Genomes and Genes
Summary: The process of accumulation of genetic and epigenetic changes over time in individual cells and the effect of the changes on CELL PROLIFERATION.
- Prandi D, Baca S, Romanel A, Barbieri C, Mosquera J, Fontugne J, et al. Unraveling the clonal hierarchy of somatic genomic aberrations. Genome Biol. 2014;15:439 pubmed publisher..The analyses highlight the diversity of clonal evolution within and across tumor types that might be informative for risk stratification and patient selection for ..
- Whittle J, Lewis M, Lindeman G, Visvader J. Patient-derived xenograft models of breast cancer and their predictive power. Breast Cancer Res. 2015;17:17 pubmed publisher..Here we review the utility of breast cancer PDX models to study the clonal evolution of tumors and to evaluate novel therapies and drug resistance.
- Villacorta Martin C, Craig A, Villanueva A. Divergent evolutionary trajectories in transplanted tumor models. Nat Genet. 2017;49:1565-1566 pubmed publisher..Human-derived tumor models are becoming popular in the context of personalized medicine, but a new study shows that these models could be less representative of primary tumors than previously thought, particularly when using late passages...
- Wan J, Massie C, Garcia Corbacho J, Mouliere F, Brenton J, Caldas C, et al. Liquid biopsies come of age: towards implementation of circulating tumour DNA. Nat Rev Cancer. 2017;17:223-238 pubmed publisher..This is an opportune time to appraise potential approaches to ctDNA analysis, and to consider their applications in personalized oncology and in cancer research. ..
- Smith E, Jepsen K, Khosroheidari M, Rassenti L, D Antonio M, Ghia E, et al. Biased estimates of clonal evolution and subclonal heterogeneity can arise from PCR duplicates in deep sequencing experiments. Genome Biol. 2014;15:420 pubmed publisherAccurate allele frequencies are important for measuring subclonal heterogeneity and clonal evolution. Deep-targeted sequencing data can contain PCR duplicates, inflating perceived read depth...
- Porter S, Baker L, Mittelman D, Porteus M. Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo. Genome Biol. 2014;15:R75 pubmed publisher..Aside from clonal cell lines, we propose that cellular barcoding could prove valuable in modeling the clonal behavior of heterogeneous cell populations over time, including tumor populations treated with chemotherapeutic agents. ..
- Andrade V, Ostrovnaya I, Seshan V, Morrogh M, Giri D, Olvera N, et al. Clonal relatedness between lobular carcinoma in situ and synchronous malignant lesions. Breast Cancer Res. 2012;14:R103 pubmed publisher..Our results support the role of LCIS as a precursor in the development of both high-grade and low-grade ductal and lobular cancers. ..
- Roshan A, Jones P, Greenman C. Exact, time-independent estimation of clone size distributions in normal and mutated cells. J R Soc Interface. 2014;11: pubmed publisher..This approach can be extended beyond neutral models of mutant clonal evolution. Applications of these approaches are twofold...
- Russo M, Broach J, Sheldon K, Houser K, Liu D, Kesterson J, et al. Clonal evolution in paired endometrial intraepithelial neoplasia/atypical hyperplasia and endometrioid adenocarcinoma. Hum Pathol. 2017;67:69-77 pubmed publisher..However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized...
- Kunimoto H, Nakajima H. Epigenetic dysregulation of hematopoietic stem cells and preleukemic state. Int J Hematol. 2017;106:34-44 pubmed publisher..Further studies are required to decipher the exact mechanism by which preleukemic stem cells originate and transform into a full-blown leukemic state. ..
- Blakely C, Watkins T, Wu W, Gini B, Chabon J, McCoach C, et al. Evolution and clinical impact of co-occurring genetic alterations in advanced-stage EGFR-mutant lung cancers. Nat Genet. 2017;49:1693-1704 pubmed publisher..This study calls for revisiting the prevailing single-gene driver-oncogene view and links clinical outcomes to co-occurring genetic alterations in patients with advanced-stage EGFR-mutant lung cancer. ..
- Andersen M, Sajid Z, Pedersen R, Gudmand Hoeyer J, Ellervik C, Skov V, et al. Mathematical modelling as a proof of concept for MPNs as a human inflammation model for cancer development. PLoS ONE. 2017;12:e0183620 pubmed publisher..the development of MPNs by mathematical models, and none have addressed the role of inflammation for clonal evolution and disease progression...
- Jaiswal S, Natarajan P, Silver A, Gibson C, Bick A, Shvartz E, et al. Clonal Hematopoiesis and Risk of Atherosclerotic Cardiovascular Disease. N Engl J Med. 2017;377:111-121 pubmed publisher..Funded by the National Institutes of Health and others.). ..
- Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N. BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies. Genome Biol. 2015;16:36 pubmed publisher..In two case studies, we demonstrate how BitPhylogeny BitPhylogeny reconstructs tumor phylogenies from methylation patterns in colon cancer and from single-cell exomes in myeloproliferative neoplasm. ..
- Cai Z, Chen G, Zeng Y, Dong X, Lin M, Huang X, et al. Circulating tumor DNA profiling reveals clonal evolution and real-time disease progression in advanced hepatocellular carcinoma. Int J Cancer. 2017;141:977-985 pubmed publisher..Taken together, study of mutation profiles in biopsy and plasma samples in HCC patients showed that ctDNA could overcome tumor heterogeneity and real-time track the therapeutic responses in the longitudinal monitoring. ..
- Degn S, van der Poel C, Firl D, Ayoglu B, Al Qureshah F, Bajic G, et al. Clonal Evolution of Autoreactive Germinal Centers. Cell. 2017;170:913-926.e19 pubmed publisher..Our data provide insight into the maturation of the self-reactive B cell response, contextualizing the epitope spreading observed in autoimmune disease. ..
- Ruscito I, Cacsire Castillo Tong D, Vergote I, Ignat I, Stanske M, Vanderstichele A, et al. Exploring the clonal evolution of CD133/aldehyde-dehydrogenase-1 (ALDH1)-positive cancer stem-like cells from primary to recurrent high-grade serous ovarian cancer (HGSOC). A study of the Ovarian Cancer Therapy-Innovative Models Prolong Survival (OCT. Eur J Cancer. 2017;79:214-225 pubmed publisher
- Qu X, Hei Y, Kang L, Yang X, Wang Y, Lu X, et al. Establishment of a combination scoring method for diagnosis of ocular adnexal lymphoproliferative disease. PLoS ONE. 2017;12:e0160175 pubmed publisher..7% (18/21) for MALToma and 35.3% (6/17) for ALH. Our study provides a method that may be useful for the differential diagnosis of RFH, ALH, and MALToma. ..
- Finazzi M, Lussana F, Salmoiraghi S, Spinelli O, Rambaldi A. Detection of driver and subclonal mutations in myelofibrosis: clinical impact on pharmacologic and transplant based treatment strategies. Expert Rev Hematol. 2017;10:627-636 pubmed publisher..Prospective clinical studies are needed to validate the use of this molecular data in the routine clinical practice. ..
- Sacco A, Kawano Y, Moschetta M, Zavidij O, Huynh D, Reagan M, et al. A novel in vivo model for studying conditional dual loss of BLIMP-1 and p53 in B-cells, leading to tumor transformation. Am J Hematol. 2017;92:E138-E145 pubmed publisher..This model mirrors what reported in patients with ABC DLBLC, and therefore represents a novel model for studying the biology of ABC-DLBCL harboring the dual loss of BLIMP-1/p53 and c-Myc over-expression. ..
- Peterson E, Chavan S, Bauer M, Heuck C, Johann D. Revealing the inherent heterogeneity of human malignancies by variant consensus strategies coupled with cancer clonal analysis. BMC Bioinformatics. 2014;15 Suppl 11:S9 pubmed publisher..New tools and methods to provide an improved understanding of tumor clonal architecture are needed to guide therapy. ..
- Kawamura S, Onai N, Miya F, Sato T, Tsunoda T, Kurabayashi K, et al. Identification of a Human Clonogenic Progenitor with Strict Monocyte Differentiation Potential: A Counterpart of Mouse cMoPs. Immunity. 2017;46:835-848.e4 pubmed publisher..Within the cGMP population, we also identified revised GMPs that completely lacked DC and lymphoid potential. Collectively, our findings expand and revise the current understanding of human myeloid cell differentiation pathways. ..
- ..This paradigm shift has been fueled by the development of single-cell sequencing technologies, which provide a powerful new approach to study complex biological processes in human cancers. ..
- Petrovska L, Mather A, Abuoun M, Branchu P, Harris S, Connor T, et al. Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010. Emerg Infect Dis. 2016;22:617-24 pubmed publisher..This high level of microevolution may affect antigenicity, pathogenicity, and transmission. ..
- Peterson E, Bauer M, Chavan S, Ashby C, Weinhold N, Heuck C, et al. Enhancing cancer clonality analysis with integrative genomics. BMC Bioinformatics. 2015;16 Suppl 13:S7 pubmed publisher..The iCloneViz approach can be used for analysis of clonal evolution and mutational dynamics of multi-omic data sets...
- Biasco L, Rothe M, Schott J, Schambach A. Integrating Vectors for Gene Therapy and Clonal Tracking of Engineered Hematopoiesis. Hematol Oncol Clin North Am. 2017;31:737-752 pubmed publisher..Moreover, outlined is how these vectors can be used for cancer gene discovery and clonal tracking of benign and malignant hematopoiesis to gain insights into the dynamics of hematopoiesis. ..
- Shlush L, Hershkovitz D. Clonal evolution models of tumor heterogeneity. Am Soc Clin Oncol Educ Book. 2015;:e662-5 pubmed publisherSomatic/clonal evolution is the process of sequential acquisition of vertically transmittable genetic/epigenetic elements in multicellular organisms. Cancer is the result of somatic evolution...
- Visentini M, Fiorilli M, Casato M. From the pathogenesis to the cure of indolent B-cell lymphoproliferative disorders associated with hepatitis C virus infection: which role for direct-acting antivirals?. Expert Rev Hematol. 2017;10:719-727 pubmed publisher..Large studies are needed to determine the values and limits of DAA for treating HCV-associated indolent lymphomas and to identify subgroups at risk of non-response. ..
- Hiley C, de Bruin E, McGranahan N, Swanton C. Deciphering intratumor heterogeneity and temporal acquisition of driver events to refine precision medicine. Genome Biol. 2014;15:453 pubmed publisher..Resolving the spatial and temporal heterogeneity of subclones with cancer driver events may offer insight into therapy response, tumor evolutionary histories and clinical trial design. ..