Citations

Nononcogenic somatic mutations are thought to be uncommon and inconsequential. To test this, we analyzed 43,693 National Heart, Lung and Blood Institute Trans-Omics for Precision Medicine blood whole genomes from 37 cohorts and identified 7131 non-missense somatic mutations that are recurrently mutated in at least 50 individuals. These recurrent non-missense somatic mutations (RNMSMs) are not clearly explained by other clonal phenomena such as clonal hematopoiesis. RNMSM prevalence increased with age, with an average 50-year-old having 27 RNMSMs. Inherited germline variation associated with RNMSM acquisition. These variants were found in genes involved in adaptive immune function, proinflammatory cytokine production, and lymphoid lineage commitment. In addition, the presence of eight specific RNMSMs associated with blood cell traits at effect sizes comparable to Mendelian genetic mutations. Overall, we found that somatic mutations in blood are an unexpectedly common phenomenon with ancestry-specific determinants and human health consequences.

Importance For many types of epithelial malignant neoplasms that are treated with definitive radiotherapy (RT), treatment prolongation and interruptions have an adverse effect on outcomes. Objective To analyze the association between RT duration and outcomes in patients with esophageal cancer who were treated with definitive chemoradiotherapy (CRT). Design, Setting, and Participants This study was an unplanned, post hoc secondary analysis of 3 prospective, multi-institutional phase 3 randomized clinical trials (Radiation Therapy Oncology Group [RTOG] 8501, RTOG 9405, and RTOG 0436) of the National Cancer Institute–sponsored NRG Oncology (formerly the National Surgical Adjuvant Breast and Bowel Project, RTOG, and Gynecologic Oncology Group). Enrolled patients with nonmetastatic esophageal cancer underwent definitive CRT in the trials between 1986 and 2013, with follow-up occurring through 2014. Data analyses were conducted between March 2022 to February 2023. Exposures Treatment groups in the trials used standard-dose RT (50 Gy) and concurrent chemotherapy. Main Outcomes and Measures The outcomes were local-regional failure (LRF), distant failure, disease-free survival (DFS), and overall survival (OS). Multivariable models were used to examine the associations between these outcomes and both RT duration and interruptions. Radiotherapy duration was analyzed as a dichotomized variable using an X-Tile software to choose a cut point and its median value as a cut point, as well as a continuous variable. Results The analysis included 509 patients (median [IQR] age, 64 [57-70] years; 418 males [82%]; and 376 White individuals [74%]). The median (IQR) follow-up was 4.01 (2.93-4.92) years for surviving patients. The median cut point of RT duration was 39 days or less in 271 patients (53%) vs more than 39 days in 238 patients (47%), and the X-Tile software cut point was 45 days or less in 446 patients (88%) vs more than 45 days in 63 patients (12%). Radiotherapy interruptions occurred in 207 patients (41%). Female (vs male) sex and other (vs White) race and ethnicity were associated with longer RT duration and RT interruptions. In the multivariable models, RT duration longer than 45 days was associated with inferior DFS (hazard ratio [HR], 1.34; 95% CI, 1.01-1.77; P = .04). The HR for OS was 1.33, but the results were not statistically significant (95% CI, 0.99-1.77; P = .05). Radiotherapy duration longer than 39 days (vs ≤39 days) was associated with a higher risk of LRF (HR, 1.32; 95% CI, 1.06-1.65; P = .01). As a continuous variable, RT duration (per 1 week increase) was associated with DFS failure (HR, 1.14; 95% CI, 1.01-1.28; P = .03). The HR for LRF 1.13, but the result was not statistically significant (95% CI, 0.99-1.28; P = .07). Conclusions and Relevance Results of this study indicated that in patients with esophageal cancer receiving definitive CRT, prolonged RT duration was associated with inferior outcomes; female patients and those with other (vs White) race and ethnicity were more likely to have longer RT duration and experience RT interruptions. Radiotherapy interruptions should be minimized to optimize outcomes.

Abstract Purpose/Background A recent article in this journal presented a US perspective regarding the modernization of clozapine prescription and proposed an escape from the long shadow cast by agranulocytosis. Methods Here, an international group of collaborators discusses a point of view complementary to the US view by focusing on worldwide outcomes of clozapine usage that may be uneven in terms of frequency of clozapine adverse drug reactions. Findings/Results Studies from the Scandinavian national registries (Finland and Denmark) did not find increased mortality in clozapine patients or any clear evidence of the alleged toxicity of clozapine. Data on clozapine-associated fatal outcomes were obtained from 2 recently published pharmacovigilance studies and from the UK pharmacovigilance database. A pharmacovigilance study focused on physician reports to assess worldwide lethality of drugs from 2010 to 2019 found 968 clozapine-associated fatal outcomes in the United Kingdom. Moreover, the United Kingdom accounted for 55% (968 of 1761) of worldwide and 90% (968 of 1073) of European fatal clozapine-associated outcomes. In a pharmacovigilance study from the UK database (from 2008 to 2017), clozapine was associated with 383 fatal outcomes/year including all reports from physicians and nonphysicians. From 2018 to 2021, UK clozapine-associated fatal outcomes increased to 440/year. Implications/Conclusions The interpretation of fatal outcomes in each country using pharmacovigilance databases is limited and only allows gross comparisons; even with those limitations, the UK data seem concerning. Pneumonia and myocarditis may be more important than agranulocytosis in explaining the uneven distribution of fatal outcomes in clozapine patients across countries.

Abstract Background: Spatial molecular analysis can provide functional characteristics of cellular components and their interactions present in the tumor immune microenvironment (TME), thus improving our understanding of the cancer ecosystem at a systemic level. We investigated the spatial and functional characteristics of the tumor, stroma, and immune cells, and their roles in the TME in facilitating cancer development, progression, and metastasis in pancreatic cancer. Methods: We performed spatial profiles of multiple regional TMEs of 13 pancreatic cancers (7 pancreatic adenocarcinoma, 3 pancreatic neuroendocrine, and 3 acinar cell carcinomas) using NanoString GeoMX at the whole transcriptome level (18,676 genes). We collected a total of 23 tissue samples containing matched primary tumors, adjacent normal pancreatic tissue, or normal/metastatic lymph node. Tumor, stroma, and immune cells are stained by PanCK, αSMA, and CD45 markers, respectively. We selected 234 regions of interest (ROIs) in the tumor core, border, adjacent normal pancreas, and lymph node to investigate spatial patterns of different cells and their cellular interactions in neighborhoods from paired primary and metastatic tumors. Results: TMEs in different ROIs are spatially correlated within a tumor but showed distinct phenotypes across tumors and tumor types. Each cell type in the ROIs has a unique role to drive cancer evolution in TMEs. Diverse types of cancer-associated fibroblasts (CAFs) are present in primary and metastatic TME, while CAFs in tumor border and metastatic lymph nodes showed mainly enriched with antigen-presenting CAF (apCAF) subtypes with higher extracellular matrix (ECM) and collagen fibrils components. Similarly, we found diverse functional phenotypes of the immune cell in TMEs. The immune response signaling pathway is activated in the stroma-infiltrated immune cells, but, in fact, not in the tumor-infiltrated immune cells. Instead, higher dysfunctional T cell and growth factors are present in the stroma-infiltrated immune cells from primary and metastatic tumors, but not in stromal immune normal pancreatic and lymph node tissues. The tumor-infiltrated immune cells showed suppressive immune activities by increasing TGFβ receptor signaling. We also discovered CCL5-driven metastatic patterns in TMEs from primary tumors and metastatic lymph nodes. Lastly, we concluded that these functional phenotypes of cells in TMEs are preserved in a certain pancreatic cancer type, suggesting the origin and evolution of different pancreatic tumors could be driven by diverse cellular and functional phenotypes of cells in TMEs. Conclusion: Our comprehensive analysis results demonstrate that the spatial analysis could provide insights into the spatial patterns that drive cancer evolution in pancreatic TMEs, thus helping understand the cellular microenvironment governing pancreatic cancer metastasis. Citation Format: Changjin Hong, Jean R. Clemenceau, Rondell P. Graham, Tae Hyun Hwang. Spatial transcriptomic landscape of primary and lymph node metastatic pancreatic cancer [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 2362.

Abstract Introduction As total neoadjuvant therapy for locally advanced rectal cancer (LARC) emerged, the possibility of skipping radiotherapy for poorly responsive patients arose. Machine-learning algorithms have focused on the radiopathologic features of tumor segmentation in order to predict responsiveness to radiotherapy. However, in addition to the tumor itself, there are several factors related to responsiveness, such as vasculature affecting hypoxia or MRI-detected extramural vascular invasion status. We aimed to predict poor responders using pretreatment rectal MRI images without segmentation and to identify which factors mainly contribute to the prediction algorithm. Methods Between Jan 1, 2000, and Dec 30, 2020, 689 consecutive patients were retrospectively included in two hospitals. Poor responders were defined by tumor regression grades (TRG) 2 and 3 that were determined through surgical resection. The ResNet-50 model was trained to predict poor responders from pretreatment rectal MRIs (T2-weighted axial, sagittal, and coronal images). We adopted a tenfold cross-validation for training and testing the model and used Gradient-weighted Class Activation Mapping (Grad-CAM) to highlight the important regions in the MRI scans that help predict poor responders. Results The number in each group of TRG was 108 (15.7%), 250 (36.3%), 265 (38.5%), and 66 (9.6%) for TRG0, TRG1, TRG2, and TRG3, respectively. There were 618 patients in the training cohort and 71 patients in the validation cohort. In the training and validation cohort, the accuracy for the prediction of poor responders was 85.6% (area under the curve (AUC) 0.856 [95% CI 0.761-0.950]) and 70.2% (AUC 0.703 [0.682-0.724]), although without segmentation. Our prediction model achieved a sensitivity of 0.724 (95% CI 0.700-0.748), a specificity of 0.684 (0.658-0.710), a positive predictive value of 0.697 (0.656-0.737), and a negative predictive value of 0.708 (0.666-0.751) in the validation cohort. Grad-CAM showed that the most important part of the accurately predicted images to contribute to the prediction was not the tumor (7/355, 1.9%) but the pelvic vasculature (353/355, 99.4%), including iliac vessels, femoral vessels, and presacral plexus, and followed by the mesorectum (38/355, 10.7%). Conclusion The pelvic vasculature contributes more to predicting poor responders to radiotherapy than the tumor itself. Therefore, when creating a prediction model for responsiveness to radiotherapy in LARC, this should be considered. Citation Format: Rumi Shin, Byunho Jo, Inyeop Jang, Cheong-Il Shin, Jin Sun Choi, Seung-Yong Jeong, Seung Chul Heo, Ji Won Park, Min Jung Kim, Tae Hyun Hwang. Why only focus on the tumor?: The crucial role of the extra-tumor environment to predict poor responders for locally advanced rectal cancer. [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 5374.

Abstract Background: The Tumor Immune microenvironment (TME) plays an important role in tumor development, progression, and treatment response. Recent studies show that spatial heterogeneity of Tumor-Infiltrating Lymphocytes (TILs), consisting of lymphocytic cell populations, is an important histopathologic feature and a powerful prognostic and predictive marker correlating with cancer progression and treatment response. Detecting and quantifying TIL density in Whole Slide Images (WSIs) is, however, labor-intensive, and it is difficult to assess differences in the composition of immune cells. Therefore, it remains a challenge to establish the analysis of TILs in the complex TME. We present an automated spatial image analysis of TILs on gastric cancer to address cancer immunotherapy. Method: 1,031WSIs of hematoxylin and eosin-stained (H&E) formalin-fixed paraffin-embedded (FFPE) sections from four patient cohorts: TCGA-STAD (329), Yonsei-1 (620 patients), Yonsei-2 (45), and St. Mary (37), were analyzed. Two treatment groups in response were classified as CR + PR, while another two treatment groups in non-response were classified as PD + SD. H&E stained WSIs were normalized using the Reinhard normalization method at 20X magnification for reducing the color variability of the stained tissue images. We used U-Net architecture to predict the normalized H&E stained WSIs. Three U-Net models were trained for predicting tumor, TILs, and stroma, using Adam optimizer, 1e-4 learning rate, a binary loss function, L2 regularization, and 50 epochs. The normalized H&E stained WSIs were predicted using the trained U-Net models. Spatial analysis of TILs was conducted on the predicted WSIs. Regional quantification of TILs was performed by two immune phenotype groups: immune-immersed (TILs enriched in tumor cells) and immune-excluded (TILs not enriched in tumor cells but in stromal cells). Kaplan-Meier with a log-rank test was used to evaluate the survival differences between the groups. Results: In TCGA-STAD, the proportion of immune-immersed composition is significantly different from the immune-excluded (p-value 0.05). In Yonsei-1, the immune-excluded composition is significantly different among the three risk groups (p-value 3e-05). In the Yonsei-2 and St. Mary cohorts, including anti-PD1 treated gastric cancer patients, the immune-immersed composition is significantly different between two response groups (p-value 0.007) and represented the diagnostic accuracy (AUROC: 0.78) on CR + PR groups. Conclusion: These findings suggest that the proposed TIL quantification in the complex TME is strongly associated with patient prognosis and anti-PD1 treatment response in gastric cancer. Citation Format: Sanghoon Lee, Sunho Park, Jae-Ho Cheong, Sam C. Wang, Matthew R. Porembka, In-Ho Kim, Sung Hak Lee, Tae Hyun Hwang. Spatial image analysis of tumor-infiltrating lymphocytes on gastric cancer to predict anti-PD1 inhibitor response [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 1360.

Abstract Background: COVID-19 causes significant morbidity and mortality, albeit with considerable heterogeneity among affected individuals. It remains unclear which host factors determine disease severity and survival. Given the propensity of clonal hematopoiesis (CH) to promote inflammation in healthy individuals, we investigated its effect on COVID-19 outcomes. Methods: We performed a multi-omics interrogation of the genome, epigenome, transcriptome, and proteome of peripheral blood mononuclear cells from COVID-19 patients (n=227). We obtained clinical data, laboratory studies, and survival outcomes. We determined CH status and TET2-related DNA methylation. We performed single-cell proteogenomics to understand clonal composition in relation to cell phenotype. We interrogated single-cell gene expression in isolation and in conjunction with DNA accessibility. We integrated these multi-omics data to understand the effect of CH on clonal composition, gene expression, methylation of cis-regulatory elements, and lineage commitment in COVID-19 patients. We performed shRNA knockdowns to validate the effect of one candidate transcription factor in myeloid cell lines. Results: The presence of CH was strongly associated with COVID-19 severity and all-cause mortality, independent of age (HR 3.48, 95% CI 1.45-8.36, p=0.005). Differential methylation of promoters and enhancers was prevalent in TET2-mutant, but not DNMT3A-mutant CH. TET2-mutant CH was associated with enhanced classical/intermediate monocytosis and single-cell proteogenomics confirmed an enrichment of TET2 mutations in these cell types. We identified cell-type specific gene expression changes associated with TET2 mutations in 102,072 single cells (n=34). Single-cell RNA-seq confirmed the skewing of hematopoiesis towards classical and intermediate monocytes and demonstrated the downregulation of EGR1 (a transcription factor important for monocyte differentiation) along with up-regulation of the lncRNA MALAT1 in monocytes. Combined scRNA-/scATAC-seq in 43,160 single cells (n=18) confirmed the skewing of hematopoiesis and up-regulation of MALAT1 in monocytes along with decreased accessibility of EGR1 motifs in known cis-regulatory elements. Using myeloid cell lines for functional validation, shRNA knockdowns of EGR1 confirmed the up-regulation of MALAT1 (in comparison to wildtype controls). Conclusions: CH is an independent prognostic factor in COVID-19 and skews hematopoiesis towards monocytosis. TET2-mutant CH is characterized by differential methylation and accessibility of enhancers binding myeloid transcriptions factors including EGR1. The ensuing loss of EGR1 expression in monocytes causes MALAT1 overexpression, a factor known to promote monocyte differentiation and inflammation. These data provide a mechanistic insight to the adverse prognostic impact of CH in COVID-19. Citation Format: Moritz Binder, Terra L. Lasho, Wazim Mohammed Ismail, Nana A. Ben-Crentsil, Jenna A. Fernandez, Minsuk Kim, Susan M. Geyer, Amelia Mazzone, Christy M. Finke, Abhishek A. Mangaonkar, Jeong-Heon Lee, Kwan Hyun Kim, Vernadette A. Simon, Fariborz Rakhshan Rohakthar, Amik Munankarmy, Susan M. Schwager, Jonathan J. Harrington, Melissa R. Snyder, Nathalie M. Droin, Eric Solary, Keith D. Robertson, Eric D. Wieben, Eric Padron, Nicholas Chia, Alexandre Gaspar-Maia, Mrinal M. Patnaik. Enhancer deregulation inTET2-mutant clonal hematopoiesis is associated with increased COVID-19 severity and mortality [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 806.

Abstract Background: While immune checkpoint inhibitors (ICI) extend survival for patients suffering from a variety of cancers, most gastric cancer (GC) patients do not respond to ICI. There is a critical need to identify novel biomarkers that guide the use of ICI or strategies to improve outcomes for GC patients. We aim to gain a deeper understanding of the GC tumor microenvironment (TME) to refine the use of ICI using spatial transcriptomes from ICI-treated gastric tumors. Method: We collected 12 pre-ICI treatment gastric tumor samples from five responders and seven nonresponders and performed spatial profiling to investigate spatial heterogeneity, functions, and phenotypes of tumor and neighboring stromal and immune cells to identify features associated with ICI response. We used pan-cytokeratin (pan-CK) to mark epithelial cells, CD45 for immune cells, and smooth muscle actin (SMA) for fibroblasts. We generated gene expression profiles of each cell type within regions of interest (ROI) with a NanoString GeoMx Cancer Transcriptome Atlas panel, comprised of 1,800 genes. A total of 58 ROIs were analyzed from responders and 62 ROIs from nonresponders. Results: We measured the spatial heterogeneity of each cell type in ROIs within and across tumors. We found the tumor, immune, and fibroblasts from nonresponders are transcriptionally more heterogeneous, compared to those from responders. This might indicate a higher degree of intratumor transcriptional heterogeneity is linked to ICI resistance. We found that nonresponse was associated with higher expression of VEGFA and VEGFB in tumor cells and higher ACTA2 in fibroblasts, not in other cell types. These findings are intriguing when considering our other finding that increased endothelial cell and fibroblast proportions in the TME are associated with ICI nonresponse. We also found that the TME of nonresponders had fewer M1 and more M2 macrophages, and there were more T cells that overexpressed gene programs consistent with dysfunction and exhaustion. These findings indicate that ICI-resistant TMEs are densely surrounded by immune-suppressive cellular components which might reduce ICI efficacy and result in ICI resistance. Finally, we performed cell-cell interaction and identified ligand-receptor interactions that are stronger in nonresponders, including CXCL12-CXCR4, CD74-MIF, and LGALS9-LRP1 ligand-receptor interactions. The predicted ligand-receptor interactions are present in cell-type-specific manners, indicating the functional role of each cell type in facilitating ICI response. Conclusion: We investigated how tumor and neighboring stromal and immune cells interact within GC TME to mediate ICI response, which demonstrate that spatial analysis could be used to identify novel biomarkers that predict response to ICI, and new therapies to enhance ICI efficacy in GC patients. Citation Format: Sunho Park, Changjing Hong, Jae-Ho Cheong, Sam C. Wang, Matthew R. Porembka, In-Ho Kim, Sung Hak Lee, Tae Hyun Hwang. Spatial architecture and cellular interactions of tumor immune microenvironment to discover biomarkers and predict immune checkpoint inhibitor response in gastric cancer [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 2262.

Abstract Chemotherapy-induced cognitive impairment (CICI, also termed “chemobrain”) is a major neurotoxic side effect exhibited by a wide range of chemotherapeutic agents. These side effects affect approximately 14 million cancer survivors. More importantly, CICI persists well after cessation of therapy, severely interfering with quality of life. Unfortunately, there is no treatment and novel therapies are urgently needed. Utilizing cisplatin, a platinum-based chemotherapy, to model chemobrain mice in vivo, we have established that cisplatin accelerates the brain aging process thus leading to long-term memory impairment in mice similar to what is clinically reported. We further show that cisplatin causes oxidative DNA damage, mitochondrial defects, impaired neurogenesis, synaptic defects, and increased gliosis in the adult hippocampus, a brain region critical for learning and memory. Mechanistically, our RNA-sequencing and qRT-PCR analysis revealed that cisplatin dramatically increases COX-2 (Ptgs2) expression and its major product, prostaglandin E2 (PGE2) in adult mouse brain and human cortical neurons derived from induced pluripotent stem cells (iPSCs). Similar as cisplatin treatment, the levels of COX-2 expression began to increase at 0.1 µM methotrexate treatment, which significantly increased at 1 µM in human cortical neurons, indicating that COX-2 induction is a common pathogenic mechanism mediating cognitive impairment associated with cisplatin and methotrexate in spite of the fact that these compounds have different mechanisms of action for cancer eradication. Most importantly, NS-398, a selective COX-2 inhibitor, effectively prevents cognitive deficits in mice and reduction in cell viability of human neurons associated with these chemotherapies, without promoting tumor growth or interfering with cisplatin’s anti-tumor activity. Taken together, our findings strongly suggest that COX-2 induction is a main cause of CICI, making COX-2 inhibition a therapeutic target for CICI. Given that COX-2 inhibitors are currently being tested in cancer prevention as well as age-related memory loss in clinical trials, inhibiting COX-2 may have far-reaching therapeutic effects on CICI and cancer treatment, which can be applied quickly, safely, and effectively to clinical trials, in the effort to improve cancer survivor quality of life. Citation Format: Mohammad Abdur Rashid, Jason J. Tang, Ki-Hyun Yoo, Ana Corujo-Ramirez, Sang Hoon Kim, Alfredo Oliveros, Peter Cole, John R. Hawse, Mi-Hyeon Jang. Blockade of the cyclooxygenase-2 prevents chemotherapy-induced cognitive impairments [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 2694.