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Article ; Online: The transcriptomic landscape of normal and ineffective erythropoiesis at single-cell resolution.

Doty, Raymond T / Lausted, Christopher G / Munday, Adam D / Yang, Zhantao / Yan, Xiaowei / Meng, Changting / Tian, Qiang / Abkowitz, Janis L

Blood advances

2023 Volume 7, Issue 17, Page(s) 4848–4868

Abstract: The anemias of myelodysplastic syndrome (MDS) and Diamond Blackfan anemia (DBA) are generally macrocytic and always reflect ineffective erythropoiesis yet result from diverse genetic mutations. To delineate shared mechanisms that lead to cell death, we ... ...

Abstract	The anemias of myelodysplastic syndrome (MDS) and Diamond Blackfan anemia (DBA) are generally macrocytic and always reflect ineffective erythropoiesis yet result from diverse genetic mutations. To delineate shared mechanisms that lead to cell death, we studied the fate of single erythroid marrow cells from individuals with DBA or MDS-5q. We defined an unhealthy (vs healthy) differentiation trajectory using transcriptional pseudotime and cell surface proteins. The pseudotime trajectories diverge immediately after cells upregulate transferrin receptor (CD71), import iron, and initiate heme synthesis, although cell death occurs much later. Cells destined to die express high levels of heme-responsive genes, including ribosomal protein and globin genes, whereas surviving cells downregulate heme synthesis and upregulate DNA damage response, hypoxia, and HIF1 pathways. Surprisingly, 24% ± 12% of cells from control subjects follow the unhealthy trajectory, implying that heme might serve as a rheostat directing cells to live or die. When heme synthesis was inhibited with succinylacetone, more DBA cells followed the healthy trajectory and survived. We also noted high numbers of messages with retained introns that increased as erythroid cells matured, confirmed the rapid cycling of colony forming unit-erythroid, and demonstrated that cell cycle timing is an invariant property of differentiation stage. Including unspliced RNA in pseudotime determinations allowed us to reliably align independent data sets and accurately query stage-specific transcriptomic changes. MDS-5q (unlike DBA) results from somatic mutation, so many normal (unmutated) erythroid cells persist. By independently tracking erythroid differentiation of cells with and without chromosome 5q deletions, we gained insight into why 5q+ cells cannot expand to prevent anemia.
MeSH term(s)	Humans ; Erythropoiesis/genetics ; Transcriptome ; Anemia/genetics ; Ribosomal Proteins/genetics ; Anemia, Diamond-Blackfan/genetics ; Myelodysplastic Syndromes/genetics ; Myelodysplastic Syndromes/metabolism ; Chromosome Deletion ; Heme/metabolism
Chemical Substances	Ribosomal Proteins ; Heme (42VZT0U6YR)
Language	English
Publishing date	2023-06-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2023010382
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Article ; Online: Single-cell analysis of erythropoiesis in Rpl11 haploinsufficient mice reveals insight into the pathogenesis of Diamond-Blackfan anemia.

Doty, Raymond T / Yan, Xiaowei / Meng, Changting / Lausted, Christopher / Tian, Qiang / Abkowitz, Janis L

Experimental hematology

2021 Volume 97, Page(s) 66–78.e6

Abstract: Rpl11 haploinsufficient mice develop a macrocytic anemia similar to patients with DBA. Here, we fully characterize this model from clinical and pathophysiological perspectives. Early erythroid precursors have increased heme content and high cytoplasmic ... ...

Abstract	Rpl11 haploinsufficient mice develop a macrocytic anemia similar to patients with DBA. Here, we fully characterize this model from clinical and pathophysiological perspectives. Early erythroid precursors have increased heme content and high cytoplasmic reactive oxygen species, impairing erythroid differentiation at the colony-forming unit-erythroid (CFU-E)/proerythroblast stage and subsequently. Using single-cell analyses that link a cell's surface protein expression to its total transcriptome and unbiased analyses, we found GATA1, GATA1 target gene, and mitotic spindle pathway gene transcription were the pathways that decreased the most. Expression of ribosome protein and globin genes was amplified. These changes, as well as the other transcriptional changes that were identified, closely resemble findings in mice that lack the heme export protein FLVCR and, thus, suggest that heme excess and toxicity are the primary drivers of the macrocytic anemia. Consistent with this, treating Rpl11 haploinsufficient mice with corticosteroids increased the numbers of earliest erythroblasts but failed to overcome heme toxicity and improve the anemia. Rpl11 haploinsufficient mice uniquely upregulated mitochondrial genes, p53 and CDKN1A pathway genes, and DNA damage checkpoint genes, which should contribute further to erythroid marrow failure. Together our data establish Rpl11 haploinsufficient mice as an excellent model of DBA that can be used to study DBA pathogenesis and test novel therapies.
MeSH term(s)	Anemia, Diamond-Blackfan/genetics ; Anemia, Diamond-Blackfan/pathology ; Animals ; Erythroid Precursor Cells/metabolism ; Erythroid Precursor Cells/pathology ; Erythropoiesis ; Female ; Haploinsufficiency ; Humans ; Male ; Mice ; Single-Cell Analysis
Language	English
Publishing date	2021-02-22
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	185107-x
ISSN	1873-2399 ; 0531-5573 ; 0301-472X
ISSN (online)	1873-2399
ISSN	0531-5573 ; 0301-472X
DOI	10.1016/j.exphem.2021.02.010
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Article ; Online: Novel metrics for quantifying bacterial genome composition skews.

Joesch-Cohen, Lena M / Robinson, Max / Jabbari, Neda / Lausted, Christopher G / Glusman, Gustavo

BMC genomics

2018 Volume 19, Issue 1, Page(s) 528

Abstract: Background: Bacterial genomes have characteristic compositional skews, which are differences in nucleotide frequency between the leading and lagging DNA strands across a segment of a genome. It is thought that these strand asymmetries arise as a result ... ...

Abstract	Background: Bacterial genomes have characteristic compositional skews, which are differences in nucleotide frequency between the leading and lagging DNA strands across a segment of a genome. It is thought that these strand asymmetries arise as a result of mutational biases and selective constraints, particularly for energy efficiency. Analysis of compositional skews in a diverse set of bacteria provides a comparative context in which mutational and selective environmental constraints can be studied. These analyses typically require finished and well-annotated genomic sequences. Results: We present three novel metrics for examining genome composition skews; all three metrics can be computed for unfinished or partially-annotated genomes. The first two metrics, (dot-skew and cross-skew) depend on sequence and gene annotation of a single genome, while the third metric (residual skew) highlights unusual genomes by subtracting a GC content-based model of a library of genome sequences. We applied these metrics to 7738 available bacterial genomes, including partial drafts, and identified outlier species. A phylogenetically diverse set of these outliers (i.e., Borrelia, Ehrlichia, Kinetoplastibacterium, and Phytoplasma) display similar skew patterns but share lifestyle characteristics, such as intracellularity and biosynthetic dependence on their hosts. Conclusions: Our novel metrics appear to reflect the effects of biosynthetic constraints and adaptations to life within one or more hosts on genome composition. We provide results for each analyzed genome, software and interactive visualizations at http://db.systemsbiology.net/gestalt/ skew_metrics .
MeSH term(s)	Bacteria/genetics ; Computational Biology/methods ; Genome, Bacterial ; Internet Access ; Models, Genetic ; User-Computer Interface
Language	English
Publishing date	2018-07-11
Publishing country	England
Document type	Journal Article
ISSN	1471-2164
ISSN (online)	1471-2164
DOI	10.1186/s12864-018-4913-5
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Article ; Online: Whole genome sequence and comparative analysis of Borrelia burgdorferi MM1.

Jabbari, Neda / Glusman, Gustavo / Joesch-Cohen, Lena M / Reddy, Panga Jaipal / Moritz, Robert L / Hood, Leroy / Lausted, Christopher G

PloS one

2018 Volume 13, Issue 6, Page(s) e0198135

Abstract: Lyme disease is caused by spirochaetes of the Borrelia burgdorferi sensu lato genospecies. Complete genome assemblies are available for fewer than ten strains of Borrelia burgdorferi sensu stricto, the primary cause of Lyme disease in North America. MM1 ... ...

Abstract	Lyme disease is caused by spirochaetes of the Borrelia burgdorferi sensu lato genospecies. Complete genome assemblies are available for fewer than ten strains of Borrelia burgdorferi sensu stricto, the primary cause of Lyme disease in North America. MM1 is a sensu stricto strain originally isolated in the midwestern United States. Aside from a small number of genes, the complete genome sequence of this strain has not been reported. Here we present the complete genome sequence of MM1 in relation to other sensu stricto strains and in terms of its Multi Locus Sequence Typing. Our results indicate that MM1 is a new sequence type which contains a conserved main chromosome and 15 plasmids. Our results include the first contiguous 28.5 kb assembly of lp28-8, a linear plasmid carrying the vls antigenic variation system, from a Borrelia burgdorferi sensu stricto strain.
MeSH term(s)	Animals ; Bacterial Typing Techniques ; Borrelia burgdorferi/classification ; Borrelia burgdorferi/genetics ; Borrelia burgdorferi Group/genetics ; Chromosome Mapping ; Comparative Genomic Hybridization ; DNA, Bacterial/analysis ; Genetic Variation ; Genome, Bacterial ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lyme Disease/microbiology ; Multilocus Sequence Typing
Chemical Substances	DNA, Bacterial
Language	English
Publishing date	2018-06-11
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0198135
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Article ; Online: Modulation of Immune Checkpoints by Chemotherapy in Human Colorectal Liver Metastases.

Jabbari, Neda / Kenerson, Heidi L / Lausted, Christopher / Yan, Xiaowei / Meng, Changting / Sullivan, Kevin M / Baloni, Priyanka / Bergey, Dani / Pillarisetty, Venu G / Hood, Leroy E / Yeung, Raymond S / Tian, Qiang

Cell reports. Medicine

2020 Volume 1, Issue 9, Page(s) 100160

Abstract: Metastatic colorectal cancer (CRC) is a major cause of cancer-related death, and incidence is rising in younger populations (younger than 50 years). Current chemotherapies can achieve response rates above 50%, but immunotherapies have limited value for ... ...

Abstract	Metastatic colorectal cancer (CRC) is a major cause of cancer-related death, and incidence is rising in younger populations (younger than 50 years). Current chemotherapies can achieve response rates above 50%, but immunotherapies have limited value for patients with microsatellite-stable (MSS) cancers. The present study investigates the impact of chemotherapy on the tumor immune microenvironment. We treat human liver metastases slices with 5-fluorouracil (5-FU) plus either irinotecan or oxaliplatin, then perform single-cell transcriptome analyses. Results from eight cases reveal two cellular subtypes with divergent responses to chemotherapy. Susceptible tumors are characterized by a stemness signature, an activated interferon pathway, and suppression of PD-1 ligands in response to 5-FU+irinotecan. Conversely, immune checkpoint TIM-3 ligands are maintained or upregulated by chemotherapy in CRC with an enterocyte-like signature, and combining chemotherapy with TIM-3 blockade leads to synergistic tumor killing. Our analyses highlight chemomodulation of the immune microenvironment and provide a framework for combined chemo-immunotherapies.
MeSH term(s)	Antineoplastic Combined Chemotherapy Protocols ; Camptothecin/therapeutic use ; Colorectal Neoplasms/drug therapy ; Colorectal Neoplasms/immunology ; Hepatitis A Virus Cellular Receptor 2/immunology ; Humans ; Irinotecan/therapeutic use ; Liver Neoplasms/drug therapy ; Liver Neoplasms/pathology ; Neoplasm Metastasis/pathology ; Organoplatinum Compounds/therapeutic use ; Oxaliplatin/therapeutic use ; Programmed Cell Death 1 Receptor/immunology ; Tumor Microenvironment/immunology
Chemical Substances	HAVCR2 protein, human ; Hepatitis A Virus Cellular Receptor 2 ; Organoplatinum Compounds ; PDCD1 protein, human ; Programmed Cell Death 1 Receptor ; Oxaliplatin (04ZR38536J) ; Irinotecan (7673326042) ; Camptothecin (XT3Z54Z28A)
Language	English
Publishing date	2020-12-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ISSN	2666-3791
ISSN (online)	2666-3791
DOI	10.1016/j.xcrm.2020.100160
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Article ; Online: Label-free detection with surface plasmon resonance imaging.

Lausted, Christopher / Hu, Zhiyuan / Hood, Leroy

Methods in molecular biology (Clifton, N.J.)

2011 Volume 723, Page(s) 321–333

Abstract: Sensors based on surface plasmon resonance have demonstrated, over the last 2 decades, to be an effective method of studying biomolecular interactions without the need for labeling. Recently, it has been adapted to high-throughput use for imaging ... ...

Abstract	Sensors based on surface plasmon resonance have demonstrated, over the last 2 decades, to be an effective method of studying biomolecular interactions without the need for labeling. Recently, it has been adapted to high-throughput use for imaging microarray binding in real time. This provides a promising platform - a label-free protein microarray system - for the study of disease. In this example, antibody microarrays are used to efficiently profile the secretion of proteins from a cell line exposed to varying concentrations of a toxic compound.
MeSH term(s)	Antibodies/immunology ; Chromans/pharmacology ; Culture Media/metabolism ; Hep G2 Cells ; Humans ; Printing ; Protein Array Analysis ; Proteins/analysis ; Proteins/immunology ; Proteins/secretion ; Surface Plasmon Resonance/methods ; Thiazolidinediones/pharmacology
Chemical Substances	Antibodies ; Chromans ; Culture Media ; Proteins ; Thiazolidinediones ; troglitazone (I66ZZ0ZN0E)
Language	English
Publishing date	2011
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-61779-043-0_20
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Article ; Online: Blockade of interleukin 10 potentiates antitumour immune function in human colorectal cancer liver metastases.

Gut

2022 Volume 72, Issue 2, Page(s) 325–337

Abstract: Objective: Programmed cell death protein 1 (PD-1) checkpoint inhibition and adoptive cellular therapy have had limited success in patients with microsatellite stable colorectal cancer liver metastases (CRLM). We sought to evaluate the effect of ... ...

Abstract	Objective: Programmed cell death protein 1 (PD-1) checkpoint inhibition and adoptive cellular therapy have had limited success in patients with microsatellite stable colorectal cancer liver metastases (CRLM). We sought to evaluate the effect of interleukin 10 (IL-10) blockade on endogenous T cell and chimeric antigen receptor T (CAR-T) cell antitumour function in CRLM slice cultures. Design: We created organotypic slice cultures from human CRLM (n=38 patients' tumours) and tested the antitumour effects of a neutralising antibody against IL-10 (αIL-10) both alone as treatment and in combination with exogenously administered carcinoembryonic antigen (CEA)-specific CAR-T cells. We evaluated slice cultures with single and multiplex immunohistochemistry, in situ hybridisation, single-cell RNA sequencing, reverse-phase protein arrays and time-lapse fluorescent microscopy. Results: αIL-10 generated a 1.8-fold increase in T cell-mediated carcinoma cell death in human CRLM slice cultures. αIL-10 significantly increased proportions of CD8 Conclusion: Neutralising the effects of IL-10 in human CRLM has therapeutic potential as a stand-alone treatment and to augment the function of adoptively transferred CAR-T cells.
MeSH term(s)	Animals ; Humans ; Mice ; Carcinoembryonic Antigen/immunology ; Carcinoma/immunology ; Carcinoma/secondary ; CD8-Positive T-Lymphocytes/immunology ; Colorectal Neoplasms/pathology ; Immunotherapy, Adoptive ; Interleukin-10/antagonists & inhibitors ; Liver Neoplasms/immunology ; Liver Neoplasms/secondary ; Lymphocyte Activation ; Receptors, Antigen, T-Cell/metabolism ; Receptors, Chimeric Antigen/genetics ; Receptors, Chimeric Antigen/metabolism ; Receptors, Interleukin-10/antagonists & inhibitors ; Antibodies, Blocking/immunology
Chemical Substances	Carcinoembryonic Antigen ; Interleukin-10 (130068-27-8) ; Receptors, Antigen, T-Cell ; Receptors, Chimeric Antigen ; Receptors, Interleukin-10 ; Antibodies, Blocking
Language	English
Publishing date	2022-06-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	80128-8
ISSN	1468-3288 ; 0017-5749
ISSN (online)	1468-3288
ISSN	0017-5749
DOI	10.1136/gutjnl-2021-325808
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Article ; Online: Author Correction: Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers.

Watanabe, Kengo / Wilmanski, Tomasz / Baloni, Priyanka / Robinson, Max / Garcia, Gonzalo G / Hoopmann, Michael R / Midha, Mukul K / Baxter, David H / Maes, Michal / Morrone, Seamus R / Crebs, Kelly M / Kapil, Charu / Kusebauch, Ulrike / Wiedrick, Jack / Lapidus, Jodi / Pflieger, Lance / Lausted, Christopher / Roach, Jared C / Glusman, Gwênlyn /

Cummings, Steven R / Schork, Nicholas J / Price, Nathan D / Hood, Leroy / Miller, Richard A / Moritz, Robert L / Rappaport, Noa

Communications biology

2023 Volume 6, Issue 1, Page(s) 1208

Language	English
Publishing date	2023-11-27
Publishing country	England
Document type	Published Erratum
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05549-9
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Article ; Online: Lifespan-extending interventions induce consistent patterns of fatty acid oxidation in mouse livers.

Cummings, Steven R / Schork, Nicholas J / Price, Nathan D / Hood, Leroy / Miller, Richard A / Moritz, Robert L / Rappaport, Noa

Communications biology

2023 Volume 6, Issue 1, Page(s) 768

Abstract: Aging manifests as progressive deteriorations in homeostasis, requiring systems-level perspectives to investigate the gradual molecular dysregulation of underlying biological processes. Here, we report systemic changes in the molecular regulation of ... ...

Abstract	Aging manifests as progressive deteriorations in homeostasis, requiring systems-level perspectives to investigate the gradual molecular dysregulation of underlying biological processes. Here, we report systemic changes in the molecular regulation of biological processes under multiple lifespan-extending interventions. Differential Rank Conservation (DIRAC) analyses of mouse liver proteomics and transcriptomics data show that mechanistically distinct lifespan-extending interventions (acarbose, 17α-estradiol, rapamycin, and calorie restriction) generally tighten the regulation of biological modules. These tightening patterns are similar across the interventions, particularly in processes such as fatty acid oxidation, immune response, and stress response. Differences in DIRAC patterns between proteins and transcripts highlight specific modules which may be tightened via augmented cap-independent translation. Moreover, the systemic shifts in fatty acid metabolism are supported through integrated analysis of liver transcriptomics data with a mouse genome-scale metabolic model. Our findings highlight the power of systems-level approaches for identifying and characterizing the biological processes involved in aging and longevity.
MeSH term(s)	Animals ; Mice ; Longevity ; Lipid Metabolism ; Aging ; Disease Models, Animal ; Liver ; Fatty Acids
Chemical Substances	Fatty Acids
Language	English
Publishing date	2023-07-22
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-023-05128-y
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Article: Plain Silver Surface Plasmon Resonance for Microarray Application

Cheng, Zhiqiang / Gillespie Doreen E / Lausted Christopher / Wang Zhiyou / Yang Mo / Zheng Zheng / Zhu Jinsong

Analytical chemistry. 2015 Feb. 03, v. 87, no. 3

2015

Abstract: The application scope of surface plasmon resonance (SPR) and SPR imaging (SPRi) is rapidly growing, and tools such as high-performance and low-cost slides could enable more rapid growth of the field. We describe herein a novel silver slide, addressing ... ...

Abstract	The application scope of surface plasmon resonance (SPR) and SPR imaging (SPRi) is rapidly growing, and tools such as high-performance and low-cost slides could enable more rapid growth of the field. We describe herein a novel silver slide, addressing the inherent instability of plain silver structure by improving adhesion between the glass substrate and the silver layer with a thin buffer layer of gold. Covered by a self-assembled monolayer (SAM) only, SPR characteristics of the slide remain steady for more than 3 months under regular storage. In a bioassay, the slide substantiates the predicted nearly 100% sensitivity improvement over gold slides and exhibits exceptional performance stability as determined by sensitivity and resolution measurements during the extended 40â¯000 s multicycle experiment. We demonstrate the suitability of this new slide for large-area SPRi, describing analysis results from a 1â¯296-ligand protein microarray. We predict this slide structure will provide a stable, high-sensitivity solution for high-throughput SPRi applications and other surface analysis platforms.
Keywords	adhesion ; bioassays ; glass ; gold ; image analysis ; microarray technology ; silver ; surface plasmon resonance
Language	English
Dates of publication	2015-0203
Size	p. 1466-1469.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021%2Fac504110t
Database	NAL-Catalogue (AGRICOLA)

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