Single-cell RNA-seq can precisely resolve cellular states, but applying this method to low-input samples is challenging. Here, we present Seq-Well, a portable, low-cost platform for massively ...parallel single-cell RNA-seq. Barcoded mRNA capture beads and single cells are sealed in an array of subnanoliter wells using a semipermeable membrane, enabling efficient cell lysis and transcript capture. We use Seq-Well to profile thousands of primary human macrophages exposed to Mycobacterium tuberculosis.
Barrier tissue dysfunction is a fundamental feature of chronic human inflammatory diseases
. Specialized subsets of epithelial cells-including secretory and ciliated cells-differentiate from basal ...stem cells to collectively protect the upper airway
. Allergic inflammation can develop from persistent activation
of type 2 immunity
in the upper airway, resulting in chronic rhinosinusitis, which ranges in severity from rhinitis to severe nasal polyps
. Basal cell hyperplasia is a hallmark of severe disease
, but it is not known how these progenitor cells
contribute to clinical presentation and barrier tissue dysfunction in humans. Here we profile primary human surgical chronic rhinosinusitis samples (18,036 cells, n = 12) that span the disease spectrum using Seq-Well for massively parallel single-cell RNA sequencing
, report transcriptomes for human respiratory epithelial, immune and stromal cell types and subsets from a type 2 inflammatory disease, and map key mediators. By comparison with nasal scrapings (18,704 cells, n = 9), we define signatures of core, healthy, inflamed and polyp secretory cells. We reveal marked differences between the epithelial compartments of the non-polyp and polyp cellular ecosystems, identifying and validating a global reduction in cellular diversity of polyps characterized by basal cell hyperplasia, concomitant decreases in glandular cells, and phenotypic shifts in secretory cell antimicrobial expression. We detect an aberrant basal progenitor differentiation trajectory in polyps, and propose cell-intrinsic
, epigenetic
and extrinsic factors
that lock polyp basal cells into this uncommitted state. Finally, we functionally demonstrate that ex vivo cultured basal cells retain intrinsic memory of IL-4/IL-13 exposure, and test the potential for clinical blockade of the IL-4 receptor α-subunit to modify basal and secretory cell states in vivo. Overall, we find that reduced epithelial diversity stemming from functional shifts in basal cells is a key characteristic of type 2 immune-mediated barrier tissue dysfunction. Our results demonstrate that epithelial stem cells may contribute to the persistence of human disease by serving as repositories for allergic memories.
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KISLJ, NUK, SBMB, UL, UM, UPUK
To explore the distinct genotypic and phenotypic states of melanoma tumors, we applied single-cell RNA sequencing (RNA-seq) to 4645 single cells isolated from 19 patients, profiling malignant, ...immune, stromal, and endothelial cells. Malignant cells within the same tumor displayed transcriptional heterogeneity associated with the cell cycle, spatial context, and a drug-resistance program. In particular, all tumors harbored malignant cells from two distinct transcriptional cell states, such that tumors characterized by high levels of the MITF transcription factor also contained cells with low MITF and elevated levels of the AXL kinase. Single-cell analyses suggested distinct tumor microenvironmental patterns, including cell-to-cell interactions. Analysis of tumor-infiltrating T cells revealed exhaustion programs, their connection to T cell activation and clonal expansion, and their variability across patients. Overall, we begin to unravel the cellular ecosystem of tumors and how single-cell genomics offers insights with implications for both targeted and immune therapies.
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BFBNIB, NMLJ, NUK, ODKLJ, PNG, SAZU, UL, UM, UPUK
Guanidinium organosulfonates (GSs) are a large and well‐explored archetypal family of hydrogen‐bonded organic host frameworks that have, over the past 25 years, been regarded as nonporous. Reported ...here is the only example to date of a conventionally microporous GS host phase, namely guanidinium 1,4‐benzenedisulfonate (p‐G2BDS). p‐G2BDS is obtained from its acetone solvate, AcMe@G2BDS, by single‐crystal‐to‐single‐crystal (SC‐SC) desolvation, and exhibits a Type I low‐temperature/pressure N2 sorption isotherm (SABET=408.7(2) m2 g−1, 77 K). SC‐SC sorption of N2, CO2, Xe, and AcMe by p‐G2BDS is explored under various conditions and X‐ray diffraction provides a measurement of the high‐pressure, room temperature Xe and CO2 sorption isotherms. Though p‐G2BDS is formally metastable relative to the “collapsed”, nonporous polymorph, np‐G2BDS, a sample of p‐G2BDS survived for almost two decades under ambient conditions. np‐G2BDS reverts to zCO2@p‐G2BDS or yXe@p‐G2BDS (y,z=variable) when pressure of CO2 or Xe, respectively, is applied.
Pores now found! The porous polymorph of guanidinium 1,4‐benzenedisulfonate, G2BDS, one of the simplest members of an archetypal class of hydrogen‐bonded frameworks, was prepared from its acetone solvate by single‐crystal‐to‐single‐crystal (SC‐SC) desolvation. The persistent porosity, phase behavior, and gas sorption characteristics are described.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Acute myeloid leukemia (AML) is a heterogeneous disease that resides within a complex microenvironment, complicating efforts to understand how different cell types contribute to disease progression. ...We combined single-cell RNA sequencing and genotyping to profile 38,410 cells from 40 bone marrow aspirates, including 16 AML patients and five healthy donors. We then applied a machine learning classifier to distinguish a spectrum of malignant cell types whose abundances varied between patients and between subclones in the same tumor. Cell type compositions correlated with prototypic genetic lesions, including an association of FLT3-ITD with abundant progenitor-like cells. Primitive AML cells exhibited dysregulated transcriptional programs with co-expression of stemness and myeloid priming genes and had prognostic significance. Differentiated monocyte-like AML cells expressed diverse immunomodulatory genes and suppressed T cell activity in vitro. In conclusion, we provide single-cell technologies and an atlas of AML cell states, regulators, and markers with implications for precision medicine and immune therapies.
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•Technology for high-throughput single-cell RNA sequencing and genotyping•Variable cell-type composition of AML correlates to genetics and outcome•Primitive AML cells aberrantly co-express stemness and myeloid priming genes•Differentiated AML cells express immunomodulatory factors and suppress T cells
A combination of transcriptomics and mutational analyses in single cells from acute myeloid leukemia patients reveals the existence of distinct functional subsets and their associated drivers.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Cell-to-cell communication mediates a plethora of cellular decisions and behaviors that are crucial for the correct and robust development of multicellular organisms. Many of these signals are ...encoded in secreted hormones or growth factors that bind to and activate cell surface receptors, to transmit the cue intracellularly. One of the major superfamilies of cell surface receptors are the receptor tyrosine kinases (RTKs). For nearly half a century RTKs have been the focus of intensive study due to their ability to alter fundamental aspects of cell biology, such as cell proliferation, growth, and shape, and because of their central importance in diseases such as cancer. Studies in model organisms such a
have proved invaluable for identifying new conserved RTK pathway components, delineating their contributions, and for the discovery of conserved mechanisms that control RTK-signaling events. Here we provide a brief overview of the RTK superfamily and the general mechanisms used in their regulation. We further highlight the functions of several RTKs that govern distinct cell-fate decisions in
and explore how their activities are developmentally controlled.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
The hydroperoxyl radical (HO2) is a major precursor of OH and tropospheric ozone. OH is the main atmospheric oxidant, while tropospheric ozone is an important surface pollutant and greenhouse gas. ...Standard gas-phase models for atmospheric chemistry tend to overestimate observed HO2 concentrations, and this has been tentatively attributed to heterogeneous uptake by aerosol particles. It is generally assumed that HO2 uptake by aerosol involves conversion to H2O2, but this is of limited efficacy as an HO2 sink because H2O2 can photolyze to regenerate OH and from there HO2. Joint atmospheric observations of HO2 and H2O2 suggest that HO2 uptake by aerosols may in fact not produce H2O2. Here we propose a catalytic mechanism involving coupling of the transition metal ions Cu(I)/Cu(II) and Fe(II)/Fe(III) to rapidly convert HO2 to H2O in aqueous aerosols. The implied HO2 uptake and conversion to H2O significantly affects global model predictions of tropospheric OH, ozone, carbon monoxide (CO) and other species, improving comparisons to observations in the GEOS-Chem model. It represents a previously unrecognized positive radiative forcing of aerosols through the effects on the chemical budgets of major greenhouse gases including methane and hydrofluorocarbons (HFCs).
Metagenomic analyses have indicated that the female bladder harbors an indigenous microbiota. However, there are few cultured reference strains with sequenced genomes available for functional and ...experimental analyses. Here we isolate and genome-sequence 149 bacterial strains from catheterized urine of 77 women. This culture collection spans 78 species, representing approximately two thirds of the bacterial diversity within the sampled bladders, including Proteobacteria, Actinobacteria, and Firmicutes. Detailed genomic and functional comparison of the bladder microbiota to the gastrointestinal and vaginal microbiotas demonstrates similar vaginal and bladder microbiota, with functional capacities that are distinct from those observed in the gastrointestinal microbiota. Whole-genome phylogenetic analysis of bacterial strains isolated from the vagina and bladder in the same women identifies highly similar Escherichia coli, Streptococcus anginosus, Lactobacillus iners, and Lactobacillus crispatus, suggesting an interlinked female urogenital microbiota that is not only limited to pathogens but is also characteristic of health-associated commensals.
Gynecologic cancer in pregnancy Korenaga, Travis-Riley K.; Tewari, Krishnansu S.
Gynecologic oncology,
06/2020, Volume:
157, Issue:
3
Journal Article
Peer reviewed
Open access
Cancer complicates 1 in 1000 pregnancies. Multidisciplinary consensus comprised of Gynecologic Oncology, Pathology, Neonatology, Radiology, Anesthesiology, Maternal Fetal Medicine, and Social Work ...should be convened. Pregnancy provides an opportunity for cervical cancer screening, with deliberate delays in treatment permissible for early stage carcinoma. Vaginal delivery is contraindicated in the presence of gross lesion(s) and radical hysterectomy with lymphadenectomy at cesarean delivery is recommended. Women with locally advanced and metastatic/recurrent disease should commence treatment at diagnosis with chemoradiation and systemic therapy, respectively; neoadjuvant chemotherapy to permit gestational advancement may be considered in select cases. Most adnexal masses are benign and resolve by the second trimester. Persistent, asymptomatic, benign-appearing masses can be managed conservatively; surgery, if indicated, is best deferred to 15–20 weeks, with laparoscopy preferable over laparotomy whenever possible. Benign and malignant germ cell tumors and borderline tumors are occasionally encountered, with unilateral adnexectomy and preservation of the uterus and contralateral ovary being the rule. Epithelial ovarian cancer is exceedingly rare. Ultrasonography and magnetic resonance imaging lack ionizing radiation and can be employed to evaluate disease extent. Tumor markers, including CA-125, AFP, LDH, inhibin-B, and even CEA and ßhCG may be informative. If required, chemotherapy can be administered following organogenesis during the second and third trimesters. Because platinum and other anti-neoplastic agents cross the placenta, chemotherapy should be withheld after 34 weeks to avoid neonatal myelosuppression. Bevacizumab, immune checkpoint inhibitors, and PARP inhibitors should be avoided throughout pregnancy. Although antenatal glucocorticoids to facilitate fetal pulmonary maturation and amniotic fluid index assessment can be considered, there is no demonstrable benefit of tocolytics, antepartum fetal heart rate monitoring, and/or amniocentesis. Endometrial, vulvar, and vaginal cancer in pregnancy are curiosities, although leiomyosarcoma and the dreaded twin fetus/hydatidiform mole have been reported. For gynecologic malignancies, pregnancy does not impart aggressive clinical behavior and/or worse prognosis.
•Cancer affects 1 in 1000 pregnancies.•Diagnostic workup for cancer must be carefully selected and interpreted in pregnancy.•Cervical cancer is the most common gynecologic malignancy diagnosed in pregnancy.•Surgery and chemotherapy can be appropriately used with preservation of pregnancy.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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