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2. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines
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Thery, C, Witwer, KW, Aikawa, E, Jose Alcaraz, M, Anderson, JD, Andriantsitohaina, R, Antoniou, A, Arab, T, Archer, F, Atkin-Smith, GK, Ayre, DC, Bach, J-M, Bachurski, D, Baharvand, H, Balaj, L, Baldacchino, S, Bauer, NN, Baxter, AA, Bebawy, M, Beckham, C, Zavec, AB, Benmoussa, A, Berardi, AC, Bergese, P, Bielska, E, Blenkiron, C, Bobis-Wozowicz, S, Boilard, E, Boireau, W, Bongiovanni, A, Borras, FE, Bosch, S, Boulanger, CM, Breakefield, X, Breglio, AM, Brennan, MA, Brigstock, DR, Brisson, A, Broekman, MLD, Bromberg, JF, Bryl-Gorecka, P, Buch, S, Buck, AH, Burger, D, Busatto, S, Buschmann, D, Bussolati, B, Buzas, E, Byrd, JB, Camussi, G, Carter, DRF, Caruso, S, Chamley, LW, Chang, Y-T, Chen, C, Chen, S, Cheng, L, Chin, AR, Clayton, A, Clerici, SP, Cocks, A, Cocucci, E, Coffey, RJ, Cordeiro-da-Silva, A, Couch, Y, Coumans, FAW, Coyle, B, Crescitelli, R, Criado, MF, D'Souza-Schorey, C, Das, S, Chaudhuri, AD, de Candia, P, De Santana Junior, EF, De Wever, O, del Portillo, HA, Demaret, T, Deville, S, Devitt, A, Dhondt, B, Di Vizio, D, Dieterich, LC, Dolo, V, Dominguez Rubio, AP, Dominici, M, Dourado, MR, Driedonks, TAP, Duarte, F, Duncan, HM, Eichenberger, RM, Ekstrom, K, Andaloussi, SEL, Elie-Caille, C, Erdbrugger, U, Falcon-Perez, JM, Fatima, F, Fish, JE, Flores-Bellver, M, Forsonits, A, Frelet-Barrand, A, Fricke, F, Fuhrmann, G, Gabrielsson, S, Gamez-Valero, A, Gardiner, C, Gaertner, K, Gaudin, R, Gho, YS, Giebel, B, Gilbert, C, Gimona, M, Giusti, I, Goberdhan, DC, Goergens, A, Gorski, SM, Greening, DW, Gross, JC, Gualerzi, A, Gupta, GN, Gustafson, D, Handberg, A, Haraszti, RA, Harrison, P, Hegyesi, H, Hendrix, A, Hill, AF, Hochberg, FH, Hoffmann, KF, Holder, B, Holthofer, H, Hosseinkhani, B, Hu, G, Huang, Y, Huber, V, Hunt, S, Ibrahim, AG-E, Ikezu, T, Inal, JM, Isin, M, Ivanova, A, Jackson, HK, Jacobsen, S, Jay, SM, Jayachandran, M, Jenster, G, Jiang, L, Johnson, SM, Jones, JC, Jong, A, Jovanovic-Talisman, T, Jung, S, Kalluri, R, Kano, S-I, Kaur, S, Kawamura, Y, Keller, ET, Khamari, D, Khomyakova, E, Khvorova, A, Kierulf, P, Kim, KP, Kislinger, T, Klingeborn, M, Klinke, DJ, Kornek, M, Kosanovic, MM, Kovacs, AF, Kraemer-Albers, E-M, Krasemann, S, Krause, M, Kurochkin, I, Kusuma, GD, Kuypers, S, Laitinen, S, Langevin, SM, Languino, LR, Lannigan, J, Lasser, C, Laurent, LC, Lavieu, G, Lazaro-Ibanez, E, Le Lay, S, Lee, M-S, Lee, YXF, Lemos, DS, Lenassi, M, Leszczynska, A, Li, ITS, Liao, K, Libregts, SF, Ligeti, E, Lim, R, Lim, SK, Line, A, Linnemannstoens, K, Llorente, A, Lombard, CA, Lorenowicz, MJ, Lorincz, AM, Lotvall, J, Lovett, J, Lowry, MC, Loyer, X, Lu, Q, Lukomska, B, Lunavat, TR, Maas, SLN, Malhi, H, Marcilla, A, Mariani, J, Mariscal, J, Martens-Uzunova, ES, Martin-Jaular, L, Martinez, MC, Martins, VR, Mathieu, M, Mathivanan, S, Maugeri, M, McGinnis, LK, McVey, MJ, Meckes, DG, Meehan, KL, Mertens, I, Minciacchi, VR, Moller, A, Jorgensen, MM, Morales-Kastresana, A, Morhayim, J, Mullier, F, Muraca, M, Musante, L, Mussack, V, Muth, DC, Myburgh, KH, Najrana, T, Nawaz, M, Nazarenko, I, Nejsum, P, Neri, C, Neri, T, Nieuwland, R, Nimrichter, L, Nolan, JP, Nolte-'t Hoen, ENM, Noren Hooten, N, O'Driscoll, L, O'Grady, T, O'Loghlen, A, Ochiya, T, Olivier, M, Ortiz, A, Ortiz, LA, Osteikoetxea, X, Ostegaard, O, Ostrowski, M, Park, J, Pegtel, DM, Peinado, H, Perut, F, Pfaffl, MW, Phinney, DG, Pieters, BCH, Pink, RC, Pisetsky, DS, von Strandmann, EP, Polakovicova, I, Poon, IKH, Powell, BH, Prada, I, Pulliam, L, Quesenberry, P, Radeghieri, A, Raffai, RL, Raimondo, S, Rak, J, Ramirez, M, Raposo, G, Rayyan, MS, Regev-Rudzki, N, Ricklefs, FL, Robbins, PD, Roberts, DD, Rodrigues, SC, Rohde, E, Rome, S, Rouschop, KMA, Rughetti, A, Russell, AE, Saa, P, Sahoo, S, Salas-Huenuleo, E, Sanchez, C, Saugstad, JA, Saul, MJ, Schiffelers, RM, Schneider, R, Schoyen, TH, Scott, A, Shahaj, E, Sharma, S, Shatnyeva, O, Shekari, F, Shelke, GV, Shetty, AK, Shiba, K, Siljander, PR-M, Silva, AM, Skowronek, A, Snyder, OL, Soares, RP, Sodar, BW, Soekmadji, C, Sotillo, J, Stahl, PD, Stoorvogel, W, Stott, SL, Strasser, EF, Swift, S, Tahara, H, Tewari, M, Timms, K, Tiwari, S, Tixeira, R, Tkach, M, Toh, WS, Tomasini, R, Torrecilhas, AC, Pablo Tosar, J, Toxavidis, V, Urbanelli, L, Vader, P, van Balkom, BWM, van der Grein, SG, Van Deun, J, van Herwijnen, MJC, Van Keuren-Jensen, K, van Niel, G, van Royen, ME, van Wijnen, AJ, Helena Vasconcelos, M, Vechetti, IJ, Veit, TD, Vella, LJ, Velot, E, Verweij, FJ, Vestad, B, Vinas, JL, Visnovitz, T, Vukman, KV, Wahlgren, J, Watson, DC, Wauben, MHM, Weaver, A, Webber, JP, Weber, V, Wehman, AM, Weiss, DJ, Welsh, JA, Wendt, S, Wheelock, AM, Wiener, Z, Witte, L, Wolfram, J, Xagorari, A, Xander, P, Xu, J, Yan, X, Yanez-Mo, M, Yin, H, Yuana, Y, Zappulli, V, Zarubova, J, Zekas, V, Zhang, J-Y, Zhao, Z, Zheng, L, Zheutlin, AR, Zickler, AM, Zimmermann, P, Zivkovic, AM, Zocco, D, Zuba-Surma, EK, Thery, C, Witwer, KW, Aikawa, E, Jose Alcaraz, M, Anderson, JD, Andriantsitohaina, R, Antoniou, A, Arab, T, Archer, F, Atkin-Smith, GK, Ayre, DC, Bach, J-M, Bachurski, D, Baharvand, H, Balaj, L, Baldacchino, S, Bauer, NN, Baxter, AA, Bebawy, M, Beckham, C, Zavec, AB, Benmoussa, A, Berardi, AC, Bergese, P, Bielska, E, Blenkiron, C, Bobis-Wozowicz, S, Boilard, E, Boireau, W, Bongiovanni, A, Borras, FE, Bosch, S, Boulanger, CM, Breakefield, X, Breglio, AM, Brennan, MA, Brigstock, DR, Brisson, A, Broekman, MLD, Bromberg, JF, Bryl-Gorecka, P, Buch, S, Buck, AH, Burger, D, Busatto, S, Buschmann, D, Bussolati, B, Buzas, E, Byrd, JB, Camussi, G, Carter, DRF, Caruso, S, Chamley, LW, Chang, Y-T, Chen, C, Chen, S, Cheng, L, Chin, AR, Clayton, A, Clerici, SP, Cocks, A, Cocucci, E, Coffey, RJ, Cordeiro-da-Silva, A, Couch, Y, Coumans, FAW, Coyle, B, Crescitelli, R, Criado, MF, D'Souza-Schorey, C, Das, S, Chaudhuri, AD, de Candia, P, De Santana Junior, EF, De Wever, O, del Portillo, HA, Demaret, T, Deville, S, Devitt, A, Dhondt, B, Di Vizio, D, Dieterich, LC, Dolo, V, Dominguez Rubio, AP, Dominici, M, Dourado, MR, Driedonks, TAP, Duarte, F, Duncan, HM, Eichenberger, RM, Ekstrom, K, Andaloussi, SEL, Elie-Caille, C, Erdbrugger, U, Falcon-Perez, JM, Fatima, F, Fish, JE, Flores-Bellver, M, Forsonits, A, Frelet-Barrand, A, Fricke, F, Fuhrmann, G, Gabrielsson, S, Gamez-Valero, A, Gardiner, C, Gaertner, K, Gaudin, R, Gho, YS, Giebel, B, Gilbert, C, Gimona, M, Giusti, I, Goberdhan, DC, Goergens, A, Gorski, SM, Greening, DW, Gross, JC, Gualerzi, A, Gupta, GN, Gustafson, D, Handberg, A, Haraszti, RA, Harrison, P, Hegyesi, H, Hendrix, A, Hill, AF, Hochberg, FH, Hoffmann, KF, Holder, B, Holthofer, H, Hosseinkhani, B, Hu, G, Huang, Y, Huber, V, Hunt, S, Ibrahim, AG-E, Ikezu, T, Inal, JM, Isin, M, Ivanova, A, Jackson, HK, Jacobsen, S, Jay, SM, Jayachandran, M, Jenster, G, Jiang, L, Johnson, SM, Jones, JC, Jong, A, Jovanovic-Talisman, T, Jung, S, Kalluri, R, Kano, S-I, Kaur, S, Kawamura, Y, Keller, ET, Khamari, D, Khomyakova, E, Khvorova, A, Kierulf, P, Kim, KP, Kislinger, T, Klingeborn, M, Klinke, DJ, Kornek, M, Kosanovic, MM, Kovacs, AF, Kraemer-Albers, E-M, Krasemann, S, Krause, M, Kurochkin, I, Kusuma, GD, Kuypers, S, Laitinen, S, Langevin, SM, Languino, LR, Lannigan, J, Lasser, C, Laurent, LC, Lavieu, G, Lazaro-Ibanez, E, Le Lay, S, Lee, M-S, Lee, YXF, Lemos, DS, Lenassi, M, Leszczynska, A, Li, ITS, Liao, K, Libregts, SF, Ligeti, E, Lim, R, Lim, SK, Line, A, Linnemannstoens, K, Llorente, A, Lombard, CA, Lorenowicz, MJ, Lorincz, AM, Lotvall, J, Lovett, J, Lowry, MC, Loyer, X, Lu, Q, Lukomska, B, Lunavat, TR, Maas, SLN, Malhi, H, Marcilla, A, Mariani, J, Mariscal, J, Martens-Uzunova, ES, Martin-Jaular, L, Martinez, MC, Martins, VR, Mathieu, M, Mathivanan, S, Maugeri, M, McGinnis, LK, McVey, MJ, Meckes, DG, Meehan, KL, Mertens, I, Minciacchi, VR, Moller, A, Jorgensen, MM, Morales-Kastresana, A, Morhayim, J, Mullier, F, Muraca, M, Musante, L, Mussack, V, Muth, DC, Myburgh, KH, Najrana, T, Nawaz, M, Nazarenko, I, Nejsum, P, Neri, C, Neri, T, Nieuwland, R, Nimrichter, L, Nolan, JP, Nolte-'t Hoen, ENM, Noren Hooten, N, O'Driscoll, L, O'Grady, T, O'Loghlen, A, Ochiya, T, Olivier, M, Ortiz, A, Ortiz, LA, Osteikoetxea, X, Ostegaard, O, Ostrowski, M, Park, J, Pegtel, DM, Peinado, H, Perut, F, Pfaffl, MW, Phinney, DG, Pieters, BCH, Pink, RC, Pisetsky, DS, von Strandmann, EP, Polakovicova, I, Poon, IKH, Powell, BH, Prada, I, Pulliam, L, Quesenberry, P, Radeghieri, A, Raffai, RL, Raimondo, S, Rak, J, Ramirez, M, Raposo, G, Rayyan, MS, Regev-Rudzki, N, Ricklefs, FL, Robbins, PD, Roberts, DD, Rodrigues, SC, Rohde, E, Rome, S, Rouschop, KMA, Rughetti, A, Russell, AE, Saa, P, Sahoo, S, Salas-Huenuleo, E, Sanchez, C, Saugstad, JA, Saul, MJ, Schiffelers, RM, Schneider, R, Schoyen, TH, Scott, A, Shahaj, E, Sharma, S, Shatnyeva, O, Shekari, F, Shelke, GV, Shetty, AK, Shiba, K, Siljander, PR-M, Silva, AM, Skowronek, A, Snyder, OL, Soares, RP, Sodar, BW, Soekmadji, C, Sotillo, J, Stahl, PD, Stoorvogel, W, Stott, SL, Strasser, EF, Swift, S, Tahara, H, Tewari, M, Timms, K, Tiwari, S, Tixeira, R, Tkach, M, Toh, WS, Tomasini, R, Torrecilhas, AC, Pablo Tosar, J, Toxavidis, V, Urbanelli, L, Vader, P, van Balkom, BWM, van der Grein, SG, Van Deun, J, van Herwijnen, MJC, Van Keuren-Jensen, K, van Niel, G, van Royen, ME, van Wijnen, AJ, Helena Vasconcelos, M, Vechetti, IJ, Veit, TD, Vella, LJ, Velot, E, Verweij, FJ, Vestad, B, Vinas, JL, Visnovitz, T, Vukman, KV, Wahlgren, J, Watson, DC, Wauben, MHM, Weaver, A, Webber, JP, Weber, V, Wehman, AM, Weiss, DJ, Welsh, JA, Wendt, S, Wheelock, AM, Wiener, Z, Witte, L, Wolfram, J, Xagorari, A, Xander, P, Xu, J, Yan, X, Yanez-Mo, M, Yin, H, Yuana, Y, Zappulli, V, Zarubova, J, Zekas, V, Zhang, J-Y, Zhao, Z, Zheng, L, Zheutlin, AR, Zickler, AM, Zimmermann, P, Zivkovic, AM, Zocco, D, and Zuba-Surma, EK
- Abstract
The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.
- Published
- 2018
3. Use of the stromal cell-derived factor-1/CXCR4 pathway in prostate cancer metastasis to bone
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Taichman, RS, Cooper, C, Keller, ET, Pienta, KJ, Taichman, NS, and McCauley, LK
- Abstract
Neoplasms have a striking tendency to metastasize or "home" to bone. Hematopoietic cells also home to bone during embryonic development, where evidence points to the chemokine stromal cell-derived factor-1 (SDF-1 or CXCL12; expressed by osteoblasts and endothelial cells) and its receptor (CXCR4) as key elements in these processes. We hypothesized that metastatic prostate carcinomas also use the SDF-1/CXCR4 pathway to localize to the bone. To test this, levels of CXCR4 expression were determined for several human prostate cancer cell lines by reverse transcription-PCR and Western blotting. Positive results were obtained for cell lines derived from malignancies that had spread to bone and marrow. Prostate cancer cells were also observed migrating across bone marrow endothelial cell monolayers in response to SDF-1. In in vitro adhesion assays, pretreatment of the prostate cancer cells with SDF-1 significantly increased their adhesion to osteosarcomas and endothelial cell lines in a dose-dependent manner. Invasion of the cancer cell lines through basement membranes was also supported by SDF-1 and inhibited by antibody to CXCR4. Collectively, these results suggest that prostate cancers and perhaps other neoplasms may use the SDF-1/CXCR4 pathway to spread to bone.
- Published
- 2016
4. Cultures of computation and quantification in the ancient world: An introduction (in dialogue with Agathe Keller and Christine Proust)
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Chemla, Karine, Sciences, Philosophie, Histoire (SPHERE (UMR_7219)), Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS), K. Chemla, A. Keller et C. Proust, and European Project: 269804,EC:FP7:ERC,ERC-2010-AdG_20100407,ERC Project SAW(2011)
- Subjects
[SHS.HISPHILSO]Humanities and Social Sciences/History, Philosophy and Sociology of Sciences ,history of mathematics in the ancient world ,mathematical cultures ,numbers ,practices ,arithmetical operations ,[SHS.HIST]Humanities and Social Sciences/History - Abstract
International audience; This introduction pleads for resuming research on the history of numbers and computation: topics in the history of mathematics that, to many, seem exhausted. One of the main reasons for revisiting these topics is the problematic division of the historiography of number into two branches: on the one hand, the history of the concept of number and, on the other, the history of numerical signs designed to express integers and the history of computations that relied on these inscriptions. Upon closer examination, this split — which has hitherto been unquestioned in the literature — looks untenable, and the book offers evidence showing the actual intertwinement between the history of the concept of number and that of numeration systems and computations. The book further aims at developing a contextualized approach to systems of numeration and computation, which the introduction discusses. To this end, the introduction argues why, in most social contexts of the ancient world, numbers cannot be discussed independently from measurement values, and it explains how the various authors of this book share the goal of identifying, in these social contexts, different ‘cultures of computation and quantification’. Thanks to this effort of contextualization, the book yields a better understanding of both the contexts of emergence and the diversity of uses of place-value numeration systems, which the introduction synthesizes.
- Published
- 2022
5. Inflammation-induced epigenetic imprinting regulates intestinal stem cells.
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Zhao D, Ravikumar V, Leach TJ, Kraushaar D, Lauder E, Li L, Sun Y, Oravecz-Wilson K, Keller ET, Chen F, Maneix L, Jenq RR, Britton R, King KY, Santibanez AE, Creighton CJ, Rao A, and Reddy P
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- Animals, Mice, Genomic Imprinting, Mice, Inbred C57BL, Graft vs Host Disease, Regeneration, Cell Differentiation, Receptors, G-Protein-Coupled metabolism, Receptors, G-Protein-Coupled genetics, Organoids metabolism, Inflammation pathology, Inflammation genetics, Epigenesis, Genetic, Stem Cells metabolism, Stem Cells cytology, Intestines cytology
- Abstract
It remains unknown whether and how intestinal stem cells (ISCs) adapt to inflammatory exposure and whether the adaptation leaves scars that will affect their subsequent regeneration. We investigated the consequences of inflammation on Lgr5
+ ISCs in well-defined clinically relevant models of acute gastrointestinal graft-versus-host disease (GI GVHD). Utilizing single-cell transcriptomics, as well as organoid, metabolic, epigenomic, and in vivo models, we found that Lgr5+ ISCs undergo metabolic changes that lead to the accumulation of succinate, which reprograms their epigenome. These changes reduced the ability of ISCs to differentiate and regenerate ex vivo in serial organoid cultures and also in vivo following serial transplantation. Furthermore, ISCs demonstrated a reduced capacity for in vivo regeneration despite resolution of the initial inflammatory exposure, demonstrating the persistence of the maladaptive impact induced by the inflammatory encounter. Thus, inflammation imprints the epigenome of ISCs in a manner that persists and affects their sensitivity to adapt to future stress or challenges., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 The Author(s). Published by Elsevier Inc. All rights reserved.)- Published
- 2024
- Full Text
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6. Differences in mutations across tumour sizes in clear-cell renal cell carcinoma.
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Monda SM, Carney BW, May AM, Gulati S, Salami SS, Chandrasekar T, Keller ET, Huebner NA, Palapattu GS, and Dall'Era MA
- Abstract
Objective: To assess the distribution of key mutations across tumour sizes in clear-cell renal cell carcinoma (ccRCC), and secondarily to examine the prognostic impact of aggressive mutations in smaller ccRCCs., Patient and Methods: The distribution of mutations (VHL, PBRM1, SETD2, BAP1 and CDKN2A loss) across tumour sizes was assessed in 1039 ccRCCs treated with nephrectomy in cohorts obtained from the Tracking Cancer Evolution (TRACERx), The Cancer Genome Atlas (TCGA) and the Cancer Genomics of the Kidney (CAGEKID) projects. Logistic regression was used to model the presence of each mutation against size. In our secondary analysis, we assessed a subset of ccRCCs ≤7 cm for associations of key aggressive mutations (SETD2, BAP1, and CDKN2A loss) with metastasis, invasive disease and overall survival, while controlling for size. A subset of localised tumours ≤7 cm was also used to assess associations with recurrence after nephrectomy., Results: On logistic regression, each 1-cm increase in tumour size was associated with aggressive mutations, SETD2, BAP1, and CDKN2A loss, at odds ratios (ORs) of 1.09, 1.10 and 1.19 (P < 0.001), whereas no significant association was observed between tumour size and PBRM1 (OR 1.02; P = 0.23). VHL was mildly negatively associated with a 1-cm increase in size (OR 0.95; P = 0.01). Among tumours ≤7 cm, SETD2 and CDKN2A loss were associated with metastatic disease at ORs of 3.86 and 3.84 (P < 0.05) while controlling for tumour size. CDKN2A loss was associated with worse overall survival, with a hazard ratio (HR) of 2.19 (P = 0.03). Among localised tumours ≤7 cm, SETD2 was associated with worse recurrence-free survival (HR 2.00; P = 0.03)., Conclusion: Large and small ccRCCs are genomically different. Aggressive mutations, namely, SETD2, BAP1, and CDKN2A loss, are rarely observed in small ccRCCs and are observed more frequently in larger tumours. However, when present in tumours ≤7 cm, SETD2 mutations and CDKN2A loss were still independently associated with invasive disease, metastasis, worse survival, and recurrence after resection, after controlling for size., (© 2024 The Author(s). BJU International published by John Wiley & Sons Ltd on behalf of BJU International.)
- Published
- 2024
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7. Urinary extracellular vesicle-derived miR-126-3p predicts lymph node invasion in patients with high-risk prostate cancer.
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Dong L, Hu C, Ma Z, Huang Y, Shelley G, Kuczler MD, Kim CJ, Witwer KW, Keller ET, Amend SR, Xue W, and Pienta KJ
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- Humans, Male, Aged, Middle Aged, Prostatic Hyperplasia genetics, Prostatic Hyperplasia pathology, Prostatic Hyperplasia urine, Lymph Nodes pathology, Prostatectomy, Prospective Studies, MicroRNAs urine, MicroRNAs genetics, Prostatic Neoplasms genetics, Prostatic Neoplasms pathology, Prostatic Neoplasms urine, Extracellular Vesicles genetics, Extracellular Vesicles metabolism, Lymphatic Metastasis genetics, Lymphatic Metastasis pathology, Biomarkers, Tumor genetics, Biomarkers, Tumor urine
- Abstract
To investigate extracellular vesicles (EVs), biomarkers for predicting lymph node invasion (LNI) in patients with high-risk prostate cancer (HRPCa), plasma, and/or urine samples were prospectively collected from 45 patients with prostate cancer (PCa) and five with benign prostatic hyperplasia (BPH). Small RNA sequencing was performed to identify miRNAs in the EVs. All patients with PCa underwent radical prostatectomy and extended pelvic lymph node dissection. Differentially expressed miRNAs were identified in patients with and without pathologically-verified LNI. The candidate miRNAs were validated in low-risk prostate cancer (LRPCa) and BPH. Four miRNA species (e.g., miR-126-3p) and three miRNA species (e.g., miR-27a-3p) were more abundant in urinary and plasma EVs, respectively, of patients with PCa. None of these miRNA species were shared between urinary and plasma EVs. miR-126-3p was significantly more abundant in patients with HR PCa with LNI than in those without (P = 0.018). miR-126-3p was significantly more abundant in the urinary EVs of patients with HRPCa than in those with LRPCa (P = 0.017) and BPH (P = 0.011). In conclusion, urinary EVs-derived miR-126-3p may serve as a good biomarker for predicting LNI in patients with HRPCa., (© 2024. The Author(s).)
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- 2024
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8. Dysregulated Ribosome Biogenesis Is a Targetable Vulnerability in Triple-Negative Breast Cancer: MRPS27 as a Key Mediator of the Stemness-inhibitory Effect of Lovastatin.
- Author
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Zheng C, Yao H, Lu L, Li H, Zhou L, He X, Xu X, Xia H, Ding S, Yang Y, Wang X, Wu M, Xue L, Chen S, Peng X, Cheng Z, Wang Y, He G, Fu S, Keller ET, Liu S, Jiang YZ, and Deng X
- Subjects
- Humans, Lovastatin pharmacology, Lovastatin therapeutic use, Ribosomal Proteins genetics, Nuclear Proteins, Ribosomes genetics, Mitochondrial Proteins, Triple Negative Breast Neoplasms drug therapy, Triple Negative Breast Neoplasms genetics
- Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer with limited effective therapeutic options readily available. We have previously demonstrated that lovastatin, an FDA-approved lipid-lowering drug, selectively inhibits the stemness properties of TNBC. However, the intracellular targets of lovastatin in TNBC remain largely unknown. Here, we unexpectedly uncovered ribosome biogenesis as the predominant pathway targeted by lovastatin in TNBC. Lovastatin induced the translocation of ribosome biogenesis-related proteins including nucleophosmin (NPM), nucleolar and coiled-body phosphoprotein 1 (NOLC1), and the ribosomal protein RPL3. Lovastatin also suppressed the transcript levels of rRNAs and increased the nuclear protein level and transcriptional activity of p53, a master mediator of nucleolar stress. A prognostic model generated from 10 ribosome biogenesis-related genes showed outstanding performance in predicting the survival of TNBC patients. Mitochondrial ribosomal protein S27 (MRPS27), the top-ranked risky model gene, was highly expressed and correlated with tumor stage and lymph node involvement in TNBC. Mechanistically, MRPS27 knockdown inhibited the stemness properties and the malignant phenotypes of TNBC. Overexpression of MRPS27 attenuated the stemness-inhibitory effect of lovastatin in TNBC cells. Our findings reveal that dysregulated ribosome biogenesis is a targetable vulnerability and targeting MRPS27 could be a novel therapeutic strategy for TNBC patients., Competing Interests: Competing Interests: The authors have declared that no competing interest exists., (© The author(s).)
- Published
- 2024
- Full Text
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9. A CXCR4 inhibitor (balixafortide) enhances docetaxel-mediated antitumor activity in a murine model of prostate cancer bone metastasis.
- Author
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Robinson T, Escara-Wilke J, Dai J, Zimmermann J, and Keller ET
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- Humans, Male, Animals, Mice, Docetaxel pharmacology, Docetaxel therapeutic use, Caspase 3, Disease Models, Animal, Interleukin-2, Ki-67 Antigen, Tartrate-Resistant Acid Phosphatase, Cell Line, Tumor, Receptors, CXCR4, Prostatic Neoplasms pathology, Bone Neoplasms drug therapy, Bone Neoplasms secondary
- Abstract
Background: Prostate cancer (PCa) bone metastases have been shown to be more resistant to docetaxel than soft tissue metastases. The proinflammatory chemokine receptor CXCR4 has been shown to confer resistance to docetaxel (DOC) in PCa cells. Balixafortide (BLX) is a protein epitope mimetic inhibitor of CXCR4. Accordingly, we hypothesized that BLX would enhance DOC-mediated antitumor activity in PCa bone metastases., Methods: PC-3 luciferase-labeled cells were injected into the tibia of mice to model bone metastases. Four treatment groups were created: vehicle, DOC (5 mg/kg), BLX (20 mg/kg), and combo (receiving both DOC and BLX). Mice were injected twice daily subcutaneously with either vehicle or BLX starting on Day 1 and weekly intraperitoneally with DOC starting on Day 1. Tumor burden was measured weekly via bioluminescent imaging. At end of study (29 days), radiographs were taken of the tibiae and blood was collected. Serum levels of TRAcP, IL-2, and IFNγ levels were measured using ELISA. Harvested tibiae were decalcified and stained for Ki67, cleaved caspase-3, and CD34 positive cells or microvessels were quantified., Results: Tumor burden was lower in the combo group compared to the DOC alone group. Treatment with the combination had no impact on the number of mice with osteolytic lesions, however the area of osteolytic lesions was lower in the combo group compared to the vehicle and BLX groups, but not the DOC group. Serum TRAcP levels were lower in the combo compared to vehicle group, but not the other groups. No significant difference in Ki67 staining was found among the groups; whereas, cleaved caspase-3 staining was lowest in the Combo group and highest in the BLX group. The DOC and combo groups had more CD34+ microvessels than the control and BLX groups. There was no difference between the treatment groups for IL-2, but the combo group had increased levels of IFNγ compared to the DOC group., Conclusions: Our data demonstrate that a combination of BAL and DOC has greater antitumor activity in a model of PCa bone metastases than either drug alone. These data support further evaluation of this combination in metastatic PCa., (© 2023 The Authors. The Prostate published by Wiley Periodicals LLC.)
- Published
- 2023
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10. A Zeb1/MtCK1 metabolic axis controls osteoclast activation and skeletal remodeling.
- Author
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Zhu L, Tang Y, Li XY, Kerk SA, Lyssiotis CA, Feng W, Sun X, Hespe GE, Wang Z, Stemmler MP, Brabletz S, Brabletz T, Keller ET, Ma J, Cho JS, Yang J, and Weiss SJ
- Subjects
- Mice, Animals, Humans, Creatine Kinase, Mitochondrial Form metabolism, Bone and Bones, Cell Differentiation, Zinc Finger E-box-Binding Homeobox 1 genetics, Zinc Finger E-box-Binding Homeobox 1 metabolism, Osteoclasts metabolism, Bone Resorption genetics, Bone Resorption metabolism
- Abstract
Osteoclasts are bone-resorbing polykaryons responsible for skeletal remodeling during health and disease. Coincident with their differentiation from myeloid precursors, osteoclasts undergo extensive transcriptional and metabolic reprogramming in order to acquire the cellular machinery necessary to demineralize bone and digest its interwoven extracellular matrix. While attempting to identify new regulatory molecules critical to bone resorption, we discovered that murine and human osteoclast differentiation is accompanied by the expression of Zeb1, a zinc-finger transcriptional repressor whose role in normal development is most frequently linked to the control of epithelial-mesenchymal programs. However, following targeting, we find that Zeb1 serves as an unexpected regulator of osteoclast energy metabolism. In vivo, Zeb1-null osteoclasts assume a hyperactivated state, markedly decreasing bone density due to excessive resorptive activity. Mechanistically, Zeb1 acts in a rheostat-like fashion to modulate murine and human osteoclast activity by transcriptionally repressing an ATP-buffering enzyme, mitochondrial creatine kinase 1 (MtCK1), thereby controlling the phosphocreatine energy shuttle and mitochondrial respiration. Together, these studies identify a novel Zeb1/MtCK1 axis that exerts metabolic control over bone resorption in vitro and in vivo., (© 2023 The Authors. Published under the terms of the CC BY NC ND 4.0 license.)
- Published
- 2023
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11. The Role of Tumor Epithelial-Mesenchymal Transition and Macrophage Crosstalk in Cancer Progression.
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May AM, Batoon L, McCauley LK, and Keller ET
- Subjects
- Humans, Cell Movement, Macrophages, Tumor Microenvironment, Epithelial-Mesenchymal Transition, Neoplasms pathology
- Abstract
Purpose of Review: The purpose of this review is to summarize the recently published findings regarding the role of epithelial to mesenchymal transition (EMT) in tumor progression, macrophages in the tumor microenvironment, and crosstalk that exists between tumor cells and macrophages., Recent Findings: EMT is a crucial process in tumor progression. In association with EMT changes, macrophage infiltration of tumors occurs frequently. A large body of evidence demonstrates that various mechanisms of crosstalk exist between macrophages and tumor cells that have undergone EMT resulting in a vicious cycle that promotes tumor invasion and metastasis. Tumor-associated macrophages and tumor cells undergoing EMT provide reciprocal crosstalk which leads to tumor progression. These interactions provide potential targets to exploit for therapy., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2023
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12. Virtual teaching kitchen classes and cardiovascular disease prevention counselling among medical trainees.
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Razavi AC, Latoff A, Dyer A, Albin JL, Artz K, Babcock A, Cimino F, Daghigh F, Dollinger B, Fiellin M, Johnston EA, Jones GM, Karch RD, Keller ET, Nace H, Parekh NK, Petrosky SN, Robinson A, Rosen J, Sheridan EM, Warner SW, Willis JL, and Harlan TS
- Abstract
Background: Hands-on culinary medicine education for medical trainees has emerged as a promising tool for cardiovascular health promotion., Purpose: To determine whether virtual culinary medicine programming associates with Mediterranean diet (MedDiet) adherence and lifestyle medicine competencies among medical trainees across the USA., Method: A total of 1433 medical trainees across 19 sites over a 12-month period were included. The Cooking for Health Optimisation with Patients-Medical Trainees survey composed of 61 questions regarding demographics, nutritional attitudes, dietary habits including MedDiet score and lifestyle medicine counselling competencies. Multivariable logistic regression assessed the association of virtual culinary medicine education with MedDiet intake and nutritional attitudes., Results: There were 519 medical trainees who participated in virtual culinary medicine education and 914 medical trainees who participated in their standard nutrition curricula. More than one-half of participants were women (n=759) and the mean age was 27 years old. Compared with students enrolled in traditional nutrition curricula, participants in virtual culinary medicine education were 37% more likely to adhere to MedDiet guidelines for fruit intake (OR 1.37, 95% CI 1.03 to 1.83, p=0.03). Virtual culinary medicine education was associated with higher proficiency in lifestyle medicine counselling categories, notably recommendations involving fibre (OR 4.03; 95% CI 3.05 to 5.34), type 2 diabetes prevention (OR 4.69; 95% CI 3.51 to 6.27) and omega fatty acids (OR 5.21; 95% CI 3.87 to 7.02). Virtual culinary medicine education had a similar, although higher magnitude association with MedDiet counselling competency (OR 5.73, 95% CI 4.26 to 7.70) when compared with historical data previously reported using hands-on, in-person culinary medicine courseware (OR 4.97, 95% CI 3.89 to 6.36)., Conclusions: Compared with traditional nutritional educational curricula, virtual culinary medicine education is associated with higher MedDiet adherence and lifestyle medicine counselling competencies among medical trainees. Both virtual and hands-on culinary medicine education may be useful for cardiovascular health promotion., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2023. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2023
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13. Integration of Single-Cell RNA-Sequencing and Network Analysis to Investigate Mechanisms of Drug Resistance.
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The S, Schnepp PM, Shelley G, Keller JM, Rao A, and Keller ET
- Subjects
- Single-Cell Analysis methods, Sequence Analysis, RNA methods, Gene Expression Profiling methods, RNA
- Abstract
Innate resistance and therapeutic-driven development of resistance to anticancer drugs is a common complication of cancer therapy. Understanding mechanisms of drug resistance can lead to development of alternative therapies. One strategy is to subject drug-sensitive and drug-resistant variants to single-cell RNA-seq (scRNA-seq) and to subject the scRNA-seq data to network analysis to identify pathways associated with drug resistance. This protocol describes a computational analysis pipeline to study drug resistance by subjecting scRNA-seq expression data to Passing Attributes between Networks for Data Assimilation (PANDA), an integrative network analysis tool that incorporates protein-protein interactions (PPI) and transcription factor (TF)-binding motifs., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
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- 2023
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14. Bone Marrow Macrophages Induce Inflammation by Efferocytosis of Apoptotic Prostate Cancer Cells via HIF-1α Stabilization.
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Mendoza-Reinoso V, Schnepp PM, Baek DY, Rubin JR, Schipani E, Keller ET, McCauley LK, and Roca H
- Subjects
- Male, Humans, Macrophages metabolism, Phagocytosis, Cytokines metabolism, Inflammation pathology, Hypoxia metabolism, Tumor Microenvironment, Bone Marrow metabolism, Prostatic Neoplasms pathology
- Abstract
The clearance of apoptotic cancer cells by macrophages, known as efferocytosis, fuels the bone-metastatic growth of prostate cancer cells via pro-inflammatory and immunosuppressive processes. However, the exact molecular mechanisms remain unclear. In this study, single-cell transcriptomics of bone marrow (BM) macrophages undergoing efferocytosis of apoptotic prostate cancer cells revealed a significant enrichment in their cellular response to hypoxia. Here, we show that BM macrophage efferocytosis increased hypoxia inducible factor-1alpha (HIF-1α) and STAT3 phosphorylation (p-STAT3 at Tyr705) under normoxic conditions, while inhibitors of p-STAT3 reduced HIF-1α. Efferocytosis promoted HIF-1α stabilization, reduced its ubiquitination, and induced HIF-1α and p-STAT3 nuclear translocation. HIF-1α stabilization in efferocytic BM macrophages resulted in enhanced expression of pro-inflammatory cytokine MIF, whereas BM macrophages with inactive HIF-1α reduced MIF expression upon efferocytosis. Stabilization of HIF-1α using the HIF-prolyl-hydroxylase inhibitor, Roxadustat, enhanced MIF expression in BM macrophages. Furthermore, BM macrophages treated with recombinant MIF protein activated NF-κB (p65) signaling and increased the expression of pro-inflammatory cytokines. Altogether, these findings suggest that the clearance of apoptotic cancer cells by BM macrophages triggers p-STAT3/HIF-1α/MIF signaling to promote further inflammation in the bone tumor microenvironment where a significant number of apoptotic cancer cells are present.
- Published
- 2022
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15. RhoB affects colitis through modulating cell signaling and intestinal microbiome.
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Yang J, Pei G, Sun X, Xiao Y, Miao C, Zhou L, Wang B, Yang L, Yu M, Zhang ZS, Keller ET, Yao Z, and Wang Q
- Subjects
- Animals, Biomarkers, Dextran Sulfate, Humans, Mice, Signal Transduction, p38 Mitogen-Activated Protein Kinases metabolism, Colitis chemically induced, Colitis pathology, Colitis, Ulcerative metabolism, Colitis, Ulcerative microbiology, Colitis, Ulcerative pathology, Gastrointestinal Microbiome, rhoB GTP-Binding Protein metabolism
- Abstract
Background: The pathogenesis of inflammatory bowel diseases (IBD) is multifactorial, and diagnostic and treatment strategies for IBD remain to be developed. RhoB regulates multiple cell functions; however, its role in colitis is unexplored., Results: Here, we found RhoB was dramatically increased in colon tissues of ulcerative colitis (UC) patients and mice with DSS-induced colitis. Compared with wild type mice, RhoB
+/- and RhoB-/- mice developed milder DSS-induced colitis and increased goblet cell numbers and IEC proliferation. Decreased RhoB promoted goblet cell differentiation and epithelial regeneration through inhibiting Wnt signaling pathway and activating p38 MAPK signaling pathway. Moreover, increased SCFA-producing bacteria and SCFA concentrations were detected in intestinal microbiome of both RhoB+/- and RhoB-/- mice and upregulated SCFA receptor expression was also observed., Conclusions: Taken together, a higher level of RhoB is associated with UC, which also contributes to UC development through modulating cell signaling and altering intestinal bacterial composition and metabolites. These observations suggest that RhoB has potential as a biomarker and a treatment target for UC. Video Abstract., (© 2022. The Author(s).)- Published
- 2022
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16. Enterobacter ludwigii protects DSS-induced colitis through choline-mediated immune tolerance.
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Li Q, Sun X, Yu K, Lv J, Miao C, Yang J, Wang S, Fu Z, Sun Y, Zhang H, Zhang ZS, Keller ET, Yao Z, and Wang Q
- Subjects
- Animals, Dendritic Cells metabolism, Dextran Sulfate toxicity, Disease Models, Animal, Enterobacter, Immune Tolerance, Mice, Mice, Inbred C57BL, T-Lymphocytes, Regulatory, Choline metabolism, Colitis
- Abstract
Commensal intestinal bacteria play key roles in regulating host immune tolerance; however, bacterial strains and related metabolites directly involved in this regulation are largely unknown. Here, using a mouse model of dextran sulfate sodium (DSS)-induced colitis combined with different antibiotic treatment, Enterobacter ludwigii, abundant in microbiota of mice treated with metronidazole, is screened out to have prophylactic and therapeutic effects on DSS-induced colitis with or without the presence of complex intestinal bacteria. E. ludwigii is found to induce CD103
+ DC and regulatory T (Treg)-mediated immune tolerance for colitis remission using in vitro and in vivo experiments. Moreover, choline, one metabolite of E. ludwigii, is identified to increase dendritic cells' (DCs) immune tolerance to promote Treg differentiation. E. ludwigii is found to induce DCs' immune tolerance ability for Treg differentiation through choline and α7nAChR-mediated retinoic acid (RA) and transforming growth factor beta (TGF-β) upregulation, resulting in protecting mice against DSS-induced colitis. This study suggests potential therapeutic approaches for inflammatory bowel diseases (IBDs)., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)- Published
- 2022
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17. Integrated Workflow for the Label-Free Isolation and Genomic Analysis of Single Circulating Tumor Cells in Pancreatic Cancer.
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Rupp B, Owen S, Ball H, Smith KJ, Gunchick V, Keller ET, Sahai V, and Nagrath S
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- Biomarkers, Tumor, DNA Copy Number Variations, Genomics, Humans, Workflow, Neoplastic Cells, Circulating pathology, Pancreatic Neoplasms genetics
- Abstract
As pancreatic cancer is the third deadliest cancer in the U.S., the ability to study genetic alterations is necessary to provide further insight into potentially targetable regions for cancer treatment. Circulating tumor cells (CTCs) represent an especially aggressive subset of cancer cells, capable of causing metastasis and progressing the disease. Here, we present the Labyrinth-DEPArray pipeline for the isolation and analysis of single CTCs. Established cell lines, patient-derived CTC cell lines and freshly isolated CTCs were recovered and sequenced to reveal single-cell copy number variations (CNVs). The resulting CNV profiles of established cell lines showed concordance with previously reported data and highlight several gains and losses of cancer-related genes such as FGFR3 and GNAS. The novel sequencing of patient-derived CTC cell lines showed gains in chromosome 8q, 10q and 17q across both CTC cell lines. The pipeline was used to process and isolate single cells from a metastatic pancreatic cancer patient revealing a gain of chromosome 1q and a loss of chromosome 5q. Overall, the Labyrinth-DEPArray pipeline offers a validated workflow combining the benefits of antigen-free CTC isolation with single cell genomic analysis.
- Published
- 2022
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18. Differential immune landscapes in appendicular versus axial skeleton.
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Ahmed AA, Strong MJ, Zhou X, Robinson T, Rocco S, Siegel GW, Clines GA, Moore BB, Keller ET, and Szerlip NJ
- Subjects
- Animals, Bone Marrow, Humans, Male, Mice, Mice, Inbred C57BL, Spine, Tumor Microenvironment, Bone Neoplasms secondary, Bone and Bones
- Abstract
Roughly 400,000 people in the U.S. are living with bone metastases, the vast majority occurring in the spine. Metastases to the spine result in fractures, pain, paralysis, and significant health care costs. This predilection for cancer to metastasize to the bone is seen across most cancer histologies, with the greatest incidence seen in prostate, breast, and lung cancer. The molecular process involved in this predilection for axial versus appendicular skeleton is not fully understood, although it is likely that a combination of tumor and local micro-environmental factors plays a role. Immune cells are an important constituent of the bone marrow microenvironment and many of these cells have been shown to play a significant role in tumor growth and progression in soft tissue and bone disease. With this in mind, we sought to examine the differences in immune landscape between axial and appendicular bones in the normal noncancerous setting in order to obtain an understanding of these landscapes. To accomplish this, we utilized mass cytometry by time-of-flight (CyTOF) to examine differences in the immune cell landscapes between the long bone and vertebral body bone marrow from patient clinical samples and C57BL/6J mice. We demonstrate significant differences between immune populations in both murine and human marrow with a predominance of myeloid progenitor cells in the spine. Additionally, cytokine analysis revealed differences in concentrations favoring a more myeloid enriched population of cells in the vertebral body bone marrow. These differences could have clinical implications with respect to the distribution and permissive growth of bone metastases., Competing Interests: The authors have declared that no competing interests exist.
- Published
- 2022
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19. A Bioreactor for 3D In Vitro Modeling of the Mechanical Stimulation of Osteocytes.
- Author
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Aw Yong KM, Horst E, Neale D, Royzenblat S, Lahann J, Greineder C, Weivoda M, Mehta G, and Keller ET
- Abstract
The bone is a mechanosensitive organ that is also a common metastatic site for prostate cancer. However, the mechanism by which the tumor interacts with the bone microenvironment to further promote disease progression remains to be fully understood. This is largely due to a lack of physiological yet user-friendly models that limit our ability to perform in-depth mechanistic studies. Here, we report a tunable bioreactor which facilitates the 3D culture of the osteocyte cell line, MLO-Y4, in a hydroxyapatite/tricalcium phosphate (HA/TCP) scaffold under constant fluidic shear stress and tunable hydrostatic pressure within physiological parameters. Increasing hydrostatic pressure was sufficient to induce a change in the expression of several bone remodeling genes such as Dmp1, Rankl, and Runx2. Furthermore, increased hydrostatic pressure induced the osteocytes to promote the differentiation of the murine macrophage cell line RAW264.7 toward osteoclast-like cells. These results demonstrate that the bioreactor recapitulates the mechanotransduction response of osteocytes to pressure including the measurement of their functional ability in a 3D environment. In conclusion, the bioreactor would be useful for exploring the mechanisms of osteocytes in bone health and disease., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Aw Yong, Horst, Neale, Royzenblat, Lahann, Greineder, Weivoda, Mehta and Keller.)
- Published
- 2022
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20. Pheno-SELEX: Engineering Anti-Metastatic Aptamers through Targeting the Invasive Phenotype Using Systemic Evolution of Ligands by Exponential Enrichment.
- Author
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Shelley G, Dai J, Keller JM, and Keller ET
- Abstract
Multiple methods (e.g., small molecules and antibodies) have been engineered to target specific proteins and signaling pathways in cancer. However, many mediators of the cancer phenotype are unknown and the ability to target these phenotypes would help mitigate cancer. Aptamers are small DNA or RNA molecules that are designed for therapeutic use. The design of aptamers to target cancers can be challenging. Accordingly, to engineer functionally anti-metastatic aptamers we used a modification of systemic evolution of ligands by exponential enrichment (SELEX) we call Pheno-SELEX to target a known phenotype of cancer metastasis, i.e., invasion. A highly invasive prostate cancer (PCa) cell line was established and used to identify aptamers that bound to it with high affinity as opposed to a less invasive variant to the cell line. The anti-invasive aptamer (AIA1) was found to inhibit in vitro invasion of the original highly invasive PCa cell line, as well as an additional PCa cell line and an osteosarcoma cell line. AIA1 also inhibited in vivo development of metastasis in both a PCa and osteosarcoma model of metastasis. These results indicate that Pheno-SELEX can be successfully used to identify aptamers without knowledge of underlying molecular targets. This study establishes a new paradigm for the identification of functional aptamers.
- Published
- 2021
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21. Transcription factor network analysis based on single cell RNA-seq identifies that Trichostatin-a reverses docetaxel resistance in prostate Cancer.
- Author
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Schnepp PM, Ahmed A, Escara-Wilke J, Dai J, Shelley G, Keller J, Mizokami A, and Keller ET
- Subjects
- Animals, Antineoplastic Agents adverse effects, Antineoplastic Agents pharmacology, Cell Line, Tumor, Humans, Male, Mice, Protein Interaction Maps drug effects, RNA-Seq, Single-Cell Analysis, Docetaxel adverse effects, Drug Resistance, Neoplasm drug effects, Hydroxamic Acids pharmacology, Prostatic Neoplasms genetics, Prostatic Neoplasms metabolism, Transcription Factors genetics, Transcription Factors metabolism
- Abstract
Background: Overcoming drug resistance is critical for increasing the survival rate of prostate cancer (PCa). Docetaxel is the first cytotoxic chemotherapeutical approved for treatment of PCa. However, 99% of PCa patients will develop resistance to docetaxel within 3 years. Understanding how resistance arises is important to increasing PCa survival., Methods: In this study, we modeled docetaxel resistance using two PCa cell lines: DU145 and PC3. Using the Passing Attributes between Networks for Data Assimilation (PANDA) method to model transcription factor (TF) activity networks in both sensitive and resistant variants of the two cell lines. We identified edges and nodes shared by both PCa cell lines that composed a shared TF network that modeled changes which occur during acquisition of docetaxel resistance in PCa. We subjected the shared TF network to connectivity map analysis (CMAP) to identify potential drugs that could disrupt the resistant networks. We validated the candidate drug in combination with docetaxel to treat docetaxel-resistant PCa in both in vitro and in vivo models., Results: In the final shared TF network, 10 TF nodes were identified as the main nodes for the development of docetaxel resistance. CMAP analysis of the shared TF network identified trichostatin A (TSA) as a candidate adjuvant to reverse docetaxel resistance. In cell lines, the addition of TSA to docetaxel enhanced cytotoxicity of docetaxel resistant PCa cells with an associated reduction of the IC50 of docetaxel on the resistant cells. In the PCa mouse model, combination of TSA and docetaxel reduced tumor growth and final weight greater than either drug alone or vehicle., Conclusions: We identified a shared TF activity network that drives docetaxel resistance in PCa. We also demonstrated a novel combination therapy to overcome this resistance. This study highlights the usage of novel application of single cell RNA-sequencing and subsequent network analyses that can reveal novel insights which have the potential to improve clinical outcomes., (© 2021. The Author(s).)
- Published
- 2021
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22. Author Correction: Litchi seed extracts diminish prostate cancer progression via induction of apoptosis and attenuation of EMT through Akt/GSK-3β signaling.
- Author
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Guo H, Luo H, Yuan H, Xia Y, Shu P, Huang X, Lu Y, Liu X, Keller ET, Sun D, Deng J, and Zhang J
- Published
- 2021
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23. Extracellular Vesicles and Bone-Associated Cancer.
- Author
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Dai J, Shupp AB, Bussard KM, and Keller ET
- Subjects
- Bone Neoplasms drug therapy, Cell Communication, Disease Progression, Humans, Signal Transduction physiology, Tumor Microenvironment physiology, Bone Neoplasms pathology, Extracellular Vesicles physiology
- Abstract
Purpose of Review: In this review, we describe the biology of extracellular vesicles (EV) and how they contribute to bone-associated cancers., Recent Findings: Crosstalk between tumor and bone has been demonstrated to promote tumor and metastatic progression. In addition to direct cell-to-cell contact and soluble factors, such as cytokines, EVs mediate crosstalk between tumor and bone. EVs are composed of a heterogenous group of membrane-delineated vesicles of varying size range, mechanisms of formation, and content. These include apoptotic bodies, microvesicles, large oncosomes, and exosomes. EVs derived from primary tumors have been shown to alter bone remodeling and create formation of a pre-metastatic niche that favors development of bone metastasis. Similarly, EVs from marrow stromal cells have been shown to promote tumor progression. Additionally, EVs can act as therapeutic delivery vehicles due to their low immunogenicity and targeting specificity. EVs play critical roles in intercellular communication. Multiple classes of EVs exist based on size on mechanism of formation. In addition to a role in pathophysiology, EVs can be exploited as therapeutic delivery vehicles., (© 2021. The Author(s), under exclusive licence to Springer Science+Business Media, LLC part of Springer Nature.)
- Published
- 2021
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24. An infection-induced RhoB-Beclin 1-Hsp90 complex enhances clearance of uropathogenic Escherichia coli.
- Author
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Miao C, Yu M, Pei G, Ma Z, Zhang L, Yang J, Lv J, Zhang ZS, Keller ET, Yao Z, and Wang Q
- Subjects
- Animals, Autophagosomes genetics, Autophagosomes ultrastructure, Beclin-1 genetics, Cell Line, Epithelium metabolism, Epithelium microbiology, Escherichia coli Infections genetics, Escherichia coli Infections microbiology, Female, Gene Knockdown Techniques, HSP90 Heat-Shock Proteins genetics, Humans, Mice, Mice, Inbred C57BL, Mice, Knockout, Microscopy, Electron, Transmission, Microtubule-Associated Proteins metabolism, Protein Binding, Protein Stability, RNA, Small Interfering, Recombinant Proteins, Urinary Bladder metabolism, Urinary Bladder microbiology, Urinary Tract Infections genetics, Urinary Tract Infections microbiology, Uropathogenic Escherichia coli pathogenicity, rhoB GTP-Binding Protein genetics, Autophagosomes metabolism, Beclin-1 metabolism, Escherichia coli Infections metabolism, HSP90 Heat-Shock Proteins metabolism, Urinary Tract Infections metabolism, Uropathogenic Escherichia coli growth & development, rhoB GTP-Binding Protein metabolism
- Abstract
Host cells use several anti-bacterial pathways to defend against pathogens. Here, using a uropathogenic Escherichia coli (UPEC) infection model, we demonstrate that bacterial infection upregulates RhoB, which subsequently promotes intracellular bacteria clearance by inducing LC3 lipidation and autophagosome formation. RhoB binds with Beclin 1 through its residues at 118 to 140 and the Beclin 1 CCD domain, with RhoB Arg133 being the key binding residue. Binding of RhoB to Beclin 1 enhances the Hsp90-Beclin 1 interaction, preventing Beclin 1 degradation. RhoB also directly interacts with Hsp90, maintaining RhoB levels. UPEC infections increase RhoB, Beclin 1 and LC3 levels in bladder epithelium in vivo, whereas Beclin 1 and LC3 levels as well as UPEC clearance are substantially reduced in RhoB
+/- and RhoB-/- mice upon infection. We conclude that when stimulated by UPEC infections, host cells promote UPEC clearance through the RhoB-Beclin 1-HSP90 complex, indicating RhoB may be a useful target when developing UPEC treatment strategies.- Published
- 2021
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25. IgV somatic mutation of human anti-SARS-CoV-2 monoclonal antibodies governs neutralization and breadth of reactivity.
- Author
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de Mattos Barbosa MG, Liu H, Huynh D, Shelley G, Keller ET, Emmer BT, Sherman E, Ginsburg D, Kennedy AA, Tai AW, Wobus C, Mirabeli C, Lanigan TM, Samaniego M, Meng W, Rosenfeld AM, Prak ETL, Platt JL, and Cascalho M
- Subjects
- Adult, Aged, Antibodies, Monoclonal genetics, Antibodies, Monoclonal immunology, Antibody Specificity, B-Lymphocytes immunology, Broadly Neutralizing Antibodies genetics, COVID-19 therapy, COVID-19 virology, Humans, Immunoglobulin Heavy Chains genetics, Immunoglobulin Variable Region genetics, Immunologic Memory, Middle Aged, Neutralization Tests, Pandemics, SARS-CoV-2 genetics, Somatic Hypermutation, Immunoglobulin, Spike Glycoprotein, Coronavirus genetics, Spike Glycoprotein, Coronavirus immunology, Antibodies, Neutralizing genetics, Antibodies, Viral genetics, COVID-19 immunology, SARS-CoV-2 immunology
- Abstract
Abs that neutralize SARS-CoV-2 are thought to provide the most immediate and effective treatment for those severely afflicted by this virus. Because coronavirus potentially diversifies by mutation, broadly neutralizing Abs are especially sought. Here, we report a possibly novel approach to rapid generation of potent broadly neutralizing human anti-SARS-CoV-2 Abs. We isolated SARS-CoV-2 spike protein-specific memory B cells by panning from the blood of convalescent subjects after infection with SARS-CoV-2 and sequenced and expressed Ig genes from individual B cells as human mAbs. All of 43 human mAbs generated in this way neutralized SARS-CoV-2. Eighteen of the forty-three human mAbs exhibited half-maximal inhibitory concentrations (IC50) of 6.7 × 10-12 M to 6.7 × 10-15 M for spike-pseudotyped virus. Seven of the human mAbs also neutralized (with IC50 < 6.7 × 10-12 M) viruses pseudotyped with mutant spike proteins (including receptor-binding domain mutants and the S1 C-terminal D614G mutant). Neutralization of the Wuhan Hu-1 founder strain and of some variants decreased when coding sequences were reverted to germline, suggesting that potency of neutralization was acquired by somatic hypermutation and selection of B cells. These results indicate that infection with SARS-CoV-2 evokes high-affinity B cell responses, some products of which are broadly neutralizing and others highly strain specific. We also identify variants that would potentially resist immunity evoked by infection with the Wuhan Hu-1 founder strain or by vaccines developed with products of that strain, suggesting evolutionary courses that SARS-CoV-2 could take.
- Published
- 2021
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26. Effects of Analgesics on Tumor Growth in Mouse Models of Prostate Cancer Bone Metastasis.
- Author
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Xu JJ, Thurston SE, Robinson TJ, Escara-Wilke JF, Daignault-Newton S, Martin TL, Keller ET, and Keller JM
- Subjects
- Analgesics therapeutic use, Animals, Humans, Male, Mice, Mice, Inbred C57BL, Mice, SCID, Bone Neoplasms drug therapy, Bone Neoplasms veterinary, Prostatic Neoplasms drug therapy, Prostatic Neoplasms veterinary
- Abstract
Murine models of tumor development often require invasive procedures for tumor implantation, potentially causing pain or distress. However, analgesics are often withheld during implantation because of concerns that they may adversely affect tumor development. Previous studies examining the effects of analgesics on the development and metastasis of various tumor lines show that the effect of analgesics depends on the tumor line and analgesic used. A blanket statement that analgesics affect the general growth of tumors is not adequate scientific justification for withholding pain relief, and pilot studies or references are recommended for each specific tumor cell line and treatment combination. In this study, we evaluated the effects of 2 commonly used analgesics on tumor growth in 2 models of prostate cancer (PCa) bone metastasis. We hypothesized that a one-time injection of analgesics at the time of intratibial injection of tumor cells would not significantly impact tumor growth. Either C57BL/6 or SCID mice were injected subcutaneously with an analgesic (carprofen [5 mg/kg], or buprenorphine [0.1 mg/kg]) or vehicle (0.1 mL of saline) at the time of intratibial injection with a PCa cell line (RM1 or PC3, n = 10 to 11 per group). Tumor growth (measured by determination of tumor burden and the extent of bone involvement) and welfare (measured by nociception, locomotion, and weight) were monitored for 2 to 4 wk. Neither carprofen or buprenorphine administration consistently affected tumor growth or indices of animal welfare as compared with the saline control for either cell line. This study adds to the growing body of literature demonstrating that analgesia can be compatible with scientific objectives, and that a decision to withhold analgesics must be scientifically justified and evaluated on a model-specific basis.
- Published
- 2021
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27. Cigarette smoke-associated inflammation impairs bone remodeling through NFκB activation.
- Author
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Lu Y, Di YP, Chang M, Huang X, Chen Q, Hong N, Kahkonen BA, Di ME, Yu C, Keller ET, and Zhang J
- Subjects
- Animals, Bone Remodeling, Inflammation, Mice, Smoke, NF-kappa B, Smoking adverse effects
- Abstract
Background: Cigarette smoking constitutes a major lifestyle risk factor for osteoporosis and hip fracture. It is reported to impair the outcome of many clinical procedures, such as wound infection treatment and fracture healing. Importantly, although several studies have already demonstrated the negative correlation between cigarette consume and impaired bone homeostasis, there is still a poor understanding of how does smoking affect bone health, due to the lack of an adequately designed animal model. Our goal was to determine that cigarette smoke exposure impairs the dynamic bone remodeling process through induction of bone resorption and inhibition of bone formation., Methods: We developed cigarette smoke exposure protocols exposing mice to environmental smoking for 10 days or 3 months to determine acute and chronic smoke exposure effects. We used these models, to demonstrate the effect of smoking exposure on the cellular and molecular changes of bone remodeling and correlate these early alterations with subsequent bone structure changes measured by microCT and pQCT. We examined the bone phenotype alterations in vivo and ex vivo in the acute and chronic smoke exposure mice by measuring bone mineral density and bone histomorphometry. Further, we measured osteoclast and osteoblast differentiation gene expression levels in each group. The function changes of osteoclast or osteoblast were evaluated., Results: Smoke exposure caused a significant imbalance between bone resorption and bone formation. A 10-day exposure to cigarette smoke sufficiently and effectively induced osteoclast activity, leading to the inhibition of osteoblast differentiation, although it did not immediately alter bone structure as demonstrated in mice exposed to smoke for 3 months. Cigarette smoke exposure also induced DNA-binding activity of nuclear factor kappaB (NFκB) in osteoclasts, which subsequently gave rise to changes in bone remodeling-related gene expression., Conclusions: Our findings suggest that smoke exposure induces RANKL activation-mediated by NFκB, which could be a "smoke sensor" for bone remodeling.
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- 2021
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28. Retraction: A Glycolytic Mechanism Regulating an Angiogenic Switch in Prostate Cancer.
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Wang J, Wang J, Dai J, Jung Y, Wei CL, Wang Y, Havens AM, Hogg PJ, Keller ET, Pienta KJ, Nor JE, Wang CY, and Taichman RS
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- 2021
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29. 'Educated' Osteoblasts Reduce Osteoclastogenesis in a Bone-Tumor Mimetic Microenvironment.
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Kolb AD, Dai J, Keller ET, and Bussard KM
- Abstract
Breast cancer (BC) metastases to bone disrupt the balance between osteoblasts and osteoclasts, leading to excessive bone resorption. We identified a novel subpopulation of osteoblasts with tumor-inhibitory properties, called educated osteoblasts (EOs). Here we sought to examine the effect of EOs on osteoclastogenesis during tumor progression. We hypothesized that EOs affect osteoclast development in the bone-tumor niche, leading to suppressed pre-osteoclast fusion and bone resorption. Conditioned media (CM) was analyzed for protein expression of osteoclast factors receptor activator of nuclear factor kappa-β ligand (RANKL), osteoprotegerin (OPG), and tumor necrosis factor alpha (TNFα) via ELISA. EOs were co-cultured with pre-osteoclasts on a bone mimetic matrix to assess osteoclast resorption. Pre-osteoclasts were tri-cultured with EOs plus metastatic BC cells and assessed for tartrate-resistance acid phosphatase (TRAP)-positive, multinucleated (≥3 nuclei), mature osteoclasts. Tumor-bearing murine tibias were stained for TRAP to determine osteoclast number in-vivo. EO CM expressed reduced amounts of soluble TNFα and OPG compared to naïve osteoblast CM. Osteoclasts formed in the presence of EOs were smaller and less in number. Upon co-culture on a mimetic bone matrix, a 50% reduction in the number of TRAP-positive osteoclasts formed in the presence of EOs was observed. The tibia of mice inoculated with BC cells had less osteoclasts per bone surface in bones with increased numbers of EO cells. These data suggest EOs reduce osteoclastogenesis and bone resorption. The data imply EOs provide a protective effect against bone resorption in bone metastatic BC.
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- 2021
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30. Photoacoustic spectral analysis at ultraviolet wavelengths for characterizing the Gleason grades of prostate cancer.
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Jo J, Siddiqui J, Zhu Y, Ni L, Kothapalli SR, Tomlins SA, Wei JT, Keller ET, Udager AM, Wang X, and Xu G
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- Animals, Cell Line, Tumor, Humans, Male, Mice, Neoplasm Grading, Neoplasm Staging, Photoacoustic Techniques methods, Prostatic Neoplasms diagnostic imaging, Prostatic Neoplasms pathology, Ultraviolet Rays
- Abstract
The diagnosis of aggressive prostate cancer (PCa) has relied on microscopic architectures, namely Gleason patterns, of tissues extracted through core biopsies. Technology capable of assessing the tissue architecture without tissue extraction will reduce the invasiveness of PCa diagnosis and improve diagnostic accuracy by allowing for more sampling locations. Our recently developed photoacoustic spectral analysis (PASA) has achieved quantification of tissue architectural heterogeneity interstitially. Taking advantage of the unique optical absorption of cell nuclei at ultraviolet (UV) wavelengths, this study investigated PASA at 266 nm for quantifying the tissue architecture heterogeneity in prostates. The results have shown significant differences among the normal, early cancer, and late cancer stages in mouse prostates ex vivo and in vivo ( n =20, p <0.05). The study with human samples ex vivo has shown a correlation of 0.80 ( n =11, p <0.05) between PASA quantification and pathologic diagnosis.
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- 2020
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31. Single-Cell Transcriptomics Analysis Identifies Nuclear Protein 1 as a Regulator of Docetaxel Resistance in Prostate Cancer Cells.
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Schnepp PM, Shelley G, Dai J, Wakim N, Jiang H, Mizokami A, and Keller ET
- Subjects
- Basic Helix-Loop-Helix Transcription Factors genetics, Cell Line, Tumor, Drug Resistance, Neoplasm, High-Throughput Nucleotide Sequencing, Humans, Male, Neoplasm Proteins genetics, Prostatic Neoplasms genetics, Prostatic Neoplasms pathology, Single-Cell Analysis, Transcriptome, Transfection, Basic Helix-Loop-Helix Transcription Factors metabolism, Docetaxel pharmacology, Neoplasm Proteins metabolism, Prostatic Neoplasms drug therapy, Prostatic Neoplasms metabolism
- Abstract
The majority of patients with prostate cancer treated with docetaxel develop resistance to it. To better understand the mechanism behind the acquisition of resistance, we conducted single-cell RNA-sequencing (scRNA-seq) of docetaxel-sensitive and -resistant variants of DU145 and PC3 prostate cancer cell lines. Overall, sensitive and resistant cells clustered separately. Differential gene expression analysis between resistant and sensitive cells revealed 182 differentially expressed genes common to both prostate cancer cell lines. A subset of these genes gave a gene expression profile in the resistant transcriptome-like-sensitive cells similar to the resistant cells. Exploration for functional gene pathways identified 218 common pathways between the two cell lines. Protein ubiquitination was the most differentially regulated pathway and was enriched in the resistant cells. Transcriptional regulator analysis identified 321 potential regulators across both cell lines. One of the top regulators identified was nuclear protein 1 (NUPR1). In contrast to the single-cell analysis, bulk analysis of the cells did not reveal NUPR1 as a promising candidate. Knockdown and overexpression of NUPR1 in the prostate cancer cells demonstrated that NUPR1 confers docetaxel resistance in both cell lines. Collectively, these data demonstrate the utility of scRNA-seq to identify regulators of drug resistance. Furthermore, NUPR1 was identified as a mediator of prostate cancer drug resistance, which provides the rationale to explore NUPR1 and its target genes for reversal of docetaxel resistance. IMPLICATIONS: Using single-cell sequencing of prostate cancer, we show that NUPR1 plays a role in docetaxel resistance., (©2020 American Association for Cancer Research.)
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- 2020
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32. Efficacy and Effect of Cabozantinib on Bone Metastases in Treatment-naive Castration-resistant Prostate Cancer.
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Smith DC, Daignault-Newton S, Grivas P, Reichert ZR, Hussain M, Cooney KA, Caram M, Alva A, Jacobson J, Yablon C, Mehra R, Escara-Wilke J, Shelley G, and Keller ET
- Subjects
- Aged, Bone Neoplasms secondary, Follow-Up Studies, Humans, Longitudinal Studies, Male, Middle Aged, Non-Randomized Controlled Trials as Topic, Prognosis, Prostatic Neoplasms, Castration-Resistant pathology, Survival Rate, Anilides therapeutic use, Bone Neoplasms drug therapy, Prostatic Neoplasms, Castration-Resistant drug therapy, Pyridines therapeutic use
- Abstract
Background: Cabozantinib is active in advanced prostate cancer with improvement on bone scans in men on phase II trials. This trial evaluated the efficacy and changes in bone lesions in men with metastatic castration-resistant prostate cancer (mCRPC) treated with cabozantinib., Patients and Methods: Eligible patients with mCRPC involving bone underwent biopsy of a bone lesion followed by cabozantinib starting at 60 mg daily and continuing until progression or intolerable toxicity. The primary study endpoint was progression-free survival at 12 weeks. The bone lesion was rebiopsied at 6 weeks. Expression of CMET, phospho-CMET, and VEGFR2 was assayed by immunohistochemistry. Serum was obtained at baseline, and at 3, 6, and 12 weeks and assayed for bone remodeling markers., Results: A total of 25 patients were enrolled: 22 were evaluable, and 3 were excluded before receiving cabozantinib. At 12 weeks, 17 (77%) of 22 patients had stable disease or better. The median time on treatment was 24 weeks (range, 3-112 weeks). The overall median progression-free survival was 43.7 weeks (95% confidence interval, 23.7-97.0 weeks). Eight (36%) of 22 patients had markedly reduced uptake on bone scan. Patients with significant response on bone scan had higher bone morphogenic protein-2 levels at baseline, stable N-telopeptides levels, increased vascular endothelial growth factor receptor 2 expression, and a trend towards increased phospho-CMET while on cabozantinib compared with patients with stable disease., Conclusions: Cabozantinib is active in men with mCRPC, inducing significant changes on bone scan in one-third of patients with changes in markers of bone formation and the tumor microenvironment., (Copyright © 2019 Elsevier Inc. All rights reserved.)
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- 2020
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33. Curcumin Nanoparticles and Their Cytotoxicity in Docetaxel-Resistant Castration-Resistant Prostate Cancer Cells.
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Tanaudommongkon I, Tanaudommongkon A, Prathipati P, Nguyen JT, Keller ET, and Dong X
- Abstract
Most prostate cancer patients develop resistance to anti-androgen therapy. This is referred to as castration-resistant prostate cancer (CRPC). Docetaxel (DTX) is the mainstay treatment against CRPC. However, over time patients eventually develop DTX resistance, which is the cause of the cancer-related mortality. Curcumin (CUR) as a natural compound has been shown to have very broad pharmacological activities, e.g., anti-inflammatory and antioxidant properties. However, CUR is very hydrophobic. The objective of this study was to develop CUR nanoparticles (NPs) and evaluate their cytotoxicity in DTX-resistant CRPC cells for the treatment of DTX-resistant CRPC. We tested solubility of CUR in different lipids and surfactants. Finally, Miglyol 812 and D-alpha-tocopheryl poly (ethylene glycol) succinate 1000 (TPGS) were chosen to prepare lipid-based NPs for CUR. We fully characterized CUR NPs that had particle size < 150 nm, high drug loading (7.5%), and entrapment efficiency (90%). Moreover, the CUR NPs were successfully lyophilized without using cryoprotectants. We tested the cytotoxicity of blank NPs, free CUR, and CUR NPs in sensitive DU145 and PC3 cells as well as their matching docetaxel-resistant cells. Cytotoxicity studies showed that blank NPs were very safe for all tested prostate cancer cell lines. Free CUR overcame the resistance in PC3 cells, but not in DU145 cells. In contrast, CUR NPs significantly increased CUR potency in all tested cell lines. Importantly, CUR NPs completely restored CUR potency in both resistant DU145 and PC3 cells. These results demonstrate that the CUR NPs have potential to overcome DTX resistance in CRPC.
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- 2020
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34. Cytotoxic necrotizing factor 1 promotes bladder cancer angiogenesis through activating RhoC.
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Guo Y, Wang J, Zhou K, Lv J, Wang L, Gao S, Keller ET, Zhang ZS, Wang Q, and Yao Z
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- Animals, Cell Line, Escherichia coli Infections metabolism, Escherichia coli Infections microbiology, HEK293 Cells, Humans, Mice, Mice, Inbred BALB C, Mice, Nude, Neovascularization, Pathologic microbiology, Neutrophils metabolism, Tumor Microenvironment physiology, Urinary Bladder microbiology, Urinary Bladder Neoplasms microbiology, Urinary Tract Infections metabolism, Urinary Tract Infections microbiology, Bacterial Toxins metabolism, Escherichia coli Proteins metabolism, Neovascularization, Pathologic metabolism, Urinary Bladder metabolism, Urinary Bladder Neoplasms metabolism, rhoC GTP-Binding Protein metabolism
- Abstract
Uropathogenic Escherichia coli (UPEC), a leading cause of urinary tract infections, is associated with prostate and bladder cancers. Cytotoxic necrotizing factor 1 (CNF1) is a key UPEC toxin; however, its role in bladder cancer is unknown. In the present study, we found CNF1 induced bladder cancer cells to secrete vascular endothelial growth factor (VEGF) through activating Ras homolog family member C (RhoC), leading to subsequent angiogenesis in the bladder cancer microenvironment. We then investigated that CNF1-mediated RhoC activation modulated the stabilization of hypoxia-inducible factor 1α (HIF1α) to upregulate the VEGF. We demonstrated in vitro that active RhoC increased heat shock factor 1 (HSF1) phosphorylation, which induced the heat shock protein 90α (HSP90α) expression, leading to stabilization of HIF1α. Active RhoC elevated HSP90α, HIF1α, VEGF expression, and angiogenesis in the human bladder cancer xenografts. In addition, HSP90α, HIF1α, and VEGF expression were also found positively correlated with the human bladder cancer development. These results provide a potential mechanism through which UPEC contributes to bladder cancer progression, and may provide potential therapeutic targets for bladder cancer., (© 2020 Federation of American Societies for Experimental Biology.)
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- 2020
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35. Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies.
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Ma Y, Sun S, Shang X, Keller ET, Chen M, and Zhou X
- Subjects
- Animals, Computer Simulation, Endoderm cytology, Endothelial Cells metabolism, Human Embryonic Stem Cells metabolism, Humans, Mice, Models, Genetic, Sensory Receptor Cells metabolism, Gene Expression Profiling, Gene Expression Regulation, RNA-Seq, Single-Cell Analysis, Statistics as Topic
- Abstract
Differential expression (DE) analysis and gene set enrichment (GSE) analysis are commonly applied in single cell RNA sequencing (scRNA-seq) studies. Here, we develop an integrative and scalable computational method, iDEA, to perform joint DE and GSE analysis through a hierarchical Bayesian framework. By integrating DE and GSE analyses, iDEA can improve the power and consistency of DE analysis and the accuracy of GSE analysis. Importantly, iDEA uses only DE summary statistics as input, enabling effective data modeling through complementing and pairing with various existing DE methods. We illustrate the benefits of iDEA with extensive simulations. We also apply iDEA to analyze three scRNA-seq data sets, where iDEA achieves up to five-fold power gain over existing GSE methods and up to 64% power gain over existing DE methods. The power gain brought by iDEA allows us to identify many pathways that would not be identified by existing approaches in these data.
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- 2020
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36. Osteoclast-mediated bone resorption is controlled by a compensatory network of secreted and membrane-tethered metalloproteinases.
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Zhu L, Tang Y, Li XY, Keller ET, Yang J, Cho JS, Feinberg TY, and Weiss SJ
- Subjects
- Animals, Bone and Bones, Cathepsins, Female, Humans, Mice, Osteoclasts, Ovariectomy, Bone Resorption, Osteoporosis
- Abstract
Osteoclasts actively remodel both the mineral and proteinaceous components of bone during normal growth and development as well as pathologic states ranging from osteoporosis to bone metastasis. The cysteine proteinase cathepsin K confers osteoclasts with potent type I collagenolytic activity; however, cathepsin K-null mice, as well as cathepsin K-mutant humans, continue to remodel bone and degrade collagen by as-yet-undefined effectors. Here, we identify a cathepsin K-independent collagenolytic system in osteoclasts that is composed of a functionally redundant network of the secreted matrix metalloproteinase MMP9 and the membrane-anchored matrix metalloproteinase MMP14. Unexpectedly, whereas deleting either of the proteinases individually leaves bone resorption intact, dual targeting of Mmp9 and Mmp14 inhibited the resorptive activity of mouse osteoclasts in vitro and in vivo and human osteoclasts in vitro. In vivo, Mmp9 / Mmp14 conditional double-knockout mice exhibited marked increases in bone density and displayed a highly protected status against either parathyroid hormone- or ovariectomy-induced pathologic bone loss. Together, these studies characterize a collagenolytic system operative in mouse and human osteoclasts and identify the MMP9/MMP14 axis as a potential target for therapeutic interventions for bone-wasting disease states., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)
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- 2020
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37. Notch3 promotes prostate cancer-induced bone lesion development via MMP-3.
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Ganguly SS, Hostetter G, Tang L, Frank SB, Saboda K, Mehra R, Wang L, Li X, Keller ET, and Miranti CK
- Subjects
- Animals, Bone Neoplasms pathology, Bone Neoplasms secondary, Cell Differentiation genetics, Cell Line, Tumor, Gene Expression Regulation, Neoplastic genetics, Heterografts, Humans, Male, Mice, Neoplasm Metastasis, Osteoblasts metabolism, Osteoblasts pathology, Osteoclasts metabolism, Osteoclasts pathology, Osteogenesis genetics, Prostatic Neoplasms pathology, Signal Transduction genetics, Bone Neoplasms genetics, Matrix Metalloproteinase 3 genetics, Prostatic Neoplasms genetics, Receptor, Notch3 genetics
- Abstract
Prostate cancer metastases primarily localize in the bone where they induce a unique osteoblastic response. Elevated Notch activity is associated with high-grade disease and metastasis. To address how Notch affects prostate cancer bone lesions, we manipulated Notch expression in mouse tibia xenografts and monitored tumor growth, lesion phenotype, and the bone microenvironment. Prostate cancer cell lines that induce mixed osteoblastic lesions in bone expressed 5-6 times more Notch3, than tumor cells that produce osteolytic lesions. Expression of active Notch3 (NICD3) in osteolytic tumors reduced osteolytic lesion area and enhanced osteoblastogenesis, while loss of Notch3 in osteoblastic tumors enhanced osteolytic lesion area and decreased osteoblastogensis. This was accompanied by a respective decrease and increase in the number of active osteoclasts and osteoblasts at the tumor-bone interface, without any effect on tumor proliferation. Conditioned medium from NICD3-expressing cells enhanced osteoblast differentiation and proliferation in vitro, while simultaneously inhibiting osteoclastogenesis. MMP-3 was specifically elevated and secreted by NICD3-expressing tumors, and inhibition of MMP-3 rescued the NICD3-induced osteoblastic phenotypes. Clinical osteoblastic bone metastasis samples had higher levels of Notch3 and MMP-3 compared with patient matched visceral metastases or osteolytic metastasis samples. We identified a Notch3-MMP-3 axis in human prostate cancer bone metastases that contributes to osteoblastic lesion formation by blocking osteoclast differentiation, while also contributing to osteoblastogenesis. These studies define a new role for Notch3 in manipulating the tumor microenvironment in bone metastases.
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- 2020
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38. Primary prostate cancer educates bone stroma through exosomal pyruvate kinase M2 to promote bone metastasis.
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Dai J, Escara-Wilke J, Keller JM, Jung Y, Taichman RS, Pienta KJ, and Keller ET
- Subjects
- Animals, Cell Line, Tumor, Cell Movement, Cell Proliferation, Chemokine CXCL12 genetics, Chemokine CXCL12 metabolism, Disease Models, Animal, Gene Expression, Humans, Hypoxia-Inducible Factor 1, alpha Subunit metabolism, Male, Mice, Models, Biological, Prostatic Neoplasms immunology, Pyruvate Kinase genetics, Stromal Cells immunology, Tumor Burden, Bone Neoplasms secondary, Exosomes metabolism, Prostatic Neoplasms metabolism, Prostatic Neoplasms pathology, Pyruvate Kinase metabolism, Stromal Cells metabolism
- Abstract
Prostate cancer (PCa) metastasizes selectively to bone through unknown mechanisms. In the current study, we identified exosome-mediated transfer of pyruvate kinase M2 (PKM2) from PCa cells into bone marrow stromal cells (BMSCs) as a novel mechanism through which primary tumor-derived exosomes promote premetastatic niche formation. We found that PKM2 up-regulates BMSC CXCL12 production in a HIF-1α-dependent fashion, which subsequently enhances PCa seeding and growth in the bone marrow. Furthermore, serum-derived exosomes from patients with either primary PCa or PCa metastasis, as opposed to healthy men, reveal that increased exosome PKM2 expression is associated with metastasis, suggesting clinical relevance of exosome PKM2 in PCa. Targeting the exosome-induced CXCL12 axis diminished exosome-mediated bone metastasis. In summary, primary PCa cells educate the bone marrow to create a premetastatic niche through primary PCa exosome-mediated transfer of PKM2 into BMSCs and subsequent up-regulation of CXCL12. This novel mechanism indicates the potential for exosome PKM2 as a biomarker and suggests therapeutic targets for PCa bone metastasis., (© 2019 Dai et al.)
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- 2019
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39. SNV identification from single-cell RNA sequencing data.
- Author
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Schnepp PM, Chen M, Keller ET, and Zhou X
- Subjects
- Databases, Genetic, Genetic Variation, Humans, RNA genetics, Polymorphism, Single Nucleotide, Sequence Analysis, RNA methods, Single-Cell Analysis methods
- Abstract
Integrating single-cell RNA sequencing (scRNA-seq) data with genotypes obtained from DNA sequencing studies facilitates the detection of functional genetic variants underlying cell type-specific gene expression variation. Unfortunately, most existing scRNA-seq studies do not come with DNA sequencing data; thus, being able to call single nucleotide variants (SNVs) from scRNA-seq data alone can provide crucial and complementary information, detection of functional SNVs, maximizing the potential of existing scRNA-seq studies. Here, we perform extensive analyses to evaluate the utility of two SNV calling pipelines (GATK and Monovar), originally designed for SNV calling in either bulk or single-cell DNA sequencing data. In both pipelines, we examined various parameter settings to determine the accuracy of the final SNV call set and provide practical recommendations for applied analysts. We found that combining all reads from the single cells and following GATK Best Practices resulted in the highest number of SNVs identified with a high concordance. In individual single cells, Monovar resulted in better quality SNVs even though none of the pipelines analyzed is capable of calling a reasonable number of SNVs with high accuracy. In addition, we found that SNV calling quality varies across different functional genomic regions. Our results open doors for novel ways to leverage the use of scRNA-seq for the future investigation of SNV function., (© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)
- Published
- 2019
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40. Macrofluidic recirculating model of skeletal metastasis.
- Author
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Osawa T, Wang W, Dai J, and Keller ET
- Subjects
- Animals, Cell Movement, Chemokine CXCL12 metabolism, Green Fluorescent Proteins genetics, Heterografts, Humans, Hydrogels, Lab-On-A-Chip Devices, Male, Mice, Mice, Nude, PC-3 Cells, Transduction, Genetic, Tumor Microenvironment, Bone Neoplasms secondary, Cancellous Bone metabolism, Femur Head, Microchip Analytical Procedures methods, Prostatic Neoplasms pathology, Stromal Cells metabolism
- Abstract
While microfluidic systems model aspects of metastasis, they are limited to artificially created tissues of limited complexity. We set out to develop an in vitro model of tumor cell migration from a primary tumor to a distant site that allows use of tissue. Accordingly, we created a macrofluidic model using culture plate wells connected with type I collagen-coated large bore tubing and has recirculating media. Green fluorescent protein-positive prostate carcinoma cells in a hydrogel or excised tumor xenografts from mice were placed into primary tumor sites and either human bone stromal cells (HS-5) in a hydrogel or human-derived bone chips were seeded into metastatic sites. Cells from the primary sites migrated to and grew in metastatic sites. Bone enhanced growth at metastatic sites and established a CXCL12 gradient that was higher in metastatic versus primary sites. AMD3100-mediated inhibition of CXCL12 function reduced the number of cells targeting the bone at the metastatic sites. In summary, we have developed a macrofluidic metastasis model that allows incorporation of tumor and metastatic microenvironment tissues and models chemotaxis. This system allows for incorporation of tumor heterogeneity and inclusion of an intact microenvironment. These features will facilitate identification of mechanisms and therapeutics for bone metastasis.
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- 2019
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41. Knockdown of Notch1 inhibits nasopharyngeal carcinoma cell growth and metastasis via downregulation of CCL2, CXCL16, and uPA.
- Author
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Guo H, Wang F, Diao Y, Zhang Z, Chen Q, Qian CN, Keller ET, Zhang J, and Lu Y
- Subjects
- Animals, Cell Proliferation genetics, Gene Expression Regulation, Neoplastic genetics, Gene Knockdown Techniques, Heterografts, Humans, Mice, Nasopharyngeal Carcinoma pathology, Neoplasm Metastasis, Neoplasm Proteins genetics, RNA, Small Interfering genetics, RNA, Small Interfering pharmacology, Receptor, Notch1 antagonists & inhibitors, Signal Transduction, Chemokine CCL2 genetics, Chemokine CXCL16 genetics, Nasopharyngeal Carcinoma genetics, Receptor, Notch1 genetics, Urokinase-Type Plasminogen Activator genetics
- Abstract
Notch pathway is a highly conserved cell signaling system that plays very important roles in controlling multiple cell differentiation processes during embryonic and adult life. Multiple lines of evidence support the oncogenic role of Notch signaling in several human solid cancers; however, the pleiotropic effects and molecular mechanisms of Notch signaling inhibition on nasopharyngeal carcinoma (NPC) remain unclear. In this study, we evaluated Notch1 expression in NPC cell lines (CNE1, CNE2, SUNE1, HONE1, and HK1) by real-time quantitative PCR and Western blot analysis, and we found that CNE1 and CNE2 cells expressed a higher level of Notch1 compared with HONE1, SUNE1, and HK1 cells. Then Notch1 expression was specifically knocked down in CNE1 and CNE2 cells by Notch1 short hairpin RNA (shRNA). In Notch1 knockdown cells, cell proliferation, migration, and invasion were significantly inhibited. The epithelial-mesenchymal transition of tumor cells was reversed in Notch1-shRNA-transfected cells, accompanied by epithelioid-like morphology changes, increased protein levels of E-cadherin, and decreased expression of vimentin. In addition, knockdown of Notch1 markedly inhibited the expression of urokinase plasminogen activator (uPA) and its receptor uPAR, and chemokines C-C motif chemokine ligand 2 and C-X-C motif chemokine ligand 16, indicating that these factors are downstream targets of Notch1. Furthermore, deleting uPA expression had similar effects as Notch1. Finally, knockdown of Notch1 significantly diminished CNE1 cell growth in a murine model concomitant with inhibition of cell proliferation and induction of apoptosis. These results suggest that Notch1 may become a novel therapeutic target for the clinical treatment of NPC., (© 2019 Wiley Periodicals, Inc.)
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- 2019
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42. Targeted Notch1 inhibition with a Notch1 antibody, OMP-A2G1, decreases tumor growth in two murine models of prostate cancer in association with differing patterns of DNA damage response gene expression.
- Author
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Ahmed AA, Robinson T, Palande M, Escara-Wilke J, Dai J, and Keller ET
- Subjects
- Amyloid Precursor Protein Secretases antagonists & inhibitors, Animals, Antineoplastic Agents, Immunological pharmacology, Cell Line, Tumor, Cell Proliferation drug effects, Disease Models, Animal, Docetaxel pharmacology, Humans, Male, Mice, Prostatic Neoplasms genetics, Prostatic Neoplasms metabolism, Receptor, Notch1 immunology, Xenograft Model Antitumor Assays, Antibodies, Monoclonal pharmacology, DNA Damage genetics, DNA Repair genetics, Prostatic Neoplasms pathology, Receptor, Notch1 antagonists & inhibitors
- Abstract
Notch plays a protumorigenic role in many cancers including prostate cancer (PCa). Global notch inhibition of multiple Notch family members using γ-secretase inhibitors has shown efficacy in suppressing PCa growth in murine models. However, global Notch inhibition is associated with marked toxicity due to the widespread function of many different Notch family members in normal cell physiology. Accordingly, in the current study, we explored if specific inhibition of Notch1 would effectively inhibit PCa growth in a murine model. The androgen-dependent VCaP and androgen-independent DU145 cell lines were injected subcutaneously into mice. The mice were treated with either control antibody 1B7.11, anti-Notch1 antibody (OMP-A2G1), docetaxel or the combination of OMP-A2G1 and docetaxel. Tumor growth was measured using calipers. At the end of the study, tumors were assessed for proliferative response, apoptotic response, Notch target gene expression, and DNA damage response (DDR) expression. OMP-A2G1 alone inhibited tumor growth of both PCa cell lines to a greater extent than docetaxel alone. There was no additive or synergistic effect of OMP-A2G1 and docetaxel. The primary toxicity was weight loss that was controlled with dietary supplementation. Proliferation and apoptosis were affected differentially in the two cell lines. OMP-A2G1 increased expression of the DDR gene GADD45α in VCaP cells but downregulated GADD45α in Du145 cells. Taken together, these data show that Notch1 inhibition decreases PCa xenograft growth but does so through different mechanisms in the androgen-dependent VCaP cell line vs the androgen-independent DU145 cell line. These results provide a rationale for further exploration of targeted Notch inhibition for therapy of PCa., (© 2019 Wiley Periodicals, Inc.)
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- 2019
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43. Targeting cathepsin K diminishes prostate cancer establishment and growth in murine bone.
- Author
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Liang W, Wang F, Chen Q, Dai J, Escara-Wilke J, Keller ET, Zimmermann J, Hong N, Lu Y, and Zhang J
- Subjects
- Adenocarcinoma drug therapy, Adenocarcinoma genetics, Adenocarcinoma pathology, Animals, Bone Neoplasms genetics, Cathepsin K genetics, Cell Proliferation drug effects, Cells, Cultured, Humans, Male, Mice, Mice, SCID, PC-3 Cells, Prostatic Neoplasms genetics, Protease Inhibitors pharmacology, RNA, Small Interfering pharmacology, RNA, Small Interfering therapeutic use, Xenograft Model Antitumor Assays, Bone Neoplasms prevention & control, Bone Neoplasms secondary, Cathepsin K antagonists & inhibitors, Molecular Targeted Therapy methods, Prostatic Neoplasms drug therapy, Prostatic Neoplasms pathology, Protease Inhibitors therapeutic use
- Abstract
Background: The processes of prostate cancer (PCa) invasion and metastasis are facilitated by proteolytic cascade involving multiple proteases, such as matrix metalloproteinases, serine proteases and cysteine proteases including cathepsin K (CatK). CatK is predominantly secreted by osteoclasts and specifically degrades collagen I leading to bone destruction. PCa and breast cancer preferentially metastasize to the bone. Importantly, CatK expression level is greater in PCa bone metastatic sites compared to primary tumor and normal prostate tissues. However, the underlying mechanism of CatK during PCa metastases into the bone remains to be elucidated. We investigated the functional role of CatK during the PCa establishment and growth process in the murine bone., Methods: CatK mRNA expression was validated by RT-PCR, protein expression by immunoblotting in PCa LNCaP, C4-2B, and PC3 cells as well as in PCa tissues. Its protein production was measured using ELISA assay. The effect of both knockdowns via siRNA and CatK inhibitor was compared in regard to PCa cell invasion. We further studied the dose-dependent CatK inhibitor effect on conditioned media-induced bone resorption. In setting up an animal model, C4-2B cells were injected into the tibiae of SCID mice. The animals treated with either vehicle or CatK inhibitor for 8 weeks at the time of tumor cell injection (tumor establishment model; protocol I) or 4 weeks after tumor cell injection (tumor progression model; protocol II) were applied to histological and histomorphometric analyses., Results: We confirmed CatK expression in PCa LNCaP, C4-2B, and PC3 cells as well as in PCa tissues. Furthermore, we observed the inhibitory effects of a selective CatK inhibitor on PCa cell invasion. The CatK inhibitor dose-dependently inhibited PCa-conditioned media-induced bone resorption. Upon injection of C4-2B cells into the tibiae of SCID mice, the selective CatK inhibitor significantly prevented the tumor establishment in protocol I, and reduced the tumor growth in bone in protocol II. It also decreased serum PSA levels in both animal models. The inhibitory effects of the CatK inhibitor were enhanced in combination with zoledronic acid (ZA)., Conclusion: The selective CatK inhibitor may prevent the establishment and progression of PCa in bone, thus making it a novel therapeutic approach for advanced PCa.
- Published
- 2019
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44. Prostate cancer promotes a vicious cycle of bone metastasis progression through inducing osteocytes to secrete GDF15 that stimulates prostate cancer growth and invasion.
- Author
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Wang W, Yang X, Dai J, Lu Y, Zhang J, and Keller ET
- Subjects
- Animals, Bone Neoplasms secondary, Cell Line, Cell Line, Tumor, Cell Movement, Cell Proliferation, Disease Progression, Humans, Male, Mice, Mice, Inbred NOD, Mice, SCID, Neoplasm Invasiveness, Neoplasm Metastasis, Prostatic Neoplasms pathology, Signal Transduction, Bone Neoplasms metabolism, Growth Differentiation Factor 15 metabolism, Osteocytes metabolism, Prostatic Neoplasms metabolism
- Abstract
Bone is the most frequent site of prostate cancer (PCa) metastasis; however, little is known about the role of the most common cell in bone, the osteocyte (OCy), in cancer biology. In this study we explored the crosstalk between PCa cells and OCys to determine if it contributes to PCa progression. PCa cells induced OCys to promote PCa proliferation, migration and invasion. A chemokine screen revealed that PCa cell induced OCys to produce growth-derived factor 15 (GDF15). Knockdown of GDF15 in OCys demonstrated that PCa cells conferred the ability on OCys to promote PCa proliferation, migration and invasion through GDF15. Consistent with this finding was the observation that the GDF15 receptor, GFRAL, was expressed on multiple PCa cell lines. Transcription factor array screening of PCa cells exposed to OCys with or without knockdown of GDF15 revealed that GDF15 in OCys promoted early growth response 1 (EGR1) expression in the PCa cells. Knockdown of EGR1 expression in PCa cells revealed it was required for the OCy-derived GDF15-mediated induction of in vitro PCa cell proliferation, migration and invasion. Subcutaneous co-injection of PCa cells and OCys into mice revealed that OCys promoted tumor growth in vivo, which was diminished by knockdown of GDF15 in the OCys. Knockdown of GDF15 in the tibiae diminished growth of PCa cancer cells injected into the tibiae, which was accompanied by decreased tumor cell proliferation and EGR1 expression. These results shed light on a novel mechanism through which PCa cells educate OCys to promote progression of PCa bone metastasis. They also suggest that targeting of GDF15-based and EGR1-based signaling pathways should be further explored for their potential to diminish progression of PCa bone metastasis.
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- 2019
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45. A surgical orthotopic approach for studying the invasive progression of human bladder cancer.
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Lorenzatti Hiles G, Cates AL, El-Sawy L, Day KC, Broses LJ, Han AL, Briggs HL, Emamdjomeh A, Chou A, Abel EV, Liebert M, Palmbos PL, Udager AM, Keller ET, and Day ML
- Subjects
- Animals, Disease Models, Animal, Humans, Mice, Inbred NOD, Mice, SCID, Neoplasm Invasiveness, Disease Progression, Urinary Bladder Neoplasms pathology, Urinary Bladder Neoplasms surgery, Xenograft Model Antitumor Assays methods
- Abstract
The invasion of bladder cancer into the sub-urothelial muscle and vasculature are key determinants leading to lethal metastatic progression. However, the molecular basis is poorly understood, partly because of the lack of uncomplicated and reliable models that recapitulate the biology of locally invasive disease. We developed a surgical grafting technique, characterized by a simple, rapid, reproducible and high-efficiency approach, to recapitulate the pathobiological events of human bladder cancer invasion in mice. This technique consists of a small laparotomy and direct implantation of human cancer cells into the bladder lumen. Unlike other protocols, it does not require debriding of the urothelial lining, injection into the bladder wall, specialized imaging equipment, bladder catheterization or costly surgical equipment. With minimal practice, the procedure can be executed in <10 min. Tumors develop with a high take rate, and most cell lines exhibit local invasion within 4 weeks of implantation.
- Published
- 2019
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46. Targeted DNA and RNA Sequencing of Paired Urothelial and Squamous Bladder Cancers Reveals Discordant Genomic and Transcriptomic Events and Unique Therapeutic Implications.
- Author
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Hovelson DH, Udager AM, McDaniel AS, Grivas P, Palmbos P, Tamura S, Lazo de la Vega L, Palapattu G, Veeneman B, El-Sawy L, Sadis SE, Morgan TM, Montgomery JS, Weizer AZ, Day KC, Neamati N, Liebert M, Keller ET, Day ML, Mehra R, and Tomlins SA
- Subjects
- Biomarkers, Tumor metabolism, Carcinoma, Squamous Cell metabolism, Carcinoma, Squamous Cell pathology, Cell Line, Tumor, DNA Copy Number Variations, DNA Mutational Analysis, DNA, Neoplasm metabolism, Gene Amplification, Gene Expression Profiling methods, Genetic Predisposition to Disease, Genome, Human, Genomics methods, Humans, Mutation, Phenotype, Predictive Value of Tests, RNA, Neoplasm metabolism, Reproducibility of Results, Sequence Analysis, RNA, Transcriptome, Urinary Bladder pathology, Urinary Bladder Neoplasms metabolism, Urinary Bladder Neoplasms pathology, Urothelium pathology, Biomarkers, Tumor genetics, Carcinoma, Squamous Cell genetics, DNA, Neoplasm genetics, Genetic Heterogeneity, RNA, Neoplasm genetics, Urinary Bladder metabolism, Urinary Bladder Neoplasms genetics, Urothelium metabolism
- Abstract
Background: Integrated molecular profiling has identified intrinsic expression-based bladder cancer molecular subtypes. Despite frequent histological diversity, robustness of subtypes in paired conventional (urothelial) and squamous components of the same bladder tumor has not been reported., Objective: To assess the impact of histological heterogeneity on expression-based bladder cancer subtypes., Design, Setting, and Participants: We performed clinically applicable, targeted DNA and/or RNA sequencing (multiplexed DNA and RNA sequencing [mxDNAseq and mxRNAseq, respectively]) on 112 formalin-fixed paraffin-embedded (FFPE) bladder cancer samples, including 12 cases with paired urothelial/squamous components and 21 bladder cancer cell lines., Outcome Measurements and Statistical Analysis: Unsupervised hierarchical and consensus clustering of target gene expression enabled derivation of basal/luminal molecular subtyping., Results and Limitation: Across 21 bladder cancer cell lines, our custom mxRNAseq panel was highly concordant with whole transcriptome sequencing, and assessed targets robustly determined expression-based basal/luminal subtypes from The Cancer Genome Atlas data (in silico) and internally sequenced FFPE tissues. Frequent deleterious TP53 (56%) and activating hotspot PIK3CA (30%) somatic mutations were seen across 69 high-quality tissue samples. Potentially targetable focal ERBB2 (6%) or EGFR (6%) amplifications were also identified, and a novel subgene copy-number detection approach is described. Combined DNA/RNA analysis showed that focally amplified samples exhibit outlier EGFR and ERBB2 expression distinct from subtype-intrinsic profiles. Critically, paired urothelial and squamous components showed divergent basal/luminal status in three of 12 cases (25%), despite identical putatively clonal prioritized somatic genomic alterations. Limitations include lack of profiled paired normal tissues for formal somatic alteration determination, and the need for formal analytical and clinical validation., Conclusions: Our results support the feasibility of clinically relevant integrative bladder cancer profiling and challenge the intrinsic nature of expression subtypes in histologically diverse bladder cancers., Patient Summary: A targeted RNA sequencing assay is capable of assessing gene expression-based subtypes in individual components of clinical bladder cancer tissue specimens. Different histological components of the same tumor may yield divergent expression profiles, suggesting that expression-based subtypes should be interpreted with caution in heterogeneous cancers., (Copyright © 2018 European Association of Urology. Published by Elsevier B.V. All rights reserved.)
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- 2018
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47. Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines.
- Author
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Théry C, Witwer KW, Aikawa E, Alcaraz MJ, Anderson JD, Andriantsitohaina R, Antoniou A, Arab T, Archer F, Atkin-Smith GK, Ayre DC, Bach JM, Bachurski D, Baharvand H, Balaj L, Baldacchino S, Bauer NN, Baxter AA, Bebawy M, Beckham C, Bedina Zavec A, Benmoussa A, Berardi AC, Bergese P, Bielska E, Blenkiron C, Bobis-Wozowicz S, Boilard E, Boireau W, Bongiovanni A, Borràs FE, Bosch S, Boulanger CM, Breakefield X, Breglio AM, Brennan MÁ, Brigstock DR, Brisson A, Broekman ML, Bromberg JF, Bryl-Górecka P, Buch S, Buck AH, Burger D, Busatto S, Buschmann D, Bussolati B, Buzás EI, Byrd JB, Camussi G, Carter DR, Caruso S, Chamley LW, Chang YT, Chen C, Chen S, Cheng L, Chin AR, Clayton A, Clerici SP, Cocks A, Cocucci E, Coffey RJ, Cordeiro-da-Silva A, Couch Y, Coumans FA, Coyle B, Crescitelli R, Criado MF, D'Souza-Schorey C, Das S, Datta Chaudhuri A, de Candia P, De Santana EF, De Wever O, Del Portillo HA, Demaret T, Deville S, Devitt A, Dhondt B, Di Vizio D, Dieterich LC, Dolo V, Dominguez Rubio AP, Dominici M, Dourado MR, Driedonks TA, Duarte FV, Duncan HM, Eichenberger RM, Ekström K, El Andaloussi S, Elie-Caille C, Erdbrügger U, Falcón-Pérez JM, Fatima F, Fish JE, Flores-Bellver M, Försönits A, Frelet-Barrand A, Fricke F, Fuhrmann G, Gabrielsson S, Gámez-Valero A, Gardiner C, Gärtner K, Gaudin R, Gho YS, Giebel B, Gilbert C, Gimona M, Giusti I, Goberdhan DC, Görgens A, Gorski SM, Greening DW, Gross JC, Gualerzi A, Gupta GN, Gustafson D, Handberg A, Haraszti RA, Harrison P, Hegyesi H, Hendrix A, Hill AF, Hochberg FH, Hoffmann KF, Holder B, Holthofer H, Hosseinkhani B, Hu G, Huang Y, Huber V, Hunt S, Ibrahim AG, Ikezu T, Inal JM, Isin M, Ivanova A, Jackson HK, Jacobsen S, Jay SM, Jayachandran M, Jenster G, Jiang L, Johnson SM, Jones JC, Jong A, Jovanovic-Talisman T, Jung S, Kalluri R, Kano SI, Kaur S, Kawamura Y, Keller ET, Khamari D, Khomyakova E, Khvorova A, Kierulf P, Kim KP, Kislinger T, Klingeborn M, Klinke DJ 2nd, Kornek M, Kosanović MM, Kovács ÁF, Krämer-Albers EM, Krasemann S, Krause M, Kurochkin IV, Kusuma GD, Kuypers S, Laitinen S, Langevin SM, Languino LR, Lannigan J, Lässer C, Laurent LC, Lavieu G, Lázaro-Ibáñez E, Le Lay S, Lee MS, Lee YXF, Lemos DS, Lenassi M, Leszczynska A, Li IT, Liao K, Libregts SF, Ligeti E, Lim R, Lim SK, Linē A, Linnemannstöns K, Llorente A, Lombard CA, Lorenowicz MJ, Lörincz ÁM, Lötvall J, Lovett J, Lowry MC, Loyer X, Lu Q, Lukomska B, Lunavat TR, Maas SL, Malhi H, Marcilla A, Mariani J, Mariscal J, Martens-Uzunova ES, Martin-Jaular L, Martinez MC, Martins VR, Mathieu M, Mathivanan S, Maugeri M, McGinnis LK, McVey MJ, Meckes DG Jr, Meehan KL, Mertens I, Minciacchi VR, Möller A, Møller Jørgensen M, Morales-Kastresana A, Morhayim J, Mullier F, Muraca M, Musante L, Mussack V, Muth DC, Myburgh KH, Najrana T, Nawaz M, Nazarenko I, Nejsum P, Neri C, Neri T, Nieuwland R, Nimrichter L, Nolan JP, Nolte-'t Hoen EN, Noren Hooten N, O'Driscoll L, O'Grady T, O'Loghlen A, Ochiya T, Olivier M, Ortiz A, Ortiz LA, Osteikoetxea X, Østergaard O, Ostrowski M, Park J, Pegtel DM, Peinado H, Perut F, Pfaffl MW, Phinney DG, Pieters BC, Pink RC, Pisetsky DS, Pogge von Strandmann E, Polakovicova I, Poon IK, Powell BH, Prada I, Pulliam L, Quesenberry P, Radeghieri A, Raffai RL, Raimondo S, Rak J, Ramirez MI, Raposo G, Rayyan MS, Regev-Rudzki N, Ricklefs FL, Robbins PD, Roberts DD, Rodrigues SC, Rohde E, Rome S, Rouschop KM, Rughetti A, Russell AE, Saá P, Sahoo S, Salas-Huenuleo E, Sánchez C, Saugstad JA, Saul MJ, Schiffelers RM, Schneider R, Schøyen TH, Scott A, Shahaj E, Sharma S, Shatnyeva O, Shekari F, Shelke GV, Shetty AK, Shiba K, Siljander PR, Silva AM, Skowronek A, Snyder OL 2nd, Soares RP, Sódar BW, Soekmadji C, Sotillo J, Stahl PD, Stoorvogel W, Stott SL, Strasser EF, Swift S, Tahara H, Tewari M, Timms K, Tiwari S, Tixeira R, Tkach M, Toh WS, Tomasini R, Torrecilhas AC, Tosar JP, Toxavidis V, Urbanelli L, Vader P, van Balkom BW, van der Grein SG, Van Deun J, van Herwijnen MJ, Van Keuren-Jensen K, van Niel G, van Royen ME, van Wijnen AJ, Vasconcelos MH, Vechetti IJ Jr, Veit TD, Vella LJ, Velot É, Verweij FJ, Vestad B, Viñas JL, Visnovitz T, Vukman KV, Wahlgren J, Watson DC, Wauben MH, Weaver A, Webber JP, Weber V, Wehman AM, Weiss DJ, Welsh JA, Wendt S, Wheelock AM, Wiener Z, Witte L, Wolfram J, Xagorari A, Xander P, Xu J, Yan X, Yáñez-Mó M, Yin H, Yuana Y, Zappulli V, Zarubova J, Žėkas V, Zhang JY, Zhao Z, Zheng L, Zheutlin AR, Zickler AM, Zimmermann P, Zivkovic AM, Zocco D, and Zuba-Surma EK
- Abstract
The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.
- Published
- 2018
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48. Novel CIL-102 derivatives as potential therapeutic agents for docetaxel-resistant prostate cancer.
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Miller DR, Tzeng CC, Farmer T, Keller ET, Caplan S, Chen YS, Chen YL, and Lin MF
- Subjects
- Antineoplastic Agents chemistry, Antineoplastic Agents metabolism, Apoptosis drug effects, Cell Line, Cell Line, Tumor, Cell Movement drug effects, Cell Proliferation drug effects, Humans, Male, Molecular Structure, Prostatic Neoplasms, Castration-Resistant drug therapy, Prostatic Neoplasms, Castration-Resistant pathology, Protein Binding, Quinolines chemistry, Quinolines metabolism, Reactive Oxygen Species metabolism, Tubulin metabolism, Antineoplastic Agents pharmacology, Docetaxel pharmacology, Drug Resistance, Neoplasm drug effects, Prostatic Neoplasms, Castration-Resistant metabolism, Quinolines pharmacology
- Abstract
The standard-of-care treatment for metastatic prostate cancer (PCa) is androgen deprivation therapy (ADT). Nevertheless, most tumors eventually relapse and develop into lethal castration-resistant prostate cancer (CRPC). Docetaxel is a FDA-approved agent for the treatment of CRPC; however, the tumor often quickly develops resistance to this drug. Thus, there is an immediate need for novel therapies to treat docetaxel-resistant PCa. In this study, we modified the structure of CIL-102 and investigated the efficacy of the derivatives against CRPC and docetaxel-resistant PCa. These novel CIL-102 derivatives inhibit CRPC tumorigenicity, including proliferation, migration and colony formation, and importantly, selectively inhibit CRPC cell proliferation over non-cancerous prostate epithelia. Computational modeling indicated the derivatives bind to β-tubulin and immunocytochemistry revealed the depolymerization of microtubules upon treatment. Western blot analyses reveal that pro-apoptotic and anti-oxidant pathways are activated, and MitoSOX and DCF-DA analyses confirmed increased reactive oxygen species (ROS) production upon treatments. Furthermore, CIL-102 derivatives effectively reduce the proliferation of docetaxel-resistant CR PCa cell lines. Our data indicate the potential of these compounds as promising therapeutic agents for CRPC as well as docetaxel-resistant CRPC., (Published by Elsevier B.V.)
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- 2018
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- View/download PDF
49. Prostate cancer tends to metastasize in the bone-mimicking microenvironment via activating NF-κB signaling.
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Tong HB, Zou CL, Qin SY, Meng J, Keller ET, Zhang J, and Lu Y
- Abstract
Prostate cancer preferentially metastasizes to the bone. However, the underlying molecular mechanisms are still unclear. To explore the effects of a bone-mimicking microenvironment on PC3 prostate cancer cell growth and metastasis, we used osteoblast differentiation medium (ODM; minimal essential medium alpha supplemented with L-ascorbic acid) to mimic the bone microenvironment. PC3 cells grown in ODM underwent epithelial-mesenchymal transition and showed enhanced colony formation, migration, and invasion abilities compared to the cells grown in normal medium. PC3 cells grown in ODM showed enhanced metastasis when injected in mice. A screening of signaling pathways related to invasion and metastasis revealed that the NF-κB pathway was activated, which could be reversed by Bay 11-7082, a NF-κB pathway inhibitor. These results indicate that the cells in different culture conditions manifested significantly different biological behaviors and the NF-κB pathway is a potential therapeutic target for prostate cancer bone metastasis.
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- 2018
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50. Crosstalk Between Androgen-sensitive and Androgen-insensitive Prostate Cancer Cells.
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Takezawa Y, Izumi K, Machioka K, Iwamoto H, Naito R, Makino T, Kadomoto S, Natsagdorj A, Kadono Y, Keller ET, Zhang J, and Mizokami A
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- Androgen Antagonists pharmacology, Androgen Antagonists therapeutic use, Cell Communication drug effects, Cell Line, Tumor, Cell Proliferation drug effects, Coculture Techniques, Drug Resistance, Neoplasm, Humans, Male, Receptors, Androgen metabolism, Signal Transduction drug effects, Androgens metabolism, Cell Communication physiology, Prostatic Neoplasms metabolism, Prostatic Neoplasms pathology, Prostatic Neoplasms, Castration-Resistant metabolism, Prostatic Neoplasms, Castration-Resistant pathology
- Abstract
Aim: To investigate how androgen-sensitive LNCaP cells crosstalk with androgen-insensitive DU145 or PC-3 cells., Materials and Methods: The numbers of LNCaP cells were counted when co-cultured with DU145 or PC-3 cells and vise versa. Androgen receptor (AR) activity in LNCaP cells was examined by luciferase reporter assay after transfection with a luciferase reporter driven by PSA promoter in the presence of DU145 or PC-3 cells. Concentration of androgens in the medium was measured by liquid chromatography-mass spectrometry (LC-MS/MS). The ability of migration and invasion of PC-3 and DU145 cells was investigated using a 2-layer chamber, in the presence of LNCaP cells., Results: Co-culture of LNCaP cells with DU145 cells resulted in the conversion of dehydroepiandrosterone (DHEA) to dihydrotestosterone (DHT), which stimulated cell proliferation and PSA promoter activity in LNCaP cells. The increased cell proliferation rate and AR activity, induced in LNCaP cells after DHT treatment, was further enhanced by co-culture with DU145 cells. LNCaP cells also stimulated the proliferation of DU145 and PC-3 cells, via secreting soluble factors. Finally, LNCaP cells promoted migration and invasion of PC-3 cells, in a co-culture system; however inhibited migration and invasion of DU145 cells., Conclusion: Crosstalk between androgen-sensitive PCa cells and androgen-insensitive PCa cells might develop the progression of PCa., (Copyright© 2018, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.)
- Published
- 2018
- Full Text
- View/download PDF
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