Search

Your search keyword '"Pera, MF"' showing total 174 results
Start Over Author "Pera, MF"
174 results on '"Pera, MF"'

1. Selective elimination of pluripotent stem cells by PIKfyve specific inhibitors.

Author

Chakraborty, AR, Vassilev, A, Jaiswal, SK, O'Connell, CE, Ahrens, JF, Mallon, BS, Pera, MF, DePamphilis, ML, Chakraborty, AR, Vassilev, A, Jaiswal, SK, O'Connell, CE, Ahrens, JF, Mallon, BS, Pera, MF, and DePamphilis, ML

Abstract

Inhibition of PIKfyve phosphoinositide kinase selectively kills autophagy-dependent cancer cells by disrupting lysosome homeostasis. Here, we show that PIKfyve inhibitors can also selectively eliminate pluripotent embryonal carcinoma cells (ECCs), embryonic stem cells, and induced pluripotent stem cells under conditions where differentiated cells remain viable. PIKfyve inhibitors prevented lysosome fission, induced autophagosome accumulation, and reduced cell proliferation in both pluripotent and differentiated cells, but they induced death only in pluripotent cells. The ability of PIKfyve inhibitors to distinguish between pluripotent and differentiated cells was confirmed with xenografts derived from ECCs. Pretreatment of ECCs with the PIKfyve specific inhibitor WX8 suppressed their ability to form teratocarcinomas in mice, and intraperitoneal injections of WX8 into mice harboring teratocarcinoma xenografts selectively eliminated pluripotent cells. Differentiated cells continued to proliferate, but at a reduced rate. These results provide a proof of principle that PIKfyve specific inhibitors can selectively eliminate pluripotent stem cells in vivo as well as in vitro.

Published
2022

2. A Splicing Mutation in Slc4a5 Results in Retinal Detachment and Retinal Pigment Epithelium Dysfunction.

Author

Collin, GB, Shi, L, Yu, M, Akturk, N, Charette, JR, Hyde, LF, Weatherly, SM, Pera, MF, Naggert, JK, Peachey, NS, Nishina, PM, Krebs, MP, Collin, GB, Shi, L, Yu, M, Akturk, N, Charette, JR, Hyde, LF, Weatherly, SM, Pera, MF, Naggert, JK, Peachey, NS, Nishina, PM, and Krebs, MP

Abstract

Fluid and solute transporters of the retinal pigment epithelium (RPE) are core components of the outer blood-retinal barrier. Characterizing these transporters and their role in retinal homeostasis may provide insights into ocular function and disease. Here, we describe RPE defects in tvrm77 mice, which exhibit hypopigmented patches in the central retina. Mapping and nucleotide sequencing of tvrm77 mice revealed a disrupted 5' splice donor sequence in Slc4a5, a sodium bicarbonate cotransporter gene. Slc4a5 expression was reduced 19.7-fold in tvrm77 RPE relative to controls, and alternative splice variants were detected. SLC4A5 was localized to the Golgi apparatus of cultured human RPE cells and in apical and basal membranes. Fundus imaging, optical coherence tomography, microscopy, and electroretinography (ERG) of tvrm77 mice revealed retinal detachment, hypopigmented patches corresponding to neovascular lesions, and retinal folds. Detachment worsened and outer nuclear layer thickness decreased with age. ERG a- and b-wave response amplitudes were initially normal but declined in older mice. The direct current ERG fast oscillation and light peak were reduced in amplitude at all ages, whereas other RPE-associated responses were unaffected. These results link a new Slc4a5 mutation to subretinal fluid accumulation and altered light-evoked RPE electrophysiological responses, suggesting that SLC4A5 functions at the outer blood-retinal barrier.

Published
2022

3. Pluripotent cell states and unexpected fates.

Author

Pera, MF and Pera, MF

Abstract

Pluripotent stem cells provide a powerful model for the study of human development and its disorders. Recent studies, including two in this issue of Stem Cell Reports, raise important questions concerning the developmental potential of human pluripotent stem cells, and how the behavior of these cells in vitro mirrors normal embryogenesis.

Published
2022

4. The genetic basis of inter-individual variation in recovery from traumatic brain injury

Author

Cortes, D, Pera, MF, Cortes, D, and Pera, MF

Abstract

Traumatic brain injury (TBI) is one of the leading causes of death among young people, and is increasingly prevalent in the aging population. Survivors of TBI face a spectrum of outcomes from short-term non-incapacitating injuries to long-lasting serious and deteriorating sequelae. TBI is a highly complex condition to treat; many variables can account for the observed heterogeneity in patient outcome. The limited success of neuroprotection strategies in the clinic has led to a new emphasis on neurorestorative approaches. In TBI, it is well recognized clinically that patients with similar lesions, age, and health status often display differences in recovery of function after injury. Despite this heterogeneity of outcomes in TBI, restorative treatment has remained generic. There is now a new emphasis on developing a personalized medicine approach in TBI, and this will require an improved understanding of how genetics impacts on long-term outcomes. Studies in animal model systems indicate clearly that the genetic background plays a role in determining the extent of recovery following an insult. A candidate gene approach in human studies has led to the identification of factors that can influence recovery. Here we review studies of the genetic basis for individual differences in functional recovery in the CNS in animals and man. The application of in vitro modeling with human cells and organoid cultures, along with whole-organism studies, will help to identify genes and networks that account for individual variation in recovery from brain injury, and will point the way towards the development of new therapeutic approaches.

Published
2021

5. Toward Guidelines for Research on Human Embryo Models Formed from Stem Cells

Author

Hyun, I, Munsie, M, Pera, MF, Rivron, NC, Rossant, J, Hyun, I, Munsie, M, Pera, MF, Rivron, NC, and Rossant, J

Abstract

Over the past few years, a number of research groups have reported striking progress on the generation of in vitro models from mouse and human stem cells that replicate aspects of early embryonic development. Not only do these models reproduce some key cell fate decisions but, especially in the mouse system, they also mimic the spatiotemporal arrangements of embryonic and extraembryonic tissues that are required for developmental patterning and implantation in the uterus. If such models could be developed for the early human embryo, they would have great potential benefits for understanding early human development, for biomedical science, and for reducing the use of animals and human embryos in research. However, guidelines for the ethical conduct of this line of work are at present not well defined. In this Forum article, we discuss some key aspects of this emerging area of research and provide some recommendations for its ethical oversight.

Published
2020

6. Unique properties of a subset of human pluripotent stem cells with high capacity for self-renewal

Author

Lau, KX, Mason, EA, Kie, J, De Souza, DP, Kloehn, J, Tull, D, McConville, MJ, Keniry, A, Beck, T, Blewitt, ME, Ritchie, ME, Naik, SH, Zalcenstein, D, Korn, O, Su, S, Romero, IG, Spruce, C, Baker, CL, McGarr, TC, Wells, CA, Pera, MF, Lau, KX, Mason, EA, Kie, J, De Souza, DP, Kloehn, J, Tull, D, McConville, MJ, Keniry, A, Beck, T, Blewitt, ME, Ritchie, ME, Naik, SH, Zalcenstein, D, Korn, O, Su, S, Romero, IG, Spruce, C, Baker, CL, McGarr, TC, Wells, CA, and Pera, MF

Abstract

Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in developmental status to mouse epiblast stem cells, which correspond to pluripotent cells at a late post-implantation stage of embryogenesis. Heterogeneity within hPSC cultures complicates this interspecies comparison. Here we show that a subpopulation of archetypal hPSC enriched for high self-renewal capacity (ESR) has distinct properties relative to the bulk of the population, including a cell cycle with a very low G1 fraction and a metabolomic profile that reflects a combination of oxidative phosphorylation and glycolysis. ESR cells are pluripotent and capable of differentiation into primordial germ cell-like cells. Global DNA methylation levels in the ESR subpopulation are lower than those in mouse epiblast stem cells. Chromatin accessibility analysis revealed a unique set of open chromatin sites in ESR cells. RNA-seq at the subpopulation and single cell levels shows that, unlike mouse epiblast stem cells, the ESR subset of hPSC displays no lineage priming, and that it can be clearly distinguished from gastrulating and extraembryonic cell populations in the primate embryo. ESR hPSC correspond to an earlier stage of post-implantation development than mouse epiblast stem cells.

Published
2020

7. Cancer Stem Cells: Notes for Authors.

Author

Eaves, CJ, Pera, MF, Eaves, CJ, and Pera, MF

Abstract

Stem Cell Reports frequently receives manuscripts dealing with the topic of cancer stem cells. Many of the submissions on this topic have major shortcomings in their content or limits to the conclusions that can be drawn from the results presented. The purpose of this Commentary is to highlight some of the underlying issues so that authors can enhance the strength of their research contributions.

Published
2020

8. Antibodies to a CA 19-9 Related Antigen Complex Identify SOX9 Expressing Progenitor Cells In Human Foetal Pancreas and Pancreatic Adenocarcinoma

Author

Farley, AM, Braxton, DR, Li, J, Trounson, K, Sakar-Dey, S, Nayer, B, Ikeda, T, Lau, KX, Hardikar, W, Hasegawa, K, Pera, MF, Farley, AM, Braxton, DR, Li, J, Trounson, K, Sakar-Dey, S, Nayer, B, Ikeda, T, Lau, KX, Hardikar, W, Hasegawa, K, and Pera, MF

Abstract

The Sialyl Lewis A antigen, or CA 19-9, is the prototype serum biomarker for adenocarcinoma of the pancreas. Despite extensive clinical study of CA 19-9 in gastrointestinal malignancies, surprisingly little is known concerning the specific cell types that express this marker during development, tissue regeneration and neoplasia. SOX9 is a transcription factor that plays a key role in these processes in foregut tissues. We report the biochemistry and tissue expression of the GCTM-5 antigen, a pancreatic cancer marker related to, but distinct from, CA19-9. This antigen, defined by two monoclonal antibodies recognising separate epitopes on a large glycoconjugate protein complex, is co-expressed with SOX9 by foregut ductal progenitors in the developing human liver and pancreas, and in pancreatic adenocarcinoma. These progenitors are distinct from cell populations identified by DCLK1, LGR5, or canonical markers of liver and pancreatic progenitor cells. Co-expression of this antigen complex and SOX9 also characterises the ductal metaplasia of submucosal glands that occurs during the development of Barrett's oesophagus. The GCTM-5 antigen complex can be detected in the sera of patients with pancreatic adenocarcinoma. The GCTM-5 epitope shows a much more restricted pattern of expression in the normal adult pancreas relative to CA19-9. Our findings will aid in the identification, characterisation, and monitoring of ductal progenitor cells during development and progression of pancreatic adenocarcinoma in man.

Published
2019

9. Assessment of established techniques to determine developmental and malignant potential of human pluripotent stem cells

Author

Allison, TF, Andrews, PW, Avior, Y, Barbaric, I, Benvenisty, N, Bock, C, Brehm, J, Bruestle, O, Damjanov, I, Elefanty, A, Felkner, D, Gokhale, PJ, Halbritter, F, Healy, LE, Hu, TX, Knowles, BB, Loring, JF, Ludwig, TE, Mayberry, R, Micallef, S, Mohamed, JS, Mueller, F-J, Mummery, CL, Nakatsuji, N, Ng, ES, Oh, SKW, O'Shea, O, Pera, MF, Reubinoff, B, Robson, P, Rossant, J, Schuldt, BM, Solter, D, Sourris, K, Stacey, G, Stanley, EG, Suemori, H, Takahashi, K, Yamanaka, S, Allison, TF, Andrews, PW, Avior, Y, Barbaric, I, Benvenisty, N, Bock, C, Brehm, J, Bruestle, O, Damjanov, I, Elefanty, A, Felkner, D, Gokhale, PJ, Halbritter, F, Healy, LE, Hu, TX, Knowles, BB, Loring, JF, Ludwig, TE, Mayberry, R, Micallef, S, Mohamed, JS, Mueller, F-J, Mummery, CL, Nakatsuji, N, Ng, ES, Oh, SKW, O'Shea, O, Pera, MF, Reubinoff, B, Robson, P, Rossant, J, Schuldt, BM, Solter, D, Sourris, K, Stacey, G, Stanley, EG, Suemori, H, Takahashi, K, and Yamanaka, S

Abstract

The International Stem Cell Initiative compared several commonly used approaches to assess human pluripotent stem cells (PSC). PluriTest predicts pluripotency through bioinformatic analysis of the transcriptomes of undifferentiated cells, whereas, embryoid body (EB) formation in vitro and teratoma formation in vivo provide direct tests of differentiation. Here we report that EB assays, analyzed after differentiation under neutral conditions and under conditions promoting differentiation to ectoderm, mesoderm, or endoderm lineages, are sufficient to assess the differentiation potential of PSCs. However, teratoma analysis by histologic examination and by TeratoScore, which estimates differential gene expression in each tumor, not only measures differentiation but also allows insight into a PSC's malignant potential. Each of the assays can be used to predict pluripotent differentiation potential but, at this stage of assay development, only the teratoma assay provides an assessment of pluripotency and malignant potential, which are both relevant to the pre-clinical safety assessment of PSCs.

Published
2018

10. Friedreich's ataxia induced pluripotent stem cell-derived cardiomyocytes display electrophysiological abnormalities and calcium handling deficiency

Author

Crombie, DE, Curl, CL, Raaijmakers, AJA, Sivakumaran, P, Kulkarni, T, Wong, RCB, Minami, I, Evans-Galea, MV, Lim, SY, Delbridge, L, Corben, LA, Dottori, M, Nakatsuji, N, Trounce, IA, Hewitt, AW, Delatycki, MB, Pera, MF, Pebay, A, Crombie, DE, Curl, CL, Raaijmakers, AJA, Sivakumaran, P, Kulkarni, T, Wong, RCB, Minami, I, Evans-Galea, MV, Lim, SY, Delbridge, L, Corben, LA, Dottori, M, Nakatsuji, N, Trounce, IA, Hewitt, AW, Delatycki, MB, Pera, MF, and Pebay, A

Abstract

We sought to identify the impacts of Friedreich's ataxia (FRDA) on cardiomyocytes. FRDA is an autosomal recessive degenerative condition with neuronal and non-neuronal manifestations, the latter including progressive cardiomyopathy of the left ventricle, the leading cause of death in FRDA. Little is known about the cellular pathogenesis of FRDA in cardiomyocytes. Induced pluripotent stem cells (iPSCs) were derived from three FRDA individuals with characterized GAA repeats. The cells were differentiated into cardiomyocytes to assess phenotypes. FRDA iPSC- cardiomyocytes retained low levels of FRATAXIN (FXN) mRNA and protein. Electrophysiology revealed an increased variation of FRDA- cardiomyocyte beating rates which was prevented by addition of nifedipine, suggestive of a calcium handling deficiency. Finally, calcium imaging was performed and we identified small amplitude, diastolic and systolic calcium transients confirming a deficiency in calcium handling. We defined a robust FRDA cardiac-specific electrophysiological profile in patient-derived iPSCs which could be used for high throughput compound screening. This cell-specific signature will contribute to the identification and screening of novel treatments for this life-threatening disease.

Published
2017

11. Using human pluripotent stem cells to study Friedreich ataxia cardiomyopathy

Author

Crombie, DE, Pera, MF, Delatycki, MB, Pebay, A, Crombie, DE, Pera, MF, Delatycki, MB, and Pebay, A

Abstract

Friedreich ataxia (FRDA) is the most common of the inherited ataxias. It is an autosomal recessive disease characterised by degeneration of peripheral sensory neurons, regions of the central nervous system and cardiomyopathy. FRDA is usually due to homozygosity for trinucleotide GAA repeat expansions found within first intron of the FRATAXIN (FXN) gene, which results in reduced levels of the mitochondrial protein FXN. Reduced FXN protein results in mitochondrial dysfunction and iron accumulation leading to increased oxidative stress and cell death in the nervous system and heart. Yet the precise functions of FXN and the underlying mechanisms leading to disease pathology remain elusive. This is particularly true of the cardiac aspect of FRDA, which remains largely uncharacterized at the cellular level. Here, we summarise current knowledge on experimental models in which to study FRDA cardiomyopathy, with a particular focus on the use of human pluripotent stem cells as a disease model.

Published
2016

12. Characterization of the retinal pigment epithelium in Friedreich ataxia.

Author

Crombie, DE, Van Bergen, N, Davidson, KC, Anjomani Virmouni, S, Mckelvie, PA, Chrysostomou, V, Conquest, A, Corben, LA, Pook, MA, Kulkarni, T, Trounce, IA, Pera, MF, Delatycki, MB, Pébay, A, Crombie, DE, Van Bergen, N, Davidson, KC, Anjomani Virmouni, S, Mckelvie, PA, Chrysostomou, V, Conquest, A, Corben, LA, Pook, MA, Kulkarni, T, Trounce, IA, Pera, MF, Delatycki, MB, and Pébay, A

Abstract

We assessed structural elements of the retina in individuals with Friedreich ataxia (FRDA) and in mouse models of FRDA, as well as functions of the retinal pigment epithelium (RPE) in FRDA using induced pluripotent stem cells (iPSCs). We analyzed the retina of the FRDA mouse models YG22R and YG8R containing a human FRATAXIN (FXN) transgene by histology. We complemented this work with post-mortem evaluation of eyes from FRDA patients. Finally, we derived RPE cells from patient FRDA-iPSCs to assess oxidative phosphorylation (OXPHOS) and phagocytosis. We showed that whilst the YG22R and YG8R mouse models display elements of retinal degeneration, they do not recapitulate the loss of retinal ganglion cells (RGCs) found in the human disease. Further, RPE cells differentiated from human FRDA-iPSCs showed normal OXPHOS and we did not observe functional impairment of the RPE in Humans.

Published
2015

13. Gene Expression Variability as a Unifying Element of the Pluripotency Network

Author

Mason, EA, Mar, JC, Laslett, AL, Pera, MF, Quackenbush, J, Wolvetang, E, Wells, CA, Mason, EA, Mar, JC, Laslett, AL, Pera, MF, Quackenbush, J, Wolvetang, E, and Wells, CA

Abstract

Heterogeneity is a hallmark of stem cell populations, in part due to the molecular differences between cells undergoing self-renewal and those poised to differentiate. We examined phenotypic and molecular heterogeneity in pluripotent stem cell populations, using public gene expression data sets. A high degree of concordance was observed between global gene expression variability and the reported heterogeneity of different human pluripotent lines. Network analysis demonstrated that low-variability genes were the most highly connected, suggesting that these are the most stable elements of the gene regulatory network and are under the highest regulatory constraints. Known drivers of pluripotency were among these, with lowest expression variability of POU5F1 in cells with the highest capacity for self-renewal. Variability of gene expression provides a reliable measure of phenotypic and molecular heterogeneity and predicts those genes with the highest degree of regulatory constraint within the pluripotency network.

Published
2014

14. Single-Cell Gene Expression Profiles Define Self-Renewing, Pluripotent, and Lineage Primed States of Human Pluripotent Stem Cells

Author

Hough, SR, Thornton, M, Mason, E, Mar, JC, Wells, CA, Pera, MF, Hough, SR, Thornton, M, Mason, E, Mar, JC, Wells, CA, and Pera, MF

Abstract

Pluripotent stem cells display significant heterogeneity in gene expression, but whether this diversity is an inherent feature of the pluripotent state remains unknown. Single-cell gene expression analysis in cell subsets defined by surface antigen expression revealed that human embryonic stem cell cultures exist as a continuum of cell states, even under defined conditions that drive self-renewal. The majority of the population expressed canonical pluripotency transcription factors and could differentiate into derivatives of all three germ layers. A minority subpopulation of cells displayed high self-renewal capacity, consistently high transcripts for all pluripotency-related genes studied, and no lineage priming. This subpopulation was characterized by its expression of a particular set of intercellular signaling molecules whose genes shared common regulatory features. Our data support a model of an inherently metastable self-renewing population that gives rise to a continuum of intermediate pluripotent states, which ultimately become primed for lineage specification.

Published
2014

15. BCL-XL Mediates the Strong Selective Advantage of a 20q11.21 Amplification Commonly Found in Human Embryonic Stem Cell Cultures

Author

Avery, S, Hirst, AJ, Baker, D, Lim, CY, Alagaratnam, S, Skotheim, RI, Lothe, RA, Pera, MF, Colman, A, Robson, P, Andrews, PW, Knowles, BB, Avery, S, Hirst, AJ, Baker, D, Lim, CY, Alagaratnam, S, Skotheim, RI, Lothe, RA, Pera, MF, Colman, A, Robson, P, Andrews, PW, and Knowles, BB

Abstract

Human embryonic stem cells (hESCs) regularly acquire nonrandom genomic aberrations during culture, raising concerns about their safe therapeutic application. The International Stem Cell Initiative identified a copy number variant (CNV) amplification of chromosome 20q11.21 in 25% of hESC lines displaying a normal karyotype. By comparing four cell lines paired for the presence or absence of this CNV, we show that those containing this amplicon have higher population doubling rates, attributable to enhanced cell survival through resistance to apoptosis. Of the three genes encoded within the minimal amplicon and expressed in hESCs, only overexpression of BCL2L1 (BCL-XL isoform) provides control cells with growth characteristics similar to those of CNV-containing cells, whereas inhibition of BCL-XL suppresses the growth advantage of CNV cells, establishing BCL2L1 as a driver mutation. Amplification of the 20q11.21 region is also detectable in human embryonal carcinoma cell lines and some teratocarcinomas, linking this mutation with malignant transformation.

Published
2013

17. Comparison of defined culture systems for feeder cell free propagation of human embryonic stem cells

Author

Akopian, V, Andrews, PW, Beil, S, Benvenisty, N, Brehm, J, Christie, M, Ford, A, Fox, V, Gokhale, PJ, Healy, L, Holm, F, Hovatta, O, Knowles, BB, Ludwig, TE, McKay, RDG, Miyazaki, T, Nakatsuji, N, Oh, SKW, Pera, MF, Rossant, J, Stacey, GN, Suemori, H, Akopian, V, Andrews, PW, Beil, S, Benvenisty, N, Brehm, J, Christie, M, Ford, A, Fox, V, Gokhale, PJ, Healy, L, Holm, F, Hovatta, O, Knowles, BB, Ludwig, TE, McKay, RDG, Miyazaki, T, Nakatsuji, N, Oh, SKW, Pera, MF, Rossant, J, Stacey, GN, and Suemori, H

Abstract

There are many reports of defined culture systems for the propagation of human embryonic stem cells in the absence of feeder cell support, but no previous study has undertaken a multi-laboratory comparison of these diverse methodologies. In this study, five separate laboratories, each with experience in human embryonic stem cell culture, used a panel of ten embryonic stem cell lines (including WA09 as an index cell line common to all laboratories) to assess eight cell culture methods, with propagation in the presence of Knockout Serum Replacer, FGF-2, and mouse embryonic fibroblast feeder cell layers serving as a positive control. The cultures were assessed for up to ten passages for attachment, death, and differentiated morphology by phase contrast microscopy, for growth by serial cell counts, and for maintenance of stem cell surface marker expression by flow cytometry. Of the eight culture systems, only the control and those based on two commercial media, mTeSR1 and STEMPRO, supported maintenance of most cell lines for ten passages. Cultures grown in the remaining media failed before this point due to lack of attachment, cell death, or overt cell differentiation. Possible explanations for relative success of the commercial formulations in this study, and the lack of success with other formulations from academic groups compared to previously published results, include: the complex combination of growth factors present in the commercial preparations; improved development, manufacture, and quality control in the commercial products; differences in epigenetic adaptation to culture in vitro between different ES cell lines grown in different laboratories.

Published
2010

18. A Continuum of Cell States Spans Pluripotency and Lineage Commitment in Human Embryonic Stem Cells

Author

Reh, TA, Hough, SR, Laslett, AL, Grimmond, SB, Kolle, G, Pera, MF, Reh, TA, Hough, SR, Laslett, AL, Grimmond, SB, Kolle, G, and Pera, MF

Abstract

BACKGROUND: Commitment in embryonic stem cells is often depicted as a binary choice between alternate cell states, pluripotency and specification to a particular germ layer or extraembryonic lineage. However, close examination of human ES cell cultures has revealed significant heterogeneity in the stem cell compartment. METHODOLOGY/PRINCIPAL FINDINGS: We isolated subpopulations of embryonic stem cells using surface markers, then examined their expression of pluripotency genes and lineage specific transcription factors at the single cell level, and tested their ability to regenerate colonies of stem cells. Transcript analysis of single embryonic stem cells showed that there is a gradient and a hierarchy of expression of pluripotency genes in the population. Even cells at the top of the hierarchy generally express only a subset of the stem cell genes studied. Many cells co-express pluripotency and lineage specific genes. Cells along the continuum show a progressively decreasing likelihood of self renewal as their expression of stem cell surface markers and pluripotency genes wanes. Most cells that are positive for stem cell surface markers express Oct-4, but only those towards the top of the hierarchy express the nodal receptor TDGF-1 and the growth factor GDF3. SIGNIFICANCE: These findings on gene expression in single embryonic stem cells are in concert with recent studies of early mammalian development, which reveal molecular heterogeneity and a stochasticity of gene expression in blastomeres. Our work indicates that only a small fraction of the population resides at the top of the hierarchy, that lineage priming (co-expression of stem cell and lineage specific genes) characterizes pluripotent stem cell populations, and that extrinsic signaling pathways are upstream of transcription factor networks that control pluripotency.

Published
2009

22. Transcriptional analysis of early lineage commitment in human embryonic stem cells

Author

Laslett, AL, Grimmond, S, Gardiner, B, Stamp, L, Lin, A, Hawes, SM, Wormald, S, Nikolic-Paterson, D, Haylock, D, Pera, MF, Laslett, AL, Grimmond, S, Gardiner, B, Stamp, L, Lin, A, Hawes, SM, Wormald, S, Nikolic-Paterson, D, Haylock, D, and Pera, MF

Abstract

BACKGROUND: The mechanisms responsible for the maintenance of pluripotency in human embryonic stem cells, and those that drive their commitment into particular differentiation lineages, are poorly understood. In fact, even our knowledge of the phenotype of hESC is limited, because the immunological and molecular criteria presently used to define this phenotype describe the properties of a heterogeneous population of cells. RESULTS: We used a novel approach combining immunological and transcriptional analysis (immunotranscriptional profiling) to compare gene expression in hESC populations at very early stages of differentiation. Immunotranscriptional profiling enabled us to identify novel markers of stem cells and their differentiated progeny, as well as novel potential regulators of hESC commitment and differentiation. The data show clearly that genes associated with the pluripotent state are downregulated in a coordinated fashion, and that they are co-expressed with lineage specific transcription factors in a continuum during the early stages of stem cell differentiation. CONCLUSION: These findings, that show that maintenance of pluripotency and lineage commitment are dynamic, interactive processes in hESC cultures, have important practical implications for propagation and directed differentiation of these cells, and for the interpretation of mechanistic studies of hESC renewal and commitment. Since embryonic stem cells at defined stages of commitment can be isolated in large numbers by immunological means, they provide a powerful model for studying molecular genetics of stem cell commitment in the embryo.

Published
2007

23. Cultured cell lines from human teratomas: windows into tumour growth and differentiation and early human development

Author

Pera Mf, W Bennett, Roach S, and S. Cooper

Subjects
Urology, medicine.medical_treatment, Models, Biological, Extracellular matrix, Embryonal carcinoma, Embryonic and Fetal Development, Biomarkers, Tumor, Mesonephroma, Tumor Cells, Cultured, Medicine, Humans, Yolk sac, Growth Substances, Transcription factor, business.industry, Growth factor, Embryogenesis, Teratoma, medicine.disease, Antigens, Differentiation, Cell biology, Hepatocyte nuclear factors, medicine.anatomical_structure, Immunology, business, Cell Division, Transcription Factors
Abstract

Cultured cell lines from human teratomas provide models to study molecules which might regulate tumour growth or normal embryonic development. Here, we describe efforts to delineate the role of transcription factors, extracellular matrix, and growth factors in controlling growth and differentiation of human embryonal carcinoma and yolk sac tumour.

Published
1993

24. An orthotopic xenograft model of human nonseminomatous germ cell tumour

Author

Douglas, ML, Boucaut, KJ, Antalis, TM, Higgins, C, Pera, MF, Stuttgen, MA, Nicol, DL, Douglas, ML, Boucaut, KJ, Antalis, TM, Higgins, C, Pera, MF, Stuttgen, MA, and Nicol, DL

Abstract

We have established the first example of an orthotopic xenograft model of human nonseminomatous germ cell tumour (NSGCT). This reproducible model exhibits many clinically relevant features including metastases to the retroperitoneal lymph nodes and lungs, making it an ideal tool for research into the development and progression of testicular germ cell tumours.

Published
2001

25. EXCEPTIONAL SENSITIVITY OF TESTICULAR GERM-CELL TUMOR-CELL LINES TO THE NEW ANTICANCER AGENT, TEMOZOLOMIDE

Author

PERA, MF, KOBERLE, B, MASTERS, JRW, PERA, MF, KOBERLE, B, and MASTERS, JRW

Abstract

Metastatic testicular germ cell tumours are cured in approximately 85% of patients using cisplatin-based combination chemotherapy. Patients who fail to respond have a poor prognosis, and there is a need for more effective treatments for cisplatin-resistant disease. In this study, it is shown that two of four cell lines derived from human non-seminomatous testicular germ cell tumours are exceptionally sensitive to temozolomide, a new imidazotetrazine which can cross the blood-brain barrier in mice. In addition, three pairs of cisplatin-resistant sublines show little cross-resistance to temozolomide. These data suggest that temozolomide might have activity against non-seminomatous testicular germ cell tumours which have relapsed following cisplatin-containing chemotherapy, and could have a role in the treatment of patients with metastatic lesions in the brain.

Published
1995

28. A brief chronicle of research on human pluripotent stem cells.

Author

Pera MF

Subjects
Humans, Animals, Gene Editing methods, Cell Culture Techniques methods, Pluripotent Stem Cells cytology, Pluripotent Stem Cells metabolism
Abstract

Today, human pluripotent stem cell technologies find widespread application across biomedical research, as models for early human development, as platforms for functional human genomics, as tools for the study of disease, drug screening and toxicology, and as a renewable source of cellular therapeutics for a range of intractable diseases. The foundations of this human pluripotent stem cell revolution rest on advances in a wide range of disciplines, including cancer biology, assisted reproduction, cell culture and organoid technology, somatic cell nuclear transfer, primate embryology, single-cell biology, and gene editing. This review surveys the slow emergence of the study of human pluripotency and the exponential growth of the field during the past several decades., (© 2024 Wiley Periodicals LLC.)

Published
2024
Full Text
View/download PDF

29. An in vitro neurogenetics platform for precision disease modeling in the mouse.

Author

Cortes DE, Escudero M, Korgan AC, Mitra A, Edwards A, Aydin SC, Munger SC, Charland K, Zhang ZW, O'Connell KMS, Reinholdt LG, and Pera MF

Subjects
Animals, Mice, Humans, Phenotype, Pluripotent Stem Cells
Abstract

The power and scope of disease modeling can be markedly enhanced through the incorporation of broad genetic diversity. The introduction of pathogenic mutations into a single inbred mouse strain sometimes fails to mimic human disease. We describe a cross-species precision disease modeling platform that exploits mouse genetic diversity to bridge cell-based modeling with whole organism analysis. We developed a universal protocol that permitted robust and reproducible neural differentiation of genetically diverse human and mouse pluripotent stem cell lines and then carried out a proof-of-concept study of the neurodevelopmental gene DYRK1A . Results in vitro reliably predicted the effects of genetic background on Dyrk1a loss-of-function phenotypes in vivo. Transcriptomic comparison of responsive and unresponsive strains identified molecular pathways conferring sensitivity or resilience to Dyrk1a1A loss and highlighted differential messenger RNA isoform usage as an important determinant of response. This cross-species strategy provides a powerful tool in the functional analysis of candidate disease variants identified through human genetic studies.

Published
2024
Full Text
View/download PDF

30. Complex regulatory networks influence pluripotent cell state transitions in human iPSCs.

Author

Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, Luchessi AD, Greenwald WWY, D'Antonio M, Pera MF, and Frazer KA

Subjects
Humans, Gene Regulatory Networks, Chromatin genetics, Cell Differentiation genetics, Octamer Transcription Factor-3 genetics, Induced Pluripotent Stem Cells metabolism
Abstract

Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discover 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which are highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlie the coordinated expression of genes in the GNMs. Epigenetic analyses reveal that regulatory networks underlying self-renewal and pluripotency are more complex than previously realized. Genetic analyses identify thousands of regulatory variants that overlapped predicted transcription factor binding sites and are associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network are significantly enriched for regulatory variants with large effects, suggesting that they play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work bins tens of thousands of regulatory elements in hiPSCs into discrete regulatory networks, shows that pluripotency and self-renewal processes have a surprising level of regulatory complexity, and suggests that genetic factors may contribute to cell state transitions in human iPSC lines., (© 2024. The Author(s).)

Published
2024
Full Text
View/download PDF

31. Analysis of regulatory network modules in hundreds of human stem cell lines reveals complex epigenetic and genetic factors contribute to pluripotency state differences between subpopulations.

Author

Arthur TD, Nguyen JP, D'Antonio-Chronowska A, Matsui H, Silva NS, Joshua IN, Luchessi AD, Young Greenwald WW, D'Antonio M, Pera MF, and Frazer KA

Abstract

Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Analyzing hundreds of hiPSCs derived from different individuals, we show the proportions of these pluripotent states vary considerably across lines. We discovered 13 gene network modules (GNMs) and 13 regulatory network modules (RNMs), which were highly correlated with each other suggesting that the coordinated co-accessibility of regulatory elements in the RNMs likely underlied the coordinated expression of genes in the GNMs. Epigenetic analyses revealed that regulatory networks underlying self-renewal and pluripotency have a surprising level of complexity. Genetic analyses identified thousands of regulatory variants that overlapped predicted transcription factor binding sites and were associated with chromatin accessibility in the hiPSCs. We show that the master regulator of pluripotency, the NANOG-OCT4 Complex, and its associated network were significantly enriched for regulatory variants with large effects, suggesting that they may play a role in the varying cellular proportions of pluripotency states between hiPSCs. Our work captures the coordinated activity of tens of thousands of regulatory elements in hiPSCs and bins these elements into discrete functionally characterized regulatory networks, shows that regulatory elements in pluripotency networks harbor variants with large effects, and provides a rich resource for future pluripotent stem cell research.

Published
2023
Full Text
View/download PDF

32. Seven days in the life cycle of Homo sapiens.

Author

Pera MF

Subjects
Female, Pregnancy, Animals, Humans, Life Cycle Stages, Morphogenesis, Stem Cells, Embryo, Mammalian, Embryonic Development
Abstract

The second week of embryonic development is a critical phase of the human life cycle and one that has been largely inaccessible to scientific investigation. Recent studies of human embryo models built from stem cells promise to yield dramatic insights into the key events of cell specification and morphogenesis that occur during this brief window of embryogenesis., Competing Interests: Declaration of interests The author declares no competing interests., (Copyright © 2023 Elsevier Inc. All rights reserved.)

Published
2023
Full Text
View/download PDF

33. An ethical framework for human embryology with embryo models.

Author

Rivron NC, Martinez Arias A, Pera MF, Moris N, and M'hamdi HI

Subjects
Humans, Pluripotent Stem Cells, Embryo, Mammalian, Embryo Research ethics
Abstract

A human embryo's legal definition and its entitlement to protection vary greatly worldwide. Recently, human pluripotent stem cells have been used to form in vitro models of early embryos that have challenged legal definitions and raised questions regarding their usage. In this light, we propose a refined legal definition of an embryo, suggest "tipping points" for when human embryo models could eventually be afforded similar protection to that of embryos, and then revisit basic ethical principles that might help to draft a roadmap for the gradual, justified usage of embryo models in a manner that aims to maximize benefits to society., Competing Interests: Declaration of interests N.C.R. is an inventor on the patents “Blastoid, cell line based artificial blastocyst” (EP2986711) and “Blastocyst-like cell aggregate and methods” (EP21151455.9) that are both licensed to dawn-bio, a company he co-founded. A.M.A. and N.M. are inventors on the patents "Polarised three-dimensional cellular aggregates” (PCT/GB2019/052668) and “human polarised three-dimensional cellular” (PCT/GB2019/052670), maintained by Cambridge Enterprise., (Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.)

Published
2023
Full Text
View/download PDF

35. Mental Health Service Utilization Rates Among Commercially Insured Adults in the US During the First Year of the COVID-19 Pandemic.

Author

McBain RK, Cantor J, Pera MF, Breslau J, Bravata DM, and Whaley CM

Subjects
Humans, Adult, Adolescent, Cohort Studies, Pandemics, Depressive Disorder, Major epidemiology, Depressive Disorder, Major therapy, Depressive Disorder, Major psychology, COVID-19 epidemiology, Mental Health Services
Abstract

Importance: The COVID-19 pandemic has been associated with an elevated prevalence of mental health conditions and disrupted mental health care throughout the US., Objective: To examine mental health service use among US adults from January through December 2020., Design, Setting, and Participants: This cohort study used county-level service utilization data from a national US database of commercial medical claims from adults (age >18 years) from January 5 to December 21, 2020. All analyses were conducted in April and May 2021., Main Outcomes and Measures: Per-week use of mental health services per 10 000 beneficiaries was calculated for 5 psychiatric diagnostic categories: major depressive disorder (MDD), anxiety disorders, bipolar disorder, adjustment disorders, and posttraumatic stress disorder (PTSD). Changes in service utilization rates following the declaration of a national public health emergency on March 13, 2020, were examined overall and by service modality (in-person vs telehealth), diagnostic category, patient sex, and age group., Results: The study included 5 142 577 commercially insured adults. The COVID-19 pandemic was associated with more than a 50% decline in in-person mental health care service utilization rates. At baseline, there was a mean (SD) of 11.66 (118.00) weekly beneficiaries receiving services for MDD per 10 000 enrollees; this declined by 6.44 weekly beneficiaries per 10 000 enrollees (β, -6.44; 95% CI, -8.33 to -4.54). For other disorders, these rates were as follows: anxiety disorders (mean [SD] baseline, 12.24 [129.40] beneficiaries per 10 000 enrollees; β, -5.28; 95% CI, -7.50 to -3.05), bipolar disorder (mean [SD] baseline, 3.32 [60.39] beneficiaries per 10 000 enrollees; β, -1.81; 95% CI, -2.75 to -0.87), adjustment disorders (mean [SD] baseline, 12.14 [129.94] beneficiaries per 10 000 enrollees; β, -6.78; 95% CI, -8.51 to -5.04), and PTSD (mean [SD] baseline, 4.93 [114.23] beneficiaries per 10 000 enrollees; β, -2.00; 95% CI, -3.98 to -0.02). Over the same period, there was a 16- to 20-fold increase in telehealth service utilization; the rate of increase was lowest for bipolar disorder (mean [SD] baseline, 0.13 [16.72] beneficiaries per 10 000 enrollees; β, 1.40; 95% CI, 1.04-1.76) and highest for anxiety disorders (mean [SD] baseline, 0.20 [9.28] beneficiaries per 10 000 enrollees; β, 9.12; 95% CI, 7.32-10.92). When combining in-person and telehealth service utilization rates, an overall increase in care for MDD, anxiety, and adjustment disorders was observed over the period., Conclusions and Relevance: In this cohort study of US adults, we found that the COVID-19 pandemic was associated with a rapid increase in telehealth services for mental health conditions, offsetting a sharp decline in in-person care and generating overall higher service utilization rates for several mental health conditions compared with prepandemic levels.

Published
2023
Full Text
View/download PDF

36. A path to translation: How 3D patient tumor avatars enable next generation precision oncology.

Author

Bose S, Barroso M, Chheda MG, Clevers H, Elez E, Kaochar S, Kopetz SE, Li XN, Meric-Bernstam F, Meyer CA, Mou H, Naegle KM, Pera MF, Perova Z, Politi KA, Raphael BJ, Robson P, Sears RC, Tabernero J, Tuveson DA, Welm AL, Welm BE, Willey CD, Salnikow K, Chuang JH, and Shen X

Subjects
Humans, Precision Medicine, Prospective Studies, Medical Oncology, Neoplasms genetics, Neoplasms therapy, Neoplasms diagnosis
Abstract

3D patient tumor avatars (3D-PTAs) hold promise for next-generation precision medicine. Here, we describe the benefits and challenges of 3D-PTA technologies and necessary future steps to realize their potential for clinical decision making. 3D-PTAs require standardization criteria and prospective trials to establish clinical benefits. Innovative trial designs that combine omics and 3D-PTA readouts may lead to more accurate clinical predictors, and an integrated platform that combines diagnostic and therapeutic development will accelerate new treatments for patients with refractory disease., Competing Interests: Declarations of interests S.B., M.B., H.M., Z.P., C.A.M., K.M.N., M.F.P., R.C.S., K.S. and J.H.C. have no competing interests to declare. S.E.K. is an advisor to Xilis, Inc. F.M.B. declares consulting/advisory fees from AbbVie, Aduro BioTech Inc., Alkermes, AstraZeneca, Daiichi Sankyo Co. Ltd., DebioPharm, eFFECTOR Therapeutics, F. Hoffman-La Roche Ltd., Genentech Inc., Harbinger Health, IBM Watson, Infinity Pharmaceuticals, Jackson Laboratory, Kolon Life Science, Lengo Therapeutics, OrigiMed, PACT Pharma, Parexel International, Pfizer Inc., Protai Bio Ltd, Samsung Bioepis, Seattle Genetics Inc., Tallac Therapeutics, Tyra Biosciences, Xencor, Zymeworks, Black Diamond, Biovica, Eisai, FogPharma, Immunomedics, Inflection Biosciences, Karyopharm Therapeutics, Loxo Oncology, Mersana Therapeutics, OnCusp Therapeutics, Puma Biotechnology Inc., Seattle Genetics, Sanofi, Silverback Therapeutics, Spectrum Pharmaceuticals, and Zentalis; sponsored research to her institution from Aileron Therapeutics, Inc., AstraZeneca, Bayer Healthcare Pharmaceutical, Calithera Biosciences Inc., Curis Inc., CytomX Therapeutics Inc., Daiichi Sankyo Co. Ltd., Debiopharm International, eFFECTOR Therapeutics, Genentech Inc., Guardant Health Inc., Klus Pharma, Takeda Pharmaceutical, Novartis, Puma Biotechnology Inc., and Taiho Pharmaceutical Co.; and honoraria for a speaking engagement from Chugai Biopharmaceuticals. S.K. is a consultant for FGH BioTech and has received research funding from FGH BioTech and Systems Oncology. K.A.P. is co-inventor on a patent for EGFRT790M mutation testing issued, licensed, and with royalties paid from Molecular Diagnostics/Memorial Sloan Kettering Cancer Center. She reports research funding to the institution from AstraZeneca, Roche/Genentech, Boehringer Ingelheim, and D2G Oncology and consulting for AstraZeneca and Jannssen. M.G.C. reports grants from NeoImmuneTech, as well as other support from Orbus Therapeutics, Incyte, Merck, and UpToDate outside the submitted work; in addition, M.G.C. has a patent for Zika virus strains for the treatment of glioblastoma pending. E.E.’s full disclosures are given here: www.bit.ly/3xuWMer. J.T. reports personal financial interest in form of scientific consultancy role for Array Biopharma, AstraZeneca, Bayer, Boehringer Ingelheim, Chugai, Daiichi Sankyo, F. Hoffmann-La Roche Ltd, Genentech Inc, HalioDX SAS, Hutchison MediPharma International, Ikena Oncology, Inspirna Inc, IQVIA, Lilly, Menarini, Merck Serono, Merus, MSD, Mirati, Neophore, Novartis, Ona Therapeutics, Orion Biotechnology, Peptomyc, Pfizer, Pierre Fabre, Samsung Bioepis, Sanofi, Scandion Oncology, Scorpion Therapeutics, Seattle Genetics, Servier, Sotio Biotech, Taiho, Tessa Therapeutics, and TheraMyc; and holds stocks in Oniria Therapeutics and also educational collaboration with Imedex/HMP, Medscape Education, MJH Life Sciences, PeerView Institute for Medical Education and Physicians Education Resource (PER). D.A.T. is a member of the Scientific Advisory Board and receives stock options from Leap Therapeutics, Surface Oncology, Cygnal Therapeutics, Mestag Therapeutics, and Xilis, Inc. outside the submitted work. D.A.T. is scientific co-founder of Mestag Therapeutics. D.A.T. has received research grant support from Fibrogen, Mestag, and ONO Therapeutics. D.A.T. receives grant funding from the Lustgarten Foundation, the NIH, and the Thompson Foundation. None of this work is related to the publication. No other disclosures were reported. C.D.W. is a part-time consultant for LifeNet Health and receives grant funding from AACR-Novocure and Varian Medical Systems. X.S. and H.C. are cofounders of Xilis, Inc. and inventors on patents related to organoid research and micro-organospheres. X.S. is CEO of Xilis, Inc. H.C.’s full disclosure is given here: www.uu.nl/staff/JCClevers/Additionalfunctions. M.S., B.J.R., P.R., X.L., B.E.W., and A.L.W. do not report any conflicts., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Published
2022
Full Text
View/download PDF

37. The consequences of recurrent genetic and epigenetic variants in human pluripotent stem cells.

Author

Andrews PW, Barbaric I, Benvenisty N, Draper JS, Ludwig T, Merkle FT, Sato Y, Spits C, Stacey GN, Wang H, and Pera MF

Subjects
Humans, Stem Cell Research, Oncogenes, Epigenesis, Genetic, Epigenomics, Pluripotent Stem Cells
Abstract

It is well established that human pluripotent stem cells (hPSCs) can acquire genetic and epigenetic changes during culture in vitro. Given the increasing use of hPSCs in research and therapy and the vast expansion in the number of hPSC lines available for researchers, the International Society for Stem Cell Research has recognized the need to reassess quality control standards for ensuring the genetic integrity of hPSCs. Here, we summarize current knowledge of the nature of recurrent genetic and epigenetic variants in hPSC culture, the methods for their detection, and what is known concerning their effects on cell behavior in vitro or in vivo. We argue that the potential consequences of low-level contamination of cell therapy products with cells bearing oncogenic variants are essentially unknown at present. We highlight the key challenges facing the field with particular reference to safety assessment of hPSC-derived cellular therapeutics., Competing Interests: Declaration of interests P.W.A. receives royalties from the Wistar Institute for sales of antibodies., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Published
2022
Full Text
View/download PDF

38. Spatial modeling of vaccine deserts as barriers to controlling SARS-CoV-2.

Author

Rader B, Astley CM, Sewalk K, Delamater PL, Cordiano K, Wronski L, Rivera JM, Hallberg K, Pera MF, Cantor J, Whaley CM, Bravata DM, Lee L, Patel A, and Brownstein JS

Abstract

Background: COVID-19 vaccine distribution is at risk of further propagating the inequities of COVID-19, which in the United States (US) has disproportionately impacted the elderly, people of color, and the medically vulnerable. We sought to measure if the disparities seen in the geographic distribution of other COVID-19 healthcare resources were also present during the initial rollout of the COVID-19 vaccine., Methods: Using a comprehensive COVID-19 vaccine database (VaccineFinder), we built an empirically parameterized spatial model of access to essential resources that incorporated vaccine supply, time-willing-to-travel for vaccination, and previous vaccination across the US. We then identified vaccine deserts-US Census tracts with localized, geographic barriers to vaccine-associated herd immunity. We link our model results with Census data and two high-resolution surveys to understand the distribution and determinates of spatially accessibility to the COVID-19 vaccine., Results: We find that in early 2021, vaccine deserts were home to over 30 million people, >10% of the US population. Vaccine deserts were concentrated in rural locations and communities with a higher percentage of medically vulnerable populations. We also find that in locations of similar urbanicity, early vaccination distribution disadvantaged neighborhoods with more people of color and older aged residents., Conclusion: Given sufficient vaccine supply, data-driven vaccine distribution to vaccine deserts may improve immunization rates and help control COVID-19., (© 2022. The Author(s).)

Published
2022
Full Text
View/download PDF

39. Pluripotent cell states and unexpected fates.

Author

Pera MF

Subjects
Cell Differentiation, Embryonic Development, Humans, Pluripotent Stem Cells
Abstract

Pluripotent stem cells provide a powerful model for the study of human development and its disorders. Recent studies, including two in this issue of Stem Cell Reports, raise important questions concerning the developmental potential of human pluripotent stem cells, and how the behavior of these cells in vitro mirrors normal embryogenesis., (Copyright © 2022 The Author. Published by Elsevier Inc. All rights reserved.)

Published
2022
Full Text
View/download PDF

40. A Splicing Mutation in Slc4a5 Results in Retinal Detachment and Retinal Pigment Epithelium Dysfunction.

Author

Collin GB, Shi L, Yu M, Akturk N, Charette JR, Hyde LF, Weatherly SM, Pera MF, Naggert JK, Peachey NS, Nishina PM, and Krebs MP

Subjects
Animals, Cells, Cultured, Disease Models, Animal, Female, Humans, Male, Mice, Mice, Inbred C57BL, Retinal Detachment pathology, Tomography, Optical Coherence methods, Mutation genetics, RNA Splicing genetics, Retina pathology, Retinal Detachment genetics, Retinal Pigment Epithelium pathology, Sodium-Bicarbonate Symporters genetics
Abstract

Fluid and solute transporters of the retinal pigment epithelium (RPE) are core components of the outer blood-retinal barrier. Characterizing these transporters and their role in retinal homeostasis may provide insights into ocular function and disease. Here, we describe RPE defects in tvrm77 mice, which exhibit hypopigmented patches in the central retina. Mapping and nucleotide sequencing of tvrm77 mice revealed a disrupted 5' splice donor sequence in Slc4a5 , a sodium bicarbonate cotransporter gene. Slc4a5 expression was reduced 19.7-fold in tvrm77 RPE relative to controls, and alternative splice variants were detected. SLC4A5 was localized to the Golgi apparatus of cultured human RPE cells and in apical and basal membranes. Fundus imaging, optical coherence tomography, microscopy, and electroretinography (ERG) of tvrm77 mice revealed retinal detachment, hypopigmented patches corresponding to neovascular lesions, and retinal folds. Detachment worsened and outer nuclear layer thickness decreased with age. ERG a- and b-wave response amplitudes were initially normal but declined in older mice. The direct current ERG fast oscillation and light peak were reduced in amplitude at all ages, whereas other RPE-associated responses were unaffected. These results link a new Slc4a5 mutation to subretinal fluid accumulation and altered light-evoked RPE electrophysiological responses, suggesting that SLC4A5 functions at the outer blood-retinal barrier.

Published
2022
Full Text
View/download PDF

41. Selective elimination of pluripotent stem cells by PIKfyve specific inhibitors.

Author

Chakraborty AR, Vassilev A, Jaiswal SK, O'Connell CE, Ahrens JF, Mallon BS, Pera MF, and DePamphilis ML

Subjects
Animals, Autophagy, Cell Line, Cell Survival drug effects, DNA metabolism, Embryonic Stem Cells cytology, Embryonic Stem Cells metabolism, Enzyme Inhibitors therapeutic use, Female, G1 Phase, Humans, Hydrazines chemistry, Hydrazines pharmacology, Hydrazines therapeutic use, Mice, Mice, Nude, Phosphatidylinositol 3-Kinases metabolism, Pluripotent Stem Cells cytology, Pluripotent Stem Cells drug effects, Pluripotent Stem Cells metabolism, Teratocarcinoma drug therapy, Teratocarcinoma pathology, Transplantation, Heterologous, Apoptosis drug effects, Enzyme Inhibitors pharmacology, Phosphatidylinositol 3-Kinases chemistry
Abstract

Inhibition of PIKfyve phosphoinositide kinase selectively kills autophagy-dependent cancer cells by disrupting lysosome homeostasis. Here, we show that PIKfyve inhibitors can also selectively eliminate pluripotent embryonal carcinoma cells (ECCs), embryonic stem cells, and induced pluripotent stem cells under conditions where differentiated cells remain viable. PIKfyve inhibitors prevented lysosome fission, induced autophagosome accumulation, and reduced cell proliferation in both pluripotent and differentiated cells, but they induced death only in pluripotent cells. The ability of PIKfyve inhibitors to distinguish between pluripotent and differentiated cells was confirmed with xenografts derived from ECCs. Pretreatment of ECCs with the PIKfyve specific inhibitor WX8 suppressed their ability to form teratocarcinomas in mice, and intraperitoneal injections of WX8 into mice harboring teratocarcinoma xenografts selectively eliminated pluripotent cells. Differentiated cells continued to proliferate, but at a reduced rate. These results provide a proof of principle that PIKfyve specific inhibitors can selectively eliminate pluripotent stem cells in vivo as well as in vitro., (Copyright © 2021. Published by Elsevier Inc.)

Published
2022
Full Text
View/download PDF

42. The exploration of pluripotency space: Charting cell state transitions in peri-implantation development.

Author

Pera MF and Rossant J

Subjects
Animals, Cell Differentiation, Embryo Implantation, Embryo, Mammalian, Germ Layers, Humans, Mice, Pluripotent Stem Cells
Abstract

Pluripotent cells in the mammalian embryo undergo state transitions marked by changes in patterns of gene expression and developmental potential as they progress from pre-implantation through post-implantation stages of development. Recent studies of cultured mouse and human pluripotent stem cells (hPSCs) have identified cells representative of an intermediate stage (referred to as the formative state) between naive pluripotency (equivalent to pre-implantation epiblast) and primed pluripotency (equivalent to late post-implantation epiblast). We examine these recent findings in light of our knowledge of peri-implantation mouse and human development, and we consider the implications of this work for deriving human embryo models from pluripotent cells., Competing Interests: Declaration of interests M.F.P. and J.R. are members of the advisory board of Cell Stem Cell., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Published
2021
Full Text
View/download PDF

44. Use of buprenorphine for those with employer-sponsored insurance during the initial phase of the COVID-19 pandemic.

Author

Cantor J, Dick AW, Haffajee R, Pera MF, Bravata DM, Stein BD, and Whaley CM

Subjects
Adult, Humans, Pandemics, SARS-CoV-2, United States, Buprenorphine therapeutic use, COVID-19, Drug Overdose epidemiology, Insurance, Opioid-Related Disorders drug therapy, Opioid-Related Disorders epidemiology
Abstract

Objective: To quantify weekly rates of use of buprenorphine for those with employer-based insurance and whether the rate differs based on county-level measures of race, historical fatal drug overdose rate, and COVID-19 case rate., Methods: We used 2020 pharmaceutical claims for 4.8 million adults from a privately insured population to examine changes in the use of buprenorphine to treat opioid use disorder in 2020 during the onset of the COVID-19 pandemic. We quantified variation by examining changes in use rates across counties based on their fatal drug overdose rate in 2018, number of COVID-19 cases per capita, and percent nonwhite., Results: Weekly use of buprenorphine was relatively stable between the first week of January (0.6 per 10,000 enrollees, 95%CI = 0.2 to 1.1) and the last week of August (0.8 per 10,000 enrollees, 95%CI = 0.4 to 1.3). We did not find evidence of any consistent change in use of buprenorphine by county-level terciles for COVID-19 rate as of August 31, 2020, age-adjusted fatal drug overdose rate, and percent nonwhite. Use was consistently higher for counties in the highest tercile of county age-adjusted fatal drug overdose rate when compared to counties in the lowest tercile of county age-adjusted fatal drug overdose rate., Discussion: Our results provide early evidence that new federal- and state-level policies may have steadied the rate of using buprenorphine for those with employer-based insurance during the pandemic., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Published
2021
Full Text
View/download PDF

45. Who Is (and Is Not) Receiving Telemedicine Care During the COVID-19 Pandemic.

Author

Cantor JH, McBain RK, Pera MF, Bravata DM, and Whaley CM

Subjects
Adult, Child, Humans, Office Visits, Pandemics, SARS-CoV-2, COVID-19, Telemedicine
Abstract

Introduction: The COVID-19 pandemic has forced telehealth to be the primary means through which patients interact with their providers. There is a concern that the pandemic will exacerbate the existing disparities in overall healthcare utilization and telehealth utilization. Few national studies have examined the changes in telehealth use during the COVID-19 pandemic., Methods: Data on 6.8 and 6.4 million employer-based health plan beneficiaries in 2020 and 2019, respectively, were collected in 2020. Unadjusted rates were compared both before and after the week of the declaration of the COVID-19 pandemic as a national emergency. Trends in weekly utilization were also examined using a difference-in-differences regression framework to quantify the changes in telemedicine and office-based care utilization while controlling for the patient's demographic and county-level sociodemographic measures. All analyses were conducted in 2020., Results: More than a 20-fold increase in the incidence of telemedicine utilization after March 13, 2020 was observed. Conversely, the incidence of office-based encounters declined by almost 50% and was not fully offset by the increase in telemedicine. The increase in telemedicine was greatest among patients in counties with low poverty levels (β=31.70, 95% CI=15.17, 48.23), among patients in metropolitan areas (β=40.60, 95% CI=30.86, 50.34), and among adults than among children aged 0-12 years (β=57.91, 95% CI=50.32, 65.49)., Conclusions: The COVID-19 pandemic has affected telehealth utilization disproportionately on the basis of patient age and both the county-level poverty rate and urbanicity., (Copyright © 2021 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.)

Published
2021
Full Text
View/download PDF

46. A case for revisiting Nodal signaling in human pluripotent stem cells.

Author

Hayes K, Kim YK, and Pera MF

Subjects
Animals, Cell Differentiation physiology, Humans, Nodal Protein genetics, Nodal Protein metabolism, Signal Transduction physiology, Transforming Growth Factor beta metabolism, Gene Expression Regulation, Developmental, Pluripotent Stem Cells metabolism
Abstract

Nodal is a transforming growth factor-β (TGF-β) superfamily member that plays a number of critical roles in mammalian embryonic development. Nodal is essential for the support of the peri-implantation epiblast in the mouse embryo and subsequently acts to specify mesendodermal fate at the time of gastrulation and, later, left-right asymmetry. Maintenance of human pluripotent stem cells (hPSCs) in vitro is dependent on Nodal signaling. Because it has proven difficult to prepare a biologically active form of recombinant Nodal protein, Activin or TGFB1 are widely used as surrogates for NODAL in hPSC culture. Nonetheless, the expression of the components of an endogenous Nodal signaling pathway in hPSC provides a potential autocrine pathway for the regulation of self-renewal in this system. Here we review recent studies that have clarified the role of Nodal signaling in pluripotent stem cell populations, highlighted spatial restrictions on Nodal signaling, and shown that Nodal functions in vivo as a heterodimer with GDF3, another TGF-β superfamily member expressed by hPSC. We discuss the role of this pathway in the maintenance of the epiblast and hPSC in light of these new advances., (© 2021 AlphaMed Press.)

Published
2021
Full Text
View/download PDF

48. The genetic basis of inter-individual variation in recovery from traumatic brain injury.

Author

Cortes D and Pera MF

Abstract

Traumatic brain injury (TBI) is one of the leading causes of death among young people, and is increasingly prevalent in the aging population. Survivors of TBI face a spectrum of outcomes from short-term non-incapacitating injuries to long-lasting serious and deteriorating sequelae. TBI is a highly complex condition to treat; many variables can account for the observed heterogeneity in patient outcome. The limited success of neuroprotection strategies in the clinic has led to a new emphasis on neurorestorative approaches. In TBI, it is well recognized clinically that patients with similar lesions, age, and health status often display differences in recovery of function after injury. Despite this heterogeneity of outcomes in TBI, restorative treatment has remained generic. There is now a new emphasis on developing a personalized medicine approach in TBI, and this will require an improved understanding of how genetics impacts on long-term outcomes. Studies in animal model systems indicate clearly that the genetic background plays a role in determining the extent of recovery following an insult. A candidate gene approach in human studies has led to the identification of factors that can influence recovery. Here we review studies of the genetic basis for individual differences in functional recovery in the CNS in animals and man. The application of in vitro modeling with human cells and organoid cultures, along with whole-organism studies, will help to identify genes and networks that account for individual variation in recovery from brain injury, and will point the way towards the development of new therapeutic approaches.

Published
2021
Full Text
View/download PDF

49. Social Determinants of Health Challenges Are Prevalent Among Commercially Insured Populations.

Author

Pera MF, Cain MM, Emerick A, Katz S, Hirsch NA, Sherman BW, and Bravata DM

Subjects
Female, Humans, Income, Poverty, Pregnancy, Patient Acceptance of Health Care, Social Determinants of Health
Abstract

Objectives: To evaluate the prevalence of social determinants of health (SDoH) factors in a large commercially-insured population and to characterize the prevalence of common conditions (eg, diabetes, behavioral health issues) and addressable health services utilization concerns (eg, lack of preventive care) for which employers offer no- and low-cost benefit programs., Methods: We identified groups with SDoH challenges within a commercially-insured population of 5.1 M through administrative data and self-report. Using medical claims and health assessment data, we identified populations with SDoH needs who had common conditions for which employers often provide no- or low-cost benefit programs (ie, diabetes, behavioral health conditions, high-risk pregnancy, overweight/obesity). Additionally, we sought populations with common addressable health services utilization concerns such as avoidable emergency room visits, lack of preventive care services, or non-adherence to medications. We used univariate analyses to describe the prevalence of SDoH risks in the population of interest., Results: Twenty-seven percent of this commercially-insured population live in a zip code where the median income is at or below 200% of the Federal Poverty Line. Respondents identified cost (55%) and family, school, or work responsibilities (26%) as key barriers to care. ER overutilization rates are higher in lower income zip codes than wealthier zip codes (34% vs 9%) as is the prevalence of diabetes, overweight/obesity, and behavioral issues, and decreased use of preventive services. Fifteen percent of the study population live in a low-access food area. There is considerable variability in access to employer-sponsored resources to address these needs (70% of employers provide behavioral health programs; 63% provide telehealth programs, but only 1% offer healthy food programs and less than 0.5% offer either child care or transportation support programs)., Conclusions: Commercially insured populations could benefit from employer-sponsored programs or benefits that address key SDoH barriers such as financial support, healthy food programs, child-care, and transportation.

Published
2021
Full Text
View/download PDF

50. Changes in Health Services Use Among Commercially Insured US Populations During the COVID-19 Pandemic.

Author

Whaley CM, Pera MF, Cantor J, Chang J, Velasco J, Hagg HK, Sood N, and Bravata DM

Subjects
Adult, COVID-19 therapy, Cross-Sectional Studies, Employment statistics & numerical data, Female, Healthcare Disparities statistics & numerical data, Humans, Male, Middle Aged, Minority Groups statistics & numerical data, Primary Health Care, COVID-19 epidemiology, Health Services Accessibility statistics & numerical data, Insurance, Health statistics & numerical data, Patient Acceptance of Health Care statistics & numerical data, Patient Preference statistics & numerical data, SARS-CoV-2
Abstract

Importance: The coronavirus disease 2019 (COVID-19) pandemic has placed unprecedented strain on patients and health care professionals and institutions, but the association of the pandemic with use of preventive, elective, and nonelective care, as well as potential disparities in use of health care, remain unknown., Objective: To examine changes in health care use during the first 2 months of the COVID-19 pandemic in March and April of 2020 relative to March and April of 2019 and 2018, and to examine whether changes in use differ by patient's zip code-level race/ethnicity or income., Design, Setting, and Participants: This cross-sectional study analyzed health insurance claims for patients from all 50 US states who receive health insurance through their employers. Changes in use of preventive services, nonelective care, elective procedures, prescription drugs, in-person office visits, and telemedicine visits were examined during the first 2 months of the COVID-19 pandemic in 2020 relative to existing trends in 2019 and 2018. Disparities in the association of the pandemic with health care use based on patient's zip code-level race and income were also examined., Results: Data from 5.6, 6.4, and 6.8 million US individuals with employer-sponsored insurance in 2018, 2019, and 2020, respectively, were analyzed. Patient demographics were similar in all 3 years (mean [SD] age, 34.3 [18.6] years in 2018, 34.3 [18.5] years in 2019, and 34.5 [18.5] years in 2020); 50.0% women in 2018, 49.5% women in 2019, and 49.5% women in 2020). In March and April 2020, regression-adjusted use rate per 10 000 persons changed by -28.2 (95% CI, -30.5 to -25.9) and -64.5 (95% CI, -66.8 to -62.2) for colonoscopies; -149.1 (95% CI, -162.0 to -16.2) and -342.1 (95% CI, -355.0 to -329.2) for mammograms; -60.0 (95% CI, -63.3 to -54.7) and -118.1 (95% CI, -112.4 to -113.9) for hemoglobin A1c tests; -300.5 (95% CI, -346.5 to -254.5) and -369.0 (95% CI, -414.7 to -323.4) for child vaccines; -4.6 (95% CI, -5.3 to -3.9) and -10.9 (95% CI, -11.6 to -10.2) for musculoskeletal surgery; -1.1 (95% CI, -1.4 to -0.7) and -3.4 (95% CI, -3.8 to -3.0) for cataract surgery; -13.4 (95% CI, -14.6 to -12.2) and -31.4 (95% CI, -32.6 to -30.2) for magnetic resonance imaging; and -581.1 (95% CI, -612.9 to -549.3) and -1465 (95% CI, -1496 to -1433) for in-person office visits. Use of telemedicine services increased by 227.9 (95% CI, 221.7 to 234.1) per 10 000 persons and 641.6 (95% CI, 635.5 to 647.8) per 10 000 persons. Patients living in zip codes with lower-income or majority racial/ethnic minority populations experienced smaller reductions in in-person visits (≥80% racial/ethnic minority zip code: 200.0 per 10 000 [95% CI, 128.9-270.1]; 79%-21% racial/ethnic minority zip code: 54.2 per 10 000 [95% CI, 33.6-74.9]) but also had lower rates of adoption of telemedicine (≥80% racial/ethnic minority zip code: -71.6 per 10 000 [95% CI, -87.6 to -55.5]; 79%-21% racial/ethnic minority zip code: -15.1 per 10 000 [95% CI, -19.8 to -10.4])., Conclusions and Relevance: In this cross-sectional study of a large US population with employer-sponsored insurance, the first 2 months of the COVID-19 pandemic were associated with dramatic reductions in the use of preventive and elective care. Use of telemedicine increased rapidly but not enough to account for reductions in in-person primary care visits. Race and income disparities at the zip code level exist in use of telemedicine.

Published
2020
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results