Single-Cell Epigenomics Reveals Mechanisms of Cancer Progression

Cancer initiation is driven by the cooperation between genetic and epigenetic aberrations that disrupt gene regulatory programs critical to maintain specialized cellular functions. After initiation, cells acquire additional genetic and epigenetic alterations influenced by tumor-intrinsic and -extrinsic mechanisms, which increase intratumoral heterogeneity, reshape the cell's underlying gene regulatory network, and promote cancer evolution. Furthermore, environmental or therapeutic insults drive the selection of heterogeneous cell states, with implications for cancer initiation, maintenance, and drug resistance. The advancement of single-cell genomics has begun to uncover the full repertoire of chromatin and gene expression states (cell states) that exist within individual tumors. These single-cell analyses suggest that cells diversify in their regulatory states upon transformation by co-opting damage-induced and nonlineage regulatory programs that can lead to epigenomic plasticity. Here, we review these recent studies related to regulatory state changes in cancer progression and highlight the growing single-cell epigenomics toolkit poised to address unresolved questions in the field. Expected final online publication date for the Annual Review of Cancer Biology, Volume 6 is April 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Exploring the Cell Stemness and the Complexity of theAdipose Tissue Niche

Adipose tissue is a complex organ composed of different cellular populations, including mesenchymal stem and progenitor cells, adipocytes, and immune cells such as macrophages and lymphocytes. These cellular populations alter dynamically during aging or as a response to pathophysiology such as obesity. Changes in the various inflammatory cells are associated with metabolic complications and the development of insulin resistance, indicating that immune cells crosstalk with the adipocytes. Therefore, a study of the cell populations in the adipose tissue and the extracellular matrix maintaining the tissue niche is important for the knowledge on the regulatory state of the organ. We used a combination of methods to study various parameters to identify the composition of the resident cells in the adipose tissue and evaluate their profile. We analyzed the tissue structure and cells based on histology, immune fluorescence staining, and flow cytometry of cells present in the tissue in vivo and these markers’ expression in vitro. Any shift in cells’ composition influences self-renewal of the mesenchymal progenitors, and other cells affect the functionality of adipogenesis.

The RNA chaperone StpA enables fast RNA refolding by destabilization of mutually exclusive base pairs within competing secondary structure elements

In bacteria RNA gene regulatory elements refold dependent on environmental clues between two or more long-lived conformational states each associated with a distinct regulatory state. The refolding kinetics are strongly temperature-dependent and especially at lower temperatures they reach timescales that are biologically not accessible. To overcome this problem, RNA chaperones have evolved. However, the precise molecular mechanism of how these proteins accelerate RNA refolding reactions remains enigmatic. Here we show how the RNA chaperone StpA of Escherichia coli leads to an acceleration of a bistable RNA’s refolding kinetics through the selective destabilization of key base pairing interactions. We find in laser assisted real-time NMR experiments on photocaged bistable RNAs that the RNA chaperone leads to a two-fold increase in refolding rates at low temperatures due to reduced stability of ground state conformations. Further, we can show that upon interaction with StpA, base pairing interactions in the bistable RNA are modulated to favor refolding through the dominant pseudoknotted transition pathway. Our results shed light on the molecular mechanism of the interaction between RNA chaperones and bistable RNAs and are the first step into a functional classification of chaperones dependent on their biophysical mode of operation.

Fractured China

Is China's rise a threat to international order? Fractured China shows that it depends on what one means by 'China', for China is not the monolithic, unitary actor that many assume. Forty years of state transformation – the fragmentation, decentralisation and internationalisation of party-state apparatuses – have profoundly changed how its foreign policy is made and implemented. Today, Chinese behaviour abroad is often not the product of a coherent grand strategy, but results from a sometimes-chaotic struggle for power and resources among contending politico-business interests, within a surprisingly permissive Chinese-style regulatory state. Presenting a path-breaking new analytical framework, Fractured China transforms the central debate in International Relations and provides new tools for scholars and policymakers seeking to understand and respond to twenty-first century rising powers. Drawing on extensive fieldwork in China and Southeast Asia, it includes three major case studies – the South China Sea, non-traditional security cooperation, and development financing–to demonstrate the framework's explanatory power.

Quantitative phosphoproteomics reveals regulatory state dependent efficacy of chemical Cdk1 inhibition and distinct Cdk5 complexes as novel Wee1 substrates

Wee1 kinase plays a central role in the eukaryotic cell cycle via its well-known negative regulation of Cdk1 activity at the G2/M transition, preventing progression into mitosis until DNA replication and/or DNA damage repair is complete. Recent genetic evidence in yeast, flies and human cells have suggested additional functions of Wee1 in mitosis and during mitotic exit, respectively. To discover new candidate substrates of Wee1 kinase, we used SILAC-based phosphoproteomics and selective chemical inhibition to quantitatively compare phosphorylation site abundances in the presence and absence of Wee1 activity. Unexpectedly, we uncovered a role for the Wee1-dependent phosphorylation of Cdk1-cyclin B at tyrosine 15 (Y15) in facilitating chemical inhibition of Cdk1-cyclin B by the inhibitor RO3306. Thermal shift stability assays demonstrated greater binding affinity of RO3306 for Y15-phosphorylated Cdk1-cyclin B versus unphosphorylated complex, providing an additional molecular basis for the observed Wee1 inhibitor-based toxicity in human cells. In addition, our experiments identified Cdk5-CABLES and Cdk5-cyclin B as novel substrates of Wee1 during chemically induced exit from mitosis. Collectively, these experiments facilitate a greater understanding of the Wee1-Cdk1 signaling axis and uncover new candidate substrates for Wee1.

Single-cell analysis of cell fate bifurcation in the chordate Ciona

Background Inductive signaling interactions between different cell types are a major mechanism for the further diversification of embryonic cell fates. Most blastomeres in the model chordate Ciona robusta become restricted to a single predominant fate between the 64-cell and mid-gastrula stages. The deeply stereotyped and well-characterized Ciona embryonic cell lineages allow the transcriptomic analysis of newly established cell types very early in their divergence from sibling cell states without the pseudotime inference needed in the analysis of less synchronized cell populations. This is the first ascidian study to use droplet scRNAseq with large numbers of analyzed cells as early as the 64-cell stage when major lineages such as primary notochord first become fate restricted. Results and conclusions We identify 59 distinct cell states, including new subregions of the b-line neural lineage and the early induction of the tail tip epidermis. We find that 34 of these cell states are directly or indirectly dependent on MAPK-mediated signaling critical to early Ciona patterning. Most of the MAPK-dependent bifurcations are canalized with the signal-induced cell fate lost upon MAPK inhibition, but the posterior endoderm is unique in being transformed into a novel state expressing some but not all markers of both endoderm and muscle. Divergent gene expression between newly bifurcated sibling cell types is dominated by upregulation in the induced cell type. The Ets family transcription factor Elk1/3/4 is uniquely upregulated in nearly all the putatively direct inductions. Elk1/3/4 upregulation together with Ets transcription factor binding site enrichment analysis enables inferences about which bifurcations are directly versus indirectly controlled by MAPK signaling. We examine notochord induction in detail and find that the transition between a Zic/Ets-mediated regulatory state and a Brachyury/FoxA-mediated regulatory state is unexpectedly late. This supports a “broad-hourglass” model of cell fate specification in which many early tissue-specific genes are induced in parallel to key tissue-specific transcriptional regulators via the same set of transcriptional inputs.

Recursive feedforward regulatory logic underlies robustness of the specification-to-differentiation transition and fidelity of terminal cell fate during C. elegans endoderm development

Development is driven by gene regulatory networks (GRNs) that progressively dictate specification and differentiation of cell fates. The architecture of GRNs directly determines the specificity and accuracy of developmental outcomes. We report here that the core regulatory circuitry for endoderm development in C. elegans is comprised of a recursive series of interlocked feedforward modules linking a cascade of six sequentially expressed GATA-type transcription factors. This structure results in a reiterated sequential redundancy, in which removal of a single factor or alternate factors in the cascade results in no, or a mild, effect on endoderm development and gut differentiation, while elimination of any two factors that are sequentially deployed in the cascade invariably results in a strong phenotype. The strength of the observed phenotypes is successfully predicted by a computational model based on the timing and levels of transcriptional states. The feedforward regulatory logic in the GRN appears to ensure timely onset of terminal differentiation genes and allow rapid and robust lockdown of cell fate during early embryogenesis. We further found that specification-to-differentiation transition is linked through a common regulator, the END-1 GATA factor that straddles the two processes. Finally, we revealed roles for key GATA factors in establishing spatial regulatory state domains by acting as transcriptional repressors that appear to define the boundaries of the digestive tract. Our findings support a comprehensive model of the core gene network that describes how robust endoderm development is achieved during C. elegans embryogenesis.

Administrative and legal status of the National Agency of Ukraine for Detection, Investiga- tion and Management of Assets Obtained from Corruption and Other Crimes

In the work, using general and special scientific research methods, and the specific combination de-pends on the purpose and objectives of the study. The use of methods of formal logic makes it possible to define, clarify and supplement certain concepts and supplement certain terminological categories and, accordingly, to sys-tematize the conceptual and categorical apparatus. Methods of formal logic and logic of essence, as well as methods of analysis and synthesis, deduction and induction, analogy and induction are also used. The scientific novelty of this article is that it is the result of scientific research on a number of problematic issues of the administrative and legal status of ARMA. The author concludes that the administrative and legal status of the National Agency of Ukraine for Detection, Investigation and Management of Assets Obtained from Corruption and Other Crimes is based on powers in the field of property confiscation management and successful implementation of relevant EU practice in Ukrainian legislation. These powers are not just a typical regulatory state activity, they form fundamen-tally new mechanisms of public-private partnership, which have no analogues in Ukraine so far. The consequence of the implementation of these powers was the creation of a new market for services for the management of seized property, as well as a stock market for seized property, different from the market for confiscated property. In the future, it would be interesting to examine the case law on appealing decisions on the transfer of financial assets to the management of ARMA. As well as expanding the powers of the National Agency of Ukraine for the detection, search and management of assets derived from corruption and other crimes

The Gendered Construction of Border-Crossing in Canada: Immigrant and Indigenous Women’s Life Histories in the Tracks of Gloria Anzaldúa

Our paper offers a new direction for Canadian scholarship on women and border studies by contextualizing women border- crossers within Anzaldúa’s conocimiento model. Based on the narratives of six women border-crossers in Canada, we argue that citizenship is a form of regulatory state-power where “belonging” is bureaucratically defined. For these women, belonging to a homeland is embodied in the interplay between Anzaldúa’s facultad and shadowbeast—between the agency of spirituality and the vagaries of political subjectivity. They crossed the border into Canada, and as a result, the whole of Canada became a borderzone within which they negotiated nepantla (the experience of being “in-between” culture and identity categories). We demonstrate how applying Anzaldúa’s framework to the Canadian context yields new insights into secularism, citizenships, multiculturalism, and belonging.

REGULATORY FIT EFFECTS ON THE ACQUISITION OF LEXICAL STRESS

Higgins’s (2000) regulatory fit theory proposes that a fit between one’s regulatory state and strategic means for reaching a goal increases motivational strength and engagement. This study investigates how regulatory fit affects the L2 acquisition of lexical stress in an authentic learning context. Ninety EFL students were assigned to either gain frame or loss frame conditions. They engaged in speech practice in which they mimicked a model speech in English to win a chance to enter a prize raffle. The reward system was framed differently in the two framing conditions, with the intention of eliciting the participants’ use of eager or vigilant strategies, thus creating fit and nonfit conditions. Acquisition of lexical stress was assessed using pre- and posttest scores. Multiple regression analysis showed no regulatory fit effects and no loss frame effects but did show a significant beneficial effect of the gain frame on the acquisition of lexical stress.