Neoadjuvant talazoparib in patients with germline BRCA1/2 mutation-positive, early-stage triple-negative breast cancer: exploration of tumor BRCA mutational status.

BACKGROUND: Talazoparib monotherapy in patients with germline BRCA-mutated, early-stage triple-negative breast cancer (TNBC) showed activity in the neoadjuvant setting in the phase II NEOTALA study (NCT03499353). These biomarker analyses further assessed the mutational landscape of the patients enrolled in the NEOTALA study. METHODS: Baseline tumor tissue from the NEOTALA study was tested retrospectively using FoundationOne®CDx. To further hypothesis-driven correlative analyses, agnostic heat-map visualizations of the FoundationOne®CDx tumor dataset were used to assess overall mutational landscape and identify additional candidate predictive biomarkers of response. RESULTS: All patients enrolled (N = 61) had TNBC. In the biomarker analysis population, 75.0% (39/52) and 25.0% (13/52) of patients exhibited BRCA1 and BRCA2 mutations, respectively. Strong concordance (97.8%) was observed between tumor BRCA and germline BRCA mutations, and 90.5% (38/42) of patients with tumor BRCA mutations evaluable for somatic-germline-zygosity were predicted to exhibit BRCA loss of heterozygosity (LOH). No patients had non-BRCA germline DNA damage response (DDR) gene variants with known/likely pathogenicity, based on a panel of 14 non-BRCA DDR genes. Ninety-eight percent of patients had TP53 mutations. Genomic LOH, assessed continuously or categorically, was not associated with response. CONCLUSION: The results from this exploratory biomarker analysis support the central role of BRCA and TP53 mutations in tumor pathobiology. Furthermore, these data support assessing germline BRCA mutational status for molecular eligibility for talazoparib in patients with TNBC.

Myeloid neoplasm with histiocytosis and spleen tyrosine kinase fusion responds to fostamatinib.

Not available.

Genomic analysis of advanced breast cancer tumors from talazoparib-treated gBRCA1/2mut carriers in the ABRAZO study.

These analyses explore the impact of homologous recombination repair gene mutations, including BRCA1/2 mutations and homologous recombination deficiency (HRD), on the efficacy of the poly(ADP-ribose) polymerase (PARP) inhibitor talazoparib in the open-label, two-cohort, Phase 2 ABRAZO trial in germline BRCA1/2-mutation carriers. In the evaluable intent-to-treat population (N = 60), 58 (97%) patients harbor ≥1 BRCA1/2 mutation(s) in tumor sequencing, with 95% (53/56) concordance between germline and tumor mutations, and 85% (40/47) of evaluable patients have BRCA locus loss of heterozygosity indicating HRD. The most prevalent non-BRCA tumor mutations are TP53 in patients with BRCA1 mutations and PIK3CA in patients with BRCA2 mutations. BRCA1- or BRCA2-mutated tumors show comparable clinical benefit within cohorts. While low patient numbers preclude correlations between HRD and efficacy, germline BRCA1/2 mutation detection from tumor-only sequencing shows high sensitivity and non-BRCA genetic/genomic events do not appear to influence talazoparib sensitivity in the ABRAZO trial.ClinicalTrials.gov identifier: NCT02034916.

Comprehensive genomic profiling and treatment patterns across ancestries in advanced prostate cancer: a large-scale retrospective analysis.

BACKGROUND: Men of African ancestry experience the greatest burden of prostate cancer globally, but they are under-represented in genomic and precision medicine studies. Therefore, we sought to characterise the genomic landscape, comprehensive genomic profiling (CGP) utilisation patterns, and treatment patterns across ancestries in a large, diverse, advanced prostate cancer cohort, to determine the impact of genomics on ancestral disparities. METHODS: In this large-scale retrospective analysis, the CGP-based genomic landscape was evaluated in biopsy sections from 11 741 patients with prostate cancer, with ancestry inferred using a single nucleotide polymorphism-based approach. Admixture-derived ancestry fractions for each patient were also interrogated. Independently, clinical and treatment information was retrospectively reviewed for 1234 patients in a de-identified US-based clinicogenomic database. Prevalence of gene alterations, including actionable gene alterations, was assessed across ancestries (n=11 741). Furthermore, real-world treatment patterns and overall survival was assessed in the subset of patients with linked clincogenomic information (n=1234). FINDINGS: The CGP cohort included 1422 (12%) men of African ancestry and 9244 (79%) men of European ancestry; the clinicogenomic database cohort included 130 (11%) men of African ancestry and 1017 (82%) men of European ancestry. Men of African ancestry received more lines of therapy before CGP than men of European ancestry (median of two lines [IQR 0-8] vs one line [0-10], p=0·029). In genomic analyses, ancestry-specific mutational landscapes were observed, but the prevalence of alterations in AR, the DNA damage response pathway, and other actionable genes were similar across ancestries. Similar genomic landscapes were observed in analyses that accounted for admixture-derived ancestry fractions. After undergoing CGP, men of African ancestry were less likely to receive a clinical study drug compared with men of European ancestry (12 [10%] of 118 vs 246 [26%] of 938, p=0·0005). INTERPRETATION: Similar rates of gene alterations with therapy implications suggest that differences in actionable genes (including AR and DNA damage response pathway genes) might not be a main driver of disparities across ancestries in advanced prostate cancer. Later CGP utilisation and a lower rate of clinical trial enrolment observed in men of African ancestry could affect genomics, outcomes, and disparities. FUNDING: American Society for Radiation Oncology, Department of Defense, Flatiron Health, Foundation Medicine, Prostate Cancer Foundation, and Sylvester Comprehensive Cancer Center.

Pan-cancer Landscape of Programmed Death Ligand-1 and Programmed Death Ligand-2 Structural Variations.

PURPOSE: Programmed cell death protein-1 (PD-1) receptor and ligand interactions are the target of immunotherapies for more than 20 cancer types. Biomarkers that predict response to immunotherapy are microsatellite instability, tumor mutational burden, and programmed death ligand-1 (PD-L1) immunohistochemistry. Structural variations (SVs) in PD-L1 (CD274) and PD-L2 (PDCD1LG2) have been observed in cancer, but the comprehensive landscape is unknown. Here, we describe the genomic landscape of PD-L1 and PD-L2 SVs, their potential impact on the tumor microenvironment, and evidence that patients with these alterations can benefit from immunotherapy. METHODS: We analyzed sequencing data from cancer cases with PD-L1 and PD-L2 SVs across 22 publications and four data sets, including Foundation Medicine Inc, The Cancer Genome Atlas, International Cancer Genome Consortium, and the Oncology Research Information Exchange Network. We leveraged RNA sequencing to evaluate immune signatures. We curated literature reporting clinical outcomes of patients harboring PD-L1 or PD-L2 SVs. RESULTS: Using data sets encompassing 300,000 tumors, we curated 486 cases with SVs in PD-L1 and PD-L2 and observed consistent breakpoint patterns, or hotspots. Leveraging The Cancer Genome Atlas, we observed significant upregulation in PD-L1 expression and signatures for interferon signaling, macrophages, T cells, and immune cell proliferation in samples harboring PD-L1 or PD-L2 SVs. Retrospective review of 12 studies that identified patients with SVs in PD-L1 or PD-L2 revealed > 50% (52/71) response rate to PD-1 immunotherapy with durable responses. CONCLUSION: Our findings show that the 3'-UTR is frequently affected, and that SVs are associated with increased expression of ligands and immune signatures. Retrospective evidence from curated studies suggests this genomic alteration could help identify candidates for PD-1/PD-L1 immunotherapy. We expect these findings will better define PD-L1 and PD-L2 SVs in cancer and lend support for prospective clinical trials to target these alterations.

HRAS Mutations Define a Distinct Subgroup in Head and Neck Squamous Cell Carcinoma.

PURPOSE: In head and neck squamous cell carcinoma (HNSCC), HRAS mutation is a new actionable oncogene driver. We aimed to evaluate HRAS mutational variants, comutation profile, and survival outcomes of this molecularly defined population. METHODS: We leveraged four deidentified patient data sets with HRAS-mutant HNSCC, MD Anderson Cancer Center, Kura Oncology, Inc trial, Foundation Medicine, and American Association for Cancer Research GENIE v.12. Patient demographic information and clinical courses were extracted, when available, in addition to HRAS mutation type and co-occurring mutations. Survival outcomes were analyzed (Kaplan-Meier method). RESULTS: Two hundred forty-nine patients with HRAS-mutant HNSCC were identified from the four data sets. Median age ranged from 55 to 65 years, with a higher frequency in male patients (64%); the majority of HRAS-mutant HNSCC occurred in human papillomavirus-negative HNSCC. HRAS mutation patterns were similar across data sets; G12S was the most common (29%). Treatment responses to tipifarnib were not codon-specific. Compared with wild-type, significantly co-occurring mutations with HRAS were Casp8 (Fisher's exact test, P < .00013), TERT (P < .0085), and NOTCH1 (P < .00013). Analysis of clinical courses from the MD Anderson Cancer Center and Kura Oncology, Inc data sets demonstrated poor clinical outcomes with a high rate of recurrence following primary definitive treatment (50%-67% relapse < 6 months) and short disease-free survival (4.0 months; 95% CI, 1.0 to 36.0) and overall survival (OS; 15.0 months; 95% CI, 6.0 to 52.0). Use of tipifarnib in this data set demonstrated improved OS (25.5 months; 95% CI, 18.0 to 48.0). CONCLUSION: Oncogenic mutations in HRAS occur in 3%-4% of HNSCC, with G12S being the most frequent. Without targeted therapy, patients with HRAS-mutant HNSCC had poor clinic outcomes; observable trend toward improvement in OS has been noted in cohorts receiving treatments such as tipifarnib. The comutation pattern of HRAS-mutant in HNSCC is distinct, which may provide insight to future therapeutic combination strategies.

Computational and Functional Analyses of HER2 Mutations Reveal Allosteric Activation Mechanisms and Altered Pharmacologic Effects.

Amplification of HER2 can drive the proliferation of cancer cells, and several inhibitors of HER2 have been successfully developed. Recent advances in next-generation sequencing now reveal that HER2 is subject to mutation, with over 2,000 unique variants observed in human cancers. Several examples of oncogenic HER2 mutations have been described, and these primarily occur at allosteric sites outside the ATP-binding site. To identify the full spectrum of oncogenic HER2 driver mutations aside from a few well-studied mutations, we developed mutation-allostery-pharmacology (MAP), an in silico prediction algorithm based on machine learning. By applying this computational approach to 820 single-nucleotide variants, a list of 222 known and potential driver mutations was produced. Of these 222 mutations, 111 were screened by Ba/F3-retrovirus proliferation assays; 37 HER2 mutations were experimentally determined to be driver mutations, comprising 15 previously characterized and 22 newly identified oncogenic mutations. These oncogenic mutations mostly affected allosteric sites in the extracellular domain (ECD), transmembrane domain, and kinase domain of HER2, with only a single mutation in the HER2 orthosteric ATP site. Covalent homodimerization was established as a common mechanism of activation among HER2 ECD allosteric mutations, including the most prevalent HER2 mutation, S310F. Furthermore, HER2 allosteric mutants with enhanced covalent homodimerization were characterized by altered pharmacology that reduces the activity of existing anti-HER2 agents, including the mAb trastuzumab and the tyrosine kinase inhibitor lapatinib. Overall, the MAP-scoring and functional validation analyses provided new insights into the oncogenic activity and therapeutic targeting of HER2 mutations in cancer. SIGNIFICANCE: This study identified new oncogenic HER2 allosteric mutations, including ECD mutations that share covalent dimerization as a mechanism of oncogenicity, suggesting the need for novel inhibitors to treat HER2-mutant cancers.

Are Undergraduates Familiar with Nephrology as a Medical Specialty? A Single Site Survey of Undergraduate Students.

Background: Over the past decade, nephrology has experienced a 43% decline in the number of fellowship applicants. Previous studies examining why residents choose a fellowship program cite lack of exposure as a main factor having an effect against a career in nephrology; however, no studies have surveyed the undergraduate population to inquire whether they recognize nephrology as a medical specialty compared with other medical specialties. We conducted a survey at a primarily undergraduate institution in the Southeast United States to test whether undergraduate students identified the word "nephrology." Methods: A total of 274 undergraduates responded to a survey that requested them to select every medical specialty that they recognized by name (15 real specialties and one fictitious specialty). Demographics regarding sex, race, collegiate level, high school location, premedical track, and household income were collected. Correlations between survey findings and rates of application and average salary per specialty were assessed. Results: Out of 15 medical specialties, nephrology (29%) and pulmonology (40%) were the least recognized. Pediatrics (97%) and surgery (97%) ranked highest. Sex, race, collegiate level, and household income were not different between those students who recognized "nephrology" and those who did not. Premedical students were about twice as likely to have recognized nephrology versus nonpremedical students (49% versus 22%, respectively; P<0.001). STEM majors were about twice as likely to identify nephrology versus non-STEM majors (40% versus 20%, respectively; P<0.001). The proportion of undergraduate students who recognized a specific medical specialty significantly correlated only with the number of US applicants per fellowship position across different medical specialties in 2020 (P<0.05). Conclusions: On the basis of word association alone, nephrology is the one of the least recognized specialties by undergraduates. The discrepancy between nephrology and other specialties highlights a gap in name recognition at an early career stage, even among premedical students.

Molecular Characterization of Mesothelioma: Impact of Histologic Type and Site of Origin on Molecular Landscape.

PURPOSE: Mesothelioma is an aggressive malignancy with heterogeneous outcomes that are partly driven by the differential efficacy of existing therapies across histologic types and sites of origin. Large-scale molecular analysis of mesothelioma and its subtypes has the potential to inform future therapeutic strategies. MATERIALS AND METHODS: We analyzed 1,294 mesotheliomas {980 pleural (malignant pleural mesothelioma [MPM]) and 314 peritoneal (malignant peritoneal mesothelioma [MPeM])} using next-generation sequencing, determined programmed death ligand-1 (PD-L1) expression and histology in a subset of cases, and assessed MTAP/CDKN2A copy-number status by fluorescence in situ hybridization and T-cell infiltration in an independent cohort. RESULTS: The molecular landscape of MPM was characterized by inactivating alterations in CDKN2A (49%), BAP1 (44%), CDKN2B (42%), MTAP (34%), and NF2 (33%). Compared with epithelioid MPM, nonepithelioid (ie, biphasic and sarcomatoid) MPM had identical tumor mutational burden (median 1.25 mut/Mb, P = .63), more commonly expressed PD-L1 (74% v 51%, P = .02), and was more likely to harbor MTAP, CDKN2A, and CDKN2B copy loss (P < .05). Fluorescence in situ hybridization confirmed that homozygous MTAP loss was enriched in nonepithelioid MPM. Relative to MPM, MPeM had comparable tumor mutational burden and PD-L1 expression. The molecular profile of MPeM was similar to MPM, with the distinction that PBRM1 alterations occurred at higher frequency (16% v 7%, P < .01). ALK rearrangements were only observed in MPeM. CONCLUSION: Regardless of histology and location, the molecular landscape of mesothelioma primarily consists of inactivating alterations in tumor suppressor genes, with enrichment of certain alterations in distinct subsets (eg, MTAP loss in nonepithelioid tumors). Given the limited efficacy of current therapies for this disease, novel approaches targeting recurring alterations should be explored.

A pan-cancer landscape of telomeric content shows that RAD21 and HGF alterations are associated with longer telomeres.

BACKGROUND: Cancer cells can proliferate indefinitely through telomere maintenance mechanisms. These mechanisms include telomerase-dependent elongation, mediated by TERT activation, and alternative lengthening of telomeres (ALT), linked to loss of ATRX or DAXX. METHODS: We analyzed the telomeric content of 89,959 tumor samples within the Foundation Medicine dataset and investigated the genomic determinants of high telomeric content, linking them to clinical outcomes, when available. RESULTS: Telomeric content varied widely by disease type with leiomyosarcoma having the highest and Merkel cell carcinoma having the lowest telomeric content. In agreement with previous studies, telomeric content was significantly higher in samples with alterations in TERC, ATRX, and DAXX. We further identified that amplifications in two genes, RAD21 and HGF, were enriched in samples with high telomeric content, which was confirmed using the PCAWG/ICGC dataset. We identified the minimal amplified region associated with high telomeric content for RAD21 (8q23.1-8q24.12), which excludes MYC, and for HGF (7q21.11). Our results demonstrated that RAD21 and HGF exerted an additive telomere lengthening effect on samples with existing alterations in canonical genes previously associated with telomere elongation. Furthermore, patients with breast cancer who harbor RAD21 alterations had poor median overall survival and trended towards higher levels of Ki-67 staining. CONCLUSIONS: This study highlights the importance of the role played by RAD21 (8q23.1-8q24.12) and HGF (7q21.11) in the lengthening of telomeres, supporting unlimited replication in tumors. These findings open avenues for work aimed at targeting this crucial pathway in tumorigenesis.

TreeTuner: A pipeline for minimizing redundancy and complexity in large phylogenetic datasets.

Various bioinformatics protocols have been developed for trimming the number of operational taxonomic units (OTUs) in phylogenetic datasets, but they typically require significant manual intervention. Here we present TreeTuner, a semiautomated pipeline that allows both coarse and fine-scale tuning of large protein sequence phylogenetic datasets via the minimization of OTU redundancy. TreeTuner facilitates preliminary investigation of such datasets as well as more rigorous downstream analysis of specific subsets of OTUs. For complete details on the use and execution of this protocol, please refer to Maruyama et al. (2013) and Sibbald et al. (2019).

Determinants of Response to Talazoparib in Patients with HER2-Negative, Germline BRCA1/2-Mutated Breast Cancer.

PURPOSE: PARP inhibitors (PARPi) have demonstrated efficacy in tumors with germline breast cancer susceptibility genes (gBRCA) 1 and 2 mutations, but further factors influencing response to PARPi are poorly understood. EXPERIMENTAL DESIGN: Breast cancer tumor tissue from patients with gBRCA1/2 mutations from the phase III EMBRACA trial of the PARPi talazoparib versus chemotherapy was sequenced using FoundationOne CDx. RESULTS: In the evaluable intent-to-treat population, 96.1% (296/308) had ≥1 tumor BRCA (tBRCA) mutation and there was strong concordance (95.3%) between tBRCA and gBRCA mutational status. Genetic/genomic characteristics including BRCA loss of heterozygosity (LOH; identified in 82.6% of evaluable patients), DNA damage response (DDR) gene mutational burden, and tumor homologous recombination deficiency [assessed by genomic LOH (gLOH)] demonstrated no association with talazoparib efficacy. CONCLUSIONS: Overall, BRCA LOH status, DDR gene mutational burden, and gLOH were not associated with talazoparib efficacy; however, these conclusions are qualified by population heterogeneity and low patient numbers in some subgroups. Further investigation in larger patient populations is warranted.

Avoidant/restrictive food intake disorder and autism spectrum disorder: clinical implications for assessment and management.

AIM: We examined clinical and neurodevelopmental presentations of children with avoidant/restrictive food intake disorder (ARFID) to inform clinical assessment and management. METHOD: Five hundred and thirty-six patients (mean age 6y 10mo, SD 3y 5mo, range 10mo-20y; 401 males, 135 females) seen by the tertiary multidisciplinary feeding service at the Evelina London Children's Hospital between January 2013 and June 2019 were included in this case-control study. These children experienced significant feeding difficulties impacting nutrition, development, and psychosocial functioning requiring tertiary specialized input. Data on ARFID diagnosis, demographics, comorbidity, and nutrition was extracted from electronic patient records. RESULTS: Forty-nine per cent of children met ARFID criteria. The remaining participants had other difficulties including feeding, medical, and/or neurodevelopmental conditions. ARFID is more prevalent among younger patients (4-9 years) and in children with comorbid autism spectrum disorder (ASD). Younger age, comorbid ASD, and male sex significantly predicted ARFID. Diet range and male sex significantly predicted nutritional inadequacy, while comorbid ASD did not. A trend was seen between younger age and nutritional inadequacy. INTERPRETATION: Young children with ARFID should raise suspicion for ASD. Although significant nutritional deficiencies are common in children with comorbid ARFID and ASD, they are correctable with nutritional supplementation. Specialty perspective potentially limits generalizability of findings to community feeding services. We also emphasize the importance of early identification of nutritional deficits and management.

Monitor gastrointestinal tolerance in children who have switched to an "enteral formula with food-derived ingredients": A national, multicenter retrospective chart review (RICIMIX study).

BACKGROUND: Enteral tube feeding intolerances, such as diarrhea, are commonly reported in children. In the pediatric population, interest is growing in the use of blended diets for the management of enteral feeding intolerances. Fiber within a blended diet stimulates the growth of beneficial gut bacteria, which in turn produce short-chain fatty acids, which are utilized as energy substrates for enterocytes. Enteral formula manufacturers have responded to this trend towards "real-food" blended diets and developed an enteral formula with food-derived ingredients. The aim of this study was to collect data relating to feed tolerance in children who had switched to an "enteral formula with food-derived ingredients." METHODS: A national multicenter retrospective study. RESULTS: Dietitians collected data from 43 medically unwell children between March 2021 and July 2021. Significant improvements were reported in children who had switched to an "enteral formula with food-derived ingredients" in retching 17 of 18 children (95%), flatulence 6 of 8 children (85%), loose stools 10 of 11 children (90%), and constipation 10 of 11 children (90%). These improvements in gastrointestinal symptoms were reflected in weight change during the one month period measurements were collected (baseline, 19.5 kg [SD, 9]; 1 month, 20.1 kg [SD, 9]; P = 0.002). CONCLUSION: We have observed beneficial outcomes in medically complex children who have switched to an "enteral formula with food-derived ingredients." Our data should motivate healthcare professionals to implement more research to better evaluate the clinical impact and mechanisms of action of blended diets and enteral formulas with food-derived ingredients.

Action learning sets for supporting postgraduate mental health nurses' transition to professional practice: A qualitative study.

This paper reports on a qualitative case study of postgraduate mental health nurses participating in a monthly facilitated action learning set (ALS) in order to support them while they transition from PGMHN to independent professional practice. The aim of the study was to determine what the impact of participating in an ALS would have on how they perceived clinical practice issues. The ALS comprised a small group of PGMHN supported by a facilitator in order to explore issues from clinical practice by using Socratic questions to challenge their thinking. Data were collected via a single focus group and a 20-item survey. Focus group textual data were coded line by line, and codes were synthesized thematically. The major theme to emerge from the qualitative results was as follows: 'Learning from doing an action learning set'. Three subthemes were identified: Think outside the box: Developing Socratic questions; there's rarely one right way: Applying action learning to practice; and Not easy to implement: Action plans in action. A 20-item evaluative survey indicated that ALS increased participant's confidence as a mental health nurse. Using critical questions increased participants' confidence to explore different perspectives when engaged in problem-solving.

Prospective evaluation of a novel enteral feeding guideline based on individual gastric emptying times: an improvement project in a pediatric intensive care unit.

BACKGROUND: On a 20-bed, mixed cardiac and general, UK pediatric intensive care unit (PICU), we aimed to determine if a physiologically based enteral feeding guideline for critically ill children, using feed frequency tailored to individual gastric emptying times, resulted in earlier establishment of full feeds (when 100% of fluid allowance (FA) available to be given as intravenous maintenance fluid or feed, defined as free FA [FFA], is given as enteral nutrition [EN]) and an increase in FFA given as EN. METHODS: Four prospective audits (totaling 331 patients and 19,771 hours) were conducted at 1 year before guideline introduction and 1, 5, and 10 years after. Patient feeding data were collected from admission until day 4 or discharge, including reasons why feed was withheld. RESULTS: The median time from admission to establishing full feeds decreased from 18 to 10 hours preguideline and postguideline and was sustained over 10 years. After adjustment for 5 confounders, this represented a reduction in the geometric mean time to full feeds of 30% (2009), 29% (2013), and 48% (2019) compared with 2007 (all P < .01). Nil-per-oral (NPO) hours were categorized as due to modifiable and nonmodifiable factors. Preguideline and postguideline NPO hours from modifiable factors decreased from 21 (2007) to 10 (2009) per 100 audit hours, which was sustained across 10 years (all P < .01). Conversely, NPO hours from nonmodifiable factors ranged from 27 to 36 per 100 audit hours throughout the audits, with no consistent trend over time. Similar inconsistency was shown in the proportion of FFA given as EN: 48% (2007), 71% (2009), 51% (2013), and 64% (2019). Continuous nasogastric and hourly bolus feeds decreased over time; they comprised 66% of feeds in 2007 but only 4%-11% in subsequent periods, being replaced with more 2-6 hour bolus, on-demand, or continuous nasojejunal feeds. CONCLUSION: The guideline was associated with sustained reduction in the time to establishing full feeds and NPO hours due to modifiable factors and more or no less FFA being given as EN.

Pan-cancer analysis of the effect of biopsy site on tumor mutational burden observations.

Background: Tumor mutational burden (TMB) has been proposed as a predictive biomarker of response to immunotherapy. Efforts to standardize TMB scores for use in the clinic and to identify the factors that could impact TMB scores are of high importance. However, the biopsy collection site has not been assessed as a factor that may influence TMB scores. Methods: We examine a real-world cohort comprising 137,771 specimens across 47 tissues in 12 indications profiled by the FoundationOne assay (Foundation Medicine, Cambridge, MA) to assess the prevalence of biopsy sites for each indication and their TMB scores distribution. Results: We observe a wide variety of biopsy sites from which specimens are sent for genomic testing and show that TMB scores differ in a cancer- and tissue-specific manner. For example, brain or adrenal gland specimens from NSCLC patients show higher TMB scores than local lung specimens (mean difference 3.31 mut/Mb; p < 0.01, 3.90 mut/Mb; p < 0.01, respectively), whereas bone specimens show no difference. Conclusions: Our data shed light on the biopsied tissue as a driver of TMB measurement variability in clinical practice.

Preharvest Detection and Postharvest Incidence of Phlyctema vagabunda on 'Cripps Pink' Apples in South Africa.

Phlyctema vagabunda is responsible for significant postharvest losses in 'Cripps Pink' apples in South Africa. The first objective of this study was to determine the presence and incidence of P. vagabunda on stored commercial 'Cripps Pink' apple in five major pome fruit growing regions in the Western Cape. As the fungus remains latent until postharvest, the second objective was to develop a rapid molecular detection tool to determine the presence of P. vagabunda on asymptomatic 'Cripps Pink' apples from two commercial orchards. Postharvest disease incidence in 'Cripps Pink' apples in the Western Cape ranged from 0 to 73% in the 2010/2011, 0 to 6% in 2011/2012, and 0 to 30% in 2012/2013 seasons. P. vagabunda spores were also detected on 'Cripps Pink' fruit from December to February and from March to April. In December and January, P. vagabunda spores were detected on the 'Hillieri' crab apple pollinator. The knowledge that P. vagabunda conidia are present on the surface of 'Cripps Pink' apples and 'Hillieri' crab apples during the growing season could be applied to improving current management practices in the orchards.

Ubiquitin fusion proteins in algae: implications for cell biology and the spread of photosynthesis.

BACKGROUND: The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protein products can evolve new functions. The presence-absence of gene fusions can also be useful characters for inferring evolutionary relationships between organisms. RESULTS: Here we show that the nuclear genomes of two unrelated single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans, possess an unexpected diversity of genes for ubiquitin fusion proteins, including novel arrangements in which ubiquitin occupies amino-terminal, carboxyl-terminal, and internal positions relative to its fusion partners. We explore the evolution of the ubiquitin multigene family in both genomes, and show that both algae possess a gene encoding an ubiquitin-nickel superoxide dismutase fusion protein (Ubiq-NiSOD) that is widely but patchily distributed across the eukaryotic tree of life - almost exclusively in phototrophs. CONCLUSION: Our results suggest that ubiquitin fusion proteins are more common than currently appreciated; because of its small size, the ubiquitin coding region can go undetected when gene predictions are carried out in an automated fashion. The punctate distribution of the Ubiq-NiSOD fusion across the eukaryotic tree could serve as a beacon for the spread of plastids from eukaryote to eukaryote by secondary and/or tertiary endosymbiosis.

Mutations in Mitochondrial DNA From Pancreatic Ductal Adenocarcinomas Associate With Survival Times of Patients and Accumulate as Tumors Progress.

Somatic mutations have been found in the mitochondria in different types of cancer cells, but it is not clear whether these affect tumorigenesis or tumor progression. We analyzed mitochondrial genomes of 268 early-stage, resected pancreatic ductal adenocarcinoma tissues and paired non-tumor tissues. We defined a mitochondrial somatic mutation (mtSNV) as a position where the difference in heteroplasmy fraction between tumor and normal sample was ≥0.2. Our analysis identified 304 mtSNVs, with at least 1 mtSNV in 61% (164 of 268) of tumor samples. The noncoding control region had the greatest proportion of mtSNVs (60 of 304 mutations); this region contains sites that regulate mitochondrial DNA transcription and replication. Frequently mutated genes included ND5, RNR2, and CO1, plus 29 mutations in transfer RNA genes. mtSNVs in 2 separate mitochondrial genes (ND4 and ND6) were associated with shorter overall survival time. This association appeared to depend on the level of mtSNV heteroplasmy. Non-random co-occurrence between mtSNVs and mutations in nuclear genes indicates interactions between nuclear and mitochondrial DNA. In an analysis of primary tumors and metastases from 6 patients, we found tumors to accumulate mitochondrial mutational mutations as they progress.