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TABLE OF CONTENTS GENERAL INFORMATION TITLE AUTHORS AND BEST CONTACT LICENSES USEFUL LINKS DATE OF DATA COLLECTION FILE ORGANIZATION FUNDING ---- Release Notes:This is a pre-publication placeholder for primary data release for the publication listed below. In common with GEO, PRIDE, and other data repositories, this will be populated with final data following peer review. ---- GENERAL INFORMATION Publication Title:Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence Authors:Zoltan Maliga, Daniel Y. Kim, Ai-Tram N. Bui, Jia-Ren Lin, Anna K. Dewan, George G. Murphy, Ajit J. Nirmal, Christine G. Lian, Peter K. Sorger, Nicole R. LeBoeuf Contact Information Nicole LeBoeuf, MD, MPH Vice Chair of Dermatology,Dana-FarberCancer Institute,; Chief, Division of Oncodermatology, Brigham and Women's Hospital; Clinical Director, Center for Cutaneous Oncology, Dana-Farber/Brigham Cancer Center, HarvardMedical School nleboeuf@partners.org Publications that cite or use the data:** Maliga, M, Kim, DY, Tram, B, Lin, JR, Dewan, AK, Jadeja, S, Murphy, G, Nirmal, AJ, Lian, C, Sorger, PK, LeBoeuf, NR. Immune Profiling of Dermatologic Adverse Events from Checkpoint Blockade using Tissue Cyclic Immunofluorescence.https://doi.org/10.1101/2023.04.03.535435 Licenses/restrictions placed on the data:CC BYhttps://creativecommons.org/licenses/by/4.0/ ---- FILE ORGANIZATION FILE TYPES/SUMMARY:Each folder corresponds to a patient sample (N). The following files are available for each patient and are located on [Synapse/AWS/Etc]. File Type Description Location N.ome.tif Stitched multiplex CyCIF image pyramid in ome.tif format AWS N_IHC.ome.tiff Immunohistochemistry stained image of serial FFPE tissue section in .ome.tiff format AWS N_HE.ome.tiff Hematoxylin and eosin stained image of FFPE tissue section in .ome.tiff format AWS markers.csv List of all markers in ome.tif image Synapse N_Quantification.csv Single-cell feature table, including intensity data for all channels Synapse segmentation/ Folder of segmentation maps for tissue image in .tif format AWS Synapse Library:Edit this to link directly to your public Synapse Library Free account registration is required to download files from Synapse. Images and metadata are available in the bucket at the following AWS location:[ADD BUCKET DETAILS] To browse and download the data use either a graphical file transfer application that supports S3 such asCyberDuck, or theAWS CLI tools. A graphical tool may be more convenient but the CLI tools will likely offer higher download speeds. FILE LIST N.ome.tif LSP Slide ID File Name File Size LSP10925 LSP10925_CyCIF_Image.ome.tif 9.3 GB LSP10929 LSP10929_CyCIF_Image.ome.tif 6.0 GB LSP10931 LSP10931_CyCIF_Image.ome.tif 8.7 GB LSP10933 LSP10933_CyCIF_Image.ome.tif 6.7 GB LSP10951 LSP10951_CyCIF_Image.ome.tif 11 GB LSP10980 LSP10980_CyCIF_Image.ome.tif 9.3 GB 51 GB markers.csv File name File Size Synapse ID markers.csv 0.7 KB N_Quantification.csv LSP Slide ID File Name File Size Synapse ID LSP10925 LSP10925_CyCIF_Quantification.csv 20 MB LSP10929 LSP10929_CyCIF_Quantification.csv 12 MB LSP10931 LSP10931_CyCIF_Quantification.csv 5.9 MB LSP10933 LSP10933_CyCIF_Quantification.csv 7.5 MB LSP10951 LSP10951_CyCIF_Quantification.csv 8.3 MB LSP10980 LSP10980_CyCIF_Quantification.csv 12 MB segmentation/ LSP Slide ID File Name File Size LSP10925 LSP10925_cellRingMask.tif 20 MB LSP10929 LSP10929_cellRingMask.tif 12 MB LSP10931 LSP10931_cellRingMask.tif 5.9 MB LSP10933 LSP10933_cellRingMask.tif 7.5 MB LSP10951 LSP10951_cellRingMask.tif 8.3 MB LSP10980 LSP10980_cellRingMask.tif 12 MB 66 MB N_IHC.ome.tiff LSP Slide ID Description File name File Size LSP16237 CD103 Image LSP16237_IHC_CD103.ome.tiff 2.8 GB LSP16240 PD1 Image LSP16240_IHC_PD1.ome.tiff 3.1 GB LSP16241 MART1 Image LSP16241_IHC_MART1.ome.tiff 2.9 GB LSP16242 FOXP3 Image LSP16242_IHC_FOXP3.ome.tiff 3.5 GB LSP16243 CD3 Image LSP16243_IHC_CD3.ome.tiff 2.9 GB LSP16244 CD4 Image LSP16244_IHC_CD4.ome.tiff 3.2 GB LSP16245 CD8 Image LSP16245_IHC_CD8.ome.tiff 3.2 GB LSP16246 CD20 Image LSP16246_IHC_CD20.ome.tiff 3.2 GB LSP16247 CD19 Image LSP16247_IHC_CD19.ome.tiff 3.7 GB LSP16248 CD163 Image LSP16248_IHC_CD163.ome.tiff 4.0 GB LSP16249 PDL1 Image LSP16249_IHC_PDL1.ome.tiff 3.7 GB LSP16250 CD69 Image LSP16250_IHC_CD69.ome.tiff 3.2 GB 39 GB N_HE.ome.tiff LSP Slide ID Description File name File Size LSP16237 H&E Image LSP16234_HE.ome.tiff 14 GB 14 GB ---- FUNDING R50-CA252138, U2C-CA233262 and Ludwig Cancer Research

Immune checkpoint blockade (ICB) has shown immense promise for treating patients with various cancer types, but its effectiveness relies on our ability to identify likely responders. Here, we examined the association between mutations in 25 core DNA repair genes and ICB outcomes in 6619 patients across 9 cancer types with advanced disease and MSK-IMPACT tumor sequencing. Notably, we observed that mutations in 7 of the DNA repair genes (ATM, ATR, POLE, ERCC4, NBN, RAD50, PARP1) were significantly associated with improved overall survival in ICB-treated patients (p0.05 for all) and had significant interaction with treatment (p

Purpose:Perineural invasion (PNI) is associated with aggressive tumor behavior, recurrence, and metastasis, and can influence the administration of adjuvant treatment. However, standard histopathologic examination has limited sensitivity in detecting PNI and does not provide insights into its mechanistic underpinnings.Experimental Design:A multivariate Cox regression was performed to validate associations between PNI and survival in 2,029 patients across 12 cancer types. Differential expression and gene set enrichment analysis were used to learn PNI-associated programs. Machine learning models were applied to build a PNI gene expression classifier. A blinded re-review of hematoxylin and eosin (H&E) slides by a board-certified pathologist helped determine whether the classifier could improve occult histopathologic detection of PNI.Results:PNI associated with both poor overall survival [HR, 1.73; 95% confidence interval (CI), 1.27–2.36; P < 0.001] and disease-free survival (HR, 1.79; 95% CI, 1.38–2.32; P < 0.001). Neural-like, prosurvival, and invasive programs were enriched in PNI-positive tumors (Padj < 0.001). Although PNI-associated features likely reflect in part the increased presence of nerves, many differentially expressed genes mapped specifically to malignant cells from single-cell atlases. A PNI gene expression classifier was derived using random forest and evaluated as a tool for occult histopathologic detection. On a blinded H&E re-review of sections initially described as PNI negative, more specimens were reannotated as PNI positive in the high classifier score cohort compared with the low-scoring cohort (P = 0.03, Fisher exact test).Conclusions:This study provides salient biological insights regarding PNI and demonstrates a role for gene expression classifiers to augment detection of histopathologic features.

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Objective To assess whether maternal ultra-processed food intake during peripregnancy and during the child rearing period is associated with offspring risk of overweight or obesity during childhood and adolescence. Design Population based prospective cohort study. Setting The Nurses’ Health Study II (NHSII) and the Growing Up Today Study (GUTS I and II) in the United States. Participants 19 958 mother-child (45% boys, aged 7-17 years at study enrollment) pairs with a median follow-up of 4 years (interquartile range 2-5 years) until age 18 or the onset of overweight or obesity, including a subsample of 2925 mother-child pairs with information on peripregnancy diet. Main outcome measures Multivariable adjusted, log binomial models with generalized estimating equations and an exchangeable correlation structure were used to account for correlations between siblings and to estimate the relative risk of offspring overweight or obesity defined by the International Obesity Task Force. Results 2471 (12.4%) offspring developed overweight or obesity in the full analytic cohort. After adjusting for established maternal risk factors and offspring’s ultra-processed food intake, physical activity, and sedentary time, maternal consumption of ultra-processed foods during the child rearing period was associated with overweight or obesity in offspring, with a 26% higher risk in the group with the highest maternal ultra-processed food consumption (group 5) versus the lowest consumption group (group 1; relative risk 1.26, 95% confidence interval 1.08 to 1.47, P for trendv group 1: relative risk 1.17, 95% confidence interval 0.89 to 1.53, P for trend=0.07). These associations were not modified by age, sex, birth weight, and gestational age of offspring or maternal body weight. Conclusions Maternal consumption of ultra-processed food during the child rearing period was associated with an increased risk of overweight or obesity in offspring, independent of maternal and offspring lifestyle risk factors. Further study is needed to confirm these findings and to understand the underlying biological mechanisms and environmental determinants. These data support the importance of refining dietary recommendations and the development of programs to improve nutrition for women of reproductive age to promote offspring health.

Presenilin 1 (PS1) is a central component of γ-secretase, an enzymatic complex involved in the generation of the amyloid-β (Aβ) peptide that deposits as plaques in the Alzheimer's disease (AD) brain. The M146L mutation in the PS1 gene (

Transcriptional states in pancreatic cancer can stratify patients by response to chemotherapy and clinical outcomes. These include the classical and basal-like states as well as a newly identified neural-like progenitor (NRP) state, which we have previously found to be enriched in primary patient tumors treated with neoadjuvant chemotherapy and radiotherapy. While several transcription factor drivers of classical and basal-like identity have been described, key regulators of the NRP state are unknown. Through in silico approaches, we identified candidate transcription factors of the NRP state, including GLIS3, a Krüppel-like zinc finger protein that mediates neuroendocrine fate during pancreatic development and differentiation of human embryonic stem cells into posterior neural progenitor cells. Our understanding of biologic and clinically-relevant attributes of transcriptional cell states remains limited by state-specific biases in various preclinical models. Existing human cell lines maintained as two-dimensional cultures tend to preferentially represent the basal-like state, whereas human three-dimensional organoid models grown in standard culture conditions best reflect the classical state. These phenotypes are therefore impacted by culture conditions as well as underlying genetic features. Furthermore, most murine pancreatic cancer models do not fully reflect the classical vs. basal-like state heterogeneity observed in humans. To enable systematic study of the classical, basal-like and NRP phenotypes, we developed isogenic KP (KrasG12D/+;Trp53FL/FL) murine organoids with a germline dCas9-VPR system to enable facile overexpression of state-specific transcription factors through CRISPR activation approaches. Quantitative PCR, RNA-sequencing, and proteomics confirmed Gata6, deltaN Trp63, and Glis3 as drivers of classical, basal-like, and NRP identity, respectively. DeltaN Trp63 organoids were further differentiated by loss of luminal morphology. Pairwise comparisons of global transcriptional alterations suggest the greatest similarities between the Gata6- and Glis3-overexpressed models, which is consistent with enhanced associations between classical and NRP states in patient tumors. Finally, although basal-like and NRP states are associated with poorer response to multi-agent chemotherapy, state-specific therapeutic sensitivities to other treatments remain incompletely defined. We therefore performed drug sensitivity assays with a panel of targeted therapies and unveiled state-specific sensitivities. These data were corroborated by drug sensitivity profiling of human patient-derived organoids and cell lines. Taken together, these results suggest a framework for defining cell state-specific vulnerabilities that may aid in stratifying and treating pancreatic cancer patients with new therapies. Citation Format: Jimmy A. Guo, Jennifer Su, Ananya Jambhale, Julien Dilly, Connor J. Hennessey, Carina Shiau, Patrick Yu, Steven Wang, Junning Wang, Laleh Abbassi, James Neiswender, Tate Bertea, Annan Yang, Qijia Yu, Peter Westcott, Jason Schenkel, Daniel Y. Kim, Hannah I. Hoffman, Grissel Cervantes Jaramillo, Giselle A. Uribe, Westley W. Wu, Arnav Mehta, David Ting, Julian A. Pacheco, Amy Deik, Clary Clish, Francisca Vazquez, Brian Wolpin, Aviv Regev, William A. Freed-Pastor, Joseph D. Mancias, Tyler Jacks, William L. Hwang, Andrew J. Aguirre. Systematic dissection of transcriptional states 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 A052.

CRISPR-Cas9 nuclease-based gene drives have been developed toward the aim of control of the human malaria vector Anopheles gambiae . Gene drives are based on an active source of Cas9 nuclease in the germline that promotes super-Mendelian inheritance of the transgene by homology-directed repair (“homing”). Understanding whether CRISPR-induced off-target mutations are generated in Anopheles mosquitoes is an important aspect of risk assessment before any potential field release of this technology. We compared the frequencies and the propensity of off-target events to occur in four different gene-drive strains, including a deliberately promiscuous set-up, using a nongermline restricted promoter for SpCas9 and a guide RNA with many closely related sites (two or more mismatches) across the mosquito genome. Under this scenario we observed off-target mutations at frequencies no greater than 1.42%. We witnessed no evidence that CRISPR-induced off-target mutations were able to accumulate (or drive) in a mosquito population, despite multiple generations’ exposure to the CRISPR-Cas9 nuclease construct. Furthermore, judicious design of the guide RNA used for homing of the CRISPR construct, combined with tight temporal constriction of Cas9 expression to the germline, rendered off-target mutations undetectable. The findings of this study represent an important milestone for the understanding and managing of CRISPR-Cas9 specificity in mosquitoes, and demonstrates that CRISPR off-target editing in the context of a mosquito gene drive can be reduced to minimal levels.

Prognostication for patients with cancer is important for clinical planning and management, but remains challenging given the large number of factors that can influence outcomes. As such, there is a need to identify features that can robustly predict patient outcomes. We evaluated 8608 patient tumor samples across 16 cancer types from The Cancer Genome Atlas and generated distinct survival classifiers for each using clinical and histopathological data accessible to standard oncology workflows. For cancers that had poor model performance, we deployed a random-forest-embedded sequential forward selection approach that began with an initial subset of the 15 most predictive clinicopathological features before sequentially appending the next most informative gene as an additional feature. With classifiers derived from clinical and histopathological features alone, we observed cancer-type-dependent model performance and an area under the receiver operating curve (AUROC) range of 0.65 to 0.91 across all 16 cancer types for 1- and 3-year survival prediction, with some classifiers consistently outperforming those for others. As such, for cancers that had poor model performance, we posited that the addition of more complex biomolecular features could enhance our ability to prognose patients where clinicopathological features were insufficient. With the inclusion of gene expression data, model performance for 3 select cancers (glioblastoma, stomach/gastric adenocarcinoma, ovarian serous carcinoma) markedly increased from initial AUROC scores of 0.66, 0.69, and 0.67 to 0.76, 0.77, and 0.77, respectively. As a whole, this study provides a thorough examination of the relative contributions of clinical, pathological, and gene expression data in predicting overall survival and reveals cancer types for which clinical features are already strong predictors and those where additional biomolecular information is needed.

Purpose: Perineural invasion (PNI) is associated with aggressive tumor behavior, recurrence, and metastasis, and can influence the administration of adjuvant treatment. However, standard histopathologic examination has limited sensitivity in detecting PNI and does not provide insights into its mechanistic underpinnings. Experimental Design: A multivariate Cox regression was performed to validate associations between PNI and survival in 2,029 patients across 12 cancer types. Differential expression and gene set enrichment analysis were used to learn PNI-associated programs. Machine learning models were applied to build a PNI gene expression classifier. A blinded re-review of hematoxylin and eosin (H&E) slides by a board-certified pathologist helped determine whether the classifier could improve occult histopathologic detection of PNI. Results: PNI associated with both poor overall survival [HR, 1.73; 95% confidence interval (CI), 1.27–2.36; P < 0.001] and disease-free survival (HR, 1.79; 95% CI, 1.38–2.32; P < 0.001). Neural-like, prosurvival, and invasive programs were enriched in PNI-positive tumors (Padj < 0.001). Although PNI-associated features likely reflect in part the increased presence of nerves, many differentially expressed genes mapped specifically to malignant cells from single-cell atlases. A PNI gene expression classifier was derived using random forest and evaluated as a tool for occult histopathologic detection. On a blinded H&E re-review of sections initially described as PNI negative, more specimens were reannotated as PNI positive in the high classifier score cohort compared with the low-scoring cohort (P = 0.03, Fisher exact test). Conclusions: This study provides salient biological insights regarding PNI and demonstrates a role for gene expression classifiers to augment detection of histopathologic features.

Prime editors have been delivered using DNA or RNA vectors. Here we demonstrate prime editing with purified ribonucleoprotein complexes. We introduced somatic mutations in zebrafish embryos with frequencies as high as 30% and demonstrate germline transmission. We also observed unintended insertions, deletions and prime editing guide RNA (pegRNA) scaffold incorporations. In HEK293T and primary human T cells, prime editing with purified ribonucleoprotein complexes introduced desired edits with frequencies of up to 21 and 7.5%, respectively. Prime editors are delivered as ribonucleoproteins to zebrafish embryos and human primary cells.

Human noroviruses are a major cause of diarrheal illness, but pathogenesis is poorly understood. Here, we investigate the cellular tropism of norovirus in specimens from four immunocompromised patients. Abundant norovirus antigen and RNA are detected throughout the small intestinal tract in jejunal and ileal tissue from one pediatric intestinal transplant recipient with severe gastroenteritis. Negative-sense viral RNA, a marker of active viral replication, is found predominantly in intestinal epithelial cells, with chromogranin A-positive enteroendocrine cells (EECs) identified as a permissive cell type in this patient. These findings are consistent with the detection of norovirus-positive EECs in the other three immunocompromised patients. Investigation of the signaling pathways induced in EECs that mediate communication between the gut and brain may clarify mechanisms of pathogenesis and lead to the development of in vitro model systems in which to evaluate norovirus vaccines and treatment., Human norovirus pathogenesis is incompletely understood due to a lack of appropriate animal disease models. Here, Green et al. show norovirus replication in chromogranin A-positive enteroendocrine cells and other epithelial cells in tissue from a pediatric intestinal transplant recipient with severe gastroenteritis.

Targeted therapies for molecularly-defined subtypes have led to immense clinical benefit for many cancer types but have generally not been successful for pancreatic cancer. Given that the mainstay of treatment remains multi-agent chemotherapy with FOLFIRINOX or gemcitabine/nab-paclitaxel, there remains an urgent need to identify novel actionable vulnerabilities for subsets of PDAC patients. Toward this end, we conducted an integrative, genome-scale examination of genetic dependencies and cell surface targets for PDAC by leveraging CRISPR and RNAi screening data from The Cancer Dependency Map Project, genomic data of bulk patient tumors from The Cancer Genome Atlas, and custom single-nucleus RNA-seq of a 43-patient cohort comprised of untreated and treated specimens. Our results re-affirm the prominence of Ras/MAPK signaling and a synthetically-lethal interaction between VPS4A/B, but also reveal recurrent susceptibilities to genes within the fatty acid metabolism, vesicular transport and exocytosis, and nucleobase synthesis pathways that otherwise have minor to moderate depleting effects on the majority of cell lines. Aberrations in frequent tumor suppressor genes and chromosomal arm-level variations appear to modify the strength of dependencies, including that of KRAS, CCND1, and GPX4, and may serve as predictive biomarkers of response. In addition, we leveraged mRNA profiling of bulk primary tumors as well as metastatic organoid models to conduct a genome-wide search for cell surface targets that are highly-expressed in tumors while lowly or not expressed in other toxicity-prone, non-malignant tissues. These putative drug targets do not need to be cancer dependencies and can be compatible with antibody-based therapeutic strategies that leverage alternative modes of cellular toxicity. Our approach identifies MSLN, NECTIN4, TROP2, and other antigens which have previously been shown to be largely tumor-specific but also reveals the expression of multiple putative targets within the CEACAM, claudin, and tetraspanin families. Finally, molecular subtyping efforts over the past decade have yielded classical and basal-like as consensus subtypes with variations therein, but genetic dependencies and cell surface expression patterns unique to either are insufficiently understood. We identified CLDN18, CEACAM5, and CEACAM6 as cell surface antigens for the classical subtype and MSLN, AQP5, and SLC6A14 for basal-like. Dependency on TLK2 and CCND1 is associated with the basal-like and classical subtype, respectively. Taken together, our integrative genomic approach may provide a precision medicine blueprint for stratifying and targeting pancreatic cancer. Citation Format: Jimmy A. Guo, Daniel Zhao, Scott P. Ginebaugh, Steven Wang, Ananya D. Jambhale, Patrick Z. Yu, Westley W. Wu, Peter Chen, Maryann Zhao, Kristen E. Lowder, Kevin S. Kapner, Hannah I. Hoffman, Stephanie W. Cheng, Daniel Y. Kim, Rebecca Boiarsky, Francois Aguet, Brenton Paolella, John M. Krill-Burger, James M. McFarland, Tobiloba Oni, Tyler Jacks, Aviv Regev, Gad Getz, William L. Hwang, Harshabad Singh, Andrew J. Aguirre. Integrative genomic characterization of therapeutic targets for pancreatic cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference on Pancreatic Cancer; 2021 Sep 29-30. Philadelphia (PA): AACR; Cancer Res 2021;81(22 Suppl):Abstract nr PR-006.

The bacterial pathogen Pseudomonas aeruginosa activates expression of many virulence genes in a cell density-dependent manner by using an intricate quorum-sensing (QS) network. QS in P. aeruginosa involves two acyl-homoserine-lactone circuits, LasI-LasR and RhlI-RhlR. LasI-LasR is required to activate many genes including those coding for RhlI-RhlR. P. aeruginosa causes chronic infections in the lungs of people with cystic fibrosis (CF). In these infections, LasR mutants are common, but rhlR-rhlI expression has escaped LasR regulation in many CF isolates. To better understand the evolutionary trajectory of P. aeruginosa QS in chronic infections, we grew LasR mutants of the well-studied P. aeruginosa strain, PAO1, in conditions that recapitulate an environment where QS signal synthesis by other bacteria might still occur. When QS is required for growth, addition of the RhlI product butyryl-homoserine lactone (C4-HSL), or bacteria that produce C4-HSL, to LasR mutants results in the rapid emergence of a population with a LasR-independent RhlI-RhlR QS system. These evolved populations exhibit subsequent growth without added C4-HSL. The variants that emerge have mutations in mexT , which codes for a transcription factor that controls expression of multiple genes. LasR-MexT mutants have a competitive advantage over both the parent LasR mutant and a LasR-MexT-RhlR mutant. Our findings suggest a plausible evolutionary trajectory for QS in P. aeruginosa CF infections where LasR mutants arise during infection, but because these mutants are surrounded by C4-HSL–producing P. aeruginosa, variants rewired to have a LasR-independent RhlIR system quickly emerge.

Image-guided surgery (IGS) can assist surgeons by modeling and visualizing objects of interest (tumors, nerves, etc.) that may be obstructed or difficult to recognize during surgery. Models based on pre-operative images are often not applicable during surgery because of motion and deformation. Therefore, real-time updates to IGS models are required. We propose an automated intra-operative tumor tracking system in which the initial tumor location is predicted using near infrared (NIR) fluorescence with indocyanine green (ICG), and the tumor is tracked using the Lucas-Kanade (LK) algorithm, a multi-resolution coarse-to-fine optical flow method. We simulate various conditions of intra-operative tumor movement, including movement speed and variations in image brightness. The LK method can accurately track tumors when speed of tumor movement and image brightness changes are low. However, when the speed of tumor movement increases or when image brightness changes by more than 30%, the LK method fails to track the tumor location. We compare the LK method to several other optical flow algorithms and find that LK has relatively high accuracy and tolerance in both speed and brightness changes, although each algorithm has strengths and weaknesses. In addition to the proposed intra-operative system, the simulations and metrics that we use in this study may serve as benchmarks to assess the performance of intra-operative tumor tracking algorithms.

3621 Background: Tumor invasion of nerves, blood vessels, and lymphatics are a primary means of local recurrence and escape from the local microenvironment, resulting in metastases and poor clinical outcomes. However, the genetic drivers that are most pertinent to these malignant processes are not well understood, and few therapeutics successfully target perineural invasion (PNI) and lympho-vascular invasion (LVI). Identifying genetic drivers and biomarkers can be valuable for therapeutic targeting and prognostication. Methods: We analyzed surgical pathology reports and bulk RNA-seq data of 1,624 patients across 12 cancer types from The Cancer Genome Atlas (TCGA). Differential gene expression analysis between patients with and without PNI/LVI was performed using DEseq2 in Python while adjusting for age, sex, race, and cancer type. Genes with an adjusted p-value < 0.001 were then used to derive parsimonious signatures using random forest classifier and recursive feature selection algorithms. Results: To assess whether these invasive histological phenotypes have clinical ramifications, we examined outcomes data and found that patients with PNI or LVI have reduced overall (OS) and disease-free survival (DFS) ( p < 0.05) relative to those without. In addition, patients with both PNI and LVI have the lowest DFS from our pan-cancer analysis, suggesting that each may have non-redundant contributions to poor outcomes. From the differential gene expression analysis, we identified a set of 621 and 606 genes that were highly associated with PNI and LVI, respectively (padj < 0.001). Many of these genes such as TEKT5 (padj = 3.18 x 10−64), which is canonically associated with ciliary and flagellar microtubules, and SCRIB (padj = 1.60 x 10−21), which helps establish apico-basal cell polarity, have not been described previously in relevance to PNI and LVI, and warrant further scientific and clinical investigation. These genes were ultimately condensed into a signature that optimizes for both model simplicity and goodness of fit with up to 90% accuracy as determined by trials on both a logistic regression and neural network model. Conclusions: We concluded from a pan-cancer analysis that PNI and LVI are associated with poor outcomes, and we were able to robustly identify sets of genes that characterize each invasive mechanism for further functional investigation.

Since the late 1990s, a growing number of US authors has been drawn to the Korean War, hoping to undo its status as “The Forgotten War.” The fact that it has served as the focus of novels by eminent Korean American authors like Chang-rae Lee and Susan Choi is not entirely surprising, given that they are the children of immigrants whose early lives had been shaped by the conflict. Given the extraordinarily high number of civilian deaths that resulted from the war and the many families that were fractured, the war is clearly a defining event that helped create a Korean diaspora. It has also become the focus, however, of novels by non-Korean American authors, including Toni Morrison, Rolando Hinojosa, and Ha Jin, which testifies to the fact that it was an event in which a number of domestic histories of race and transnational histories of empire converged. The body of literary works that have emerged around this event can be thought of as constituting an archive of what Michael Rothberg has termed “multidirectional memory,” one that suggests the intimacies of multiple histories involving not only Koreans and Korean Americans, but also other US racialized groups including African, Mexican, Chinese, and Japanese Americans as well as their connections to the complicated formations of empire that have shaped the relationships between Asian nations. Contending with the complexity and range of literary works that have centered on this event enables a reconsideration and expansion of what the proper subjects and objects of Asian American literary criticism are. If the field has outgrown its origins, in which the projection of a cultural nationalist vision of Asian American identity was a paramount goal, the vibrancy of these works stems from their soundings of a subject that is not univocal but multivocal. The political desires they seek to animate in their readers are not reducible to an agenda of combating domestic racism or consolidating a nativist notion of Asian American cultural identity, though they may contribute to such endeavors. More expansively, however, they articulate a multivalent range of progressive political aspirations and proliferate an array of identificatory possibilities.

This essay reads the work of Rolando Hinojosa for the ways in which it invites a consideration of the two wars that the United States fought in the middle of the nineteenth and twentieth centuries—the US-Mexico War and the Korean War, respectively—as part of a continuous history of US empire. It examines the array of cross-racial identifications operant in his Korean War trilogy—Korean Love Songs, Rites and Witnesses, and The Useless Servants—which attach variously to Japanese and Korean civilians as well as to North Korean and Chinese soldiers. In so doing, this article shows how Hinojosa's war writings are part of an Orientalism that is deployed in the service of anticolonial and antiracist critique but that also recapitulates aspects of the colonial imaginary. These works also engage in an auto-critique of how certain segments of the Chicana/o population came to be beneficiaries of a liberal Cold War racial dispensation that enabled limited forms of upward mobility for some communities of color.

This article examines the coverage of the Korean War in the popular American magazine Life, focusing on its depiction of Koreans. In these depictions, Koreans figure as an epistemological enigma: as ambiguously friendly/hostile, loyal/disloyal, and as worthy/unworthy of life. But in journalism’s attempted management of that inscrutability we glimpse a crucial element of the shift in epistemes that defined the emergence of what cultural theorist Rey Chow has described as the Age of the World Target: an epoch in which the “countries of East Asia, Southeast Asia, Eastern Europe, Latin America, and the Middle East took on the significance of ‘target fields’ — as fields of information retrieval and dissemination that were necessary to the United States’ continual political and ideological hegemony.” To understand this emergent episteme, however, it is also necessary to engage with the work of cultural critic Christina Klein, who has described the post-1945 period as one in which middlebrow cultural works like Life reveal a U.S. Cold War ideology oriented as much by a desire to integrate subjects of the decolonizing world into the American sphere of influence as by an impulse to contain the Soviet menace.

To the extent that Americanist scholars have begun to fill in what Amy Kaplan famously described as “The Absence of Empire in the Study of American Culture,” they have done so largely by remembering forgotten wars. While the Mexican-American War and the Spanish-American War have not eclipsed the US Civil War in significance (or, for that matter, either of the World Wars or the Vietnam War), studies that have stressed the historical significance of these events have been vital to the project of illuminating “the multiple historical trajectories of the anarchy of empire” that connect the middle of the nineteenth century to the beginning of this one (Anarchy 170). What to do, then, with the American military conflict that is most closely associated with, and certainly merits, the epithet “the forgotten war”? For there are no images that come readily to mind in reference to the Korean War (1950–53), a somewhat surprising state of affairs given the superabundance of images and narratives associated with the conflict that preceded it by five years and the one that followed it by six: World War II (1940–45) and the Vietnam War (1959–75), respectively. There is, moreover, relatively little scholarship in American literary and cultural studies that focuses primarily on this event or on its representation.