Search

Clonal hematopoiesis (CH) is an age-related clonal expansion of hematopoietic stem cells (HSCs). Factors that shape the progression of CH are only beginning to be characterized. HSCs are a heterogeneous population of cells with distinct clonal outputs over time, which are hypothesized to be largely scripted in epigenetic and transcriptional cell state. Molecular properties of HSC states that mediate clonal behaviors of two major driver mutations in CH - DNMT3A and TET2 - represent potential therapeutical targets. Recent studies have identified the landscape of human CH mutant cells compared to non-mutated ones. However, the notion of a specific molecular target identified in CH cells associated with selective advantage or predisposition for subsequent transformation requires a formal validation by longitudinal studies. To uncover molecular underpinnings of CH-driven clonal phenotypes in human HSCs in vivo, we combined clonal analysis using heritable expressed DNA barcodes with single-cell transcriptomics using transplant in immunodeficient mice. We developed a statistical approach to associate transcriptional differences of HSCs with the clone phenotypes, such as size and HSC density, across more than a hundred of detected clones. It revealed robust transcriptional signatures underlying clone size and HSC density, which are largely complementary to transcriptional programs activated in TET2 and DNMT3A mutant HSCs. Of note, the clone size and density of HSCs in the clone tend to be uncoupled and associated with distinct transcriptional processes. Citation Format: Ruslan Soldatov, Giulia Schiroli, Peter Kharchenko, David Scadden. Transcriptional signatures of stem cell phenotypes in normal and clonal hematopoiesis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2456.

SummaryThe treatment of primary prostate cancer delicately balances an active surveillance approach for low-risk disease with multimodal treatment including surgery, radiation therapy, and hormonal therapy for high-risk disease. Recurrence and development of metastatic disease remains a clinical problem, without a clear understanding of what drives immune escape and tumor progression. Here, we sought to comprehensively describe the tumor microenvironment of localized prostate cancer contrasting this with adjacent normal samples and healthy controls. We performed single-cell RNA sequencing and high-resolution spatial transcriptomic analysis. This revealed tumor context dependent changes in gene expression. Our data point towards an immune suppressive tumor microenvironment associated with suppressive myeloid populations and exhausted T-cells, in addition to high stromal angiogenic activity. We inferred cell-to-cell relationships at an unprecedented scale for ligand-receptor interactions within undissociated tissue sections. Our work provides a highly detailed and comprehensive resource of the prostate tumor microenvironment as well as tumor-stromal cell interactions.HighlightsCharacterization of prostate cancer by combined scRNA-seq and spatial transcriptomic analysisPrimary prostate cancer establishes a suppressive immune microenvironmentThe prostate tumor microenvironment exhibits a high angiogenic gene expression patternA new computational analysis pipeline to deconvolute context-specific differential gene expression

Modern drill bits designs have become more efficient using static modelling, and in more advanced cases, time-based dynamic modelling. These methods have created improved cutting structures that fail rock more effectively, however, at-bit vibrations are difficult to estimate because of the high-frequency nature of the vibration and its proximity to typical vibration sensors. In conventional applications, vibration is not measured near the bit. A solution to capture this data on conventional assemblies and use the data in an actual bit design is presented in this paper with subsequent performance and vibration results. The relative efficiency, bit dull grading, and vibration performance are compared across these designs and explored in depth. This new generation of vibration tool fits inside the bit pin, enabling accurate at-bit vibration measurements by a suite of sensors. The tool includes a tri-axis accelerometer that measures lateral and axial acceleration, and gyro sensors to measure rpm and torsional acceleration. Together, these outputs combine with the rig surface data to have time- and depth-based vibration data in the context of the run. When used to quantify the dynamic model, this represents a modelling calibration that improves bit design performance. The lower-vibration environment created by the new bit design enables the operator to run increased parameters with a lower likelihood for measurement-while-drilling (MWD) failures, motor failures, and premature catastrophic bit failures leading to faster run times and less nonproductive time (NPT). These results also prove that meaningful bit design changes can take place more frequently than through traditional means, translating value to the operator in the form more successful BHA improvements and less drilling time. Using the new in-bit sensor in a baseline design to start the design cycle, a baseline mechanical specific energy (MSE) and vibration model was developed foot-by-foot. The worst areas of vibration were seen as the bit became dull in the lower section of the drilling interval. A new dull bit model was created in parallel to capture this section of data. A new design was proposed to Whiting Petroleum to improve both sharp and dull efficiency and vibration, and subsequently run with sensor in an offset well.

Extract: Stem cells modulate tissue formation and repair based on a complex interaction of cell autonomous and non-autonomous regulatory mechanisms. While reductionist approaches to understanding stem cell control continue to be extremely productive, understanding the physiological contexts in which stem cells function, will ultimately require definition of the microenvironments in which they live. The location of stem or precursor populations within numerous solid tissues has been described, but delineating specific associated cells and how they participate in regulating stem cell function has generally been lacking for mammalian tissues. However, the use of invertebrate-based models has created particularly productive systems in which to examine the niche context of stem cells. Gonadal tissue from C. elegans and D. melanogaster has permitted the definition and identification of ancillary niche cells, physical interactions and the molecular pathways such as Notch paralogues that govern the interplay between the stem cell and its local environment. We sought to determine a niche component for a mammalian tissue and focused on the hematopoietic system. We focused on hematopoiesis for multiple reasons, but in particular because of the potential for applying the information gained to a medical context.

Electroporation has been used in biological laboratories for many years to transiently porate cell membranes and permit plasmid or protein transfection. It has been shown that the application of pulsed electric fields (PEFs) of defined strength will kill off larger cells and select for viable small cells, in samples containing heterogeneous cells. This permits the selective killing of several blood and bone marrow-resident tumor cells. PEF technology is being applied to tumor purging of progenitor-cell transfusions, in support of high-dose chemotherapy, for the treatment of cancers such as lymphoma and multiple myeloma. Autologous stem-cell transplantation, in the setting of hematologic malignancies such as lymphoma, improves disease-free survival if the graft has undergone tumor purging. Progenitor cells are preserved or enriched. To overcome issues of electrical resistance, purging fidelity, and large sample volume, a flowing chamber PEF apparatus was designed and constructed for large-scale purging of clinical quantities of progenitor-cell transfusions. The specifics of this technique are described here. Treatment of greater than 10(9) cells is achieved in 30 min, under optimized flow conditions designed to overcome surface area or resistance issues and to optimize exposure of cells to electric fields. Efficient, large volume tumor purging of greater than 3 logs, for mixtures of tumor cells and mononuclear cells, is routinely achieved under defined conditions.

It has been realized that different cell states employ different metabolic modes. Whether metabolism is a determinant of cell state is unclear, but studies in cancer suggest that altering metabolic activity can modify cellular function. Cancer cells metabolize glucose through glycolysis even in the presence of oxygen, a phenomenon called Warburg effect. Normal somatic cells thought to also preferentially use glycolytic metabolism are tissue stem cells, particularly the hematopoietic stem cells (HSC) resident in the hypoxic microenvironment of the bone marrow. Recently the molecular basis for Warburg effect in cancer cells has been identified as due to a specific isoform of pyruvate kinase M2 (PKM2). Interestingly, HSC also express PKM2. Using a mouse strain that allows conditional deletion of PKM2, we observed that PKM2 depletion enhances normal HSC function as revealed by a competitive transplantation assay. The altered cellular function is accompanied with decreased glycolysis and increased oxidative phosphorylation specifically in the primitive stem/progenitor cell population. Notably however, PKM2 deletion markedly disadvantages disease development in mouse models of both acute and chronic myeloid leukemia. Such a distinction in response between normal and malignant cells is unprecedented to our knowledge and may offer a highly unique opportunity to advantage normal while disadvantaging malignant cells of the hematopoietic lineage by targeting a single metabolic enzyme.