Minorities Face Delays to Pancreatic Cancer Treatment Regardless of Diagnosis Setting

INTRODUCTION

Our analysis was designed to characterize the demographics and disparities between the diagnosis of pancreas cancer during emergency presentation (EP) and the outpatient setting (OP) and to see the impact of our institutions pancreatic multidisciplinary clinic (PMDC) on these disparities.

METHODS

Institutional review board-approved retrospective review of our institutional cancer registry and PMDC databases identified patients diagnosed/treated for pancreatic ductal adenocarcinoma between 2014 and 2022. Chi-square tests were used for categorical variables, and one-way ANOVA with a Bonferroni correction was used for continuous variables. Statistical significance was set at p < 0.05.

RESULTS

A total of 286 patients met inclusion criteria. Eighty-nine patients (31.1%) were underrepresented minorities (URM). Fifty-seven (64.0%) URMs presented during an EP versus 100 (50.8%) non-URMs (p = 0.037). Forty-one (46.1%) URMs were reviewed at PMDC versus 71 (36.0%) non-URMs (p = 0.10). No differences in clinical and pathologic stage between the cohorts (p = 0.28) were present. URMs took 22 days longer on average to receive treatment (66.5 days vs. 44.8 days, p = 0.003) in the EP cohort and 18 days longer in OP cohort (58.0 days vs. 40.5 days, p < 0.001) compared with non-URMs. Pancreatic Multidisciplinary Clinic enrollment in EP cohort eliminated the difference in time to treatment between cohorts (48.3 days vs. 37.0 days; p = 0.151).

RESULTS

Underrepresented minorities were more likely to be diagnosed via EP and showed delayed times to treatment compared with non-URM counterparts. Our PMDC alleviated some of these observed disparities. Future studies are required to elucidate the specific factors that resulted in these findings and to identify solutions.

Distinct Hodgkin lymphoma subtypes defined by noninvasive genomic profiling

The scarcity of malignant Hodgkin and Reed-Sternberg cells hampers tissue-based comprehensive genomic profiling of classic Hodgkin lymphoma (cHL). By contrast, liquid biopsies show promise for molecular profiling of cHL due to relatively high circulating tumour DNA (ctDNA) levels1-4. Here we show that the plasma representation of mutations exceeds the bulk tumour representation in most cases, making cHL particularly amenable to noninvasive profiling. Leveraging single-cell transcriptional profiles of cHL tumours, we demonstrate Hodgkin and Reed-Sternberg ctDNA shedding to be shaped by DNASE1L3, whose increased tumour microenvironment-derived expression drives high ctDNA concentrations. Using this insight, we comprehensively profile 366 patients, revealing two distinct cHL genomic subtypes with characteristic clinical and prognostic correlates, as well as distinct transcriptional and immunological profiles. Furthermore, we identify a novel class of truncating IL4R mutations that are dependent on IL-13 signalling and therapeutically targetable with IL-4Rα-blocking antibodies. Finally, using PhasED-seq5, we demonstrate the clinical value of pretreatment and on-treatment ctDNA levels for longitudinally refining cHL risk prediction and for detection of radiographically occult minimal residual disease. Collectively, these results support the utility of noninvasive strategies for genotyping and dynamic monitoring of cHL, as well as capturing molecularly distinct subtypes with diagnostic, prognostic and therapeutic potential.

Muscle of dark and normal beef differs metabolically

Reduction in muscle glycogen triggered by adverse antemortem handling events alters postmortem energy metabolism and results in a high ultimate pH and dark, firm and dry beef, often referred to as 'dark-cutting'. However, the relationship between atypical dark (AT) beef, postmortem energy metabolism and underlying tissue characteristics remains somewhat unclear. Cattle harvested in the US and Canada representing normal (pH < 5.6), AT dark (pH 5.6-5.8) and dark cutting (DC; pH > 5.8) beef were analyzed for tissue characteristics related to energy metabolism. Results show AT dark beef is more oxidative but similar to normal beef in glycolytic potential and nucleotide abundance. Mitochondria DNA content (P < 0.05, Canada; P < 0.005, US) and oxidative enzymes for DC and AT dark beef were greater (P < 0.01; Canada and US) compared to normal beef. Myoglobin tracked (P < 0.01) with color classification. These findings show both DC and AT beef are inherently more oxidative and raise the possibility that more oxidative muscle may be more prone to develop dark beef.

Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies against self-antigens

Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA sequencing (scRNA-Seq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from 7 primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. Ig sequencing identified plasma cell (PC) clones expressing isotype-switched and hypermutated Igs, suggesting the occurrence of T cell-dependent B cell responses. We assessed the reactivity of 41 recombinant antibodies that represented the products of 235 PCs and 12 B cells toward multiple cell lines and PDAC tissues and observed frequent staining of intracellular self-antigens. Three of these antigens were identified: the filamentous actin (F-actin), the nucleic protein RuvB like AAA ATPase 2 (RUVBL2), and the mitochondrial protein heat shock protein family D (Hsp60) member 1 (HSPD1). Antibody titers against F-actin and HSPD1 were substantially elevated in the plasma of patients with PDAC compared with healthy donors. Thus, PCs in PDAC produce autoantibodies reacting with intracellular self-antigens, which may result from promotion of preexisting, autoreactive B cell responses. These observations indicate the chronic inflammatory microenvironment of PDAC can support the adaptive immune response.

Abstract 3150: Computational cohort discovery and coordinator-led validation to navigate potential research candidates to clinical trials

The purpose of this study was to improve the identification and solicitation of human subject candidates to augment patient enrollment to clinical trials. In the past, our enrollment efforts involved manual mechanisms that began at the time that cancer patients were presented for care, most commonly at our chemotherapy clinics. We reasoned that computational review of pathology records may be far more efficient, allowing us to screen larger numbers of patients, and may allow us to intercept patients at the time of diagnosis, rather than time of care. We thus implemented a new workflow: (1) computational query of pathology database to filter candidates based on key eligibility criteria; (2) validation of the query using a clinical research coordinator, who can then (3) navigate the patient to the trial. As a proof of concept, starting in August of 2022, we selected two gastrointestinal oncology trials, the COBRA and PACES trial, based on trial eligibility that could be easily extracted using pathologic criteria, and because these trials had low enrollment. We designed computational queries to extract cohorts of potential patients whose surgery dates and pathology staging identified potential clinical trial candidates. A coordinator performed chart-review to validate these candidates. The trial coordinator then contacted the patient’s surgical oncologist, facilitated referral to a medical oncologist, and tracked the number of patients approached and consented. Whereas in a 12-month period preceding this new workflow, we had 0 and 1 patients approached for the PACES and COBRA trial, in the 3-month period following the new intervention, we had 8 and 2 patients approached. These data suggest computational cohort building and subsequent navigation have the potential to improve enrollment onto clinical trials and motivate extension of this work to additional trials. Table(s)

Trial # of patients approached pre-intervention Computational Criteria Meeting computational criteria Coordinator validation criteria # of patients validated by coordinator # of patients connected with medical oncologist # of patients approached post-intervention PACES 0 Colorectal cancer, stage T0-T3,N0-1 Date Aug 2021 – July 2022 23 Facility location, No evidence of disease on colonoscopy performed 120 -456 days post-surgery, No chemotherapy, No other malignancy 18 8 8 COBRA 1 Colorectal cancer pT3N0resection date August 2022 – October 2022 18 ≥ 12 lymph nodes assessedPatient locationIf the subject appropriate for active surveillanceSurgery within 14-60 days of randomization 4 0 2

Citation Format: Yonah Ziemba, Kaitlin Parnahay, Paul Ward, Nalan Yurtsever, Sharon Fox, Cheryl Schleicher, Priya Singh-Shiwsankar, Vincent Vinciguerra, Joseph Herman, James M. Crawford, Daniel A. King. Computational cohort discovery and coordinator-led validation to navigate potential research candidates to clinical trials [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 3150.

Abstract 4394: Feasibility analysis of querying EHR databases for cancer clinical trial criteria

Background: In order to enroll patients for clinical trials (CT), it is common to run queries in clinical databases using CT eligibility criteria as filters and specifications. However, CT eligibility criteria are often unavailable as discrete data fields, which can interfere with CT recruitment. The purpose of this study was to identify the most commonly needed eligibility criteria that are specified in cancer CT to investigate whether and how they could be found in clinical databases.

Design: We examined the data elements needed for the trial eligibility criteria that would be used in queries for all the Breast, Gastrointestinal, Genitourinary, Head and Neck, and Cutaneous Cancer treatment trials open for enrollment across our health system. We then performed a sort-rank exercise for these eligibility criteria terms.

Results: The analysis included 33 trials and 12 data elements. Table 1 shows the number of times each eligibility criterion appeared in the 33 CTs and its feasibility for an EHR query. The data elements that appeared most frequently were Organ/Cancer Site (100%), Tumor Morphology (66.7%), Presence of Metastases (51.5%), TN Staging (39.4%), and Days Since Diagnosis (24.2%). Of these, only Organ/Cancer Site and Days Since Diagnosis were accessible as structured datapoints in our clinical databases.

Conclusions: The lack of feasibility for EHR query is likely due to the fact that healthcare information is generally stored in a discrete, structured form as a means of completing care transactions (drug orders or laboratory values) and ensuring billing compliance (ICD and outpatient CPT codes). This presents a critical challenge when data are required for CT enrollment, quality assurance metrics, and prospective and retrospective clinical research. Health systems—and by extension, their patients—would benefit from investing in structured data schemas involving AJCC staging, tumor morphology, and presence of metastases.

Eligibility criteria with corresponding number of appearances in CTs and feasibility for EHR query Eligibility criterion Number of trials with each criterion Feasibility for EHR query Organ/Cancer Site 33 (100%) Accessible (ICD codes very detailed for site and used consistently for purpose of billing) Tumor Morphology 22 (66.7%) Not accessible (Code have not been created in ICD system, SNOMED is not widely adopted, not needed for billing) Presence of Metastases 17 (51.5%) Not accessible (Not coded consistently, coded in ICD as a “secondary” malignancy but generally does not affect billing) TN Staging 13 (39.4%) Not accessible (Not coded in ICD system) Days Since Diagnosis 8 (24.2%) Accessible (Structured data captured for purpose of initial transaction) Tumor Markers and Other Lab Results 4 (12.1%) Accessible (Structured data captured by laboratory instrument for purpose of initial transaction) Immunohistochemical Biomarkers 4 (12.1%) Not accessible (Pathologist assessment documented as narrative text) History of Systemic Therapy 3 (9.1%) Accessible (NDC drug code captured with initial order in order to complete the initial transaction) Feasibility of Resection 3 (9.1%) Not accessible (Surgeon assessment documented as narrative text) Disease progression 3 (9.1%) Not accessible (Radiologist assessment documented as narrative text) Surgical Procedure 2 (6.1%) Accessible as CPT codes for outpatient surgeries as needed for billing. Not accessible for inpatient surgeries where billing is capitated as a single fee for entire hospitalization based on disease related groups Margins 2 (6.1%) Not accessible (Pathologist assessment documented as narrative text)

Citation Format: Dylan J. Cooper, Joseph Herman, Nalan Yurtsever, Sergio Garza, Daniel A. King, Yonah Ziemba. Feasibility analysis of querying EHR databases for cancer clinical trial criteria. [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 4394.

Immunotherapy and Targeted Therapy for Advanced Gastroesophageal Cancer: ASCO Guideline

PURPOSE

To develop recommendations involving targeted therapies for patients with advanced gastroesophageal cancer.

METHODS

The American Society of Clinical Oncology convened an Expert Panel to conduct a systematic review of relevant studies and develop recommendations for clinical practice.

RESULTS

Eighteen randomized controlled trials met the inclusion criteria for the systematic review.

RECOMMENDATIONS

For human epidermal growth factor receptor 2 (HER2)-negative patients with gastric adenocarcinoma (AC) and programmed death-ligand 1 (PD-L1) combined positive score (CPS) ≥ 5, first-line therapy with nivolumab and chemotherapy (CT) is recommended. For HER2-negative patients with esophageal or gastroesophageal junction (GEJ) AC and PD-L1 CPS ≥ 5, first-line therapy with nivolumab and CT is recommended. First-line therapy with pembrolizumab and CT is recommended for HER2-negative patients with esophageal or GEJ AC and PD-L1 CPS ≥ 10. For patients with esophageal squamous cell carcinoma and PD-L1 tumor proportion score ≥ 1%, nivolumab plus CT, or nivolumab plus ipilimumab is recommended; for patients with esophageal squamous cell carcinoma and PD-L1 CPS ≥ 10, pembrolizumab plus CT is recommended. For patients with HER2-positive gastric or GEJ previously untreated, unresectable or metastatic AC, trastuzumab plus pembrolizumab is recommended, in combination with CT. For patients with advanced gastroesophageal or GEJ AC whose disease has progressed after first-line therapy, ramucirumab plus paclitaxel is recommended. For HER2-positive patients with gastric or GEJ AC who have progressed after first-line therapy, trastuzumab deruxtecan is recommended. In all cases, participation in a clinical trial is recommended as it is the panel's expectation that targeted treatment options for gastroesophageal cancer will continue to evolve.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.

Immunotherapy and Targeted Therapy for Advanced Gastroesophageal Cancer: ASCO Guideline

PURPOSE

To develop recommendations involving targeted therapies for patients with advanced gastroesophageal cancer.

METHODS

The American Society of Clinical Oncology convened an Expert Panel to conduct a systematic review of relevant studies and develop recommendations for clinical practice.

RESULTS

Eighteen randomized controlled trials met the inclusion criteria for the systematic review.

RECOMMENDATIONS

For human epidermal growth factor receptor 2 (HER2)-negative patients with gastric adenocarcinoma (AC) and programmed death-ligand 1 (PD-L1) combined positive score (CPS) ≥ 5, first-line therapy with nivolumab and chemotherapy (CT) is recommended. For HER2-negative patients with esophageal or gastroesophageal junction (GEJ) AC and PD-L1 CPS ≥ 5, first-line therapy with nivolumab and CT is recommended. First-line therapy with pembrolizumab and CT is recommended for HER2-negative patients with esophageal or GEJ AC and PD-L1 CPS ≥ 10. For patients with esophageal squamous cell carcinoma and PD-L1 tumor proportion score ≥ 1%, nivolumab plus CT, or nivolumab plus ipilimumab is recommended; for patients with esophageal squamous cell carcinoma and PD-L1 CPS ≥ 10, pembrolizumab plus CT is recommended. For patients with HER2-positive gastric or GEJ previously untreated, unresectable or metastatic AC, trastuzumab plus pembrolizumab is recommended, in combination with CT. For patients with advanced gastroesophageal or GEJ AC whose disease has progressed after first-line therapy, ramucirumab plus paclitaxel is recommended. For HER2-positive patients with gastric or GEJ AC who have progressed after first-line therapy, trastuzumab deruxtecan is recommended. In all cases, participation in a clinical trial is recommended as it is the panel's expectation that targeted treatment options for gastroesophageal cancer will continue to evolve.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.

Immunotherapy and Targeted Therapy for Advanced Gastroesophageal Cancer: ASCO Guideline

PURPOSE

To develop recommendations involving targeted therapies for patients with advanced gastroesophageal cancer.

METHODS

The American Society of Clinical Oncology convened an Expert Panel to conduct a systematic review of relevant studies and develop recommendations for clinical practice.

RESULTS

Eighteen randomized controlled trials met the inclusion criteria for the systematic review.

RECOMMENDATIONS

For human epidermal growth factor receptor 2 (HER2)-negative patients with gastric adenocarcinoma (AC) and programmed death-ligand 1 (PD-L1) combined positive score (CPS) ≥ 5, first-line therapy with nivolumab and chemotherapy (CT) is recommended. For HER2-negative patients with esophageal or gastroesophageal junction (GEJ) AC and PD-L1 CPS ≥ 5, first-line therapy with nivolumab and CT is recommended. First-line therapy with pembrolizumab and CT is recommended for HER2-negative patients with esophageal or GEJ AC and PD-L1 CPS ≥ 10. For patients with esophageal squamous cell carcinoma and PD-L1 tumor proportion score ≥ 1%, nivolumab plus CT, or nivolumab plus ipilimumab is recommended; for patients with esophageal squamous cell carcinoma and PD-L1 CPS ≥ 10, pembrolizumab plus CT is recommended. For patients with HER2-positive gastric or GEJ previously untreated, unresectable or metastatic AC, trastuzumab plus pembrolizumab is recommended, in combination with CT. For patients with advanced gastroesophageal or GEJ AC whose disease has progressed after first-line therapy, ramucirumab plus paclitaxel is recommended. For HER2-positive patients with gastric or GEJ AC who have progressed after first-line therapy, trastuzumab deruxtecan is recommended. In all cases, participation in a clinical trial is recommended as it is the panel's expectation that targeted treatment options for gastroesophageal cancer will continue to evolve.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.

Immunotherapy and Targeted Therapy for Advanced Gastroesophageal Cancer: ASCO Guideline

PURPOSE

To develop recommendations involving targeted therapies for patients with advanced gastroesophageal cancer.

METHODS

The American Society of Clinical Oncology convened an Expert Panel to conduct a systematic review of relevant studies and develop recommendations for clinical practice.

RESULTS

Eighteen randomized controlled trials met the inclusion criteria for the systematic review.

RECOMMENDATIONS

For human epidermal growth factor receptor 2 (HER2)-negative patients with gastric adenocarcinoma (AC) and programmed death-ligand 1 (PD-L1) combined positive score (CPS) ≥ 5, first-line therapy with nivolumab and chemotherapy (CT) is recommended. For HER2-negative patients with esophageal or gastroesophageal junction (GEJ) AC and PD-L1 CPS ≥ 5, first-line therapy with nivolumab and CT is recommended. First-line therapy with pembrolizumab and CT is recommended for HER2-negative patients with esophageal or GEJ AC and PD-L1 CPS ≥ 10. For patients with esophageal squamous cell carcinoma and PD-L1 tumor proportion score ≥ 1%, nivolumab plus CT, or nivolumab plus ipilimumab is recommended; for patients with esophageal squamous cell carcinoma and PD-L1 CPS ≥ 10, pembrolizumab plus CT is recommended. For patients with HER2-positive gastric or GEJ previously untreated, unresectable or metastatic AC, trastuzumab plus pembrolizumab is recommended, in combination with CT. For patients with advanced gastroesophageal or GEJ AC whose disease has progressed after first-line therapy, ramucirumab plus paclitaxel is recommended. For HER2-positive patients with gastric or GEJ AC who have progressed after first-line therapy, trastuzumab deruxtecan is recommended. In all cases, participation in a clinical trial is recommended as it is the panel's expectation that targeted treatment options for gastroesophageal cancer will continue to evolve.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.

Immunotherapy and Targeted Therapy for Advanced Gastroesophageal Cancer: ASCO Guideline

PURPOSE

To develop recommendations involving targeted therapies for patients with advanced gastroesophageal cancer.

METHODS

The American Society of Clinical Oncology convened an Expert Panel to conduct a systematic review of relevant studies and develop recommendations for clinical practice.

RESULTS

Eighteen randomized controlled trials met the inclusion criteria for the systematic review.

RECOMMENDATIONS

For human epidermal growth factor receptor 2 (HER2)-negative patients with gastric adenocarcinoma (AC) and programmed death-ligand 1 (PD-L1) combined positive score (CPS) ≥ 5, first-line therapy with nivolumab and chemotherapy (CT) is recommended. For HER2-negative patients with esophageal or gastroesophageal junction (GEJ) AC and PD-L1 CPS ≥ 5, first-line therapy with nivolumab and CT is recommended. First-line therapy with pembrolizumab and CT is recommended for HER2-negative patients with esophageal or GEJ AC and PD-L1 CPS ≥ 10. For patients with esophageal squamous cell carcinoma and PD-L1 tumor proportion score ≥ 1%, nivolumab plus CT, or nivolumab plus ipilimumab is recommended; for patients with esophageal squamous cell carcinoma and PD-L1 CPS ≥ 10, pembrolizumab plus CT is recommended. For patients with HER2-positive gastric or GEJ previously untreated, unresectable or metastatic AC, trastuzumab plus pembrolizumab is recommended, in combination with CT. For patients with advanced gastroesophageal or GEJ AC whose disease has progressed after first-line therapy, ramucirumab plus paclitaxel is recommended. For HER2-positive patients with gastric or GEJ AC who have progressed after first-line therapy, trastuzumab deruxtecan is recommended. In all cases, participation in a clinical trial is recommended as it is the panel's expectation that targeted treatment options for gastroesophageal cancer will continue to evolve.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.

Immunotherapy and Targeted Therapy for Advanced Gastroesophageal Cancer: ASCO Guideline

PURPOSE

To develop recommendations involving targeted therapies for patients with advanced gastroesophageal cancer.

METHODS

The American Society of Clinical Oncology convened an Expert Panel to conduct a systematic review of relevant studies and develop recommendations for clinical practice.

RESULTS

Eighteen randomized controlled trials met the inclusion criteria for the systematic review.

RECOMMENDATIONS

For human epidermal growth factor receptor 2 (HER2)-negative patients with gastric adenocarcinoma (AC) and programmed death-ligand 1 (PD-L1) combined positive score (CPS) ≥ 5, first-line therapy with nivolumab and chemotherapy (CT) is recommended. For HER2-negative patients with esophageal or gastroesophageal junction (GEJ) AC and PD-L1 CPS ≥ 5, first-line therapy with nivolumab and CT is recommended. First-line therapy with pembrolizumab and CT is recommended for HER2-negative patients with esophageal or GEJ AC and PD-L1 CPS ≥ 10. For patients with esophageal squamous cell carcinoma and PD-L1 tumor proportion score ≥ 1%, nivolumab plus CT, or nivolumab plus ipilimumab is recommended; for patients with esophageal squamous cell carcinoma and PD-L1 CPS ≥ 10, pembrolizumab plus CT is recommended. For patients with HER2-positive gastric or GEJ previously untreated, unresectable or metastatic AC, trastuzumab plus pembrolizumab is recommended, in combination with CT. For patients with advanced gastroesophageal or GEJ AC whose disease has progressed after first-line therapy, ramucirumab plus paclitaxel is recommended. For HER2-positive patients with gastric or GEJ AC who have progressed after first-line therapy, trastuzumab deruxtecan is recommended. In all cases, participation in a clinical trial is recommended as it is the panel's expectation that targeted treatment options for gastroesophageal cancer will continue to evolve.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.

Immunotherapy and Targeted Therapy for Advanced Gastroesophageal Cancer: ASCO Guideline

PURPOSE

To develop recommendations involving targeted therapies for patients with advanced gastroesophageal cancer.

METHODS

The American Society of Clinical Oncology convened an Expert Panel to conduct a systematic review of relevant studies and develop recommendations for clinical practice.

RESULTS

Eighteen randomized controlled trials met the inclusion criteria for the systematic review.

RECOMMENDATIONS

For human epidermal growth factor receptor 2 (HER2)-negative patients with gastric adenocarcinoma (AC) and programmed death-ligand 1 (PD-L1) combined positive score (CPS) ≥ 5, first-line therapy with nivolumab and chemotherapy (CT) is recommended. For HER2-negative patients with esophageal or gastroesophageal junction (GEJ) AC and PD-L1 CPS ≥ 5, first-line therapy with nivolumab and CT is recommended. First-line therapy with pembrolizumab and CT is recommended for HER2-negative patients with esophageal or GEJ AC and PD-L1 CPS ≥ 10. For patients with esophageal squamous cell carcinoma and PD-L1 tumor proportion score ≥ 1%, nivolumab plus CT, or nivolumab plus ipilimumab is recommended; for patients with esophageal squamous cell carcinoma and PD-L1 CPS ≥ 10, pembrolizumab plus CT is recommended. For patients with HER2-positive gastric or GEJ previously untreated, unresectable or metastatic AC, trastuzumab plus pembrolizumab is recommended, in combination with CT. For patients with advanced gastroesophageal or GEJ AC whose disease has progressed after first-line therapy, ramucirumab plus paclitaxel is recommended. For HER2-positive patients with gastric or GEJ AC who have progressed after first-line therapy, trastuzumab deruxtecan is recommended. In all cases, participation in a clinical trial is recommended as it is the panel's expectation that targeted treatment options for gastroesophageal cancer will continue to evolve.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.

Immunotherapy in the Management of Esophagogastric Cancer: A Practical Review

Recent data support incorporation of immune checkpoint inhibitors into the treatment armamentarium for esophageal, gastroesophageal junction, and gastric (esophagogastric) cancer. This practical review focuses on clinical trials that influenced US Food and Drug Administration approvals and treatment guidelines in esophagogastric cancer, including the impact of location, stage, histology, human epidermal growth factor receptor 2 status, and PD-(L)1 expression on these guidelines. The role of immunotherapy in the locally advanced and metastatic setting is constantly expanding. Over the next few years, the many ongoing trials exploring immunotherapy are anticipated to bring new treatment regimens into the frontline setting with the potential to improve survival in patients with advanced disease.

Attention-deficit/hyperactivity disorder and ischemic stroke: A Mendelian randomization study

BACKGROUND

Observational studies have found an association between attention-deficit/hyperactivity disorder (ADHD) and ischemic stroke.

AIMS

The purpose of this study was to investigate whether genetic liability to ADHD has a causal effect on ischemic stroke and its subtypes.

METHODS

In this two-sample Mendelian randomization (MR) study, genetic variants (nine single-nucleotide polymorphisms; P < 5 × 10^-8) using as instrumental variables for the analysis was obtained from a genome-wide association study of ADHD with 19,099 cases and 34,194 controls. The outcome datasets for stroke and its subtypes were obtained from the MEGASTROKE consortium, with 40,585 cases and 406,111 controls. MR inverse variance-weighted method was conducted to investigate the effect of genetic liability to ADHD on ischemic stroke and its subtypes. Sensitivity analyses (median-based methods, MR-Egger, MR-robust adjusted profile scores, MR-pleiotropy residual sum and outlier) were also utilized to assess horizontal pleiotropy and remove outliers. Multivariable MR (MVMR) analyses were conducted to explore potential mediators.

RESULTS

Genetically determined ADHD (per 1 SD) was significantly associated with a higher risk of any ischemic stroke (AIS) (odds ratio (OR) = 1.15, 95% confidence interval (CI) = 1.05-1.25, P = 0.002) and large-artery atherosclerotic stroke (LAS) (OR = 1.40, 95% CI = 1.10-1.76, P = 0.005). The significant association was also found in sensitivity analyses and MVMR analyses.

CONCLUSIONS

Genetic liability to ADHD was significantly associated with an increased risk of AIS, especially LAS. The association between ADHD and LAS was independent of age of smoking initiation but mediated by coronary artery disease.

Immunotherapy and Targeted Therapy for Advanced Gastroesophageal Cancer: ASCO Guideline

PURPOSE

To develop recommendations involving targeted therapies for patients with advanced gastroesophageal cancer.

METHODS

The American Society of Clinical Oncology convened an Expert Panel to conduct a systematic review of relevant studies and develop recommendations for clinical practice.

RESULTS

Eighteen randomized controlled trials met the inclusion criteria for the systematic review.

RECOMMENDATIONS

For human epidermal growth factor receptor 2 (HER2)-negative patients with gastric adenocarcinoma (AC) and programmed death-ligand 1 (PD-L1) combined positive score (CPS) ≥ 5, first-line therapy with nivolumab and chemotherapy (CT) is recommended. For HER2-negative patients with esophageal or gastroesophageal junction (GEJ) AC and PD-L1 CPS ≥ 5, first-line therapy with nivolumab and CT is recommended. First-line therapy with pembrolizumab and CT is recommended for HER2-negative patients with esophageal or GEJ AC and PD-L1 CPS ≥ 10. For patients with esophageal squamous cell carcinoma and PD-L1 tumor proportion score ≥ 1%, nivolumab plus CT, or nivolumab plus ipilimumab is recommended; for patients with esophageal squamous cell carcinoma and PD-L1 CPS ≥ 10, pembrolizumab plus CT is recommended. For patients with HER2-positive gastric or GEJ previously untreated, unresectable or metastatic AC, trastuzumab plus pembrolizumab is recommended, in combination with CT. For patients with advanced gastroesophageal or GEJ AC whose disease has progressed after first-line therapy, ramucirumab plus paclitaxel is recommended. For HER2-positive patients with gastric or GEJ AC who have progressed after first-line therapy, trastuzumab deruxtecan is recommended. In all cases, participation in a clinical trial is recommended as it is the panel's expectation that targeted treatment options for gastroesophageal cancer will continue to evolve.Additional information is available at www.asco.org/gastrointestinal-cancer-guidelines.

Multiomic analysis for optimization of combined focal and immunotherapy protocols in murine pancreatic cancer

Background: Although combination immunotherapies incorporating local and systemic components have shown promising results in treating solid tumors, varied tumor microenvironments (TMEs) can impact immunotherapeutic efficacy. Method: We designed and evaluated treatment strategies for breast and pancreatic cancer combining magnetic resonance-guided focused ultrasound (MRgFUS) ablation and antibody therapies. With a combination of single-cell sequencing, spectral flow cytometry, and histological analyses, we profiled an immune-suppressed KPC (Kras^+/LSL-G12D; Trp53^+/LSL-R172H; Pdx1-Cre) pancreatic adenocarcinoma (MT4) model and a dense epithelial neu deletion (NDL) HER2⁺ mammary adenocarcinoma model with a greater fraction of lymphocytes, natural killer cells and activated dendritic cells. We then performed gene ontology analysis, spectral and digital cytometry to assess the immune response to combination immunotherapies and correlation with survival studies. Result: Based on gene ontology analysis, adding ablation to immunotherapy enriched immune cell migration pathways in the pancreatic cancer model and extensively enriched wound healing pathways in the breast cancer model. With CIBERSORTx digital cytometry, aCD40 + aPD-1 immunotherapy combinations enhanced dendritic cell activation in both models. In the MT4 TME, adding the combination of aCD40 antibody and checkpoint inhibitors (aPD-1 and aCTLA-4) with ablation was synergistic, increasing activated natural killer cells and T cells in distant tumors. Furthermore, ablation with immunotherapy upregulated critical Ly6c myeloid remodeling phenotypes that enhance T-cell effector function and increased granzyme and protease encoding genes by as much as 100-fold. Ablation combined with immunotherapy then extended survival in the MT4 model to a greater extent than immunotherapy alone. Conclusion: In summary, TME profiling informed a successful multicomponent treatment protocol incorporating ablation and facilitated differentiation of TMEs in which ablation is most effective.

Pancreatic Cancer Patient-derived Organoids Can Predict Response to Neoadjuvant Chemotherapy

OBJECTIVE

To evaluate if patient-derived organoids (PDOs) may predict response to neoadjuvant (NAT) chemotherapy in patients with pancreatic adenocarcinoma.

BACKGROUND

PDOs have been explored as a biomarker of therapy response and for personalized therapeutics in patients with pancreatic cancer.

METHODS

During 2017-2021, patients were enrolled into an IRB-approved protocol and PDO cultures were established. PDOs of interest were analyzed through a translational pipeline incorporating molecular profiling and drug sensitivity testing.

RESULTS

One hundred thirty-six samples, including both surgical resections and fine needle aspiration/biopsy from 117 patients with pancreatic cancer were collected. This biobank included diversity in stage, sex, age, and race, with minority populations representing 1/3 of collected cases (16% Black, 9% Asian, 7% Hispanic/Latino). Among surgical specimens, PDO generation was successful in 71% (15 of 21) of patients who had received NAT prior to sample collection and in 76% (39 of 51) of patients who were untreated with chemotherapy or radiation at the time of collection. Pathological response to NAT correlated with PDO chemotherapy response, particularly oxaliplatin. We demonstrated the feasibility of a rapid PDO drug screen and generated data within 7 days of tissue resection.

CONCLUSION

Herein we report a large single-institution organoid biobank, including ethnic minority samples. The ability to establish PDOs from chemotherapy-naive and post-NAT tissue enables longitudinal PDO generation to assess dynamic chemotherapy sensitivity profiling. PDOs can be rapidly screened and further development of rapid screening may aid in the initial stratification of patients to the most active NAT regimen.

Structure of the MRAS-SHOC2-PP1C phosphatase complex

RAS-MAPK signalling is fundamental for cell proliferation and is altered in most human cancers1-3. However, our mechanistic understanding of how RAS signals through RAF is still incomplete. Although studies revealed snapshots for autoinhibited and active RAF-MEK1-14-3-3 complexes4, the intermediate steps that lead to RAF activation remain unclear. The MRAS-SHOC2-PP1C holophosphatase dephosphorylates RAF at serine 259, resulting in the partial displacement of 14-3-3 and RAF-RAS association3,5,6. MRAS, SHOC2 and PP1C are mutated in rasopathies-developmental syndromes caused by aberrant MAPK pathway activation6-14-and SHOC2 itself has emerged as potential target in receptor tyrosine kinase (RTK)-RAS-driven tumours15-18. Despite its importance, structural understanding of the SHOC2 holophosphatase is lacking. Here we determine, using X-ray crystallography, the structure of the MRAS-SHOC2-PP1C complex. SHOC2 bridges PP1C and MRAS through its concave surface and enables reciprocal interactions between all three subunits. Biophysical characterization indicates a cooperative assembly driven by the MRAS GTP-bound active state, an observation that is extendible to other RAS isoforms. Our findings support the concept of a RAS-driven and multi-molecular model for RAF activation in which individual RAS-GTP molecules recruit RAF-14-3-3 and SHOC2-PP1C to produce downstream pathway activation. Importantly, we find that rasopathy and cancer mutations reside at protein-protein interfaces within the holophosphatase, resulting in enhanced affinities and function. Collectively, our findings shed light on a fundamental mechanism of RAS biology and on mechanisms of clinically observed enhanced RAS-MAPK signalling, therefore providing the structural basis for therapeutic interventions.

Inferring gene expression from cell-free DNA fragmentation profiles

Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.

Non-invasive metabolomics biomarkers of production efficiency and beef carcass quality traits

The inter-cattle growth variations stem from the interaction of many metabolic processes making animal selection difficult. We hypothesized that growth could be predicted using metabolomics. Urinary biomarkers of cattle feed efficiency were explored using mass spectrometry-based untargeted and targeted metabolomics. Feed intake and weight-gain was measured in steers (n = 75) on forage-based growing rations (stage-1, 84 days) followed by high-concentrate finishing rations (stage-2, 84 days). Urine from days 0, 21, 42, 63, and 83 in each stage were analyzed from steers with the greater (n = 14) and least (n = 14) average-daily-gain (ADG) and comparable dry-matter-intake (DMI; within 0.32 SD of the mean). Steers were slaughtered after stage-2. Adjusted fat-thickness and carcass-yield-grade increased in greater-ADG-cattle selected in stage-1, but carcass traits did not differ between ADG-selected in stage-2. Overall 85 untargeted metabolites segregated greater- and least-ADG animals, with overlap across diets (both stages) and breed type, despite sampling time effects. Total 18-bile acids (BAs) and 5-steroids were quantified and associated with performance and carcass quality across ADG-classification depending on the stage. Stepwise logistic regression of urinary BA and steroids had > 90% accuracy identifying efficient-ADG-steers. Urine metabolomics provides new insight into the physiological mechanisms and potential biomarkers for feed efficiency.

Chylothorax associated with sarcoidosis: a review of the literature

OBJECTIVE

To review the medical literature regarding chylothorax associated with sarcoidosis.

METHODS

A literature review of all reported cases of sarcoidosis-associated chylothorax, we included a novel case report to the analysis.

RESULTS

Of sixteen cases included in the study, 10 were women (62.5%), mean age 47±17years. In 6 subjects (37.5%) chylothorax was part of the initial presentation of sarcoidosis. Four subjects (25%) additionally suffered from lymphedema and chylous ascites, and one from chylous ascites only. Thoracic lymphadenopathy was reported for 13/16 subjects (81.3%) and lung parenchymal disease in 8/16 (50%). Compression of the thoracic duct was considered as a causative factor in 10 cases (62.5%). One case was attributed to granulomatous pleural inflammation, one to generalized lymphangiectasia, and no specific causative factors were identified in 4 remaining cases (25%). Overall mortality rate was 18.8% (3/16 subjects). Of note, all the subjects treated with corticosteroids survived.

CONCLUSIONS

Since the association of sarcoidosis with chylothorax is exceedingly rare, alternative etiologies should be pursued even when chylothorax develops in a subject with preexisting sarcoidosis. However, the possibility of sarcoidosis should be entertained when other etiologies for a newly diagnosed chylothorax are ruled out. A multidisciplinary approach is required for optimal management, both for elucidating the diagnosis and for employing therapy, which could be multimodal. A trial of immunosuppressive therapy with corticosteroids should be considered.

PAGEANT: personal access to genome and analysis of natural traits

GWASs have identified numerous genetic variants associated with a wide variety of diseases, yet despite the wide availability of genetic testing the insights that would enhance the interpretability of these results are not widely available to members of the public. As a proof of concept and demonstration of technological feasibility, we developed PAGEANT (Personal Access to Genome & Analysis of Natural Traits), usable through Graphical User Interface or command line-based version, aiming to serve as a protocol and prototype that guides the overarching design of genetic reporting tools. PAGEANT is structured across five core modules, summarized by five Qs: (i) quality assurance of the genetic data; (ii) qualitative assessment of genetic characteristics; (iii) quantitative assessment of health risk susceptibility based on polygenic risk scores and population reference; (iv) query of third-party variant databases (e.g. ClinVAR and PharmGKB) and (v) quick Response code of genetic variants of interest. Literature review was conducted to compare PAGEANT with academic and industry tools. For 2504 genomes made publicly available through the 1000 Genomes Project, we derived their genomic characteristics for a suite of qualitative and quantitative traits. One exemplary trait is susceptibility to COVID-19, based on the most up-to-date scientific findings reported.

Mechanical ventilation for older medical patients in a large tertiary medical care center

Aim

The aim of the study is to determine the factors influencing the outcomes of older ventilated medical patients in a large tertiary medical center.

Findings

Of 554 older patients (mean age 79 years) who underwent mechanical ventilation for the first time during the study period in-hospital mortality was 64.1% and overall 6-months survival was 26%. A combination of age 85 years and older, poor functional status prior to ventilation, and associated morbidity were the strongest negative predictors of survival after discharge from the hospital.

Message

The identification of factors predicting poor survival of mechanical ventilation will assist policy makers in clinical decision-making particularly at times of limited health resources.

Background

The development of technologies for the prolongation of life has resulted in an increase in the number of older ventilated patients in internal medicine and chronic care wards. Our study aimed to determine the factors influencing the outcomes of older ventilated medical patients in a large tertiary medical center.

Methods

We performed a prospective observational cohort study including all newly ventilated medical patients aged 65 years and older over a period of 18 months. Data were acquired from computerized medical records and from an interview of the medical personnel initiating mechanical ventilation.

Results

A total of 554 patients underwent mechanical ventilation for the first time during the study period. The average age was 79 years, and 80% resided at home. Following mechanical ventilation, 8% died in the emergency room, and the majority of patients (351; 63%) were hospitalized in internal medicine wards. In-hospital mortality was 64.1%, with 48% dying during the first week of hospitalization. Overall 6-months survival was 26%. We found that a combination of age 85 years and older, functional status prior to ventilation, and associated morbidity (diabetes with target organ injury and/or oncological solid organ disease) were the strongest negative predictors of survival after discharge from the hospital.

Conclusion

Mechanical ventilation at older age is associated with poor survival and it is possible to identify factors predicting survival. In the midst of the COVID-19 pandemic, the findings of this study may help in the decision-making process regarding mechanical ventilation for older people.

Interaction between genetic predisposition, smoking, and dementia risk: a population-based cohort study

We evaluated whether the association between cigarette smoking and dementia risk is modified by genetic predisposition including apolipoprotein E (APOE) genotype and polygenic risk (excluding the APOE region). We included 193,198 UK Biobank participants aged 60–73 years without dementia at baseline. Of non-APOE-ε4 carriers, 0.89% (95% CI 0.73–1.08%) current smokers developed dementia compared with 0.49% (95% CI 0.44–0.55%) of never smokers (adjusted HR 1.78; 95% CI 1.39–2.29). In contrast, of one APOE-ε4 allele carriers, 1.69% (95% CI 1.31–2.12%) current smokers developed dementia compared with 1.40% (95% CI 1.25–1.55%) of never smokers (adjusted HR 1.06; 95% CI 0.77–1.45); of two APOE-ε4 alleles carriers, 4.90% (95% CI 2.92–7.61%) current smokers developed dementia compared with 3.87% (95% CI 3.11–4.74%) of never smokers (adjusted HR 0.94; 95% CI 0.49–1.79). Of participants with high polygenic risk, 1.77% (95% CI 1.35–2.27%) current smokers developed dementia compared with 1.05% (95% CI 0.91–1.21%) of never smokers (adjusted HR 1.63; 95% CI 1.16–2.28). A significant interaction was found between APOE genotype and smoking status (P = 0.002) while no significant interaction was identified between polygenic risk and smoking status (P = 0.25). APOE genotype but not polygenic risk modified the effect of smoking on dementia risk.

Polygenic Scores and Parental Predictors: An Adult Height Study Based on the United Kingdom Biobank and the Framingham Heart Study

Human height is a polygenic trait, influenced by a large number of genomic loci. In the pre-genomic era, height prediction was based largely on parental height. More recent predictions of human height have made great strides by integrating genotypic data from large biobanks with improved statistical techniques. Nevertheless, recent studies have not leveraged parental height, an added feature that we hypothesized would offer complementary predictive value. In this study, we assessed the predictive power of polygenic risk scores (PRS) combined with the traditional parental height predictors. Our study analyzed genotypic data and parental height from 1,071 trios from the United Kingdom Biobank and 444 trios from the Framingham Heart Study. We explored a series of statistical models to fully evaluate the performance of several PRS constructed together with parental information and proposed a model we call PRS++ that includes gender, parental height, and PRSs of parents and proband. Our estimate of height with an R² of ∼0.82 is, to our knowledge, the most accurate estimate yet achieved for predicting human adult height. Without parental information, the R² from the best PRS-driven model is ∼0.73. In summary, using adult height prediction as an example, we demonstrated that traditional predictors still play important roles and merit integration into the current trends of intensive PRS approaches.

Pancreatic INI1-deficient undifferentiated rhabdoid carcinoma achieves complete clinical response on gemcitabine and nab-paclitaxel following immediate progression on FOLFIRINOX: a case report

INTRODUCTION

INI1-deficient undifferentiated rhabdoid carcinoma is a rare pancreatic carcinoma for which the optimal treatment is unknown. Pancreatic ductal adenocarcinoma, the most common histology of pancreas cancer, is treated with combination chemotherapy in the advanced setting, a strategy supported by strong evidence in well powered studies. In patients with excellent performance status, first-line treatment usually consists of the three-drug regimen FOLFIRINOX, with the combination of gemcitabine with nab-paclitaxel, typically less toxic than the three-drug regimen, reserved for second-line therapy. Given the lack of published reports describing treatment outcomes for patients with rare forms of pancreatic cancer, the same treatment approach used for pancreatic ductal adenocarcinoma is typically employed.

OBSERVATION

This case describes a patient with metastatic pancreatic INI1-deficient undifferentiated rhabdoid carcinoma who was primarily resistant to FOLFIRINOX therapy but who then achieved an immediate, marked and sustained response to gemcitabine with nab-paclitaxel.

CONCLUSION

Given the lack of data informing on optimal management of INI1-deficient pancreatic undifferentiated rhabdoid carcinoma, and the exceptional response achieved by gemcitabine with nab-paclitaxel, this case report highlights a surprising and potentially informative anecdote. Additional studies are needed to confirm responses observed in this report which when taken together may strongly influence first-line therapy choice for this rare malignancy. Given the difficult in acquiring sufficient numbers of these rare histologies in any one institution, multi-institution collaboration in studying outcomes of rare pancreatic malignancies is likely essential.

Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy

Immunotherapy fails to cure most cancer patients. Preclinical studies indicate that radiotherapy synergizes with immunotherapy, promoting radiation-induced antitumor immunity. Most preclinical immunotherapy studies utilize transplant tumor models, which overestimate patient responses. Here, we show that transplant sarcomas are cured by PD-1 blockade and radiotherapy, but identical treatment fails in autochthonous sarcomas, which demonstrate immunoediting, decreased neoantigen expression, and tumor-specific immune tolerance. We characterize tumor-infiltrating immune cells from transplant and primary tumors, revealing striking differences in their immune landscapes. Although radiotherapy remodels myeloid cells in both models, only transplant tumors are enriched for activated CD8+ T cells. The immune microenvironment of primary murine sarcomas resembles most human sarcomas, while transplant sarcomas resemble the most inflamed human sarcomas. These results identify distinct microenvironments in murine sarcomas that coevolve with the immune system and suggest that patients with a sarcoma immune phenotype similar to transplant tumors may benefit most from PD-1 blockade and radiotherapy.

PERHAPS: Paired-End short Reads-based HAPlotyping from next-generation Sequencing data

The identification of rare haplotypes may greatly expand our knowledge in the genetic architecture of both complex and monogenic traits. To this aim, we developed PERHAPS (Paired-End short Reads-based HAPlotyping from next-generation Sequencing data), a new and simple approach to directly call haplotypes from short-read, paired-end Next Generation Sequencing (NGS) data. To benchmark this method, we considered the APOE classic polymorphism (*1/*2/*3/*4), since it represents one of the best examples of functional polymorphism arising from the haplotype combination of two Single Nucleotide Polymorphisms (SNPs). We leveraged the big Whole Exome Sequencing (WES) and SNP-array data obtained from the multi-ethnic UK BioBank (UKBB, N=48,855). By applying PERHAPS, based on piecing together the paired-end reads according to their FASTQ-labels, we extracted the haplotype data, along with their frequencies and the individual diplotype. Concordance rates between WES directly called diplotypes and the ones generated through statistical pre-phasing and imputation of SNP-array data are extremely high (>99%), either when stratifying the sample by SNP-array genotyping batch or self-reported ethnic group. Hardy-Weinberg Equilibrium tests and the comparison of obtained haplotype frequencies with the ones available from the 1000 Genome Project further supported the reliability of PERHAPS. Notably, we were able to determine the existence of the rare APOE*1 haplotype in two unrelated African subjects from UKBB, supporting its presence at appreciable frequency (approximatively 0.5%) in the African Yoruba population. Despite acknowledging some technical shortcomings, PERHAPS represents a novel and simple approach that will partly overcome the limitations in direct haplotype calling from short read-based sequencing.

Clinical and Radiological Characteristics of Patients Diagnosed with Spontaneous Pneumothorax: Treatment Options and Clinical Outcomes. A Retrospective Analysis 2004 to 2017

BACKGROUND

Primary spontaneous pneumothorax (PSP) tends to occur in young adults without underlying lung diseases and is usually followed by limited symptoms, while secondary spontaneous pneumothorax (SSP) is a complication of a pre-existing lung disease. Surprisingly, for such common conditions, there is a considerable inconsistency regarding management guidelines.

OBJECTIVES

To evaluate the risk factors for spontaneous pneumothoraxes and to summarize outcomes and complications based on our clinical experience.

METHODS

This retrospective study group was comprised of 250 consecutive patients older than 18 years of age who were diagnosed with spontaneous pneumothorax and hospitalized at the Meir Medical Center (2004-2017). Data on demographic characteristics, indicating symptoms, chest X-rays, and chest computed tomography (CT) results were collected. Our experience and outcomes were then compared to a large multicenter study.

RESULTS

Most of the patients were male (85%) and past or current smokers; 69% presented with PSP, while the rest were SSP. No occupational relation was noted. About 55% of the cases presented with a moderate or large pneumothorax (over 1/3 hemithorax). Most patients (56%) required chest tube drainage and 20% undergone surgery. Nearly 10% presented with a recurrent pneumothorax with the mean time to recurrence being 11 ± 20 days. Although the length of hospital stay of patients that underwent surgery was the longest (P < 0.001) for both PSP and SSP, the recurrence rate was actually reduced, suggesting some benefit for the surgical treatment option.

CONCLUSIONS

Our experience showed that the traditional approach to the PSP treatment should be further considered, as previously suggested.

Marked Decrease in CA 19-9 Level Belies Rapidly Progressive Lymphangitic Carcinomatosis in a Case of Metastatic Pancreatic Cancer

Background: The CA 19-9 tumor marker is commonly used alongside imaging to trend chemotherapy response in patients with pancreatic ductal adenocarcinoma.

Presentation: We describe an unusual clinical case of metastatic pancreatic cancer who achieved a marked decline in CA 19-9 but paradoxically developed widespread pulmonary lymphangitic carcinomatosis leading to rapid clinical decline and death.

Conclusions: This case highlights the limitations of using the CA 19-9 tumor marker in isolation.

Admission Rate of Patients With Major Psychiatric Disorders to the Intensive Care Unit

BACKGROUND

Major psychiatric disorders such as major depression and schizophrenia interfere with patients' life activities and ability to function. These disorders correlate with a higher prevalence of medical and psychiatric comorbidities.

OBJECTIVE

To compare the admission rate of patients with major psychiatric disorders between the intensive care unit and other departments in a tertiary care center.

METHODS

In a retrospective study of records of 238 721 patients, data were collected from admission files and the intensive care unit computer system. The study group was 245 patients with psychiatric disorders admitted to the intensive care unit. Control groups were 9226 psychiatric patients in other hospital departments and 3032 nonpsychiatric patients in the intensive care unit.

RESULTS

A major psychiatric disorder was diagnosed twice as often in the 3277 patients admitted to the intensive care unit as in patients admitted to other departments (7.5% vs 3.8%, P < .001). The study group had fewer male patients than did the nonpsychiatric intensive care unit group (52% vs 66%, P < .001); the age distribution was similar. Patients with a psychiatric disorder required longer stays than other intensive care unit patients. However, their mortality rate was significantly lower (8.57% vs 17.1%, P = .001). A direct correlation between the admission and a psychiatric condition was found in one-third of admissions in the study group.

CONCLUSIONS

Psychiatric patients' admission rate to the intensive care unit was significantly higher than their admission rate to other departments. Their intensive care unit stays were also longer, which may increase resource use.

The Profile of COPD Patients with Prolonged Hospitalizations: A Retrospective Analysis of 200 Hospital Admissions

BACKGROUND

Patients with severe chronic obstructive pulmonary disease (COPD) experience frequent exacerbations and need to be hospitalized, resulting in an economic and social burden. Although data exist regarding reasons of frequent hospitalizations, there is no data available about the impact on the length of stay (LOS).

OBJECTIVES

To characterize the causes of prolonged hospitalizations in COPD patients.

METHODS

A retrospective study was conducted of patients who were diagnosed and treated in the pulmonary department for severe COPD exacerbations. All patient demographic data and medical history were collected. Data regarding the disease severity were also collected (including Global Initiative for Obstructive Lung Disease [GOLD] criteria, pulmonologist follow-up, prior hospitalizations, and LOS).

RESULTS

The study comprised 200 patients, average age 69.5 ± 10.8 years, 61% males. Of these patients, 89 (45%) were hospitalized for up to 4 days, 111 (55%) for 5 days or more, and 34 (17%) for more than 7 days. Single patients had longer LOS compared with married patients (48% vs. 34%, P = 0.044). Multivariate analysis showed that the number of prior hospital admissions in the last year was a predictor of LOS (P = 0.038, odds ratio [OR] = 0.807, 95% confidence interval [95%CI] = 0.659-0.988), as well as the use of non-invasive respiratory support by bilevel positive airway pressure (BiPAP) during the hospitalization (P = 0.024, OR = 4.662, 95%CI = 1.229-17.681).

CONCLUSIONS

Fewer previous hospitalizations due to COPD exacerbations and the need for non-invasive respiratory support by BiPAP were found as predictors of longer LOS.

Direct on-the-spot detection of SARS-CoV-2 in patients

IMPACT STATEMENT

Humanity is currently experiencing a global pandemic with devastating implications on human health and the economy. Most countries are gradually exiting their lockdown state. We are currently lacking rapid and simple viral detections, especially methods that can be performed in the household. Here, we applied RT-LAMP directly on human clinical swabs and self-collected saliva samples. We adjusted the method to allow simple and rapid viral detection, with no RNA purification steps. By testing our method on over 180 human samples, we determined its sensitivity, and by applying it to other viruses, we determined its specificity. We believe this method has a promising potential to be applied world-wide as a simple and cheap surveillance test for SARS-CoV-2.

Abstract 4334: Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer

Little is known about the genomic features of brain metastases from colorectal cancer (CRC) and the contributing genetic factors. We conducted an analysis of large-scale structural aberrations, including chromosome aneuploidies, with a method called linked-read whole genome sequencing and a new somatic rearrangement detection software tool (ZoomX) to better understand the genomic architecture of brain metastases from CRC. We resolved on average 145 distal inter- and intra-chromosomal somatic junctions per sample with their exact haplotype information and basepair level breakpoints. In addition, we used a new haplotyping method based on these imbalances to generate cancer chromosome haplotypes of up to 146 Mbp long. We identified extensive chromosomal-level instability (CIN) in these cancer genomes, with an average of 90 large-scale copy number aberrations per sample in sizes ranging from hundreds of Kbp to hundreds of Mbp. A substantial fraction of CIN is likely attributable to earlier chromothripsis events. For example, we identified multiple chromothripsis events disrupting the loci of known cancer genes such as TP53, an essential colon cancer driver. We identified novel rearrangements including an oncogenic gene fusion; e.g. SET/DPP10 among these metastatic samples. A majority of chromosome arms demonstrated an allelic imbalance across all of the samples. In summary, the analysis revealed pervasive chromosome-level genome instability as a potential contributor to devastating brain invasion by CRC. It also demonstrated the advantages of linked-read whole genome sequencing. This approach is cost-effective and represents a high-resolution tool to assess genome-wide rearrangements and to generate megabase-scale haplotypes.

Citation Format: Li C. Xia, John M. Bell, Christina Wood-Bouwens, Daniel A. King, GiWon Shin, Stephanie Greer, Ian D. Connolly, Melanie H. Gephart, Hanlee P. Ji. Linked read whole genome sequencing reveals pervasive chromosomal level instability and novel rearrangements in brain metastases from colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4334.

Characterization of variability in pork carcass composition and primal quality,

The objective was to characterize the factors and production practices that contribute to variation in pork composition and quality. It is possible the variation in pork quality traits, such as color, marbling, and tenderness, contributes to reduced customer confidence in the predictability of finished product quality and, therefore, pork products becoming less competitive for consumer dollars. Pigs raised in 8 different barns representing 2 seasons (hot and cold) and 2 production focuses (lean and quality) were used in this study. Pigs were marketed in 3 groups from each barn and marketing procedures followed commercial marketing procedures. Data were collected on a total of 7,684 pigs. The mivque0 option of the VARCOMP procedure in SAS was used to evaluate the proportion of variation each independent variable (season, production focus, marketing group, sex, and random variation) contributed to total variance. Random variation including inherent biological differences, as well as factors not controlled in this study, contributed the greatest proportion to total variation for each carcass composition and quality trait. Pig and other factors contributed to 93.5% of the variation in HCW, and marketing group, sex, season, and production focus accounted for 4.1, 1.4, 0.8, and 0.3%, respectively. Variation in percent carcass lean was attributed to production focus (36.4%), sex (15.8%), and season (10.2%). Pig and other factors contributed the greatest percentage of total variation (39.4%). Loin weight variation was attributed to production focus (21.4%), sex (5.4%), season (2.7%), marketing group (1.8%), and pig (68.7%). Belly weight variation was attributed to pig (88.9%), sex (4.1%), marketing group (3.8%), production focus (3.0%), and season (0.1%). Variation in ham weight was attributed to pig and other factors (93.9%), marketing group (2.8%), production focus (2.2%), and season (1.1%). Ultimate pH variation was attributed to pig (88.5%), season (6.2%), production focus (2.4%), marketing group (2.2%), and sex (0.7%). Aside from pig (71.9%), production focus (14.0%) was the next largest contributor to variation in iodine value followed by sex (13.2%) and marketing group (0.9%). Variation in carcass quality and composition could be accounted for, but the greatest percentage of variation was due to factors not accounted for in normal marketing practices.

Predicting aged pork quality using a portable Raman device

The utility of Raman spectroscopic signatures of fresh pork loin (1 d & 15 d postmortem) in predicting fresh pork tenderness and slice shear force (SSF) was determined. Partial least square models showed that sensory tenderness and SSF are weakly correlated (R² = 0.2). Raman spectral data were collected in 6 s using a portable Raman spectrometer (RS). A PLS regression model was developed to predict quantitatively the tenderness scores and SSF values from Raman spectral data, with very limited success. It was discovered that the prediction accuracies for day 15 post mortem samples are significantly greater than that for day 1 postmortem samples. Classification models were developed to predict tenderness at two ends of sensory quality as "poor" vs. "good". The accuracies of classification into different quality categories (1st to 4th percentile) are also greater for the day 15 postmortem samples for sensory tenderness (93.5% vs 76.3%) and SSF (92.8% vs 76.1%). RS has the potential to become a rapid on-line screening tool for the pork producers to quickly select meats with superior quality and/or cull poor quality to meet market demand/expectations.

Effect of packaging type during postmortem aging and degree of doneness on pork chop sensory traits of loins selected to vary in color and marbling

The objective was to determine the interactions between packaging type and degree of doneness on sensory traits of pork loins classified based on the newly proposed USDA quality grades. A total of 144 loins were selected from 2 groups of pigs (lean growth or meat quality production focus) to represent as much variation in visual color and marbling as possible. Selection was achieved with a VQG grading camera. The ventral surface of the loins was evaluated for loin quality traits at 1 d postmortem. At 2 d postmortem loins were sliced into 28-mm-thick chops. Chop within each loin was randomly assigned to either individual vacuum packages or to individual Styrofoam trays and overwrapped in polyvinyl chloride (PVC) oxygen permeable film. Overwrapped PVC packages were then placed in bulk packages and flushed with a gas mixture that contained approximately 0.4% carbon monoxide, 30% carbon dioxide, and 80% nitrogen. Vacuum-packaged chops were aged until 14 d postmortem. Chops packaged in PVC overwrap were aged until 9 d postmortem in the bulk packages, then placed on simulated retail display until 14 d postmortem. Chops from each packaging type were cooked to an internal temperature of either 63 °C or 71 °C for the evaluation of slice shear force (SSF) or for evaluation of tenderness, juiciness, and flavor by a trained panel. Data were analyzed as split-split plot design with production focus of the pigs, proposed USDA quality grade, packaging type, and degree of doneness as fixed effects. While there were main effect differences between production focuses, there were no interactions with production focus. There were also no 3-way (P ≥ 0.19) interactions and only one 2-way interaction among quality grade, packaging type, or degree of doneness. There were no differences in sensory tenderness (P = 0.30), juiciness (P = 0.49), flavor (P = 0.89), SSF (P = 0.13), or cook loss (P = 0.06) among USDA quality grades. There were no differences in sensory tenderness (P = 0.06), juiciness (P = 0.32), flavor (P = 0.74), SSF (P = 0.99), or cook loss (P = 0.12) between chops aged in vacuum packages or PVC packages. Chops cooked to 63 °C were 4.6% more tender (P < 0.0001), 10.1% juicier (P < 0.0001), and 2.9% less flavorful (P = 0.01) than chops cooked to 71 °C. These data suggest that cooking chops to 63 °C rather than 71 °C was a more effective way to improve tenderness and juiciness than selecting chops of a certain quality grade or altering packaging postmortem.

Detection of structural mosaicism from targeted and whole-genome sequencing data

Structural mosaic abnormalities are large post-zygotic mutations present in a subset of cells and have been implicated in developmental disorders and cancer. Such mutations have been conventionally assessed in clinical diagnostics using cytogenetic or microarray testing. Modern disease studies rely heavily on exome sequencing, yet an adequate method for the detection of structural mosaicism using targeted sequencing data is lacking. Here, we present a method, called MrMosaic, to detect structural mosaic abnormalities using deviations in allele fraction and read coverage from next-generation sequencing data. Whole-exome sequencing (WES) and whole-genome sequencing (WGS) simulations were used to calculate detection performance across a range of mosaic event sizes, types, clonalities, and sequencing depths. The tool was applied to 4911 patients with undiagnosed developmental disorders, and 11 events among nine patients were detected. For eight of these 11 events, mosaicism was observed in saliva but not blood, suggesting that assaying blood alone would miss a large fraction, possibly >50%, of mosaic diagnostic chromosomal rearrangements.

Postmortem protein degradation is a key contributor to fresh pork loin tenderness

The objective of this study was to determine factors that influence tenderness independent of variation in pH, color, or marbling. To achieve the objective, 2 sample groups were chosen from a population of 159 pork loins aged 11 to 16 d. Predetermined ranges (ultimate pH, 5.54 to 5.86; marbling score, 1.0 to 3.0; percent total lipid, 1.61 to 3.37%) were defined for inclusion of individual loins in the study. The pork loins with the greatest ( = 12) and least ( = 12) Instron star probe values were assigned to 2 classification groups. The high star probe group had an average star probe that was 2.8 kg greater than the low star probe group (7.75 vs. 4.95 kg). Pork quality and sensory characteristics of pH, subjective and instrumental color values, cook loss, sensory tenderness, chewiness, juiciness, pork flavor, and off flavor were determined on fresh, never frozen pork chops. Lipid content, sarcomere length, myosin heavy-chain profile, and calpain autolysis were determined. Degradation of troponin-T, desmin, filamin, and titin were evaluated on the protein extracts from each sample. Pork loin pH, subjective color scores, Minolta L values, sarcomere length, and myosin heavy-chain composition were not different across groups. Chops from the low star probe group had a significantly greater marbling score (2.3 vs. 1.9) and lipid content (2.61 vs. 2.23%). Calpain-1 was completely autolyzed in both high and low star probe samples, demonstrating that calpain-1 potentially had been active in all samples. Low star probe whole-muscle protein extracts had more troponin-T ( < 0.01), desmin ( < 0.01), and filamin degradation ( < 0.01) than high star probe samples. Both classification groups showed degradation of titin. Remarkably, some high star probe samples still had observable intact bands of titin on SDS-PAGE gels. These results demonstrate that significant variation in instrumental tenderness is observed within a moderate pH range. Lipid content and proteolysis both appear to contribute to this variation.

Effects of dietary protein concentration and ractopamine hydrochloride on performance and carcass characteristics of finishing beef steers

Ractopamine hydrochloride (RAC) is used in the feedlot industry to increase daily gain, improve feed efficiency, and increase HCW. However, little work has been done to determine whether additional protein is needed in the diet to maximize the benefit of RAC in beef cattle. Objectives of our experiment were to determine if feeding additional CP in conjunction with RAC would improve animal performance and carcass characteristics. Therefore, an experiment was conducted using finishing diets containing 13.5 or 17.5% CP with 0 or 300 mg of RAC for 30 to 33 d at the end of the finishing period. Beef steers ( = 438; 387.8 ± 1.9 kg initial BW) were randomly assigned to 1 of 4 treatments in a 2 × 2 factorial arrangement (16 pens total, 4 pens/treatment). No interactions between feeding RAC and CP level were detected ( > 0.19) for animal performance or carcass traits. Final BW did not differ among treatment ( = 0.37); however, final BW had a tendency to be 2% greater ( = 0.07) when the 13.5% CP diet was fed. Dry matter intake was not different between steers fed 0 or 300 mg/d of RAC ( = 0.20), yet DMI was 12% greater for cattle fed the 13.5% CP compared with steers fed the 17.5% CP diet ( < 0.01). Daily gain did not differ for cattle fed different levels of RAC or CP ( > 0.16). The G:F was 3.6% greater for cattle fed 300 vs. 0 mg/d of RAC ( = 0.04). The G:F was 8.7% greater for cattle fed the 17.5% diet vs. the 13.5% CP diet ( < 0.01), which can be attributed to the decreased DMI for cattle fed the 17.5% CP diet. Hot carcass weight was not different for steers fed 0 or 300 mg/d of RAC ( = 0.36) or for steers fed the 13.5% diet vs. 17.5% CP diet ( = 0.93). Dressing percentage was 1.5% greater for cattle fed 300 vs. 0 mg/d of RAC ( = 0.05) but was not different between cattle fed the different CP levels in the diet ( = 0.16). Longissimus area, adjusted 12th-rib fat, and marbling score did not differ across RAC or CP treatments ( > 0.26). Additionally, no differences in USDA yield grade or percentage of cattle grading USDA Choice were detected for RAC or CP treatments ( > 0.26), which also supports the idea that quality grade of cattle fed RAC at the same level of fatness is not impacted. Our data indicate excess protein did not enhance the response to RAC, and furthermore, the improved performance from RAC reported by others was not observed other than a small increase in G:F.

The effects of degree of dark cutting on tenderness and sensory attributes of beef

The objective of this study was to determine the effect of degree of dark cutting (DC) on the tenderness, juiciness, and flavor attributes of beef. During carcass grading at a large U.S. commercial beef harvesting facility, DC carcasses ( = 160) and matching normal control (NC) carcasses ( = 160) were selected. Longissimus lumborum (LL) pH was determined and DC carcasses were classified as severe (severe dark cutter [SEDC]; mean pH = 6.9; = 40), moderate (moderate dark cutter [MODC]; mean pH = 6.6; n = 40), mild (mild dark cutter [MIDC]; mean pH = 6.4; = 40), or shady (shady dark cutter [SHDC]; mean pH = 6.1; = 40). Strip loins were obtained from the left carcass sides, vacuum-packaged, and aged at 1°C. Slice shear force (SSF) was measured (14 d postmortem) fresh (never frozen), and trained descriptive sensory analysis of tenderness, juiciness, and flavor was measured (13 d postmortem) on frozen/thawed LL steaks. Cooked SSF pieces were frozen and used for western blotting of desmin to determine extent of postmortem proteolysis. Thaw and cook loss decreased as intensity of DC increased, with SEDC having the lowest loss (1.83 and 10.1%, respectively) compared with NC (3.37 and 14.9%, respectively). Slice shear force was higher (P < 0.05) for SHDC (25.6 kg) and MIDC (22.9 kg) compared with SEDC (16.8 kg), MODC (19.4 kg), and NC (17.8 kg). Sarcomere length was shorter ( < 0.05) between DC class (1.66, 1.67, 1.71, and 1.73 μm for SEDC, MODC, MIDC, and SHDC, respectively) and NC (1.86 μm). Postmortem proteolysis of desmin was greater ( < 0.05) for NC compared with all DC classes (59.83% vs. 49.20, 40.31, 42.07, and 43.30% for SEDC, MODC, MIDC, and SHDC, respectively). Trained sensory panel ratings for tenderness differed ( < 0.05) among DC class with SEDC (6.51) the most tender followed by MODC (6.04) and then MIDC (5.19), whereas SHDC (4.66) and NC (4.93) were the toughest. Juiciness ratings differed ( < 0.05) among each DC class (5.9, 5.7, 5.4, and 5.2 for SEDC, MODC, MIDC, and SHDC, respectively), with no difference between MIDC or SHDC compared with NC (5.23). Fat-like, rancid, heated oil, chemical, and musty/earthy/hummus flavors increased ( < 0.05) whereas metallic, sour, and salty flavors decreased as severity of DC increased. This study showed DC and NC differed in LL tenderness, juiciness, and flavor. The direction and/or magnitude of those differences were greatly dependent on severity of DC. Steaks with intermediate pH (SHDC and MIDC) are most likely to be tough and are regularly included in U.S. Select and U.S. Choice product lines.

Comparison of variability in pork carcass composition and quality between barrows and gilts

Pigs ( = 8,042) raised in 8 different barns representing 2 seasons (cold and hot) and 2 production focuses (lean growth and meat quality) were used to characterize variability of carcass composition and quality traits between barrows and gilts. Data were collected on 7,684 pigs at the abattoir. Carcass characteristics, subjective loin quality, and fresh ham face color (muscles) were measured on a targeted 100% of carcasses. Fresh belly characteristics, boneless loin weight, instrumental loin color, and ultimate loin pH measurements were collected from 50% of the carcasses each slaughter day. Adipose tissue iodine value (IV), 30-min loin pH, LM slice shear force, and fresh ham muscle characteristic measurements were recorded on 10% of carcasses each slaughter day. Data were analyzed using the MIXED procedure of SAS as a 1-way ANOVA in a randomized complete block design with 2 levels (barrows and gilts). Barn (block), marketing group, production focus, and season were random variables. A 2-variance model was fit using the REPEATED statement of the MIXED procedure, grouped by sex for analysis of least squares means. Homogeneity of variance was tested on raw data using Levene's test of the GLM procedure. Hot carcass weight of pigs (94.6 kg) in this study was similar to U.S. industry average HCW (93.1 kg). Therefore, these data are representative of typical U.S. pork carcasses. There was no difference ( ≥ 0.09) in variability of HCW or loin depth between barrow and gilt carcasses. Back fat depth and estimated carcass lean were more variable ( ≤ 0.0001) and IV was less variable ( = 0.05) in carcasses from barrows than in carcasses from gilts. Fresh belly weight and thickness were more variable ( ≤ 0.01) for bellies of barrows than bellies of gilts, but there was no difference in variability for belly length, width, or flop distance ( ≥ 0.06). Fresh loin subjective color was less variable ( < 0.01) and subjective marbling was more variable ( < 0.0001) in loins from barrows than in those from gilts, but there were no differences ( ≥ 0.08) in variability for any other loin traits or fresh ham traits. Overall, traits associated with carcass fatness, including back fat depth, belly thickness, and marbling, but not IV, were more variable in carcasses from barrows than in carcasses from gilts, whereas minimal differences in variability existed between carcasses of barrows and carcasses of gilts for traits associated with carcass muscling and lean quality.