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Immunotherapy is used to treat almost all patients with advanced non-small cell lung cancer (NSCLC); however, identifying robust predictive biomarkers remains challenging. Here we show the predictive capacity of integrating medical imaging, histopathologic and genomic features to predict immunotherapy response using a cohort of 247 patients with advanced NSCLC with multimodal baseline data obtained during diagnostic clinical workup, including computed tomography scan images, digitized programmed death ligand-1 immunohistochemistry slides and known outcomes to immunotherapy. Using domain expert annotations, we developed a computational workflow to extract patient-level features and used a machine-learning approach to integrate multimodal features into a risk prediction model. Our multimodal model (area under the curve (AUC) = 0.80, 95% confidence interval (CI) 0.74–0.86) outperformed unimodal measures, including tumor mutational burden (AUC = 0.61, 95% CI 0.52–0.70) and programmed death ligand-1 immunohistochemistry score (AUC = 0.73, 95% CI 0.65–0.81). Our study therefore provides a quantitative rationale for using multimodal features to improve prediction of immunotherapy response in patients with NSCLC using expert-guided machine learning.

Additional results for dual probe EGFR and ERBB2 FISH from Patients 9, 30 and 32.

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Human cancers arise from environmental, heritable and somatic factors, but how these mechanisms interact in tumorigenesis is poorly understood. Studying 17,152 prospectively sequenced patients with cancer, we identified pathogenic germline variants in cancer predisposition genes, and assessed their zygosity and co-occurring somatic alterations in the concomitant tumors. Two major routes to tumorigenesis were apparent. In carriers of pathogenic germline variants in high-penetrance genes (5.1% overall), lineage-dependent patterns of biallelic inactivation led to tumors exhibiting mechanism-specific somatic phenotypes and fewer additional somatic oncogenic drivers. Nevertheless, 27% of cancers in these patients, and most tumors in patients with pathogenic germline variants in lower-penetrance genes, lacked particular hallmarks of tumorigenesis associated with the germline allele. The dependence of tumors on pathogenic germline variants is variable and often dictated by both penetrance and lineage, a finding with implications for clinical management. A study of 17,152 patients with cancer identified pathogenic germline variants in cancer predisposition genes. Although tumors showed biallelic inactivation for high-penetrance genes, this was not the case in most patients with pathogenic variants in low-penetrance genes, suggesting alternative routes to tumorigenesis.

BACKGROUND: Patterns of metastasis in cancer are increasingly relevant to prognostication and treatment planning but have historically been documented by means of autopsy series. PURPOSE: To show the feasibility of using natural language processing (NLP) to gather accurate data from radiology reports for assessing spatial and temporal patterns of metastatic spread in a large patient cohort. MATERIALS AND METHODS: In this retrospective longitudinal study, consecutive patients who underwent CT from July 2009 to April 2019 and whose CT reports followed a departmental structured template were included. Three radiologists manually curated a sample of 2219 reports for the presence or absence of metastases across 13 organs; these manually curated reports were used to develop three NLP models with an 80%-20% split for training and test sets. A separate random sample of 448 manually curated reports was used for validation. Model performance was measured by accuracy, precision, and recall for each organ. The best-performing NLP model was used to generate a final database of metastatic disease across all patients. For each cancer type, statistical descriptive reports were provided by analyzing the frequencies of metastatic disease at the report and patient levels. RESULTS: In 91 665 patients (mean age ± standard deviation, 61 years ± 15; 46 939 women), 387 359 reports were labeled. The best-performing NLP model achieved accuracies from 90% to 99% across all organs. Metastases were most frequently reported in abdominopelvic (23.6% of all reports) and thoracic (17.6%) nodes, followed by lungs (14.7%), liver (13.7%), and bones (9.9%). Metastatic disease tropism is distinct among common cancers, with the most common first site being bones in prostate and breast cancers and liver among pancreatic and colorectal cancers. CONCLUSION: Natural language processing may be applied to cancer patients’ CT reports to generate a large database of metastatic phenotypes. Such a database could be combined with genomic studies and used to explore prognostic imaging phenotypes with relevance to treatment planning. © RSNA, 2021 Online supplemental material is available for this article.

Mucinous carcinomas can arise in any organ with epithelial cells that produce mucus. While mucinous tumors from different organs are histologically similar, it remains to be elucidated whether they share molecular alterations. Here we analyzed a total of 902 patients across six cancer types by comparing mucinous and non-mucinous samples, integrating text mining of pathology reports, gene expression, methylation, mutational and copy-number profiling. We found that, in addition to genes involved in mucin processing and secretion, MUC2 up-regulation is a multi-cancer biomarker of mucinous histology and is regulated by DNA methylation in colorectal, breast and stomach cancer. The majority of carcinomas with mucinous differentiation had fewer DNA copy-number alterations than non-mucinous tumors. The tumor mutational burden was lower in breast and lung with mucinous differentiation compared to their non-mucinous counterparts. We found several differences in the frequency of oncogenic gene and pathway alterations between mucinous and non-mucinous carcinomas, including a lower frequency of p53 pathway alterations in colorectal and lung cancer, and a lower frequency of PI-3-Kinase/Akt pathway alterations in breast and stomach cancer with mucinous differentiation. This study shows that carcinomas with mucinous differentiation originating from different organs share transcriptomic and genomic similarities. These results might pave the way for a more biologically relevant taxonomy for these rare cancers., info:eu-repo/semantics/published

Stably acquired mutations in hematopoietic cells represent substrates of selection that may lead to clonal hematopoiesis (CH), a common state in cancer patients that is associated with a heightened risk of leukemia development. Owing to technical and sample size limitations, most CH studies have characterized gene mutations or mosaic chromosomal alterations (mCAs) individually. Here we leverage peripheral blood sequencing data from 32,442 cancer patients to jointly characterize gene mutations (n = 14,789) and mCAs (n = 383) in CH. Recurrent composite genotypes resembling known genetic interactions in leukemia genomes underlie 23% of all detected autosomal alterations, indicating that these selection mechanisms are operative early in clonal evolution. CH with composite genotypes defines a patient group at high risk of leukemia progression (3-year cumulative incidence 14.6%, CI: 7–22%). Multivariable analysis identifies mCA as an independent risk factor for leukemia development (HR = 14, 95% CI: 6–33, P, Patients with solid cancers have high rates of clonal haematopoiesis associated with increased risk of secondary leukemias. Here, by using peripheral blood sequencing data from patients with solid non-hematologic cancer, the authors profile the landscape of mosaic chromosomal alterations and gene mutations, defining patients at high risk of leukemia progression.

There is conflicting data regarding the role of PBAF complex mutations and response to immune checkpoint blockade (ICB) therapy in clear cell renal cell carcinoma (ccRCC) and other solid tumors. We assess the prevalence of PBAF complex mutations from two large cohorts including the pan-cancer TCGA project (n = 10,359) and the MSK-IMPACT pan-cancer immunotherapy cohort (n = 3700). Across both cohorts, PBAF complex mutations, predominantly PBRM1 mutations, are most common in ccRCC. In multivariate models of ccRCC patients treated with ICB (n = 189), loss-of-function (LOF) mutations in PBRM1 are not associated with overall survival (OS) (HR = 1.24, p = 0.47) or time to treatment failure (HR = 0.85, p = 0.44). In a series of 11 solid tumors (n = 2936), LOF mutations are not associated with improved OS in a stratified multivariate model (HR = 0.9, p = 0.7). In a current series of solid tumors treated with ICB, we are unable to demonstrate favorable response to ICB in patients with PBAF complex mutations. The clinical benefit from immunotherapy response in patients with mutations of genes forming the chromatin remodelling complex PBAF remains controversial. Here the authors show that PBAF complex mutations are not associated with favourable response in pan-cancer cohorts of patients treated with immune-checkpoint blockade.

Compared with previous standards of care, the use of immune checkpoint inhibitors (ICI) has brought significant improvements in survival and quality of life for lung cancer patients. However, only a small proportion of these patients respond durably. People with different ancestries differ probabilistically in genetic factors, environmental exposures, and socio-economic conditions. Whether patients of different ancestry benefit equally from ICIs remains unclear. We studied the impact of genomic ancestry, tumor genomics, and social determinants of health (SDH) factors and factors that are impacted from SDH including recorded race/ethnicity, inferred low-income status from patient zip codes, exposure to smoking, and BMI on ICI response, defined by cancer progression-free survival (PFS, minimum 6 months FU), for non-small cell lung cancer (NSCLC) patients with MSK-IMPACT targeted panel sequencing. This FDA approved assay includes matched tumor-white blood cell sequencing to distinguish germline from somatic variants and has been applied to 1,802 NSCLC patients who received ICI treatment, including 81 and 117 patients with at least 80% of African (AFR) and East Asian (EAS) ancestry, respectively. Moreover, 173 samples were derived from admixed patients with more than one major ancestry. We first used a natural language processing (NLP) model to obtain PFS from free-text clinical notes. A multivariable cox proportional hazard model was then used to associate PFS with ancestry, race, smoking status, ICI drug regimen, PD-L1 status, disease stage, tumor mutational burden (TMB), inferred income, and BMI. Neither genetic ancestry nor self-reported race/ethnicity was associated with the PFS. Moreover, ICI drug regimen types, low-income status, and BMI were not associated with PFS in our cohort. TMB-high was associated with longer PFS across all ancestries, although TMB was lower in patients with EAS ancestry (Median 7.9 vs. 5.3 mut/Mb, p These results suggest that the benefits of ICI extend across ancestry, race, and income lines in a single institution, arguing for more equitable patient access to these medications. We also show that TMB is a generalizable biomarker for ICI outcome across ancestries. However, more diverse patient populations are needed to understand whether there is ancestry-specificity in other ICI outcome biomarkers. Citation Format: Christopher J. Fong, Michele Waters, Karl Pichotta, Justin Jee, Devika R. Jutagir, David Ma, Tomin Perea-Chamblee, Susie Kim, Kanika Arora, Brooke Mastrogiacomo, Thinh Tran, Steven Maron, Mirella Altoe, Anisha Luthra, Joseph Kholodenko, Arfath Patha, Doori Rose, Michael F. Berger, Gregory J. Riely, Nikolaus Schultz, Sanna Goyert, Adam Schoenfeld, Francesca Gany, Jian Carrot-Zhang. Understanding genomic and social determinants of cancer immunotherapy outcome across ancestry. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4260.

Objectives Negative effusion cytology is more common in certain forms of Malignant Pleural Effusion (MPE) and results in pathway delay. Local Anaesthetic Thoracoscopy (LAT) is extremely sensitive and safe but cannot be offered to all. A stratified pathway, including ‘Direct to LAT’ in selected cases could enhance patient experience but requires reliable baseline predictors of unhelpful cytology, including both negative (no malignant cells) and incomplete results (malignant cells identified but predictive markers failed), since pleural biopsies will be required in the latter for optimal management. This retrospective analysis of a prospective multi-centre study, sought to identify baseline features for pathway rationalization. Materials and methods 363/638 (57%) of patients recruited to the DIAPHRAGM study (ISRCTN10079972) were included. Prospective data, including final diagnoses, asbestos exposure and fluid cytology results were supplemented by retrospective Computed Tomography (CT) and predictive marker reports. Independent predictors of negative and incomplete cytology were determined by multivariable logistic regression. Contingency tables were used to assess diagnostic value of cytology in associated phenotypes. Results 238/363 (66%) patients were diagnosed with MPE (18 tumour types). Fluid cytology was negative in 151/238 (63%) and independently associated with asbestos-exposure (Odds Ratio (OR) 5.34) and a malignant CT (OR 2.25). When both features were recorded the sensitivity and negative predictive value of fluid cytology were 19% (95% CI 11–30%) and 9% (95% CI 4–20%)), respectively. Cytology was incomplete in 34/238 (14%), i.e. 47% of positive cytology cases) but was not associated with any baseline feature. ORs for incomplete cytology in Ovarian, Breast, Renal and Lung Cancer were 83, 22, 21 and 9, respectively. Conclusion Negative cytology is extremely likely in patients with asbestos exposure and a malignant CT report. A ‘Direct-to-LAT’ approach may be appropriate in this setting. No baseline predictors of incomplete cytology were identified.

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability1–4 patterned by distinct mutational processes5,6, tumour heterogeneity7–9 and intraperitoneal spread7,8,10. Immunotherapies have had limited efficacy in HGSOC11–13, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumour sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumours harboured inflammatory signalling and ongoing immunoediting, reflected in loss of HLA diversity and tumour infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback-inversion-bearing tumours exhibited elevated immunosuppressive TGFβ signalling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumours and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, intratumoral heterogeneity and intraperitoneal spread. We investigated determinants of immune recognition and evasion in HGSOC to elucidate co- evolutionary processes underlying malignant progression and tumor immunity. Mutational processes and anatomic sites of tumor foci were key determinants of tumor microenvironment cellular phenotypes, inferred from whole genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumor sites from 42 treatment-naive HGSOC patients. Homologous recombination-deficient (HRD)-Dup (BRCA1 mutant-like) and HRD- Del (BRCA2 mutant-like) tumors harbored increased neoantigen burden, inflammatory signaling and ongoing immunoediting, reflected in loss of HLA diversity and tumor infiltration with highly- differentiated dysfunctional CD8+ T cells. Foldback inversion (FBI, non-HRD) tumors exhibited elevated TGFβ signaling and immune exclusion, with predominantly naive/stem-like and memory T cells. Our findings implicate distinct immune resistance mechanisms across HGSOC subtypes which can inform future immunotherapeutic strategies.HIGHLIGHTSMulti-region, multi-modal profiling of malignant and immune cell phenotypes in ovarian cancerAnatomic site specificity is a determinant of cancer cell and intratumoral immune phenotypesTumor mutational processes impact mechanisms of immune control and immune evasionSpatial topology of HR-deficient tumors is defined by immune interactions absent from immune inert HR-proficient subtypes

Progression to metastatic disease remains the main cause of cancer death. Yet, the underlying genomic mechanisms driving metastasis remain largely unknown. Here, we present MSK-MET, an integrated pan-cancer cohort of tumor genomic and clinical outcome data from more than 25,000 patients. We analyzed this dataset to identify associations between tumor genomic alterations and patterns of metastatic dissemination across 50 tumor types. We found that chromosomal instability is strongly correlated with metastatic burden in some tumor types, including prostate adenocarcinoma, lung adenocarcinoma and HR-positive breast ductal carcinoma, but not in others, such as colorectal adenocarcinoma, pancreatic adenocarcinoma and high-grade serous ovarian cancer. We also identified specific somatic alterations associated with increased metastatic burden and specific routes of metastatic spread. Our data offer a unique resource for the investigation of the biological basis for metastatic spread and highlight the crucial role of chromosomal instability in cancer progression.

PURPOSE Tumor mutational profiling is increasingly performed in patients with advanced cancer. We determined the extent to which germline mutation profiling guides therapy selection in patients with advanced cancer. METHODS Patients with cancer undergoing tumor genomic profiling were prospectively consented for germline cancer predisposition gene analysis (2015-2019). In patients harboring germline likely pathogenic or pathogenic (LP/P) alterations, therapeutic actionability was classified using a precision oncology knowledge base. Patients with metastatic or recurrent cancer receiving germline genotype–directed therapy were determined. RESULTS Among 11,947 patients across > 50 malignancies, 17% (n = 2,037) harbored a germline LP/P variant. By oncology knowledge base classification, 9% (n = 1042) had an LP/P variant in a gene with therapeutic implications (4% level 1; 4% level 3B; < 1% level 4). BRCA1/2 variants accounted for 42% of therapeutically actionable findings, followed by CHEK2 (13%), ATM (12%), mismatch repair genes (11%), and PALB2 (5%). When limited to the 9,079 patients with metastatic or recurrent cancer, 8% (n = 710) harbored level 1 or 3B genetic findings and 3.2% (n = 289) received germline genotype–directed therapy. Germline genotype–directed therapy was received by 61% and 18% of metastatic cancer patients with level 1 and level 3B findings, respectively, and by 54% of BRCA1/2, 75% of mismatch repair, 43% of PALB2, 35% of RAD51C/D, 24% of BRIP1, and 19% of ATM carriers. Of BRCA1/2 patients receiving a poly(ADP-ribose) polymerase inhibitor, 45% (84 of 188) had tumors other than breast or ovarian cancer, wherein the drug, at time of delivery, was delivered in an investigational setting. CONCLUSION In a pan-cancer analysis, 8% of patients with advanced cancer harbored a germline variant with therapeutic actionability with 40% of these patients receiving germline genotype–directed treatment. Germline sequence analysis is additive to tumor sequence analysis for therapy selection and should be considered for all patients with advanced cancer.

Reports suggest an increased risk of tuberculosis (TB) in people with chronic airway diseases (CADs) such as chronic obstructive pulmonary disease (COPD), but evidence has not been systematically reviewed. We performed a systematic review by searching MEDLINE and Embase for studies published from 1 January 1993 to 15 January 2021 reporting the association between the incident risk of TB in people with CADs (asthma, COPD and bronchiectasis). Two reviewers independently assessed the quality of individual studies. We included nine studies, with two from low-income high TB burden countries. Three cohort studies reported a statistically significant independent association between COPD and the risk of TB in high-income countries (n=711 389). Hazard ratios for incident TB ranged from 1.44 to 3.14 adjusted for multiple confounders including age, sex and comorbidity. There was large between-study heterogeneity (I2=97.0%) across studies. The direction of effect on the TB risk from asthma was inconsistent. Chronic bronchitis or bronchiectasis studies were limited. The small number of available studies demonstrated an increased risk of TB in people with COPD; however, the magnitude of the increase varies by setting and population. Data in high TB burden countries and for other CADs are limited.

Introduction Neutrophil extracellular traps (NETs) are a form of antimicrobial defence which have been implicated in multiple inflammatory diseases. This study investigated the role of NETs in bronchiectasis, a neutrophilic disease which lacks therapies that directly target neutrophilic inflammation, through a series of UK and international studies. Methods LC/MS proteomics was used to compare protein profiles in sputum between severe and mild bronchiectasis (20 vs 20 patients). Microbiome changes, using 16S rRNA sequencing, clinical characteristics and NET levels using a validated histone-elastase immunoassay were analysed. Results were validated in an independent European cohort. Proteomics was used to identify proteins associated with treatment response of acute exacerbations of bronchiectasis in 20 patients treated with intravenous antibiotics for 14 days. Two studies of long-term macrolide treatment, one in bronchiectasis and a post-hoc analysis of the AMAZES trial in asthma, investigated the effect of macrolide treatment on NETs. Results 96 proteins were differentially expressed in sputum between severe and mild bronchiectasis, with known NET proteins being the most abundant and discriminating. The relationship between NETs and associated proteins were validated in two independent cohorts, a UK cohort (n=175) and a European cohort (n=275). Sputum NETs were associated with BSI (p Conclusion NET-associated proteins are elevated in bronchiectasis sputum and are associated with disease severity, bacterial infection and mortality. Treatment response is linked to successfully reducing NET levels with intravenous antibiotic or macrolide therapies suggesting that NETs may be an important therapeutic target in bronchiectasis.

Purpose: We report our experience with next-generation sequencing to characterize the landscape of actionable genomic alterations in renal cell carcinoma (RCC). Experimental Design: A query of our institutional clinical sequencing database (MSK-IMPACT) was performed that included tumor samples from 38,468 individuals across all cancer types. Somatic variations were annotated using a precision knowledge database (OncoKB) and the available clinical data stratified by level of evidence. Alterations associated with response to immune-checkpoint blockade (ICB) were analyzed separately; these included DNA mismatch repair (MMR) gene alterations, tumor mutational burden (TMB), and microsatellite instability (MSI). Data from The Cancer Genome Atlas (TCGA) consortium as well as public data from several clinical trials in metastatic RCC were used for validation purposes. Multiregional sequencing data from the TRAcking Cancer Evolution through Therapy (TRACERx) RENAL cohort were used to assess the clonality of somatic mutations. Results: Of the 753 individuals with RCC identified in the MSK-IMPACT cohort, 115 showed evidence of targetable alterations, which represented a prevalence of 15.3% [95% confidence interval (CI), 12.7%–17.8%). When stratified by levels of evidence, the alterations identified corresponded to levels 2 (11.3%), 3A (5.2%), and 3B (83.5%). A low prevalence was recapitulated in the TCGA cohort at 9.1% (95% CI, 6.9%–11.2%). Copy-number variations predominated in papillary RCC tumors, largely due to amplifications in the MET gene. Notably, higher rates of actionability were found in individuals with metastatic disease (stage IV) compared with those with localized disease (OR, 2.50; 95% CI, 1.16–6.16; Fisher's P = 0.01). On the other hand, the prevalence of alterations associated with response to ICB therapy was found to be approximately 5% in both the MSK-IMPACT and TCGA cohorts and no associations with disease stage were identified (OR, 1.35; 95% CI, 0.46–5.40; P = 0.8). Finally, multiregional sequencing revealed that the vast majority of actionable mutations occurred later during tumor evolution and were only present subclonally in RCC tumors. Conclusions: RCC harbors a low prevalence of clinically actionable alterations compared with other tumors and the evidence supporting their clinical use is limited. These aberrations were found to be more common in advanced disease and seem to occur later during tumor evolution. Our study provides new insights on the role of targeted therapies for RCC and highlights the need for additional research to improve treatment selection using genomic profiling.

Summary Background Bronchiectasis is predominantly a neutrophilic inflammatory disease. There are no established therapies that directly target neutrophilic inflammation because little is understood of the underlying mechanisms leading to severe disease. Neutrophil extracellular trap (NET) formation is a method of host defence that has been implicated in multiple inflammatory diseases. We aimed to investigate the role of NETs in disease severity and treatment response in bronchiectasis. Methods In this observational study, we did a series of UK and international studies to investigate the role of NETs in disease severity and treatment response in bronchiectasis. First, we used liquid chromatography-tandem mass spectrometry to identify proteomic biomarkers associated with disease severity, defined using the bronchiectasis severity index, in patients with bronchiectasis (n=40) in Dundee, UK. Second, we validated these biomarkers in two cohorts of patients with bronchiectasis, the first comprising 175 patients from the TAYBRIDGE study in the UK and the second comprising 275 patients from the BRIDGE cohort study from centres in Italy, Spain, and UK, using an immunoassay to measure NETs. Third, we investigated whether pathogenic bacteria had a role in NET concentrations in patients with severe bronchiectasis. In a separate study, we enrolled patients with acute exacerbations of bronchiectasis (n=20) in Dundee, treated with intravenous antibiotics for 14 days and proteomics were used to identify proteins associated with treatment response. Findings from this cohort were validated in an independent cohort of patients who were admitted to the same hospital (n=20). Fourth, to assess the potential use of macrolides to reduce NETs in patients with bronchiectasis, we examined two studies of long-term macrolide treatment, one in patients with bronchiectasis (n=52 from the UK) in which patients were given 250 mg of azithromycin three times a week for a year, and a post-hoc analysis of the Australian AMAZES trial in patients with asthma (n=47) who were given 500 mg of azithromycin 3 times per week for a year. Findings Sputum proteomics identified that NET-associated proteins were the most abundant and were the proteins most strongly associated with disease severity. This finding was validated in two observational cohorts, in which sputum NETs were associated with bronchiectasis severity index, quality of life, future risk of hospital admission, and mortality. In a subgroup of 20 patients with acute exacerbations, clinical response to intravenous antibiotic treatment was associated with successfully reducing NETs in sputum. Patients with Pseudomonas aeruginosa infection had a lessened proteomic and clinical response to intravenous antibiotic treatment compared with those without Pseudomonas infections, but responded to macrolide therapy. Treatment with low dose azithromycin was associated with a significant reduction in NETs in sputum over 12 months in both bronchiectasis and asthma. Interpretation We identified NETs as a key marker of disease severity and treatment response in bronchiectasis. These data support the concept of targeting neutrophilic inflammation with existing and novel therapies. Funding Scottish Government, British Lung Foundation, and European Multicentre Bronchiectasis Audit and Research Collaboration (EMBARC).

INTRODUCTION AND OBJECTIVE:We report our experience with next-generation sequencing to characterize the prevalence and genomic landscape of actionable genomic alterations in renal cell carcinoma (R...

While progression to metastatic disease is the main cause of cancer death, little is known about the genomic mechanisms that drive metastasis. Rapidly growing clinical genomic data sets have the potential to identify genomic biomarkers of cancer metastasis, however, manual curation of clinical data is quickly emerging as a bottleneck. To overcome this challenge, we have developed a natural language processing (NLP) pipeline to identify organs affected by metastasis from radiology reports of patients with cancer. To develop our NLP models, we leveraged the AACR GENIE Biopharma Collaborative lung and colorectal cancer datasets generated in part at Memorial Sloan Kettering Cancer Center (MSK), containing curated labels of ten metastatic disease sites derived from 31,445 corresponding free-text radiology reports (2,310 patients). Using these data, we trained three machine learning models for identifying metastatic events from clinical text, using logistic regression, convolutional neural networks (CNN), and Bidirectional Encoder Representations from Transformers (BERT). We split patients into a training set (80% of patients) and validation set (20%). The BERT model yielded superior performance across evaluation metrics, with an average per metastatic disease site area under the receiver operating characteristic curve (AUC) of 0.981, average accuracy of 97.3%, macro-average precision/recall of 85.1/85.6, and micro-average precision/recall of 87.5/89.6. We applied our method to radiology reports from 52,000 patients with tumors prospectively profiled using the MSK-IMPACT clinical sequencing cohort. A comparison with the MSK-MET cohort, which contains metastatic events derived from billing codes in a subset of 25,000 patients, showed strong concordance (79.7% of metastatic events matched), with the NLP-based method identified an average of 1.4 additional metastatic sites per patient, an expected result given the incomplete nature of the billing code data. Analyzing genomic and clinical data in this cohort, we confirmed that chromosomal instability, as inferred by the fraction of genome altered (FGA), is strongly correlated with metastatic burden (defined as the number of distinct organs affected by metastases) in several tumor types, including prostate adenocarcinoma, lung adenocarcinoma and HR-positive breast ductal carcinoma, and we identified this trend in 10 additional cancer types not previously identified, including lobular HR-positive breast carcinoma and esophageal adenocarcinoma.We demonstrate that mining of electronic health records can be used to extract rich, structured clinical information. Our models, applied at scale, offer a unique resource for the investigation of the biological basis for metastatic spread. We hope our automated clinical data extractions can enable further large-scale studies of associations between genomic biomarkers and metastatic behavior. Citation Format: Anisha Luthra, Karl Pichotta, Brooke Mastrogiacomo, Samantha McCarthy, Steven Maron, Jianjiong Gao, Justin Jee, Christopher J. Fong, Nikolaus Schultz. A.I.-assisted clinical data curation to determine genomic biomarkers of cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1158.

Although the majority of cancer genes show a high degree of specificity for certain lineages, genomic profiling of cancer patients routinely identify alterations in genes that are atypical to the presented cancer type but are canonical drivers in a different lineage. It is often unclear if these atypical drivers arose early in tumorigenesis or were acquired during progression. A complete understanding of lineage associated genes (LAGs) will enable better interpretation of the molecular etiology of each diagnosed tumor. Here, we used a cohort of 38,912 patients across 122 cancer histologies (each with 50 or more patients) profiled for somatic alterations (mutations, copy number alterations and gene fusions) using the MSK-IMPACT assay. Tumors with TMB > 15 were already excluded. All alterations were classified as drivers using OncoKB. Allele-specific copy number calls were assessed using FACETS. Overall, 95% of patients harbored at least one oncogenic alteration, with a median of 4 drivers per tumor. We observed widespread prevalence of drivers across lineages with each gene mutated in a median of 36 different lineages. Conversely, a median of 103 genes were mutated at least once in each lineage. Hypothesizing that cancer genes are influenced by cell of origin, we sought to identify lineages harboring significantly higher rates of drivers in a given gene compared to its pancancer driver rate. We identified 1781 significant (adjusted P < 0.05) gene and lineage associations, and an additional 109 involving genes mutated at >10% in the respective lineages but which did not reach significance were also included. Lineage-agnostic genes such as TP53 and CDKN2A were associated with a broad spectrum of lineages (90 and 55, respectively). However, overall, each gene we profiled was found to be associated with a median of 3 distinct lineages. For example, while BRAF drivers are found in nearly all histologies (n=91), it is enriched for drivers in only 8 lineages: melanoma (acral and cutaneous), thyroid (poorly differentiated, anaplastic and papillary) and bowel (mucinous adenocarc. of colon/rectum, colon adenocarc. and neuroendocrine carc. of colon/rectum). In all, nearly a third of all drivers were observed in non-associated lineages. We next compared the somatic properties of drivers among genes in associated lineages vs. the same genes in non-associated lineages. We observed that mutations in LAGs were more often clonal (83% vs. 73%, associated vs. non-associated, P = 0) and showed enrichment for mutant allele imbalance in oncogenes (40% vs. 23%, P = 2e-111) and biallelic inactivation in tumor suppressor LAGs (71% vs. 58%, P = 4e-130). Furthermore, 93% of all OncoKB Level 1/2/3A actionable alterations, which are classified based on their histology, were in LAGs. In conclusion, our findings enable classification of drivers that are relevant for lineage-specific malignant transformation and advance our understanding of tumor biology. Citation Format: Chaitanya Bandlamudi, Walid K. Chatila, Shaleigh A. Smith, Subhiksha Nandakumar, Craig Bielski, Bastien Nguyen, Henry S. Walch, Christoph K. Kreitzer, Kanika S. Arora, Tran Thinh Ngoc, Miika Mehine, Irina Ostrovnaya, Ino de Bruijn, Hyung Jun Woo, Ritika Kundra, Christopher J. Fong, Satshil Rana, Gaofei Zhao, Mingxuan Zhang, Mark R. Zucker, Hongxin Zhang, Ryan Ptashkin, Rose Brannon, Eduard Reznik, JianJiong Gao, Maria E. Arcila, Ryma Benayed, Debyani Chakravarty, David Solit, Mark T. Donoghue, Marc Ladanyi, Nikolaus D. Schultz, Michael F. Berger, Ahmet Zehir. Comprehensive identification of lineage associated cancer genes in 122 histologies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3628.

Neutrophil elastase (NE) is a 29kDa serine protease released from the azurophilic granules of neutrophils. It may be directly involved in the pathogenesis and disease progression in cystic fibrosis, bronchiectasis and COPD through the degradation of airway elastin and by impairing host defence. Areas covered: Measurement of NE activity has emerged as a promising biomarker strategy in inflammatory lung disease. The authors review studies where NE activity has been linked with clinical outcomes such as lung function decline, exacerbation frequency or other cross-sectional and longitudinal markers of disease severity. In this article the evidence for NE measurement, and the strengths and weaknesses of a commercially available immunoassay which can specifically detect NE activity in human biological samples such as sputum and bronchoalveolar lavage are reviewed. Expert commentary: NE is a promising biomarker for stratifying severity disease. NE also appears to be responsive to antibiotic and other treatments, potentially therefore allowing it to be used as an indicator of treatment response in clinical trials.

Background Stably acquired mutations in hematopoietic cells represent substrates of selection that may lead to clonal hematopoiesis (CH), a common state in cancer patients that is associated with a heightened risk of leukemia development. Owing to technical and sample size limitations most CH studies have characterized gene mutations or mosaic chromosomal alterations (mCAs) individually. The relationship between acquired gene mutations and mCAs in CH and their joint roles in leukemia development have not been systematically investigated. Methods We developed a method to reliably map mCAs at low cell fractions from deep targeted sequencing data. We applied this method in a cohort of 32,442 solid tumor patients who have undergone prospective clinical sequencing (MSK-IMPACT). We characterized gene mutations in our patient cohort using an established variant calling procedure from our previous studies. Results We jointly characterized 383 mCA events (median aberrant cell fraction 32%, range 10%-90%) and 14,789 mutations across 457 genes. mCA was significantly associated with age (OR=1.8, P20% VAF, compared to 1% of the general cohort. We identify co-mutational patterns characteristic of diverse mechanisms of clonal selection. We observe that mutations in DNMT3A, TET2, JAK2, MPL, EZH2, TP53 and ATM form recurrent double-hits with deletions or CNLOHs, resulting in either oncogene mutant dosage adjustment or inactivation of tumor suppressors. Notably, certain mCA events were highly directed events acting on previously acquired gene mutations in the corresponding loci. Of six events of 7qCNLOH, all six co-localized with an EZH2 (7q36.1) mutation (q During patient follow-up, the 3-year cumulative incidence of leukemias was significantly higher in patients with composite CH genotypes (14.6%, CI: 7-22%) as compared to patients with either mCA, gene mutation alone or no CH, of which all had a 3-year cumulative incidence of Conclusions Our joint characterization of gene mutations and mCAs in a large prospective sequencing cohort reveals a previously unrecognized layer of complexity in the evolutionary dynamics of clonal hematopoiesis that converges towards characteristic genotypes associated with distinct leukemia subtypes. This puts mCAs in the context of the continuous evolutionary process of oncogenesis that can often span years and sheds new lights on its patterns of acquisition and progression. We demonstrate that the integration of chromosomal aberrations provides additional resolution to risk stratification as well as interpretation of clinical phenotypes and that mCAs should be screened in conjunction with gene mutations to improve existing CH surveillance programs in cancer patients. Disclosures Bolton: GRAIL: Research Funding. Medina:Isabl: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees. Mantha:MJH Associates: Honoraria; Physicians Education Resource: Honoraria. Solit:Pfizer: Honoraria; Loxo Oncology: Honoraria; Lilly Oncology: Honoraria; Illumina: Honoraria; Vivideon Therapeutics: Honoraria. Diaz:Neophore: Consultancy, Current equity holder in private company; Merck: Consultancy; Johns Hopkins University: Patents & Royalties; Jounce Therapeutics: Current equity holder in private company; Thrive Earlier Detection: Current equity holder in private company; Personal Genome Diagnostics: Consultancy, Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees. Berger:Illumina: Research Funding; Roche: Consultancy; Grail: Research Funding. Levine:Lilly: Consultancy, Honoraria; Janssen: Consultancy; Roche: Consultancy, Honoraria, Research Funding; Loxo: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Imago: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Isoplexis: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Honoraria, Research Funding; Prelude Therapeutics: Research Funding; Gilead: Honoraria; Amgen: Honoraria; Morphosys: Consultancy; Novartis: Consultancy; Astellas: Consultancy; Qiagen: Current equity holder in publicly-traded company, Membership on an entity's Board of Directors or advisory committees. Zehir:Memorial Sloan Kettering Cancer Center: Current Employment; Illumina: Honoraria. Papaemmanuil:Celgene: Consultancy, Honoraria, Research Funding; Prime Oncology: Consultancy, Honoraria; Novartis: Consultancy, Honoraria; Illumina: Consultancy, Honoraria; Kyowa Hakko Kirin: Consultancy, Honoraria; Isabl: Current equity holder in private company, Membership on an entity's Board of Directors or advisory committees; MSKCC: Patents & Royalties.

Background: Bronchiectasis is predominantly a neutrophilic inflammatory disease. There are no established therapies that directly target neutrophilic inflammation because of a lack of understanding of the underlying mechanisms leading to severe disease. Neutrophil extracellular trap (NET) formation is a mode of host defence that has been implicated in multiple inflammatory diseases. Methods: We conducted a series of UK and international studies to investigate the role of NETs in disease severity and treatment response in bronchiectasis. Nano LC/MS-MS was used to identify proteomic markers associated with disease severity, defined using the bronchiectasis severity index (BSI) (n=40). These were validated in two cohorts (n=175 and n=275) using a validated immunoassay to measure NETs. 20 patients with acute exacerbations of bronchiectasis were treated with intravenous antibiotics for 14 days and proteomics used to identify proteins associated with treatment response. Two studies of long-term macrolide treatment, one in bronchiectasis and a post-hoc analysis of the AMAZES trial in asthma, investigated the effect of macrolide treatment on NETs. Findings: 96 proteins were differentially expressed in sputum between severe and mild bronchiectasis. The most abundant and most discriminating were proteins known to be NET proteins. This was validated in two observational cohorts where sputum NETs were associated with BSI, quality of life, lung function, future risk of hospital admissions and mortality. Antibiotic treatment in 20 patients was associated with 23 significantly down-regulated and 16 up-regulated proteins, with the “neutrophil degranulation” pathway being most strongly implicated in response. Patients with Pseudomonas aeruginosa infection had a blunted proteomic and clinical response to treatment. Treatment with low dose azithromycin was associated with a significant reduction in NETs in sputum over 12 months in both bronchiectasis and asthma. Interpretation: NETs are identified as a key marker of disease severity and treatment response in bronchiectasis. Funding: Supported by the Scottish Government Chief Scientist Office (Senior Clinical Fellowship to JDC) and British Lung Foundation through the BLF Chair of Respiratory Research. Supported by the European Bronchiectasis Network (EMBARC), a European Respiratory Society Clinical Research Collaboration. Declaration of Interests: None to declare Ethics Approval Statement: The studies were approved by local research ethics committees and patients provided informed consent.

There is conflicting data regarding the role of PBAF complex mutations and response to immune checkpoint blockade (ICB) therapy in clear cell renal cell carcinoma (ccRCC) and other solid tumors. We assess the prevalence of PBAF complex mutations from two large cohorts including the pan-cancer TCGA project (n = 10,359) and the MSK-IMPACT pan-cancer immunotherapy cohort (n = 3700). Across both cohorts, PBAF complex mutations, predominantly PBRM1 mutations, are most common in ccRCC. In multivariate models of ccRCC patients treated with ICB (n = 189), loss-of-function (LOF) mutations in PBRM1 are not associated with overall survival (OS) (HR = 1.24, p = 0.47) or time to treatment failure (HR = 0.85, p = 0.44). In a series of 11 solid tumors (n = 2936), LOF mutations are not associated with improved OS in a stratified multivariate model (HR = 0.9, p = 0.7). In a current series of solid tumors treated with ICB, we are unable to demonstrate favorable response to ICB in patients with PBAF complex mutations.

Background The sputum microbiome has a potential role in disease phenotyping and risk stratification in chronic obstructive pulmonary disease (COPD), but few large longitudinal cohort studies exist. Objective Our aim was to investigate the COPD sputum microbiome and its association with inflammatory phenotypes and mortality. Methods 16S ribosomal RNA gene sequencing was performed on sputum from 253 clinically stable COPD patients (4-year median follow-up). Samples were classified as Proteobacteria or Firmicutes (phylum level) and Haemophilus or Streptococcus (genus level) dominant. Alpha diversity was measured by using Shannon-Wiener diversity and Berger-Parker dominance indices. Survival was modeled by using Cox proportional hazards regression. A subset of 78 patients had label-free liquid chromatography with tandem mass spectrometry performed, with partial least square discriminant analysis integrating clinical, microbiome, and proteomics data. Results Proteobacteria dominance and lower diversity was associated with more severe COPD according to the Global Initiative for Chronic Obstructive Lung Disease classification system (P = .0015), more frequent exacerbations (P = .0042), blood eosinophil level less than or equal to 100 cells/μL (P Conclusion The sputum microbiome is associated with clinical and inflammatory phenotypes in COPD. Reduced microbiome diversity, associated with Proteobacteria (predominantly Haemophilus) dominance, is associated with neutrophil-associated protein profiles and an increased risk of mortality.

Background: Neutrophil Extracellular Traps (NETs) are composed of DNA, histones and over 30 granular proteins. NETs are ineffective at killing bronchiectasis pathogens such as Pseudomonas aeruginosa. We hypothesised that NETs would be present in the bronchiectasis lung and would be associated with an altered microbiome. Methods: 218 bronchiectasis patients were enrolled. We performed microbiome analysis on patient sputum using 16s rRNA PCR and sequencing. Lung inflammation was evaluated using LC/MS proteomics and NET quantification in sputum supernatant using immunoassays. Results: 218 patients were studied. Mean age was 68 years, 58% female. The bronchiectasis microbiome was heterogeneous but was dominated by proteobacteria dysbiosis, such as Pseudomonas and Haemophilus (n=94) and to a lesser extent firmicutes dysbiosis, such as Streptococcus (n=52). Proteobacteria dysbiosis was associated with moderate and severe bronchiectasis, and a higher frequency of exacerbations. Integration of inflammatory and microbiota data showed severe bronchiectasis associated with proteobacteria, MMP9, LL-37, Olfactomedin-4, neutrophil elastase, resistin and other NET components, while firmicutes were associated with eosinophilic inflammation, and high levels of epithelial markers such as cystatin and SLPI. NETs were abundant in the bronchiectasis sputum and were higher in patients with proteobacteria dysbiosis (mean histone-elastase complexes 35.8 sd 44.6 vs 11.6 sd 13.3, p=0.0002). Higher NETs were associated with lower diversity measured by the Shannon index (p=0.01), and Berger-Parker index (p=0.02). Conclusion: NETs are associated with proteobacteria dysbiosis and loss of microbiome diversity in bronchiectasis.

Introduction: COPD is a heterogenous disease which makes identifying patients more likely to respond to a particular treatment or at higher risk of poor clinical outcomes challenging. Methods: Microbiome characterization by 16S bacterial rRNA gene sequencing was performed on sputum samples obtained from 297 COPD patients studied during stable disease with a median follow up of 4 years. Samples were classified at the phyla level as proteobacteria or firmicutes dominant whilst at the genera level samples were classed as Haemophilus or Streptococcus dominant. If no phyla or genera was represented at greater than 40% these were classed as “balanced microbiomes”. The results were compared to clinical characteristics to determine the utility of stable disease microbiome in predicting outcomes. Results: Proteobacteria dysbiosis and loss of microbiota diversity (Shannon-Wiener Diversity Index) was associated with more severe COPD by GOLD stage (P=0.0007), more frequent prior exacerbations (P=0.0057), low blood eosinophil counts ( Proteobacteria dysbiosis was associated with an increased risk of mortality (HR 2.39 95% CI 1.23-4.66, p=0.01) compared to those with a balanced or firmicutes dominated microbiome. Uniquely among Firmicutes, patients with a Streptococcus dominated microbiome had an increased mortality risk (HR 2.58 95% CI 1.03-6.46, p= 0.043) when compared to those with balanced microbiomes. Conclusions: Reduced microbiome diversity, driven by Proteobacteria (predominantly Haemophilus) or Streptococcus dysbiosis is associated with increased mortality and may indicate COPD endotypes at increased risk of negative outcomes. Funder: GSK

Although most cancer deaths are due to metastatic spread, we are not able to predict if, when and where a tumor will metastasize. So far, large-scale cancer sequencing efforts have either focused on primary tumors (TCGA), or have characterized the overall genomic landscape of metastases without investigating the interplay between genomic profiles and specific routes of metastatic dissemination. Here, we have investigated associations between genomic alterations and metastatic patterns using a cohort of 25,763 patients treated at Memorial Sloan Kettering with available targeted DNA sequencing data (MSK-IMPACT, 468 genes). Our cohort consists of 15,662 (60%) sequenced primaries and 10,101 (40%) sequenced metastases from 44 different tumor types. A total of 99,220 distant metastatic events were automatically extracted from ICD billing codes from electronic medical records and mapped to a reference set of 21 anatomic locations. Metastases had significantly more copy-number alterations (CNA) (inferred by fraction genome altered, FGA) than primaries in 15/44 tumor types. Metastases also exhibited significantly higher fractions of clonal mutations in 11/44 types and higher rates of whole-genome duplication in 7/44 types. Driver genes that were most often altered at higher frequencies in metastases included TP53, CDKN2A, PTEN and MYC, while most frequently altered oncogenic pathways in metastases included TP53, Cell Cycle and DNA damage repair. Importantly, we found that FGA was positively correlated with metastatic burden (defined as the number of distinct metastatic organs throughout the entire clinical history) in 19/44 tumor types. This trend, which was observed even when restricting the analysis to primary tumors, was most pronounced in prostate, breast and endometrioid adenocarcinoma. In other tumor types, including MSS colorectal and serous ovarian tumors, there was no such trend. These findings suggest that CNA burden can be predictive of metastatic potential in some tumor types. The relationship between TMB and metastatic burden was not straightforward: we observed a positive correlation in six tumor types, and a negative correlation in four tumor types. Finally, we explored associations between somatic alterations and metastatic organotropisms. For example, BRAF mutation was enriched in MSS colorectal cancer patients with brain metastasis (7% vs 12%, qval < .05), AR amplification and PTEN deletion were enriched in prostate cancer patients with bone metastasis (5% vs 21%, qval < .05 and 9% vs 19%, qval < .05) whereas ERG fusion was less frequent in patients with bone metastasis (30% vs 24%, qval < .05). In summary, we present a comprehensive, spatiotemporal map of metastasis that integrates clinical and molecular information and serves as an initial proof of concept that genomic profiling of tumors could be used to predict patterns of metastatic spread. Citation Format: Bastien Nguyen, Christopher Fong, Renzo DiNatale, Anisha Luthra, Subhiksha Nandakumar, Henry Walch, Walid K. Chatila, Arjun Rajanna, David B. Solit Solit, Michael F. Berger, Ahmet Zehir, Jianjiong Gao, Francisco Sanchez-Vega, Nikolaus Schultz. Integration of genomic and clinical data from 25,000 patients identifies molecular determinants of metastatic potential and organotropisms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2834.

Despite the fact that the majority of cancer related deaths are due to metastatic disease, existing large-scale cancer sequencing projects such as The Cancer Genome Atlas have so far focused mainly on primary tumors. Moreover, most publicly available datasets in cancer genomics lack information about spatiotemporal patterns of metastatic spread. We have developed new clinical data extraction methods and performed an integrative analysis of clinical and genomic features from 34,836 patients treated at Memorial Sloan Kettering Cancer Center (MSK), stratified into 45 cancer subtypes. Tumors were sequenced with MSK-IMPACT, a targeted next-generation sequencing assay that identifies genomic alterations in 468 genes. Indications of metastatic events, including affected organs and detailed timeline annotations, were extracted from the electronic medical records. This allowed us to distinguish not only sequenced primaries (58%) from sequenced metastases (42%), but also primaries in patients with evidence of metastatic disease (33%) from patients without evidence of metastatic disease (25%) at the time of sequencing. Tumors from patients with evidence of metastatic disease exhibited increased copy-number alterations, measured as fraction of genome altered (FGA) in multiple cancer types, including prostate adenocarcinoma, endometrial endometrioid, HR+/HER2- breast invasive carcinoma and lung adenocarcinoma (all p < 0.001). This supports the existence of a positive correlation between disease burden and chromosomal instability, although this effect is weaker or non-existent in some cancer types, including hepatocellular carcinoma, ovarian serous, and cholangiocarcinoma. We investigated associations between somatic alterations and metastatic organotropisms. For example, among patients with microsatellite stable colorectal cancer, tumors that metastasized exclusively to the peritoneum were enriched in BRAF alterations when compared to patients that never metastasized to that site (21% vs. 6%; p=0.003), while tumors that metastasized exclusively to the lung were enriched in KRAS alterations (69% vs. 41%; p=0.002). By analyzing primary tumors in patients with no evidence of metastatic disease at the time of sequencing, and comparing those that would eventually metastasize with those that would not, we identified predictive markers of metastatic risk. For example, in bladder cancer, tumors with altered TP53 were twice as likely to metastasize (54% vs. 27%; p We present a comprehensive, spatiotemporal map of metastasis that integrates clinical and molecular information and can be used to build personalized risk models of metastatic spread at target-organ resolution based on individual molecular profiles, which can enhance precision medical care and optimize clinical outcomes. Citation Format: Christopher J. Fong, Francisco Sanchez-Vega, Bastien Ngyuen, Anisha Luthra, Subhiksha Nandakumar, Henry Walch, Walid Chatila, Arjun Rajanna, Ahmet Zehir, Michael Berger, Jianjiong Gao, Nikolaus Schultz. Integrative analysis of clinical and genomic information identifies predictive markers of metastatic risk [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1109.

Introduction: Bronchiectasis (BE) is a heterogeneous disease and antibiotics are a main treatment. Recent trials suggest clinical response to antibiotics is unpredictable. We used proteomic approaches to study patients with BE when clinically stable and following antibiotic treatment. Methods: Sputum samples were collected from 20 BE patients on day one of an exacerbation, and 14 days post-antibiotic treatment. Label Free LC/MS was used to profile sputum samples. Biomarkers, including neutrophil extracellular traps (NETs) were measured using immunoassays. Results were validated in 333 stable patients with BE. Results: 20 patients were included in the proteomic study. 55% of patients had Pseudomonas aeruginosa (PA) infection. In the proteomic analysis, there was a differential response to antibiotics in patients with baseline PA. The expression of NET proteins showed a greater decrease after antibiotic treatment in the non-PA group. Three endotypes of BE treatment response were identified with distinct proteomic patterns: type 1 events associated with NET clearance and improvements in symptoms/FEV1, type 2 events with minimal proteomic changes and minimal clinical response, type 3 events where response was mixed. Candidate biomarkers were validated which showed heterogeneous responses post antibiotics. In a validation study in 333 stable patients, sputum NET complexes correlated with FEV1% predicted(p Conclusion: We identified novel endotypes of BE exacerbations and treatment responses which may be used in future for personalised therapy.

Background Neutrophil elastase (NE) has been linked to lung neutrophil dysfunction in bronchiectasis and cystic fibrosis (CF), making NE inhibition a potential therapeutic target. NE inhibitor trials have given mixed result perhaps because not all patients have elevated airway NE activity. Methods We tested whether a single baseline sputum NE measurement or a combination of clinical parameters could enrich patient populations with elevated NE activity for “personalised medicine”. Intra- and interindividual variations of total and active NE levels in induced sputum from patients with CF or bronchiectasis were monitored over 14 days. Patients with established CF and bronchiectasis (n=5 per group) were recruited. NE was measured using three different methods: one total and two active NE assays. Subsequently, we analysed the association between clinical parameters and NE from a large bronchiectasis cohort study (n=381). Results All three assays showed a high degree of day-to-day variability (0–233% over 14 days). There were strong correlations found between all assays (p, NE at baseline can enrich studies for “high” NE patients, while in bronchiectasis, inclusion of patients with Pseudomonas aeruginosa, purulent sputum and frequent exacerbations provides a high degree of certainty of including patients with high NE http://ow.ly/mPTS30nI8ec

Introduction: Infection is a key component of the pathophysiology of bronchiectasis. Characterisation of the microbiome offers a higher degree of sensitivity and resolution than traditional culture to evaluate the importance of infection in determining the risk of exacerbation and long-term outcomes, including mortality, in bronchiectasis. Methods: Sputum samples from 281 patients with bronchiectasis included in a longitudinal cohort of patients from two hospitals in the East of Scotland underwent 16S rRNA amplicon sequencing. Sputum supernatant was used to measure neutrophil elastase activity by immunoassay. Patients were enrolled from 2012-2015 and followed up until January 2019 for long term outcomes. Repeat sputum samples were obtained at exacerbation and stable visits during follow-up. Dominant genera was assigned based on a previously published method. Microbiome characteristics were compared to measures of clinical disease severity and long term outcomes. Results: In both stable bronchiectasis and during exacerbations, a microbiome dominated by Proteobacteria and Firmicutes was observed. Beta diversity analysis indicated that patients' microbiomes were relatively stable over time and showed less variation than that observed between patients. During disease stability, reduced Shannon-Wiener Diversity Index was associated with higher bronchiectasis severity (P

The anti-HER2 antibody trastuzumab is standard care for advanced esophagogastric (EG) cancer with ERBB2 (HER2) amplification or overexpression, but intrinsic and acquired resistance are common. We conducted a phase II study of afatinib, an irreversible pan-HER kinase inhibitor, in trastuzumab-resistant EG cancer. We analyzed pretreatment tumor biopsies and, in select cases, performed comprehensive characterization of postmortem metastatic specimens following acquisition of drug resistance. Afatinib response was associated with coamplification of EGFR and ERBB2. Heterogeneous 89Zr-trastuzumab PET uptake was associated with genomic heterogeneity and mixed clinical response to afatinib. Resistance to afatinib was associated with selection for tumor cells lacking EGFR amplification or with acquisition of MET amplification, which could be detected in plasma cell-free DNA. The combination of afatinib and a MET inhibitor induced complete tumor regression in ERBB2 and MET coamplified patient-derived xenograft models established from a metastatic lesion progressing on afatinib. Collectively, differential intrapatient and interpatient expression of HER2, EGFR, and MET may determine clinical response to HER kinase inhibitors in ERBB2-amplified EG cancer. Significance: Analysis of patients with ERBB2-amplified, trastuzumab-resistant EG cancer who were treated with the HER kinase inhibitor afatinib revealed that sensitivity and resistance to therapy were associated with EGFR/ERBB2 coamplification and MET amplification, respectively. HER2-directed PET imaging and cell-free DNA sequencing could help guide strategies to overcome the emergence of resistant clones. See related commentary by Klempner and Catenacci, p. 166. This article is highlighted in the In This Issue feature, p. 151

We propose a perfusion model that can quantify blood flow in relation to arterial occlusion due to plaque accumulation in peripheral arterial disease patients. Model parameters can be of help to PAD diagnosis.

We present initial results from monitoring surgical interventions in peripheral-artery-disease (PAD) patients with diffuse optical spectroscopy (DOS). DOS measures show promise as an early predictor of treatment success.

A diffuse optical spectroscopic system suitable for intraoperative use for vascular surgery is characterized. A case example of its use for a patient before and after angioplasty is presented.

Introduction: Neutrophil extracellular traps (NETs) are composed of DNA, histones and antimicrobial peptides. NETs are designed to trap and kill pathogens but have been linked to disease severity in bronchiectasis (BE) and cystic fibrosis (CF). We studied the effect of airway mediators on NET formation in BE and CF. Methods: Peripheral blood neutrophils were stimulated with PMA and C5a to generate NETs. We simulated the airway environment by treating neutrophils with autologous sputum supernatant. Phagocytosis was assessed with FITC-labelled Pseudomonas aeruginosa. Results: We recruited 5 patients with CF and 5 with BE. We observed similar levels of spontaneous NET formation in BE, CF and healthy controls (HC). Sputum pre-treatment of neutrophils enhanced NET formation in response to PMA (mean increase 82.5% 95% CI 55-109%, p An increase in the NET component neutrophil elastase resulted in a decrease in phagocytosis of P. aeruginosa by sputum neutrophils (figure), r-0.74, p=0.01. Phagocytosis failure could be replicated by treating peripheral neutrophils with sputum. Conclusion: Sputum from patients with BE and CF contains mediators that promote NET formation and inhibit phagocytosis of bacteria.

Background/Objectives Infantile hemangiomas (IHs) are vascular tumors with the potential for significant morbidity. There is a lack of validated objective tools to assess IH severity and response to treatment. Diffuse optical spectroscopy (DOS), a noninvasive, nonionizing imaging modality, can measure total hemoglobin concentration and hemoglobin oxygen saturation in tissue to assess IH vascularity and response to treatment. Our objective was to evaluate the utility of a wireless, handheld DOS system to assess IH characteristics at selected points during their clinical course. Methods Thirteen subjects (initial age 5.8 ± 2.0 mos) with 15 IHs were enrolled. IHs were classified as proliferative, plateau phase, or involuting. Nine patients with 11 IHs were untreated; four patients with 4 IHs were treated with timolol or propranolol. Each IH was evaluated by placing the DOS system directly on the lesion as well a normal contralateral skin site. IH vascularity and oxygenation were scored using a newly defined normalized hypoxia fraction (NHF) coefficient. Measurements were recorded at various intervals from the initial visit to 1 to 2 years of age. Results For the nine untreated IHs, the NHF was highest at 6 months of age, during proliferation. Differences in NHFs between the proliferation and the plateau (p = 0.02) and involuting (p < 0.001) stages were statistically significant. In treated patients, the NHF normalized to 60% after 2 months. One treated IH came within 5% of the NHF for normal skin after 12 months. Conclusions DOS can be used to assess the vascularity and tissue oxygenation of IHs and monitor their progression and response to treatment.

Background Neutrophil extracellular traps (NETs) have been observed in the airway in patients with chronic obstructive pulmonary disease (COPD), but their clinical and pathophysiologic implications have not been defined. Objective We sought to determine whether NETs are associated with disease severity in patients with COPD and how they are associated with microbiota composition and airway neutrophil function. Methods NET protein complexes (DNA-elastase and histone-elastase complexes), cell-free DNA, and neutrophil biomarkers were quantified in soluble sputum and serum from patients with COPD during periods of disease stability and during exacerbations and compared with clinical measures of disease severity and the sputum microbiome. Peripheral blood and airway neutrophil function were evaluated by means of flow cytometry ex vivo and experimentally after stimulation of NET formation. Results Sputum NET complexes were associated with the severity of COPD evaluated by using the composite Global Initiative for Obstructive Lung Disease scale (P, Graphical abstract

616 Background: We report our experience with next-generation sequencing to characterize the prevalence and genomic landscape of actionable genomic alterations in renal cell carcinoma (RCC). Methods: A query of our institutional clinical sequencing database was performed to include tumor samples sequenced across all cancers. Actionable alterations with clinical or biologic evidence supporting an association with response to targeted therapy were stratified by level of evidence using an oncology knowledge database (OncoKB). Results: Data from 35,668 patients was included, and the 15 cancer types with the highest prevalence of actionable alterations were selected for subsequent analysis (28,027 patients). Of these cancers, RCC ranked 13th in prevalence of actionable alterations. Of 708 RCC samples included, 259 (37%) were from metastatic sites. However, of the remaining 449 primary samples, 208 (29%) belonged to patients who had metastatic disease at the time of sequencing. Although 69% of patients with any RCC harbored at least one known oncogenic mutation, only 90/687 (13%) harbored alterations for which compelling clinical data currently exist to justify the use of a standard or an investigational agent (levels of evidence 1 to 3B). This represents an increase from the previously reported prevalence (5% in 2017). The most common histologic subtype, clear cell RCC harbored the vast majority of actionable alterations (52/421; 12%). Regarding the specific genes that harbor these alterations, 31 level 2A alterations were identified, all of which were TSC1/TSC2 mutations; 30 level 2B alterations were identified, of which PIK3CA (22) and BRCA1/BRCA2 (5) mutations were most common; 11 level 3A alterations, all of which were MTOR mutations, and 8 level 3B alterations, of which AKT1 (4) mutation was most common. Conclusions: Although the prevalence of actionable mutations in RCC seems to have doubled in recent years, the role of genetic testing in identifying candidates for targeted therapy in RCC is currently limited relative to other cancer types, emphasizing the need for additional research in this area to further inform targeted therapy decisions.

Metastatic disease is responsible for the vast majority of cancer-related deaths. Patterns of metastatic spread and colonization are, however, not random: routes of metastatic dissemination are cancer-type specific, and different cancer types exhibit varying levels of affinity for specific organs as metastatic target sites. We analyzed a cohort of more than 30,000 patients that were treated at Memorial Sloan Kettering Cancer Center (MSK) and had their tumors sequenced using the clinical MSK-IMPACT test, a targeted next-generation sequencing assay that identifies mutations, copy number changes and structural rearrangements in 468 genes. By querying the electronic medical record, we catalogued all metastatic events in the clinical history of these patients and mapped them to a set of 32 tissue sites. The primary diagnoses spanned 30 different cancer types, which were further stratified into >50 relevant molecular subtypes, based on a combination of molecular and histopathological features. Observed patterns of metastatic dissemination were cancer type specific and, in some cases, exhibited strong differences across molecular subtypes of the same cancer type. For example, HER2+ subtypes of breast cancer exhibited increased rates of brain (34% vs. 18%, p The median number of organs affected by metastatic disease per patient was 4 (range 1-14). The number of affected organs exhibited a strong positive correlation with the overall level of aneuploidy, as measured by the total fraction of genome altered by copy number changes (P We present the first pan-cancer study that combines molecular and histopathological features to draw a comprehensive atlas of tumor metastasis. Our results provide novel insights into the biology of metastatic tumors and can have a direct impact on patient management and care by optimizing the use and frequency of specific imaging studies for metastasis surveillance. Citation Format: Francisco Sanchez-Vega, Christopher Fong, Walid Chatila, Philip Jonsson, Alexander V. Penson, Renzo G. DiNatale, Michael F. Berger, Ahmet Zehir, Ed Reznik, Jianjiong Gao, Karuna Ganesh, Barry S. Taylor, Nikolaus Schultz. A molecular and histopathologic map of cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2736.