Cold Spring Harbor Laboratory

About: Cold Spring Harbor Laboratory is a nonprofit organization based out in Cold Spring Harbor, New York, United States. It is known for research contribution in the topics: Gene & Genome. The organization has 3772 authors who have published 6603 publications receiving 1010873 citations. The organization is also known as: CSHL.

Patterns of gene action in plant development revealed by enhancer trap and gene trap transposable elements.

Abstract: The crucifer Arabidopsis thaliana has been used widely as a model organism for the study of plant development. We describe here the development of an efficient insertional mutagenesis system in Arabidopsis that permits identification of genes by their patterns of expression during development. Transposable elements of the Ac/Ds system carrying the GUS reporter gene have been designed to act as enhancer traps or gene traps. A novel selection scheme maximizes recovery of unlinked transposition events. In this study 491 plants carrying independent transposon insertions were generated and screened for expression patterns. One-half of the enhancer trap insertions and one-quarter of the gene trap insertions displayed GUS expression in seedlings or flowers, including expression patterns specific to organs, tissues, cell types, or developmental stages. The patterns identify genes that act during organogenesis, pattern formation, or cell differentiation. Transposon insertion lines with specific GUS expression patterns provide valuable markers for studies of Arabidopsis development and identify new cell types or subtypes in plants. The diversity of gene expression patterns generated suggests that the identification and cloning of Arabidopsis genes expressed in any developmental process is feasible using this system.

Neutrophil extracellular traps produced during inflammation awaken dormant cancer cells in mice.

Abstract: INTRODUCTION Most cancer patients die from cancer that recurs after spreading to a different tissue, rather than from their original tumor. After successful treatment of the original tumor, cancer cells that have disseminated to other sites can undergo dormancy, remaining viable but not proliferating. In breast, prostate, and other cancers, cancer cells can remain dormant and clinically undetectable for years and even decades before recurring, or awakening, as metastatic cancer. Little is known about what might initiate cancer awakening, and this in turn reduces our opportunities to prevent metastasis. RATIONALE Epidemiological studies have suggested that inflammation is linked to a higher risk of breast cancer recurrence after a period of clinical dormancy. Smoking, which causes chronic lung inflammation, is also associated with a higher risk of recurrence. However, whether inflammation can cause awakening is not clear. Inflammatory cells, such as neutrophils, can provide many different signals that promote cancer progression. Neutrophils can kill harmful microorganisms by the release of neutrophil extracellular traps (NETs) into the extracellular space. NETs are scaffolds of DNA with associated cytotoxic proteins and proteases [e.g., neutrophil elastase (NE) and matrix metalloproteinase 9 (MMP9)]. NETs induced by bacteria or by cancer cells can promote metastasis, but the mechanism by which this occurs is not known. In this study, we tested whether NETs formed during lung inflammation could induce awakening. RESULTS We found that sustained experimental lung inflammation—induced by either tobacco smoke exposure or nasal instillation of lipopolysaccharide (LPS)—converted dormant cancer cells to aggressive lung metastases in mice. Both types of sustained inflammation also caused the formation of NETs. Inhibiting NET formation or digesting the NETs’ DNA scaffold prevented conversion of single disseminated cancer cells to growing metastases in mouse models of breast and prostate cancer. The NET DNA bound to the extracellular matrix (ECM) protein laminin, thus bringing two NET-associated proteases, NE and MMP9, to their substrate. This in turn facilitated a sequential cleavage of laminin, first by NE and then by MMP9. The NET-mediated proteolytic remodeling of laminin revealed an epitope that triggered proliferation of dormant cancer cells through integrin activation and FAK/ERK/MLCK/YAP signaling. We generated a blocking antibody against NET-remodeled laminin, and this antibody prevented or reduced tobacco smoke exposure– or LPS-induced inflammation from awakening dormant cancer cells in mice. CONCLUSION Our data implicate NETs and NET-mediated ECM remodeling as critical mediators of inflammation-induced awakening in mouse models of dormancy. We propose that NETs awaken cancer by concentrating neutrophil proteases at the ECM protein laminin, allowing for sequential proteolytic remodeling of laminin and leading to integrin-mediated signaling in the cancer cells. Our findings set the stage for epidemiological studies to test possible links among inflammation or smoking, NETs, and recurrence after dormancy in human patients. If such links can be established, we envision that approaches similar to the ones used in mouse models in our study could be used to target NETs and their downstream effectors to reduce the risk of cancer recurrence in human patients.

Identification of unique neoantigen qualities in long-term survivors of pancreatic cancer.

Abstract: Pancreatic ductal adenocarcinoma is a lethal cancer with fewer than 7% of patients surviving past 5 years. T-cell immunity has been linked to the exceptional outcome of the few long-term survivors, yet the relevant antigens remain unknown. Here we use genetic, immunohistochemical and transcriptional immunoprofiling, computational biophysics, and functional assays to identify T-cell antigens in long-term survivors of pancreatic cancer. Using whole-exome sequencing and in silico neoantigen prediction, we found that tumours with both the highest neoantigen number and the most abundant CD8+ T-cell infiltrates, but neither alone, stratified patients with the longest survival. Investigating the specific neoantigen qualities promoting T-cell activation in long-term survivors, we discovered that these individuals were enriched in neoantigen qualities defined by a fitness model, and neoantigens in the tumour antigen MUC16 (also known as CA125). A neoantigen quality fitness model conferring greater immunogenicity to neoantigens with differential presentation and homology to infectious disease-derived peptides identified long-term survivors in two independent datasets, whereas a neoantigen quantity model ascribing greater immunogenicity to increasing neoantigen number alone did not. We detected intratumoural and lasting circulating T-cell reactivity to both high-quality and MUC16 neoantigens in long-term survivors of pancreatic cancer, including clones with specificity to both high-quality neoantigens and predicted cross-reactive microbial epitopes, consistent with neoantigen molecular mimicry. Notably, we observed selective loss of high-quality and MUC16 neoantigenic clones on metastatic progression, suggesting neoantigen immunoediting. Our results identify neoantigens with unique qualities as T-cell targets in pancreatic ductal adenocarcinoma. More broadly, we identify neoantigen quality as a biomarker for immunogenic tumours that may guide the application of immunotherapies.