Clinical Benefit from Docetaxel +/- Ramucirumab Is Not Associated with Mutation Status in Metastatic Non-Small-Cell Lung Cancer Patients Who Progressed on Platinum Doublets and Immunotherapy

Docetaxel +/- ramucirumab remains the standard-of-care therapy for patients with metastatic non-small-cell lung cancer (NSCLC) after progression on platinum doublets and immune checkpoint inhibitors (ICIs). The aim of our study was to investigate whether the cancer gene mutation status was associated with clinical benefits from docetaxel +/- ramucirumab. We also investigated whether platinum/taxane-based regimens offered a better clinical benefit in this patient population. A total of 454 patients were analyzed (docetaxel +/- ramucirumab n=381; platinum/taxane-based regimens n=73). Progression-free survival (PFS) and overall survival (OS) were compared among different subpopulations with different cancer gene mutations and between patients who received docetaxel +/- ramucirumab versus platinum/taxane-based regimens. Among patients who received docetaxel +/- ramucirumab, the top mutated cancer genes included TP53 (n=167), KRAS (n=127), EGFR (n=65), STK11 (n=32), ERBB2 (HER2) (n=26), etc. None of these cancer gene mutations or PD-L1 expression was associated with PFS or OS. Platinum/taxane-based regimens were associated with a significantly longer mQS (13.00 m, 95% Cl: 11.20-14.80 m versus 8.40 m, 95% Cl: 7.12-9.68 m, LogRank P=0.019) than docetaxel +/- ramcirumab. Key prognostic factors including age, histology, and performance status were not different between these two groups. In conclusion, in patients with metastatic NSCLC who have progressed on platinum doublets and ICIs, the clinical benefit from docetaxel +/- ramucirumab is not associated with the cancer gene mutation status. Platinum/taxane-based regimens may offer a superior clinical benefit over docetaxel +/- ramucirumab in this patient population.

A novel Bayesian model for assessing intratumor heterogeneity of tumor infiltrating leukocytes with multi-region gene expression sequencing

Intratumor heterogeneity (ITH) of tumor-infiltrated leukocytes (TILs) is an important phenomenon of cancer biology with potentially profound clinical impacts. Multi-region gene expression sequencing data provide a promising opportunity that allows for explorations of TILs and their intratumor heterogeneity for each subject. Although several existing methods are available to infer the proportions of TILs, considerable methodological gaps exist for evaluating intratumor heterogeneity of TILs with multi-region gene expression data. Here, we develop ICeITH, immune cell estimation reveals intratumor heterogeneity, a Bayesian hierarchical model that borrows cell type profiles as prior knowledge to decompose mixed bulk data while accounting for the within-subject correlations among tumor samples. ICeITH quantifies intratumor heterogeneity by the variability of targeted cellular compositions. Through extensive simulation studies, we demonstrate that ICeITH is more accurate in measuring relative cellular abundance and evaluating intratumor heterogeneity compared with existing methods. We also assess the ability of ICeITH to stratify patients by their intratumor heterogeneity score and associate the estimations with the survival outcomes. Finally, we apply ICeITH to two multi-region gene expression datasets from lung cancer studies to classify patients into different risk groups according to the ITH estimations of targeted TILs that shape either pro- or anti-tumor processes. In conclusion, ICeITH is a useful tool to evaluate intratumor heterogeneity of TILs from multi-region gene expression data.

Conservation of Glutathione Transferase mRNA and Protein Sequences Similar to Human and Horse Alpha Class GST A3-3 across Dog, Goat, and Opossum Species

The glutathione transferase A3-3 (GST A3-3) homodimeric enzyme is the most efficient enzyme that catalyzes isomerization of the precursors of testosterone, estradiol, and progesterone in the gonads of humans and horses. However, the presence of GST A3-3 orthologs with equally high ketosteroid isomerase activity has not been verified in other mammalian species, even though pig and cattle homologs have been cloned and studied. Identifying GSTA3 genes is a challenge because of multiple GSTA gene duplications (e.g., 12 in the human genome); consequently, the GSTA3 gene is not annotated in most genomes. To improve our understanding of GSTA3 gene products and their functions across diverse mammalian species, we cloned homologs of the horse and human GSTA3 mRNAs from the testes of a dog, goat, and gray short-tailed opossum, the genomes of which all currently lack GSTA3 gene annotations. The resultant novel GSTA3 mRNA and inferred protein sequences had a high level of conservation with human GSTA3 mRNA and protein sequences (≥70% and ≥64% identities, respectively). Sequence conservation was also apparent for the 12 residues of the "H-site" in the 222 amino acid GSTA3 protein that is known to interact with the steroid substrates. Modeling predicted that the dog GSTA3-3 may be a more active ketosteroid isomerase than the corresponding goat or opossum enzymes. However, expression of the GSTA3 gene was higher in liver than in other dog tissue. Our results improve understanding of the active sites of mammalian GST A3-3 enzymes, inhibitors of which might be useful for reducing steroidogenesis for medical purposes, such as fertility control or treatment of steroid-dependent diseases.

Abstract 6524: Single-cell transcriptomic analysis reveals immune landscape in the malignant transformation of normal lung to lung adenocarcinoma in genetic murine models

Background: Our understanding of the initiation and progression of lung precancers is rudimentary, which has impeded advance for lung cancer prevention and interception. Although human specimens are the gold standard to study human cancer biology, lung precancer specimens designated for research are often very limited. Furthermore, human specimens are not amendable for preclinical intervention studies. We sought to establish and characterize human-relevant murine lung precancer models to study evolution of lung precancers and to provide insights for lung cancer interception.

Methods: We established two mouse models, KrasG12D (a genetically engineered mouse model with KrasG12D activating mutation) and CITMs (a carcinogen urethane-induced model) in the same 129S4 background. We performed single-cell transcriptome sequencing of lung tissues collected at 5 time points after induction for each model to characterize the dynamics of immune response along with the initiation and progression of lung adenocarcinoma.

Results: A total of 82,198 immune cells were analyzed and 23 immune cell subpopulations were identified. The results demonstrated dynamic changes of immune cell compositions and cell states along with the evolution from normal lung to lung precancers, and to lung adenocarcinomas in both models. CD4+ effector T cells, CD4+ regulatory T cells, mucosal associated invariant T cells (MAIT) and macrophages progressively increased during tumor progression, in contrast to progressively decreasing naive CD4+ T cells, naive CD8+ T cells and naive B cells. In contrast to CITMs, KrasG12D model harbors a clear decrease in conventional dendritic cells (cDCs) and activated B cells, but significantly more neutrophils (Wilcoxon test, P < 0.01).

Conclusion: These data provide a temporal atlas of lung cancer evolution during early lung carcinogenesis and a resource for interception preclinical study. Our results revealed progressive immunosuppression along with progression of lung precancers in both genetic and carcinogen-induced models, but the immune features underlying immunosuppression may be different.

Citation Format: Hong Chen, Bo Zhu, Junya Fujimoto, Yanhua Tian, Jian-Rong Li, Pingjun Chen, Alexandre Reuben, Monique B. Nilsson, Xiuning Le, Alissa Poteete, Shawna M. Hubert, Don L. Gibbons, Ignacio I. Wistuba, Jia Wu, Chao Cheng, John V. Heymach, Jianjun Zhang. Single-cell transcriptomic analysis reveals immune landscape in the malignant transformation of normal lung to lung adenocarcinoma in genetic murine models [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 6524.

Cold and heterogeneous T cell repertoire is associated with copy number aberrations and loss of immune genes in small-cell lung cancer

Small-cell lung cancer (SCLC) is speculated to harbor complex genomic intratumor heterogeneity (ITH) associated with high recurrence rate and suboptimal response to immunotherapy. Here, using multi-region whole exome/T cell receptor (TCR) sequencing as well as immunohistochemistry, we reveal a rather homogeneous mutational landscape but extremely cold and heterogeneous TCR repertoire in limited-stage SCLC tumors (LS-SCLCs). Compared to localized non-small cell lung cancers, LS-SCLCs have similar predicted neoantigen burden and genomic ITH, but significantly colder and more heterogeneous TCR repertoire associated with higher chromosomal copy number aberration (CNA) burden. Furthermore, copy number loss of IFN-γ pathway genes is frequently observed and positively correlates with CNA burden. Higher mutational burden, higher T cell infiltration and positive PD-L1 expression are associated with longer overall survival (OS), while higher CNA burden is associated with shorter OS in patients with LS-SCLC.

Immune evolution from preneoplasia to invasive lung adenocarcinomas and underlying molecular features

The mechanism by which anti-cancer immunity shapes early carcinogenesis of lung adenocarcinoma (ADC) is unknown. In this study, we characterize the immune contexture of invasive lung ADC and its precursors by transcriptomic immune profiling, T cell receptor (TCR) sequencing and multiplex immunofluorescence (mIF). Our results demonstrate that anti-tumor immunity evolved as a continuum from lung preneoplasia, to preinvasive ADC, minimally-invasive ADC and frankly invasive lung ADC with a gradually less effective and more intensively regulated immune response including down-regulation of immune-activation pathways, up-regulation of immunosuppressive pathways, lower infiltration of cytotoxic T cells (CTLs) and anti-tumor helper T cells (Th), higher infiltration of regulatory T cells (Tregs), decreased T cell clonality, and lower frequencies of top T cell clones in later-stages. Driver mutations, chromosomal copy number aberrations (CNAs) and aberrant DNA methylation may collectively impinge host immune responses and facilitate immune evasion, promoting the outgrowth of fit subclones in preneoplasia into dominant clones in invasive ADC.

Multiomics profiling of primary lung cancers and distant metastases reveals immunosuppression as a common characteristic of tumor cells with metastatic plasticity

BACKGROUND

Metastasis is the primary cause of cancer mortality accounting for 90% of cancer deaths. Our understanding of the molecular mechanisms driving metastasis is rudimentary.

RESULTS

We perform whole exome sequencing (WES), RNA sequencing, methylation microarray, and immunohistochemistry (IHC) on 8 pairs of non-small cell lung cancer (NSCLC) primary tumors and matched distant metastases. Furthermore, we analyze published WES data from 35 primary NSCLC and metastasis pairs, and transcriptomic data from 4 autopsy cases with metastatic NSCLC and one metastatic lung cancer mouse model. The majority of somatic mutations are shared between primary tumors and paired distant metastases although mutational signatures suggest different mutagenesis processes in play before and after metastatic spread. Subclonal analysis reveals evidence of monoclonal seeding in 41 of 42 patients. Pathway analysis of transcriptomic data reveals that downregulated pathways in metastases are mainly immune-related. Further deconvolution analysis reveals significantly lower infiltration of various immune cell types in metastases with the exception of CD4+ T cells and M2 macrophages. These results are in line with lower densities of immune cells and higher CD4/CD8 ratios in metastases shown by IHC. Analysis of transcriptomic data from autopsy cases and animal models confirms that immunosuppression is also present in extracranial metastases. Significantly higher somatic copy number aberration and allelic imbalance burdens are identified in metastases.

CONCLUSIONS

Metastasis is a molecularly late event, and immunosuppression driven by different molecular events, including somatic copy number aberration, may be a common characteristic of tumors with metastatic plasticity.

Prognostic Value of Pro-Inflammatory Neutrophils and C-Reactive Protein in Cancer Patient With Coronavirus Disease 2019: A Multi-Center, Retrospective Study

Background: At present, the epidemic of the novel coronavirus disease 2019 (COVID-19) has quickly engulfed the world. Inflammatory cytokines are associated with the severity and outcomes of patients with COVID-19. However, the prognostic value of pro-inflammatory factors in cancer patients with COVID-19 are unknown. Methods: A multi-center, retrospective, cross-sectional study, based on five designated tertiary hospitals for the treatment of COVID-19 in Hubei Province, China. 112 cancer patients with COVID-19, and 105 COVID-19 patients without cancer were enrolled in the study between January 1st, 2020 and April 30th, 2020. The risk assessment of pro-inflammatory factors for disease severity and clinical adverse outcomes was identified by univariable and multivariable logistic regression models. Results: Of the 112 cancer patients with COVID-19, 40 (35.7%) patients were in critical condition and 18 (16.1%) patients died unfortunately. Univariate and multivariate analysis demonstrated that hemoglobin level and pro-inflammatory neutrophils and C-reactive protein (CRP), can be used as independent factors affecting the severity of COVID-19; Meanwhile, pro-inflammatory neutrophils and CRP can be used as an independent influencing factor for adverse clinical outcome of death. Moreover, the dynamic changes of neutrophils and CRP were also presented, and compared with COVID-19 patients without cancer, cancer patients with COVID-19 showed higher neutrophil counts and CRP levels. Conclusion: In cancer patients with COVID-19, the significant increase in pro-inflammatory neutrophils and CRP indicated a more critical illness and adverse clinical outcome, and pro-inflammatory neutrophils and CRP played a greater adverse role compare with COVID-19 patients without cancer, which may be the cause of critical illness and adverse clinical outcomes of cancer patients with COVID-19.

Characteristics and Outcomes of 35 Breast Cancer Patients Infected With COVID-19

Since December 2019, a novel coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly engulfed the world. Cancer patients infected with COVID-19 are considered to carry higher severity of the disease and higher mortality rate than common COVID-19 patients in previous studies. However, due to the poor clinical information on COVID-19 patients with cancer, the evidences that supported this conclusion are insufficient. At present, rather limited reports have analyzed the clinical data of breast cancer patients infected with COVID-19. Therefore, in this retrospective study, we described the clinical characteristics and the outcomes of 35 COVID-19 patients with breast cancer and compared 55 COVID-19 patients without cancer and 81 COVID-19 patients with other types of cancer as controls. Our data showed that there were no differences in disease severity and outcomes between the COVID-19 patients with breast cancer and the common COVID-19 patients, which was in contrast to previous studies. In addition, compared with other types of cancer patients, asymptomatic infections and mild cases among breast cancer patients made up a substantially larger proportion. Our results indicated that the clinical characteristics of breast cancer patients were milder than those of other types of cancer patients, but there were no significant differences in outcomes between the two groups.

Energy metabolism and sources of oxidative stress in wooden breast - a review

Modern broilers show dramatic growth over a short interval and contribute directly to the success of the poultry meat industry. The growth performance of commercial broilers is a result of genetic selection for "performance traits", such as body size, meat yield, and feed conversion rate. However, due to the rapid growth rate of modern commercial broilers, several growth-related conditions have arisen, increasing economic losses and consumer concerns. Among the most economically consequential is the muscle disorder called wooden breast. Together with associated myopathies such as white striping and spaghetti meat, wooden breast is causing losses of $200 million a year in the U.S. alone and occurs worldwide. No causative factors are known for wooden breast to date. Wooden breast can affect over 80% of broilers in a flock, yet no methods of amelioration are currently available. Overall, the evidence suggests that wooden breast is a genetic, age-dependent condition associated with fast growth rate. The primary features of wooden breast are muscle degeneration and fibrosis, high levels of oxidative stress, hypoxia, and altered energy metabolism. Recent work has also implicated reduced pectoral vessel density in the pathogenesis of wooden breast. This review examines the history of myopathies in commercial broilers and the relationship of myopathies to metabolism and oxidative performance. This review summarizes the foundational knowledge of wooden breast and provides a platform for further investigation of wooden breast.

Impacts of Dietary Protein and Prebiotic Inclusion on Liver and Spleen Gene Expression in Hy-Line Brown Caged Layers

Simple Summary

Eggs are one of the most affordable and nutritious animal proteins available, and with increasing human population, there is an increased demand for production. As feed is the main expense in poultry production, novel protein sources and feed additives need to be evaluated for their benefits for poultry health and performance. In this study, we evaluated the standard soybean-based diets against an alternate source—cottonseed meal, in the context of prebiotic addition. Prebiotics putatively improves health and production. We assessed the homeostatic and immune balance by assaying the expression of select marker genes. We find that the inclusion of yeast cell wall products as prebiotic alters homeostatic balance. Particularly, the upregulation of apoptosis—a normal cell process—suggests that these products may promote homeostatic balance.

Abstract

The ingredients of poultry feeds are chosen based on the least-cost formulation to meet nutritional requirements. However, this approach can lead to the introduction of anti-nutritional ingredients in the feed. The objective of this study was to evaluate the impacts of two diets (with or without prebiotic) on homeostatic genes in the liver and spleen of laying hens. Hy-Line Brown layers were raised either on a soybean meal or cottonseed meal-based diets with and without an added prebiotic (yeast cell wall), totaling four experimental diets. A total of 120, 63-week old layers were housed individually in a wire cage system. We investigated differences in the expression of select homeostatic marker genes in the liver and spleen of hens from each treatment. We then used the ΔΔCT and generalized linear models to assess significance. Results show that the inclusion of prebiotic yeast cell-wall (YCW) increased the expression of the BAK gene in the liver tissue for both the soybean meal (SBM) and cottonseed meal (CSM) diets. For splenic tissue, the combination of YCW with the CSM diet increased the POR gene over six log2 fold. Altogether, our results suggest altered homeostasis, which can have consequences for health and performance.