Publications by authors named "Matthew Vincent"

22 Publications

  • Page 1 of 1

Protocol for Cloning Epithelial Stem Cell Variants from Human Lung.

STAR Protoc 2020 Sep 9;1(2). Epub 2020 Jul 9.

Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

The plurality of clonogenic cells derived from human lung includes a spectrum of diverse p63+ stem cells responsible for the regeneration of normal epithelial tissue and disease-associated metaplastic lesions. Here, we report protocols for the cloning, expansion, and characterization of these stem cell variants, which in general assist in analyses of stem cell heterogeneity, genome editing, drug screening, and regenerative medicine. For complete details on the use and execution of this protocol, please refer to Kumar et al. (2011), Zuo et al. (2015), and Rao et al. (2020).
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http://dx.doi.org/10.1016/j.xpro.2020.100063DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529324PMC
September 2020

Mapping the Effects of Genetic Variation on Chromatin State and Gene Expression Reveals Loci That Control Ground State Pluripotency.

Cell Stem Cell 2020 09 13;27(3):459-469.e8. Epub 2020 Aug 13.

The Jackson Laboratory, Bar Harbor, ME 04609, USA. Electronic address:

Mouse embryonic stem cells (mESCs) cultured in the presence of LIF occupy a ground state with highly active pluripotency-associated transcriptional and epigenetic circuitry. However, ground state pluripotency in some inbred strain backgrounds is unstable in the absence of ERK1/2 and GSK3 inhibition. Using an unbiased genetic approach, we dissect the basis of this divergent response to extracellular cues by profiling gene expression and chromatin accessibility in 170 genetically heterogeneous mESCs. We map thousands of loci affecting chromatin accessibility and/or transcript abundance, including 10 QTL hotspots where genetic variation at a single locus coordinates the regulation of genes throughout the genome. For one hotspot, we identify a single enhancer variant ∼10 kb upstream of Lifr associated with chromatin accessibility and mediating a cascade of molecular events affecting pluripotency. We validate causation through reciprocal allele swaps, demonstrating the functional consequences of noncoding variation in gene regulatory networks that stabilize pluripotent states in vitro.
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http://dx.doi.org/10.1016/j.stem.2020.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7484384PMC
September 2020

Regenerative Metaplastic Clones in COPD Lung Drive Inflammation and Fibrosis.

Cell 2020 05 15;181(4):848-864.e18. Epub 2020 Apr 15.

Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, TX 77003, USA. Electronic address:

Chronic obstructive pulmonary disease (COPD) is a progressive condition of chronic bronchitis, small airway obstruction, and emphysema that represents a leading cause of death worldwide. While inflammation, fibrosis, mucus hypersecretion, and metaplastic epithelial lesions are hallmarks of this disease, their origins and dependent relationships remain unclear. Here we apply single-cell cloning technologies to lung tissue of patients with and without COPD. Unlike control lungs, which were dominated by normal distal airway progenitor cells, COPD lungs were inundated by three variant progenitors epigenetically committed to distinct metaplastic lesions. When transplanted to immunodeficient mice, these variant clones induced pathology akin to the mucous and squamous metaplasia, neutrophilic inflammation, and fibrosis seen in COPD. Remarkably, similar variants pre-exist as minor constituents of control and fetal lung and conceivably act in normal processes of immune surveillance. However, these same variants likely catalyze the pathologic and progressive features of COPD when expanded to high numbers.
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http://dx.doi.org/10.1016/j.cell.2020.03.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7294989PMC
May 2020

Cloning of ground-state intestinal stem cells from endoscopic biopsy samples.

Nat Protoc 2020 05 1;15(5):1612-1627. Epub 2020 Apr 1.

Stem Cell Center, Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.

'Adult' or 'somatic' stem cells harbor an intrinsic ability to regenerate tissues. Heterogeneity of such stem cells along the gastrointestinal tract yields the known segmental specificity of this organ and may contribute to the pathology of certain enteric conditions. Here we detail technology for the generation of 'libraries' of clonogenic cells from 1-mm-diamter endoscopic biopsy samples from the human gastrointestinal tract. Each of the 150-300 independent clones in a typical stem cell library can be clonally expanded to billions of cells in a few weeks while maintaining genomic stability and the ability to undergo multipotent differentiation to the specific epithelia from which the sample originated. The key to this methodology is the intrinsic immortality of normal intestinal stem cells (ISCs) and culture systems that maintain them as highly immature, ground-state ISCs marked by a single-cell clonogenicity of 70% and a corresponding 250-fold proliferative advantage over spheroid technologies. Clonal approaches such as this enhance the resolution of molecular genetics, make genome editing easier, and may be useful in regenerative medicine, unravelling heterogeneity in disease, and facilitating drug discovery.
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http://dx.doi.org/10.1038/s41596-020-0298-4DOI Listing
May 2020

NMDA Receptor in Vasopressin 1b Neurons Is Not Required for Short-Term Social Memory, Object Memory or Aggression.

Front Behav Neurosci 2019 8;13:218. Epub 2019 Nov 8.

Section on Neural Gene Expression, National Institute of Mental Health, National Institutes of Health, Bethesda, MD, United States.

The arginine vasopressin 1b receptor (Avpr1b) plays an important role in social behaviors including aggression, social learning and memory. Genetic removal of Avpr1b from mouse models results in deficits in aggression and short-term social recognition in adults. Avpr1b gene expression is highly enriched in the pyramidal neurons of the hippocampal cornu ammonis 2 (CA2) region. Activity of the hippocampal CA2 has been shown to be required for normal short-term social recognition and aggressive behaviors. Vasopressin acts to enhance synaptic responses of CA2 neurons through a NMDA-receptor dependent mechanism. Genetic removal of the obligatory subunit of the NMDA receptor (Grin1) within distinct hippocampal regions impairs non-social learning and memory. However, the question of a direct role for NMDA receptor activity in Avpr1b neurons to modulate social behavior remains unclear. To answer this question, we first created a novel transgenic mouse line with Cre recombinase knocked into the Avpr1b coding region to genetically target Avpr1b neurons. We confirmed this line has dense Cre expression throughout the dorsal and ventral CA2 regions of the hippocampus, along with scattered expression within the caudate-putamen and olfactory bulb (OB). Conditional removal of the NMDA receptor was achieved by crossing our line to an available floxed Grin1 line. The resulting mice were measured on a battery of social and memory behavioral tests. Surprisingly, we did not observe any differences between Avpr1b-Grin1 knockout mice and their wildtype siblings. We conclude that mice without typical NMDA receptor function in Avpr1b neurons can develop normal aggression as well as short-term social and object memory performance.
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http://dx.doi.org/10.3389/fnbeh.2019.00218DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6856057PMC
November 2019

Unlimited expansion of intestinal stem cells from a wide range of ages.

Integr Mol Med 2019 Aug 15;6(4). Epub 2019 Jul 15.

Institute of Molecular Medicine, McGovern Medical School of The University of Texas, Health Science Center, Houston, Texas 77030, USA.

The recent technical advance in cloning and culturing ground-state intestinal stem cells (ISC) provides us an opportunity of accurate assessment of age-related impact on the function of highly proliferative intestinal stem cells. Our ability of indefinitely and robustly expanding single-stem-cell derived pedigrees allows us to study intestinal stem cells at the clonal level. Interestingly, comparable number of ISC clones was yielded from 1mm endoscopic biopsy of all donors despite the age. They were passaged as pedigrees and expanded to 1 billion cells in approximately sixty days without changes in stemness demonstrated by clonogenicity and multipotency. Therefore, our study shows that ISCs from a wide range of ages can be cloned and expanded to unlimited number with similar efficiency and stability. These patient-derived ISCs harbor intrinsic immortality and are ideal for autologous transplantation, supporting the promise of adult-stem-cell based personalized medicine.
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http://dx.doi.org/10.15761/IMM.1000375DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6713279PMC
August 2019

Exploration of Multiple Signaling Pathways Through Which Sodium Tanshinone IIA Sulfonate Attenuates Pathologic Remodeling Experimental Infarction.

Front Pharmacol 2019 12;10:779. Epub 2019 Jul 12.

Physiology & Experimental Medicine, Hospital for Sick Children, Toronto, ON, Canada.

The level of maladaptive myocardial remodeling consistently contributes to the poor prognosis of patients following a myocardial infarction (MI). In this study, we investigated whether and how sodium tanshinone IIA sulfonate (STS) would attenuate the post-infarct cardiac remodeling in mice model of MI developing after surgical ligation of the left coronary artery. All mice subjected to experimental MI or to the sham procedure were then treated for the following 4 weeks, either with STS or with a vehicle alone. Results of our studies indicated that STS treatment of MI mice prevented the left ventricular dilatation and improved their cardiac function. Results of further tests, aimed at mechanistic explanation of the beneficial effects of STS, indicated that treatment with this compound enhanced the autophagy and, at the same time, inhibited apoptosis of the cardiomyocytes. Meaningfully, we have also established that myocardium of STS-treated mice displayed significantly higher levels of adenosine monophosphate kinase than their untreated counterparts and that this effect additionally associated with the significantly diminished activities of apoptotic promoters: mammalian target of rapamycin and P70S6 kinase. Moreover, we also found that additional administration of the adenosine monophosphate kinase inhibitor (compound C) or autophagy inhibitor (chloroquine) practically eliminated the observed beneficial effects of STS. In conclusion, we suggest that the described multistage mechanism triggered by STS treatment enhanced autophagy, thereby attenuating pathologic remodeling of the post-infarct hearts.
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http://dx.doi.org/10.3389/fphar.2019.00779DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639725PMC
July 2019

Gene loci associated with insulin secretion in islets from non-diabetic mice.

J Clin Invest 2019 07 25;129(10):4419-4432. Epub 2019 Jul 25.

University of Wisconsin-Madison, Biochemistry Department, Madison, Wisconsin, USA.

Genetic susceptibility to type 2 diabetes is primarily due to β-cell dysfunction. However, a genetic study to directly interrogate β-cell function ex vivo has never been previously performed. We isolated 233,447 islets from 483 Diversity Outbred (DO) mice maintained on a Western-style diet, and measured insulin secretion in response to a variety of secretagogues. Insulin secretion from DO islets ranged >1,000-fold even though none of the mice were diabetic. The insulin secretory response to each secretagogue had a unique genetic architecture; some of the loci were specific for one condition, whereas others overlapped. Human loci that are syntenic to many of the insulin secretion QTL from mouse are associated with diabetes-related SNPs in human genome-wide association studies. We report on three genes, Ptpn18, Hunk and Zfp148, where the phenotype predictions from the genetic screen were fulfilled in our studies of transgenic mouse models. These three genes encode a non-receptor type protein tyrosine phosphatase, a serine/threonine protein kinase, and a Krϋppel-type zinc-finger transcription factor, respectively. Our results demonstrate that genetic variation in insulin secretion that can lead to type 2 diabetes is discoverable in non-diabetic individuals.
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http://dx.doi.org/10.1172/JCI129143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6763251PMC
July 2019

Biobanking Organoids or Ground-State Stem Cells?

J Clin Med 2018 Dec 16;7(12). Epub 2018 Dec 16.

Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA.

Autologous transplantation of human epidermal stem cells cultured in Green's method is one of the first examples of utilizing adult stem cells in regenerative medicine. Using the same method, we cloned p63-expressing distal airway stem cells and showed their essential role in lung regeneration in a mouse model of acute respiratory distress syndrome. However, adult stem cells of columnar epithelial tissues had until recently evaded all attempts at cloning. To address this issue, we developed a novel technology that enabled cloning ground-state stem cells of the columnar epithelium. The adaption of this technology to clone stem cells of cancer precursors furthered our understanding of the dynamics of processes such as clonal evolution and dominance in Barrett's esophagus, as well as for testing platforms for chemical screening. Taken together, the properties of these ground-state stem cells, including unlimited propagation, genomic stability, and regio-specificity, make them ideal for regenerative medicine, disease modeling and drug discovery.
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http://dx.doi.org/10.3390/jcm7120555DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6306851PMC
December 2018

An Efficient Method for Cloning Gastrointestinal Stem Cells From Patients via Endoscopic Biopsies.

Gastroenterology 2019 01 6;156(1):20-23. Epub 2018 Oct 6.

Institute of Molecular Medicine, McGovern Medical School of University of Texas Health Science Center, Houston, Texas; Department of Biochemistry and Molecular Biology, McGovern Medical School of University of Texas Health Science Center, Houston, Texas. Electronic address:

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http://dx.doi.org/10.1053/j.gastro.2018.08.062DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309951PMC
January 2019

Genetic Drivers of Pancreatic Islet Function.

Genetics 2018 05 22;209(1):335-356. Epub 2018 Mar 22.

Department of Biochemistry, University of Wisconsin-Madison, Wisconsin 53706-1544

The majority of gene loci that have been associated with type 2 diabetes play a role in pancreatic islet function. To evaluate the role of islet gene expression in the etiology of diabetes, we sensitized a genetically diverse mouse population with a Western diet high in fat (45% kcal) and sucrose (34%) and carried out genome-wide association mapping of diabetes-related phenotypes. We quantified mRNA abundance in the islets and identified 18,820 expression QTL. We applied mediation analysis to identify candidate causal driver genes at loci that affect the abundance of numerous transcripts. These include two genes previously associated with monogenic diabetes ( and ), as well as three genes with nominal association with diabetes-related traits in humans (, , and ). We grouped transcripts into gene modules and mapped regulatory loci for modules enriched with transcripts specific for α-cells, and another specific for δ-cells. However, no single module enriched for β-cell-specific transcripts, suggesting heterogeneity of gene expression patterns within the β-cell population. A module enriched in transcripts associated with branched-chain amino acid metabolism was the most strongly correlated with physiological traits that reflect insulin resistance. Although the mice in this study were not overtly diabetic, the analysis of pancreatic islet gene expression under dietary-induced stress enabled us to identify correlated variation in groups of genes that are functionally linked to diabetes-associated physiological traits. Our analysis suggests an expected degree of concordance between diabetes-associated loci in the mouse and those found in human populations, and demonstrates how the mouse can provide evidence to support nominal associations found in human genome-wide association mapping.
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http://dx.doi.org/10.1534/genetics.118.300864DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5937189PMC
May 2018

Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression.

Bioinformatics 2018 07;34(13):2177-2184

The Jackson Laboratory, Bar Harbor, USA.

Motivation: Allele-specific expression (ASE) refers to the differential abundance of the allelic copies of a transcript. RNA sequencing (RNA-seq) can provide quantitative estimates of ASE for genes with transcribed polymorphisms. When short-read sequences are aligned to a diploid transcriptome, read-mapping ambiguities confound our ability to directly count reads. Multi-mapping reads aligning equally well to multiple genomic locations, isoforms or alleles can comprise the majority (>85%) of reads. Discarding them can result in biases and substantial loss of information. Methods have been developed that use weighted allocation of read counts but these methods treat the different types of multi-reads equivalently. We propose a hierarchical approach to allocation of read counts that first resolves ambiguities among genes, then among isoforms, and lastly between alleles. We have implemented our model in EMASE software (Expectation-Maximization for Allele Specific Expression) to estimate total gene expression, isoform usage and ASE based on this hierarchical allocation.

Results: Methods that align RNA-seq reads to a diploid transcriptome incorporating known genetic variants improve estimates of ASE and total gene expression compared to methods that use reference genome alignments. Weighted allocation methods outperform methods that discard multi-reads. Hierarchical allocation of reads improves estimation of ASE even when data are simulated from a non-hierarchical model. Analysis of RNA-seq data from F1 hybrid mice using EMASE reveals widespread ASE associated with cis-acting polymorphisms and a small number of parent-of-origin effects.

Availability And Implementation: EMASE software is available at https://github.com/churchill-lab/emase.

Supplementary Information: Supplementary data are available at Bioinformatics online.
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http://dx.doi.org/10.1093/bioinformatics/bty078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022640PMC
July 2018

Ground-State Stem Cells: A Novel Approach for Adult Stem Cell Research.

J Pediatr Pediatr Med 2018 31;2(6):7-10. Epub 2018 Dec 31.

Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204, USA.

A robust and reliable culture system of adult stem cells is essential for applying the cutting-edge technologies of drug screening, gene editing, and genomics to stem cell research necessary for breakthroughs in this field. In addition, personalized regenerative medicine based on autologous transplantation requires our ability to clone and expand the numbers of these stem cells . In comparison to the 3D "organoid" culture system that shows limited ability to propagate stem cells as the majority of cells are differentiated or transit amplifying cells, ground-state stem cell culture system is a novel technology that permits long-lived adult stem cells to maintain immaturity, self-renewal capacity, multi-potency and genomic stability despite long-term culturing in a 2D system. The robustness, reliability and easy-to-use features of this new technology bypass the deficiencies of 3D organoid culture systems and provided unlimited stem cell sources for research, therapeutic use, and drug discovery.
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http://dx.doi.org/10.29245/2578-2940/2018/6.1140DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6448798PMC
December 2018

Mutational spectrum of Barrett's stem cells suggests paths to initiation of a precancerous lesion.

Nat Commun 2016 Jan 19;7:10380. Epub 2016 Jan 19.

Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.

The precancerous lesion known as Barrett's oesophagus can evolve to oesophageal adenocarcinoma in decades-long processes of regenerative growth. Here we report the isolation and propagation of distinct, patient-matched stem cells of Barrett's, gastric and oesophageal epithelia that yield divergent tumour types following in vitro transformation and xenografting. Genomic analyses reveal a broad mutational spectrum unique to Barrett's stem cells that likely reflects their risk for oncogenesis. Remarkably, 25% of cases show no cancer-related genomic changes, suggesting that Barrett's initiates without driver mutations. Most cases, however, sustain patterns of deletions almost identical to adenocarcinoma though tumour-associated gene amplifications were absent. Notably, those suspected of low-grade dysplasia have p53 mutations or undergo amplifications of proto-oncogenes and receptor tyrosine kinases, implicating these events in lethal transitions. Our findings suggest paths for the initiation and progression of Barrett's and define a discrete stem cell underlying its regenerative growth whose eradication could prevent oesophageal adenocarcinoma.
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http://dx.doi.org/10.1038/ncomms10380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4735693PMC
January 2016

Synthetic ligands of the elastin receptor induce elastogenesis in human dermal fibroblasts via activation of their IGF-1 receptors.

J Dermatol Sci 2015 Dec 9;80(3):175-85. Epub 2015 Oct 9.

Physiology & Experimental Medicine Program, Hospital for Sick Children, ON, Canada; Institute of Medical Science, University of Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, ON, Canada. Electronic address:

Background: We have previously reported that a mixture of peptides obtained after chemical or enzymatic degradation of bovine elastin, induced new elastogenesis in human skin.

Objective: Now, we investigated the elastogenic potential of synthetic peptides mimicking the elastin-derived, VGVAPG sequence, IGVAPG sequence that we found in the rice bran, and a similar peptide, VGVTAG that we identified in the IGF-1-binding protein-1 (IGFBP-1).

Results: We now demonstrate that treatment with each of these xGVxxG peptides (recognizable by the anti-elastin antibody), up-regulated the levels of elastin-encoding mRNA, tropoelastin protein, and the deposition of new elastic fibers in cultures of human dermal fibroblasts and in cultured explants of human skin. Importantly, we found that such induction of new elastogenesis may involve two parallel signaling pathways triggered after activation of IGF-1 receptor. In the first one, the xGVxxG peptides interact with the cell surface elastin receptor, thereby causing the downstream activation of the c-Src kinase and a consequent cross-activation of the adjacent IGF-1R, even in the absence of its principal ligand. In the second pathway their hydrophobic association with the N-terminal domain (VGVTAG) of the serum-derived IGFBP-1 induces conformational changes of this IGF-1 chaperone allowing for the release of its cargo and a consequent ligand-specific phosphorylation of IGF-1R.

Conclusion: We present a novel, clinically relevant mechanism in which products of partial degradation of dermal elastin may stimulate production of new elastic fibers by dermal fibroblasts. Our findings particularly encourage the use of biologically safe synthetic xGVxxG peptides for regeneration of the injured or aged human skin.
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http://dx.doi.org/10.1016/j.jdermsci.2015.10.001DOI Listing
December 2015

Human embryonic stem cell-derived retinal pigment epithelium in patients with age-related macular degeneration and Stargardt's macular dystrophy: follow-up of two open-label phase 1/2 studies.

Lancet 2015 Feb 15;385(9967):509-16. Epub 2014 Oct 15.

Advanced Cell Technology, Marlborough, MA, USA. Electronic address:

Background: Since they were first derived more than three decades ago, embryonic stem cells have been proposed as a source of replacement cells in regenerative medicine, but their plasticity and unlimited capacity for self-renewal raises concerns about their safety, including tumour formation ability, potential immune rejection, and the risk of differentiating into unwanted cell types. We report the medium-term to long-term safety of cells derived from human embryonic stem cells (hESC) transplanted into patients.

Methods: In the USA, two prospective phase 1/2 studies were done to assess the primary endpoints safety and tolerability of subretinal transplantation of hESC-derived retinal pigment epithelium in nine patients with Stargardt's macular dystrophy (age >18 years) and nine with atrophic age-related macular degeneration (age >55 years). Three dose cohorts (50,000, 100,000, and 150,000 cells) were treated for each eye disorder. Transplanted patients were followed up for a median of 22 months by use of serial systemic, ophthalmic, and imaging examinations. The studies are registered with ClinicalTrials.gov, numbers NCT01345006 (Stargardt's macular dystrophy) and NCT01344993 (age-related macular degeneration).

Findings: There was no evidence of adverse proliferation, rejection, or serious ocular or systemic safety issues related to the transplanted tissue. Adverse events were associated with vitreoretinal surgery and immunosuppression. 13 (72%) of 18 patients had patches of increasing subretinal pigmentation consistent with transplanted retinal pigment epithelium. Best-corrected visual acuity, monitored as part of the safety protocol, improved in ten eyes, improved or remained the same in seven eyes, and decreased by more than ten letters in one eye, whereas the untreated fellow eyes did not show similar improvements in visual acuity. Vision-related quality-of-life measures increased for general and peripheral vision, and near and distance activities, improving by 16-25 points 3-12 months after transplantation in patients with atrophic age-related macular degeneration and 8-20 points in patients with Stargardt's macular dystrophy.

Interpretation: The results of this study provide the first evidence of the medium-term to long-term safety, graft survival, and possible biological activity of pluripotent stem cell progeny in individuals with any disease. Our results suggest that hESC-derived cells could provide a potentially safe new source of cells for the treatment of various unmet medical disorders requiring tissue repair or replacement.

Funding: Advanced Cell Technology.
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http://dx.doi.org/10.1016/S0140-6736(14)61376-3DOI Listing
February 2015

p63(+)Krt5(+) distal airway stem cells are essential for lung regeneration.

Nature 2015 Jan 12;517(7536):616-20. Epub 2014 Nov 12.

1] Genome Institute of Singapore, A-STAR, 138672 Singapore [2] The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut 06032, USA [3] Department of Medicine, National University Health System, 119228 Singapore.

Lung diseases such as chronic obstructive pulmonary disease and pulmonary fibrosis involve the progressive and inexorable destruction of oxygen exchange surfaces and airways, and have emerged as a leading cause of death worldwide. Mitigating therapies, aside from impractical organ transplantation, remain limited and the possibility of regenerative medicine has lacked empirical support. However, it is clinically known that patients who survive sudden, massive loss of lung tissue from necrotizing pneumonia or acute respiratory distress syndrome often recover full pulmonary function within six months. Correspondingly, we recently demonstrated lung regeneration in mice following H1N1 influenza virus infection, and linked distal airway stem cells expressing Trp63 (p63) and keratin 5, called DASC(p63/Krt5), to this process. Here we show that pre-existing, intrinsically committed DASC(p63/Krt5) undergo a proliferative expansion in response to influenza-induced lung damage, and assemble into nascent alveoli at sites of interstitial lung inflammation. We also show that the selective ablation of DASC(p63/Krt5) in vivo prevents this regeneration, leading to pre-fibrotic lesions and deficient oxygen exchange. Finally, we demonstrate that single DASC(p63/Krt5)-derived pedigrees differentiate to type I and type II pneumocytes as well as bronchiolar secretory cells following transplantation to infected lung and also minimize the structural consequences of endogenous stem cell loss on this process. The ability to propagate these cells in culture while maintaining their intrinsic lineage commitment suggests their potential in stem cell-based therapies for acute and chronic lung diseases.
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http://dx.doi.org/10.1038/nature13903DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7095488PMC
January 2015

The antidiabetic hormone glucagon-like peptide-1 induces formation of new elastic fibers in human cardiac fibroblasts after cross-activation of IGF-IR.

Endocrinology 2015 Jan;156(1):90-102

Physiology and Experimental Medicine Program (N.Q., Y.W., A.W., S.M., M.V., A.H.), Heart Center, The Hospital for Sick Children, Ontario, Canada M5G 0A4; Institute of Medical Science (N.Q., A.H.), University of Toronto, Ontario, Canada M5S 1A8; Department of Laboratory Medicine and Pathobiology (M.V., M.H., A.H.), University of Toronto, Ontario, Canada M5S 1A8; Heart and Stroke Richard Lewar Center of Excellence in Cardiovascular Research (M.H., A.H.), University of Toronto, Ontario, Canada M5S 1A8; and Toronto General Research Institute (M.H.), Toronto, Ontario, Canada M5G 2M9.

Glucagon-like peptide 1 (GLP-1) is a metabolic hormone involved in the stimulation of insulin biosynthesis and secretion. It has been recently reported that GLP-1 also exerts cardioprotective effects and facilitates functional recovery after myocardial infarction through GLP-1 receptor-mediated signaling in cardiomyocytes. GLP-1 treatment has been also demonstrated to produce sustained improvement in cardiac function in long-term studies, suggesting the involvement of mechanisms beyond the acute metabolic and cytoprotective effects. For example, the possible interaction of GLP-1 with the cardiac fibroblasts, which are responsible for the postinfarct remodeling and extracellular matrix production, has not been previously explored. Here, we report that cultures of human cardiac fibroblasts treated with GLP-1 peptides display a selective up-regulation in elastin gene expression and a consequent increase in elastic fibers production, in the absence of the classic GLP-1 receptor. Importantly, we provide experimental evidence that this GLP-1-induced elastogenesis is triggered through the cross-activation of the IGF-I receptor. Because GLP-1 does not stimulate deposition of collagen I, nor promote the proliferation or apoptosis of cultured cardiac fibroblasts, we speculate that its elastogenic effect may also contribute to the beneficial remodeling of the human heart after myocardial infarction.
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http://dx.doi.org/10.1210/en.2014-1519DOI Listing
January 2015

Residual embryonic cells as precursors of a Barrett's-like metaplasia.

Cell 2011 Jun;145(7):1023-35

Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.

Barrett's esophagus is an intestine-like metaplasia and precursor of esophageal adenocarcinoma. Triggered by gastroesophageal reflux disease, the origin of this metaplasia remains unknown. p63-deficient mice, which lack squamous epithelia, may model acid-reflux damage. We show here that p63 null embryos rapidly develop intestine-like metaplasia with gene expression profiles similar to Barrett's metaplasia. We track its source to a unique embryonic epithelium that is normally undermined and replaced by p63-expressing cells. Significantly, we show that a discrete population of these embryonic cells persists in adult mice and humans at the squamocolumnar junction, the source of Barrett's metaplasia. We show that upon programmed damage to the squamous epithelium, these embryonic cells migrate toward adjacent, specialized squamous cells in a process that may recapitulate early Barrett's. Our findings suggest that certain precancerous lesions, such as Barrett's, initiate not from genetic alterations but from competitive interactions between cell lineages driven by opportunity.
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http://dx.doi.org/10.1016/j.cell.2011.05.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125107PMC
June 2011

Mouse Tumor Biology Database (MTB): status update and future directions.

Nucleic Acids Res 2007 Jan 29;35(Database issue):D638-42. Epub 2006 Nov 29.

The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, USA.

The Mouse Tumor Biology (MTB) database provides access to data about endogenously arising tumors (both spontaneous and induced) in genetically defined mice (inbred, hybrid, mutant and genetically engineered mice). Data include information on the frequency and latency of mouse tumors, pathology reports and images, genomic changes occurring in the tumors, genetic (strain) background and literature or contributor citations. Data are curated from the primary literature or submitted directly from researchers. MTB is accessed via the Mouse Genome Informatics web site (http://www.informatics.jax.org). Integrated searches of MTB are enabled through use of multiple controlled vocabularies and by adherence to standardized nomenclature, when available. Recently MTB has been redesigned and its database infrastructure replaced with a robust relational database management system (RDMS). Web interface improvements include a new advanced query form and enhancements to already existing search capabilities. The Tumor Frequency Grid has been revised to enhance interactivity, providing an overview of reported tumor incidence across mouse strains and an entrée into the database. A new pathology data submission tool allows users to submit, edit and release data to the MTB system.
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http://dx.doi.org/10.1093/nar/gkl983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1751545PMC
January 2007

The Mouse Tumor Biology Database: integrated access to mouse cancer biology data.

Exp Lung Res 2005 Mar;31(2):259-70

The Jackson Laboratory, Bar Harbor, Maine, USA.

Mice have long been used as models for the study of human cancer. The National Cancer Institute has included among its research areas of extraordinary opportunity the development of new mouse genetic models of human cancer and the exploration of cancer imaging as a research tool. Because of the volume and interconnectedness of relevant data, the creation and maintenance of bioinformatics resources of mouse tumor biology is necessary to facilitate current and future cancer research. The Mouse Tumor Biology (MTB) Database provides electronic access to data generated through the study of spontaneous and induced tumors in genetically defined mice (inbred, hybrid, spontaneous and induced mutant, and genetically engineered strains of mice).
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http://dx.doi.org/10.1080/01902140490495633DOI Listing
March 2005

Tautomerism, acid-base equilibria, and H-bonding of the six histidines in subtilisin BPN' by NMR.

Protein Sci 2003 Apr;12(4):794-810

Pulmonary and Critical Care Division, Department of Medicine, New England Medical Center/Tupper Research Institute, Boston, Massachusetts 02111, USA.

We have determined by (15)N, (1)H, and (13)C NMR, the chemical behavior of the six histidines in subtilisin BPN' and their PMSF and peptide boronic acid complexes in aqueous solution as a function of pH in the range of from 5 to 11, and have assigned every (15)N, (1)H, C(epsilon 1), and C(delta2) resonance of all His side chains in resting enzyme. Four of the six histidine residues (17, 39, 67, and 226) are neutrally charged and do not titrate. One histidine (238), located on the protein surface, titrates with pK(a) = 7.30 +/- 0.03 at 25 degrees C, having rapid proton exchange, but restricted mobility. The active site histidine (64) in mutant N155A titrates with a pK(a) value of 7.9 +/- 0.3 and sluggish proton exchange behavior, as shown by two-site exchange computer lineshape simulation. His 64 in resting enzyme contains an extremely high C(epsilon 1)-H proton chemical shift of 9.30 parts per million (ppm) owing to a conserved C(epsilon 1)-H(.)O=C H-bond from the active site imidazole to a backbone carbonyl group, which is found in all known serine proteases representing all four superfamilies. Only His 226, and His 64 at high pH, exist as the rare N(delta1)-H tautomer, exhibiting (13)C(delta1) chemical shifts approximately 9 ppm higher than those for N(epsilon 2)-H tautomers. His 64 in the PMSF complex, unlike that in the resting enzyme, is highly mobile in its low pH form, as shown by (15)N-(1)H NOE effects, and titrates with rapid proton exchange kinetics linked to a pK(a) value of 7.47 +/- 0.02.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323859PMC
http://dx.doi.org/10.1110/ps.0235203DOI Listing
April 2003