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Zusammenfassung: Nicht medikamentöse Interventionen für Menschen mit Demenz sollen die Lebensqualität und das Wohlbefinden steigern, psychopathologische und Verhaltenssymptome lindern und auch den versorgenden Angehörigen Unterstützungsmöglichkeiten und Resilienz-Förderung bieten. Vor dem Hintergrund der ausbleibenden Erfolge im Bereich der pharmakologisch-therapeutischen Forschung haben diese Ansätze zunehmend an Bedeutung gewonnen. Es handelt sich um eine aktuelle Übersicht der wichtigsten nicht medikamentösen Interventionen für Menschen mit Demenz und diesbezügliche Empfehlungen zur therapeutischen Anwendung unter Berücksichtigung des aktuellen Forschungsstands und der AWMF-S3-Leitlinie «Demenzen». Die vielversprechendsten Interventionen aus diesem therapeutischen Spektrum sind Massnahmen zur Förderung zentraler kognitiver Funktionen, Angebote zur Steigerung und Stabilisierung des körperlichen Aktivitätsniveaus sowie kreativtherapeutische Angebote zur Förderung der Kommunikationsfähigkeit und sozialer Teilhabe. Inzwischen werden viele dieser psychosozialen Interventionen durch den Einsatz digitaler Zugänge weiterentwickelt. Gemeinsam ist ihnen, dass sie sich an den individuellen kognitiven und körperlichen Ressourcen der Betroffenen orientieren, Lebensqualität und Stimmung verbessern sowie Partizipation und Selbstwirksamkeit fördern sollen. Neben den psychosozialen Interventionen haben in den vergangenen Jahren auch ernährungsbezogene Ansätze («Medical Food») und nichtinvasive Neurostimulation Potenziale im Rahmen der nicht medikamentösen Demenz-Therapie erkennen lassen.

Die im Folgenden dargestellten Fallberichte beschreiben exemplarisch die Interventionsmodule im Rahmen des Innovationsfondsprojektes DAVOS. DAVOS (Depression im Altenpflegeheim: Verbesserung der Behandlung durch ein gestuftes kollaboratives Versorgungsmodell) wurde als innovatives, gestuftes und strukturiertes Case-Management-Programm zur Verbesserung der Depressionsbehandlung für Bewohnende von Altenpflegeeinrichtungen implementiert und hinsichtlich seiner Wirksamkeit unter Alltagsbedingungen evaluiert. Weder systematische Identifikation depressiver Symptomatik noch adäquate psychotherapeutische Versorgung der Betroffenen finden in den Pflegeeinrichtungen gegenwärtig statt. Die Fallberichte zeigen deutlich, welchen Zuwachs an Aktivität und Funktionsniveau, an Wohlbefinden und Lebensqualität man bei depressiven Pflegeheimbewohnenden durch eine optimierte psychotherapeutische Versorgung erzielen kann.

Objectives The emergence of MDR strains is a public health problem in the management of associated infections. Several resistance mechanisms are present, and antibiotic efflux is often found at the same time as enzyme resistance and/or target mutations. However, in the laboratory routinely, only the latter two are identified and the prevalence of antibiotic expulsion is underestimated, causing a misinterpretation of the bacterial resistance phenotype. The development of a diagnostic system to quantify the efflux routinely would thus improve the management of patients. Methods A quantitative technique based on detection of clinically used fluoroquinolones was investigated in Enterobacteriaceae clinical strains with a high or basal efflux activity. The detail of efflux involvement was studied from MIC determination and antibiotic accumulation inside bacteria. WGS was carried out on selected strains to determine the genetic background associated with efflux expression. Results Only 1 Klebsiella pneumoniae isolate exhibited a lack of efflux whereas 13 isolates had a basal efflux and 8 presented efflux pump overexpression. The antibiotic accumulation evidenced the efficacy of the efflux mechanism in strains, and the contribution of dynamic expulsion versus target mutations in fluoroquinolone susceptibility. Conclusions We confirmed that phenylalanine arginine β-naphthylamide is not a reliable marker of efflux due to the affinity of the AcrB efflux pump for different substrates. We have developed an accumulation test that can be used efficiently on clinical isolates collected by the biological laboratory. The experimental conditions and protocols ensure a robust assay that with improvements in practice, expertise and equipment could be transferred to the hospital laboratory to diagnose the contribution of efflux in Gram-negative bacteria.

International audience; Current trends in the aerospace industry for the digitization of data, tools, and services call for novel solutions that can keep track of the latest technological advancements. Moreover, the increasing drive toward model-based approaches imposes the use of models for the development of complex systems, such as satellites. New types of methods and tools are needed in order to manage the still-growing complexity of embedded systems and their corresponding models. This paper addresses issues related to space systems (in-service) operations and proposes a multimodel approach to address them. The multimodel approach aims at facilitating the task of operational diagnosis by creating a monitoring and diagnosis-dedicated system model derived from existing system design (architecture, functional behavior, and safety) models. The purpose of the diagnosis-dedicated model is to enable the codesign of the system and its diagnosis tools in order to improve the performance of diagnosis activities and the system’s availability. This paper demonstrates the interests of the suggested approach with regard to the limitations of current practices.

Zusammenfassung Einleitung Motorische Symptome bei Morbus Parkinson lassen sich durch körperliche Aktivität modifizieren. Inwiefern dies auch für nicht-motorische, autonome Symptome gilt, ist weitaus weniger bekannt. Die Erkrankung weist zudem eine Vielzahl an geschlechterspezifischen Unterschieden auf. Epidemiologische Untersuchungen deuten zum Beispiel auf einen besseren primärpräventiven Effekt durch körperliche Aktivität bei Männern als bei Frauen hin. Daten zu geschlechterspezifischen Effekten auf das autonome Nervensystem sind jedoch limitiert. Im Rahmen der vorliegenden Pilotstudie sollen mögliche geschlechterspezifische Effekte einer Bewegungsintervention auf Störungen der hämodynamischen Regulation als Manifestation nicht-motorischer Symptome untersucht werden. Diese sind aufgrund ihrer oft gegensätzlichen hypo- und hypertonen Ausprägung schwierig medikamentös zu behandeln, lassen sich aber gegebenenfalls durch Bewegungsinterventionen modifizieren. Methodik Bei 42 Patienten und Patientinnen (Alter: 70,3 Jahre; 24 Männer; 18 Frauen) wurden vor und nach einer mehrwöchigen, stationären Parkinsonkomplexbehandlung hämodynamische Parameter in einem Schellongtest untersucht. Mittels anschließender Regressionsanalyse erfolgte eine Quantifizierung der Abhängigkeit von den Faktoren Alter, Body Mass Index, Krankheitsdauer, Vorerkrankungen, Sitzendblutdruck und hypotensiv wirkender Medikamente. Ergebnis Bei 44% der Männer und 46% der Frauen traten hämodynamische Regulationsstörungen im Stand und in Rückenlage mindestens einmal auf. Eine vor Therapiebeginn präsentierte Regulationsstörung im Stand zeigte sich in keiner Geschlechtergruppe durch die Parkinsonkomplexbehandlung verändert. Frauen zeigten zu Therapieende jedoch einen signifikant niedrigeren Blutdruck im Liegen (p=0,022*). Unabhängig von der Komplextherapie fiel der Blutdruck in Rückenlage bei Frauen nach Orthostasebelastung höher aus als davor (vor Therapie: p=0,015 *; nach Therapie: p=0,021*). Jedes Lebensjahr erhöhte das Risiko für eine hämodynamische Regulationsstörung in Rückenlage in der Gesamtgruppe um 12,4% (Regressionskoeffizient B=0,117; p=0,014 *; Exp(B)=1,124). Schlussfolgerung Systematische Effekte auf Blutdruckwerte im Rahmen von Orthostasereaktionen durch eine Parkinsonkomplexbehandlung konnten nicht nachgewiesen werden. Allerdings zeigte sich bei Frauen nach Parkinsonkomplexbehandlung eine Senkung der Blutdruckwerte in Rückenlage. Das scheinbar unsystematische, teils geschlechterspezifische Auftreten hämodynamischer Regulationsstörungen fordert ein individualmedizinisch angelegtes Vorgehen im therapeutischen Alltag.

The optimal in-hospital observation periods associated with minimal risks of complications and unplanned readmission after laparoscopic liver resection are unknown. The purpose of this study was to assess changes in the risks of postoperative complications over time.Surgical complexity of laparoscopic liver resection was stratified into grades I (low complexity), II (intermediate), and III (high) using our 3-level complexity classification. The cumulative incidence rate and conditional probability of postoperative complication and risk factors for complication Clavien-Dindo grade ≥II (defined as treatment-requiring complications) were assessed.The cumulative incidence of treatment-requiring complications was higher in patients undergoing grade III resection than in patients undergoing grade I resection (32.3% vs 10.4%, P.001) and grade II resection (32.3% vs 20.7%, P = .019). The conditional probability of postoperative complication stratified by our complexity classification decreased over time and was10% for patients undergoing grade I resection on postoperative day 1, grade II resection on postoperative day 4, and grade III resection on postoperative day 10.The conditional cumulative incidence of treatment-requiring complications for patients undergoing laparoscopic liver resection is well stratified based on the 3-level complexity classification. Conditional complication risk analysis stratified by the 3 complexity grades may be useful for optimizing in-hospital observation after laparoscopic liver resection.

Background Diabetic foot infections (DFIs) represent a public health problem because of their frequency and the severity of their consequences, i.e. amputation and mortality. Polymicrobial biofilms on the skin surface of these ulcers complicate wound healing. Few in vitro models exist to study the antibiotics activity in this context. Objectives This study evaluated the in vitro activity of antibiotics against the two main bacteria isolated in DFI, Staphylococcus aureus and Pseudomonas aeruginosa, using a dynamic system (BioFlux™ 200) and a chronic wound-like medium (CWM) that mimic the foot ulcer environment. Methods Reference strains and two pairs of clinical S. aureus and P. aeruginosa isolated together from a DFI were cultivated in brain heart infusion and CWM media during 72 h at 37°C, alone and combined in the BioFlux™ 200 system. Antibiotic activity was evaluated after a mechanical debridement. The activities were measured by the reduction of biofilm percentage of bacteria in the microfluidic system using microscopy. Results Daptomycin for S. aureus and ceftazidime for P. aeruginosa showed excellent activity to reduce biofilm biomass, whereas linezolid action was more mitigated and dalbavancin was ineffective. Ceftazidime + daptomycin presented the most potent in vitro activity on a mixed biofilm. Conclusions The combination of CWM and the BioFlux™ microfluidic system represents a valuable tool to screen the potential antimicrobial activity of antibiotics under conditions mimicking those encountered in DFI. It could help clinicians in their management of chronic wounds.

Androgen deprivation therapy has a central role in the treatment of advanced prostate cancer, often causing initial tumour remission before increasing independence from signal transduction mechanisms of the androgen receptor and then eventual disease progression. Novel treatment approaches are urgently needed, but only a fraction of promising drug candidates from the laboratory will eventually reach clinical approval, highlighting the demand for critical assessment of current preclinical models. Such models include standard, genetically modified and patient-derived cell lines, spheroid and organoid culture models, scaffold and hydrogel cultures, tissue slices, tumour xenograft models, patient-derived xenograft and circulating tumour cell eXplant models as well as transgenic and knockout mouse models. These models need to account for inter-patient and intra-patient heterogeneity, the acquisition of primary or secondary resistance, the interaction of tumour cells with their microenvironment, which make crucial contributions to tumour progression and resistance, as well as the effects of the 3D tissue network on drug penetration, bioavailability and efficacy.

Starting in 2021, Centers for Medicare and Medicaid Services required hospitals to provide pricing information to allow consumers to compare prices. Patients perceived that the quality of these services also impacts decision-making. This study examines the relationship between procedure price and quality from the patients' perspective.Unnegotiated prices of procedures were extracted from hospital websites. Hospital quality was defined as the U.S. NewsWorld Report's score for the specialty performing the procedure. Regional differences in markets were corrected with the Wage Price Index. Spearman's correlations were used for analysis between price and quality.Overall, 67% (1225/1815) of hospitals had a pricing document. Compliance by procedure was poor with a low of 7% for Current Procedural Terminology (CPT) 93000 and a high of 27% for CPTs 93452 and 62323. Wide variability of prices for all procedures was noted. The smallest difference in price range listed was for CPT 45380 with a 32× difference between the minimum and maximum ($310-$10,023) with the first, second, and third quartiles being $1457, $2759, and $4276, respectively. The largest difference in price range was for CPT 55700 with a 5036× difference between the minimum and maximum ($9-$45,322) with the first, second, and third quartiles being $1638, $2971, and $5342, respectively. Correlation between price and quality was low, with the strongest being rho = 0.369 (P = 0.02) for CPT 93000.Compliance with price transparency was low with large variability in prices for the same procedure. There was no correlation between hospital price and quality. As currently implemented, poor compliance and wide price variability may limit patients' understanding of procedure costs.

In this study we aimed to identify the molecular genetic cause of a progressive multisystem disease with prominent lipodystrophy.In total, 5 affected individuals were investigated using exome sequencing. Dermal fibroblasts were characterized using RNA sequencing, proteomics, immunoblotting, immunostaining, and electron microscopy. Subcellular localization and rescue studies were performed.We identified a lipodystrophy phenotype with a typical facial appearance, corneal clouding, achalasia, progressive hearing loss, and variable severity. Although 3 individuals showed stunted growth, intellectual disability, and died within the first decade of life (A1, A2, and A3), 2 are adults with normal intellectual development (A4 and A5). All individuals harbored an identical homozygous nonsense variant affecting the retention and splicing complex component BUD13. The nucleotide substitution caused alternative splicing of BUD13 leading to a stable truncated protein whose expression positively correlated with disease expression and life expectancy. In dermal fibroblasts, we found elevated intron retention, a global reduction of spliceosomal proteins, and nuclei with multiple invaginations, which were more pronounced in A1, A2, and A3. Overexpression of both BUD13 isoforms normalized the nuclear morphology.Our results define a hitherto unknown syndrome and show that the alternative splice product converts a loss-of-function into a hypomorphic allele, thereby probably determining the severity of the disease and the survival of affected individuals.

Rationale and Objectives High-grade gastroenteropancreatic neuroendocrine neoplasms (G3 GEP-NENs) are pathologically classified into well differentiated neuroendocrine tumors (G3 NETs) and poorly differentiated neuroendocrine carcinomas (G3 NECs). Using a novel parameter, we examined the prognostic value of 18F-FDG and 68Ga-DOTATATE PET/CT quantification in comparison to pathologic assessment in G3 GEP-NENs. Materials and Methods A total of 31 patients with G3 GEP-NENs were reviewed. For each patient, the SUVmax on 18F-FDG and 68Ga-DOTATATE PET/CT were used to calculate the FDG-DOTATATE-Z (FDZ) score: a continuous parameter that increases with 68Ga-DOTATATE uptake and decreases with 18F-FDG uptake. The variation in the FDZ score with respect to pathologic variables was examined. Kaplan-Meier and Cox regression analyses were performed to evaluate the effect of FDZ score on overall survival. An external cohort of 21 patients was used for validation. Results The FDZ score was significantly higher in G3 NETs compared to G3 NECs (p 0.05 group showed significantly longer survival compared to those in the FDZ≤0.05 group, with median of 34.9 vs. 12.0 months (p 0.05 (p=0.005), well differentiated disease (p=0.044), and lower Ki67 index (p=0.042) were predictors of survival. On multivariate regression, only FDZ>0.05 could independently predict longer survival with HR=0.16 (p=0.018), which was reproduced in the external validation cohort. Conclusion Combined quantification of 18F-FDG and 68Ga-DOTATATE PET/CT into a novel parameter, the FDZ score, reflects the pathologic characteristics of G3 GEP-NENs and is a prognostic indicator of overall survival independent of differentiation.

Summary Preneoplastic high-risk lesions in the pancreas need to be differentiated from low-risk lesions warranting surveillance and eventually surgical intervention. Imaging is used so far; however, certain imaging features are subject to interpretation and hence have their intrinsic flaws. In a recent article, a liquid biopsy with protein and RNA markers demonstrates differentiation based on a blood test. See related article by Zhang et al., p. 1535

La mort des dirigeants politiques du Vème siècle à Athènes telle que Plutarque la met en scène permet de réfléchir au lien étroit construit par les Grecs entre les rituels funéraires et l’idéologie politique.

Human papilloma virus (HPV) is an infectious carcinogenic agent. Nearly all cervical cancers are positive for one of the high-risk HPV subtypes. Although the introduction of the HPV vaccines in many countries have shown tremendous positive effects on the incidence of both cervical intraepithelial lesions (CIN) and invasive cancer, the large majority of females worldwide are still not vaccinated. Patients with diagnosed high-grade CIN need a lifelong close monitoring of possible relapse or development of invasive cancer. Different blood-based liquid biopsy approaches have shown great promise as an easily obtainable minimally invasive tool for early detection and monitoring of disease. Among the different liquid biopsy approaches the clinical relevance of cell-free DNA (cfDNA) in cervical cancer has been best investigated. In cervical cancer, the DNA fragments can be of both, human as well as viral origin. Thus, the mutation and methylation status of genes related to carcinogenesis as well as the HPV status can be analysed in plasma from cervical cancer patients. This review describes recent advances in different cfDNA approaches for early detection and monitoring of cervical cancer and its precursor lesions.

Background Revealing molecular mechanisms linked to androgen receptor activity can help to improve diagnosis and treatment of prostate cancer. Retinoic acid-induced 2 (RAI2) protein is thought to act as a transcriptional coregulator involved in hormonal responses and epithelial differentiation. We evaluated the clinical relevance and biological function of the RAI2 protein in prostate cancer. Methods We assessed RAI2 gene expression in the Cancer Genome Atlas prostate adenocarcinoma PanCancer cohort and protein expression in primary tumors (n = 199) by immunohistochemistry. We studied RAI2 gene expression as part of a multimarker panel in an enriched circulating tumor cell population isolated from blood samples (n = 38) of patients with metastatic prostate cancer. In prostate cancer cell lines, we analyzed the consequences of androgen receptor inhibition on RAI2 protein expression and the consequences of RAI2 depletion on the expression of the androgen receptor and selected target genes. Results Abundance of the RAI2 protein in adenocarcinomas correlated with the androgen receptor; keratins 8, 18, and 19; and E-cadherin as well as with an early biochemical recurrence. In circulating tumor cells, detection of RAI2 mRNA significantly correlated with gene expression of FOLH1, KLK3, RAI2, AR, and AR-V7. In VCaP and LNCaP cell lines, sustained inhibition of hormone receptor activity induced the RAI2 protein, whereas RAI2 depletion augmented the expression of MME, STEAP4, and WIPI1. Conclusions The RAI2 protein functions as a transcriptional coregulator of the androgen response in prostate cancer cells. Detection of RAI2 gene expression in blood samples from patients with metastatic prostate cancer indicated the presence of circulating tumor cells.

Most individuals with rare diseases initially consult their primary care physician. For a subset of rare diseases, efficient diagnostic pathways are available. However, ultra-rare diseases often require both expert clinical knowledge and comprehensive genetic diagnostics, which poses structural challenges for public healthcare systems. To address these challenges within Germany, a novel structured diagnostic concept, based on multidisciplinary expertise at established university hospital centers for rare diseases (CRDs), was evaluated in the three year prospective study TRANSLATE NAMSE. A key goal of TRANSLATE NAMSE was to assess the clinical value of exome sequencing (ES) in the ultra-rare disease population. The aims of the present study were to perform a systematic investigation of the phenotypic and molecular genetic data of TRANSLATE NAMSE patients who had undergone ES in order to determine the yield of both ultra-rare diagnoses and novel gene-disease associations; and determine whether the complementary use of machine learning and artificial intelligence (AI) tools improved diagnostic effectiveness and efficiency.ES was performed for 1,577 patients (268 adult and 1,309 pediatric). Molecular genetic diagnoses were established in 499 patients (74 adult and 425 pediatric). A total of 370 distinct molecular genetic causes were established. The majority of these concerned known disorders, most of which were ultra-rare. During the diagnostic process, 34 novel and 23 candidate genotype-phenotype associations were delineated, mainly in individuals with neurodevelopmental disorders.To determine the likelihood that ES will lead to a molecular diagnosis in a given patient, based on the respective clinical features only, we developed a statistical framework called YieldPred. The genetic data of a subcohort of 224 individuals that also gave consent to the computer-assisted analysis of their facial images were processed with the AI tool Prioritization of Exome Data by Image Analysis (PEDIA) and showed superior performance in variant prioritization.The present analyses demonstrated that the novel structured diagnostic concept facilitated the identification of ultra-rare genetic disorders and novel gene-disease associations on a national level and that the machine learning and AI tools improved diagnostic effectiveness and efficiency for ultra-rare genetic disorders.

PDX models treated with PARPi therapies.

Purpose:PARP inhibitors have become the standard-of-care treatment for homologous recombination deficient (HRD) high-grade serous ovarian cancer (HGSOC). However, not all HRD tumors respond to PARPi. Biomarkers to predict response are needed. [18F]FluorThanatrace ([18F]FTT) is a PARPi-analog PET radiotracer that noninvasively measures PARP-1 expression. Herein, we evaluate [18F]FTT as a biomarker to predict response to PARPi in patient-derived xenograft (PDX) models and subjects with HRD HGSOC.Experimental Design:In PDX models, [18F]FTT-PET was performed before and after PARPi (olaparib), ataxia-telangiectasia inhibitor (ATRi), or both (PARPi-ATRi). Changes in [18F]FTT were correlated with tumor volume changes. Subjects were imaged with [18F]FTT-PET at baseline and after ∼1 week of PARPi. Changes in [18F]FTT-PET uptake were compared with changes in tumor size (RECISTv1.1), CA-125, and progression-free survival (PFS).Results:A decrease in [18F]FTT tumor uptake after PARPi correlated with response to PARPi, or PARPi-ATRi treatment in PARPi-resistant PDX models (r = 0.77–0.81). In subjects (n = 11), percent difference in [18F]FTT-PET after ∼7 days of PARPi compared with baseline correlated with best RECIST response (P = 0.01), best CA-125 response (P = 0.033), and PFS (P = 0.027). All subjects with >50% reduction in [18F]FTT uptake had >6-month PFS and >50% reduction in CA-125. Utilizing only baseline [18F]FTT uptake did not predict such responses.Conclusions:The decline in [18F]FTT uptake shortly after PARPi initiation provides a measure of drug-target engagement and shows promise as a biomarker to guide PARPi therapies in this pilot study. These results support additional preclinical mechanistic and clinical studies in subjects receiving PARPi ± combination therapy.See related commentary by Liu and Zamarin, p. 1384

PARPi treatment and response.

Background: Given the scarce donor supply, an increasing number of so-called marginal or extended criteria donor (ECD) organs are used for liver transplantation. These ECD liver grafts are however known to be associated with a higher rate of early allograft dysfunction and primary non-function because of a greater vulnerability to ischemia-reperfusion injury. The end-ischemic Hypothermic Oxygenated Machine Perfusion (HOPE) technique may improve outcomes of liver transplantation with ECD grafts by decreasing reperfusion injury. Methods: HOPExt trial is a comparative open-label, multicenter, national, prospective, randomized, controlled study, in two parallel groups, using static cold storage, the gold standard procedure, as control. The trial will enroll adult patients on the transplant waiting list for liver failure or liver cirrhosis and/or liver malignancy requiring liver transplantation and receiving an ECD liver graft from a brain-dead donor. In the experimental group, ECD liver grafts will first undergo a classical static cold (4°C) storage followed by a hypothermic oxygenated perfusion (HOPE) for a period of 1 to 4 hours. The control group will consist of the classic static cold storage which is the gold standard procedure in liver transplantation. The primary objective of this trial is to study the efficacy of HOPE used before transplantation of ECD liver grafts from brain-dead donors in reducing postoperative early allograft dysfunction within the first 7 postoperative days compared to simple cold static storage. Discussion: We present in this protocol all study procedures in regard to the achievement of the HOPExt trial, to prevent biased analysis of trial outcomes and improve the transparency of the trial results. Enrollment of patients in the HOPExt trial has started on June 31, 2021, and is ongoing Trial registration: ClinicalTrials.gov NCT03929523. Registered on April 29, 2019, before the start of inclusion.

Supplementary Figure S4. Data base analysis of correlation between RAI2 and ESR1 mRNA expression.

Supplementary Figure S3. qPCR verification of RAI2 expression and correlative analysis of RAI2 mRNA expression in primary breast tumors.

ORF overexpression screen data

Supplementary detailed methods

Supplementary Figure S6. Analysis of adherents junction formation following RAI2 depletion in MCF-7 and KPL-1.

Supplementary Figure S7. Gene expression profiling of MDA-MD-231 cells over expressing wild type and CtBP binding deficient RAI2 proteins.

Secondary mini-pool overexpression screen data

Supplementary Figure S1. Genome-scale CRISPR-Cas9 screening identifies a strong correlation between copy number and sensitivity to CRISPR-Cas9 genome editing. Supplementary Figure S2. Global summary of the relationship of CRISPR-Cas9 guide scores to genomic copy number for all 33 cell lines screened. Supplementary Figure S3. Amplified genes represent the strongest perceived dependencies in pooled CRISPR-Cas9 screening data. Figure S4. Evaluation of the influence of copy number on CRISPR-Cas9 dependency scores in published data from Hart et al. (25). Figure S5. Representative examples of structural variations leading to copy number amplification underlying the gene-independent anti-proliferative response to CRISPRCas9 targeting of loci within these regions.

Table S1: Detailed information on all CpGs of interest Table S2: Cancer-associated CpGs in TRGs by pathway at FDR < 0.05, with unspecified skin malignancies excluded Table S3: Methylation trajectory over time by cancer status Table S4: Logistic regression results for DNA methylation measured over 8 years before diagnosis/censoring Table S5: Regulatory elements enrichment analysis results Figure S1: Plots of Beta-coefficients by genomic location for all CpGs on six genes of interest Figure S2: DNA methylation by years to cancer diagnosis/censoring and cancers status with 95% confidence intervals Figure S3: DNA methylation by years to cancer diagnosis/censoring and cancer status for CpG additional sites Figure S4: Regulatory enrichment analysis results

Supplementary Figure S6. Representative example of complex amplified locus showing a CRISPR-CN correlation. Supplementary Figure S7. Comparative analysis of the relationship of CRISPR-Cas9 guide scores to the predicted number of CRISPR-Cas9-induced DNA cuts based on either copy number or total predicted perfect-match on- and off-target alignments. Supplementary Figure S8. Comprehensive analysis of CRISPR-Cas9 sensitivity correlated to the total predicted number of DNA cuts conferred by each sgRNA. Supplementary Figure S9. (A) PANC-1 infection efficiency corresponding to Figure 6 in vitro validation experiment measuring short-term proliferation and viability response of PANC-1 cells transduced at high multiplicity of infection. (B) Immunoblot of protein from PANC-1 cells harvested 48 hours after infection at high MOI with the indicated sgRNAs targeting inside (19q8) or outside (19q4) the PANC-1 19q13 amplicon shown in Figure 6A. Supplementary Figure S10. CRISPR-Cas9 targeting of amplified regions or multiple genomic loci induces DNA damage and a G2 cell cycle arrest in CAL120 cells.

Supplementary Figure S5. Quantification of CAMA-1 cells with mesenchymal transformed cellular morphology.

ORF constructs in secondary mini-pool overexpression screen

Sample Information: Table with cell line identities and relevant information for this manuscript.