Validation of a Non-Targeted LC-MS Approach for Identifying Ancient Proteins: Method Development on Bone to Improve Artifact Residue Analysis

Barker, Andrew; Dombrosky, Jonathan; Chaput, Dale; Venbles, Barney; Wolverton, Steve; Stevens, Stanley M.

doi:10.14237/ebl.6.1.2015.294

Cited by 22 publications

(4 citation statements)

References 43 publications

(63 reference statements)

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“…The TME mainly consists of the tumor stroma, adjacent tissue cells, microvessels, immune cells, and immune molecules. 415 CSCs not only adapt to changes in the TME but also affect the TME. Concurrently, the microenvironment also promotes the self-renewal of CSCs, induces angiogenesis, recruits immune and stromal cells, and promotes tumor invasion and metastasis (Fig.…”

Section: Major Signaling Pathways In Cscsmentioning

confidence: 99%

Targeting cancer stem cell pathways for cancer therapy

Yang

Shi

Zhao

et al. 2020

Sig Transduct Target Ther

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998

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Since cancer stem cells (CSCs) were first identified in leukemia in 1994, they have been considered promising therapeutic targets for cancer therapy. These cells have self-renewal capacity and differentiation potential and contribute to multiple tumor malignancies, such as recurrence, metastasis, heterogeneity, multidrug resistance, and radiation resistance. The biological activities of CSCs are regulated by several pluripotent transcription factors, such as OCT4, Sox2, Nanog, KLF4, and MYC. In addition, many intracellular signaling pathways, such as Wnt, NF-κB (nuclear factor-κB), Notch, Hedgehog, JAK-STAT (Janus kinase/signal transducers and activators of transcription), PI3K/AKT/mTOR (phosphoinositide 3-kinase/AKT/mammalian target of rapamycin), TGF (transforming growth factor)/SMAD, and PPAR (peroxisome proliferator-activated receptor), as well as extracellular factors, such as vascular niches, hypoxia, tumor-associated macrophages, cancer-associated fibroblasts, cancer-associated mesenchymal stem cells, extracellular matrix, and exosomes, have been shown to be very important regulators of CSCs. Molecules, vaccines, antibodies, and CAR-T (chimeric antigen receptor T cell) cells have been developed to specifically target CSCs, and some of these factors are already undergoing clinical trials. This review summarizes the characterization and identification of CSCs, depicts major factors and pathways that regulate CSC development, and discusses potential targeted therapy for CSCs.Signal Transduction and Targeted Therapy (2020) 5:8; https://doi.

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Section: Major Signaling Pathways In Cscsmentioning

confidence: 99%

Targeting cancer stem cell pathways for cancer therapy

Yang

Shi

Zhao

et al. 2020

Sig Transduct Target Ther

1,246

998

View full text Add to dashboard Cite

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“…Plasma proteins and blood clotting proteins are also typically present in bone and dentine proteomes, including prothrombin (F2), coagulation factor IX (F9), and coagulation factor X (F10). To date, ancient bone proteomes have been studied in humans, ,,,, mammoths, , moas, cattle, , horses, , turkeys, rabbits, squirrels, extinct rhinoceros, and ancient dentine proteomes have been studied in humans ,, and extinct rhinoceros …”

Section: Applications In Paleoproteomicsmentioning

confidence: 99%

Paleoproteomics

2022

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Paleoproteomics, the study of ancient proteins, is a rapidly growing field at the intersection of molecular biology, paleontology, archaeology, paleoecology, and history. Paleoproteomics research leverages the longevity and diversity of proteins to explore fundamental questions about the past. While its origins predate the characterization of DNA, it was only with the advent of soft ionization mass spectrometry that the study of ancient proteins became truly feasible. Technological gains over the past 20 years have allowed increasing opportunities to better understand preservation, degradation, and recovery of the rich bioarchive of ancient proteins found in the archaeological and paleontological records. Growing from a handful of studies in the 1990s on individual highly abundant ancient proteins, paleoproteomics today is an expanding field with diverse applications ranging from the taxonomic identification of highly fragmented bones and shells and the phylogenetic resolution of extinct species to the exploration of past cuisines from dental calculus and pottery food crusts and the characterization of past diseases. More broadly, these studies have opened new doors in understanding past human−animal interactions, the reconstruction of past environments and environmental changes, the expansion of the hominin fossil record through large scale screening of nondiagnostic bone fragments, and the phylogenetic resolution of the vertebrate fossil record. Even with these advances, much of the ancient proteomic record still remains unexplored. Here we provide an overview of the history of the field, a summary of the major methods and applications currently in use, and a critical evaluation of current challenges. We conclude by looking to the future, for which innovative solutions and emerging technology will play an important role in enabling us to access the still unexplored "dark" proteome, allowing for a fuller understanding of the role ancient proteins can play in the interpretation of the past.

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“…Immunoprecipitation methodology could also increase confidence in the use of antibodies for direct analysis of fossil soft tissues because it can remove the concerns of nonspecific binding by validating the antibody target . Because mass spectrometry provides direct identification of isolated/enriched proteins, it is possible to directly evaluate the specificity of the antibodies/aptamers and rule out cross-reactivity with humics or other diagenetic molecules as the source of immunological response . Further, we have found that some low-abundance bone proteins (e.g., hemoglobin) solubilize better in extraction buffers that are nonoptimal for general proteome, suggesting that extraction reagents may themselves be optimized for more targeted investigations.…”

Section: Future Directions In Dtppmentioning

confidence: 99%

Deep Time Paleoproteomics: Looking Forward

2021

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The goal of paleoproteomics is to characterize proteins from specimens that have been subjected to the degrading and obscuring effects of time, thus obtaining biological information about tissues or organisms both unobservable in the present and unobtainable through morphological study. Although the description of sequences from Tyrannosaurus rex and Brachylophosaurus canadensis suggested that proteins may persist over tens of millions of years, the majority of paleoproteomic analyses have focused on historical, archeological, or relatively young paleontological samples that rarely exceed 1 million years in age. However, recent advances in methodology and analyses of diverse tissues types (e.g., fossil eggshell, dental enamel) have begun closing the large window of time that remains unexplored in the fossil history of the Cenozoic. In this perspective, we discuss the history and current state of deep time paleoproteomics (DTPp), here defined as paleoproteomic study of samples ∼1 million years (1 Ma) or more in age. We then discuss the future of DTPp research, including what we see as critical ways the field can expand, advancements in technology that can be utilized, and the types of questions DTPp can address if such a future is realized.

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Validation of a Non-Targeted LC-MS Approach for Identifying Ancient Proteins: Method Development on Bone to Improve Artifact Residue Analysis

Cited by 22 publications

References 43 publications

Targeting cancer stem cell pathways for cancer therapy

Targeting cancer stem cell pathways for cancer therapy

Paleoproteomics

Deep Time Paleoproteomics: Looking Forward

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