Citations

Abstract Sequencing efforts have identified key oncogenic drivers and transcriptomic subtypes of high-grade gliomas (HGGs), but this knowledge has not resulted in individualized therapy or improved patient outcomes. Here, we used a functional genomics approach combining integrated genomic/transcriptomic analyses with patient-derived 3D micro-cancers (mCancers) to rapidly identify individualized therapeutic vulnerabilities and determine predictive response biomarkers. 30 primary/recurrent HGGs, including 20 glioblastomas, 5 astrocytomas, and 5 oligodendrogliomas, were included for drug testing. mCancers recapitulated the structural and molecular alterations, cellularity, and heterogeneity, of parental patient tumors. A total of 119 single-agent drugs and 183 drug combinations were tested, while a pre-selected drug panel comprising 25 glioma-relevant treatment strategies was tested across all cases. In general, mCancer efficacy corresponded well to historical responses to previously tested agents (EGFR, HDAC inhibitors, etc.). Combined, strong efficacy (i.e. >70% growth inhibition at Cmax) of single treatments targeting deregulated receptor tyrosine kinase (RTK), p53/apoptosis, cell cycle, DNA damage repair, IDH, or telomere maintainance pathways, was observed in 14 out of 30 cases. Surprisingly, transcriptional signatures, but not specific genetic alterations, were found to stratify drug responses. For example, mCancers enriched for the most aggressive mesenchymal (MES) and glycolytic/plurimetabolic (GPM) transcriptional subtypes exhibited stronger response to the BET inhibitor JQ1 (and other clinical BET inhibitors) and the DNA-PKcs/mTOR dual inhibitor CC-115. This therapeutic vulnerability was associated with enrichment of YAP/TAZ signaling, and the glioblastoma stem cell G-STEM signature. Notably, individual combination strategies were effective across tumors, with strong responses ranging from 38% to 77% of all tumors tested. Overall, this study underscores the value of functional genomics in identifying novel vulnerabilities of HGGs and associated response biomarkers. It also highlights the need for further clinical validation of several novel therapies and especially drug combination strategies with strong efficacy in the ex vivo setting.

Recognizing the early signs of cancer risk is vital for informing prevention, early detection, and survival. To investigate whether changes in circulating metabolites characterise the early stages of colorectal cancer (CRC) development, we examined associations between a genetic risk score (GRS) associated with CRC liability (72 single nucleotide polymorphisms) and 231 circulating metabolites measured by nuclear magnetic resonance spectroscopy in the Avon Longitudinal Study of Parents and Children (N=6,221). Linear regression models were applied to examine associations between genetic liability to colorectal cancer and circulating metabolites measured in the same individuals at age 8, 16, 18 and 25 years. The GRS for CRC was associated with up to 28% of the circulating metabolites at FDR-P<0.05 across all time points, particularly with higher fatty acids and very-low- and low-density lipoprotein subclass lipids. Two-sample reverse Mendelian randomization (MR) analyses investigating CRC liability (52,775 cases, 45,940 controls) and metabolites measured in a random subset of UK Biobank participants (N=118,466, median age 58y) revealed broadly consistent effect estimates with the GRS analysis. In conventional (forward) MR analyses, genetically predicted polyunsaturated fatty acid concentrations were most strongly associated with higher CRC risk. These analyses suggest that higher genetic liability to CRC can cause early alterations in systemic metabolism, and suggest that fatty acids may play an important role in CRC development.

Context.— In 2018 the College of American Pathologists Diagnostic Immunology and Flow Cytometry Committee designed and implemented a new plasma cell neoplasia flow cytometry proficiency testing program—PCNEO—to allow clinical flow cytometry laboratories to monitor and assess their performance compared with a peer group. Objective.— To report the results from the first 4 years of the PCNEO program. Design.— Program participants were sent 2 sets of challenges per year, each including 1 wet challenge and 2 dry challenges, with associated clinical and laboratory findings. The wet challenges were composed of myeloma cell line specimens (with or without dilution in preserved whole blood) for flow cytometric analysis. The dry (paper) challenges were composed of clinical case summaries and images of flow cytometric test results from various flow cytometry laboratories of committee members. Results.— A total of 116 to 145 laboratories from 17 countries enrolled in the proficiency testing program. For the wet challenges, almost all participants (97%–100%; cumulative, 98.2%) correctly identified the presence of neoplastic plasma cell populations based on flow cytometric analysis of undiluted myeloma cell lines. Slightly fewer participants (89.0%–97.4%; cumulative, 95.2%) correctly identified the presence of neoplastic plasma cell populations based on flow cytometric analysis of diluted myeloma cell lines (10% or 50% dilutions into peripheral blood) intended to better represent a typical clinical sample. There was generally agreement among 80% or more of participants for positive or negative staining for CD38, CD138, CD19, CD20, and surface and cytoplasmic κ and λ light chains. Similarly, 84% to 100% of participants were able to correctly identify the presence of neoplastic plasma cell populations in paper challenges, including the presence of small, neoplastic plasma cell populations (0.01%–5.0% clonal plasma cells) and the presence of nonneoplastic plasma cell populations (correctly identified by 91%–96% of participants). Conclusions.— Participant performance in the new proficiency testing program was excellent overall, with the vast majority of participants able to perform flow cytometric analysis and identify neoplastic plasma cell populations and to identify small plasma cell clones or expanded populations of reactive plasma cells in dry challenge flow cytometry results. This program will allow laboratories to verify the accuracy of their testing program and test interpretations for the assessment of patients suspected of having a plasma cell neoplasm.

Background: Tobacco smoking during pregnancy is associated with metabolic dysfunction in children, but mechanistic insights remain limited. Hypomethylation of cg05575921 in the aryl hydrocarbon receptor repressor (AHRR) gene is associated with in utero tobacco smoke exposure. In this study, we evaluated whether AHRR hypomethylation mediates the association between maternal smoking and metabolic dysfunction in children. Methods: We assessed metabolic dysfunction using liver fat content (LFC), serum, and clinical data in children aged 7–12 years (n=78) followed since birth. Maternal smoking was self-reported at 12 weeks gestation. Methylation was measured by means of pyrosequencing at 3 sequential CpG sites, including cg05575921, at birth and at ages 7–12. Regression models were used to evaluate whether AHRR methylation mediated the association between maternal smoking and child metabolic dysfunction. Results: Average AHRR methylation at birth was significantly higher among children of nonsmoking mothers compared with children of mothers who smoked (69.8% ± 4.4% vs. 63.5% ± 5.5, p=0.0006). AHRR hypomethylation at birth was associated with higher liver fat content (p=0.01), triglycerides (p=0.01), and alanine aminotransferase levels (p=0.03), and lower HDL cholesterol (p=0.01) in childhood. AHRR hypomethylation significantly mediated associations between maternal smoking and liver fat content (indirect effect=0.213, p=0.018), triglycerides (indirect effect=0.297, p=0.044), and HDL cholesterol (indirect effect = -0.413, p=0.007). AHRR methylation in childhood (n=78) was no longer significantly associated with prenatal smoke exposure or child metabolic parameters (p>0.05). Conclusions: AHRR hypomethylation significantly mediates the association between prenatal tobacco smoke exposure and features of childhood metabolic dysfunction, despite the lack of persistent hypomethylation of AHRR into childhood. Further studies are needed to replicate these findings and to explore their causal and long-term significance.

A large number of variants identified through clinical genetic testing in disease susceptibility genes are of uncertain significance (VUS). Following the recommendations of the American College of Medical Genetics and Genomics (ACMG) and Association for Molecular Pathology (AMP), the frequency in case-control datasets (PS4 criterion) can inform their interpretation. We present a novel case-control likelihood ratio-based method that incorporates gene-specific age-related penetrance. We demonstrate the utility of this method in the analysis of simulated and real datasets. In the analysis of simulated data, the likelihood ratio method was more powerful compared to other methods. Likelihood ratios were calculated for a case-control dataset of BRCA1 and BRCA2 variants from the Breast Cancer Association Consortium (BCAC) and compared with logistic regression results. A larger number of variants reached evidence in favor of pathogenicity, and a substantial number of variants had evidence against pathogenicity—findings that would not have been reached using other case-control analysis methods. Our novel method provides greater power to classify rare variants compared with classical case-control methods. As an initiative from the ENIGMA Analytical Working Group, we provide user-friendly scripts and preformatted Excel calculators for implementation of the method for rare variants in BRCA1, BRCA2, and other high-risk genes with known penetrance.

Background: Meniscal root repair can improve patient outcomes significantly; however, several contraindications exist, including arthritic change to the medial or lateral tibiofemoral compartments. Purpose/Hypothesis: The purpose of this study was to evaluate the outcomes of meniscal root repair in patients with advanced patellofemoral chondromalacia (PFC). It was hypothesized that the presence of advanced PFC would not significantly affect the postoperative outcomes. Study Design: Cohort study; Level of evidence, 3. Methods: A retrospective review was conducted of patients who underwent meniscal root repair with at least 2 years of follow-up data. Patients with chondromalacia as determined by arthroscopic visualization (defined as Outerbridge grade 3 or 4) were placed in the PFC group; patients with Outerbridge grade 0 to 2 chondromalacia were placed in the non-PFC group. Outcomes were measured by the Lysholm knee scoring scale and the International Knee Documentation Committee (IKDC) Subjective Knee Form. Clinical outcomes including complications were also recorded. Quantitative data between the groups were analyzed using the 2-tailed independent-samples t test. Results: Overall, this study included 81 patients (35 in the PFC group, 46 in the non-PFC group). The mean follow-up times were 25.1 months in the PFC group and 24.8 months in the non-PFC group. In both groups, Lysholm and IKDC scores improved significantly with 24-month Lysholm scores averaging 85.86 in the PFC group and 86.61 in the non-PFC group ( P = .62) and 24-month IKDC scores averaging 77.66 for the PFC group and 79.59 for the non-PFC group ( P = .45). The cohorts demonstrated similar rates of retear, arthrofibrosis, infection, and progression to total knee arthroplasty. Conclusion: The presence of advanced PFC was not associated with inferior outcomes in patients who underwent posterior meniscal root repair, and rates of recurrent tears, postoperative infection, arthrofibrosis, and conversion to total knee arthroplasty were similar between the study groups. These findings suggest that PFC may not significantly alter the results of meniscal root repair and should not be considered an absolute contraindication for this procedure.

ImportanceRespiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections (LRTIs) and infant hospitalization worldwide.ObjectiveTo evaluate the characteristics and outcomes of RSV-related critical illness in US infants during peak 2022 RSV transmission.Design, Setting, and ParticipantsThis cross-sectional study used a public health prospective surveillance registry in 39 pediatric hospitals across 27 US states. Participants were infants admitted for 24 or more hours between October 17 and December 16, 2022, to a unit providing intensive care due to laboratory-confirmed RSV infection.ExposureRespiratory syncytial virus.Main Outcomes and MeasuresData were captured on demographics, clinical characteristics, signs and symptoms, laboratory values, severity measures, and clinical outcomes, including receipt of noninvasive respiratory support, invasive mechanical ventilation, vasopressors or extracorporeal membrane oxygenation, and death. Mixed-effects multivariable log-binomial regression models were used to assess associations between intubation status and demographic factors, gestational age, and underlying conditions, including hospital as a random effect to account for between-site heterogeneity.ResultsThe first 15 to 20 consecutive eligible infants from each site were included for a target sample size of 600. Among the 600 infants, the median (IQR) age was 2.6 (1.4-6.0) months; 361 (60.2%) were male, 169 (28.9%) were born prematurely, and 487 (81.2%) had no underlying medical conditions. Primary reasons for admission included LRTI (594 infants [99.0%]) and apnea or bradycardia (77 infants [12.8%]). Overall, 143 infants (23.8%) received invasive mechanical ventilation (median [IQR], 6.0 [4.0-10.0] days). The highest level of respiratory support for nonintubated infants was high-flow nasal cannula (243 infants [40.5%]), followed by bilevel positive airway pressure (150 infants [25.0%]) and continuous positive airway pressure (52 infants [8.7%]). Infants younger than 3 months, those born prematurely (gestational age &amp;lt;37 weeks), or those publicly insured were at higher risk for intubation. Four infants (0.7%) received extracorporeal membrane oxygenation, and 2 died. The median (IQR) length of hospitalization for survivors was 5 (4-10) days.Conclusions and RelevanceIn this cross-sectional study, most US infants who required intensive care for RSV LRTIs were young, healthy, and born at term. These findings highlight the need for RSV preventive interventions targeting all infants to reduce the burden of severe RSV illness.

Abstract Observational studies have suggested a protective role for eosinophils in colorectal cancer (CRC) development and implicated neutrophils, but the causal relationships remain unclear. Here, we aimed to estimate the causal effect of circulating white blood cell (WBC) counts (N = ~550 000) for basophils, eosinophils, monocytes, lymphocytes and neutrophils on CRC risk (N = 52 775 cases and 45 940 controls) using Mendelian randomisation (MR). For comparison, we also examined this relationship using individual‐level data from UK Biobank (4043 incident CRC cases and 332 773 controls) in a longitudinal cohort analysis. The inverse‐variance weighted (IVW) MR analysis suggested a protective effect of increased basophil count and eosinophil count on CRC risk [OR per 1‐SD increase: 0.88, 95% CI: 0.78‐0.99, P = .04; OR: 0.93, 95% CI: 0.88‐0.98, P = .01]. The protective effect of eosinophils remained [OR per 1‐SD increase: 0.88, 95% CI: 0.80‐0.97, P = .01] following adjustments for all other WBC subtypes, to account for genetic correlation between the traits, using multivariable MR. A protective effect of increased lymphocyte count on CRC risk was also found [OR: 0.84, 95% CI: 0.76‐0.93, P = 6.70e‐4] following adjustment. Consistent with MR results, a protective effect for eosinophils in the cohort analysis in the fully adjusted model [RR per 1‐SD increase: 0.96, 95% CI: 0.93‐0.99, P = .02] and following adjustment for the other WBC subtypes [RR: 0.96, 95% CI: 0.93‐0.99, P = .001] was observed. Our study implicates peripheral blood immune cells, in particular eosinophils and lymphocytes, in CRC development, highlighting a need for mechanistic studies to interrogate these relationships.

Objectives: Meniscal root tears have been shown to accelerate cartilage breakdown and increase the risk of total knee arthroplasty (TKA) if left unaddressed. Unfortunately, many patients with meniscal root tears already have associated chondromalacia which can impact surgical outcomes. The presence of advanced chondromalacia in the medial or lateral compartmentsof the knee is a known contraindication to performing meniscal root repair; however, the effect of advanced patellofemoral chondromalacia on meniscal root outcomes is not known. The purpose of this study was to compare the outcomes of meniscal root repair in patients with and without advanced patellofemoral chondromalacia (PFC). Methods: A retrospective review of prospectively collected data of patients undergoing meniscal root repair by a single surgeon was conducted between January 2016 and December 2019. Patients were included if they had undergone an isolated posterior medial or lateral meniscal root repair. The meniscal root repair was performed using a transtibial suture technique. Patients were placed into one of two groups depending on the amount of patellofemoral chondromalacia present at the time of surgery. Patients with Outerbridge grade 0-2 were placed in the Minimal Patellofemoral Chondromalacia (MPFC) Group. Patients with Outerbridge 3-4 changes found the time of surgery were placed in the Patellofemoral Chondromalacia (PFC) Group. Patients with Outerbridge 3-4 changes found in the medial or lateral compartment were excluded from the study. Lysholm Knee Scoring Scale and the International Knee Documentation (IKDC) Subjective Knee Form were collected preoperatively, 6,12 and 24 months after surgery. Clinical outcomes followed included recurrent meniscal tear, conversion to total knee arthroplasty, knee arthrofibrosis requiring manipulation under anesthesia/lysis of adhesions and infection. PASS and MCID were determined using data on meniscal repairs in other literature. Continuous data was compared using two-tailed student-T test while categorical data was compared utilizing chi-square testing. Results: A total of 27 patients made up the PFC group and 54 in the MPFC group. There was no difference between the groups with regards to age, sex, BMI or laterality of the procedure. The PFC group had 26 medial and 1 lateral meniscal root repairs. The MPFC group had 51 medial and 3 lateral repairs. The average Outerbridge score of the patella for the PFC group was 3.2 compared to 1.8 in the MPFC group (p<.001). The Outerbridge score for the trochlea in each group was 3.4 vs. 1.6 for the PFC and MPFC groups respectively (p<.001). No difference was identified between the Outerbridge score for the medial compartment for the PFC and MPFC groups (1.48 vs 1.46 respectively) or the lateral compartments (0.48 vs. 0.61 respectively). Lysholm and IKDC scores rose significantly over the pre- operative value at all time points in the study for both groups. No difference was seen between the two groups for the Lysholm or IKDC scores at any timepoint during study. PASS rates for IKDC between the two groups were similar with 6,12 and 24-month PASS rates being 66.7%, 87.5% and 81.4% respectively for the PFC group and 62.9%, 77.8% and 85.2% for the MPFC group. There was also no difference between the groups with regards to the percentage of patients reaching MCID for IKDC. The PFC group showed the percentage of patients reaching MCID to be 81.5%, 100% and 92.6% at the 6,12, and 24 month time points respectively while the MPFC group showed the percentage of patients reaching MCID to be 75.9%, 88.9% and 94.4% at the 6,12 and 24 month postoperative time points respectively. There was 1 (3.7%) recurrent tear in the PFC group and 3 (5.6%) in the MPFC group (p=.72). One patient (3.7%) in the PFC and none of the MPFC group were converted to TKA by the 2-year follow up (p=.15). Each group had 1 patient develop arthrofibrosis requiring MUA/LOA. There were no infections in the PFC group and one in the MPFC group which was a superficial wound infection that resolved after a course of oral antibiotics. Conclusions: In our series, the presence of advanced patellofemoral chondromalacia did not lead to inferior short-term outcomes in patients undergoing meniscal root repair compared to patients without patellofemoral chondromalacia. IKDC and Lysholm scores were similar between the PFC and MPFC group at all time points while scores for both groups were significantly higher than preoperative levels at all time points. The ability to reach MCID and PASS for IKDC was not significantly different between the two groups. In addition, there was not a significant difference between the two groups in the number of recurrent tears, conversion to total knee arthroplasty or complications identified. Our results show meniscal root repair can be performed in patients with severe patellofemoral chondromalacia with similar results as patients undergoing root repair without severe patellofemoral chondromalacia. Patellofemoral chondromalacia should not be considered a contraindication to meniscal root repair.

Background: Recognizing the early signs of cancer risk is vital for informing prevention, early detection, and survival. Methods: To investigate whether changes in circulating metabolites characterize the early stages of colorectal cancer (CRC) development, we examined the associations between a genetic risk score (GRS) associated with CRC liability (72 single-nucleotide polymorphisms) and 231 circulating metabolites measured by nuclear magnetic resonance spectroscopy in the Avon Longitudinal Study of Parents and Children (N = 6221). Linear regression models were applied to examine the associations between genetic liability to CRC and circulating metabolites measured in the same individuals at age 8 y, 16 y, 18 y, and 25 y. Results: The GRS for CRC was associated with up to 28% of the circulating metabolites at FDR-P < 0.05 across all time points, particularly with higher fatty acids and very-low- and low-density lipoprotein subclass lipids. Two-sample reverse Mendelian randomization (MR) analyses investigating CRC liability (52,775 cases, 45,940 controls) and metabolites measured in a random subset of UK Biobank participants (N = 118,466, median age 58 y) revealed broadly consistent effect estimates with the GRS analysis. In conventional (forward) MR analyses, genetically predicted polyunsaturated fatty acid concentrations were most strongly associated with higher CRC risk. Conclusions: These analyses suggest that higher genetic liability to CRC can cause early alterations in systemic metabolism and suggest that fatty acids may play an important role in CRC development. Funding: This work was supported by the Elizabeth Blackwell Institute for Health Research, University of Bristol, the Wellcome Trust, the Medical Research Council, Diabetes UK, the University of Bristol NIHR Biomedical Research Centre, and Cancer Research UK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. This work used the computational facilities of the Advanced Computing Research Centre, University of Bristol - http://www.bristol.ac.uk/acrc/ .