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Phase III+: The University is open for expanded research operations; only authorized personnel will be admitted on campus. More info here.
Phase III+: The University is open for expanded research operations; only authorized personnel will be admitted on campus. More info here.
Phase III+: The University is open for expanded research operations; only authorized personnel will be admitted on campus. More info here.

Publications search

Found 36604 matches. Displaying 31-40
Zou CH, El Dika I, Vercauteren KOA, Capanu M, Chou JN, Shia JR, Pilet J, Quirk C, Lalazar G, Andrus L, Kabbani M, Yaqubie A, Khalil D, Mergoub T, Chiriboga L, Rice CM, Abou-Alfa GK, de Jong YP
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Mouse characteristics that affect establishing xenografts from hepatocellular carcinoma patient biopsies in the United States

CANCER MEDICINE 2022 FEB; 11(3):602-617
Background Hepatocellular carcinoma (HCC) patient-derived xenograft (PDX) models hold potential to advance knowledge in HCC biology to help improve systemic therapies. Beside hepatitis B virus-associated tumors, HCC is poorly established in PDX. Methods PDX formation from fresh HCC biopsies were obtained and implanted intrahepatically or in subrenal capsule (SRC). Mouse liver injury was induced in immunodeficient Fah(-/-) mice through cycling off nitisinone after HCC biopsy implantation, versus continuous nitisinone as non-liver injury controls. Mice with macroscopically detectable PDX showed rising human alpha1-antitrypsin (hAAT) serum levels, and conversely, no PDX was observed in mice with undetectable hAAT. Results Using rising hAAT as a marker for PDX formation, 20 PDX were established out of 45 HCC biopsy specimens (44%) reflecting the four major HCC etiologies most commonly identified at Memorial SloanKettering similar to many other institutions in the United States. PDX was established only in severely immunodeficient mice lacking lymphocytes and NK cells. Implantation under the renal capsule improved PDX formation two-fold compared to intrahepatic implantation. Two out of 18 biopsies required murine liver injury to establish PDX, one associated with hepatitis C virus and one with alcoholic liver disease. PDX tumors were histologically comparable to biopsy specimens and 75% of PDX lines could be passaged. Conclusions Using cycling off nitisinone-induced liver injury, HCC biopsies implanted under the renal capsule of severely immunodeficient mice formed PDX with 57% efficiency as determined by rising hAAT levels. These findings facilitate a more efficient make-up of PDX for research into subset-specific HCC.
Rex MR, Williams R, Birsoy K, Llman MST, Stahl M
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Targeting mitochondrial metabolism in acute myeloid leukemia

LEUKEMIA & LYMPHOMA 2022 FEB 23; 63(3):530-537
Cancer cells reprogram their metabolism to maintain sustained proliferation, which creates unique metabolic dependencies between malignant and healthy cells that can be exploited for therapy. In acute myeloid leukemia (AML), mitochondrial inhibitors that block tricarboxylic acid cycle enzymes or electron transport chain complexes have recently shown clinical promise. The isocitrate dehydrogenase 1 inhibitor ivosidenib, the isocitrate dehydrogenase 2 inhibitor enasidenib, and the BH3 mimetic venetoclax received FDA approval for treatment of AML in the last few years. Other mitochondrial inhibitors including CPI-613, CB-839, dihydroorotate dehydrogenase inhibitors, IACS-010759, and mubritinib, have shown encouraging preclinical efficacy and are currently being evaluated in clinical trials. In this review, we summarize recent metabolism-based therapies and their ability to target altered cancer metabolism in AML.
Toker IA, Lev I, Mor Y, Gurevich Y, Fisher D, Houri-Zeevi L, Antonova O, Doron H, Anava S, Gingold H, Hadany L, Shaham S, Rechavi O
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Transgenerational inheritance of sexual attractiveness via small RNAs enhances evolvability in C. elegans

DEVELOPMENTAL CELL 2022 FEB 7; 57(3):298-+
It is unknown whether transient transgenerational epigenetic responses to environmental challenges affect the process of evolution, which typically unfolds over many generations. Here, we show that in C. elegans, inherited small RNAs control genetic variation by regulating the crucial decision of whether to self-fertilize or outcross. We found that under stressful temperatures, younger hermaphrodites secrete a male-attracting pheromone. Attractiveness transmits transgenerationally to unstressed progeny via heritable small RNAs and the Argonaute Heritable RNAi Deficient-1 (HRDE-1). We identified an endogenous small interfering RNA pathway, enriched in endo-siRNAs that target sperm genes, that transgenerationally regulates sexual attraction, male prevalence, and outcrossing rates. Multigenerational mating competition experiments and mathematical simulations revealed that over generations, animals that inherit attractiveness mate more and their alleles spread in the population. We propose that the sperm serves as a "stress-sensor"that, via small RNA inheritance, promotes outcrossing in challenging environments when increasing genetic variation is advantageous.
Shabanan SH, Seyedmirzaei H, Barnea A, Hanaei S, Rezaei N
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Stem cell transplantation as a progressing treatment for retinitis pigmentosa

CELL AND TISSUE RESEARCH 2022 FEB; 387(2):177-205
Retinal degenerative diseases such as retinitis pigmentosa (RP) are of the major causes of vision loss in developed countries. Despite the unclear pathophysiology, treatment methods have been investigated vastly in the past decades. This review article mainly discusses the advances in application of stem cell and progenitor transplantation for retinitis pigmentosa. Stem cell sources such as mesenchymal stem cells, embryonic stem cells, induced pluripotent stem cells, neural stem cells, retinal progenitor cells, and olfactory ensheathing cells are discussed separately in addition to a brief description of two approaches for treatment of early-stage RP, including gene therapy and nutritional therapy.
Park J, Foox J, Hether T, Danko DC, Warren S, Kim Y, Reeves J, Butler DJ, Mozsary C, Rosiene J, Shaiber A, Afshin EE, MacKay M, Rendeiro AF, Bram Y, Chandar V, Geiger H, Craney A, Velu P, Melnick AM, Hajirasouliha I, Beheshti A, Taylor D, Saravia-Butler A, Singh U, Wurtele ES, Schisler J, Fennessey S, Corvelo A, Zody MC, Germer S, Salvatore S, Levy S, Wu SX, Tatonetti NP, Shapira S, Salvatore M, Westblade LF, Cushing M, Rennert H, Kriegel AJ, Elemento O, Imielinski M, Rice CM, Borczuk AC, Meydan C, Schwartz RE, Mason CE
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System-wide transcriptome damage and tissue identity loss in COVID-19 patients

CELL REPORTS MEDICINE 2022 FEB 15; 3(2):? Article 100522
The molecular mechanisms underlying the clinical manifestations of coronavirus disease 2019 (COVID-19), and what distinguishes them from common seasonal influenza virus and other lung injury states such as acute respiratory distress syndrome, remain poorly understood. To address these challenges, we combine transcriptional profiling of 646 clinical nasopharyngeal swabs and 39 patient autopsy tissues to define body wide transcriptome changes in response to COVID-19. We then match these data with spatial protein and expression profiling across 357 tissue sections from 16 representative patient lung samples and identify tissue-compartment-specific damage wrought by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, evident as a function of varying viral loads during the clinical course of infection and tissue-type-specific expression states. Overall, our findings reveal a systemic disruption of canonical cellular and transcriptional pathways across all tissues, which can inform subsequent studies to combat the mortality of COVID-19 and to better understand the molecular dynamics of lethal SARS-CoV-2 and other respiratory infections.
Monaco H, Liu KS, Sereno T, Deforet M, Taylor BP, Chen YY, Reagor CC, Xavier JB
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Spatial-temporal dynamics of a microbial cooperative behavior resistant to cheating

NATURE COMMUNICATIONS 2022 FEB 7; 13(1):? Article 721
Much of our understanding of bacterial behavior stems from studies in liquid culture. In nature, however, bacteria frequently live in densely packed spatially-structured communities. How does spatial structure affect bacterial cooperative behaviors? In this work, we examine rhamnolipid production-a cooperative and virulent behavior of Pseudomonas aeruginosa. Here we show that, in striking contrast to well-mixed liquid culture, rhamnolipid gene expression in spatially-structured colonies is strongly associated with colony specific growth rate, and is impacted by perturbation with diffusible quorum signals. To interpret these findings, we construct a data-driven statistical inference model which captures a length-scale of bacterial interaction that develops over time. Finally, we find that perturbation of P. aeruginosa swarms with quorum signals preserves the cooperating genotype in competition, rather than creating opportunities for cheaters. Overall, our data demonstrate that the complex response to spatial localization is key to preserving bacterial cooperative behaviors. Bacteria often live in densely packed, spatially-structured communities; however, much of our understanding of their behavior stems from studies in liquid culture. Here, Monaco et al. show how spatial structure and quorum sensing modulate a cooperative behavior in colonies of Pseudomonas aeruginosa.
Sahajpal NS, Lai CYJ, Hastie A, Mondal AK, Dehkordi SR, van der Made CI, Fedrigo O, Al-Ajli F, Jalnapurkar S, Byrska-Bishop M, Kanagal-Shamanna R, Levy B, Schieck M, Illig T, Bacanu SA, Chou JS, Randolph AG, Rojiani AM, Zody MC, Brownstein CA, Beggs AH, Bafna V, Jarvis ED, Hoischen A, Chaubey A, Kolhe R
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Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19

ISCIENCE 2022 FEB 18; 25(2):? Article 103760
Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to accurately detect several classes of variants, especially large structural variants (SVs), which account for a substantial proportion of genetic diversity including clinically relevant variation. We performed optical genome mapping on 52 severely ill COVID-19 patients to identify rare/ unique SVs as decisive predisposition factors associated with COVID-19. We identified 7 SVs involving genes implicated in two key host-viral interaction pathways: innate immunity and inflammatory response, and viral replication and spread in nine patients, of which SVs in STK26 and DPP4 genes are the most intriguing candidates. This study is the first to systematically assess the potential role of SVs in the pathogenesis of COVID-19 severity and highlights the need to evaluate SVs along with sequencing variants to comprehensively associate genomic information with interindividual variability in COVID-19 phenotypes.
Bader-Meunier B, Hadchouel A, Berteloot L, Polivka L, Beziat V, Casanova JL, Levy R
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Effectiveness and safety of ruxolitinib for the treatment of refractory systemic idiopathic juvenile arthritis like associated with interstitial lung disease : a case report

Kaczmarek E, Pyman B, Nanayakkara J, Tuschl T, Tyryshkin K, Renwick N, Mousavi P
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Discriminating Neoplastic from Nonneoplastic Tissues Using an miRNA-Based Deep Cancer Classifier

Next-generation sequencing has enabled the collection of large biological data sets, allowing novel molecular-based classification methods to be developed for increased understanding of disease. miRNAs are small regulatory RNA molecules that can be quantified using next-generation sequencing and are excellent classificatory markers. Herein, a deep cancer classifier (DCC) was adapted to differentiate neoplastic from nonneoplastic samples using comprehensive miRNA expression profiles from 1031 human breast and skin tissue samples. The classifier was fine-tuned and evaluated using 750 neoplastic and 281 nonneoplastic breast and skin tissue samples. Performance of the DCC was compared with two machine-learning classifiers: support vector machine and random forests. In addition, performance of feature extraction through the DCC was also compared with a developed feature selection algorithm, cancer specificity. The DCC had the highest performance of area under the receiver operating curve and high performance in both sensitivity and specificity, unlike machine-learning and feature selection models, which often performed well in one metric compared with the other. In particular, deep learning had noticeable advantages with highly heterogeneous data sets. In addition, our cancer specificity algorithm identified candidate biomarkers for differentiating neoplastic and nonneoplastic tissue samples (eg, miR-144 and miR-375 in breast cancer and miR-375 and miR-451 in skin cancer).
Ghosn M, Elsakka AS, Ridouani F, Doustaly R, Mingione L, Royalty K, Ziv E, Alexander E, Maxwell A, Monette S, Kim HS, Short RF, Tam AL, Suh RD, Solomon SB
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Augmented fluoroscopy guided transbronchial pulmonary microwave ablation using a steerable sheath

Background: Transbronchial microwave ablation (MWA) is a promising novel therapy. Despite advances in bronchoscopy and virtual navigation, real time image guidance of probe delivery is lacking, and distal maneuverability is limited. Cone-beam computed tomography (CBCT) based augmented fluoroscopy guidance using steerable sheaths may help overcome these shortcomings. The aim of this study was to evaluate feasibility and accuracy of augmented fluoroscopy guided transbronchial MWA with a steerable sheath and without a bronchoscope. Methods: In this prospective study, procedures were performed under general anesthesia. Extra-bronchial lung synthetic targets were placed percutaneously. Target and airways extracted from CBCT, with planned bronchial parking point close to the target were overlaid on live fluoroscopy. Endobronchial navigation was solely performed under augmented fluoroscopy guidance. A 6.5 Fr steerable sheath was parked in the bronchus per plan, and a flexible MWA probe was inserted coaxially then advanced through the bronchus wall towards the target. Final in-target position was confirmed by CBCT. Only one ablation of 100 W-5 min was performed per target. Animals were euthanized and pathology analysis of the lungs was performed. Results: Eighteen targets with a median largest diameter of 9 mm (interquartile range, 7-11 mm) were ablated in 9 pigs. Median needle-target center distance was 2 mm (interquartile range, 0-4 mm), and was higher for lower/middle than for upper lobes [0 mm (interquartile range, 0-4 mm) vs. 4 mm (interquartile range, 3-8 mm), P=0.04]. No severe complications or pneumothorax occurred. Two cases of rib fractures in the ablation zone resolved after medical treatment. Median longest axis of the ablation zone on post-ablation computed tomography was 38 mm (interquartile range, 30-40 mm). Histology showed coagulation necrosis of ablated tissue. Conclusions: Transbronchial MWA under augmented fluoroscopy guidance using a steerable sheath is feasible and accurate.