Germline genetic variation and predicting immune checkpoint inhibitor induced toxicity

Immune checkpoint inhibitor (ICI) therapy has revolutionised the treatment of various cancer types. ICIs reinstate T-cell function to elicit an anti-cancer immune response. The resulting immune response can however have off-target effects which manifest as autoimmune type serious immune-related adverse events (irAE) in ~10–55% of patients treated. It is currently challenging to predict both who will experience irAEs and to what severity. Identification of patients at high risk of serious irAE would revolutionise patient care. While the pathogenesis driving irAE development is still unclear, host genetic factors are proposed to be key determinants of these events. This review presents current evidence supporting the role of the host genome in determining risk of irAE. We summarise the spectrum and timing of irAEs following treatment with ICIs and describe currently reported germline genetic variation associated with expression of immuno-modulatory factors within the cancer immunity cycle, development of autoimmune disease and irAE occurrence. We propose that germline genetic determinants of host immune function and autoimmune diseases could also explain risk of irAE development. We also endorse genome-wide association studies of patients being treated with ICIs to identify genetic variants that can be used in polygenic risk scores to predict risk of irAE

Common Variants in the Glycerol Kinase Gene Reduce Tuberculosis Drug Efficacy

Despite the administration of multiple drugs that are highly effective in vitro, tuberculosis (TB) treatment requires prolonged drug administration and is confounded by the emergence of drug-resistant strains. To understand the mechanisms that limit antibiotic efficacy, we performed a comprehensive genetic study to identify Mycobacterium tuberculosis genes that alter the rate of bacterial clearance in drug-treated mice. Several functionally distinct bacterial genes were found to alter bacterial clearance, and prominent among these was the glpK gene that encodes the glycerol-3-kinase enzyme that is necessary for glycerol catabolism. Growth on glycerol generally increased the sensitivity of M. tuberculosis to antibiotics in vitro, and glpK-deficient bacteria persisted during antibiotic treatment in vivo, particularly during exposure to pyrazinamide-containing regimens. Frameshift mutations in a hypervariable homopolymeric region of the glpK gene were found to be a specific marker of multidrug resistance in clinical M. tuberculosis isolates, and these loss-of-function alleles were also enriched in extensively drug-resistant clones. These data indicate that frequently observed variation in the glpK coding sequence produces a drug-tolerant phenotype that can reduce antibiotic efficacy and may contribute to the evolution of resistance. IMPORTANCE: TB control is limited in part by the length of antibiotic treatment needed to prevent recurrent disease. To probe mechanisms underlying survival under antibiotic pressure, we performed a genetic screen for M. tuberculosis mutants with altered susceptibility to treatment using the mouse model of TB. We identified multiple genes involved in a range of functions which alter sensitivity to antibiotics. In particular, we found glycerol catabolism mutants were less susceptible to treatment and that common variation in a homopolymeric region in the glpK gene was associated with drug resistance in clinical isolates. These studies indicate that reversible high-frequency variation in carbon metabolic pathways can produce phenotypically drug-tolerant clones and have a role in the development of resistance

Mortality Among Adults With Cancer Undergoing Chemotherapy or Immunotherapy and Infected With COVID-19

Importance: Large cohorts of patients with active cancers and COVID-19 infection are needed to provide evidence of the association of recent cancer treatment and cancer type with COVID-19 mortality. // Objective: To evaluate whether systemic anticancer treatments (SACTs), tumor subtypes, patient demographic characteristics (age and sex), and comorbidities are associated with COVID-19 mortality. // Design, Setting, and Participants: The UK Coronavirus Cancer Monitoring Project (UKCCMP) is a prospective cohort study conducted at 69 UK cancer hospitals among adult patients (≥18 years) with an active cancer and a clinical diagnosis of COVID-19. Patients registered from March 18 to August 1, 2020, were included in this analysis. // Exposures: SACT, tumor subtype, patient demographic characteristics (eg, age, sex, body mass index, race and ethnicity, smoking history), and comorbidities were investigated. // Main Outcomes and Measures: The primary end point was all-cause mortality within the primary hospitalization. // Results: Overall, 2515 of 2786 patients registered during the study period were included; 1464 (58%) were men; and the median (IQR) age was 72 (62-80) years. The mortality rate was 38% (966 patients). The data suggest an association between higher mortality in patients with hematological malignant neoplasms irrespective of recent SACT, particularly in those with acute leukemias or myelodysplastic syndrome (OR, 2.16; 95% CI, 1.30-3.60) and myeloma or plasmacytoma (OR, 1.53; 95% CI, 1.04-2.26). Lung cancer was also significantly associated with higher COVID-19–related mortality (OR, 1.58; 95% CI, 1.11-2.25). No association between higher mortality and receiving chemotherapy in the 4 weeks before COVID-19 diagnosis was observed after correcting for the crucial confounders of age, sex, and comorbidities. An association between lower mortality and receiving immunotherapy in the 4 weeks before COVID-19 diagnosis was observed (immunotherapy vs no cancer therapy: OR, 0.52; 95% CI, 0.31-0.86). // Conclusions and Relevance: The findings of this study of patients with active cancer suggest that recent SACT is not associated with inferior outcomes from COVID-19 infection. This has relevance for the care of patients with cancer requiring treatment, particularly in countries experiencing an increase in COVID-19 case numbers. Important differences in outcomes among patients with hematological and lung cancers were observed

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Functional Outcomes After Upper Extremity Surgery for Cerebral Palsy: Comparison of High and Low Manual Ability Classification System Levels

Purpose The heterogeneity of cerebral palsy makes interpretation and prediction of outcome after upper extremity surgery difficult. We hypothesized that the outcome of upper extremity surgery for cerebral palsy is related to the Manual Ability Classification System (MACS) level. Methods We reviewed 27 patients with a mean age of 22 years, who underwent upper extremity surgery for spastic cerebral palsy at a mean follow-up of 29 months. Patients were classified into 5 MACS levels using a standardized questionnaire completed by their primary caregivers. Preoperatively and at most recent follow-up visits, patients were assessed using the House scale and patient-reported functional outcomes on a 5-point scale. We compared the outcomes of patients with high (I-II, independence in daily activities) and low (III-V, dependence in daily activities) MACS levels. Results The overall mean House scale improved from 2.9 to 4.6 postoperatively (p<.001), dressing ability from 3.7 to 4.2 (p=.005), hygiene from 4.2 to 4.9 (p=.005), and appearance from 2.4 to 4.2 (p<.001). A total of 13 patients had a high MACS level (7 had I and 6 had II) and 14 had a low MACS level (8 had III, 6 had IV, and none had V). The high-MACS group had a greater improvement according to the House scale (p=.009) and the low-MACS group had a larger improvement in hygiene status (p=.043). There were no differences in the amount of improvement in dressing ability (p=.169) and appearance (p=.765). Overall satisfaction with surgery was higher for the high-MACS group (p=.038). Conclusions The high-MACS group had a greater improvement in rating according to the House scale and higher satisfaction than the low-MACS group after upper extremity surgery for cerebral palsy in our small number of patients. This study suggests that the MACS level can be used to predict upper extremity surgery outcomes for cerebral palsy. (J Hand Surg 2010;35A:277-283. Copyright (C) 2010 by the American Society for Surgery of the Hand. All rights reserved.)N

Relationships between isometric muscle strength, gait parameters, and gross motor function measure in patients with cerebral palsy

Purpose: This study investigated the correlation between isometric muscle strength, gross motor function, and gait parameters in patients with spastic cerebral palsy and to find which muscle groups play an important role for gait pattern in a flexed knee gait. Materials and Methods: Twenty-four ambulatory patients (mean age, 10.0 years) with spastic cerebral palsy who were scheduled for single event multilevel surgery, including distal hamstring lengthening, were included. Preoperatively, peak isometric muscle strength was measured for the hip flexor, hip extensor, knee flexor, and knee extensor muscle groups using a handheld dynamometer, and three-dimensional (3D) gait analysis and gross motor function measure (GMFM) scoring were also performed. Correlations between peak isometric strength and GMFM, gait kinematics, and gait kinetics were analyzed. Results: Peak isometric muscle strength of all muscle groups was not related to the GMFM score and the gross motor function classification system level. Peak isometric strength of the hip extensor and knee extensor was significantly correlated with the mean pelvic tilt (r=-0.588, p=0.003 and r=-0.436, p=0.033) and maximum pelvic obliquity (r=-0.450, p=0.031 and r=-0.419, p=0.041). There were significant correlations between peak isometric strength of the knee extensor and peak la-lee extensor moment in early stance (r=0.467, p=0.021) and in terminal stance (r=0.416, p=0.043). Conclusion: There is no correlation between muscle strength and gross motor function. However, this study showed that muscle strength, especially of the extensor muscle group of the hip and knee joints, might play a critical role in gait by stabilizing pelvic motion and decreasing energy consumption in a flexed knee gait.Y