisms driving dependence toward this degradation machinery upon asparagine starvation in cancer cells. We show the independence of known stress response pathways including the integrated stress response mediated with GCN2. Additionally, we demonstrate the independence of changes in cell cycle progression and expression levels of the asparagine-synthesizing enzyme ASNS. Instead, RNA sequencing revealed that GSK3α inhibition and asparagine starvation leads to the temporally dynamic downregulation of distinct ribosomal proteins, which have been shown to display anti-proliferative functions. Using a CRISPR/Cas9 viability screen, we demonstrate that the downregulation of these specific ribosomal proteins can rescue cell death upon GSK3α inhibition and asparagine starvation. Thus, our findings suggest the vital role of the previously unrecognized regulation of ribosomal proteins in bridging GSK3α activity and tolerance of asparagine starvation.

A critical spotlight on the paradigms of FFPE-DNA sequencing

In the late 19th century, formalin fixation with paraffin-embedding (FFPE) of tissues was developed as a fixation and conservation method and is still used to this day in routine clinical and pathological practice. The implementation of state-of-the-art nucleic acid sequencing technologies has sparked much interest for using historical FFPE samples stored in biobanks as they hold promise in extracting new information from these valuable samples. However, formalin fixation chemically modifies DNA, which potentially leads to incorrect sequences or misinterpretations in downstream processing and data analysis. Many publications have concentrated on one type of DNA damage, but few have addressed the complete spectrum of FFPE-DNA damage. Here, we review mitigation strategies in (I) pre-analytical sample quality control, (II) DNA repair treatments, (III) analytical sample preparation and (IV) bioinformatic analysis of FFPE-DNA. We then provide recommendations that are tested and illustrated with DNA from 13-year-old liver specimens, one FFPE preserved and one fresh frozen, applying target-enriched sequencing. Thus, we show how DNA damage can be compensated, even when using low quantities (50 ng) of fragmented FFPE-DNA (DNA integrity number 2.0) that cannot be amplified well (Q129 bp/Q41 bp = 5%). Finally, we provide a checklist called 'ERROR-FFPE-DNA' that summarises recommendations for the minimal information in publications required for assessing fitness-for-purpose and inter-study comparison when using FFPE samples.

Comparing in-person, blended and virtual training interventions; a real-world evaluation of HIV capacity building programs in 16 countries in sub-Saharan Africa

We sought to evaluate the impact of transitioning a multi-country HIV training program from in-person to online by comparing digital training approaches implemented during the pandemic with in-person approaches employed before COVID-19. We evaluated mean changes in pre-and post-course knowledge scores and self-reported confidence scores for learners who participated in (1) in-person workshops (between October 2019 and March 2020), (2) entirely asynchronous, Virtual Workshops [VW] (between May 2021 and January 2022), and (3) a blended Online Course [OC] (between May 2021 and January 2022) across 16 SSA countries. Learning objectives and evaluation tools were the same for all three groups. Across 16 SSA countries, 3023 participants enrolled in the in-person course, 2193 learners participated in the virtual workshop, and 527 in the online course. The proportions of women who participated in the VW and OC were greater than the proportion who participated in the in-person course (60.1% and 63.6%, p<0.001). Nursing and midwives constituted the largest learner group overall (1145 [37.9%] vs. 949 [43.3%] vs. 107 [20.5%]). Across all domains of HIV knowledge and self-perceived confidence, there was a mean increase between pre- and post-course assessments, regardless of how training was delivered. The greatest percent increase in knowledge scores was among those participating in the in-person course compared to VW or OC formats (13.6% increase vs. 6.0% and 7.6%, p<0.001). Gains in self-reported confidence were greater among learners who participated in the in-person course compared to VW or OC formats, regardless of training level (p<0.001) or professional cadre (p<0.001). In this multi-country capacity HIV training program, in-person, online synchronous, and blended synchronous/asynchronous strategies were effective means of training learners from diverse clinical settings. Online learning approaches facilitated participation from more women and more diverse cadres. However, gains in knowledge and clinical confidence were greater among those participating in in-person learning programs.

Combining Solid and Liquid Biopsy for Therapy Monitoring in Esophageal Cancer

Esophageal cancer (EC) has one of the highest mortality rates among cancers, making it imperative that therapies are optimized and dynamically adapted to individuals. In this regard, liquid biopsy is an increasingly important method for residual disease monitoring. However, conflicting detection rates (14% versus 60%) and varying cell-free circulating tumor DNA (ctDNA) levels (0.07% versus 0.5%) have been observed in previous studies. Here, we aim to resolve this discrepancy. For 19 EC patients, a complete set of cell-free DNA (cfDNA), formalin-fixed paraffin-embedded tumor tissue (TT) DNA and leukocyte DNA was sequenced (139 libraries). cfDNA was examined in biological duplicates and/or longitudinally, and TT DNA was examined in technical duplicates. In baseline cfDNA, mutations were detected in 12 out of 19 patients (63%); the median ctDNA level was 0.4%. Longitudinal ctDNA changes were consistent with clinical presentation. Considerable mutational diversity was observed in TT, with fewer mutations in cfDNA. The most recurrently mutated genes in TT were TP53, SMAD4, TSHZ3, and SETBP1, with SETBP1 being reported for the first time. ctDNA in blood can be used for therapy monitoring of EC patients. However, a combination of solid and liquid samples should be used to help guide individualized EC therapy.

Design and Optimization of Novel Benzimidazole- and Imidazo[4,5-b]pyridine-Based ATM Kinase Inhibitors with Subnanomolar Activities

The ATM kinase is a promising target in cancer treatment as an important regulator of the cellular response to DNA double-strand breaks. In this work, we present a new class of specific benzimidazole-based ATM inhibitors with picomolar potency against the isolated enzyme and favorable selectivity within relative PIKK and PI3K kinases. We could identify two promising inhibitor subgroups with significantly different physicochemical properties, which we developed simultaneously. These efforts lead to numerous highly active inhibitors with picomolar enzymatic activities. Furthermore, initial low cellular activities on A549 cells could be increased significantly in numerous examples resulting in cellular IC₅₀ values in the subnanomolar range. Further characterization of the highly potent inhibitors 90 und 93 revealed promising pharmacokinetic properties and strong activities in organoids in combination with etoposide. Additionally, 93 showed no off-target activities within a kinome-representative mini kinase panel, with favorable selectivities within the PIKK- and PI3K-families.

The Influence of the Side Chain Structure on the Photostability of Low Band Gap Polymers

Side chains play an important role in the photo-oxidation process of low band gap (LBG) polymers. For example, it has been shown that their photostability can be increased by the introduction of aromatic-oxy-alkyl links. We studied the photostability of prototypical LBG polymers with alkyl and oxyalkyl side chains during irradiation with white light (AM 1.5 conditions) in dry air using UV/vis and IR spectroscopy. Though its degradation kinetics were distinctly affected by the presence or absence of oxygen in the structure of the side chains, in particular cases, the stability was more affected by the presence of linear or branched side chains. Moreover, we showed that the exact position of the alkyl/oxyalkyl side chain at the polymer backbone could be crucial. Although minor effects of chemical modifications on the electronic parameters (ionization potential and gap) were observed, the molecular orientation, determined by polarization modulation-infrared reflection-absorption spectroscopy (PMIRRAS), could be affected. The aggregation and crystallinity of these polymers may distinctly affect their stability.

Thin Polymer Films by Oxidative or Reductive Electropolymerization and Their Application in Electrochromic Windows and Thin-Film Sensors

Electrically conducting and semiconducting polymers represent a special and still very attractive class of functional chromophores, especially due to their unique optical and electronic properties and their broad device application potential. They are potentially suitable as materials for several applications of high future relevance, for example flexible photovoltaic modules, components of displays/screens and batteries, electrochromic windows, or photocatalysts. Therefore, their synthesis and structure elucidation are still intensely investigated. This article will demonstrate the very fruitful interplay of current electropolymerization research and its exploitation for science education issues. Experiments involving the synthesis of conducting polymers and their assembly into functional devices can be used to teach basic chemical and physical principles as well as to motivate students for an innovative and interdisciplinary field of chemistry.

Chemotherapy-related hyperbilirubinemia in pediatric acute lymphoblastic leukemia: a genome-wide association study from the AIEOP-BFM ALL study group

BACKGROUND

Characterization of clinical phenotypes in context with tumor and host genomic information can aid in the development of more effective and less toxic risk-adapted and targeted treatment strategies. To analyze the impact of therapy-related hyperbilirubinemia on treatment outcome and to identify contributing genetic risk factors of this well-recognized adverse effect we evaluated serum bilirubin levels in 1547 pediatric patients with acute lymphoblastic leukemia (ALL) and conducted a genome-wide association study (GWAS).

PATIENTS AND METHODS

Patients were treated in multicenter trial AIEOP-BFM ALL 2000 for pediatric ALL. Bilirubin toxicity was graded 0 to 4 according to the Common Toxicity Criteria (CTC) of the National Cancer Institute. In the GWAS discovery cohort, including 650 of the 1547 individuals, genotype frequencies of 745,895 single nucleotide variants were compared between 435 patients with hyperbilirubinemia (CTC grades 1-4) during induction/consolidation treatment and 215 patients without it (grade 0). Replication analyses included 224 patients from the same trial.

RESULTS

Compared to patients with no (grade 0) or moderate hyperbilirubinemia (grades 1-2) during induction/consolidation, patients with grades 3-4 had a poorer 5-year event free survival (76.6 ± 3% versus 87.7 ± 1% for grades 1-2, P = 0.003; 85.2 ± 2% for grade 0, P < 0.001) and a higher cumulative incidence of relapse (15.6 ± 3% versus 9.0 ± 1% for grades 1-2, P = 0.08; 11.1 ± 1% for grade 0, P = 0.007). GWAS identified a strong association of the rs6744284 variant T allele in the UGT1A gene cluster with risk of hyperbilirubinemia (allelic odds ratio (OR) = 2.1, P = 7 × 10^- 8). TT-homozygotes had a 6.5-fold increased risk of hyperbilirubinemia (grades 1-4; 95% confidence interval (CI) = 2.9-14.6, P = 7 × 10^- 6) and a 16.4-fold higher risk of grade 3-4 hyperbilirubinemia (95% CI 6.1-43.8, P = 2 × 10^- 8). Replication analyses confirmed these associations with joint analysis yielding genome-wide significance (allelic OR = 2.1, P = 6 × 10^- 11; 95% CI 1.7-2.7). Moreover, rs6744284 genotypes were strongly linked to the Gilbert's syndrome-associated UGT1A1*28/*37 allele (r² = 0.70), providing functional support for study findings. Of clinical importance, the rs6744284 TT genotype counterbalanced the adverse prognostic impact of high hyperbilirubinemia on therapy outcome.

CONCLUSIONS

Chemotherapy-related hyperbilirubinemia is a prognostic factor for treatment outcome in pediatric ALL and genetic variation in UGT1A aids in predicting the clinical impact of hyperbilirubinemia.

TRIAL REGISTRATION

http://www.

CLINICALTRIALS

gov ; #NCT00430118.

High-throughput method for the hybridisation-based targeted enrichment of long genomic fragments for PacBio third-generation sequencing

Hybridisation-based targeted enrichment is a widely used and well-established technique in high-throughput second-generation short-read sequencing. Despite the high potential to genetically resolve highly repetitive and variable genomic sequences by, for example PacBio third-generation sequencing, targeted enrichment for long fragments has not yet established the same high-throughput due to currently existing complex workflows and technological dependencies. We here describe a scalable targeted enrichment protocol for fragment sizes of >7 kb. For demonstration purposes we developed a custom blood group panel of challenging loci. Test results achieved > 65% on-target rate, good coverage (142.7×) and sufficient coverage evenness for both non-paralogous and paralogous targets, and sufficient non-duplicate read counts (83.5%) per sample for a highly multiplexed enrichment pool of 16 samples. We genotyped the blood groups of nine patients employing highly accurate phased assemblies at an allelic resolution that match reference blood group allele calls determined by SNP array and NGS genotyping. Seven Genome-in-a-Bottle reference samples achieved high recall (96%) and precision (99%) rates. Mendelian error rates were 0.04% and 0.13% for the included Ashkenazim and Han Chinese trios, respectively. In summary, we provide a protocol and first example for accurate targeted long-read sequencing that can be used in a high-throughput fashion.

Aesthetic Preference for Negatively-Valenced Artworks Remains Stable in Pathological Aging: A Comparison Between Cognitively Impaired Patients With Alzheimer's Disease and Healthy Controls

Background

Despite severe cognitive dysfunction in Alzheimer's disease (AD), aesthetic preferences in AD patients seem to retain some stability over time, similarly to healthy controls. However, the underlying mechanisms of aesthetic preference stability in AD remain unclear. We therefore aimed to study the role of emotional valence of stimuli for stability of aesthetic preferences in patients with AD compared to cognitively unimpaired elderly adults.

Methods

Fifteen AD patients (Mini-Mental State Examination (MMSE) score 12–26) without visual impairment and/or psychiatric disorder, as well as 15 healthy controls without cognitive impairment (MMSE ≥ 27) matched in age, sex, art interest and highest level of education were included in this study. All participants were asked to rank-order eight artworks per stimulus category (positive, negative, neutral in emotional valence) according to their preference twice with a 2-week span in-between. Based on these two rankings a preference change score was calculated. In order to assess explicit recognition memory of the artworks in the second testing session, four artworks of each stimulus category used in the preference ranking task were presented together with a content-matched distractor artwork painted by the same artist. Participants had to indicate which of the stimuli they had seen 2 weeks previously.

Results

AD patients [MMSE (M) = 18.9 ± 3.6; Age (M) = 85.4 ± 6.9; 33.3% male] had no explicit recognition memory of the artworks (recognition at chance level), whereas healthy controls [MMSE (M) = 27.7 ± 1.4; Age (M) = 84.3 ± 6.7; 33.3% male] correctly recognized 85% of stimuli after 2 weeks. AD patients had equally stable preferences compared to the control group for negative artworks, but less stable preferences for positive and neutral images (Bonferroni-corrected significance levels; p < 0.017).

Conclusion

Even in cognitively impaired AD patients, aesthetic preference for negatively-valenced artworks remains relatively stable. Our study provides novel evidence that AD patients may have a somewhat preserved implicit valence system for negative compared to neutral or positive visual information, especially in the domain of aesthetics. However, more studies need to further uncover the details of the underlying neurocognitive mechanisms of preference stability in pathological aging.

Decisive role of water and protein dynamics in residence time of p38α MAP kinase inhibitors

Target residence time plays a crucial role in the pharmacological activity of small molecule inhibitors. Little is known, however, about the underlying causes of inhibitor residence time at the molecular level, which complicates drug optimization processes. Here, we employ all-atom molecular dynamics simulations (~400 μs in total) to gain insight into the binding modes of two structurally similar p38α MAPK inhibitors (type I and type I½) with short and long residence times that otherwise show nearly identical inhibitory activities in the low nanomolar IC₅₀ range. Our results highlight the importance of protein conformational stability and solvent exposure, buried surface area of the ligand and binding site resolvation energy for residence time. These findings are further confirmed by simulations with a structurally diverse short residence time inhibitor SB203580. In summary, our data provide guidance in compound design when aiming for inhibitors with improved target residence time.

The molecular determinants of the residence time of a small molecule inhibitor at its target protein are not well understood. Here, Pantsar et al. show that the target protein’s conformational stability and solvent exposure are key factors governing the target residence time of kinase inhibitors.

High-Throughput Screening Platform in Postnatal Heart Cells and Chemical Probe Toolbox to Assess Cardiomyocyte Proliferation

Restoring lost heart muscle is an attractive goal for cardiovascular regenerative medicine. One appealing strategy is the therapeutic stimulation of cardiomyocyte proliferation, which inter alia remains challenging due to available assay technologies capturing the complex biology. Here, a high-throughput-formatted phenotypic assay platform was established using rodent whole heart-derived cells to preserve the cellular environment of cardiomyocytes. Several readouts allowed the quantification of cycling cardiomyocytes, including a transgenic H2B-mCherry system for unequivocal, automated detection of cardiomyocyte nuclei. A chemical genetics approach revealed pronounced species differences and furnished pan-kinase inhibitors 5 and 36 as potent and robust inducers of endoreplication and acytokinetic mitosis. Combined profiling of the commonly used p38 MAPK inhibitors SB203580 (1), SB239063 (2) and a novel set of skepinone-L (6) derivatives pointed to off-target effects beyond p38 that might be critical for effective cardiomyocyte cytokinesis. Kinome-focused screening eventually furnished TG003 (38) as a novel candidate for stimulating cardiomyocyte proliferation.

Deficiency in X-linked inhibitor of apoptosis protein promotes susceptibility to microbial triggers of intestinal inflammation

Inflammatory bowel disease (IBD) is characterized by inappropriate immune responses to the microbiota in genetically susceptible hosts, but little is known about the pathways that link individual genetic alterations to microbiota-dependent inflammation. Here, we demonstrated that the loss of X-linked inhibitor of apoptosis protein (XIAP), a gene associated with Mendelian IBD, rendered Paneth cells sensitive to microbiota-, tumor necrosis factor (TNF)–, receptor-interacting protein kinase 1 (RIPK1)–, and RIPK3-dependent cell death. This was associated with deficiency in Paneth cell–derived antimicrobial peptides and alterations in the stratification and composition of the microbiota. Loss of XIAP was not sufficient to elicit intestinal inflammation but provided susceptibility to pathobionts able to promote granulomatous ileitis, which could be prevented by administration of a Paneth cell–derived antimicrobial peptide. These data reveal a pathway critical for host-microbial cross-talk, which is required for intestinal homeostasis and the prevention of inflammation and which is amenable to therapeutic targeting.

Deficiency in X-linked inhibitor of apoptosis protein promotes susceptibility to microbial triggers of intestinal inflammation

Inflammatory bowel disease (IBD) is characterized by inappropriate immune responses to the microbiota in genetically susceptible hosts, but little is known about the pathways that link individual genetic alterations to microbiota-dependent inflammation. Here, we demonstrated that the loss of X-linked inhibitor of apoptosis protein (XIAP), a gene associated with Mendelian IBD, rendered Paneth cells sensitive to microbiota-, tumor necrosis factor (TNF)–, receptor-interacting protein kinase 1 (RIPK1)–, and RIPK3-dependent cell death. This was associated with deficiency in Paneth cell–derived antimicrobial peptides and alterations in the stratification and composition of the microbiota. Loss of XIAP was not sufficient to elicit intestinal inflammation but provided susceptibility to pathobionts able to promote granulomatous ileitis, which could be prevented by administration of a Paneth cell–derived antimicrobial peptide. These data reveal a pathway critical for host-microbial cross-talk, which is required for intestinal homeostasis and the prevention of inflammation and which is amenable to therapeutic targeting.

Genetic Variation in ABCC4 and CFTR and Acute Pancreatitis during Treatment of Pediatric Acute Lymphoblastic Leukemia

Background: Acute pancreatitis (AP) is a serious, mechanistically not entirely resolved side effect of L-asparaginase-containing treatment for acute lymphoblastic leukemia (ALL). To find new candidate variations for AP, we conducted a genome-wide association study (GWAS). Methods: In all, 1,004,623 single-nucleotide variants (SNVs) were analyzed in 51 pediatric ALL patients with AP (cases) and 1388 patients without AP (controls). Replication used independent patients. Results: The top-ranked SNV (rs4148513) was located within the ABCC4 gene (odds ratio (OR) 84.1; p = 1.04 × 10⁻¹⁴). Independent replication of our 20 top SNVs was not supportive of initial results, partly because rare variants were neither present in cases nor present in controls. However, results of combined analysis (GWAS and replication cohorts) remained significant (e.g., rs4148513; OR = 47.2; p = 7.31 × 10⁻⁹). Subsequently, we sequenced the entire ABCC4 gene and its close relative, the cystic fibrosis associated CFTR gene, a strong AP candidate gene, in 48 cases and 47 controls. Six AP-associated variants in ABCC4 and one variant in CFTR were detected. Replication confirmed the six ABCC4 variants but not the CFTR variant. Conclusions: Genetic variation within the ABCC4 gene was associated with AP during the treatment of ALL. No association of AP with CFTR was observed. Larger international studies are necessary to more conclusively assess the risk of rare clinical phenotypes.

Liquid Biopsy in Gastric Cancer: Analysis of Somatic Cancer Tissue Mutations in Plasma Cell-Free DNA for Predicting Disease State and Patient Survival

INTRODUCTION

Gastric cancer (GC) diagnosis in late stages and high mortality rates are the main issues that require new noninvasive molecular tools. We aimed to assess somatic mutational profiles in GC tissue and plasma cell-free DNA (cfDNA), evaluate their concordance rate, and analyze the role of multilayer molecular profiling to predict disease state and prognosis.

METHODS

Treatment-naive GC patient group (n = 29) was selected. Whole exome sequencing (WES) of GC tissue was performed, and a unique 38-gene panel for deep targeted sequencing of plasma cfDNA was developed. Oncoproteins were measured by enzyme-linked immunosorbent assay, and other variables such as tumor mutational burden and microsatellite instability were evaluated using WES data.

RESULTS

The yield of cfDNA was increased 43.6-fold; the integrity of fragments was decreased in GC compared with controls. WES analysis of cancerous tissue and plasma cfDNA (targeted sequencing) mutational profiles revealed 47.8% concordance. The increased quantity of GC tissue-derived alterations detected in cfDNA was associated with worse patients' survival. Analysis of importance of multilayer variables and receiver operating characteristic curve showed that combination of 2 analytes: (i) quantity of tissue matching alterations and (ii) presence of any somatic alteration in plasma cfDNA resulted in area under curve 0.744 when discriminating patients with or without distant metastasis. Furthermore, cfDNA sequence alterations derived from tumor tissue were detected in patients who had even relatively small GC tumors (T1-T2).

DISCUSSION

Our results indicate that quantitative and qualitative cfDNA mutational profile analysis is a promising tool for evaluating GC disease status or poorer prognosis.

P14.11 Severe treatment-induced myelosuppression is more frequent in female malignant glioma patients and associated with reduced overall survival

BACKGROUND

An association of treatment-related myelotoxicity with female gender has been previously suggested. However, a systematic analysis of the prognostic relevance of radiochemotherapy-related cytopenia involving the different blood cell lineages is lacking.

MATERIAL AND METHODS

We retrospectively analyzed cytopenia during temozolomide-based concomitant radiochemotherapy (RCT) in 493 glioma patients. Histological grading, molecular pathology, surgical procedures and median overall survival (OS) were recorded. The extent of cytopenia was correlated with gender and outcome.

RESULTS

Treatment-induced severe cytopenia (leuko-, lympho-, neutro- and thrombocytopenia) occurred much more often in female than in male glioma patients (40.8 vs. 13.9%, p-value &lt;0.0001). In female patients with IDH-wildtype high-grade astrocytomas there was a negative correlation of severe leuko-, lympho- and thrombocytopenia during temozolomide RCT with OS (36 vs. 54, 37 vs. 54 and 36 vs. 57 weeks, respectively; all p-values &lt;0.05). In male patients there was also a trend for this unfavorable effect. Additionally, severe cytopenia correlated with reduced temozolomide dose exposure during RCT (all p-values &lt;0.05 in total cohort) and reduced dose exposure was independently associated with worse OS (p-values &lt;0.05 in the total and female cohort).

CONCLUSION

Our data confirm that women are at higher risk for treatment-induced cytopenia during RCT which is associated with a significant decrease in OS. From our data, it appears plausible that reduced temozolomide dose exposure during RCT is at least in part responsible for this finding. Immunosuppression of patients with severe cytopenia may be an independent contributor to adverse outcome.

Cationic Diazapentacenium Polymers Made in a Sequence of CN Cross Coupling Polymerization and Acid-Mediated Postpolymerization Cyclization

Polycationic stepladder polymers containing 5,12-diazapentacenium bistriflate repeat units are made in a two-step sequence of a carbon-nitrogen cross coupling polymerization and subsequent postpolymerization cyclization. The deeply colored products show a rather weak conjugative interaction between the dicationic diazapentacenium repeat units along the polymer chains.

Genome-wide analysis of 944 133 individuals provides insights into the etiology of haemorrhoidal disease

OBJECTIVE

Haemorrhoidal disease (HEM) affects a large and silently suffering fraction of the population but its aetiology, including suspected genetic predisposition, is poorly understood. We report the first genome-wide association study (GWAS) meta-analysis to identify genetic risk factors for HEM to date.

DESIGN

We conducted a GWAS meta-analysis of 218 920 patients with HEM and 725 213 controls of European ancestry. Using GWAS summary statistics, we performed multiple genetic correlation analyses between HEM and other traits as well as calculated HEM polygenic risk scores (PRS) and evaluated their translational potential in independent datasets. Using functional annotation of GWAS results, we identified HEM candidate genes, which differential expression and coexpression in HEM tissues were evaluated employing RNA-seq analyses. The localisation of expressed proteins at selected loci was investigated by immunohistochemistry.

RESULTS

We demonstrate modest heritability and genetic correlation of HEM with several other diseases from the GI, neuroaffective and cardiovascular domains. HEM PRS validated in 180 435 individuals from independent datasets allowed the identification of those at risk and correlated with younger age of onset and recurrent surgery. We identified 102 independent HEM risk loci harbouring genes whose expression is enriched in blood vessels and GI tissues, and in pathways associated with smooth muscles, epithelial and endothelial development and morphogenesis. Network transcriptomic analyses highlighted HEM gene coexpression modules that are relevant to the development and integrity of the musculoskeletal and epidermal systems, and the organisation of the extracellular matrix.

CONCLUSION

HEM has a genetic component that predisposes to smooth muscle, epithelial and connective tissue dysfunction.

Early loss of cerebellar Purkinje cells in human and a transgenic mouse model of Alzheimer's disease

BACKGROUND

The cerebellum's involvement in AD has been under-appreciated by historically labeling as a normal control in AD research.

METHODS

We determined the involvement of the cerebellum in AD progression. Postmortem human and APPswe/PSEN1dE9 mice cerebellums were used to assess the cerebellar Purkinje cells (PC) by immunohistochemistry. The locomotor and spatial cognitive functions were assessed in 4- to 5-month-old APPswe/PSEN1dE9 mice. Aβ plaque and APP processing were determined in APPswe/PSEN1dE9 mice at different age groups by immunohistochemistry and Western blot.

RESULTS

We observed loss of cerebellar PC in mild cognitive impairment and AD patients compared with cognitively normal controls. A strong trend towards PC loss was found in AD mice as early as 5 months. Impairment of balance beam and rotorod performance, but no spatial learning and memory dysfunction was observed in AD mice at 4-5 months. Aβ plaque in the cerebral cortex was evidenced in AD mice at 2 months and dramatically increased at 6 months. Less and smaller Aβ plaques were observed in the cerebellum than in the cerebrum of AD mice. Similar intracellular APP staining was observed in the cerebellum and cerebrum of AD mice at 2 to 10 months. Similar expression of full-length APP and C-terminal fragments were indicated in the cerebrum and cerebellum of AD mice during aging.

DISCUSSION

Our study in post-mortem human brains and transgenic AD mice provided neuropathological and functional evidence that cerebellar dysfunction may occur at the early stage of AD and likely independent of Aβ plaque.

Discovery of a Novel Class of Covalent Dual Inhibitors Targeting the Protein Kinases BMX and BTK

The nonreceptor tyrosine TEC kinases are key regulators of the immune system and play a crucial role in the pathogenesis of diverse hematological malignancies. In contrast to the substantial efforts in inhibitor development for Bruton's tyrosine kinase (BTK), specific inhibitors of the other TEC kinases, including the bone marrow tyrosine kinase on chromosome X (BMX), remain sparse. Here we present a novel class of dual BMX/BTK inhibitors, which were designed from irreversible inhibitors of Janus kinase (JAK) 3 targeting a cysteine located within the solvent-exposed front region of the ATP binding pocket. Structure-guided design exploiting the differences in the gatekeeper residues enabled the achievement of high selectivity over JAK3 and certain other kinases harboring a sterically demanding residue at this position. The most active compounds inhibited BMX and BTK with apparent IC50 values in the single digit nanomolar range or below showing moderate selectivity within the TEC family and potent cellular target engagement. These compounds represent an important first step towards selective chemical probes for the protein kinase BMX.

Longitudinal Multi-omics Analyses Identify Responses of Megakaryocytes, Erythroid Cells, and Plasmablasts as Hallmarks of Severe COVID-19

Temporal resolution of cellular features associated with a severe COVID-19 disease trajectory is needed for understanding skewed immune responses and defining predictors of outcome. Here, we performed a longitudinal multi-omics study using a two-center cohort of 14 patients. We analyzed the bulk transcriptome, bulk DNA methylome, and single-cell transcriptome (>358,000 cells, including BCR profiles) of peripheral blood samples harvested from up to 5 time points. Validation was performed in two independent cohorts of COVID-19 patients. Severe COVID-19 was characterized by an increase of proliferating, metabolically hyperactive plasmablasts. Coinciding with critical illness, we also identified an expansion of interferon-activated circulating megakaryocytes and increased erythropoiesis with features of hypoxic signaling. Megakaryocyte- and erythroid-cell-derived co-expression modules were predictive of fatal disease outcome. The study demonstrates broad cellular effects of SARS-CoV-2 infection beyond adaptive immune cells and provides an entry point toward developing biomarkers and targeted treatments of patients with COVID-19.

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SARS-CoV2 infection elicits dynamic changes of circulating cells in the blood

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Severe COVID-19 is characterized by increased metabolically active plasmablasts

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Elevation of IFN-activated megakaryocytes and erythroid cells in severe COVID-19

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Cell-type-specific expression signatures are associated with a fatal COVID-19 outcome

An Organic Borate Salt with Superior p-Doping Capability for Organic Semiconductors

Molecular doping allows enhancement and precise control of electrical properties of organic semiconductors, and is thus of central technological relevance for organic (opto-) electronics. Beyond single-component molecular electron acceptors and donors, organic salts have recently emerged as a promising class of dopants. However, the pertinent fundamental understanding of doping mechanisms and doping capabilities is limited. Here, the unique capabilities of the salt consisting of a borinium cation (Mes2B+; Mes: mesitylene) and the tetrakis(penta-fluorophenyl)borate anion [B(C6F5)4]- is demonstrated as p-type dopant for polymer semiconductors. With a range of experimental methods, the doping mechanism is identified to comprise electron transfer from the polymer to Mes2B+, and the positive charge on the polymer is stabilized by [B(C6F5)4]-. Notably, the former salt cation leaves during processing and is not present in films. The anion [B(C6F5)4]- even enables the stabilization of polarons and bipolarons in poly(3-hexylthiophene), not yet achieved with other molecular dopants. From doping studies with high ionization energy polymer semiconductors, the effective electron affinity of Mes2B+[B(C6F5)4]- is estimated to be an impressive 5.9 eV. This significantly extends the parameter space for doping of polymer semiconductors.

Abstract 3617: Very low coverage whole genome sequencing improves clinically relevant copy number variation calling compared to targeted sequencing

Introduction

Despite many advances, the treatment for most patients with advanced solid tumors in the abdomen continues to be a clinical challenge. Copy number variants (CNVs) are an important part of the genomic landscape of these patients. Next-generation sequencing (NGS) tests used in the clinical setting are predominantly multi-gene targeted panels (FM, Guardant, NeoGenomics). Although this is the current standard, there is still doubt about the reliability and accuracy of such panels (PMID: 28472276), and panel based CNV-calling in clinical labs use stringent thresholds that may filter out many CNVs. The purpose of our study was to evaluate the clinical utility of a 125-gene targeted sequencing panel in detecting actionable CNVs in a cohort of colorectal cancer patients, with the eventual goal of identifying appropriate genome-guided therapy options.

Materials and Methods

We performed (i) targeted (350X) NGS based on the IDT xGen 125-gene Pan-Cancer panel on tumor and matched normal blood samples of 54 patients as well as (ii) very low-coverage (LC-WGS, 0.1X) whole genome sequencing on tumor and matched blood samples for the same set of patients. Bioinformatics methods included adapter trimming with bbduk, alignment with bwa-mem, quality control with FASTQC and Qualimap. CNVkit, ichorNCA, and Control-FREEC were used to call CNVs. For CNVkit and ichorNCA, the normal samples were combined to create a ‘reference normal'. Multiple window sizes were utilized to call CNVs at different scales.

Results

We compared the results of CNV calls from CNVkit, ichorCNA and Control-FREEC from targeted and LC-WGS data. This analysis indicates that targeted panels are at least currently not capable of reliably identifying the copy number landscape of clinical colorectal samples when matched normal samples are utilized. While within the targeted region we identified a median of five clinically actionable CNVs per sample for both targeted and whole genome sequencing (CNV amplification threshold of 5 copies), discordance of called CNVs on average was 56 percent. Numerical copy number calls tend to be higher for the targeted panel (mean: 10) vs LC-WGS (mean: 6) Beyond the targeted regions, LC-WGS detected a median of one additional clinical actionable CNV in genes such as PD-L1, JAK2, LRP1B, VEGFA, BCL2, and CCND3 which are not part of the targeted gene panel.

Conclusions

Our analysis suggests that CNV calling from targeted panels can be improved upon by incorporating very low-coverage whole genome sequencing.

Citation Format: Anu Amallraja, Janina Fuß, Casey B. Williams, Michael Forster, Sebastian Hinz, Tobias Meißner, Alexander Hendricks. Very low coverage whole genome sequencing improves clinically relevant copy number variation calling compared to targeted sequencing [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3617.

Clinical responses to PD-1 inhibition and their molecular characterization in six patients with mismatch repair-deficient metastatic cancer of the digestive system

Purpose

Immune checkpoint inhibitors have shown efficacy in patients with microsatellite instability-high/mismatch repair-deficient (MSI-H/dMMR) gastrointestinal (GI) cancers. However, depth and duration of clinical response is not uniform. We assessed tumor mutation burden (TMB) as a response marker in patients with GI cancers treated with immune checkpoint inhibitors.

Methods

Detailed clinical and response data were collected from six patients with metastatic MSI-H/dMMR GI cancers treated with immune checkpoint inhibitors. Efficacy was assessed by Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. Tumors and matched normal tissue were profiled by targeted next generation sequencing (127 gene panel, size 0.8 Mb). Impact of included mutation types, germline filtering methodology and different variant allele frequency thresholds on TMB estimation was assessed.

Results

Objective radiographic responses were observed in all six patients, and complete response was achieved in two of the six patients. Responses were durable (minimum 25 months). TMB estimates were clearly above the two recently reported cut-offs for metastatic colorectal cancer of 12 or 37 mutations per megabase for five of six patients, respectively, while one patient had borderline TMB elevation. TMB did not show an association with extent and duration of response but was influenced by included mutation types, germline filtering method and variant allele frequency threshold.

Conclusion

Our case series confirms the clinical benefit of immune checkpoint blockade in patients with metastatic MSI-H/dMMR GI cancers and illustrates the vulnerability of TMB as predictive marker in a subset of patients.

Electronic supplementary material

The online version of this article (10.1007/s00432-020-03335-2) contains supplementary material, which is available to authorized users.

Two Prevalent ∼100-kb GYPB Deletions Causative of the GPB-Deficient Blood Group MNS Phenotype S-s-U- in Black Africans

The U antigen (MNS5) is one of 49 antigens belonging to the MNS blood group system (ISBT002) carried on glycophorins A (GPA) and B (GPB). U is present on the red blood cells in almost all Europeans and Asians but absent in approximately 1.0% of Black Africans. U negativity coincides with negativity for S (MNS3) and s (MNS4) on GPB, thus be called S-s-U-, and is thought to arise from homozygous deletion of GYPB. Little is known about the molecular background of these deletions. Bioinformatic analysis of the 1000 Genomes Project data revealed several candidate regions with apparent deletions in GYPB. Highly specific Gap-PCRs, only resulting in positive amplification from DNAs with deletions present, allowed for the exact genetic localization of 3 different breakpoints; 110.24- and 103.26-kb deletions were proven to be the most frequent in Black Americans and Africans. Among 157 CEPH DNAs, deletions in 6 out of 8 African ethnicities were present. Allele frequencies of the deletions within African ethnicities varied greatly and reached a cumulative 23.3% among the Mbuti Pygmy people from the Congo. Similar observations were made for U+var alleles, known to cause strongly reduced GPB expression. The 110- and 103-kb deletional GYPB haplotypes were found to represent the most prevalent hereditary factors causative of the MNS blood group phenotype S-s-U-. Respective GYPB deletions are now accessible by molecular detection of homo- and hemizygous transmission.

Warm, lively, rough? Assessing agreement on aesthetic effects of artworks

The idea that simple visual elements such as colors and lines have specific, universal associations-for example red being warm-appears rather intuitive. Such associations have formed a basis for the description of artworks since the 18th century and are still fundamental to discourses on art today. Art historians might describe a painting where red is dominant as "warm," "aggressive," or "lively," with the tacit assumption that beholders would universally associate the works' certain key forms with specific qualities, or "aesthetic effects". However, is this actually the case? Do we actually share similar responses to the same line or color? In this paper, we tested whether and to what extent this assumption of universality (sharing of perceived qualities) is justified. We employed-for the first time-abstract artworks as well as single elements (lines and colors) extracted from these artworks in an experiment in which participants rated the stimuli on 14 "aesthetic effect" scales derived from art literature and empirical aesthetics. To test the validity of the assumption of universality, we examined on which of the dimensions there was agreement, and investigated the influence of art expertise, comparing art historians with lay people. In one study and its replication, we found significantly lower agreement than expected. For the whole artworks, participants agreed on the effects of warm-cold, heavy-light, and happy-sad, but not on 11 other dimensions. Further, we found that the image type (artwork or its constituting elements) was a major factor influencing agreement; people agreed more on the whole artwork than on single elements. Art expertise did not play a significant role and agreement was especially low on dimensions usually of interest in empirical aesthetics (e.g., like-dislike). Our results challenge the practice of interpreting artworks based on their aesthetic effects, as these effects may not be as universal as previously thought.