269 results on '"Varn, Frederick S."'
Search Results
2. Glioma progression is shaped by genetic evolution and microenvironment interactions
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Varn, Frederick S, Johnson, Kevin C, Martinek, Jan, Huse, Jason T, Nasrallah, MacLean P, Wesseling, Pieter, Cooper, Lee AD, Malta, Tathiane M, Wade, Taylor E, Sabedot, Thais S, Brat, Daniel, Gould, Peter V, Wöehrer, Adelheid, Aldape, Kenneth, Ismail, Azzam, Sivajothi, Santhosh K, Barthel, Floris P, Kim, Hoon, Kocakavuk, Emre, Ahmed, Nazia, White, Kieron, Datta, Indrani, Moon, Hyo-Eun, Pollock, Steven, Goldfarb, Christine, Lee, Ga-Hyun, Garofano, Luciano, Anderson, Kevin J, Nehar-Belaid, Djamel, Barnholtz-Sloan, Jill S, Bakas, Spyridon, Byrne, Annette T, D’Angelo, Fulvio, Gan, Hui K, Khasraw, Mustafa, Migliozzi, Simona, Ormond, D Ryan, Paek, Sun Ha, Van Meir, Erwin G, Walenkamp, Annemiek ME, Watts, Colin, Weiss, Tobias, Weller, Michael, Palucka, Karolina, Stead, Lucy F, Poisson, Laila M, Noushmehr, Houtan, Iavarone, Antonio, Verhaak, Roel GW, Consortium, The GLASS, Alfaro, Kristin D, Amin, Samirkumar B, Ashley, David M, Bock, Christoph, Brodbelt, Andrew, Bulsara, Ketan R, and Castro, Ana Valeria
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Biological Sciences ,Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Rare Diseases ,Brain Disorders ,Brain Cancer ,Genetics ,Cancer ,Neurosciences ,2.1 Biological and endogenous factors ,Aetiology ,Adult ,Brain Neoplasms ,Evolution ,Molecular ,Genes ,p16 ,Glioma ,Humans ,Isocitrate Dehydrogenase ,Mutation ,Neoplasm Recurrence ,Local ,Tumor Microenvironment ,GLASS Consortium ,genomics ,glioblastoma ,glioma ,hypermutation ,macrophages ,microenvironment ,neurons ,single-cell ,spatial imaging ,treatment resistance ,Medical and Health Sciences ,Developmental Biology ,Biological sciences ,Biomedical and clinical sciences - Abstract
The factors driving therapy resistance in diffuse glioma remain poorly understood. To identify treatment-associated cellular and genetic changes, we analyzed RNA and/or DNA sequencing data from the temporally separated tumor pairs of 304 adult patients with isocitrate dehydrogenase (IDH)-wild-type and IDH-mutant glioma. Tumors recurred in distinct manners that were dependent on IDH mutation status and attributable to changes in histological feature composition, somatic alterations, and microenvironment interactions. Hypermutation and acquired CDKN2A deletions were associated with an increase in proliferating neoplastic cells at recurrence in both glioma subtypes, reflecting active tumor growth. IDH-wild-type tumors were more invasive at recurrence, and their neoplastic cells exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. Mesenchymal transition was associated with the presence of a myeloid cell state defined by specific ligand-receptor interactions with neoplastic cells. Collectively, these recurrence-associated phenotypes represent potential targets to alter disease progression.
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- 2022
3. Multifactorial Deep Learning Reveals Pan-Cancer Genomic Tumor Clusters with Distinct Immunogenomic Landscape and Response to Immunotherapy
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Xie, Feng, Zhang, Jianjun, Wang, Jiayin, Reuben, Alexandre, Xu, Wei, Yi, Xin, Varn, Frederick S, Ye, Yongsheng, Cheng, Junwen, Yu, Miao, Wang, Yue, Liu, Yufeng, Xie, Mingchao, Du, Peng, Ma, Ke, Ma, Xin, Zhou, Penghui, Yang, Shengli, Chen, Yaobing, Wang, Guoping, Xia, Xuefeng, Liao, Zhongxing, Heymach, John V, Wistuba, Ignacio I, Futreal, P Andrew, Ye, Kai, Cheng, Chao, and Xia, Tian
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Immunology ,Cancer ,Immunization ,Human Genome ,Genetics ,Vaccine Related ,Biomarkers ,Tumor ,DNA Copy Number Variations ,Deep Learning ,Follow-Up Studies ,Gene Expression Regulation ,Neoplastic ,Genomics ,Humans ,Immunotherapy ,Microsatellite Instability ,Neoplasms ,Prognosis ,Survival Rate ,Tumor Microenvironment ,Oncology & Carcinogenesis ,Clinical sciences ,Oncology and carcinogenesis - Abstract
PurposeTumor genomic features have been of particular interest because of their potential impact on the tumor immune microenvironment and response to immunotherapy. Due to the substantial heterogeneity, an integrative approach incorporating diverse molecular features is needed to characterize immunologic features underlying primary resistance to immunotherapy and for the establishment of novel predictive biomarkers.Experimental designWe developed a pan-cancer deep machine learning model integrating tumor mutation burden, microsatellite instability, and somatic copy-number alterations to classify tumors of different types into different genomic clusters, and assessed the immune microenvironment in each genomic cluster and the association of each genomic cluster with response to immunotherapy.ResultsOur model grouped 8,646 tumors of 29 cancer types from The Cancer Genome Atlas into four genomic clusters. Analysis of RNA-sequencing data revealed distinct immune microenvironment in tumors of each genomic class. Furthermore, applying this model to tumors from two melanoma immunotherapy clinical cohorts demonstrated that patients with melanoma of different genomic classes achieved different benefit from immunotherapy. Interestingly, tumors in cluster 4 demonstrated a cold immune microenvironment and lack of benefit from immunotherapy despite high microsatellite instability burden.ConclusionsOur study provides a proof for principle that deep learning modeling may have the potential to discover intrinsic statistical cross-modality correlations of multifactorial input data to dissect the molecular mechanisms underlying primary resistance to immunotherapy, which likely involves multiple factors from both the tumor and host at different molecular levels.
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- 2020
4. Comparative Molecular Life History of Spontaneous Canine and Human Gliomas
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Amin, Samirkumar B, Anderson, Kevin J, Boudreau, C Elizabeth, Martinez-Ledesma, Emmanuel, Kocakavuk, Emre, Johnson, Kevin C, Barthel, Floris P, Varn, Frederick S, Kassab, Cynthia, Ling, Xiaoyang, Kim, Hoon, Barter, Mary, Lau, Ching C, Ngan, Chew Yee, Chapman, Margaret, Koehler, Jennifer W, Long, James P, Miller, Andrew D, Miller, C Ryan, Porter, Brian F, Rissi, Daniel R, Mazcko, Christina, LeBlanc, Amy K, Dickinson, Peter J, Packer, Rebecca A, Taylor, Amanda R, Rossmeisl, John H, Woolard, Kevin D, Heimberger, Amy B, Levine, Jonathan M, and Verhaak, Roel GW
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Biological Sciences ,Bioinformatics and Computational Biology ,Genetics ,Brain Cancer ,Human Genome ,Rare Diseases ,Cancer ,Brain Disorders ,Neurosciences ,Animals ,Brain Neoplasms ,DNA Methylation ,Dogs ,Exome ,Glioma ,Humans ,Isocitrate Dehydrogenase ,Mutation ,Tumor Suppressor Protein p53 ,adult glioma ,canine glioma ,comparative genomics ,comparative oncology ,computational biology ,life history ,mutagenesis ,pediatric glioma ,Oncology and Carcinogenesis ,Oncology & Carcinogenesis ,Biochemistry and cell biology ,Oncology and carcinogenesis - Abstract
Sporadic gliomas in companion dogs provide a window on the interaction between tumorigenic mechanisms and host environment. We compared the molecular profiles of canine gliomas with those of human pediatric and adult gliomas to characterize evolutionarily conserved mammalian mutational processes in gliomagenesis. Employing whole-genome, exome, transcriptome, and methylation sequencing of 83 canine gliomas, we found alterations shared between canine and human gliomas such as the receptor tyrosine kinases, TP53 and cell-cycle pathways, and IDH1 R132. Canine gliomas showed high similarity with human pediatric gliomas per robust aneuploidy, mutational rates, relative timing of mutations, and DNA-methylation patterns. Our cross-species comparative genomic analysis provides unique insights into glioma etiology and the chronology of glioma-causing somatic alterations.
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- 2020
5. Longitudinal molecular trajectories of diffuse glioma in adults
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Barthel, Floris P, Johnson, Kevin C, Varn, Frederick S, Moskalik, Anzhela D, Tanner, Georgette, Kocakavuk, Emre, Anderson, Kevin J, Abiola, Olajide, Aldape, Kenneth, Alfaro, Kristin D, Alpar, Donat, Amin, Samirkumar B, Ashley, David M, Bandopadhayay, Pratiti, Barnholtz-Sloan, Jill S, Beroukhim, Rameen, Bock, Christoph, Brastianos, Priscilla K, Brat, Daniel J, Brodbelt, Andrew R, Bruns, Alexander F, Bulsara, Ketan R, Chakrabarty, Aruna, Chakravarti, Arnab, Chuang, Jeffrey H, Claus, Elizabeth B, Cochran, Elizabeth J, Connelly, Jennifer, Costello, Joseph F, Finocchiaro, Gaetano, Fletcher, Michael N, French, Pim J, Gan, Hui K, Gilbert, Mark R, Gould, Peter V, Grimmer, Matthew R, Iavarone, Antonio, Ismail, Azzam, Jenkinson, Michael D, Khasraw, Mustafa, Kim, Hoon, Kouwenhoven, Mathilde CM, LaViolette, Peter S, Li, Meihong, Lichter, Peter, Ligon, Keith L, Lowman, Allison K, Malta, Tathiane M, Mazor, Tali, McDonald, Kerrie L, Molinaro, Annette M, Nam, Do-Hyun, Nayyar, Naema, Ng, Ho Keung, Ngan, Chew Yee, Niclou, Simone P, Niers, Johanna M, Noushmehr, Houtan, Noorbakhsh, Javad, Ormond, D Ryan, Park, Chul-Kee, Poisson, Laila M, Rabadan, Raul, Radlwimmer, Bernhard, Rao, Ganesh, Reifenberger, Guido, Sa, Jason K, Schuster, Michael, Shaw, Brian L, Short, Susan C, Smitt, Peter A Sillevis, Sloan, Andrew E, Smits, Marion, Suzuki, Hiromichi, Tabatabai, Ghazaleh, Van Meir, Erwin G, Watts, Colin, Weller, Michael, Wesseling, Pieter, Westerman, Bart A, Widhalm, Georg, Woehrer, Adelheid, Yung, WK Alfred, Zadeh, Gelareh, Huse, Jason T, De Groot, John F, Stead, Lucy F, and Verhaak, Roel GW
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Neurosciences ,Brain Disorders ,Cancer ,Rare Diseases ,Brain Cancer ,Genetics ,Adult ,Chromosomes ,Human ,Pair 1 ,Chromosomes ,Human ,Pair 19 ,Disease Progression ,Glioma ,Humans ,Isocitrate Dehydrogenase ,Mutation ,Polymorphism ,Single Nucleotide ,Recurrence ,GLASS Consortium ,General Science & Technology - Abstract
The evolutionary processes that drive universal therapeutic resistance in adult patients with diffuse glioma remain unclear1,2. Here we analysed temporally separated DNA-sequencing data and matched clinical annotation from 222 adult patients with glioma. By analysing mutations and copy numbers across the three major subtypes of diffuse glioma, we found that driver genes detected at the initial stage of disease were retained at recurrence, whereas there was little evidence of recurrence-specific gene alterations. Treatment with alkylating agents resulted in a hypermutator phenotype at different rates across the glioma subtypes, and hypermutation was not associated with differences in overall survival. Acquired aneuploidy was frequently detected in recurrent gliomas and was characterized by IDH mutation but without co-deletion of chromosome arms 1p/19q, and further converged with acquired alterations in the cell cycle and poor outcomes. The clonal architecture of each tumour remained similar over time, but the presence of subclonal selection was associated with decreased survival. Finally, there were no differences in the levels of immunoediting between initial and recurrent gliomas. Collectively, our results suggest that the strongest selective pressures occur during early glioma development and that current therapies shape this evolution in a largely stochastic manner.
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- 2019
6. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response
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Johnson, Kevin C., Anderson, Kevin J., Courtois, Elise T., Gujar, Amit D., Barthel, Floris P., Varn, Frederick S., Luo, Diane, Seignon, Martine, Yi, Eunhee, Kim, Hoon, Estecio, Marcos R. H., Zhao, Dacheng, Tang, Ming, Navin, Nicholas E., Maurya, Rahul, Ngan, Chew Yee, Verburg, Niels, de Witt Hamer, Philip C., Bulsara, Ketan, Samuels, Michael L., Das, Sunit, Robson, Paul, and Verhaak, Roel G. W.
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- 2021
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7. Radiotherapy is associated with a deletion signature that contributes to poor outcomes in patients with cancer
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Kocakavuk, Emre, Anderson, Kevin J., Varn, Frederick S., Johnson, Kevin C., Amin, Samirkumar B., Sulman, Erik. P., Lolkema, Martijn P., Barthel, Floris P., and Verhaak, Roel G. W.
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- 2021
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8. The epigenetic evolution of glioma is determined by the IDH1 mutation status and treatment regimen
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Malta, Tathiane M; https://orcid.org/0000-0003-1129-5791, Sabedot, Thais S; https://orcid.org/0000-0002-7813-483X, Morosini, Natalia S; https://orcid.org/0000-0002-9294-9461, Datta, Indrani; https://orcid.org/0000-0001-7548-9881, Garofano, Luciano; https://orcid.org/0000-0001-8582-0865, Vallentgoed, Wies R; https://orcid.org/0000-0001-6373-7710, Varn, Frederick S; https://orcid.org/0000-0001-6307-016X, Aldape, Kenneth; https://orcid.org/0000-0001-5119-7550, D'Angelo, Fulvio; https://orcid.org/0000-0002-4940-4693, Bakas, Spyridon; https://orcid.org/0000-0001-8734-6482, Barnholtz-Sloan, Jill S; https://orcid.org/0000-0001-6190-9304, Gan, Hui K; https://orcid.org/0000-0001-7319-8546, Hasanain, Mohammad; https://orcid.org/0000-0001-5207-101X, Hau, Ann-Christin; https://orcid.org/0000-0002-4412-2355, Johnson, Kevin C; https://orcid.org/0000-0003-0016-5158, Cazacu, Simona; https://orcid.org/0000-0002-6085-4177, deCarvalho, Ana C; https://orcid.org/0000-0003-1183-4548, Khasraw, Mustafa; https://orcid.org/0000-0003-3249-9849, Kocakavuk, Emre; https://orcid.org/0000-0003-1920-0494, Kouwenhoven, Mathilde C M; https://orcid.org/0000-0001-5252-4365, Migliozzi, Simona; https://orcid.org/0000-0002-4870-8943, Niclou, Simone P; https://orcid.org/0000-0002-3417-9534, Niers, Johanna M; https://orcid.org/0000-0002-0366-8247, Ormond, D Ryan; https://orcid.org/0000-0001-7027-2915, Paek, Sun Ha; https://orcid.org/0000-0003-3007-8653, Reifenberger, Guido; https://orcid.org/0000-0002-1419-9837, Sillevis Smitt, Peter A; https://orcid.org/0000-0001-8044-6798, Smits, Marion; https://orcid.org/0000-0001-5563-2871, Weiss, Tobias; https://orcid.org/0000-0002-5533-9429, Weller, Michael; https://orcid.org/0000-0002-1748-174X, et al, Malta, Tathiane M; https://orcid.org/0000-0003-1129-5791, Sabedot, Thais S; https://orcid.org/0000-0002-7813-483X, Morosini, Natalia S; https://orcid.org/0000-0002-9294-9461, Datta, Indrani; https://orcid.org/0000-0001-7548-9881, Garofano, Luciano; https://orcid.org/0000-0001-8582-0865, Vallentgoed, Wies R; https://orcid.org/0000-0001-6373-7710, Varn, Frederick S; https://orcid.org/0000-0001-6307-016X, Aldape, Kenneth; https://orcid.org/0000-0001-5119-7550, D'Angelo, Fulvio; https://orcid.org/0000-0002-4940-4693, Bakas, Spyridon; https://orcid.org/0000-0001-8734-6482, Barnholtz-Sloan, Jill S; https://orcid.org/0000-0001-6190-9304, Gan, Hui K; https://orcid.org/0000-0001-7319-8546, Hasanain, Mohammad; https://orcid.org/0000-0001-5207-101X, Hau, Ann-Christin; https://orcid.org/0000-0002-4412-2355, Johnson, Kevin C; https://orcid.org/0000-0003-0016-5158, Cazacu, Simona; https://orcid.org/0000-0002-6085-4177, deCarvalho, Ana C; https://orcid.org/0000-0003-1183-4548, Khasraw, Mustafa; https://orcid.org/0000-0003-3249-9849, Kocakavuk, Emre; https://orcid.org/0000-0003-1920-0494, Kouwenhoven, Mathilde C M; https://orcid.org/0000-0001-5252-4365, Migliozzi, Simona; https://orcid.org/0000-0002-4870-8943, Niclou, Simone P; https://orcid.org/0000-0002-3417-9534, Niers, Johanna M; https://orcid.org/0000-0002-0366-8247, Ormond, D Ryan; https://orcid.org/0000-0001-7027-2915, Paek, Sun Ha; https://orcid.org/0000-0003-3007-8653, Reifenberger, Guido; https://orcid.org/0000-0002-1419-9837, Sillevis Smitt, Peter A; https://orcid.org/0000-0001-8044-6798, Smits, Marion; https://orcid.org/0000-0001-5563-2871, Weiss, Tobias; https://orcid.org/0000-0002-5533-9429, Weller, Michael; https://orcid.org/0000-0002-1748-174X, and et al
- Abstract
Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histological progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neo-angiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution towards an IDHwt-like phenotype.
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- 2024
9. The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen
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Malta, Tathiane M., Sabedot, Thais S., Morosini, Natalia S., Datta, Indrani, Garofano, Luciano, Vallentgoed, Wies, Varn, Frederick S., Aldape, Kenneth, D'Angelo, Fulvio, Bakas, Spyridon, Barnholtz-Sloan, Jill S., Gan, Hui K., Hasanain, Mohammad, Hau, Ann Christin, Johnson, Kevin C., Cazacu, Simona, deCarvalho, Ana C., Khasraw, Mustafa, Kocakavuk, Emre, Kouwenhoven, Mathilde C.M., Migliozzi, Simona, Niclou, Simone P., Niers, Johanna M., Ormond, D. Ryan, Paek, Sun Ha, Reifenberger, Guido, Smitt, Peter A.Sillevis, Smits, Marion, Stead, Lucy F., van den Bent, Martin J., Van Meir, Erwin G., Walenkamp, Annemiek, Weiss, Tobias, Weller, Michael, Westerman, Bart A., Ylstra, Bauke, Wesseling, Pieter, Lasorella, Anna, French, Pim J., Poisson, Laila M., Verhaak, Roel G.W., Iavarone, Antonio, Noushmehr, Houtan, Malta, Tathiane M., Sabedot, Thais S., Morosini, Natalia S., Datta, Indrani, Garofano, Luciano, Vallentgoed, Wies, Varn, Frederick S., Aldape, Kenneth, D'Angelo, Fulvio, Bakas, Spyridon, Barnholtz-Sloan, Jill S., Gan, Hui K., Hasanain, Mohammad, Hau, Ann Christin, Johnson, Kevin C., Cazacu, Simona, deCarvalho, Ana C., Khasraw, Mustafa, Kocakavuk, Emre, Kouwenhoven, Mathilde C.M., Migliozzi, Simona, Niclou, Simone P., Niers, Johanna M., Ormond, D. Ryan, Paek, Sun Ha, Reifenberger, Guido, Smitt, Peter A.Sillevis, Smits, Marion, Stead, Lucy F., van den Bent, Martin J., Van Meir, Erwin G., Walenkamp, Annemiek, Weiss, Tobias, Weller, Michael, Westerman, Bart A., Ylstra, Bauke, Wesseling, Pieter, Lasorella, Anna, French, Pim J., Poisson, Laila M., Verhaak, Roel G.W., Iavarone, Antonio, and Noushmehr, Houtan
- Abstract
Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histologic progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neoangiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution toward an IDHwt-like phenotype.
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- 2024
10. Whole transcriptome signature for prognostic prediction (WTSPP): application of whole transcriptome signature for prognostic prediction in cancer
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Schaafsma, Evelien, Zhao, Yanding, Wang, Yue, Varn, Frederick S., Zhu, Kenneth, Yang, Huan, and Cheng, Chao
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- 2020
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11. Very low mutation burden is a feature of inflamed recurrent glioblastomas responsive to cancer immunotherapy
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Gromeier, Matthias, Brown, Michael C., Zhang, Gao, Lin, Xiang, Chen, Yeqing, Wei, Zhi, Beaubier, Nike, Yan, Hai, He, Yiping, Desjardins, Annick, Herndon, II, James E., Varn, Frederick S., Verhaak, Roel G., Zhao, Junfei, Bolognesi, Dani P., Friedman, Allan H., Friedman, Henry S., McSherry, Frances, Muscat, Andrea M., Lipp, Eric S., Nair, Smita K., Khasraw, Mustafa, Peters, Katherine B., Randazzo, Dina, Sampson, John H., McLendon, Roger E., Bigner, Darell D., and Ashley, David M.
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- 2021
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12. Perspective of mesenchymal transformation in glioblastoma
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Kim, Yona, Varn, Frederick S., Park, Sung-Hye, Yoon, Byung Woo, Park, Hye Ran, Lee, Charles, Verhaak, Roel G. W., and Paek, Sun Ha
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- 2021
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13. Identifying New Immune Response Dynamics in Virus-Associated Cancers
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Varn, Frederick S. and Cheng, Chao
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- 2019
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14. Integrative Analysis Identifies Transcription Factor–DNA Methylation Relationships and Introduces New Avenues for Translating Cancer Epigenetics into the Clinic
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Ung, Matthew H., Lou, Shaoke, Varn, Frederick S., Cheng, Chao, Wu, Wei, editor, and Choudhry, Hani, editor
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- 2015
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15. Whole transcriptome signature for prognostic prediction (WTSPP): application of whole transcriptome signature for prognostic prediction in cancer
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Schaafsma, Evelien, Zhao, Yanding, Wang, Yue, Varn, Frederick S., Zhu, Kenneth, Yang, Huan, and Cheng, Chao
- Abstract
Developing prognostic biomarkers for specific cancer types that accurately predict patient survival is increasingly important in clinical research and practice. Despite the enormous potential of prognostic signatures, proposed models have found limited implementations in routine clinical practice. Herein, we propose a generic, RNA sequencing platform independent, statistical framework named whole transcriptome signature for prognostic prediction to generate prognostic gene signatures. Using ovarian cancer and lung adenocarcinoma as examples, we provide evidence that our prognostic signatures overperform previous reported signatures, capture prognostic features not explained by clinical variables, and expose biologically relevant prognostic pathways, including those involved in the immune system and cell cycle. Our approach demonstrates a robust method for developing prognostic gene expression signatures. In conclusion, our statistical framework can be generally applied to all cancer types for prognostic prediction and might be extended to other human diseases. The proposed method is implemented as an R package (PanCancerSig) and is freely available on GitHub (https://github.com/Cheng-Lab-GitHub/PanCancer_Signature).
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- 2024
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16. Single-cell RNA sequencing reveals the impact of chromosomal instability on glioblastoma cancer stem cells
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Zhao, Yanding, Carter, Robert, Natarajan, Sivaraman, Varn, Frederick S., Compton, Duane A., Gawad, Charles, Cheng, Chao, and Godek, Kristina M.
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- 2019
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17. Radiotherapy is associated with a deletion signature that contributes to poor outcomes in cancer patients
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Kocakavuk, Emre, Anderson, Kevin J., Varn, Frederick S., Johnson, Kevin C., Amin, Samirkumar B., Sulman, Erik. P., Lolkema, Martijn P., Barthel, Floris P., and Verhaak, Roel G.W.
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Radiotherapy ,Mutagenesis ,Neoplasms ,Radiation, Ionizing ,Humans ,Neoplasm Recurrence, Local ,Prognosis ,Article ,DNA Damage ,Sequence Deletion - Abstract
Ionizing radiation causes DNA damage and is a mainstay for cancer treatment, but understanding of its genomic impact is limited. We analyzed mutational spectra following radiotherapy in 190 paired primary and recurrent gliomas from the Glioma Longitudinal Analysis Consortium and 3,693 post-treatment metastatic tumors from the Hartwig Medical Foundation. We identified radiotherapy-associated significant increases in the burden of small deletions (5-15 bp) and large deletions (20+ bp to chromosome-arm length). Small deletions were characterized by a larger span size, lacking breakpoint microhomology and were genomically more dispersed when compared to pre-existing deletions and deletions in non-irradiated tumors. Mutational signature analysis implicated classical non-homologous end-joining-mediated DNA damage repair and APOBEC mutagenesis following radiotherapy. A high radiation-associated deletion burden was associated with worse clinical outcomes, suggesting that effective repair of radiation-induced DNA damage is detrimental to patient survival. These results may be leveraged to predict sensitivity to radiation therapy in recurrent cancer.
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- 2021
18. GBMdeconvoluteR accurately infers proportions of neoplastic and immune cell populations from bulk glioblastoma transcriptomics data.
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Ajaib, Shoaib, Lodha, Disha, Pollock, Steven, Hemmings, Gemma, Finetti, Martina A, Gusnanto, Arief, Chakrabarty, Aruna, Ismail, Azzam, Wilson, Erica, Varn, Frederick S, Hunter, Bethany, Filby, Andrew, Brockman, Asa A, McDonald, David, Verhaak, Roel G W, Ihrie, Rebecca A, and Stead, Lucy F
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- 2023
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19. Immunoregulatory functions of VISTA
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Nowak, Elizabeth C., Lines, J. Louise, Varn, Frederick S., Deng, Jie, Sarde, Aurelien, Mabaera, Rodwell, Kuta, Anna, Le Mercier, Isabelle, Cheng, Chao, and Noelle, Randolph J.
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- 2017
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20. Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ERM+ breast cancer.
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Kevin Shee, Amanda Jiang, Varn, Frederick S., Stephanie Liu, Traphagen, Nicole A., Owens, Philip, Ma, Cynthia X., Jeremy Hoog, Chao Cheng, Golub, Todd R., Straussman, Ravid, and Miller, Todd W.
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- 2019
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21. A P53-Deficiency Gene Signature Predicts Recurrence Risk of Patients with Early-Stage Lung Adenocarcinoma.
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Yanding Zhao, Varn, Frederick S., Guoshuai Cai, Feifei Xiao, Amos, Christopher I., and Chao Cheng
- Abstract
Background: Lung cancer is associated with the highest mortality rate of all cancer types, and the most common histologic subtype of lung cancer is adenocarcinoma. To apply more effective therapeutic treatment, molecular markers that are able to predict the recurrence risk of patients with adenocarcinoma are critically needed. Mutations in TP53 tumor suppressor gene have been found in approximately 50% of lung adenocarcinoma cases, but the presence of a TP53 mutation does not always associate with increased mortality. Methods: The Cancer Genome Atlas RNA sequencing data of lung adenocarcinoma were used to define a novel gene signature for P53 deficiency. This signature was then used to calculate a sample-specific P53 deficiency score based on a patient's transcriptomic profile and tested in four independent lung adenocarcinoma microarray datasets. Results: In all datasets, P53 deficiency score was a significant predictor for recurrence-free survival where high P53 deficiency score was associated with poor survival. The score was prognostic even after adjusting for several key clinical variables including age, tumor stage, smoking status, and P53 mutation status. Furthermore, the score was able to predict recurrence-free survival in patients with stage I adenocarcinoma and was also associated with smoking status. Conclusions: The P53 deficiency score was a better predictor of recurrence-free survival compared with P53 mutation status and provided additional prognostic values to established clinical factors. Impact: The P53 deficiency score can be used to stratify early-stage patients into subgroups based on their risk of recurrence for aiding physicians to decide personalized therapeutic treatment. [ABSTRACT FROM AUTHOR]
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- 2018
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22. The E2F4 prognostic signature predicts pathological response to neoadjuvant chemotherapy in breast cancer patients.
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Mark, Kenneth M. K., Varn, Frederick S., Ung, Matthew H., Feng Qian, Chao Cheng, Qian, Feng, and Cheng, Chao
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BREAST cancer patients , *ADJUVANT treatment of cancer , *CANCER chemotherapy , *BREAST cancer treatment , *GENE expression profiling , *ONCOLOGY , *ESTROGEN receptors , *PROTEIN analysis , *PROTEIN metabolism , *BREAST tumors , *COMBINED modality therapy , *DATABASES , *PROGNOSIS , *PROTEINS , *RESEARCH funding , *RECEIVER operating characteristic curves - Abstract
Background: Neoadjuvant chemotherapy is a key component of breast cancer treatment regimens and pathologic complete response to this therapy varies among patients. This is presumably due to differences in the molecular mechanisms that underlie each tumor's disease pathology. Developing genomic clinical assays that accurately categorize responders from non-responders can provide patients with the most effective therapy for their individual disease.Methods: We applied our previously developed E2F4 genomic signature to predict neoadjuvant chemotherapy response in breast cancer. E2F4 individual regulatory activity scores were calculated for 1129 patient samples across 5 independent breast cancer neoadjuvant chemotherapy datasets. Accuracy of the E2F4 signature in predicting neoadjuvant chemotherapy response was compared to that of the Oncotype DX and MammaPrint predictive signatures.Results: In all datasets, E2F4 activity level was an accurate predictor of neoadjuvant chemotherapy response, with high E2F4 scores predictive of achieving pathologic complete response and low scores predictive of residual disease. These results remained significant even after stratifying patients by estrogen receptor (ER) status, tumor stage, and breast cancer molecular subtypes. Compared to the Oncotype DX and MammaPrint signatures, our E2F4 signature achieved similar performance in predicting neoadjuvant chemotherapy response, though all signatures performed better in ER+ tumors compared to ER- ones. The accuracy of our signature was reproducible across datasets and was maintained when refined from a 199-gene signature down to a clinic-friendly 33-gene panel.Conclusion: Overall, we show that our E2F4 signature is accurate in predicting patient response to neoadjuvant chemotherapy. As this signature is more refined and comparable in performance to other clinically available gene expression assays in the prediction of neoadjuvant chemotherapy response, it should be considered when evaluating potential treatment options. [ABSTRACT FROM AUTHOR]- Published
- 2017
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23. Adaptive immunity programmes in breast cancer.
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Varn, Frederick S., Mullins, David W., Arias‐Pulido, Hugo, Fiering, Steven, and Cheng, Chao
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- *
BREAST cancer , *IMMUNE system , *T cells , *IMMUNOSUPPRESSION , *LYMPHOCYTES - Abstract
The role of the immune system in shaping cancer development and patient prognosis has recently become an area of intense focus in industry and academia. Harnessing the adaptive arm of the immune system for tumour eradication has shown great promise in a variety of tumour types. Differences between tissues, however, necessitate a greater understanding of the adaptive immunity programmes that are active within each tumour type. In breast cancer, adaptive immune programmes play diverse roles depending on the cellular infiltration found in each tumour. Cytotoxic T lymphocytes and T helper type 1 cells can induce tumour eradication, whereas regulatory T cells and T helper type 2 cells are known to be involved in tumour-promoting immunosuppressive responses. Complicating these matters, heterogeneous expression of hormone receptors and growth factors in different tumours leads to disparate, patient-specific adaptive immune responses. Despite this non-conformity in adaptive immune behaviours, encouraging basic and clinical results have been observed that suggest a role for immunotherapeutic approaches in breast cancer. Here, we review the literature pertaining to the adaptive immune response in breast cancer, summarize the primary findings relating to the breast tumour's biology, and discuss potential clinical immunotherapies. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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24. Therapeutically targeting tumor microenvironment–mediated drug resistance in estrogen receptor–positive breast cancer
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Shee, Kevin, Yang, Wei, Hinds, John W., Hampsch, Riley A., Varn, Frederick S., Traphagen, Nicole A., Patel, Kishan, Cheng, Chao, Jenkins, Nicole P., Kettenbach, Arminja N., Demidenko, Eugene, Owens, Philip, Faber, Anthony C., Golub, Todd R., Straussman, Ravid, and Miller, Todd W.
- Abstract
Drug resistance to approved systemic therapies in estrogen receptor–positive (ER+) breast cancer remains common. We hypothesized that factors present in the human tumor microenvironment (TME) drive drug resistance. Screening of a library of recombinant secreted microenvironmental proteins revealed fibroblast growth factor 2 (FGF2) as a potent mediator of resistance to anti-estrogens, mTORC1 inhibition, and phosphatidylinositol 3-kinase inhibition in ER+ breast cancer. Phosphoproteomic analyses identified ERK1/2 as a major output of FGF2 signaling via FGF receptors (FGFRs), with consequent up-regulation of Cyclin D1 and down-regulation of Bim as mediators of drug resistance. FGF2-driven drug resistance in anti-estrogen–sensitive and –resistant models, including patient-derived xenografts, was reverted by neutralizing FGF2 or FGFRs. A transcriptomic signature of FGF2 signaling in primary tumors predicted shorter recurrence-free survival independently of age, grade, stage, and FGFR amplification status. These findings delineate FGF2 signaling as a ligand-based drug resistance mechanism and highlights an underdeveloped aspect of precision oncology: characterizing and treating patients according to their TME constitution.
- Published
- 2018
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25. In silicoframeworks for systematic pre-clinical screening of potential anti-leukemia therapeutics
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Ung, Matthew H., Varn, Frederick S., and Cheng, Chao
- Abstract
ABSTRACTIntroduction: Leukemia is a collection of highly heterogeneous cancers that arise from neoplastic transformation and clonal expansion of immature hematopoietic cells. Post-treatment recurrence is high, especially among elderly patients, thus necessitating more effective treatment modalities. Development of novel anti-leukemic compounds relies heavily on traditional in vitroscreens which require extensive resources and time. Therefore, integration of in silicoscreens prior to experimental validation can improve the efficiency of pre-clinical drug development.Areas covered: This article reviews different methods and frameworks used to computationally screen for anti-leukemic agents. In particular, three approaches are discussed including molecular docking, transcriptomic integration, and network analysis.Expert opinion: Today’s data deluge presents novel opportunities to develop computational tools and pipelines to screen for likely therapeutic candidates in the treatment of leukemia. Formal integration of these methodologies can accelerate and improve the efficiency of modern day anti-leukemic drug discovery and ease the economic and healthcare burden associated with it.
- Published
- 2016
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26. Regulators Associated with Clinical Outcomes Revealed by DNA Methylation Data in Breast Cancer.
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Ung, Matthew H., Varn, Frederick S., Lou, Shaoke, and Cheng, Chao
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- *
DNA methylation , *GENETICS of breast cancer , *BREAST cancer prognosis , *GENETIC transcription , *TRANSCRIPTION factors - Abstract
The regulatory architecture of breast cancer is extraordinarily complex and gene misregulation can occur at many levels, with transcriptional malfunction being a major cause. This dysfunctional process typically involves additional regulatory modulators including DNA methylation. Thus, the interplay between transcription factor (TF) binding and DNA methylation are two components of a cancer regulatory interactome presumed to display correlated signals. As proof of concept, we performed a systematic motif-based in silico analysis to infer all potential TFs that are involved in breast cancer prognosis through an association with DNA methylation changes. Using breast cancer DNA methylation and clinical data derived from The Cancer Genome Atlas (TCGA), we carried out a systematic inference of TFs whose misregulation underlie different clinical subtypes of breast cancer. Our analysis identified TFs known to be associated with clinical outcomes of p53 and ER (estrogen receptor) subtypes of breast cancer, while also predicting new TFs that may also be involved. Furthermore, our results suggest that misregulation in breast cancer can be caused by the binding of alternative factors to the binding sites of TFs whose activity has been ablated. Overall, this study provides a comprehensive analysis that links DNA methylation to TF binding to patient prognosis. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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27. Integrative analysis of survival-associated gene sets in breast cancer.
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Varn, Frederick S., Ung, Matthew H., Ke Lou, Shao, and Chao Cheng
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- *
GENE expression , *BREAST cancer , *COMEDO carcinoma , *HUMAN anatomy , *INCURABLE diseases - Abstract
Background: Patient gene expression information has recently become a clinical feature used to evaluate breast cancer prognosis. The emergence of prognostic gene sets that take advantage of these data has led to a rich library of information that can be used to characterize the molecular nature of a patient's cancer. Identifying robust gene sets that are consistently predictive of a patient's clinical outcome has become one of the main challenges in the field. Methods: We inputted our previously established BASE algorithm with patient gene expression data and gene sets from MSigDB to develop the gene set activity score (GSAS), a metric that quantitatively assesses a gene set's activity level in a given patient. We utilized this metric, along with patient time-to-event data, to perform survival analyses to identify the gene sets that were significantly correlated with patient survival. We then performed cross-dataset analyses to identify robust prognostic gene sets and to classify patients by metastasis status. Additionally, we created a gene set network based on component gene overlap to explore the relationship between gene sets derived from MSigDB. We developed a novel gene set based on this network's topology and applied the GSAS metric to characterize its role in patient survival. Results: Using the GSAS metric, we identified 120 gene sets that were significantly associated with patient survival in all datasets tested. The gene overlap network analysis yielded a novel gene set enriched in genes shared by the robustly predictive gene sets. This gene set was highly correlated to patient survival when used alone. Most interestingly, removal of the genes in this gene set from the gene pool on MSigDB resulted in a large reduction in the number of predictive gene sets, suggesting a prominent role for these genes in breast cancer progression. Conclusions: The GSAS metric provided a useful medium by which we systematically investigated how gene sets from MSigDB relate to breast cancer patient survival. We used this metric to identify predictive gene sets and to construct a novel gene set containing genes heavily involved in cancer progression. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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28. CASCADES, a novel SOX2 super‐enhancer‐associated long noncoding RNA, regulates cancer stem cell specification and differentiation in glioblastoma.
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Shahzad, Uswa, Nikolopoulos, Marina, Li, Christopher, Johnston, Michael, Wang, Jenny J., Sabha, Nesrin, Varn, Frederick S., Riemenschneider, Alexandra, Krumholtz, Stacey, Krishnamurthy, Pranathi Meda, Smith, Christian A., Karamchandani, Jason, Watts, Jonathan K., Verhaak, Roel G. W., Gallo, Marco, Rutka, James T., and Das, Sunit
- Subjects
- *
LINCRNA , *CANCER stem cells , *BRAIN tumors , *ISOCITRATE dehydrogenase , *CELL differentiation - Abstract
Glioblastoma is the most common primary malignant brain tumor in adults, with a median survival of just over 1 year. The failure of available treatments to achieve remission in patients with glioblastoma (GBM) has been attributed to the presence of cancer stem cells (CSCs), which are thought to play a central role in tumor development and progression and serve as a treatment‐resistant cell repository capable of driving tumor recurrence. In fact, the property of “stemness” itself may be responsible for treatment resistance. In this study, we identify a novel long noncoding RNA (lncRNA), cancer stem cell‐associated distal enhancer of SOX2 (CASCADES), that functions as an epigenetic regulator in glioma CSCs (GSCs). CASCADES is expressed in isocitrate dehydrogenase (IDH)‐wild‐type GBM and is significantly enriched in GSCs. Knockdown of CASCADES in GSCs results in differentiation towards a neuronal lineage in a cell‐ and cancer‐specific manner. Bioinformatics analysis reveals that CASCADES functions as a super‐enhancer‐associated lncRNA epigenetic regulator of SOX2. Our findings identify CASCADES as a critical regulator of stemness in GSCs that represents a novel epigenetic and therapeutic target for disrupting the CSC compartment in glioblastoma. [ABSTRACT FROM AUTHOR]
- Published
- 2024
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29. A B cell-derived gene expression signature associates with an immunologically active tumor microenvironment and response to immune checkpoint blockade therapy.
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Varn, Frederick S., Wang, Yue, and Cheng, Chao
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- *
B cells , *MELANOMA , *TUMOR microenvironment , *IMMUNE response , *GENE expression - Abstract
Immune checkpoint inhibitors have shown great potential in treating solid tumors, inducing durable remission and prolonged survival time in responders. Despite their promise, a large fraction of patients remains unresponsive to these treatments highlighting the need for biomarkers that can predict patient sensitivity. Pre-treatment gene expression profiles for patients receiving immune checkpoint inhibitors have recently become available, establishing a new medium by which to discover biomarkers that predict therapy response. In this study, we mined for transcriptomic correlates of response by applying immune cell-derived gene expression signatures to publicly available datasets containing matched gene expression and response efficacy information. These datasets were comprised of urothelial carcinoma patients receiving anti-PD-L1 (n = 25), melanoma patients receiving anti-PD-1 (n = 28), and melanoma patients receiving anti-CTLA-4 (n = 42). We identified one signature, derived from a subpopulation of B cells, with scores that were significantly and reproducibly elevated in patients experiencing clinical benefit following therapy targeting the PD-1/PD-L1 axis and were additionally elevated in patients responsive to anti-CTLA-4 therapy. Multivariate models revealed that this signature was associated with response independent of other response-predictive biomarkers, including tumor mutation burden. Functional annotation of the signature revealed it to be associated with features indicative of an immunologically active microenvironment, including B and T cell activation as well as antigen presentation activity. The preliminary findings presented detail a transcriptomic signature associated with response to multiple checkpoint inhibitors and suggest novel biological associations that warrant further investigation. [ABSTRACT FROM AUTHOR]
- Published
- 2019
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30. Computational immune profiling in lung adenocarcinoma reveals reproducible prognostic associations with implications for immunotherapy.
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Varn, Frederick S., Tafe, Laura J., Amos, Christopher I., and Cheng, Chao
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- *
NON-small-cell lung carcinoma , *IMMUNOTHERAPY - Abstract
Non-small cell lung cancer is one of the leading causes of cancer-related death in the world. Lung adenocarcinoma, the most common type of non-small cell lung cancer, has been well characterized as having a dense lymphocytic infiltrate, suggesting that the immune system plays an active role in shaping this cancer's growth and development. Despite these findings, our understanding of how this infiltrate affects patient prognosis and its association with lung adenocarcinoma-specific clinical factors remains limited. To address these questions, we inferred the infiltration level of six distinct immune cell types from a series of four lung adenocarcinoma gene expression datasets. We found that naive B cell, CD8+ T cell, and myeloid cell-derived expression signals of immune infiltration were significantly predictive of patient survival in multiple independent datasets, with B cell and CD8+ T cell infiltration associated with prolonged prognosis and myeloid cell infiltration associated with shorter survival. These associations remained significant even after accounting for additional clinical variables. Patients stratified by smoking status exhibited decreased CD8+ T cell infiltration and altered prognostic associations, suggesting potential immunosuppressive mechanisms in smokers. Survival analyses accounting for immune checkpoint gene expression and cellular immune infiltrate indicated checkpoint protein-specific modulatory effects on CD8+ T cell and B cell function that may be associated with patient sensitivity to immunotherapy. Together, these analyses identified reproducible associations that can be used to better characterize the role of immune infiltration in lung adenocarcinoma and demonstrate the utility in using computational approaches to systematically characterize tissue-specific tumor-immune interactions. [ABSTRACT FROM AUTHOR]
- Published
- 2018
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31. Integrative analysis of breast cancer reveals prognostic haematopoietic activity and patient-specific immune response profiles.
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Varn, Frederick S., Andrews, Erik H., Mullins, David W., and Cheng, Chao
- Published
- 2016
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32. Systematic analysis of hematopoietic gene expression profiles for prognostic prediction in acute myeloid leukemia.
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Varn, Frederick S., Andrews, Erik H., and Cheng, Chao
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- *
GENE expression , *HEMATOPOIETIC stem cells , *ACUTE myeloid leukemia , *GENETIC transcription , *GENETICS , *PROGNOSIS - Abstract
Acute myeloid leukemia (AML) is a hematopoietic disorder initiated by the leukemogenic transformation of myeloid cells into leukemia stem cells (LSCs). Preexisting gene expression programs in LSCs can be used to assess their transcriptional similarity to hematopoietic cell types. While this relationship has previously been examined on a small scale, an analysis that systematically investigates this relationship throughout the hematopoietic hierarchy has yet to be implemented. We developed an integrative approach to assess the similarity between AML patient tumor profiles and a collection of 232 murine hematopoietic gene expression profiles compiled by the Immunological Genome Project. The resulting lineage similarity scores (LSS) were correlated with patient survival to assess the relationship between hematopoietic similarity and patient prognosis. This analysis demonstrated that patient tumor similarity to immature hematopoietic cell types correlated with poor survival. As a proof of concept, we highlighted one cell type identified by our analysis, the short-term reconstituting stem cell, whose LSSs were significantly correlated with patient prognosis across multiple datasets, and showed distinct patterns in patients stratified by traditional clinical variables. Finally, we validated our use of murine profiles by demonstrating similar results when applying our method to human profiles. [ABSTRACT FROM AUTHOR]
- Published
- 2015
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33. The Epigenetic Evolution of Glioma Is Determined by the IDH1 Mutation Status and Treatment Regimen.
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Malta TM, Sabedot TS, Morosini NS, Datta I, Garofano L, Vallentgoed W, Varn FS, Aldape K, D'Angelo F, Bakas S, Barnholtz-Sloan JS, Gan HK, Hasanain M, Hau AC, Johnson KC, Cazacu S, deCarvalho AC, Khasraw M, Kocakavuk E, Kouwenhoven MCM, Migliozzi S, Niclou SP, Niers JM, Ormond DR, Paek SH, Reifenberger G, Sillevis Smitt PA, Smits M, Stead LF, van den Bent MJ, Van Meir EG, Walenkamp A, Weiss T, Weller M, Westerman BA, Ylstra B, Wesseling P, Lasorella A, French PJ, Poisson LM, Verhaak RGW, Iavarone A, and Noushmehr H
- Subjects
- Humans, Epigenesis, Genetic, Epigenomics, Mutation, Neoplasm Recurrence, Local genetics, Tumor Microenvironment, Brain Neoplasms pathology, Glioma pathology, Isocitrate Dehydrogenase genetics, Isocitrate Dehydrogenase metabolism
- Abstract
Tumor adaptation or selection is thought to underlie therapy resistance in glioma. To investigate longitudinal epigenetic evolution of gliomas in response to therapeutic pressure, we performed an epigenomic analysis of 132 matched initial and recurrent tumors from patients with IDH-wildtype (IDHwt) and IDH-mutant (IDHmut) glioma. IDHwt gliomas showed a stable epigenome over time with relatively low levels of global methylation. The epigenome of IDHmut gliomas showed initial high levels of genome-wide DNA methylation that was progressively reduced to levels similar to those of IDHwt tumors. Integration of epigenomics, gene expression, and functional genomics identified HOXD13 as a master regulator of IDHmut astrocytoma evolution. Furthermore, relapse of IDHmut tumors was accompanied by histologic progression that was associated with survival, as validated in an independent cohort. Finally, the initial cell composition of the tumor microenvironment varied between IDHwt and IDHmut tumors and changed differentially following treatment, suggesting increased neoangiogenesis and T-cell infiltration upon treatment of IDHmut gliomas. This study provides one of the largest cohorts of paired longitudinal glioma samples with epigenomic, transcriptomic, and genomic profiling and suggests that treatment of IDHmut glioma is associated with epigenomic evolution toward an IDHwt-like phenotype., Significance: Standard treatments are related to loss of DNA methylation in IDHmut glioma, resulting in epigenetic activation of genes associated with tumor progression and alterations in the microenvironment that resemble treatment-naïve IDHwt glioma., (©2023 The Authors; Published by the American Association for Cancer Research.)
- Published
- 2024
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34. Driver Mutations Dictate the Immunologic Landscape and Response to Checkpoint Immunotherapy of Glioblastoma.
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Yeo AT, Shah R, Aliazis K, Pal R, Xu T, Zhang P, Rawal S, Rose CM, Varn FS, Appleman VA, Yoon J, Varma H, Gygi SP, Verhaak RGW, Boussiotis VA, and Charest A
- Subjects
- Animals, Mice, CTLA-4 Antigen genetics, CTLA-4 Antigen metabolism, Programmed Cell Death 1 Receptor, Cell Line, Tumor, Immunotherapy, Mutation, Tumor Microenvironment genetics, Glioblastoma therapy, Glioblastoma drug therapy, Myeloid-Derived Suppressor Cells, Brain Neoplasms genetics, Brain Neoplasms therapy
- Abstract
The composition of the tumor immune microenvironment (TIME) is considered a key determinant of patients' response to immunotherapy. The mechanisms underlying TIME formation and development over time are poorly understood. Glioblastoma (GBM) is a lethal primary brain cancer for which there are no curative treatments. GBMs are immunologically heterogeneous and impervious to checkpoint blockade immunotherapies. Utilizing clinically relevant genetic mouse models of GBM, we identified distinct immune landscapes associated with expression of EGFR wild-type and mutant EGFRvIII cancer driver mutations. Over time, accumulation of polymorphonuclear myeloid-derived suppressor cells (PMN-MDSC) was more pronounced in EGFRvIII-driven GBMs and was correlated with resistance to PD-1 and CTLA-4 combination checkpoint blockade immunotherapy. We determined that GBM-secreted CXCL1/2/3 and PMN-MDSC-expressed CXCR2 formed an axis regulating output of PMN-MDSCs from the bone marrow leading to systemic increase in these cells in the spleen and GBM tumor-draining lymph nodes. Pharmacologic targeting of this axis induced a systemic decrease in the numbers of PMN-MDSC, facilitated responses to PD-1 and CTLA-4 combination checkpoint blocking immunotherapy, and prolonged survival in mice bearing EGFRvIII-driven GBM. Our results uncover a relationship between cancer driver mutations, TIME composition, and sensitivity to checkpoint blockade in GBM and support the stratification of patients with GBM for checkpoint blockade therapy based on integrated genotypic and immunologic profiles., (©2023 The Authors; Published by the American Association for Cancer Research.)
- Published
- 2023
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35. Central nervous system immune interactome is a function of cancer lineage, tumor microenvironment, and STAT3 expression.
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Najem H, Ott M, Kassab C, Rao A, Rao G, Marisetty A, Sonabend AM, Horbinski C, Verhaak R, Shankar A, Krishnan SN, Varn FS, Arrieta VA, Gupta P, Ferguson SD, Huse JT, Fuller GN, Long JP, Winkowski DE, Freiberg BA, James CD, Platanias LC, Lesniak MS, Burks JK, and Heimberger AB
- Subjects
- Central Nervous System metabolism, Humans, Macrophages metabolism, STAT3 Transcription Factor metabolism, Tumor Microenvironment, United States, Brain Neoplasms pathology, Glioblastoma pathology, Lung Neoplasms pathology
- Abstract
BACKGROUNDImmune cell profiling of primary and metastatic CNS tumors has been focused on the tumor, not the tumor microenvironment (TME), or has been analyzed via biopsies.METHODSEn bloc resections of gliomas (n = 10) and lung metastases (n = 10) were analyzed via tissue segmentation and high-dimension Opal 7-color multiplex imaging. Single-cell RNA analyses were used to infer immune cell functionality.RESULTSWithin gliomas, T cells were localized in the infiltrating edge and perivascular space of tumors, while residing mostly in the stroma of metastatic tumors. CD163+ macrophages were evident throughout the TME of metastatic tumors, whereas in gliomas, CD68+, CD11c+CD68+, and CD11c+CD68+CD163+ cell subtypes were commonly observed. In lung metastases, T cells interacted with CD163+ macrophages as dyads and clusters at the brain-tumor interface and within the tumor itself and as clusters within the necrotic core. In contrast, gliomas typically lacked dyad and cluster interactions, except for T cell CD68+ cell dyads within the tumor. Analysis of transcriptomic data in glioblastomas revealed that innate immune cells expressed both proinflammatory and immunosuppressive gene signatures.CONCLUSIONOur results show that immunosuppressive macrophages are abundant within the TME and that the immune cell interactome between cancer lineages is distinct. Further, these data provide information for evaluating the role of different immune cell populations in brain tumor growth and therapeutic responses.FUNDINGThis study was supported by the NIH (NS120547), a Developmental research project award (P50CA221747), ReMission Alliance, institutional funding from Northwestern University and the Lurie Comprehensive Cancer Center, and gifts from the Mosky family and Perry McKay. Performed in the Flow Cytometry & Cellular Imaging Core Facility at MD Anderson Cancer Center, this study received support in part from the NIH (CA016672) and the National Cancer Institute (NCI) Research Specialist award 1 (R50 CA243707). Additional support was provided by CCSG Bioinformatics Shared Resource 5 (P30 CA046592), a gift from Agilent Technologies, a Research Scholar Grant from the American Cancer Society (RSG-16-005-01), a Precision Health Investigator Award from University of Michigan (U-M) Precision Health, the NCI (R37-CA214955), startup institutional research funds from U-M, and a Biomedical Informatics & Data Science Training Grant (T32GM141746).
- Published
- 2022
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36. Hypoxia-Induced VISTA Promotes the Suppressive Function of Myeloid-Derived Suppressor Cells in the Tumor Microenvironment.
- Author
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Deng J, Li J, Sarde A, Lines JL, Lee YC, Qian DC, Pechenick DA, Manivanh R, Le Mercier I, Lowrey CH, Varn FS, Cheng C, Leib DA, Noelle RJ, and Mabaera R
- Subjects
- Adenocarcinoma genetics, Adenocarcinoma metabolism, Animals, Apoptosis, B7 Antigens genetics, Case-Control Studies, Cell Proliferation, Cohort Studies, Colorectal Neoplasms genetics, Colorectal Neoplasms metabolism, Female, Humans, Hypoxia-Inducible Factor 1, alpha Subunit genetics, Lymphocyte Activation immunology, Mice, Mice, Inbred BALB C, Prognosis, Survival Rate, T-Lymphocytes immunology, T-Lymphocytes, Regulatory immunology, Tumor Cells, Cultured, Adenocarcinoma immunology, B7 Antigens metabolism, Colorectal Neoplasms immunology, Hypoxia physiopathology, Hypoxia-Inducible Factor 1, alpha Subunit metabolism, Myeloid-Derived Suppressor Cells immunology, Tumor Microenvironment immunology
- Abstract
Tumor hypoxia is a negative prognostic factor that is implicated in oncogenic signal activation, immune escape, and resistance to treatment. Identifying the mechanistic role of hypoxia in immune escape and resistance to immune-checkpoint inhibitors may aid the identification of therapeutic targets. We and others have shown that V-domain Ig suppressor of T-cell activation (VISTA), a negative checkpoint regulator in the B7 family, is highly expressed in the tumor microenvironment in tumor models and primary human cancers. In this study, we show that VISTA and HIF1α activity are correlated in a cohort of colorectal cancer patients. High VISTA expression was associated with worse overall survival. We used the CT26 colon cancer model to investigate the regulation of VISTA by hypoxia. Compared with less hypoxic tumor regions or draining lymph nodes, regions of profound hypoxia in the tumor microenvironment were associated with increased VISTA expression on tumor-infiltrating myeloid-derived suppressor cells (MDSC). Using chromatin immunoprecipitation and genetic silencing, we show that hypoxia-inducible factor (HIF)-1α binding to a conserved hypoxia response element in the VISTA promoter upregulated VISTA on myeloid cells. Further, antibody targeting or genetic ablation of VISTA under hypoxia relieved MDSC-mediated T-cell suppression, revealing VISTA as a mediator of MDSC function. Collectively, these data suggest that targeting VISTA may mitigate the deleterious effects of hypoxia on antitumor immunity., (©2019 American Association for Cancer Research.)
- Published
- 2019
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37. Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER + breast cancer.
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Shee K, Jiang A, Varn FS, Liu S, Traphagen NA, Owens P, Ma CX, Hoog J, Cheng C, Golub TR, Straussman R, and Miller TW
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- Androgen Antagonists therapeutic use, Bone Morphogenetic Protein Receptors, Type I genetics, Bone Morphogenetic Protein Receptors, Type I metabolism, Breast Neoplasms drug therapy, Breast Neoplasms pathology, Cell Cycle Checkpoints, Cell Line, Tumor, Cyclin-Dependent Kinase 4 metabolism, Cyclin-Dependent Kinase 6 metabolism, Cyclin-Dependent Kinase Inhibitor p21 metabolism, Female, Humans, Mechanistic Target of Rapamycin Complex 1 metabolism, Receptors, Estrogen metabolism, Survival Analysis, Transcriptome, Tumor Microenvironment, Bone Morphogenetic Protein 4 metabolism, Breast Neoplasms metabolism, Cytokines metabolism, Signal Transduction
- Abstract
Despite the success of approved systemic therapies for estrogen receptor α (ER)-positive breast cancer, drug resistance remains common. We hypothesized that secreted factors from the human tumor microenvironment could modulate drug resistance. We previously screened a library of 297 recombinant-secreted microenvironmental proteins for the ability to confer resistance to the anti-estrogen fulvestrant in 2 ER
+ breast cancer cell lines. Herein, we considered whether factors that enhanced drug sensitivity could be repurposed as therapeutics and provide leads for drug development. Screening data revealed bone morphogenic protein (BMP)4 as a factor that inhibited cell growth and synergized with approved anti-estrogens and cyclin-dependent kinase 4/6 inhibitors (CDK4/6i ). BMP4-mediated growth inhibition was dependent on type I receptor activin receptor-like kinase (ALK)3-dependent phosphorylation (P) of mothers against decapentaplegic homolog (SMAD/P-SMAD)1 and 5, which could be reversed by BMP receptor inhibitors and ALK3 knockdown. The primary effect of BMP4 on cell fate was cell-cycle arrest, in which RNA sequencing, immunoblot analysis, and RNA interference revealed to be dependent on p21WAF1/Cip1 upregulation. BMP4 also enhanced sensitivity to approved inhibitors of mammalian target of rapamycin complex 1 and CDK4/6 via ALK3-mediated P-SMAD1/5 and p21 upregulation in anti-estrogen-resistant cells. Patients bearing primary ER+ breast tumors, exhibiting a transcriptomic signature of BMP4 signaling, had improved disease outcome following adjuvant treatment with anti-estrogen therapy, independently of age, tumor grade, and tumor stage. Furthermore, a transcriptomic signature of BMP4 signaling was predictive of an improved biologic response to the CDK4/6i palbociclib, in combination with an aromatase inhibitor in primary tumors. These findings highlight BMP4 and its downstream pathway activation as a therapeutic opportunity in ER+ breast cancer.-Shee, K., Jiang, A., Varn, F. S., Liu, S., Traphagen, N. A., Owens, P., Ma, C. X., Hoog, J., Cheng, C., Golub, T. R., Straussman, R., Miller, T. W. Cytokine sensitivity screening highlights BMP4 pathway signaling as a therapeutic opportunity in ER+ breast cancer.- Published
- 2019
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38. Genomic Characterization of Six Virus-Associated Cancers Identifies Changes in the Tumor Immune Microenvironment and Altered Genetic Programs.
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Varn FS, Schaafsma E, Wang Y, and Cheng C
- Subjects
- Biomarkers, Tumor metabolism, CD8-Positive T-Lymphocytes immunology, Cell Line, Tumor, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Gene Expression Regulation, Viral, Genome, Human, Humans, Immune System, Immunotherapy, Lymphocytes, Tumor-Infiltrating immunology, Macrophages metabolism, Neoplasms immunology, Oncogene Proteins chemistry, Prognosis, Receptors, Antigen, T-Cell metabolism, Transcriptome, Genomics, Neoplasms genetics, Neoplasms virology, Tumor Microenvironment
- Abstract
Viruses affect approximately 20% of all human cancers and induce expression of immunogenic viral oncoproteins that make these tumors potent targets for immune checkpoint inhibitors. In this study, we apply computational tools to The Cancer Genome Atlas (TCGA) and other genomic datasets to define how virus infection shapes the tumor immune microenvironment and genetic architecture of 6 virus-associated tumor types. Across cancers, the cellular composition of the microenvironment varied by viral status, with virus-positive tumors often exhibiting increased infiltration of cytolytic cell types compared with their virus-negative counterparts. Analyses of the infiltrating T-cell receptor repertoire in these patients revealed that Epstein-Barr virus infection was associated with decreased receptor diversity in multiple cancers, suggesting an antigen-driven clonal T-cell response. Tissue-specific gene-expression signatures capturing virus-associated transcriptomic changes successfully predicted virus status in independent datasets and were associated with both immune- and proliferation-related features that were predictive of patient prognosis. Together, the analyses presented suggest viruses have distinct effects in different tumors, with implications for immunotherapy. Significance: This study utilizes TCGA and other genomic datasets to further our understanding of how viruses affect the tumor immune response in different cancer types. Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/78/22/6413/F1.large.jpg Cancer Res; 78(22); 6413-23. ©2018 AACR ., (©2018 American Association for Cancer Research.)
- Published
- 2018
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39. A B cell-derived gene expression signature associates with an immunologically active tumor microenvironment and response to immune checkpoint blockade therapy.
- Author
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Varn FS, Wang Y, and Cheng C
- Abstract
Immune checkpoint inhibitors have shown great potential in treating solid tumors, inducing durable remission and prolonged survival time in responders. Despite their promise, a large fraction of patients remains unresponsive to these treatments highlighting the need for biomarkers that can predict patient sensitivity. Pre-treatment gene expression profiles for patients receiving immune checkpoint inhibitors have recently become available, establishing a new medium by which to discover biomarkers that predict therapy response. In this study, we mined for transcriptomic correlates of response by applying immune cell-derived gene expression signatures to publicly available datasets containing matched gene expression and response efficacy information. These datasets were comprised of urothelial carcinoma patients receiving anti-PD-L1 (n = 25), melanoma patients receiving anti-PD-1 (n = 28), and melanoma patients receiving anti-CTLA-4 (n = 42). We identified one signature, derived from a subpopulation of B cells, with scores that were significantly and reproducibly elevated in patients experiencing clinical benefit following therapy targeting the PD-1/PD-L1 axis and were additionally elevated in patients responsive to anti-CTLA-4 therapy. Multivariate models revealed that this signature was associated with response independent of other response-predictive biomarkers, including tumor mutation burden. Functional annotation of the signature revealed it to be associated with features indicative of an immunologically active microenvironment, including B and T cell activation as well as antigen presentation activity. The preliminary findings presented detail a transcriptomic signature associated with response to multiple checkpoint inhibitors and suggest novel biological associations that warrant further investigation.
- Published
- 2018
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40. A P53-Deficiency Gene Signature Predicts Recurrence Risk of Patients with Early-Stage Lung Adenocarcinoma.
- Author
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Zhao Y, Varn FS, Cai G, Xiao F, Amos CI, and Cheng C
- Subjects
- Adenocarcinoma mortality, Biomarkers, Tumor genetics, Disease-Free Survival, Gene Expression Profiling, Genes, p53 genetics, Genome-Wide Association Study, Humans, Lung Neoplasms mortality, Adenocarcinoma genetics, Lung Neoplasms genetics, Mutation genetics, Neoplasm Recurrence, Local genetics, Tumor Suppressor Protein p53 deficiency
- Abstract
Background: Lung cancer is associated with the highest mortality rate of all cancer types, and the most common histologic subtype of lung cancer is adenocarcinoma. To apply more effective therapeutic treatment, molecular markers that are able to predict the recurrence risk of patients with adenocarcinoma are critically needed. Mutations in TP53 tumor suppressor gene have been found in approximately 50% of lung adenocarcinoma cases, but the presence of a TP53 mutation does not always associate with increased mortality. Methods: The Cancer Genome Atlas RNA sequencing data of lung adenocarcinoma were used to define a novel gene signature for P53 deficiency. This signature was then used to calculate a sample-specific P53 deficiency score based on a patient's transcriptomic profile and tested in four independent lung adenocarcinoma microarray datasets. Results: In all datasets, P53 deficiency score was a significant predictor for recurrence-free survival where high P53 deficiency score was associated with poor survival. The score was prognostic even after adjusting for several key clinical variables including age, tumor stage, smoking status, and P53 mutation status. Furthermore, the score was able to predict recurrence-free survival in patients with stage I adenocarcinoma and was also associated with smoking status. Conclusions: The P53 deficiency score was a better predictor of recurrence-free survival compared with P53 mutation status and provided additional prognostic values to established clinical factors. Impact: The P53 deficiency score can be used to stratify early-stage patients into subgroups based on their risk of recurrence for aiding physicians to decide personalized therapeutic treatment. Cancer Epidemiol Biomarkers Prev; 27(1); 86-95. ©2017 AACR ., (©2017 American Association for Cancer Research.)
- Published
- 2018
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- View/download PDF
41. Systematic Pan-Cancer Analysis Reveals Immune Cell Interactions in the Tumor Microenvironment.
- Author
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Varn FS, Wang Y, Mullins DW, Fiering S, and Cheng C
- Subjects
- CD8-Positive T-Lymphocytes immunology, Gene Expression Profiling, Humans, Neoplasm Staging, Neoplasms genetics, Neoplasms pathology, Survival Rate, Biomarkers, Tumor genetics, Cell Communication immunology, Macrophages immunology, Neoplasms immunology, Tumor Microenvironment immunology
- Abstract
With the recent advent of immunotherapy, there is a critical need to understand immune cell interactions in the tumor microenvironment in both pan-cancer and tissue-specific contexts. Multidimensional datasets have enabled systematic approaches to dissect these interactions in large numbers of patients, furthering our understanding of the patient immune response to solid tumors. Using an integrated approach, we inferred the infiltration levels of distinct immune cell subsets in 23 tumor types from The Cancer Genome Atlas. From these quantities, we constructed a coinfiltration network, revealing interactions between cytolytic cells and myeloid cells in the tumor microenvironment. By integrating patient mutation data, we found that while mutation burden was associated with immune infiltration differences between distinct tumor types, additional factors likely explained differences between tumors originating from the same tissue. We concluded this analysis by examining the prognostic value of individual immune cell subsets as well as how coinfiltration of functionally discordant cell types associated with patient survival. In multiple tumor types, we found that the protective effect of CD8
+ T cell infiltration was heavily modulated by coinfiltration of macrophages and other myeloid cell types, suggesting the involvement of myeloid-derived suppressor cells in tumor development. Our findings illustrate complex interactions between different immune cell types in the tumor microenvironment and indicate these interactions play meaningful roles in patient survival. These results demonstrate the importance of personalized immune response profiles when studying the factors underlying tumor immunogenicity and immunotherapy response. Cancer Res; 77(6); 1271-82. ©2017 AACR ., (©2017 American Association for Cancer Research.)- Published
- 2017
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42. Application of pharmacologically induced transcriptomic profiles to interrogate PI3K-Akt-mTOR pathway activity associated with cancer patient prognosis.
- Author
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Ung MH, Wang GL, Varn FS, and Cheng C
- Subjects
- Algorithms, Androstadienes pharmacology, Antibiotics, Antineoplastic pharmacology, Breast Neoplasms drug therapy, Breast Neoplasms metabolism, Cell Line, Tumor, Chromones pharmacology, Female, Gene Expression Regulation, Neoplastic drug effects, HL-60 Cells, Humans, Kaplan-Meier Estimate, MCF-7 Cells, Models, Genetic, Morpholines pharmacology, Phosphatidylinositol 3-Kinases genetics, Phosphatidylinositol 3-Kinases metabolism, Prognosis, Proto-Oncogene Proteins c-akt genetics, Proto-Oncogene Proteins c-akt metabolism, Signal Transduction drug effects, Sirolimus pharmacology, TOR Serine-Threonine Kinases genetics, TOR Serine-Threonine Kinases metabolism, Transcriptome drug effects, Wortmannin, Breast Neoplasms genetics, Gene Expression Regulation, Neoplastic genetics, Signal Transduction genetics, Transcriptome genetics
- Abstract
The PI3K-Akt-mTOR signaling pathway has been identified as a key driver of carcinogenesis in several cancer types. As such, a major area of focus in cancer biology is the development of genomic biomarkers that can measure the activity level of the PI3K-Akt-mTOR pathway. In this study, we systematically estimate PI3K-Akt-mTOR pathway activity in breast primary tumor samples using transcriptomic profiles derived from drug treatment in MCF7 cell lines. We demonstrate that gene expression profiles derived from chemically-induced protein inhibition allows us to measure PI3K-Akt-mTOR pathway activity in patient tumor samples. With this approach, we predict prognosis and response to chemotherapy in cancer patients, and screen for potential pharmacological modulators of PI3K-Akt-mTOR pathway inhibitors.
- Published
- 2016
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43. In silico frameworks for systematic pre-clinical screening of potential anti-leukemia therapeutics.
- Author
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Ung MH, Varn FS, and Cheng C
- Subjects
- Animals, Computer-Aided Design, Drug Design, Drug Discovery methods, Drug Evaluation, Preclinical methods, Humans, Leukemia pathology, Molecular Docking Simulation, Antineoplastic Agents pharmacology, Computer Simulation, Leukemia drug therapy
- Abstract
Introduction: Leukemia is a collection of highly heterogeneous cancers that arise from neoplastic transformation and clonal expansion of immature hematopoietic cells. Post-treatment recurrence is high, especially among elderly patients, thus necessitating more effective treatment modalities. Development of novel anti-leukemic compounds relies heavily on traditional in vitro screens which require extensive resources and time. Therefore, integration of in silico screens prior to experimental validation can improve the efficiency of pre-clinical drug development. Areas covered: This article reviews different methods and frameworks used to computationally screen for anti-leukemic agents. In particular, three approaches are discussed including molecular docking, transcriptomic integration, and network analysis. Expert opinion: Today's data deluge presents novel opportunities to develop computational tools and pipelines to screen for likely therapeutic candidates in the treatment of leukemia. Formal integration of these methodologies can accelerate and improve the efficiency of modern day anti-leukemic drug discovery and ease the economic and healthcare burden associated with it.
- Published
- 2016
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44. Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value.
- Author
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Cheng C, Lou S, Andrews EH, Ung MH, and Varn FS
- Subjects
- Algorithms, Cell Line, Tumor, Gene Expression Profiling methods, Gene Expression Regulation, Neoplastic, Gene Regulatory Networks, Humans, Liposarcoma genetics, Prognosis, Survival Analysis, Cell Cycle Checkpoints, Computational Biology methods, E2F1 Transcription Factor genetics, E2F4 Transcription Factor genetics, Liposarcoma pathology
- Abstract
Unlabelled: Liposarcoma is the second most common form of sarcoma, which has been categorized into four molecular subtypes, which are associated with differential prognosis of patients. However, the transcriptional regulatory programs associated with distinct histologic and molecular subtypes of liposarcoma have not been investigated. This study uses integrative analyses to systematically define the transcriptional regulatory programs associated with liposarcoma. Likewise, computational methods are used to identify regulatory programs associated with different liposarcoma subtypes, as well as programs that are predictive of prognosis. Further analysis of curated gene sets was used to identify prognostic gene signatures. The integration of data from a variety of sources, including gene expression profiles, transcription factor-binding data from ChIP-Seq experiments, curated gene sets, and clinical information of patients, indicated discrete regulatory programs (e.g., controlled by E2F1 and E2F4), with significantly different regulatory activity in one or multiple subtypes of liposarcoma with respect to normal adipose tissue. These programs were also shown to be prognostic, wherein liposarcoma patients with higher E2F4 or E2F1 activity associated with unfavorable prognosis. A total of 259 gene sets were significantly associated with patient survival in liposarcoma, among which > 50% are involved in cell cycle and proliferation., Implications: These integrative analyses provide a general framework that can be applied to investigate the mechanism and predict prognosis of different cancer types., (©2016 American Association for Cancer Research.)
- Published
- 2016
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45. E2F4 Program Is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer.
- Author
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Cheng C, Varn FS, and Marsit CJ
- Subjects
- Cell Line, Tumor, Disease-Free Survival, Female, Humans, Immunotherapy, Male, Mycobacterium bovis metabolism, Treatment Outcome, Urinary Bladder Neoplasms genetics, Urinary Bladder Neoplasms immunology, Urinary Bladder Neoplasms pathology, Disease Progression, E2F4 Transcription Factor genetics, E2F4 Transcription Factor metabolism, Mycobacterium bovis immunology, Urinary Bladder Neoplasms therapy
- Abstract
Unlabelled: Bladder cancer is a common malignant disease, with non-muscle-invasive bladder cancer (NMIBC) representing the majority of tumors. This cancer subtype is typically treated by transurethral resection. In spite of treatment, up to 70% of patients show local recurrences. Intravesical BCG (Bacillus Calmette-Guerin) immunotherapy has been widely used to treat NMIBC, but it fails to suppress recurrence of bladder tumors in up to 40% of patients. Therefore, the development of prognostic markers is needed to predict the progression of bladder cancer and the efficacy of intravesical BCG treatment. This study demonstrates the effectiveness of an E2F4 signature for prognostic prediction of bladder cancer. E2F4 scores for each sample in a bladder cancer expression dataset were calculated by summarizing the relative expression levels of E2F4 target genes identified by ChIP-seq, and then the scores were used to stratify patients into good- and poor-outcome groups. The molecular signature was investigated in a single bladder cancer dataset and then its effectiveness was confirmed in two meta-bladder datasets consisting of specimens from multiple independent studies. These results were consistent in different datasets and demonstrate that the E2F4 score is predictive of clinical outcomes in bladder cancer, with patients whose tumors exhibit an E2F4 score >0 having significantly shorter survival times than those with an E2F4 score <0, in both non-muscle-invasive, and muscle-invasive bladder cancer. Furthermore, although intravesical BCG immunotherapy can significantly improve the clinical outcome of NMIBC patients with positive E2F4 scores (E2F4>0 group), it does not show significant treatment effect for those with negative scores (E2F4<0 group)., Implications: The E2F4 signature can be applied to predict the progression/recurrence and the responsiveness of patients to intravesical BCG immunotherapy in bladder cancer., (©2015 American Association for Cancer Research.)
- Published
- 2015
- Full Text
- View/download PDF
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