Alcohol and colorectal cancer risk subclassified by mutational signatures of DNA mismatch repair deficiency

BACKGROUND

We examined whether the association between alcohol consumption and CRC incidence was stronger for tumors with higher contributions of defective MMR (dMMR)-related tumor mutational signatures (TMSs).

METHODS

We used data from 227,916 men and women who participated in the Nurses' Health Study (1980-2016), the Nurses' Health Study II (1991-2017), and the Health Professionals Follow-up Study (1986-2016). Dietary data was collected every 4 years through validated food frequency questionnaires. Relative contributions of two dMMR-related TMSs (c-dMMRa/SBS15 and c-dMMRb/SBS26) were quantified using whole-exome sequencing data in a subset of incident CRC cases. Duplication-method Cox proportional hazards regression models were used to assess the association between alcohol consumption and the risk of CRC subtypes according to different contributions of the TMSs. All statistical tests were 2-sided.

RESULTS

We documented 825 incident CRC cases with available TMS data over 26-36 years of follow-up. The association between alcohol consumption and CRC incidence was stronger for tumors with higher contributions of c-dMMRb/SBS26 (P-heterogeneitytrend = 0.02) compared to tumors with lower contributions of this TMS. Compared with nondrinkers, drinkers with ≥15 g/d of alcohol had a high risk of c-dMMRb/SBS26-high CRC [multivariable-adjusted HR: 2.43 (95% CI: 1.55-3.82)], but not c-dMMRb/SBS26-low CRC [0.86 (95% CI: 0.57-1.28)] or c-dMMRb/SBS26-moderate CRC [1.14 (95% CI: 0.76-1.71)]. No significant differential associations were observed for c-dMMRa/SBS15 (P-heterogeneitytrend = 0.41).

CONCLUSIONS

High alcohol consumption was associated with an increased incidence of CRC containing higher contributions of c-dMMRb/SBS26, suggesting that alcohol consumption may be involved in colorectal carcinogenesis through the DNA mismatch repair pathway.

Protein biomarkers and alternatively methylated cell-free DNA detect early stage pancreatic cancer

OBJECTIVE

Pancreatic ductal adenocarcinoma (PDAC) is commonly diagnosed at an advanced stage. Liquid biopsy approaches may facilitate detection of early stage PDAC when curative treatments can be employed.

DESIGN

To assess circulating marker discrimination in training, testing and validation patient cohorts (total n=426 patients), plasma markers were measured among PDAC cases and patients with chronic pancreatitis, colorectal cancer (CRC), and healthy controls. Using CA19-9 as an anchor marker, measurements were made of two protein markers (TIMP1, LRG1) and cell-free DNA (cfDNA) pancreas-specific methylation at 9 loci encompassing 61 CpG sites.

RESULTS

Comparative methylome analysis identified nine loci that were differentially methylated in exocrine pancreas DNA. In the training set (n=124 patients), cfDNA methylation markers distinguished PDAC from healthy and CRC controls. In the testing set of 86 early stage PDAC and 86 matched healthy controls, CA19-9 had an area under the receiver operating characteristic curve (AUC) of 0.88 (95% CI 0.83 to 0.94), which was increased by adding TIMP1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.06), LRG1 (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02) or exocrine pancreas-specific cfDNA methylation markers at nine loci (AUC 0.92; 95% CI 0.88 to 0.96; p=0.02). In the validation set of 40 early stage PDAC and 40 matched healthy controls, a combined panel including CA19-9, TIMP1 and a 9-loci cfDNA methylation panel had greater discrimination (AUC 0.86, 95% CI 0.77 to 0.95) than CA19-9 alone (AUC 0.82; 95% CI 0.72 to 0.92).

CONCLUSION

A combined panel of circulating markers including proteins and methylated cfDNA increased discrimination compared with CA19-9 alone for early stage PDAC.

Search for Heavy Neutral Leptons in Electron-Positron and Neutral-Pion Final States with the MicroBooNE Detector

We present the first search for heavy neutral leptons (HNLs) decaying into νe^{+}e^{-} or νπ^{0} final states in a liquid-argon time projection chamber using data collected with the MicroBooNE detector. The data were recorded synchronously with the NuMI neutrino beam from Fermilab's main injector corresponding to a total exposure of 7.01×10^{20} protons on target. We set upper limits at the 90% confidence level on the mixing parameter |U_{μ4}|^{2} in the mass ranges 10≤m_{HNL}≤150  MeV for the νe^{+}e^{-} channel and 150≤m_{HNL}≤245  MeV for the νπ^{0} channel, assuming |U_{e4}|^{2}=|U_{τ4}|^{2}=0. These limits represent the most stringent constraints in the mass range 35 Collapse

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Affiliation(s)

P Abratenko Tufts University, Medford, Massachusetts 02155, USA
O Alterkait Tufts University, Medford, Massachusetts 02155, USA
D Andrade Aldana Illinois Institute of Technology (IIT), Chicago, Illinois 60616, USA
L Arellano The University of Manchester, Manchester M13 9PL, United Kingdom
J Asaadi University of Texas, Arlington, Texas 76019, USA
A Ashkenazi Tel Aviv University, Tel Aviv, Israel, 69978
S Balasubramanian Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
B Baller Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
G Barr University of Oxford, Oxford OX1 3RH, United Kingdom
D Barrow University of Oxford, Oxford OX1 3RH, United Kingdom
J Barrow Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA Tel Aviv University, Tel Aviv, Israel, 69978
V Basque Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
O Benevides Rodrigues Illinois Institute of Technology (IIT), Chicago, Illinois 60616, USA
S Berkman Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA Michigan State University, East Lansing, Michigan 48824, USA
A Bhanderi The University of Manchester, Manchester M13 9PL, United Kingdom
A Bhat University of Chicago, Chicago, Illinois 60637, USA
M Bhattacharya Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
M Bishai Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
A Blake Lancaster University, Lancaster LA1 4YW, United Kingdom
B Bogart University of Michigan, Ann Arbor, Michigan 48109, USA
T Bolton Kansas State University (KSU), Manhattan, Kansas 66506, USA
J Y Book Harvard University, Cambridge, Massachusetts 02138, USA
M B Brunetti University of Warwick, Coventry CV4 7AL, United Kingdom
L Camilleri Columbia University, New York, New York 10027, USA
Y Cao The University of Manchester, Manchester M13 9PL, United Kingdom
D Caratelli University of California, Santa Barbara, California 93106, USA
F Cavanna Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
G Cerati Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
A Chappell University of Warwick, Coventry CV4 7AL, United Kingdom
Y Chen SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
J M Conrad Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
M Convery SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
L Cooper-Troendle University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
J I Crespo-Anadón Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid E-28040, Spain
R Cross University of Warwick, Coventry CV4 7AL, United Kingdom
M Del Tutto Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
S R Dennis University of Cambridge, Cambridge CB3 0HE, United Kingdom
P Detje University of Cambridge, Cambridge CB3 0HE, United Kingdom
A Devitt Lancaster University, Lancaster LA1 4YW, United Kingdom
R Diurba Universität Bern, Bern CH-3012, Switzerland
Z Djurcic Argonne National Laboratory (ANL), Lemont, Illinois 60439, USA
R Dorrill Illinois Institute of Technology (IIT), Chicago, Illinois 60616, USA
K Duffy University of Oxford, Oxford OX1 3RH, United Kingdom
S Dytman University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
B Eberly University of Southern Maine, Portland, Maine 04104, USA
P Englezos Rutgers University, Piscataway, New Jersey 08854, USA
A Ereditato University of Chicago, Chicago, Illinois 60637, USA Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
J J Evans The University of Manchester, Manchester M13 9PL, United Kingdom
R Fine Los Alamos National Laboratory (LANL), Los Alamos, New Mexico 87545, USA
O G Finnerud The University of Manchester, Manchester M13 9PL, United Kingdom
W Foreman Illinois Institute of Technology (IIT), Chicago, Illinois 60616, USA
B T Fleming University of Chicago, Chicago, Illinois 60637, USA
D Franco University of Chicago, Chicago, Illinois 60637, USA
A P Furmanski University of Minnesota, Minneapolis, Minnesota 55455, USA
F Gao University of California, Santa Barbara, California 93106, USA
D Garcia-Gamez Universidad de Granada, Granada E-18071, Spain
S Gardiner Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
G Ge Columbia University, New York, New York 10027, USA
S Gollapinni Los Alamos National Laboratory (LANL), Los Alamos, New Mexico 87545, USA
E Gramellini The University of Manchester, Manchester M13 9PL, United Kingdom
P Green University of Oxford, Oxford OX1 3RH, United Kingdom
H Greenlee Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
L Gu Lancaster University, Lancaster LA1 4YW, United Kingdom
W Gu Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
R Guenette The University of Manchester, Manchester M13 9PL, United Kingdom
P Guzowski The University of Manchester, Manchester M13 9PL, United Kingdom
L Hagaman University of Chicago, Chicago, Illinois 60637, USA
O Hen Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
C Hilgenberg University of Minnesota, Minneapolis, Minnesota 55455, USA
G A Horton-Smith Kansas State University (KSU), Manhattan, Kansas 66506, USA
Z Imani Tufts University, Medford, Massachusetts 02155, USA
B Irwin University of Minnesota, Minneapolis, Minnesota 55455, USA
M Ismail University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
C James Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
X Ji Nankai University, Nankai District, Tianjin 300071, China
J H Jo Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
R A Johnson University of Cincinnati, Cincinnati, Ohio 45221, USA
Y-J Jwa Columbia University, New York, New York 10027, USA
D Kalra Columbia University, New York, New York 10027, USA
N Kamp Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA
G Karagiorgi Columbia University, New York, New York 10027, USA
W Ketchum Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
M Kirby Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
T Kobilarcik Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
I Kreslo Universität Bern, Bern CH-3012, Switzerland
M B Leibovitch University of California, Santa Barbara, California 93106, USA
I Lepetic Rutgers University, Piscataway, New Jersey 08854, USA
J-Y Li University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
K Li Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
Y Li Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
K Lin Rutgers University, Piscataway, New Jersey 08854, USA
B R Littlejohn Illinois Institute of Technology (IIT), Chicago, Illinois 60616, USA
H Liu Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
W C Louis Los Alamos National Laboratory (LANL), Los Alamos, New Mexico 87545, USA
X Luo University of California, Santa Barbara, California 93106, USA
C Mariani Center for Neutrino Physics, Virginia Tech, Blacksburg, Viriginia 24061, USA
D Marsden The University of Manchester, Manchester M13 9PL, United Kingdom
J Marshall University of Warwick, Coventry CV4 7AL, United Kingdom
N Martinez Kansas State University (KSU), Manhattan, Kansas 66506, USA
D A Martinez Caicedo South Dakota School of Mines and Technology (SDSMT), Rapid City, South Dakota 57701, USA
S Martynenko Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
A Mastbaum Rutgers University, Piscataway, New Jersey 08854, USA
I Mawby University of Warwick, Coventry CV4 7AL, United Kingdom
N McConkey University College London, London WC1E 6BT, United Kingdom
V Meddage Kansas State University (KSU), Manhattan, Kansas 66506, USA
J Micallef Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA Tufts University, Medford, Massachusetts 02155, USA
K Miller University of Chicago, Chicago, Illinois 60637, USA
A Mogan Colorado State University, Fort Collins, Colorado 80523, USA
T Mohayai Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA Indiana University, Bloomington, Indiana 47405, USA
M Mooney Colorado State University, Fort Collins, Colorado 80523, USA
A F Moor University of Cambridge, Cambridge CB3 0HE, United Kingdom
C D Moore Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
L Mora Lepin The University of Manchester, Manchester M13 9PL, United Kingdom
M M Moudgalya The University of Manchester, Manchester M13 9PL, United Kingdom
S Mulleriababu Universität Bern, Bern CH-3012, Switzerland
D Naples University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
A Navrer-Agasson The University of Manchester, Manchester M13 9PL, United Kingdom
N Nayak Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
M Nebot-Guinot University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
J Nowak Lancaster University, Lancaster LA1 4YW, United Kingdom
N Oza Columbia University, New York, New York 10027, USA
O Palamara Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
N Pallat University of Minnesota, Minneapolis, Minnesota 55455, USA
V Paolone University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
A Papadopoulou Argonne National Laboratory (ANL), Lemont, Illinois 60439, USA
V Papavassiliou New Mexico State University (NMSU), Las Cruces, New Mexico 88003, USA
H B Parkinson University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
S F Pate New Mexico State University (NMSU), Las Cruces, New Mexico 88003, USA
N Patel Lancaster University, Lancaster LA1 4YW, United Kingdom
Z Pavlovic Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
E Piasetzky Tel Aviv University, Tel Aviv, Israel, 69978
I Pophale Lancaster University, Lancaster LA1 4YW, United Kingdom
X Qian Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
J L Raaf Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
V Radeka Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
A Rafique Argonne National Laboratory (ANL), Lemont, Illinois 60439, USA
M Reggiani-Guzzo University of Edinburgh, Edinburgh EH9 3FD, United Kingdom The University of Manchester, Manchester M13 9PL, United Kingdom
L Ren New Mexico State University (NMSU), Las Cruces, New Mexico 88003, USA
L Rochester SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
J Rodriguez Rondon South Dakota School of Mines and Technology (SDSMT), Rapid City, South Dakota 57701, USA
M Rosenberg Tufts University, Medford, Massachusetts 02155, USA
M Ross-Lonergan Los Alamos National Laboratory (LANL), Los Alamos, New Mexico 87545, USA
C Rudolf von Rohr Universität Bern, Bern CH-3012, Switzerland
I Safa Columbia University, New York, New York 10027, USA
G Scanavini Wright Laboratory, Department of Physics, Yale University, New Haven, Connecticut 06520, USA
D W Schmitz University of Chicago, Chicago, Illinois 60637, USA
A Schukraft Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
W Seligman Columbia University, New York, New York 10027, USA
M H Shaevitz Columbia University, New York, New York 10027, USA
R Sharankova Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
J Shi University of Cambridge, Cambridge CB3 0HE, United Kingdom
E L Snider Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
M Soderberg Syracuse University, Syracuse, New York 13244, USA
S Söldner-Rembold The University of Manchester, Manchester M13 9PL, United Kingdom
J Spitz University of Michigan, Ann Arbor, Michigan 48109, USA
M Stancari Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
J St John Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
T Strauss Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
A M Szelc University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
W Tang University of Tennessee, Knoxville, Tennessee 37996, USA
N Taniuchi University of Cambridge, Cambridge CB3 0HE, United Kingdom
K Terao SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
C Thorpe Lancaster University, Lancaster LA1 4YW, United Kingdom The University of Manchester, Manchester M13 9PL, United Kingdom
D Torbunov Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
D Totani University of California, Santa Barbara, California 93106, USA
M Toups Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
Y-T Tsai SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
J Tyler Kansas State University (KSU), Manhattan, Kansas 66506, USA
M A Uchida University of Cambridge, Cambridge CB3 0HE, United Kingdom
T Usher SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
B Viren Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
M Weber Universität Bern, Bern CH-3012, Switzerland
H Wei Louisiana State University, Baton Rouge, Louisiana 70803, USA
A J White University of Chicago, Chicago, Illinois 60637, USA
S Wolbers Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
T Wongjirad Tufts University, Medford, Massachusetts 02155, USA
M Wospakrik Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
K Wresilo University of Cambridge, Cambridge CB3 0HE, United Kingdom
W Wu University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
E Yandel University of California, Santa Barbara, California 93106, USA
T Yang Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
L E Yates Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
H W Yu Brookhaven National Laboratory (BNL), Upton, New York 11973, USA
G P Zeller Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
J Zennamo Fermi National Accelerator Laboratory (FNAL), Batavia, Illinois 60510, USA
C Zhang Brookhaven National Laboratory (BNL), Upton, New York 11973, USA

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First Double-Differential Measurement of Kinematic Imbalance in Neutrino Interactions with the MicroBooNE Detector

We report the first measurement of flux-integrated double-differential quasielasticlike neutrino-argon cross sections, which have been made using the Booster Neutrino Beam and the MicroBooNE detector at Fermi National Accelerator Laboratory. The data are presented as a function of kinematic imbalance variables which are sensitive to nuclear ground-state distributions and hadronic reinteraction processes. We find that the measured cross sections in different phase-space regions are sensitive to different nuclear effects. Therefore, they enable the impact of specific nuclear effects on the neutrino-nucleus interaction to be isolated more completely than was possible using previous single-differential cross section measurements. Our results provide precision data to help test and improve neutrino-nucleus interaction models. They further support ongoing neutrino-oscillation studies by establishing phase-space regions where precise reaction modeling has already been achieved.

Characterization of different types of anxiety disorders in relation to structural integration of personality and adverse and protective childhood experiences in psychotherapy outpatients - a cross-sectional study

BACKGROUND

Current research has emphasized the role of structural integration of personality and childhood experiences for the understanding of anxiety disorders. In this study, we examined the relationship between anxiety disorders (generalized anxiety disorder vs. panic disorder vs. phobic disorders), the level of structural integration of personality, and negative and protective childhood experiences at the beginning of outpatient psychodynamic psychotherapy treatment. Differences were characterized in comparison to patients with no anxiety disorders.

METHODS

The sample included a total of 1646 outpatient psychodynamic psychotherapy treatments, of which 695 treatments included the diagnosis of at least one anxiety disorder. Levels of structural integration of personality were assessed according to the Operationalized Psychodynamic Diagnosis (OPD-2) system. Self-reported negative and protective childhood experiences were examined by using the Questionnaire for the Assessment of Adverse and Protective Childhood Experiences (APC). Associations were tested using single factor ANOVAs.

RESULTS

Patients with anxiety disorders showed lower levels of structural integration of personality and reported more adverse childhood experiences than patients with no anxiety disorders. Regarding the subscales of structural integration of personality, phobic disorders were associated with impaired external communication, whereas for generalized anxiety disorder, an (uncorrected) association with impaired self-regulation was found. Also, generalized anxiety disorder was associated with sexual abuse and other traumatization (accidents etc.) during childhood, while panic disorder and phobic disorders were associated with emotional neglect, abuse, and fewer protective childhood experiences.

CONCLUSIONS

Our findings emphasize the need of considering structural integration of personality and childhood experiences in order to understand and treat various types of anxiety disorders.

First Measurement of Quasielastic Λ Baryon Production in Muon Antineutrino Interactions in the MicroBooNE Detector

We present the first measurement of the cross section of Cabibbo-suppressed Λ baryon production, using data collected with the MicroBooNE detector when exposed to the neutrinos from the main injector beam at the Fermi National Accelerator Laboratory. The data analyzed correspond to 2.2×10^{20} protons on target running in neutrino mode, and 4.9×10^{20} protons on target running in anti-neutrino mode. An automated selection is combined with hand scanning, with the former identifying five candidate Λ production events when the signal was unblinded, consistent with the GENIE prediction of 5.3±1.1 events. Several scanners were employed, selecting between three and five events, compared with a prediction from a blinded Monte Carlo simulation study of 3.7±1.0 events. Restricting the phase space to only include Λ baryons that decay above MicroBooNE's detection thresholds, we obtain a flux averaged cross section of 2.0_{-1.7}^{+2.2}×10^{-40}  cm^{2}/Ar, where statistical and systematic uncertainties are combined.

Helicobacter pylori Seropositivity, ABO Blood Type, and Pancreatic Cancer Risk From 5 Prospective Cohorts

BACKGROUND

Helicobacter pylori infection may be a risk factor for pancreatic cancer, particularly infection by strains without the cytotoxin-associated gene A (CagA) virulence factor. Non-O blood type is a known risk factor for pancreatic cancer, and H. pylori gastric colonization occurs largely from bacterial adhesins binding to blood group antigens on gastric mucosa.

METHODS

We included 485 pancreatic cancer cases and 1,122 matched controls from 5 U.S. prospective cohorts. Prediagnostic plasma samples were assessed for H. pylori and CagA antibody titers. Conditional logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for pancreatic cancer. ABO blood type was assessed using genetic polymorphisms at the ABO gene locus or self-report.

RESULTS

Compared with H. pylori -seronegative participants, those who were seropositive did not demonstrate an increased risk of pancreatic cancer (OR 0.83, 95% CI 0.65-1.06). This lack of association was similar among CagA-seropositive (OR 0.75, 95% CI 0.53-1.04) and -seronegative (OR 0.89, 95% CI 0.65-1.20) participants. The association was also similar when stratified by time between blood collection and cancer diagnosis ( P -interaction = 0.80). Consistent with previous studies, non-O blood type was associated with increased pancreatic cancer risk, but this increase in risk was similar regardless of H. pylori seropositivity ( P -interaction = 0.51).

DISCUSSION

In this nested case-control study, history of H. pylori infection as determined by H. pylori antibody serology was not associated with pancreatic cancer risk, regardless of CagA virulence factor status. The elevated risk associated with non-O blood type was consistent in those with or without H. pylori seropositivity.

Histopathology images predict multi-omics aberrations and prognoses in colorectal cancer patients

Histopathologic assessment is indispensable for diagnosing colorectal cancer (CRC). However, manual evaluation of the diseased tissues under the microscope cannot reliably inform patient prognosis or genomic variations crucial for treatment selections. To address these challenges, we develop the Multi-omics Multi-cohort Assessment (MOMA) platform, an explainable machine learning approach, to systematically identify and interpret the relationship between patients' histologic patterns, multi-omics, and clinical profiles in three large patient cohorts (n = 1888). MOMA successfully predicts the overall survival, disease-free survival (log-rank test P-value<0.05), and copy number alterations of CRC patients. In addition, our approaches identify interpretable pathology patterns predictive of gene expression profiles, microsatellite instability status, and clinically actionable genetic alterations. We show that MOMA models are generalizable to multiple patient populations with different demographic compositions and pathology images collected from distinctive digitization methods. Our machine learning approaches provide clinically actionable predictions that could inform treatments for colorectal cancer patients.

Abstract 5760: Molecular, immune, and microbial profiles of early-onset, intermediate-onset, and later-onset CRCs

Background: Despite heightened interest in early-onset CRC, little is known about the tumor molecular, immune, and microbial characteristics of early-onset CRC. It is also unclear whether CRCs diagnosed at or shortly after age 50 are similar to early-onset CRC. We hypothesized that tumor molecular, immune, and microbial characteristics in CRC tissue might show differential heterogeneity patterns between three age groups (&lt;50 "early-onset", 50-54 "intermediate-onset", ≥55 "later-onset").

Methods: We examined 3,395 CRC cases with available tissue data, including 660 early-onset and 243 intermediate-onset cases in the Nurses' Health Study, Health Professionals Follow-up Study, and Ontario Familial Colon Cancer Registry. We profiled the in situ T-cell landscape of 959 cases using digital imaging, machine learning, and a customized 9-plex multiplexed immunofluoresence panel with antibodies directed against CD3, CD4, CD8, CD45RA, CD45RO, FOXP3, and MKI67 (Ki-67). Using chi-squared test or Spearman’s correlation test, we assessed differences in tumor characteristics including microsatellite instability, CpG island methylator phenotype (CIMP), KRAS, and BRAF mutations, LINE-1 methylation levels, pks+ E. coli and Fusobacterium nucleatum positivity, histopathologic lymphocytic reaction, and T-cell densities between early-onset, intermediate-onset, and later-onset cases.

Results: Compared to later-onset CRC (21%), early-onset (4.8%) and intermediate-onset CRCs (5.1%) exhibited a lower prevalence of CIMP-high status (P&lt;0.001). The mean tumor LINE-1 methylation level increased with increasing age [59 (SD, 12) in early-onset, 61 (SD, 10) in intermediate-onset, and 64 (SD, 9.8) in later-onset CRC (P&lt;0.001)]. Early-onset CRC (4.1%) had fewer BRAF mutations than intermediate-onset (10.4%) and later-onset CRC (15%) (P&lt;0.001). Compared to later-onset CRC, early-onset CRC tended to show lower levels of tumor-infiltrating lymphocytes (P=0.013), and intratumoral periglandular reaction (P=0.025). Compared to later-onset CRC, early-onset CRC had a lower density of memory (both CD4+ and CD8+) T-cells (median 21 vs. 48 cells/mm2; P=0.002) and a higher density of MKI67+ immune cells (median 50 vs. 19 cells/mm2; P=0.003) in tumor epithelial areas but not in the surrounding stroma. No significant differences in other tested characteristics were identified.

Conclusions: Compared to later-onset CRC, early-onset and intermediate-onset CRCs tended to have aggressive tumor phenotypes such as LINE-1 hypomethylation, lower lymphocytic immune reaction, and a higher density of MKI67+ immune cells. These findings highlight the importance of the tumor microenvironment in the etiology of early-onset and intermediate-onset CRCs.

Citation Format: Tomotaka Ugai, Yasutoshi Takashima, Andressa Dias Costa, Daniel Buchanan, Jeroen Huyghe, Li Hsu, Conghui Qu, Claire Thomas, Steve Gallinger, Robert Grant, Ulrike Peters, Amanda I. Phipps, Jonathan Nowak, Shuji Ogino. Molecular, immune, and microbial profiles of early-onset, intermediate-onset, and later-onset CRCs. [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 5760.

Defining equitable genomic testing uptake in gastrointestinal oncology: Ensuring capture of demographic data

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Background: Tumor genomic testing (GT) has increased diagnostic accuracy and treatment options for patients (pts) with cancer. Dana-Farber Cancer Institute (DFCI) has made GT accessible as an institute-supported research effort for >10 yrs. We estimate 50% standard therapies and 15-35% clinical trials in Gastrointestinal Cancer Clinic (GCC) require GT to determine eligibility. Pts in GCC with certain cancers are eligible for GT as a clinical test – these include metastatic/locally advanced colorectal, gastric, pancreatic, or biliary cancers. Clinical testing requires CLIA lab certification and insurance reimbursement; research does not. Herein we ID gaps in our GT database. Methods: We reviewed data on GT uptake in GCC between 4/2015 - 6/2022. 20,096 pts were captured by the GT tracking system. Data included: testing ordered and completed (proportion, type, time to receiving tissue for testing [TR], time to testing completion [TC]). Demographic data is not captured in the tracking system; matching unique patient identifiers with electronic health record is pending. Results: Most pts received GT (57.6%); 12% were not eligible; 30.4% declined consent. Most testing was completed (67.6%), but 21.3% of tests failed (45.5% of these from insufficient tissue). Research testing (71%) comprised most tests, but clinical tests were completed faster (median 34 days research vs 20 days clinical). Ampullary (91%), anal (90%), colon (90%) had highest completion rates; pancreatic (59%), hepatocellular carcinoma (56%) had lowest (from insufficient viable tumor in submitted specimens). Conclusions: GCC has a robust recruitment program that has yielded high GT uptake. Given the frequency that GT is used for treatment and trials, building a demographically representative dataset is crucial, especially for pts with largest burden of morbidity and mortality from cancer. We ID'd data gaps in the GT tracking system, which lacks demographics and reason for not testing. Demographic data is available in the electronic health record but does not speak with the GT tracking system so this analysis is not routinely done. Ability to visualize this data is important to ensure equitable GT uptake. Future efforts will focus on improving rates of consent in genomics databases and cancer clinical trials. Genomic testing at Dana-Farber Cancer Institute Gastrointestinal Cancer Center, 4/2015 – 6/2022.[Table: see text]

First Constraints on Light Sterile Neutrino Oscillations from Combined Appearance and Disappearance Searches with the MicroBooNE Detector

We present a search for eV-scale sterile neutrino oscillations in the MicroBooNE liquid argon detector, simultaneously considering all possible appearance and disappearance effects within the 3+1 active-to-sterile neutrino oscillation framework. We analyze the neutrino candidate events for the recent measurements of charged-current ν_{e} and ν_{μ} interactions in the MicroBooNE detector, using data corresponding to an exposure of 6.37×10^{20} protons on target from the Fermilab booster neutrino beam. We observe no evidence of light sterile neutrino oscillations and derive exclusion contours at the 95% confidence level in the plane of the mass-squared splitting Δm_{41}^{2} and the sterile neutrino mixing angles θ_{μe} and θ_{ee}, excluding part of the parameter space allowed by experimental anomalies. Cancellation of ν_{e} appearance and ν_{e} disappearance effects due to the full 3+1 treatment of the analysis leads to a degeneracy when determining the oscillation parameters, which is discussed in this Letter and will be addressed by future analyses.

Abstract PR005: Primary results of PanCAN-SR1, a phase 1b study evaluating Gemcitabine, nab-Paclitaxel, Canakinumab, and Spartalizumab to target IL-1β and PD-1 in metastatic pancreatic cancer with correlative tissue and blood biomarker analysis

In preclinical work, the inflammatory cytokine IL-1β was shown to be upregulated in pancreatic cancer tumors and to contribute to activation of pancreatic stellate cells and immunosuppression (Das et al 2020). We conducted an open-label multicenter Phase Ib study evaluating gemcitabine, nab-paclitaxel, canakinumab (ACZ885), a high-affinity human anti-interleukin-1β (IL-1β) mAb, and spartalizumab (PDR001), a PD-1 mAb. Eligible subjects had previously untreated metastatic PDA and RECIST measurable disease. The primary objective was to confirm recommended phase II dose by evaluating the incidence of dose limiting toxicities (DLTs) in the first 56 days of dosing in at least 6 evaluable subjects utilizing a Bayesian logistic regression model. Subjects underwent baseline and on-study tissue and blood collection for correlative translational research. Results: 10 subjects were enrolled between Nov 2020 and Mar 2021. At the primary data cut off of May 23, 2021, 6 subjects were evaluable for DLT. There were no DLTs, the recommended Phase II dose was established as: gemcitabine (1000mg/m2 IV) day 1,8,15; nab-paclitaxel (125mg/m2 IV) day 1,8,15; canakinumab (250mg SC) day 1, spartalizumab (400mg IV) day 1; of each 28 day cycle. At the time of an updated database extraction on June 1, 2022, 2 subjects remain on study. Adverse events were consistent with those typically seen with chemotherapy. The most common Grade 3/4 AEs were neutropenia (60%) and anemia (50%), with no fatal AEs. One patient discontinued spartalizumab due to grade 3 pneumonitis. In preliminary efficacy analysis (n=10), there are 3 confirmed PRs, 5 subjects with stable disease, 2 subjects with progression as best response. Individual site data estimates that the 12 month OS rate is 60%; updated RR, PFS and OS data will be reported. Activation of CD8 T cells in peripheral blood and increased serum levels of IFN-induced chemokines CXCL9/10 were observed in both responder and non-responder patients. Using an in vitro suppression assay, we showed that baseline serum from responders could induce myeloid derived suppressor cells, an effect that was abrogated with treatment. Single cell transcriptional profiling, multiplex immunofluorescence and spatial transcriptomics also revealed treatment-dependent shifts in T cell activation state and myeloid cells in the tumors of patients experiencing clinical response. Conclusions: PanCAN-SR1 established the Phase II dose of canakinumab and spartalizumab with chemotherapy in first line metastatic PDA, based upon favorable benefit-risk assessment. Based on our comprehensive analysis of 10 patients treated with combination therapy including IL-1b blockade, we hypothesize that the definitive role of anti-IL-1b in human patients with pancreatic cancer is to reduce systemic immune suppression and to reduce immunosuppressive myeloid cell activation in the tumor. The clinical utility of targeting IL-1β in pancreatic cancer is being evaluated in a randomized Phase II/III study through the Precision Promise clinical trial network. NCT04581343.

Citation Format: Paul E. Oberstein, Osama Rahma, Nina Beri, Amy Stoll-D'Astice, Emily A. Kawaler, Igor Dolgalev, Gregor Werba, Victoire Cardo-Ruffino, Naïma Böllenrücher, Andressa Dias Costa, Saloney Nazeer, Matthew Squires, Jonathan Nowak, Dafna Bar-Sagi, Brian Wolpin, Diane M Simeone, Stephanie K Dougan. Primary results of PanCAN-SR1, a phase 1b study evaluating Gemcitabine, nab-Paclitaxel, Canakinumab, and Spartalizumab to target IL-1β and PD-1 in metastatic pancreatic cancer with correlative tissue and blood biomarker analysis [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr PR005.

Abstract B018: Eosinophils alter metastatic spread in pancreatic cancer

Pancreatic ductal adenocarcinoma (PDA) is the third most common cause of cancer death in the US with a 11% 5-year survival rate. A key contributor of this dismal prognosis is early and frequent metastatic spread with limited treatment options for patients. Metastasis in PDA is facilitated by a robust fibroinflammatory response in the primary tumor site, a large portion of which is composed of infiltrating immune cells, and survival during transit to establish in the secondary site. In the primary tumor reactive stroma, we found increased eosinophils in both human and mouse PDA compared to the normal pancreas. Eosinophils are an innate immune cell best known for their ability to control parasite responses and have been implicated in either pro- or anti-cancer roles in various solid tumors. We used the ΔdblGata mice, which lack eosinophils, to study the role of eosinophils during metastatic spread using a resectable model of PDA metastasis. This model of metastasis was developed to facilitate consistent seeding of lung metastasis in approximately 50 percent of mice from a transient subcutaneous tumor which undergoes subsequent surgical removal and harvest to evaluate metastasis at 4 weeks. We found that mice lacking eosinophils have increased metastasis to the lung in our resectable model of PDA metastasis but no difference in establishment of IV injected PDA tumor cells, suggesting eosinophil control at the primary tumor site. Single cell sequencing of the subcutaneous tumors finds differences in the angiogenic subtypes, tip and stalk cells, in mice lacking eosinophils. Sequencing of eosinophil populations in humans and mice find an increase in angiogenic signaling suggesting a regulatory role in tumor cell access to the circulation. We conclude that eosinophils in PDA inhibit the metastatic process through control of angiogenic signaling.

Citation Format: Megan T. Hoffman, Patrick J. Lenehan, Jennifer Wang, Lestat Ali, Li Qiang, Amiko Uchida, Sara Vayrynen, Andressa Dias Costa, Michael Dougan, Max Heckler, Jonathan Nowak, Brian W. Wolpin, Stephanie K. Dougan. Eosinophils alter metastatic spread in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B018.

MiniBooNE and MicroBooNE Combined Fit to a 3+1 Sterile Neutrino Scenario

This Letter presents the results from the MiniBooNE experiment within a full "3+1" scenario where one sterile neutrino is introduced to the three-active-neutrino picture. In addition to electron-neutrino appearance at short baselines, this scenario also allows for disappearance of the muon-neutrino and electron-neutrino fluxes in the Booster Neutrino Beam, which is shared by the MicroBooNE experiment. We present the 3+1 fit to the MiniBooNE electron-(anti)neutrino and muon-(anti)neutrino data alone and in combination with MicroBooNE electron-neutrino data. The best-fit parameters of the combined fit with the exclusive charged-current quasielastic analysis (inclusive analysis) are Δm^{2}=0.209  eV^{2}(0.033  eV^{2}), |U_{e4}|^{2}=0.016(0.500), |U_{μ4}|^{2}=0.500(0.500), and sin^{2}(2θ_{μe})=0.0316(1.0). Comparing the no-oscillation scenario to the 3+1 model, the data prefer the 3+1 model with a Δχ^{2}/d.o.f.=24.7/3(17.3/3), a 4.3σ(3.4σ) preference assuming the asymptotic approximation given by Wilks's theorem.

Search for an Excess of Electron Neutrino Interactions in MicroBooNE Using Multiple Final-State Topologies

We present a measurement of ν_{e} interactions from the Fermilab Booster Neutrino Beam using the MicroBooNE liquid argon time projection chamber to address the nature of the excess of low energy interactions observed by the MiniBooNE Collaboration. Three independent ν_{e} searches are performed across multiple single electron final states, including an exclusive search for two-body scattering events with a single proton, a semi-inclusive search for pionless events, and a fully inclusive search for events containing all hadronic final states. With differing signal topologies, statistics, backgrounds, reconstruction algorithms, and analysis approaches, the results are found to be either consistent with or modestly lower than the nominal ν_{e} rate expectations from the Booster Neutrino Beam and no excess of ν_{e} events is observed.

First Measurement of Energy-Dependent Inclusive Muon Neutrino Charged-Current Cross Sections on Argon with the MicroBooNE Detector

We report a measurement of the energy-dependent total charged-current cross section σ(E_{ν}) for inclusive muon neutrinos scattering on argon, as well as measurements of flux-averaged differential cross sections as a function of muon energy and hadronic energy transfer (ν). Data corresponding to 5.3×10^{19} protons on target of exposure were collected using the MicroBooNE liquid argon time projection chamber located in the Fermilab booster neutrino beam with a mean neutrino energy of approximately 0.8 GeV. The mapping between the true neutrino energy E_{ν} and reconstructed neutrino energy E_{ν}^{rec} and between the energy transfer ν and reconstructed hadronic energy E_{had}^{rec} are validated by comparing the data and Monte Carlo (MC) predictions. In particular, the modeling of the missing hadronic energy and its associated uncertainties are verified by a new method that compares the E_{had}^{rec} distributions between data and a MC prediction after constraining the reconstructed muon kinematic distributions, energy, and polar angle to those of data. The success of this validation gives confidence that the missing energy in the MicroBooNE detector is well modeled and underpins first-time measurements of both the total cross section σ(E_{ν}) and the differential cross section dσ/dν on argon.

Search for Neutrino-Induced Neutral-Current Δ Radiative Decay in MicroBooNE and a First Test of the MiniBooNE Low Energy Excess under a Single-Photon Hypothesis

We report results from a search for neutrino-induced neutral current (NC) resonant Δ(1232) baryon production followed by Δ radiative decay, with a ⟨0.8⟩  GeV neutrino beam. Data corresponding to MicroBooNE's first three years of operations (6.80×10^{20} protons on target) are used to select single-photon events with one or zero protons and without charged leptons in the final state (1γ1p and 1γ0p, respectively). The background is constrained via an in situ high-purity measurement of NC π^{0} events, made possible via dedicated 2γ1p and 2γ0p selections. A total of 16 and 153 events are observed for the 1γ1p and 1γ0p selections, respectively, compared to a constrained background prediction of 20.5±3.65(syst) and 145.1±13.8(syst) events. The data lead to a bound on an anomalous enhancement of the normalization of NC Δ radiative decay of less than 2.3 times the predicted nominal rate for this process at the 90% confidence level (C.L.). The measurement disfavors a candidate photon interpretation of the MiniBooNE low-energy excess as a factor of 3.18 times the nominal NC Δ radiative decay rate at the 94.8% C.L., in favor of the nominal prediction, and represents a greater than 50-fold improvement over the world's best limit on single-photon production in NC interactions in the sub-GeV neutrino energy range.

Abstract P099: Radionuclide imaging of low-density-lipoprotein receptor (LDLR)-overexpressing glioblastoma: A preclinical study of Gallium-68 RMX-VH

Introduction: One of the factors that limit the efficacy of the drugs, especially in primary brain tumors, is the permeability of the blood-brain barrier (BBB). The low-density lipoprotein receptor (LDL-R) expressed at the BBB mediates the transport of endogenous ligands through the BBB. We developed a new radiolabeled peptide targeting both the human and murine LDLR and able i) to cross the BBB and ii) to target tumors such as glioblastoma that express high levels of the LDLR. The objective of this study was to determine the LDLR targeting properties, the pharmacokinetics of 68Ga radiolabeled RMX-VH in a glioblastoma model that expresses the human LDLR (hLDLR). Methods: The nonclinical studies of 68Ga-RMX-VH were completed in U87MG, A172, U373 glioblastoma cancer cell lines and xenografts mice models. The studies determined in vivo time-dependent accumulation of this agent, in vitro dose-depended cellular uptake, and cellular competition studies. We compared the tumor-specific accumulation of 68Ga-RMX-VH and normal organ distribution in female and male athymic nude mice. Radiotracer, RMX-VH (10-30ug) was labeled with isotope-Ga68 (10-25mCi, ITM GmBH). U87MG and A172- derived xenografts were generated in athymic nude mice (10 weeks) and PET/CT images were acquired using G4 PET/Xray camera (Sofie Biosciences) at 1h, 2h, 3h, and 4h post-injection. The followed up biodistribution studies were done at 30 min, 1h, 2h, and 3 hrs. post-injection. The organs and tumor were collected, weighed, and the tissue radioactivity was measured with Wizard2 Gamma Counter (Perkin-Elmer, Waltham, MA). The percentage of injected dose per gram of tissue (%ID/g) was calculated and decay-corrected. Results: Our studies confirmed the in vitro and in vivo selectivity and specificity of 68Ga-RMX-VH toward LDLR-positive tumors. 68Ga-RMX-VH is a small peptide (MW: 1432.7 g/mol) and renal excretion was expected as a route of agent elimination. The tumor-specific uptake of radiotracer in U87MG xenografts was 1.8%ID/g at 1h and remained unchanged at 3h post-injection. The kidney retention of the agent reached 12.2%ID/g and decreased to 10.2%ID/g. The accumulation of radiotracer in the liver, ovaries, and intestine correlated well with the known normal expression of LDLR. The tumor-to-muscle ratio was 5.97 at 1h; increased to 26.1 and 22.39 at 2h and 3h. The elimination t1/2 of radiotracer was only 18.6 min, with a clearance CL of 502 ml/min. Adsorption from the site of administration is rapid as the Cmax was 5 min. The tumor-specific uptake and normal organ distribution of 68Ga-RMX-VH were lower in male mice than in females. This correlated with differences in lipid and lipoproteins metabolism in males and females. Conclusions: RMX-VH showed favorable hLDLR targeting properties in vitro and in vivo in glioblastoma mice models. Our results suggest that hLDLR may serve as a target for imaging for glioblastoma. The first-in-human exploratory IND study of Ga68-RMX-VH will be initiated in Q2 of 2021.

Citation Format: Izabela Tworowska, Leo Garcia Flores II, Xuewei Qu, Cédric Malicet, Nilesh Wagh, David Ranganathan, Jonathan Nowak, Pascaline Lecorche, Jamal Temsamani, Ebrahim S. Delpassand. Radionuclide imaging of low-density-lipoprotein receptor (LDLR)-overexpressing glioblastoma: A preclinical study of Gallium-68 RMX-VH [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr P099.

960 Randomized multicenter study of neoadjuvant chemoradiation therapy (CRT) alone or in combination with pembrolizumab in patients with resectable or borderline resectable pancreatic cancer

Background

Pancreatic cancer (PC) is a challenging target for immunotherapy due to its immune-suppressive microenvironment. Neoadjuvant chemoradiation (CRT) can increase the presence of tumor-infiltrating lymphocytes (TILs). We hypothesized that the combination of CRT and pembrolizumab can further expand and activate TILs.

Methods

Patients with resectable or borderline resectable PC were randomized 2:1 to the investigational treatment (Arm A) of pembrolizumab 200mg IV every 3 weeks concurrently with CRT (capecitabine 825 mg/m2 orally twice daily and radiation 50.4 Gy in 28 fractions over 28 days) or CRT only (Arm B) prior to surgical resection. The primary endpoints were safety and difference in TILs density between Arm A and B assessed using multiplexed immunofluorescence on resected tumor specimens. As a correlate analysis, single cell RNA-sequencing (scRNA-seq) was performed to quantify gene expression in T cells from tumors and peripheral blood, and to track expanded T cell clonotypes in these compartments (n=4 patients Arm A; n=3 patients Arm B). The study was amended after enrollment of 37 patients to allow FOLFIRINOX prior to CRT, given changes in standard of care.

Results

37 patients were enrolled (24 Arm A, 13 Arm B). After neoadjuvant therapy, 13 patients had unresectable disease (9 on A, 4 on B), and 24 patients underwent surgery and were evaluable for the TILs primary endpoint (17 arm A, 7 arm B). The mean difference (A-B) in CD8+ T cell density was 36 cells/mm2 (95% CI -85 to 157, stdev 130) (p 0.48). Additional analysis did not show significant differences in activated cytotoxic T cells, regulatory T cells, M1- or M2-like polarized macrophages, or granulocytes. The median recurrence free survival (RFS) was 18.2 months on Arm A and 14.1 on Arm B (p 0.41). Overall survival was 27.8 months on Arm A and 24.3 on Arm B (p 0.68) with a median follow up of 2.2 years. The most common grade 3 treatment-related toxicities were lymphopenia reported in 29% on Arm A and 31% on Arm B, respectively followed by diarrhea in 8% on Arm A attributed to CRT. scRNA-seq revealed clonal expansion and expression of co-inhibitory markers among TIL subsets.

Conclusions

The combination of CRT and pembrolizumab is safe. Preliminary analysis shows that the addition of pembrolizumab to CRT has minimal effects on intratumoral densities of TILs and other immune cell populations. Single cell transcriptome analyses enable in-depth characterization of the functional responses of T cells to pembrolizumab in the setting of CRT.

Acknowledgements

This study was funded by Merck

Trial Registration

NCT02305186

Ethics Approval

The study was conducted at 6 sites: University of Virginia, Dana Farber Cancer Institute, MD Anderson Cancer Center (MDACC), Mayo Clinic, Hartford Healthcare Cancer Center, and University of Miami. Written informed consent was provided by the study participants and the protocol was approved by the relevant local IRBs in each site.

Search for a Higgs Portal Scalar Decaying to Electron-Positron Pairs in the MicroBooNE Detector

We present a search for the decays of a neutral scalar boson produced by kaons decaying at rest, in the context of the Higgs portal model, using the MicroBooNE detector. We analyze data triggered in time with the Fermilab NuMI neutrino beam spill, with an exposure of 1.93×10^{20} protons on target. We look for monoenergetic scalars that come from the direction of the NuMI hadron absorber, at a distance of 100 m from the detector, and decay to electron-positron pairs. We observe one candidate event, with a standard model background prediction of 1.9±0.8. We set an upper limit on the scalar-Higgs mixing angle of θ<(3.3-4.6)×10^{-4} at the 95% confidence level for scalar boson masses in the range (100-200)  MeV/c^{2}. We exclude, at the 95% confidence level, the remaining model parameters required to explain the central value of a possible excess of K_{L}^{0}→π^{0}νν[over ¯] decays reported by the KOTO collaboration. We also provide a model-independent limit on a new boson X produced in K→πX decays and decaying to e^{+}e^{-}.

LDL receptor-peptide conjugate as in vivo tool for specific targeting of pancreatic ductal adenocarcinoma

Despite clinical advances in diagnosis and treatment, pancreatic ductal adenocarcinoma (PDAC) remains the third leading cause of cancer death, and is still associated with poor prognosis and dismal survival rates. Identifying novel PDAC-targeted tools to tackle these unmet clinical needs is thus an urgent requirement. Here we use a peptide conjugate that specifically targets PDAC through low-density lipoprotein receptor (LDLR). We demonstrate by using near-infrared fluorescence imaging the potential of this conjugate to specifically detect and discriminate primary PDAC from healthy organs including pancreas and from benign mass-forming chronic pancreatitis, as well as detect metastatic pancreatic cancer cells in healthy liver. This work paves the way towards clinical applications in which safe LDLR-targeting peptide conjugate promotes tumor-specific delivery of imaging and/or therapeutic agents, thereby leading to substantial improvements of the PDAC patient’s outcome.

Acier et al. investigated a peptide cargo system, the Fc(A680)-VH4127, that targets PDAC through the LDLR cell-surface receptor. The Fc(A680)-VH4127 was found to specifically target spontaneous pancreatic tumors in KICmice, as well as metastatic pancreatic tumors in liver.

Randomized multicenter phase Ib/II study of neoadjuvant chemoradiation therapy (CRT) alone or in combination with pembrolizumab in patients with resectable or borderline resectable pancreatic cancer

4128

Background: Pancreatic cancer (PC) is a challenging target for immunotherapy due to suppressive immune-microenvironment. Neoadjuvant chemoradiation (CRT) can increase the presence of tumor-infiltrating lymphocytes (TILs). We hypothesized that the combination of CRT and pembrolizumab can lead to further increase in TILs and their activation. Methods: Patients with resectable or borderline resectable PC were randomized 2:1 to the investigational treatment (Arm A) of pembrolizumab 200mg IV every 3 weeks concurrently with CRT (capecitabine 825 mg/m2 orally twice daily and radiation 50.4 Gy in 28 fractions over 28 days) or CRT only (Arm B) prior to surgical resection. The primary endpoints were treatment safety and density of TILs with the objective to estimate differences in TILs density between the investigational and the control arms. Immune cell densities were assessed using multiplexed immunofluorescence on resected tumor specimens. Densities of CD8+TILs were measured in 2-10 representative regions containing residual cancer per case and then averaged to obtain overall densities. The study was amended after enrollment of 37 patients to allow FOLFIRINOX prior to CRT, given changes in standard of care. Results: 37 patients were enrolled (24 Arm A and 13 Arm B). Post-neoadjuvant therapy, 13 patients had unresectable disease (9 on A and 4 on B), and 24 patients underwent surgery and were evaluable for the TILs primary endpoint (17 arm A and 7 arm B). The mean difference (A-B) in CD8+ cell density was 36 cells/mm2 (95% CI -85 to 157, stdev 130) (p 0.48). Additional analysis did not show significant differences in CD8+Ki67+ (activated cytotoxic T-cells), CD4+, and CD4+FOXP3+ (regulatory T cells), M1- or M2-like polarized macrophages, or granulocytes. The median recurrence free survival (RFS) was 18.2 months on Arm A and 14.1 on Arm B (p 0.41) and Overall Survival was 27.8 months on Arm A and 24.3 on Arm B (p 0.68) with a median follow up of 2.2 years. The most common grade 3 treatment-related toxicities were lymphopenia reported in 29% on Arm A and 31% on Arm B followed by diarrhea in 8% on Arm A attributed to CRT. There was only 1 DLT of increased ALT attributed to the combination on Arm A that resolved after holding the treatment and receiving steroids. There were no major surgical complications reported within 30 days post-surgery. Conclusions: The combination of CRT and pembrolizumab is safe. Preliminary analysis shows that the addition of pembrolizumab to CRT has minimal effects on several immune cell populations including CD8+TILs in the PC microenvironment. The study is currently enrolling 25 more patients who receive FOLFIRINOX prior to randomization to CRT+/- Pembrolizumab, which will help to dissect the immune modulatory effect of chemotherapy followed by CRT. Clinical trial information: NCT02305186.

Consideration of immunomodulatory actions of morphine in COVID-19 - Short report

Cytokine storm in COVID-19 is linked to disease severity and mortality. 40% of patients with severe COVID-19 require mechanical ventilation. Analgesia and sedation are used for treatment of pain, facilitation of mechanical ventilation, or management of acute agitation. Herein, we present the immunomodulating actions of morphine that may either improve or worsen the clinical course of COVID-19 once cytokine storm develops. A literature search was performed to find articles on potential immunomodulatory effects of morphine. Taken together, the results of in vitro and in vivo models in non-COVID-19 conditions suggest that morphine could have a beneficial effect by mitigating the cytokine storm in the early stages of severe COVID-19. In contrast, it could be potentially harmful in late stages of severe COVID-19, especially in the presence of septic shock.

First Measurement of Differential Charged Current Quasielasticlike ν_{μ}-Argon Scattering Cross Sections with the MicroBooNE Detector

We report on the first measurement of flux-integrated single differential cross sections for charged-current (CC) muon neutrino (ν_{μ}) scattering on argon with a muon and a proton in the final state, ^{40}Ar (ν_{μ},μp)X. The measurement was carried out using the Booster Neutrino Beam at Fermi National Accelerator Laboratory and the MicroBooNE liquid argon time projection chamber detector with an exposure of 4.59×10^{19} protons on target. Events are selected to enhance the contribution of CC quasielastic (CCQE) interactions. The data are reported in terms of a total cross section as well as single differential cross sections in final state muon and proton kinematics. We measure the integrated per-nucleus CCQE-like cross section (i.e., for interactions leading to a muon, one proton, and no pions above detection threshold) of (4.93±0.76_{stat}±1.29_{sys})×10^{-38}  cm^{2}, in good agreement with theoretical calculations. The single differential cross sections are also in overall good agreement with theoretical predictions, except at very forward muon scattering angles that correspond to low-momentum-transfer events.

Abstract PR03: Subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer

The majority of patients with pancreatic ductal adenocarcinoma (PDAC) present at diagnosis with metastatic disease and have median survival times of less than 12 months. Recent studies have demonstrated that PDAC tumors with distinct transcriptional phenotypes are associated with different clinical outcomes. However, the mechanisms underlying this survival difference, the degree of cellular heterogeneity within a given tumor, and the subtype-specific contributions from the local immune microenvironment are not understood. In addition, there are ongoing efforts to understand if patient-derived organoid models can be used as functional surrogates for an individual patient’s disease. It remains unclear if patient transcriptional phenotypes are preserved in their matched organoid models. Here, we describe a pipeline that permits both direct characterization of the PDAC liver metastatic niche via single-cell RNA-sequencing and functional assessment of PDAC tumor biology in patient-matched organoid models. Starting from core needle biopsies of metastatic PDAC lesions containing 50-100k viable cells, we simultaneously perform: (1) single-cell RNA-sequencing using Seq-Well and (2) three-dimensional organoid culture generation. We have applied this approach to profile 23 patients and their matched early passage organoid models. Our pipeline yields high-quality single-cell measurements across diverse cell types—both malignant and non-malignant—enabling a principled dissection of tumor intrinsic and extrinsic factors. Evaluation of clinically relevant transcriptional signatures (e.g., Basal-like vs Classical) revealed extensive heterogeneity at the single-cell level. Single malignant cells are capable of co-expressing markers of both Basal-like and Classical states suggesting these phenotypes lie on a continuum rather than as discrete types. Basal cells express more stem-like features and inhabit a distinct microenvironment compared to their Classical counterparts. Microenvironmental composition differed on several levels between the two types, most notably their T/NK cell and macrophage populations with specific implications for subtype-specific microenvironmental directed therapy. Finally, we found that the microenvironment in traditional organoid culture selects against the Basal-like subtype and that these tumors are capable of significant phenotypic plasticity in vitro. We are able to recover Basal-like features by altering the organoid growth conditions. These findings suggest the need for distinct environments to support specific transcriptional subtypes in PDAC. Overall, our work provides a framework for the analysis of human cancers and their matched models using single-cell methods, and reveals novel, actionable insights into the heterogeneity and plasticity underlying survival in transcriptionally distinct forms of PDAC.

Citation Format: Peter S. Winter, Srivatsan Raghavan, Andrew Navia, Hannah Williams, Alan DenAdel, Radha Kalekar, Jennyfer Galvez-Reyes, Kristen Lowder, Nolawit Mulugeta, Manisha Raghavan, Ashir Borah, Raymond Ng, Junning Wang, Emma Reilly, Dorisanne Ragon, Lauren Brais, Kimmie Ng, James Cleary, Lorin Crawford, Scott Manalis, Jonathan Nowak, Brian Wolpin, William Hahn, Andrew Aguirre, Alex Shalek. Subtype-specific microenvironmental crosstalk and tumor cell plasticity in metastatic pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Tumor Heterogeneity: From Single Cells to Clinical Impact; 2020 Sep 17-18. Philadelphia (PA): AACR; Cancer Res 2020;80(21 Suppl):Abstract nr PR03.

Inactivation of the gene encoding the cationic antimicrobial peptide resistance factor MprF increases biofilm formation but reduces invasiveness of Listeria monocytogenes

AIMS

To understand the genetics involved in surface attachment and biofilm formation of Listeria monocytogenes.

METHODS AND RESULTS

An in vitro screen of a Himar1 transposon library of L. monocytogenes strain 15G01 identified three transposants that produced significantly different biofilm levels when compared to the wild-type strain; two mutants exhibited enhanced biofilm formation and one produced less biofilm biomass than the wild-type. The mutant 15G01 mprF::Himar1, which had a transposon insertion in the mprF gene, was selected for further analysis. The mutant produced a more densely populated biofilm on solid surfaces such as stainless steel and polystyrene, as determined using scanning electron and light microscopy. The 15G01 mprF::Himar1 mutant remained viable in biofilms, but showed an increase in sensitivity to the cationic antimicrobial gallidermin. The mutant also displayed reduced invasiveness in CaCo-2 intestinal cells, suggesting virulence properties are compromised by the inactivation of mprF.

CONCLUSIONS

Biofilm formation and gallidermin resistance of L. monocytogenes is influenced by mprF, but this trait is associated with a compromise in invasiveness.

SIGNIFICANCE AND IMPACT OF THE STUDY

The presence of pathogenic microorganisms in the food processing environment can cause a significant problem, especially when these microorganisms are established as biofilms. This study shows that the inactivation of the mprF gene results in enhanced biofilm formation and abiotic surface attachment of L. monocytogenes.

Abstract A06: The added value of examining germline variants in a precision cancer therapy study

Introduction: Tumor profiling is becoming a more routine part of clinical care. Many academic centers and commercial entities offer tumor sequencing of cancer-related genes without matched germline profiling. We hypothesize that tumor-only sequencing may limit full clinical interpretation and have decreased sensitivity to identify significant germline variants.

Methods: The Genomic Assessment Improves Novel Therapy (GAIN) Consortium is a clinical cancer genomics study for patients with high-risk solid malignancies. Patients in this study were selected for subanalysis if panel sequencing of 447 genes was performed on a tumor and interpreted by an expert panel prior to the availability of matched germline sequencing. Interpretation of tumor sequencing included both therapeutic recommendations and a curation of cancer-related variants of potential clinical significance if present in the germline. Germline sequencing was separately performed targeting 147 genes (a subset of the somatic panel) and analyzed with a germline-specific pipeline to identify and filter variants. We examined clinical recommendations in the somatic reports that were based on single-nucleotide variants identified from the 147 overlapping genes. We compared these interpretations with results from the matched germline data.

Results: We identified 159 participants with somatic and germline sequencing reports meeting the eligibility criteria. Germline sequencing identified 38 pathogenic or likely pathogenic (P/LP) germline variants in 35 of 159 patients (22%). Of those 35 patients, 17 (49%) had a P/LP variant in an autosomal dominant cancer predisposition gene, 19 (54%) in an autosomal recessive gene, and 1 (2.9%) in a noncancer gene. Of the 38 total variants, 21 (55%) were identified by the analytic pipeline used for somatic sequencing and noted as potential germline variants in the somatic reports. Forty treatment recommendations were made from the somatic data within the overlapping genes. Ten (25%) treatment recommendations were based on variants that were later determined to be germline. These included variants in TP53, SDHA, SMARCA4, TSC2, FAM175A, CHEK2, and AKT1, many of which were noted in the somatic reports to be variants of uncertain significance or possibly germline.

Conclusions: In this study, we found that clinically actionable germline variants were under-reported when relying on analytical pipelines and clinical interpretations developed for the analysis of tumor samples. In the absence of germline sequencing, we also found that cancer treatment recommendations can be made based on mutations identified from tumor sequencing that are germline variants. In many cases, these recommendations remain appropriate (e.g., PARP inhibitors for BRCA1/2) while in other cases germline data facilitated a more nuanced interpretation of actionability. These findings support the use of germline genetic testing and paired tumor-germline analysis in precision cancer medicine studies.

Citation Format: Jaclyn Schienda, Catherine M. Clinton, Laura B. Corson, Alma Imamovic-Tuco, Navin Pinto, Luke Maese, Theodore W. Laetsch, AeRang Kim, Susan I. Vear, Margaret E. Macy, Mark A. Applebaum, Rochelle Bagatell, Amit J. Sabnis, Daniel A. Weiser, Julia L. Glade-Bender, Samuel L. Volchenboum, Wenjun Kang, Danielle Manning, Jonathan Nowak, Joshua Schiffman, Neal I. Lindeman, Alanna J. Church, Katherine A. Janeway, Brian D. Crompton, Junne Kamihara. The added value of examining germline variants in a precision cancer therapy study [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr A06.

Abstract PR02: Matched metastatic pancreatic ductal adenocarcinoma biopsies and organoid models reveal tumor cell transcriptional plasticity and subtype-specific microenvironmental crosstalk

The majority of patients with pancreatic ductal adenocarcinoma (PDAC) present with metastatic disease at diagnosis and have median survival times of less than 12 months. Recent studies have demonstrated that PDAC tumors with distinct transcriptional signatures are associated with different clinical outcomes, and that the tumor microenvironment may contribute to PDAC pathogenesis. In parallel, there are ongoing efforts to understand if patient-derived organoid models can be used as functional surrogates for an individual patient’s disease. However, it remains unclear if patient transcriptional phenotypes are preserved in their matched organoid models. Here, we describe a pipeline that permits both direct characterization of the PDAC liver metastatic niche via single-cell RNA-sequencing and functional assessment of PDAC tumor biology in patient-matched organoid models. Starting from core needle biopsies of metastatic PDAC lesions containing 50-100k viable cells, we simultaneously perform (1) low-input single-cell RNA-sequencing using Seq-Well and (2) three-dimensional organoid culture generation. We have applied this approach to profile 21 patients and their matched early passage organoid models. Our pipeline yields high-quality single-cell measurements across diverse cell types—both tumor and nontumor stromal—enabling a principled dissection of tumor intrinsic and extrinsic factors. Evaluation of clinically relevant transcriptional signatures (e.g., basal-like vs. classical) revealed extensive heterogeneity at the single-cell level and identified new, hybrid expression states. We also observed evidence of significant subtype-specific crosstalk between immune populations and tumor cells—specifically between T cells and tumor cells originating from basal-like tumors. Serial sampling at different stages of treatment revealed transcriptional shifts in tumor cells suggestive of significant plasticity. We similarly found that organoids derived from basal-like tumors exhibited considerable plasticity in vitro and had decreased fitness in standard organoid culture conditions, suggesting the need for distinct environments to support specific transcriptional subtypes. Overall, our approach provides actionable insights into the heterogeneity and plasticity of human PDAC, as well as a pipeline and framework for the analysis of PDAC and other cancers.

This abstract is also being presented as Poster A50.

Citation Format: Peter S. Winter, Srivatsan Raghavan, Andrew W. Navia, Hannah Williams, Jennyfer Galvez-Reyes, Radha Kalekar, Ashir Borah, Alan DenAdel, Manisha Raghavan, Kristen Lowder, Nolawit Mulugeta, Junning Wang, Emma Reilly, Lauren Brais, Lorin Crawford, James McFarland, James M. Cleary, Jonathan Nowak, Brian M. Wolpin, Andrew J. Aguirre, William C. Hahn, Alex K. Shalek. Matched metastatic pancreatic ductal adenocarcinoma biopsies and organoid models reveal tumor cell transcriptional plasticity and subtype-specific microenvironmental crosstalk [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr PR02.

Size-dependent influence of NOx on the growth rates of organic aerosol particles

Atmospheric new-particle formation (NPF) affects climate by contributing to a large fraction of the cloud condensation nuclei (CCN). Highly oxygenated organic molecules (HOMs) drive the early particle growth and therefore substantially influence the survival of newly formed particles to CCN. Nitrogen oxide (NOx) is known to suppress the NPF driven by HOMs, but the underlying mechanism remains largely unclear. Here, we examine the response of particle growth to the changes of HOM formation caused by NOx. We show that NOx suppresses particle growth in general, but the suppression is rather nonuniform and size dependent, which can be quantitatively explained by the shifted HOM volatility after adding NOx. By illustrating how NOx affects the early growth of new particles, a critical step of CCN formation, our results help provide a refined assessment of the potential climatic effects caused by the diverse changes of NOx level in forest regions around the globe.

Search for Electron Antineutrino Appearance in a Long-Baseline Muon Antineutrino Beam

Electron antineutrino appearance is measured by the T2K experiment in an accelerator-produced antineutrino beam, using additional neutrino beam operation to constrain parameters of the Pontecorvo-Maki-Nakagawa-Sakata (PMNS) mixing matrix. T2K observes 15 candidate electron antineutrino events with a background expectation of 9.3 events. Including information from the kinematic distribution of observed events, the hypothesis of no electron antineutrino appearance is disfavored with a significance of 2.40σ and no discrepancy between data and PMNS predictions is found. A complementary analysis that introduces an additional free parameter which allows non-PMNS values of electron neutrino and antineutrino appearance also finds no discrepancy between data and PMNS predictions.

Association of naturally occurring sleep loss with reduced amygdala resting-state functional connectivity following psychosocial stress

Enduring sleep loss is a risk factor for a variety of both somatic and mental health issues. When subjected to sleep loss, the brain becomes vulnerable to critical alterations in cognitive and emotional processing. In our study, we examined the effect of psychosocial stress on amygdala resting-state functional connectivity in participants with cumulative sleep loss calculated across the seven days preceding scanning. For this purpose, forty-five healthy male participants completed a one-week sleep diary and underwent resting-state scans before and after taking part in the ScanSTRESS paradigm, which allows social stress induction during functional magnetic resonance imaging. Sleep loss was negatively associated with seed-based functional connectivity of the left amygdala with the medial prefrontal cortex, dorsal anterior cingulate cortex, anterior insula, posterior cingulate cortex, and dorsolateral prefrontal cortex. That is, participants with higher amounts of sleep loss showed reduced left amygdala connectivity after social stress induction to cortical regions encompassing main nodes of the brain's default mode network and salience network. Our results shed more light on how brain functional connectivity may shape the brain's stress response in the context of naturally occurring sleep loss, revealing a potential neural mechanism for increased vulnerability to stress-related psychopathology.

Vitamin D receptor agonist paricalcitol plus gemcitabine and nab-paclitaxel in patients with metastatic pancreatic cancer

TPS784

Background: Patients(pts) with metastatic pancreatic cancer (PC) have a median survival of less than one year even with use of multiagent chemotherapy programs. Pancreatic tumors are composed of multiple cell types and a dense extracellular matrix that may support cancer cell proliferation and impede chemotherapy delivery. Cancer-associated fibroblasts (CAF’s) in the tumor microenvironment secrete pro-inflammatory factors and components of the extracellular matrix. In PC laboratory models, engagement of the vitamin D receptor (VDR) by VDR agonists shifts CAFs toward a more quiescent phenotype with reduced tumor growth and improved chemotherapy penetration (Sherman. Cell, 2014). Paricalcitol is a synthetic VDR agonist used in patients with secondary hyperparathyroidism due to chronic kidney disease. A prior pilot study evaluated IV paricalcitol with gemcitabine (G) and nab-paclitaxel (A) before surgical resection in patients with resectable PC (NCT02030860). Methods: Pts with previously-untreated metastatic PC will be enrolled in a two-stage study consisting of a safety run-in and a randomized phase 2 study (NCT03520790). In the run-in stage, 36 pts will be randomized 1:1:1 to G (1000 mg/m2) and A (125 mg/m2) given 3 weeks on and 1 week off plus: (a) paricalcitol 25mcg IV thrice weekly, (b) paricalcitol 16mcg oral daily, or (c) placebo oral daily. Grade 3/4 hypercalcemia or genitourinary stones will be considered dose limiting toxicities.Pts will undergo paired pre- and on-treatment tumor biopsies to examine pharmacodynamic (PD) markers by bulk and single cell RNA sequencing and multiplex immunofluoresence.Assuming safety and supportive PD assessments, the phase 2 study will randomize an additional 76 pts to two treatment arms with GA plus: (a) paricalcitol or (b) placebo.Paricalcitol formulation (IV or oral) will be determined based on data from the run-in stage.The primary endpoint of the phase 2 study is overall survival, with a total of 100 pts needed to identify a hazard ratio of 0.6 with 80% power and one-sided alpha of 0.10.Secondary endpoints include safety, response rate, and progression free survival.Trial funding provided by SU2C, CRUK,Lustgarten Foundation, and AACR. Clinical trial information: NCT03520790.

Abstract PR15: Assessment of tumor heterogeneity, clonal evolution, and the stromal microenvironment in metastatic pancreatic ductal adenocarcinoma and matched patient-derived organoids

Patients with metastatic pancreatic ductal adenocarcinoma (PDAC) have few treatment options and continue to have dismal prognoses due to the rapid development of resistance to both standard-of-care and experimental therapies. Several recent studies have demonstrated that patients with distinct PDAC transcriptional subtypes have differing clinical courses, and that the tumor microenvironment can also contribute to patient outcome. However, deep cellular characterization of metastatic PDAC tumors and their stromal microenvironments has been challenging due to limited tissue availability from metastatic liver biopsies. Here, we present a focused assessment of the PDAC liver metastatic niche—encompassing tumor, immune, and stromal cells—via low-input single-cell transcriptional profiling of patient specimens with the goal of developing a deeper understanding of tumor heterogeneity and the tumor microenvironment. Our pipeline accesses core needle biopsies from liver metastases, splitting each core for 1) single-cell RNA sequencing using Seq-Well and 2) organoid generation. Using this pipeline, we have successfully profiled liver metastases from 15 patients along with matched early-passage organoid models. Assessment of clinically relevant transcriptional signatures reveals extensive heterogeneity at the single-cell level and identifies new, hybrid transcriptional states occupied by these metastases. In addition, we observe evidence of significant crosstalk between stromal and immune populations and tumor cells. Serial samples at different stages of therapy show transcriptional shifts in tumor cells suggestive of significant plasticity that likely contributes to therapeutic resistance. Initial analysis of matched organoids at successive passages demonstrates a skew in their clonal composition, as well as evolution of their transcriptional state as compared to their in vivo phenotypes. Overall, our work provides an important window into the biology of metastatic PDAC, as well as some of the first direct comparisons of clonality and transcriptional phenotypes across in vivo specimens and their in vitro organoid counterparts.

This abstract is also being presented as Poster C43.

Citation Format: Srivatsan Raghavan, Peter S. Winter, Andrew Navia, Radha Kalekar, Jennyfer Galvez-Reyes, Sanjay Prakadan, Junning Wang, Emma Reilly, Lauren Brais, James M. Cleary, Jonathan Nowak, Brian M. Wolpin, Alex K. Shalek, Andrew J. Aguirre, William C. Hahn. Assessment of tumor heterogeneity, clonal evolution, and the stromal microenvironment in metastatic pancreatic ductal adenocarcinoma and matched patient-derived organoids [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2019 Sept 6-9; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2019;79(24 Suppl):Abstract nr PR15.

Abstract C130: Precision oncology decision support within the Gastrointestinal Cancer Center at Dana-Farber Cancer Institute (GI TARGET)

Precision oncology is fast becoming the new paradigm for cancer treatment. This approach involves molecular profiling of patient tumors and tailoring of a treatment regimen based on the unique combination of targetable alterations identified therein. At Dana-Farber Cancer Institute (DFCI), over 24,000 patient tumors have been sequenced using the NGS platform OncoPanel since 2013. OncoPanel is a comprehensive genomic characterization of a tumor and it can be time-consuming to discern those alterations that are interesting from an academic or research perspective from those that can be leveraged to direct patient care. To address this issue, the GI TARGET (Treatment Assistance Regarding Genomic Evaluation of Tumors) project was initiated to provide decision support for oncologists within the DFCI Gastrointestinal Cancer Center (GCC). GI TARGET is a collaboration between the DFCI GCC, the Brigham & Women’s Hospital (BWH) Center for Advanced Molecular Diagnostics (CAMD), and the DFCI Knowledge Systems Group, developers of the precision medicine clinical trial matching platform MatchMiner. Report generation involves review of OncoPanel data in the context of patient clinical history via one of two workflows; complex genomic cases are reviewed in a weekly Molecular Tumor Board comprised of oncologists, molecular pathologists, a PhD-level Clinical Genomics Scientist, and representatives from the MatchMiner team, while ‘simple’ genomic cases are reviewed by both an oncologist and a PhD-level Clinical Genomics Scientist. Since the launch of the project in January 2018, we have signed out over 1000 GI TARGET reports. We are assessing the utility of these reports using a number of metrics including clinical trial enrollment tracking via MatchMiner, follow-up on recommendations via chart abstraction, and oncologist feedback. The aims of GI TARGET are 1) to reduce the burden of genomic analysis on the treating oncologist by providing expert-led deep review of OncoPanel and exploration of associated therapy/additional patient care considerations, 2) to support clinical trial enrollment by matching the results of somatic testing with ongoing clinical studies, and 3) to provide an example framework for how precision oncology can be incorporated into standard clinical cancer care, which may be helpful to guide efforts in other care settings, particularly in community hospitals where the vast majority (an estimated 80%-85%) of cancer patients in the United States receive their care.

Citation Format: Rachel B Keller, Tali Mazor, Marios Giannakis, Jonathan Nowak, Lynette Sholl, Andrew Aguirre, Adam Bass, Nilay Sethi, Ankur Nagaraja, Lauren Brais, Emma Reilly, Ethan Cerami, Brian Wolpin. Precision oncology decision support within the Gastrointestinal Cancer Center at Dana-Farber Cancer Institute (GI TARGET) [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr C130. doi:10.1158/1535-7163.TARG-19-C130

Abstract LB-A16: Imaging of glioblastoma using LDLR-based targeted delivery system

Introduction: Glioblastoma is the most agressive brain tumor with average life expectancy of 12-15 months from diagnosis. One of the factors that limit efficacy of drug, especially in primary brain tumor is permeability of the blood brain barrier (BBB). The low-density lipoprotein receptor (LDLR) expressed at the BBB mediates the transport of endogenous ligands through the BBB, a process referred to as receptor-mediated transcytosis. VECT-HORUS (VH) has identified and chemically optimized a family of peptide-vectors targeting both the human and murine LDLR and able i) to cross the BBB and ii) to target tumors such as glioblastoma that express high levels of the LDLR. The objective of this study was to determine the LDLR targeting properties of 68Ga/177Lu- radiolabeled peptide vectors developed by the VH proprietary platform using a glioblastoma model that expresses the human LDLR (hLDLR) at high levels. Methods: The LDLR targeted DOTA-conjugates (VH-DO31, VH-DO33) and NODAGA conjugate (VH-NO31), (10-30ug, VECT-HORUS SAS, France) were labeled with 68Ga (1.5mCi) eluted from 68Ge/68Ga generator (100mCi, ITG GmBH, Germany) or with 177Lu n.c.a (1mCi, ITG GmBH, Germany). The U87MG cell line has been shown to express high levels of the hLDLR. The LDLR targeting properties of these conjugates were thus determined in vitro in U87MG cellular uptake studies, as well as in vivo in U87MG xenografted mice. The PET/CT images of U87MG xenograft generated in athymic nude mice (10 weeks, n=3) were acquired using G4 PET/Xray camera (Sofie Biosciences; 10min/scan) at 1h, 2h, 3h and 4h post-injection. Results: All 68Ga/177Lu-labeled conjugates were synthesized with radiochemical purity higher than 91 % as determined by radio-HPLC. Radiolytic stability of agents was increased using C18 ethanol purification of the final products. 177Lu-VH-DO33 showed the highest retention of the agent in U87MG cell line at 1h (13.88± 1.6 %ID/mg) and 21h incubation time (8.7± 4 %ID/mg) compared to 177Lu-VH-DO31 (8.28 ±6.2 %ID/mg) The microPET imaging studies showed rapid accumulation and retention of all VH derivatives in tumor as monitored up to 4h post injection. All agents were eliminated through bladder and kidneys. There was no accumulation of agents in the bone marrow. The image based biodistribution studies of 68Ga-VH-DO31, 68Ga-VH-DO33 and 68Ga-VH-NO31 showed that the tumor to muscle ratios (SUV ratio) after 30 min post-injection were 4.12, 5.07 and 3.88, respectively and remained at the same levels up to 3h post-injection. The SUV ratios of tumor to kidneys were as follows: 68Ga-VH-DO31 (0.46), 68Ga-VH-DO33 (0.84) and 68Ga-VH-NO31 (0.46) confirming renal elimination of the agents. Conclusions: VH derivatives showed favorable hLDLR and tumor-targeting properties both in in vitro as well as in vivo in U87MG xenografts. These results can postulate that hLDLR may serve as a target for the development of theranostic probes for the diagnosis and radiotherapy of glioblastoma.

Citation Format: Izabela Tworowska, Leo G Flores II, Rafal Zielinski, Jonathan Nowak, Pascaline Lecorche, Cedric Malicet, Michel Khrestchatisky, Jamal Temsamani, Ebrahim Delpassand. Imaging of glioblastoma using LDLR-based targeted delivery system [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr LB-A16. doi:10.1158/1535-7163.TARG-19-LB-A16

P4510Impact of secondary tricuspid regurgitation on survival in heart failure - insights from COMMIT-HF registry

Background

Functional tricuspid regurgitation (fTR) is common in left sided heart disease, especially in patients with concomitant left-sided valvular diseases and can lead to functional impairment and reduced survival. However, the impact of fTR on survival in chronic heart failure with reduced left ventricular ejection fraction (HFrEF) without severe left valvular diseases (LVD) is not fully established. The aim of the present study was to observe if moderate to severe fTR may influence the survival in patients with HFrEF without severe LVD.

Methods

We have analyzed a large single-center registry (n=2731) of HFrEF patients treated in a large-volume cardiovascular center between 2009–2015. After exclusion of patients with severe aortic and mitral valve disease we have included 2435 patients with HFrEF (left ventricular ejection fraction (LVEF) ≤35%). Functional moderate to severe tricuspid regurgitation without severe left valvular diseases was present in 465 patients. Twelve -month vital status was available for the whole patient population. Univariate and multivariate Cox proportional hazard regression models were performed to evaluate the relationship between moderate to severe fTR and mortality in the study group.

Results

Comparison of clinical data of fTR and non-fTR in HFrEF patients revealed some significant differences (age 63.3±12.9 vs 61.3±12.4, p=0.002; female sex 25.8% vs 17,9%, p<0.001; chronic kidney disease stage III-V 45.3 vs 26.6%, p=0.001; atrial fibrillation 52.4% vs 28.5%, p<0.001). Twelve-month all-cause mortality was over 2-fold higher in the fTR group (21.2% vs 8.1%, p<0.001). There were no significant differences with regard to the medical treatment, implantable defibrillator or cardiac resynchronization therapy. The presence of fTR was identified as an independent echocardiographic factor impaired 12-month all-cause survival (HR 1.59, CI 1.2- 2.09, p<0.001, figure 1)

Conclusion

Apart from the LVEF, the presence of moderate to severe fTR may predict 12-month all-cause mortality in patients with HFrEF.

Acknowledgement/Funding

None

P5368The prevalence and management of familial hypercholesterolemia in patients with acute coronary syndrome in Poland: results of the TERCET registry

Background

Prevalence of familial hypercholesterolemia (FH) is high among patients with coronary artery disease (CAD). However, data on FH among patients with acute coronary syndrome (ACS) are still scarce.

Purpose

Therefore, we aimed to assess the prevalence, lipid-lowering therapy and short- and long-term outcomes in patients with FH among patients with ACS.

Methods

We finally included 19,582 consecutive patients from the Hyperlipidaemia Therapy in the tERtiary Cardiological cEnTer (TERCET) Registry for years 2006–2018. Among them, there were 7,319 patients admitted with ACS: 3,085 due to ST-segment elevation acute coronary syndrome (STEMI), 2,256 due to NSTEMI, and 1,978 due to unstable angina (UA). Stable CAD [sCAD] group n=12,462 that was treated as a reference one. Based on the personal and familial history of premature cardiovascular disease and low-density lipoprotein cholesterol (LDL-C) concentration, the Dutch Lipid Clinic Network (DLCN) algorithm was used for FH diagnosis.

Results

At the time of hospitalization, the overall occurrence of probable/definite FH and possible FH were 1.2% and 13.5% respectively. In patients with ACS, 1.6% had probable/definite FH and 17.0% possible FH. The highest occurrence of FH was observed in STEMI subgroup, where 20.6% of the patients had ≥3 points according to the DLCN criteria. There were significant differences in hypolipemic treatment between the FH subpopulations. In patients with definite/probable FH 92.3% and 91.5% were administered statins at discharge, respectively (including 52.9% prescribed intensive statin therapy). Patients with definite and probable FH had higher 30-day mortality than patients without FH (8.2% and 3.8% vs 2.0%, respectively; p=0.0052). However, no significant differences were observed between the FH groups in the 12-, 36- and 60-month follow-up (Figure). Propensity-score matching analysis showed that definite/probable FH patients had significantly higher all-cause mortality at the 36- and 60-month follow-up in comparison to non-FH subjects (11.4% vs 4.8% and 19.2% vs 7.2%, respectively; p≤0.021 for both).

Outcomes depending on DCLN FH diagnosis.

Conclusions

The prevalence of FH according to the DLCN criteria in the Polish very high-risk population is even 14.7% and is significantly higher in patients with ACS than in patients with sCAD. Among patients included in the Registry, the occurrence of FH rises to 20.6% in the STEMI subgroup, and to 17.2% in the NSTEMI subgroup. Propensity-score matching analysis confirmed that FH itself is a cause of increased all-cause mortality in the long-term follow-up.

Acknowledgement/Funding

None

First Measurement of Inclusive Muon Neutrino Charged Current Differential Cross Sections on Argon at E_{ν}∼0.8 GeV with the MicroBooNE Detector

We report the first measurement of the double-differential and total muon neutrino charged current inclusive cross sections on argon at a mean neutrino energy of 0.8 GeV. Data were collected using the MicroBooNE liquid argon time projection chamber located in the Fermilab Booster neutrino beam and correspond to 1.6×10^{20} protons on target of exposure. The measured differential cross sections are presented as a function of muon momentum, using multiple Coulomb scattering as a momentum measurement technique, and the muon angle with respect to the beam direction. We compare the measured cross sections to multiple neutrino event generators and find better agreement with those containing more complete treatment of quasielastic scattering processes at low Q^{2}. The total flux integrated cross section is measured to be 0.693±0.010(stat)±0.165(syst)×10^{-38}  cm^{2}.

Significant Excess of Electronlike Events in the MiniBooNE Short-Baseline Neutrino Experiment

The MiniBooNE experiment at Fermilab reports results from an analysis of ν_{e} appearance data from 12.84×10^{20} protons on target in neutrino mode, an increase of approximately a factor of 2 over previously reported results. A ν_{e} charged-current quasielastic event excess of 381.2±85.2 events (4.5σ) is observed in the energy range 200<E_{ν}^{QE}<1250  MeV. Combining these data with the ν[over ¯]_{e} appearance data from 11.27×10^{20} protons on target in antineutrino mode, a total ν_{e} plus ν[over ¯]_{e} charged-current quasielastic event excess of 460.5±99.0 events (4.7σ) is observed. If interpreted in a two-neutrino oscillation model, ν_{μ}→ν_{e}, the best oscillation fit to the excess has a probability of 21.1%, while the background-only fit has a χ^{2} probability of 6×10^{-7} relative to the best fit. The MiniBooNE data are consistent in energy and magnitude with the excess of events reported by the Liquid Scintillator Neutrino Detector (LSND), and the significance of the combined LSND and MiniBooNE excesses is 6.0σ. A two-neutrino oscillation interpretation of the data would require at least four neutrino types and indicate physics beyond the three neutrino paradigm. Although the data are fit with a two-neutrino oscillation model, other models may provide better fits to the data.

Clinical Heterogeneity of Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked Syndrome: A French Multicenter Retrospective Study

Objective

Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is an autoimmune disease caused by mutations in the forkhead box protein 3 gene (FOXP3), which encodes a key regulator of immune tolerance. The aim of this study was to describe the clinical heterogeneity of the disease in a national French cohort.

Methods

Multicenter retrospective study of patients diagnosed with IPEX syndrome caused by mutations in FOXP3.

Results

Thirty children from 26 families were included. Age at disease onset (median [first to third quartile]) was 1.5 mo [0–84] and at death 3.5 years [0–10.5] (n = 15) indicating a high heterogeneity. Initial presentation was diarrhoea (68%), type 1 diabetes (T1D; 25%), skin lesions (7%) and nephropathy (3%). During the course of the disease the following main symptoms were observed: diarrhoea (100%), skin lesions (85%), T1DM (50%), severe food allergies (39%), haematological disorders (28%), nephropathies (25%), hepatitis (14%) as well as the presence of a variety of autoantibodies. Immunosuppressive mono- or combination therapy led to improvement in eight children. Three boys displayed a stable disease course without any immunosuppressive medication. Overall 10-year survival rate was 43% (42% in transplanted patients and 52% in patients on immunosuppressive therapy). Five out of 22 identified FOXP3 mutations have not been described yet: c.−23 + 1G > A, c.−23 + 5G > A, c.264delC, c.1015C > T and c.1091A > G. The first two produced atypical, attenuated phenotypes. Missense and frameshift mutations affecting the forkhead domain were associated with poor survival (Gehan–Wilcoxon p = 0.002).

Conclusion

The broad phenotypic heterogeneity of IPEX raises questions about modifying factors and justifies early FOXP3 sequencing in suspected cases.

Search for CP Violation in Neutrino and Antineutrino Oscillations by the T2K Experiment with 2.2×10^{21} Protons on Target

The T2K experiment measures muon neutrino disappearance and electron neutrino appearance in accelerator-produced neutrino and antineutrino beams. With an exposure of 14.7(7.6)×10^{20} protons on target in the neutrino (antineutrino) mode, 89 ν_{e} candidates and seven anti-ν_{e} candidates are observed, while 67.5 and 9.0 are expected for δ_{CP}=0 and normal mass ordering. The obtained 2σ confidence interval for the CP-violating phase, δ_{CP}, does not include the CP-conserving cases (δ_{CP}=0, π). The best-fit values of other parameters are sin^{2}θ_{23}=0.526_{-0.036}^{+0.032} and Δm_{32}^{2}=2.463_{-0.070}^{+0.071}×10^{-3}  eV^{2}/c^{4}.