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Cold Spring Harbor Symposia on Quantitative Biology

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https://www.readbyqxmd.com/read/28424341/alterations-in-three-dimensional-organization-of-the-cancer-genome-and-epigenome
#1
Joanna Achinger-Kawecka, Phillippa C Taberlay, Susan J Clark
The structural and functional basis of the genome is provided by the three-dimensional (3D) chromatin state. To enable accurate gene regulation, enhancer elements and promoter regions are brought into close spatial proximity to ensure proper, cell type-specific gene expression. In cancer, genetic and epigenetic processes can deregulate the transcriptional program. To investigate whether the 3D chromatin state is also disrupted in cancer we performed Hi-C chromosome conformation sequencing in normal and prostate cancer cells and compared the chromatin interaction maps with changes to the genome and epigenome...
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28424340/a-conversation-with-valerie-weaver
#2
(no author information available yet)
No abstract text is available yet for this article.
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28424339/discovery-of-double-stranded-genomic-dna-in-circulating-exosomes
#3
Raghu Kalluri, Valerie S LeBleu
It is becoming increasingly clear that small vesicles released from cells (extracellular vesicles [EVs]) represent a heterogeneous population implicated in cell-to-cell communication. The classifications and nomenclature of EVs are evolving as enrichment strategies and specific characteristics are being unraveled. At present, physical properties of EVs-namely, size, shape, and density-are often used to identify subpopulations of EVs. A distinct group of EVs, termed exosomes, largely defined by their small size (∼40-150 nm) and proposed subcellular origin, has been extensively studied in several aspects of cancer biology...
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28424338/a-conversation-with-david-lyden
#4
(no author information available yet)
No abstract text is available yet for this article.
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28424337/physical-and-chemical-gradients-in-the-tumor-microenvironment-regulate-tumor-cell-invasion-migration-and-metastasis
#5
Madeleine J Oudin, Valerie M Weaver
Cancer metastasis requires the invasion of tumor cells into the stroma and the directed migration of tumor cells through the stroma toward the vasculature and lymphatics where they can disseminate and colonize secondary organs. Physical and biochemical gradients that form within the primary tumor tissue promote tumor cell invasion and drive persistent migration toward blood vessels and the lymphatics to facilitate tumor cell dissemination. These microenvironment cues include hypoxia and pH gradients, gradients of soluble cues that induce chemotaxis, and ions that facilitate galvanotaxis, as well as modifications to the concentration, organization, and stiffness of the extracellular matrix that produce haptotactic, alignotactic, and durotactic gradients...
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28424336/a-conversation-with-karen-cichowski
#6
(no author information available yet)
No abstract text is available yet for this article.
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28424335/a-conversation-with-raghu-kalluri
#7
(no author information available yet)
No abstract text is available yet for this article.
April 19, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28416577/normal-and-neoplastic-stem-cells
#8
Melissa N McCracken, Benson M George, Kevin S Kao, Kristopher D Marjon, Tal Raveh, Irving L Weissman
A stem cell is broadly defined as a cell that retains the capacity to self-renew, a feature that confers the ability to continuously make identical daughter cells or additional cells that will differentiate into downstream progeny. This highly regulated genetic program to retain "stemness" is under active investigation. Research in our laboratory has explored similarities and differences in embryonic, tissue-specific, and neoplastic stem cells and their terminally differentiated counterparts. In this review, we will focus on the contributions of our laboratory, in particular on the studies that identified the mouse hematopoietic stem cell (HSC) and the human leukemic stem cell...
April 17, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28416576/pathways-involved-in-formation-of-mammary-organoid-architecture-have-keys-to-understanding-drug-resistance-and-to-discovery-of-druggable-targets
#9
Saori Furuta, Mina J Bissell
Signals from the extracellular matrix (ECM) are received at the cell surface receptor, transmitted to the cytoskeletons, and transferred to the nucleus and chromatin for tissue- and context-specific gene expression. Cells, in return, modulate the cell shape and ECM, allowing for the maintenance of tissue homeostasis as well as for coevolution and adaptation to the environmental signals. We postulated the existence of dynamic and reciprocal interactions between the ECM and the nucleus more than three decades ago, but now these pathways have been proven experimentally thanks to the advances in imaging and cell/molecular biology techniques...
April 17, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28416575/moving-closer-to-victory
#10
Taru Muranen, Joan S Brugge
No abstract text is available yet for this article.
April 17, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28408647/composition-and-function-of-mammalian-swi-snf-chromatin-remodeling-complexes-in-human-disease
#11
John L Pulice, Cigall Kadoch
Mammalian SWI/SNF (BAF) chromatin remodeling complexes play critical roles in maintaining chromatin architecture and gene expression. Genomic sequencing efforts over the past several years have unveiled a major role for these complexes in the development of human cancer as well as neurologic disease, prompting the need to interrogate underlying mechanisms and to develop new methods to comprehensively understand mSWI/SNF complex function. Here we discuss the emerging insights from genetic, biochemical, and functional genomic studies in the field and suggest approaches toward further basic investigations, as well as therapeutic targeting of chromatin remodeling machinery...
April 13, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28404767/a-conversation-with-joan-brugge
#12
(no author information available yet)
No abstract text is available yet for this article.
April 12, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28396526/a-conversation-with-luis-parada
#13
(no author information available yet)
No abstract text is available yet for this article.
April 10, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28396525/trimming-the-vascular-tree-in-tumors-metabolic-and-immune-adaptations
#14
Elizabeth Allen, Rindert Missiaen, Gabriele Bergers
Angiogenesis, the formation of new blood vessels, has become a well-established hallmark of cancer. Its functional importance for the manifestation and progression of tumors has been further validated by the beneficial therapeutic effects of angiogenesis inhibitors, most notably ones targeting the vascular endothelial growth factor (VEGF) signaling pathways. However, with the transient and short-lived nature of the patient response, it has become evident that tumors have the ability to adapt to the pressures of vascular growth restriction...
April 10, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28396524/reexamining-how-cancer-cells-exploit-the-body-s-metabolic-resources
#15
Craig B Thompson, Wilhelm Palm
A key feature of multicellular life is the sharing of nutritional resources by all cells of the organism. In animals, the allocation of nutrients to individual cells is not determined in a cell-autonomous fashion. Instead, growth factor and hormonal signaling pathways have evolved to regulate cellular nutrient uptake, which prevents individual cells from parasitizing the organism's metabolic reserves. Cancer is a condition where the highly ordered regulation of nutrient distribution is disrupted. During carcinogenesis, transformed cells acquire mutations in signaling pathways that render nutrient uptake cell-autonomous...
April 10, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28389597/explaining-the-paucity-of-intratumoral-t-cells-a-construction-out-of-known-entities
#16
Douglas T Fearon
This essay addresses the question of how tumors escape control by the immune system. The literature strongly points to inadequate accumulation of T cells among cancer cells as being the proximate cause, but this observation has no acceptable explanation as yet. An approach to this problem is adopted wherein the chemokines and chemokine receptors that normally mediate the trafficking of T cells to inflamed tissues are reviewed and considered in the context of their relative levels of expression in a transplanted colorectal tumor model...
April 7, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28389596/single-cell-analysis-of-circulating-tumor-cells-as-a-window-into-tumor-heterogeneity
#17
David T Miyamoto, David T Ting, Mehmet Toner, Shyamala Maheswaran, Daniel A Haber
Recent advances in microfluidic approaches have enabled the efficient isolation and detailed molecular characterization of circulating tumor cells (CTCs) in the peripheral blood of patients with cancer. Single-cell molecular analyses of CTCs reveal a tremendous degree of intracellular heterogeneity in CTC populations, reflective of heterogeneity across different patients as well as the underlying heterogeneity of tumors within each individual patient. These studies have enabled the identification of heterogeneous drug resistance mechanisms that can coexist in treatment refractory tumors...
April 7, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28389595/cancer-immunogenomics-computational-neoantigen-identification-and-vaccine-design
#18
Jasreet Hundal, Christopher A Miller, Malachi Griffith, Obi L Griffith, Jason Walker, Susanna Kiwala, Aaron Graubert, Joshua McMichael, Adam Coffman, Elaine R Mardis
The application of modern high-throughput genomics to the study of cancer genomes has exploded in the past few years, yielding unanticipated insights into the myriad and complex combinations of genomic alterations that lead to the development of cancers. Coincident with these genomic approaches have been computational analyses that are capable of multiplex evaluations of genomic data toward specific therapeutic end points. One such approach is called "immunogenomics" and is now being developed to interpret protein-altering changes in cancer cells in the context of predicted preferential binding of these altered peptides by the patient's immune molecules, specifically human leukocyte antigen (HLA) class I and II proteins...
April 7, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28381439/tumor-stroma-interactions-in-bone-metastasis-molecular-mechanisms-and-therapeutic-implications
#19
Hanqiu Zheng, Wenyang Li, Yibin Kang
Metastasis and associated complications are the major cause of death for cancer patients. The incidence of bone metastasis is among the highest in cancers arising from breast, prostate, and lung. Common skeletal-related events caused by bone metastasis include aberrant bone remodeling (osteolytic, osteoblastic, and mixed), bone pain, fracture, spinal cord compression, and life-threatening hypercalcemia. It is now known that interactions between tumor cells and bone stroma lie at the core of major steps of bone-metastasis progression...
April 5, 2017: Cold Spring Harbor Symposia on Quantitative Biology
https://www.readbyqxmd.com/read/28381438/modeling-breast-cancer-intertumor-and-intratumor-heterogeneity-using-xenografts
#20
Alejandra Bruna, Oscar M Rueda, Carlos Caldas
Breast cancer is a heterogeneous disease that can be stratified in at least 10 different subtypes. We present here a platform for derivation of preclinical models based on patient-derived tumor xenografts (PDTXs) that represent these subgroups. These models preserve the transcriptome, methylome, copy-number, and mutational landscape features of the tumor of origin through different passaging. Furthermore, the intratumoral composition of these models is formed by communities of clones very similar to the ones present in the originating tumor...
April 5, 2017: Cold Spring Harbor Symposia on Quantitative Biology
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