bims-pimaco 2023-10-22 papers

Issue of 2023‒10‒22
six papers selected by
Lucas B. Zeiger, Beatson Institute for Cancer Research

Adv Biol Regul. 2023 Oct 04. pii: S2212-4926(23)00035-0. [Epub ahead of print] 100989

Proteomic and yeast 2-hybrid screens to identify PTEN binding partners.

Priyanka Tibarewal, Laura Spinelli, Helene Maccario, Nick R Leslie.

PTEN is a phosphoinositide lipid phosphatase and an important tumour suppressor protein. PTEN function is reduced or lost in around a third of all human cancers through diverse mechanisms, from gene deletion to changes in the function of proteins which regulate PTEN through direct protein binding. Here we present data from SILAC (Stable Isotope Labelling by Amino acids in Cell culture) proteomic screens to identify proteins which bind to PTEN. These experiments using untransformed epithelial cells and glioma cells identified several novel candidate proteins in addition to many previously identified PTEN binding partners and many proteins which are recognised as common false positives using these methods. From subsequent co-expression pull-down experiments we provide further evidence supporting the physical interaction of PTEN with MMP1, Myosin 18A and SHROOM3. We also performed yeast two-hybrid screens which identify the previously recognised PTEN binding partner MSP58 in addition to the nuclear import export receptor TNPO3. These experiments identify several novel candidate binding partners of PTEN and provide further data addressing the set of proteins that interact with this important tumour suppressor.

Keywords: PDZ; PTEN; Phosphatase; Protein-protein interaction; Proteomics; Tumour suppressor

DOI: https://doi.org/10.1016/j.jbior.2023.100989

Brief Bioinform. 2023 Sep 22. pii: bbad361. [Epub ahead of print]24(6):

Classification of PTEN missense VUS through exascale simulations.

Siddharth Sinha, Jiaheng Li, Benjamin Tam, San Ming Wang.

Phosphatase and tensin homolog (PTEN), a tumor suppressor with dual phosphatase properties, is a key factor in PI3K/AKT signaling pathway. Pathogenic germline variation in PTEN can abrogate its ability to dephosphorylate, causing high cancer risk. Lack of functional evidence lets numerous PTEN variants be classified as variants of uncertain significance (VUS). Utilizing Molecular Dynamics (MD) simulations, we performed a thorough evaluation for 147 PTEN missense VUS, sorting them into 66 deleterious and 81 tolerated variants. Utilizing replica exchange molecular dynamic (REMD) simulations, we further assessed the variants situated in the catalytic core of PTEN's phosphatase domain and uncovered conformational alterations influencing the structural stability of the phosphatase domain. There was a high degree of agreement between our results and the variants classified by Variant Abundance by Massively Parallel Sequencing, saturation mutagenesis, multiplexed functional data and experimental assays. Our extensive analysis of PTEN missense VUS should benefit their clinical applications in PTEN-related cancer.SIGNIFICANCE STATEMENT: Classification of PTEN variants affecting its lipid phosphatase activity is important for understanding the roles of PTEN variation in the pathogenesis of hereditary and sporadic malignancies. Of the 3000 variants identified in PTEN, 1296 (43%) were assigned as VUS. Here, we applied MD and REMD simulations to investigate the effects of PTEN missense VUS on the structural integrity of the PTEN phosphatase domain consisting the WPD, P and TI active sites. We classified a total of 147 missense VUS into 66 deleterious and 81 tolerated variants by referring to the control group comprising 54 pathogenic and 12 benign variants. The classification was largely in concordance with these classified by experimental approaches.

Keywords: MD simulations; PTEN; evolution selection; lipid phosphatase activity; replica exchange molecular dynamics (REMD) simulations; variants of uncertain significance (VUS)

DOI: https://doi.org/10.1093/bib/bbad361

Pathol Res Pract. 2023 Oct 10. pii: S0344-0338(23)00580-0. [Epub ahead of print]251 154879

Comparison of immunohistochemistry and next-generation sequencing results in oncogenic PTEN missense mutations.

Moonsik Kim, Jinhee Kim, An Na Seo, Ji Yun Jeong, Nora Jee-Young Park, Gun Oh Chong, Dae Gy Hong, Ji Young Park.

BACKGROUND: Phosphatase and tensin homolog (PTEN) is one of the most frequently mutated tumor suppressor genes in malignant tumors. Oncogenic PTEN mutations have diagnostic, prognostic, and therapeutic implications. Similar to TP53 mutations, oncogenic PTEN mutations can result from nonsynonymous missense mutations. However, there has been no detailed study on the immunostaining pattern of oncogenic PTEN missense mutations.METHODS: We retrospectively selected 18 cancers (13 endometrial cancers, 2 brain tumors, 1 ovarian cancer, 1 lung cancer, and 1 cancer of unknown origin) harboring oncogenic PTEN missense mutations, which were confirmed by targeted next-generation sequencing. PTEN immunohistochemistry was conducted for all cases, and the results were compared with sequencing results.
RESULTS: The immunostaining results of PTEN missense mutations revealed a diverse pattern depending on the site of mutation and co-occurring mutation. The most frequent oncogenic PTEN mutations were R130G (4/18, 22.2 %) and R130Q (3/18, 16.7 %). Eleven cases harbored PTEN missense mutations only, whereas the remaining seven cases harbored PTEN truncating mutations and PTEN missense mutations. Complete loss of cytoplasmic expression were found in five cases, of which three had missense mutation only. PTEN R130 residue mutation alone did not showed altered PTEN immunostaining pattern in this study.
CONCLUSIONS: PTEN missense mutation, which comprises a portion of oncogenic PTEN mutation, can manifest as a diverse immunostaining pattern. Complementary testing using both immunostaining and next-generation sequencing should be conducted to accurately evaluate the PTEN status in malignancy.

Keywords: Immunohistochemistry; Missense mutation; Next-generation sequencing; PTEN

DOI: https://doi.org/10.1016/j.prp.2023.154879

Proc Biol Sci. 2023 Oct 25. 290(2009): 20231020

Stochastic model for cell population dynamics quantifies homeostasis in colonic crypts and its disruption in early tumorigenesis.

Konstantinos Mamis, Ruibo Zhang, Ivana Bozic.

The questions of how healthy colonic crypts maintain their size, and how homeostasis is disrupted by driver mutations, are central to understanding colorectal tumorigenesis. We propose a three-type stochastic branching process, which accounts for stem, transit-amplifying (TA) and fully differentiated (FD) cells, to model the dynamics of cell populations residing in colonic crypts. Our model is simple in its formulation, allowing us to estimate all but one of the model parameters from the literature. Fitting the single remaining parameter, we find that model results agree well with data from healthy human colonic crypts, capturing the considerable variance in population sizes observed experimentally. Importantly, our model predicts a steady-state population in healthy colonic crypts for relevant parameter values. We show that APC and KRAS mutations, the most significant early alterations leading to colorectal cancer, result in increased steady-state populations in mutated crypts, in agreement with experimental results. Finally, our model predicts a simple condition for unbounded growth of cells in a crypt, corresponding to colorectal malignancy. This is predicted to occur when the division rate of TA cells exceeds their differentiation rate, with implications for therapeutic cancer prevention strategies.

Keywords: branching process; cell population dynamics; colonic crypts; colorectal tumorigenesis; homeostasis

DOI: https://doi.org/10.1098/rspb.2023.1020

Cancer Res. 2023 Oct 17.

Delineating a role for methionine metabolism in colorectal cancer.

Shiyu Liu, Jason W Locasale.

Advances in mass spectrometry allow for broader applications of metabolomics in research and clinical applications. In a recent issue of Nature Metabolism, Voorde and colleagues utilized metabolite profiling to investigate the metabolism of colorectal cancer (CRC) in mouse models, organoids and patients. This study underscores the utility of metabolomics in distinguishing CRC, offering potential for its use in precision medicine. It also revealed a pivotal role for adenosylhomocysteinase in the methionine cycle and highlighted its potential as a therapeutic target.

DOI: https://doi.org/10.1158/0008-5472.CAN-23-3169