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  1. Article: SMARCD1 is a "Goldilocks" metastasis modifier.

    Ross, Christina / Gong, Li-Yun / Jenkins, Lisa M / Ha, Ngoc-Han / Majocha, Megan / Hunter, Kent

    bioRxiv : the preprint server for biology

    2024  

    Abstract: Breast cancer is the most frequently diagnosed cancer worldwide, constituting around 15% of all diagnosed cancers in 2023. The predominant cause of breast cancer-related mortality is metastasis to distant essential organs, and a lack of metastasis- ... ...

    Abstract Breast cancer is the most frequently diagnosed cancer worldwide, constituting around 15% of all diagnosed cancers in 2023. The predominant cause of breast cancer-related mortality is metastasis to distant essential organs, and a lack of metastasis-targeted therapies perpetuates dismal outcomes for late-stage patients. However, through our use of meiotic genetics to study inherited transcriptional network regulation, we have identified a new class of "Goldilocks" genes that are promising candidates for the development of metastasis-targeted therapeutics. Building upon previous work that implicated the CCR4-NOT RNA deadenylase complex in metastasis, we now demonstrate that the RNA-binding proteins (RNA-BPs) NANOS1, PUM2, and CPSF4 also regulate metastatic potential. Using cell lines, 3D culture, mouse models, and clinical data, we pinpoint
    Language English
    Publishing date 2024-01-29
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.01.24.577061
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Multiplexing the Identification of Microorganisms via Tandem Mass Tag Labeling Augmented by Interference Removal through a Novel Modification of the Expectation Maximization Algorithm.

    Alves, Gelio / Ogurtsov, Aleksey Y / Porterfield, Harry / Maity, Tapan / Jenkins, Lisa M / Sacks, David / Yu, Yi-Kuo

    Journal of the American Society for Mass Spectrometry

    2024  

    Abstract: Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate ... ...

    Abstract Having fast, accurate, and broad spectrum methods for the identification of microorganisms is of paramount importance to public health, research, and safety. Bottom-up mass spectrometer-based proteomics has emerged as an effective tool for the accurate identification of microorganisms from microbial isolates. However, one major hurdle that limits the deployment of this tool for routine clinical diagnosis, and other areas of research such as culturomics, is the instrument time required for the mass spectrometer to analyze a single sample, which can take ∼1 h per sample, when using mass spectrometers that are presently used in most institutes. To address this issue, in this study, we employed, for the first time, tandem mass tags (TMTs) in multiplex identifications of microorganisms from multiple TMT-labeled samples in one MS/MS experiment. A difficulty encountered when using TMT labeling is the presence of interference in the measured intensities of TMT reporter ions. To correct for interference, we employed in the proposed method a modified version of the expectation maximization (EM) algorithm that redistributes the signal from ion interference back to the correct TMT-labeled samples. We have evaluated the sensitivity and specificity of the proposed method using 94 MS/MS experiments (covering a broad range of protein concentration ratios across TMT-labeled channels and experimental parameters), containing a total of 1931 true positive TMT-labeled channels and 317 true negative TMT-labeled channels. The results of the evaluation show that the proposed method has an identification sensitivity of 93-97% and a specificity of 100% at the species level. Furthermore, as a proof of concept, using an in-house-generated data set composed of some of the most common urinary tract pathogens, we demonstrated that by using the proposed method the mass spectrometer time required per sample, using a 1 h LC-MS/MS run, can be reduced to 10 and 6 min when samples are labeled with TMT-6 and TMT-10, respectively. The proposed method can also be used along with Orbitrap mass spectrometers that have faster MS/MS acquisition rates, like the recently released Orbitrap Astral mass spectrometer, to further reduce the mass spectrometer time required per sample.
    Language English
    Publishing date 2024-05-13
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1073671-2
    ISSN 1879-1123 ; 1044-0305
    ISSN (online) 1879-1123
    ISSN 1044-0305
    DOI 10.1021/jasms.3c00445
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: The TFIIH complex is required to establish and maintain mitotic chromosome structure.

    Haase, Julian / Chen, Richard / Parker, Wesley M / Bonner, Mary Kate / Jenkins, Lisa M / Kelly, Alexander E

    eLife

    2022  Volume 11

    Abstract: Condensins compact chromosomes to promote their equal segregation during mitosis, but the mechanism of condensin engagement with and action on chromatin is incompletely understood. Here, we show that the general transcription factor TFIIH complex is ... ...

    Abstract Condensins compact chromosomes to promote their equal segregation during mitosis, but the mechanism of condensin engagement with and action on chromatin is incompletely understood. Here, we show that the general transcription factor TFIIH complex is continuously required to establish and maintain a compacted chromosome structure in transcriptionally silent
    MeSH term(s) Animals ; Chromatin ; Chromosomes/metabolism ; DNA Topoisomerases, Type II/metabolism ; Histones ; Mice ; Mitosis ; Nucleosomes ; Xenopus laevis/metabolism
    Chemical Substances Chromatin ; Histones ; Nucleosomes ; DNA Topoisomerases, Type II (EC 5.99.1.3)
    Language English
    Publishing date 2022-03-16
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Intramural
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.75475
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: The TDRD3-USP9X complex and MIB1 regulate TOP3B homeostasis and prevent deleterious TOP3B cleavage complexes.

    Saha, Sourav / Huang, Shar-Yin Naomi / Yang, Xi / Saha, Liton Kumar / Sun, Yilun / Khandagale, Prashant / Jenkins, Lisa M / Pommier, Yves

    Nature communications

    2023  Volume 14, Issue 1, Page(s) 7524

    Abstract: TOP3B is stabilized by TDRD3. Hypothesizing that TDRD3 recruits a deubiquitinase, we find that TOP3B interacts with USP9X via TDRD3. Inactivation of USP9X destabilizes TOP3B, and depletion of both TDRD3 and USP9X does not promote further TOP3B ... ...

    Abstract TOP3B is stabilized by TDRD3. Hypothesizing that TDRD3 recruits a deubiquitinase, we find that TOP3B interacts with USP9X via TDRD3. Inactivation of USP9X destabilizes TOP3B, and depletion of both TDRD3 and USP9X does not promote further TOP3B ubiquitylation. Additionally, we observe that MIB1 mediates the ubiquitylation and proteasomal degradation of TOP3B by directly interacting with TOP3B independently of TDRD3. Combined depletion of USP9X, TDRD3 and MIB1 causes no additional increase in TOP3B levels compared to MIB1 knockdown alone indicating that the TDRD3-USP9X complex works downstream of MIB1. To comprehend why cells degrade TOP3B in the absence of TDRD3, we measured TOP3Bccs. Lack of TDRD3 increases TOP3Bccs in DNA and RNA, and induced R-loops, γH2AX and growth defect. Biochemical experiments confirm that TDRD3 increases the turnover of TOP3B. Our work provides molecular insights into the mechanisms by which TDRD3 protect cells from deleterious TOP3Bccs which are otherwise removed by TRIM41.
    MeSH term(s) Cell Line, Tumor ; Ubiquitination ; Ubiquitin Thiolesterase/metabolism
    Chemical Substances Ubiquitin Thiolesterase (EC 3.4.19.12)
    Language English
    Publishing date 2023-11-18
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-023-43151-z
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Pyruvate dehydrogenase complex integrates the metabolome and epigenome in memory T cell differentiation in vitro.

    Tarasenko, Tatiana N / Banerjee, Payal / Gomez-Rodriguez, Julio / Gildea, Derek / Zhang, Suiyuan / Wolfsberg, Tyra / Jenkins, Lisa M / McGuire, Peter J

    Research square

    2023  

    Abstract: Background: Modulation of metabolic flux through pyruvate dehydrogenase complex (PDC) plays an important role in T cell activation and differentiation. PDC sits at the transition between glycolysis and the tricarboxylic acid cycle and is a major ... ...

    Abstract Background: Modulation of metabolic flux through pyruvate dehydrogenase complex (PDC) plays an important role in T cell activation and differentiation. PDC sits at the transition between glycolysis and the tricarboxylic acid cycle and is a major producer of acetyl-CoA, marking it as a potential metabolic and epigenetic node.
    Methods: To understand the role of pyruvate dehydrogenase complex in T cell differentiation, we generated mice deficient in T cell pyruvate dehydrogenase E1A (
    Results: Herein, we show that genetic ablation of PDC activity in T cells (
    Conclusions: Collectively, our data indicate that PDC integrates the metabolome and epigenome in memory T cell differentiation. Targeting this metabolic and epigenetic node can have widespread ramifications on cellular function.
    Language English
    Publishing date 2023-01-27
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-2464392/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Linear (-)-Zampanolide: Flexibility in Conformation-Activity Relationships.

    Umaña, Christian A / Henry, Jeffrey L / Saltzman, Claire T / Sackett, Dan L / Jenkins, Lisa M / Taylor, Richard E

    ChemMedChem

    2023  Volume 18, Issue 19, Page(s) e202300292

    Abstract: Through an understanding of the conformational preferences of the polyketide natural product (-)-zampanolide, and the structural motifs that control these preferences, we developed a linear zampanolide analogue that exhibits potent cytotoxicity against ... ...

    Abstract Through an understanding of the conformational preferences of the polyketide natural product (-)-zampanolide, and the structural motifs that control these preferences, we developed a linear zampanolide analogue that exhibits potent cytotoxicity against cancer cell lines. This discovery provides a set of three structural handles for further structure-activity relationship (SAR) studies of this potent microtubule-stabilizing agent. Moreover, it provides additional evidence of the complex relationship between ligand preorganization, conformational flexibility, and biological potency. In contrast to medicinal chemistry dogma, these results demonstrate that increased overall conformational flexibility is not necessarily detrimental to protein binding affinity and biological activity.
    MeSH term(s) Macrolides/chemistry ; Molecular Conformation ; Polyketides/chemistry ; Structure-Activity Relationship
    Chemical Substances zampanolide ; Macrolides ; Polyketides
    Language English
    Publishing date 2023-08-10
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Intramural ; Research Support, N.I.H., Extramural
    ZDB-ID 2218496-X
    ISSN 1860-7187 ; 1860-7179
    ISSN (online) 1860-7187
    ISSN 1860-7179
    DOI 10.1002/cmdc.202300292
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Extracellular Proximity Labeling Reveals an Expanded Interactome for the Matrisome Protein TIMP2.

    Peeney, David / Gurung, Sadeechya / Rich, Josh A / Coates-Park, Sasha / Liu, Yueqin / Toor, Jack / Jones, Jane / Richie, Christopher T / Jenkins, Lisa M / Stetler-Stevenson, William G

    Research square

    2024  

    Abstract: Classical methods of investigating protein-protein interactions (PPIs) are generally performed in non-living systems, yet in recent years new technologies utilizing proximity labeling (PL) have given researchers the tools to explore proximal PPIs in ... ...

    Abstract Classical methods of investigating protein-protein interactions (PPIs) are generally performed in non-living systems, yet in recent years new technologies utilizing proximity labeling (PL) have given researchers the tools to explore proximal PPIs in living systems. PL has distinct advantages over traditional protein interactome studies, such as the ability to identify weak and transient interactions in vitro and in vivo. Most PL studies are performed on targets within the cell or on the cell membrane. We have adapted the original PL method to investigate PPIs within the extracellular compartment, using both BioID2 and TurboID, that we term extracellular PL (ePL). To demonstrate the utility of this modified technique, we investigate the interactome of the widely expressed matrisome protein tissue inhibitor of metalloproteinases 2 (TIMP2). Tissue inhibitors of metalloproteinases (TIMPs) are a family of multi-functional proteins that were initially defined by their ability to inhibit the enzymatic activity of metalloproteinases (MPs), the major mediators of extracellular matrix (ECM) breakdown and turnover. TIMP2 exhibits a broad expression profile and is often abundant in both normal and diseased tissues. Understanding the functional transformation of matrisome regulators, like TIMP2, during the evolution of tissue microenvironments associated with disease progression is essential for the development of ECM-targeted therapeutics. Using carboxyl- and amino-terminal fusion proteins of TIMP2 with BioID2 and TurboID, we describe the TIMP2 proximal interactome. We also illustrate how the TIMP2 interactome changes in the presence of different stimuli, in different cell types, in unique culture conditions (2D vs 3D), and with different reaction kinetics (BioID2 vs. TurboID); demonstrating the power of this technique versus classical PPI methods. We propose that the screening of matrisome targets in disease models using ePL will reveal new therapeutic targets for further comprehensive studies.
    Language English
    Publishing date 2024-01-15
    Publishing country United States
    Document type Preprint
    DOI 10.21203/rs.3.rs-3857263/v1
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: The thiol methyltransferase activity of TMT1A (METTL7A) is conserved across species.

    González Dalmasy, José M / Fitzsimmons, Christina M / Frye, William J E / Perciaccante, Andrew J / Jewell, Connor P / Jenkins, Lisa M / Batista, Pedro J / Robey, Robert W / Gottesman, Michael M

    Chemico-biological interactions

    2024  Volume 394, Page(s) 110989

    Abstract: Although few resistance mechanisms for histone deacetylase inhibitors (HDACis) have been described, we recently demonstrated that TMT1A (formerly METTL7A) and TMT1B (formerly METTL7B) can mediate resistance to HDACis with a thiol as the zinc-binding ... ...

    Abstract Although few resistance mechanisms for histone deacetylase inhibitors (HDACis) have been described, we recently demonstrated that TMT1A (formerly METTL7A) and TMT1B (formerly METTL7B) can mediate resistance to HDACis with a thiol as the zinc-binding group by methylating and inactivating the drug. TMT1A and TMT1B are poorly characterized, and their normal physiological role has yet to be determined. As animal model systems are often used to determine the physiological function of proteins, we investigated whether the ability of these methyltransferases to methylate thiol-based HDACis is conserved across different species. We found that TMT1A was conserved across rats, mice, chickens, and zebrafish, displaying 85.7%, 84.8%, 60.7%, and 51.0% amino acid sequence identity, respectively, with human TMT1A. Because TMT1B was not found in the chicken or zebrafish, we focused our studies on the TMT1A homologs. HEK-293 cells were transfected to express mouse, rat, chicken, or zebrafish homologs of TMT1A and all conferred resistance to the thiol-based HDACIs NCH-51, KD-5170, and romidepsin compared to empty vector-transfected cells. Additionally, all homologs blunted the downstream effects of HDACi treatment such as increased p21 expression, increased acetylated histone H3, and cell cycle arrest. Increased levels of dimethylated romidepsin were also found in the culture medium of cells transfected to express any of the TMT1A homologs after a 24 h incubation with romidepsin compared to empty-vector transfected cells. Our results indicate that the ability of TMT1A to methylate molecules is conserved across species. Animal models may therefore be useful in elucidating the role of these enzymes in humans.
    MeSH term(s) Animals ; Humans ; Mice ; Methyltransferases/metabolism ; Methyltransferases/genetics ; HEK293 Cells ; Zebrafish/metabolism ; Rats ; Chickens ; Histone Deacetylase Inhibitors/pharmacology ; Amino Acid Sequence ; Sulfhydryl Compounds/metabolism ; Depsipeptides/pharmacology ; Methylation ; Species Specificity ; Conserved Sequence
    Chemical Substances Methyltransferases (EC 2.1.1.-) ; Histone Deacetylase Inhibitors ; Sulfhydryl Compounds ; romidepsin (CX3T89XQBK) ; Depsipeptides
    Language English
    Publishing date 2024-04-03
    Publishing country Ireland
    Document type Journal Article
    ZDB-ID 218799-1
    ISSN 1872-7786 ; 0009-2797
    ISSN (online) 1872-7786
    ISSN 0009-2797
    DOI 10.1016/j.cbi.2024.110989
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  9. Article ; Online: The novel ATR inhibitor M1774 induces replication protein overexpression and broad synergy with DNA-targeted anticancer drugs.

    Jo, Ukhyun / Arakawa, Yashuhiro / Zimmermann, Astrid / Taniyama, Daiki / Mizunuma, Makito / Jenkins, Lisa M / Maity, Tapan / Kumar, Suresh / Zenke, Frank T / Takebe, Naoko / Pommier, Yves

    Molecular cancer therapeutics

    2024  

    Abstract: Ataxia Telangiectasia and Rad3-related (ATR) checkpoint kinase inhibitors are in clinical trials. Here we explored the molecular pharmacology and therapeutic combination strategies of the oral ATR inhibitor M1774 (Tuvusertib) with DNA damaging agents ( ... ...

    Abstract Ataxia Telangiectasia and Rad3-related (ATR) checkpoint kinase inhibitors are in clinical trials. Here we explored the molecular pharmacology and therapeutic combination strategies of the oral ATR inhibitor M1774 (Tuvusertib) with DNA damaging agents (DDAs). As single agent, M1774 suppressed cancer cell viability at nanomolar concentrations, showing greater activity than ceralasertib and berzosertib, but less potency than gartisertib and elimusertib in the small-cell lung cancer H146, H82, and DMS114 cell lines. M1774 also efficiently blocked the activation of the ATR-CHK1 checkpoint pathway caused by replication stress induced by TOP1 inhibitors. Combination with non-toxic dose of M1774 enhanced TOP1 inhibitor-induced cancer cell death by enabling unscheduled replication upon replicative damage, thereby increasing genome instability. Tandem mass tag (TMT)-based quantitative proteomics uncovered that M1774, in the presence of DDA, forces the expression of proteins activating replication (CDC45) and G2/M-progression (PLK1 and CCNB1). In particular, the fork protection complex proteins (TIMELESS and TIPIN) were enriched. Low dose of M1774 was found highly synergistic with a broad spectrum of clinical DDAs including TOP1 inhibitors (SN-38/irinotecan, topotecan, exatecan, and exatecan), the TOP2 inhibitor etoposide, cisplatin, the RNA polymerase II inhibitor lurbinectedin, and the PARP inhibitor talazoparib in various models including cancer cell lines, patient-derived organoids, and mouse xenograft models. Furthermore, we demonstrate that M1774 reverses chemoresistance to anticancer DDAs in cancer cells lacking SLFN11 expression, suggesting that SLFN11 can be utilized for patient selection in upcoming clinical trials.
    Language English
    Publishing date 2024-03-11
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2063563-1
    ISSN 1538-8514 ; 1535-7163
    ISSN (online) 1538-8514
    ISSN 1535-7163
    DOI 10.1158/1535-7163.MCT-23-0402
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: A spatial map of hepatic mitochondria uncovers functional heterogeneity shaped by nutrient-sensing signaling.

    Kang, Sun Woo Sophie / Cunningham, Rory P / Miller, Colin B / Brown, Lauryn A / Cultraro, Constance M / Harned, Adam / Narayan, Kedar / Hernandez, Jonathan / Jenkins, Lisa M / Lobanov, Alexei / Cam, Maggie / Porat-Shliom, Natalie

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 1799

    Abstract: In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal and pericentral axis. How the mitochondria sense and integrate these signals to respond and maintain homeostasis is not ...

    Abstract In the liver, mitochondria are exposed to different concentrations of nutrients due to their spatial positioning across the periportal and pericentral axis. How the mitochondria sense and integrate these signals to respond and maintain homeostasis is not known. Here, we combine intravital microscopy, spatial proteomics, and functional assessment to investigate mitochondrial heterogeneity in the context of liver zonation. We find that periportal and pericentral mitochondria are morphologically and functionally distinct; beta-oxidation is elevated in periportal regions, while lipid synthesis is predominant in the pericentral mitochondria. In addition, comparative phosphoproteomics reveals spatially distinct patterns of mitochondrial composition and potential regulation via phosphorylation. Acute pharmacological modulation of nutrient sensing through AMPK and mTOR shifts mitochondrial phenotypes in the periportal and pericentral regions, linking nutrient gradients across the lobule and mitochondrial heterogeneity. This study highlights the role of protein phosphorylation in mitochondrial structure, function, and overall homeostasis in hepatic metabolic zonation. These findings have important implications for liver physiology and disease.
    MeSH term(s) Liver/metabolism ; Oxidation-Reduction ; Mitochondria/metabolism
    Language English
    Publishing date 2024-02-28
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-45751-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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