Immunologically 'cold' triple negative breast cancers engraft at a higher rate in patient derived xenografts

Autor: Varduhi Petrosyan, Lacey E. Dobrolecki, Emily L. LaPlante, Ramakrishnan Rajaram Srinivasan, Matthew H. Bailey, Alana L. Welm, Bryan E. Welm, Michael T. Lewis, Aleksandar Milosavljevic

Publikováno v: npj Breast Cancer, Vol 8, Iss 1, Pp 1-5 (2022)

Abstract TNBC is a heterogeneous subtype of breast cancer, and only a subset of TNBC can be established as PDXs. Here, we show that there is an engraftment bias toward TNBC with low levels of immune cell infiltration. Additionally, TNBC that failed t

Externí odkaz: https://doaj.org/article/df1189d5619f478396baf68cd383f8f1

Clinical diagnosis of metabolic disorders using untargeted metabolomic profiling and disease-specific networks learned from profiling data

Autor: Lillian R. Thistlethwaite, Xiqi Li, Lindsay C. Burrage, Kevin Riehle, Joseph G. Hacia, Nancy Braverman, Michael F. Wangler, Marcus J. Miller, Sarah H. Elsea, Aleksandar Milosavljevic

Publikováno v: Scientific Reports, Vol 12, Iss 1, Pp 1-17 (2022)

Abstract Untargeted metabolomics is a global molecular profiling technology that can be used to screen for inborn errors of metabolism (IEMs). Metabolite perturbations are evaluated based on current knowledge of specific metabolic pathway deficiencie

Externí odkaz: https://doaj.org/article/310f472f536f4ec6800d411142c0cff3

Identifying biomarkers of differential chemotherapy response in TNBC patient-derived xenografts with a CTD/WGCNA approach

Autor: Varduhi Petrosyan, Lacey E. Dobrolecki, Lillian Thistlethwaite, Alaina N. Lewis, Christina Sallas, Ramakrishnan R. Srinivasan, Jonathan T. Lei, Vladimir Kovacevic, Predrag Obradovic, Matthew J. Ellis, C. Kent Osborne, Mothaffar F. Rimawi, Anne Pavlick, Maryam Nemati Shafaee, Heidi Dowst, Antrix Jain, Alexander B. Saltzman, Anna Malovannaya, Elisabetta Marangoni, Alana L. Welm, Bryan E. Welm, Shunqiang Li, Gerburg M. Wulf, Olmo Sonzogni, Chen Huang, Suhas Vasaikar, Susan G. Hilsenbeck, Bing Zhang, Aleksandar Milosavljevic, Michael T. Lewis

Publikováno v: iScience, Vol 26, Iss 1, Pp 105799- (2023)

Summary: Although systemic chemotherapy remains the standard of care for TNBC, even combination chemotherapy is often ineffective. The identification of biomarkers for differential chemotherapy response would allow for the selection of responsive pat

Externí odkaz: https://doaj.org/article/2b0f86504c374089a6c4e5c09a09e1cb

Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research

Autor: Bogdan Mateescu, Jennifer C. Jones, Roger P. Alexander, Eric Alsop, Ji Yeong An, Mohammad Asghari, Alex Boomgarden, Laura Bouchareychas, Alfonso Cayota, Hsueh-Chia Chang, Al Charest, Daniel T. Chiu, Robert J. Coffey, Saumya Das, Peter De Hoff, Andrew deMello, Crislyn D’Souza-Schorey, David Elashoff, Kiarash R. Eliato, Jeffrey L. Franklin, David J. Galas, Mark B. Gerstein, Ionita H. Ghiran, David B. Go, Stephen Gould, Tristan R. Grogan, James N. Higginbotham, Florian Hladik, Tony Jun Huang, Xiaoye Huo, Elizabeth Hutchins, Dennis K. Jeppesen, Tijana Jovanovic-Talisman, Betty Y.S. Kim, Sung Kim, Kyoung-Mee Kim, Yong Kim, Robert R. Kitchen, Vaughan Knouse, Emily L. LaPlante, Carlito B. Lebrilla, L. James Lee, Kathleen M. Lennon, Guoping Li, Feng Li, Tieyi Li, Tao Liu, Zirui Liu, Adam L. Maddox, Kyle McCarthy, Bessie Meechoovet, Nalin Maniya, Yingchao Meng, Aleksandar Milosavljevic, Byoung-Hoon Min, Amber Morey, Martin Ng, John Nolan, Getulio P. De Oliveira Junior, Michael E. Paulaitis, Tuan Anh Phu, Robert L. Raffai, Eduardo Reátegui, Matthew E. Roth, David A. Routenberg, Joel Rozowsky, Joseph Rufo, Satyajyoti Senapati, Sigal Shachar, Himani Sharma, Anil K. Sood, Stavros Stavrakis, Alessandra Stürchler, Muneesh Tewari, Juan P. Tosar, Alexander K. Tucker-Schwartz, Andrey Turchinovich, Nedyalka Valkov, Kendall Van Keuren-Jensen, Kasey C. Vickers, Lucia Vojtech, Wyatt N. Vreeland, Ceming Wang, Kai Wang, ZeYu Wang, Joshua A. Welsh, Kenneth W. Witwer, David T.W. Wong, Jianping Xia, Ya-Hong Xie, Kaichun Yang, Mikołaj P. Zaborowski, Chenguang Zhang, Qin Zhang, Angela M. Zivkovic, Louise C. Laurent

Publikováno v: iScience, Vol 25, Iss 8, Pp 104653- (2022)

Summary: The extracellular RNA communication consortium (ERCC) is an NIH-funded program aiming to promote the development of new technologies, resources, and knowledge about exRNAs and their carriers. After Phase 1 (2013–2018), Phase 2 of the progr

Externí odkaz: https://doaj.org/article/d72ed055b3ab4740b73e722d85b82959

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

Autor: Clémentine Decamps, Florian Privé, Raphael Bacher, Daniel Jost, Arthur Waguet, HADACA consortium, Eugene Andres Houseman, Eugene Lurie, Pavlo Lutsik, Aleksandar Milosavljevic, Michael Scherer, Michael G. B. Blum, Magali Richard

Publikováno v: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-15 (2020)

Abstract Background Cell-type heterogeneity of tumors is a key factor in tumor progression and response to chemotherapy. Tumor cell-type heterogeneity, defined as the proportion of the various cell-types in a tumor, can be inferred from DNA methylati

Externí odkaz: https://doaj.org/article/33510f0e09a647fc969cdf1e7068af53