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7. Isoform-Level Transcriptome Analysis of Peripheral Blood Mononuclear Cells from Breast Cancer Patients Identifies a Disease-Associated RASGEF1A Isoform.

Author

Čelešnik, Helena, Gorenjak, Mario, Krušič, Martina, Crnobrnja, Bojana, Sobočan, Monika, Takač, Iztok, Arko, Darja, and Potočnik, Uroš

Subjects
RNA analysis, NUCLEIC acid analysis, MONONUCLEAR leukocytes, RESEARCH funding, BREAST tumors, POLYMERASE chain reaction, CANCER patients, TUMOR markers, BIOINFORMATICS, GENE expression profiling, EXTRACELLULAR space, SIGNAL peptides, SEQUENCE analysis
Abstract

Simple Summary: Peripheral blood analyses can offer a minimally invasive view into systemic immunity during cancer and can lead to the identification of biomarkers for cancer screening and therapeutic management. While a limited number of studies have reported blood transcriptome in breast cancer (BC) using RNA-seq analysis, our study is the first that aimed to identify potential BC biomarkers by analyzing transcriptome at an isoform level in peripheral blood mononuclear cells (PBMCs) from BC patients and healthy women. Our approach has led to the identification of an isoform of the RASGEF1A gene, the ENST00000374459 transcriptional variant, as a promising blood mRNA biomarker for distinguishing BC and healthy subjects. Additionally, our association analysis with clinicopathological characteristics revealed that lower ENST00000374459 expression in PBMCs of breast cancer patients was associated with higher proliferation and circulating tumor DNA (ctDNA) shedding, thereby linking expression of this isoform in blood immune cells to cancer progression and spreading. Background: Breast cancer (BC) comprises multiple subtypes with distinct molecular features, which differ in their interplay with host immunity, prognosis, and treatment. Non-invasive blood analyses can provide valuable insights into systemic immunity during cancer. The aim of this study was to analyze the expression of transcriptional isoforms in peripheral blood mononuclear cells (PBMCs) from BC patients and healthy women to identify potential BC immune biomarkers. Methods: RNA sequencing and isoform-level bioinformatics were performed on PBMCs from 12 triple-negative and 13 luminal A patients. Isoform expression validation by qRT-PCR and clinicopathological correlations were performed in a larger cohort (156 BC patients and 32 healthy women). Results: Transcriptional analyses showed a significant (p < 0.001) decrease in the ENST00000374459 RASGEF1A isoform in PBMCs of BC compared to healthy subjects, indicating disease-related expression changes. The decrease was associated with higher ctDNA and Ki-67 values. Conclusions: The levels of the RASGEF1A transcriptional isoform ENST00000374459 may have the potential to distinguish between BC and healthy subjects. The downregulation of ENST00000374459 in breast cancer is associated with higher proliferation and ctDNA shedding. Specialized bioinformatics analyses such as isoform analyses hold significant promise in the detection of biomarkers, since standard RNA sequencing analyses may overlook specific transcriptional changes that may be disease-associated and biologically important. [ABSTRACT FROM AUTHOR]

Published
2024
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14. Safety and tolerability of subcutaneous trastuzumab for the adjuvant treatment of human epidermal growth factor receptor 2-positive early breast cancer: SafeHer phase III study's primary analysis of 2573 patients

Author

Koroveshi, Dhurata, Bouzid, Kamel, Casalnuovo, Monica, Cascallar, Diana, Korbenfeld, Ernesto Pablo, Bastick, Patricia, Beith, Jane, Colosimo, Maree, Friedlander, Michael, Ganju, Vinod, Green, Michael, Patterson, Kevin, Redfern, Andrew, Richardson, Gary, Ceric, Timur, Gordana, Kecman, Beato, Carlos Augusto, Ferrari, Marcela, Hegg, Roberto, Helena, Vanessa, Ismael, Gustavo Fernando, Lessa, Alvaro Edson, Mano, Max, Morelle, Alessandra, Nogueira, Jose Alberto, Timcheva, Konstanta, Tomova, Antoaneta, Tsakova, Maya, Zlatareva-Petrova, Ani, Asselah, Jamil, Assi, Hazem, Brezden-Masley, Christine, Chia, Stephen, Freedman, Ori, Harb, Mohammed, Joy, Anil Abraham, Kulkarni, Swati, Prady, Catherine, Gaete, Alejandro Andres Acevedo, Matamala, Luis, Torres, Roberto, Yanez, Eduardo, Franco, Sandra, Urrego, Marcela, Gugić, Damir, Vrbanec, Damir, Melichar, Bohuslav, Prausová, Jana, Vyzula, Rostislav, Pilarte, Rafael Gutierrez, León, María Isabel, Muñoz, Rene, Ramos, Glenda, Azeem, Hamdy Abdel, Aziz, Amr Abdel, El Zawahry, Heba, Osegueda, Finlander Rosales, Alexandre, Jerome, Artignan, Xavier, Barletta, Hugues, Beguier, Emmanuel, Berdah, Jean-François, Marty, Chantal Bernard, Bollet, Marc, Bourgeois, Hugues, Bressac, Claude, Burki, Franck, Campone, Mario, Coeffic, David, Cojocarasu, Oana Zveltlana, Dagada, Corinne, Dalenc, Florence, Del Piano, Francesco, Desauw, Christophe, Desmoulins, Isabelle, Dohollou, Nadine, Egreteau, Joelle, Ferrero, Jean-Marc, Foa, Cyril, Garidi, Reda, Gasnault, Laurent, Gligorov, Joseph, Guardiola, Emmanuel, Hamizi, Salima, Jarcau, Rosana, Jacquin, Jean-Philippe, Jaubert, Dominique, Jolimoy, Geneviève, Mineur, Hortense Laharie, Largillier, Remy, Leduc, Bernard, Martin, Philippe, Melis, Adrien, Monge, Jeremy, Moullet, Isabelle, Mousseau, Mireille, Nguyen, Suzanne, Orfeuvre, Hubert, Petit, Thierry, Pivot, Xavier, Priou, Frank, Bach, Isabelle Sillet, Simon, Helene, Stefani, Laetitia, Uwer, Lionel, Youssef, Ali, Aktas, Bahriye, von der Assen, Albert, Augustin, Doris, Balser, Christina, Bauer, Lelia-Eveline, Bechtner, Christina, Beyer, Greta, Brucker, Cosima, Bückner, Ute, Busch, Steffi, Christensen, Bernd, Deryal, Mustafa, Farrokh, Andre, Faust, Elke, Friedrichs, Kay, Graf, Heiko, Griesshammer, Martin, Grischke, Eva-Maria, Hänle, Claudia, Heider, Andrea, Henschen, Stephan, Hesse, Tobias, Jackisch, Christian, Kisro, Jens, Köhler, Andreas, Kuemmel, Sherko, Lampe, Dieter, Lantzsch, Tilmann, Latos, Kunibert, Lex, Benno, Liedtke, Cornelia, Luedders, Doerte, Maintz, Christoph, Müller, Volkmar, Overkamp, Friedrich, Park-Simon, Tjoung-won, Paul, Marion, Prechtl, Anita, Ringsdorf, Uta, Runnebaum, Ingo, Ruth, Sylvia, Salat, Christoph, Scheffen, Iris, Schilling, Jörg, Schmatloch, Sabine, Schmidt, Marcus, Schneeweiss, Andreas, Schrader, Iris, Seipelt, Gernot, Simon, Elke, Stefek, Andrea, Stickeler, Elmar, Thill, Marc, Tio, Joke, Tuczek, Anna, Warm, Mathias, Weigel, Michael, Wischnik, Arthur, Wojcinski, Sebastian, Ziegler-Löhr, Katja, Aravantinos, Gerasimos, Ardavanis, Alexandros, Fountzilas, George, Gogas, Helen, Kakolyris, Stylianos, Mavroudis, Dimitris, Papadimitriou, Christos, Papandreou, Christos, Papazisis, Konstantinos, Castro, Hugo, Hernandez-Monroy, Cesar Estuardo, Ngan, Roger, Yeo, Winnie, Bittner, Nora, Boer, Katalin, Csejtei, Andras, Horvath, Zsolt, Kocsis, Judit, Mangel, László Csaba, Mezei, Klara, Nagy, Zsuzsanna, Szanto, Janos, Atmakusuma, Djumhana, Fadjari, Heri, Kurnianda, Djohan, Prayogo, Nugroho, Tanggo, Eddie Herman, Coate, Linda, Hennessy, Bryan, Kelly, Cathy, Martin, Michael, Nasim, Saira, O'Connor, Miriam, Aieta, Michele, Allegrini, Giacomo, Amadori, Dino, Bidoli, Paolo, Biti, Giampaolo, Bordonaro, Roberto, Bottini, Alberto, Carterni, Giacomo, Cavanna, Luigi, Cazzaniga, Marina, Cognetti, Francesco, Contu, Antonio, Cruciani, Giorgio, Donadio, Michela, Falcone, Alfredo, Farci, Daniele, Forcignanò, R. Chiara, Frassoldati, Antonio, Gaion, Fernando, Gamucci, Teresa, Giotta, Francesco, de Laurentiis, Michele, Livi, Lorenzo, Lorusso, Vito, Maiello, Evaristo, Marchetti, Paolo, Mariani, Gabriella, Mion, Marta, Moscetti, Luca, Musolino, Antonino, Pazzola, Antonio, Pedrazzoli, Paolo, Pigi, Andrea, de Placido, Sabino, Caremoli, Elena Rota, Santoro, Armando, Tienghi, Amelia, Ahn, Jin-Seok, Jung, Kyung Hae, Lee, Keun Seok, Lee, Soo Hyeon, Seo, Jae Hong, Sohn, Joo-Hyuk, Cesas, Alvydas, Juozaityte, Elona, Cheah, Nellie Lay Chin, Chong, Flora Li Tze, Devi, Beena C.R., Phua, Vincent, Teoh, Darren, Ching, Lee Wei, Yusof, Mastura, Corona, Jorge, Dominguez, Adriana, Mendoza, René Lazaro González, Hernandez, Carlos Alberto, Ramiro, Alejandro Juarez, Santos, Juan Matos, Espinosa, Paola Morales, Villarreal Garza, Cynthia Mayte, Errihani, Hassan, Bakker, Sandra, van den Berkmortel, Franchette, Blaisse, R.J.B., Huinink, Daan ten Bokkel, van den Bosch, J., Braun, J.J., Dercksen, M.W., Droogendijk, Helga, Erdkamp, Frans, Haringhuizen, Annebeth, de Jongh, F.E., Kok, T.C., Los, Maartje, Madretsma, Stanley, Terwogt, Jetske M. Meerum, van der Padt, Annemieke, van Rossum-Schornagel, Quirine Clementine, Smilde, T.J., de Valk, Bart, van der Velden, Annette, van Warmerdam, Laurence, van de Wouw, A.J., North, Richard, Kersten, Christian, Mjaaland, Ingvild, Wist, Erik, Aziz, Zeba, Masood, Nehal, Rashid, Kamran, Shah, Mazhar, Alcedo, Juan Carlos, Aleman, Diana, Neciosup, Silvia, Reategui, Rocio, Valdiviezo, Natalia, Vera, Luis, Fernando, Gracieux, Roque, Fernando, Strebel, Heinrik Martin, Krzemieniecki, Krzysztof, Litwiniuk, Maria, Mruk, Andrzej, Pienkowski, Tadeusz, Sawrycki, Piotr, Slomian, Grzegorz, Tomczak, Piotr, Afonso, Noemia, Cardoso, Fátima, Damasceno, Margarida, Nave, Monica, Badulescu, Florinel, Ciule, Larisa, Curescu, Stefan, Eniu, Alexandru, Filip, Dumitru, Grecea, Daniela, Jinga, Dan-Corneliu, Lungulescu, Dan, Oprean, Cristina Marinela, Stanculeanu, Dana Lucia, Turdean, Maria, Dvornichenko, Viktoria, Emelyanov, Sergey, Lichinitser, Mikhail, Manikhas, Alexey, Sakaeva, Dina, Shirinkin, Vadim, Stroyakovskiy, Daniil, Abulkhair, Omalkhair, Zekri, Jamal, Filipovic, Sladjana, Kovcin, Vladimir, Nedovic, Jasmina, Pesic, Jasna, Vasovic, Suzana, Ng, Raymond, Bystricky, Branislav, Leskova, Jaroslava, Mardiak, Jozef, Mišurová, Etela, Wagnerova, Maria, Takač, Iztok, Demetriou, Georgia Savva, Dreosti, Lydia, Govender, Poovandren, Jordaan, Johannes Petrus, Veersamy, Petrosian, Romero, Jose Luis Alonso, Lopez, Norberto Batista, Arias, Carmen Cañabate, Chacon, Jose, Aramburo, Antonio Fernandez, Morales, Luis Antonio Fernandez, Garcia, Mirta, Estevez, Laura Garcia, Garcia-Palomo Perez, Andres, Garcia Saenz, Jose Angel, Garcia Sanchis, Laura, Cubells, Laia Garrigos, Cortijo, Lucia Gonzalez, Santiago, Santiago Gonzalez, De Aranguiz, Blanca Hernando Fernandez, Mañas, José Juan Illarramendi, Gallego, Pedro Jimenez, Cussac, Antonio Llombart, Ferrandiz, Cristina Llorca, Garrido, Maria Lomas, Alvarez, Pilar Lopez, Vega, Jose Manuel Lopez, Del Prado, Purificacion Martinez, Jañez, Noelia Martinez, Murillo, Serafin Morales, Rosales, Adolfo Murias, Jaso, Laura Murillo, Fernandez, Ignacio Pelaez, Martorell, Antonia Perello, Carrion, Ramon Perez, Simon, Sonia Pernas, Alcibar, Arrate Plazaola, Lorenzo, Jose Ponce, Garcia, Vanesa Quiroga, Asensio, Teresa Ramon y Cajal, Maicas, Maria Dolores Torregrosa, Villanueva Silva, Maria Jose, Killander, Fredrika, Svensson, Jan Henry, Fehr, Mathias, Hauser, Nik, Müller, Andreas, Pagani, Olivia, Passmann-Kegel, Heike, Popescu, Razvan, Rabaglio, Manuela, Rauch, Daniel, Schlatter, Christina, Zaman, Khalil, Chang, Tsai-Wang, Huang, Chiun-Sheng, Wang, Hwei-Chung, Yu, Jyh-Cherng, Bandidwattanawong, Chanyoot, Maneechavakajorn, Jedzada, Seetalarom, Kasan, Dejthevaporn, Thitiya (Sirisinha), Somwangprasert, Areewan, Vongsaisuwon, Mawin, Akbulut, Hakan, Altundag, Kadri, Arican, Ali, Bozcuk, Hakan, Eralp, Yesim, Idris, Mohamed, Isikdogan, Abdurrahman, Senol, Coskun Hasan, Sevinc, Alper, Uygun, Kazim, Yucel, Eftal, Yucel, Idris, Yumuk, Fulden, Shparyk, Yaroslav, Voitko, Nataliia, Jaloudi, Mohammed, Adams, Jocelyn, Agrawal, Rajiv, Ahmed, Samreen, Alhasso, Abdulla, Allerton, Rozenn, Anwar, Suhail, Archer, Caroline, Ashford, Richard, Barraclough, Lisa, Bertelli, Gianfilippo, Bishop, Jill, Branson, Tony, Butt, Mohammed, Chakrabarti, Amit, Chakraborti, Prabir, Churn, Mark, Crowley, Clare, Davis, Ruth, Dhadda, Amandeep, Eldeeb, Hany, Fraser, Judith, Hall, Julia, Hickish, Tamas, Hogg, Martin, Howe, Theresa, Joffe, Jonathan, Kelleher, Muireann, Kelly, Stephen, Kendall, Anne, Kristeleit, Hartmut, Lumsden, Graeme, Macmillan, Craig, MacPherson, Iain, Malik, Zafar, Mithal, Natasha, Neal, Anthony, Panwar, Udaiveer, Proctor, Andrew, Proctor, Steven John, Raj, Sanjay, Rehman, Shazza, Sandri, Ines, Scatchard, Kate, Sherwin, Elizabeth, Sims, Eliot, Singer, Julian, Smith, Sarah, Tahir, Saad, Taylor, Wendy, Tsalic, Medy, Verrill, Mark, Wardley, Andrew, Waters, Simon, Wheatley, Duncan, Wright, Kathryn, Yuille, Frances, Alonso, Isabel, Artagaveytia, Nora, Rodriguez, Robinson, Arbona, Esther, Garcia, Yuraima, Lion, Lorena, Marcano, Dalila, Van Thuan, Tran, Gligorov, J., Ataseven, B., Verrill, M., De Laurentiis, M., Jung, K.H., Azim, H.A., Al-Sakaff, N., Lauer, S., Shing, M., and Pivot, X.

Published
2017
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16. Survival of node-negative breast cancer patients treated at the university medical centre Maribor in the period 2000–2009

Author

Fokter Dovnik Nina, Arko Darja, Čas Sikošek Nina, and Takač Iztok

Subjects
breast cancer, survival, time trends, regional differences, slovenia, rak dojk, preživetje, časovni vzorci, regionalne razlike, slovenija, Public aspects of medicine, RA1-1270
Abstract

Breast cancer is increasingly diagnosed in the early stages without regional nodal involvement. The aim of the present study was to determine the 5-year overall (OS) and breast cancer specific survival (BCSS) for patients with node-negative breast cancer treated at the University Medical Centre Maribor, and compare it with survival at the national level.

Published
2017
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18. Recommendations for diagnosis, treatment and follow-up of patients with ovarian cancer, fallopian tube cancer and primary peritoneal cancer

Author

Kovačević, Nina, Šegedin, Barbara, Merlo, Sebastjan, Bebar, Sonja, Blatnik, Ana, Cokan, Andrej, Cvjetičanin, Branko, Fokter Dovnik, Nina, Gazič, Barbara, Grčar Kuzmanov, Biljana, Gregorič, Brigita, Horvat, Matej, Janša, Vid, Knez, Jure, Kobal, Borut, Kobav, Manja, Krajc, Mateja, Krajec, Maja, Lasič, Mateja, Novaković, Srdjan, Pakiž, Maja, Ravnik, Maja, Smrkolj, Špela, Strojnik, Ksenija, Škof, Erik, Takač, Iztok, Vivod, Gregor, Zadnik, Vesna, and Zobec Logar, Barbara Helena

Abstract

no abstract., Onkologija : a medical-scientific journal, Vol. 26 No. 2 (2022)

Published
2022
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20. Effectiveness of artificial intelligence algorithms in identification of patients with high-grade histopathology after conisation.

Author

Mlinarič, Marko, Mlinarič, Maša, Križmarić, Miljenko, Takač, Iztok, and Fokter, Alenka Repše

Abstract

The aim of this study was to compare effectiveness of various artificial intelligence classification algorithms in identifying patients with high-grade final histopathology of conisation based on last PAP smear result and risk factors for development of uterine cervical dysplasia and cancer. The data of 1475 patients who underwent conisation surgery at University Clinical Centre Maribor between 1993-2005 were analysed. Synthetic Minority Oversampling Technique (SMOTE) algorithm was employed for the imbalanced data correction. Various classification algorithms were tested with Weka open-source software. The 10-fold cross validation was used to define testing and hold-out set for analysis. Random Forest (RF) classification algorithm was better than the other tested algorithms and achieved 89.42% correct classifications (baseline ZeroR classification 63.4%, sensitivity 96.80%, specificity 76.60%, kappa 0.7632, Area under Receiver Operation Characteristic curve (AUC ROC) 0.911, Precision Recall curve (PRC) Area 0.916, and Matthews Correlation Coefficient (MCC) 0.771. Random Forest (RF) algorithm correctly identified majority of patients with final high-grade histopathology of conisation from patients dataset based on last PAP smear result and risk factors of developing high-grade dysplasia and carcinoma. Such algorithms can help clinicians to identify high-risk patients in future. An invitation could be sent to patients who did not participate in organized screening program, thus preventing the serious disease. Further studies are required in this regard. [ABSTRACT FROM AUTHOR]

Published
2023
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26. Programske smernice Državnega programa ZORA

Author

Ivanuš, Urška, Arh, Edita, Bebar, Sonja, Cvjetičanin, Branko, Deisinger, Dušan, Florjančič, Mojca, Frelih, Aljoša, Gašper, Urška, Grčar-Kuzmanov, Biljana, Jančar, Nina, Jerman, Tine, Kališnik, Kaja, Kašnik-Čas, Silvestra, Kloboves-Prevodnik, Veronika, Kobal, Borut, Duratović Konjević, Amela, Kos, Jerneja, Kupljen, Gabrijela, Lasič Pecev, Mateja, Marčec, Mateja, Meglič, Leon, Merlo, Sebastjan, Mlinarič, Marko, Nolde, Nataša, Oblak, Irena, Pakiž, Maja, Pirš, Boštjan, Pogačnik, Ana, Primic-Žakelj, Maja, Repše-Fokter, Alenka, Roškar, Luka, Salobir Gajšek, Uršula, Sitar, Špela, Smrkolj, Špela, Snoj, Vivijana, Strojan Fležar, Margareta, Štrumbelj, Tadeja, Takač, Iztok, Toff-Jovan, Renata, Tušek, Tomaž, and Uštar, Andreja

Subjects
zgodnja diagnostika, presejanje, presejalni programi, nacionalni programi, elektronske knjige, postopki, udc:618.146-006-07(082)(0.034.2), predrakave spremembe
Published
2022

30. MFUM-BrTNBC-1, a Newly Established Patient-Derived Triple-Negative Breast Cancer Cell Line: Molecular Characterisation, Genetic Stability, and Comprehensive Comparison with Commercial Breast Cancer Cell Lines

Author

Skok, Kristijan, primary, Gradišnik, Lidija, additional, Čelešnik, Helena, additional, Milojević, Marko, additional, Potočnik, Uroš, additional, Jezernik, Gregor, additional, Gorenjak, Mario, additional, Sobočan, Monika, additional, Takač, Iztok, additional, Kavalar, Rajko, additional, and Maver, Uroš, additional

Published
2021
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