Continuous multiplexed phage genome editing using recombitrons.

Bacteriophage genome editing can enhance the efficacy of phages to eliminate pathogenic bacteria in patients and in the environment. However, current methods for editing phage genomes require laborious screening, counterselection or in vitro construction of modified genomes. Here, we present a scalable approach that uses modified bacterial retrons called recombitrons to generate recombineering donor DNA paired with single-stranded binding and annealing proteins for integration into phage genomes. This system can efficiently create genome modifications in multiple phages without the need for counterselection. The approach also supports larger insertions and deletions, which can be combined with simultaneous counterselection for >99% efficiency. Moreover, we show that the process is continuous, with more edits accumulating the longer the phage is cultured with the host, and multiplexable. We install up to five distinct mutations on a single lambda phage genome without counterselection in only a few hours of hands-on time and identify a residue-level epistatic interaction in the T7 gp17 tail fiber.

Biopsychosocial Associates of Psychological Distress and Post-Traumatic Growth among Canadian Cancer Patients during the COVID-19 Pandemic.

OBJECTIVE: Understanding both the positive and negative psychological outcomes among cancer patients during the pandemic is critical for planning post-pandemic cancer care. This study (1) examined levels of psychological distress and post-traumatic growth (PTG) among Canadian cancer patients during the COVID-19 pandemic and (2) explored variables that were associated with psychological distress and PTG during the pandemic using a biopsychosocial framework. METHOD: A cross-section survey was undertaken of patients receiving ongoing care at a regional cancer centre in Ontario, Canada, between February and December 2021. Self-reported questionnaires assessing sociodemographic information, social difficulties, psychological distress (depression, anxiety fear of recurrence, and emotional distress), PTG, illness perceptions, and behavioural responses to the pandemic were administered. Disease-related information was extracted from patient health records. RESULTS: Prevalences of moderate to severe levels of depression, anxiety, fear of recurrence and emotional distress were reported by 26.0%, 21.2%, 44.2%, and 50.0% of the sample (N = 104), respectively. Approximately 43% of the sample reported experiencing high PTG, and these positive experiences were not associated with levels of distress. Social factors, including social difficulties, being female, lower education, and unemployment status were prominent associative factors of patient distress. Perceptions of the pandemic as threatening, adopting more health safety behaviours, and not being on active treatment also increased patient likelihood to experience severe psychological distress. Younger age and adopting more health safety behaviours increased the likelihood of experiencing high PTG. The discriminatory power of the predictive models was strong, with a C-statistic > 0.80. CONCLUSIONS: Examining both the positive and negative psychological patient outcomes during the pandemic has highlighted the complex range of coping responses. Interventions that adopt a multi-pronged approach to screen and address social distress, as well as to leverage health safety behaviours, may improve the adjustments in the pandemic aftermath.

Oncologists' Satisfaction with Virtual Care: A Questionnaire.

INTRODUCTION: Although virtual care (VC) has become an integral part of oncology care and healthcare delivery, clinicians' perspectives on and satisfaction with this modality are not well understood. METHODS: Using a National Network Forum framework and expert panel review, we developed a questionnaire to measure oncologists' satisfaction with VC. The questionnaire was distributed to Canadian oncologists through medical society email lists (n = 1541). We used a 5-point Likert scale to capture their responses, which included strongly disagree (1), disagree (2), undecided (3), agree (4), and strongly agree (5). RESULTS: A total of 61 oncologists and/or oncology trainees, of 768 (7.9%) who opened their email, completed questionnaires between October 2022 and January 2023. Every questionnaire item had a response rate greater than 98%. Seventy-two percent of the respondents were satisfied with VC. Oncologists who were less comfortable with technology were more likely to report lower levels of satisfaction (p < 0.001, Wilcoxon rank-sum). The questionnaire items that received the highest levels of agreement were related to VC reducing costs and improving access for patients and concerns about missing a diagnosis and assessing patients' functional status. The questionnaire items that received the greatest disagreement were related to VC improving access for patients with language barriers, VC being associated with time-savings for clinicians, improvements in clinical efficacy, and more readily available lab tests. CONCLUSIONS: Most of the oncologists surveyed are satisfied with VC; however, there are some concerns with VC that need to be addressed. Future research on optimizing VC should address clinicians' concerns, in addition to addressing the patient experience.

Pediatric Head and Neck Dog Bites in the United States: A NEISS Database Investigation of Risk Factors and Escalation of Care.

Pediatric patients experience increased morbidity secondary to head and neck dog bites. The authors examined risk factors among pediatric head and neck dog bite patients and which factors are associated with admission to inform prevention efforts. All patients who suffered head and neck dog bites from 2013-2022 in the National Electronic Injury Surveillance System (NEISS) database were reviewed. Demographics among discharged and escalation of care (EOC) patients were compared using multinomial logistic regression (MLR), and linear regression was employed to analyze yearly emergency room (ER) visit incidence. Among 949 pediatric patients, 57.2% were male, 43.4% were 2-6 years old, and 77.7% sustained face or mouth injuries. Attacks were commonly provoked (60.5%), occurred in the home (82.3%), and involved a dog known to the patient (61.7%). The most common dog breed involved was Pitbull (33.1%). MLR revealed increased EOC among patients with neck injury (OR=11.82, SE=0.68, P<0.001), orbital injury (OR=12.91, SE=0.55, P<0.001), unprovoked attacks (OR=2.67, SE=0.16, P<0.001), and those under 2 years old (OR=1.83, SE=0.19, P=0.002). There was a significant yearly rise in the number of pediatric head and neck dog bites (model coefficient=6.467, SE=1.40, P=0.002). Overall, increased caution around particular dog breeds in households with children under 2 years old may decrease head and neck dog bite injuries. While pediatricians should perform general safety education, enhanced knowledge of risk factors is essential for proper inpatient counseling by surgical specialists.

Genome-wide association study identifies high-impact susceptibility loci for HCC in North America.

BACKGROUND AND AIMS: Despite the substantial impact of environmental factors, individuals with a family history of liver cancer have an increased risk for HCC. However, genetic factors have not been studied systematically by genome-wide approaches in large numbers of individuals from European descent populations (EDP). APPROACH AND RESULTS: We conducted a 2-stage genome-wide association study (GWAS) on HCC not affected by HBV infections. A total of 1872 HCC cases and 2907 controls were included in the discovery stage, and 1200 HCC cases and 1832 controls in the validation. We analyzed the discovery and validation samples separately and then conducted a meta-analysis. All analyses were conducted in the presence and absence of HCV. The liability-scale heritability was 24.4% for overall HCC. Five regions with significant ORs (95% CI) were identified for nonviral HCC: 3p22.1, MOBP , rs9842969, (0.51, [0.40-0.65]); 5p15.33, TERT , rs2242652, (0.70, (0.62-0.79]); 19q13.11, TM6SF2 , rs58542926, (1.49, [1.29-1.72]); 19p13.11 MAU2 , rs58489806, (1.53, (1.33-1.75]); and 22q13.31, PNPLA3 , rs738409, (1.66, [1.51-1.83]). One region was identified for HCV-induced HCC: 6p21.31, human leukocyte antigen DQ beta 1, rs9275224, (0.79, [0.74-0.84]). A combination of homozygous variants of PNPLA3 and TERT showing a 6.5-fold higher risk for nonviral-related HCC compared to individuals lacking these genotypes. This observation suggests that gene-gene interactions may identify individuals at elevated risk for developing HCC. CONCLUSIONS: Our GWAS highlights novel genetic susceptibility of nonviral HCC among European descent populations from North America with substantial heritability. Selected genetic influences were observed for HCV-positive HCC. Our findings indicate the importance of genetic susceptibility to HCC development.

Dietary L-Tryptophan consumption determines the number of colonic regulatory T cells and susceptibility to colitis via GPR15.

Environmental factors are the major contributor to the onset of immunological disorders such as ulcerative colitis. However, their identities remain unclear. Here, we discover that the amount of consumed L-Tryptophan (L-Trp), a ubiquitous dietary component, determines the transcription level of the colonic T cell homing receptor, GPR15, hence affecting the number of colonic FOXP3+ regulatory T (Treg) cells and local immune homeostasis. Ingested L-Trp is converted by host IDO1/2 enzymes, but not by gut microbiota, to compounds that induce GPR15 transcription preferentially in Treg cells via the aryl hydrocarbon receptor. Consequently, two weeks of dietary L-Trp supplementation nearly double the colonic GPR15+ Treg cells via GPR15-mediated homing and substantially reduce the future risk of colitis. In addition, humans consume 3-4 times less L-Trp per kilogram of body weight and have fewer colonic GPR15+ Treg cells than mice. Thus, we uncover a microbiota-independent mechanism linking dietary L-Trp and colonic Treg cells, that may have therapeutic potential.

The Cholangiocarcinoma in the Young (CITY) Study: Tumor Biology, Treatment Patterns, and Survival Outcomes in Adolescent Young Adults With Cholangiocarcinoma.

PURPOSE: Increased awareness of the distinct tumor biology for adolescents and young adults (AYAs) with cancer has led to improvement in outcomes for this population. However, in cholangiocarcinoma (CCA), a paucity of data exist on the AYA population. To our knowledge, we present the largest study to date on AYA disease biology, treatment patterns, and survival outcomes in CCA. METHODS: A multi-institutional cohort of patients with CCA diagnosed with intrahepatic cholangiocarcinoma (ICC) or extrahepatic cholangiocarcinoma (ECC) was used for analysis. Retrospective chart review was conducted on patients who were 50 years old and younger (young; n = 124) and older than 50 years (older; n = 723). RESULTS: Among 1,039 patients screened, 847 patients met eligibility (72% ICC, 28% ECC). Young patients had a larger median tumor size at resection compared with older patients (4.2 v 3.6 cm; P = .048), more commonly had N1 disease (65% v 43%; P = .040), and were more likely to receive adjuvant therapy (odds ratio, 4.0; 95% CI, 1.64 to 9.74). Tumors of young patients were more likely to harbor an FGFR2 fusion, BRAF mutation, or ATM mutation (P < .05 for each). Young patients were more likely to receive palliative systemic therapy (96% v 69%; P < .001), targeted therapy (23% v 8%; P < .001), and treatment on a clinical trial (31% v 19%; P = .004). Among patients who presented with advanced disease, young patients had a higher median overall survival compared with their older counterparts (17.7 v 13.5 months; 95% CI, 12.6 to 22.6 v 11.4 to 14.8; P = .049). CONCLUSION: Young patients with CCA had more advanced disease at resection, more commonly received both adjuvant and palliative therapies, and demonstrated improved survival compared with older patients. Given the low clinical trial enrollment and poor outcomes among some AYA cancer populations, data to the contrary in CCA are highly encouraging.

Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy.

Primary liver cancer is a rising cause of cancer deaths in the US. Although immunotherapy with immune checkpoint inhibitors induces a potent response in a subset of patients, response rates vary among individuals. Predicting which patients will respond to immune checkpoint inhibitors is of great interest in the field. In a retrospective arm of the National Cancer Institute Cancers of the Liver: Accelerating Research of Immunotherapy by a Transdisciplinary Network (NCI-CLARITY) study, we use archived formalin-fixed, paraffin-embedded samples to profile the transcriptome and genomic alterations among 86 hepatocellular carcinoma and cholangiocarcinoma patients prior to and following immune checkpoint inhibitor treatment. Using supervised and unsupervised approaches, we identify stable molecular subtypes linked to overall survival and distinguished by two axes of aggressive tumor biology and microenvironmental features. Moreover, molecular responses to immune checkpoint inhibitor treatment differ between subtypes. Thus, patients with heterogeneous liver cancer may be stratified by molecular status indicative of treatment response to immune checkpoint inhibitors.

Molecular profiling and treatment pattern differences between intrahepatic and extrahepatic cholangiocarcinoma.

BACKGROUND: Treatment patterns for intrahepatic cholangiocarcinoma (ICC) and extrahepatic cholangiocarcinoma (ECC) differ, but limited studies exist comparing them. This study examines differences in molecular profiling rates and treatment patterns in these populations, focusing on use of adjuvant, liver-directed, targeted, and investigational therapies. METHODS: This multicenter collaboration included patients with ICC or ECC treated at 1 of 8 participating institutions. Retrospective data were collected on risk factors, pathology, treatments, and survival. Comparative statistical tests were 2-sided. RESULTS: Among 1039 patients screened, 847 patients met eligibility (ICC = 611, ECC = 236). Patients with ECC were more likely than those with ICC to present with early stage disease (53.8% vs 28.0%), undergo surgical resection (55.1% vs 29.8%), and receive adjuvant chemoradiation (36.5% vs 4.2%) (all P < .00001). However, they were less likely to undergo molecular profiling (50.3% vs 64.3%) or receive liver-directed therapy (17.9% vs 35.7%), targeted therapy (4.7% vs 18.9%), and clinical trial therapy (10.6% vs 24.8%) (all P < .001). In patients with recurrent ECC after surgery, the molecular profiling rate was 64.5%. Patients with advanced ECC had a shorter median overall survival than those with advanced ICC (11.8 vs 15.1 months; P < .001). CONCLUSIONS: Patients with advanced ECC have low rates of molecular profiling, possibly in part because of insufficient tissue. They also have low rates of targeted therapy use and clinical trial enrollment. While these rates are higher in advanced ICC, the prognosis for both subtypes of cholangiocarcinoma remains poor, and a pressing need exists for new effective targeted therapies and broader access to clinical trials.

Continuous Multiplexed Phage Genome Editing Using Recombitrons.

Bacteriophages, which naturally shape bacterial communities, can be co-opted as a biological technology to help eliminate pathogenic bacteria from our bodies and food supply1. Phage genome editing is a critical tool to engineer more effective phage technologies. However, editing phage genomes has traditionally been a low efficiency process that requires laborious screening, counter selection, or in vitro construction of modified genomes2. These requirements impose limitations on the type and throughput of phage modifications, which in turn limit our knowledge and potential for innovation. Here, we present a scalable approach for engineering phage genomes using recombitrons: modified bacterial retrons3 that generate recombineering donor DNA paired with single stranded binding and annealing proteins to integrate those donors into phage genomes. This system can efficiently create genome modifications in multiple phages without the need for counterselection. Moreover, the process is continuous, with edits accumulating in the phage genome the longer the phage is cultured with the host, and multiplexable, with different editing hosts contributing distinct mutations along the genome of a phage in a mixed culture. In lambda phage, as an example, recombitrons yield single-base substitutions at up to 99% efficiency and up to 5 distinct mutations installed on a single phage genome, all without counterselection and only a few hours of hands-on time.