RabLab January 2023

highlight

Cell metabolism

Immunoediting instructs tumor metabolic reprogramming to support immune evasion.

2023-01-04

PubMed:36599297; DOI:10.1016/j.cmet.2022.12.003

Chin-Hsien Tsai¹, Yu-Ming Chuang², Xiaoyun Li², Yi-Ru Yu², Sheue-Fen Tzeng¹, Shao Thing Teoh³, Katherine E Lindblad⁴, Mario Di Matteo⁵, Wan-Chen Cheng², Pei-Chun Hsueh², Kung-Chi Kao², Hana Imrichova⁶, Likun Duan⁷, Hector Gallart-Ayala⁸, Pei-Wen Hsiao⁹, Massimiliano Mazzone⁵, Julijana Ivanesevic⁶, Xiaojing Liu⁷, Karin E de Visser¹⁰, Amaia Lujambio⁴, Sophia Y Lunt¹¹, Susan M Kaech¹², Ping-Chih Ho¹³

Affiliations

Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland; Graduate Institute of Life Sciences, National Defense Medical Center, Taipei City, Taiwan
Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Liver Cancer Program, Division of Liver Diseases, Department of Medicine, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences at Icahn School of Medicine at Mount Sinai, New York, NY, USA
Laboratory of Tumor Inflammation and angiogenesis, Vesalius Research Center, VIB, Leuven, Belgium; Laboratory of Tumor Inflammation and angiogenesis, Department of Oncology, KU Leuven, Leuven, Belgium
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Wien, Austria
Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC, USA
Metabolomics Platform, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
Agricultural Biotechnology Research Center, Academia Sinica, Taipei City, Taiwan
Division of Tumor Biology and Immunology, Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA; Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
NOMIS Center for Immunobiology and Microbial Pathogenesis, Salk Institute for Biological Studies, La Jolla, CA, USA
Department of Oncology, University of Lausanne, Lausanne, Switzerland; Ludwig Institute of Cancer Research, University of Lausanne, Lausanne, Switzerland.

CRI Lloyd J. Old STAR Dr. Ping-Chih Ho @PCHo_Lab of @Ludwig_Cancer @OncoUNILCHUV observes that T cell mediated immunosurveillance in early-stage tumorigenesis instructs c-Myc upregulation and metabolic reprogramming in tumor cells. Discover more:

2023-01-05

Happy new year! It is great to see our 7-year work got published today in @Cell_Metabolism ! Thanks for all the support from @Tcellogic and my master study mentor, Pei-Wen.

2023-01-04

Great to see this excellent work is finally out

2023-01-04

Look at this new study from @PCHo_Lab working at @OncoUNILCHUV @Ludwig_Cancer, published in @Cell_Metabolism. It shows for the first time that T-cell-mediated immunosurveillance is guiding metabolic reprogramming in tumour cells.

Read it here: https://doi.org/10.1016/j.cmet.2022.12.003…

2023-01-20

Cool work by @PCHo_Lab “T cell-mediated immunosurveillance in early-stage tumorigenesis instructs c-Myc upregulation and metabolic reprogramming in tumor cells.”

2023-01-04

Nature metabolism

Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency.

2023-01-26

PubMed:36717752; DOI:10.1038/s42255-022-00720-8

Patrick Forny¹, Ximena Bonilla², David Lamparter³, Wenguang Shao⁴, Tanja Plessl¹, Caroline Frei¹, Anna Bingisser¹, Sandra Goetze⁴, Audrey van Drogen⁴, Keith Harshman³, Patrick G A Pedrioli⁴, Cedric Howald³, Martin Poms⁵, Florian Traversi¹, Céline Bürer¹, Sarah Cherkaoui⁶, Raphael J Morscher⁶, Luke Simmons⁷, Merima Forny¹, Ioannis Xenarios⁴, Ruedi Aebersold⁸, Nicola Zamboni⁴, Gunnar Rätsch⁹, Emmanouil T Dermitzakis¹⁰, Bernd Wollscheid¹¹, Matthias R Baumgartner¹², D Sean Froese¹³

Affiliations

Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, University of Zurich, Zurich, Switzerland
Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
Health 2030 Genome Center, Geneva, Switzerland
PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland
Division of Clinical Chemistry, University Children’s Hospital Zurich, University of Zurich, Zurich, Switzerland
Division of Oncology and Children’s Research Center, University Children’s Hospital Zurich, University of Zurich, Zurich, Switzerland
Division of Child Neurology, University Children’s Hospital Zurich, University of Zurich, Zurich, Switzerland
Department of Biology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland
Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology/ETH Zürich, Zurich, Switzerland.
Health 2030 Genome Center, Geneva, Switzerland.
PHRT Swiss Multi-Omics Center, smoc.ethz.ch, Zurich, Switzerland.
Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, University of Zurich, Zurich, Switzerland.
Division of Metabolism and Children’s Research Center, University Children’s Hospital Zurich, University of Zurich, Zurich, Switzerland.

What a tour de force in multi-omic characterisation of #raredisease MMA patient samples to identify novel #metabolomic signature, protein interactors & diagnostic features, from our collaborators @FroeseLab @PatrickForny et al from @KispiZuerich. Many congrats!

2023-01-31

Great work from @KispiZuerich , highlighting the importance of anaplerosis in #organicacidurias !

2023-01-27

Last January, @PatrickForny et al published their study of an important cohort of patients with a #RareDisease.

I made this illustration to show how these patients have an impaired metabolism. The cover wasn’t selected, but you can check out the paper: https://nature.com/articles/s42255-022-00720-8…

2023-03-06

Our new article is out today in @NatMetabolism ! Years in the works we deciphered a cohort of 210 rare metabolic disease patients by #multiomics. Grateful to the whole team at @KispiZuerich @PHRT_CH @ETH_en @UZH_en @FroeseLab !

2023-01-27

Thanks @PatrickForny for sharing this and everyone involved for their amazing contributions. A wonderful example of how clinics and technology can interface to better diagnostics and (future) treatments for rare disease.

2023-01-30

bioRxiv

Glycine homeostasis requires reverse SHMT flux

2023-01-12

DOI:10.1101/2023.01.11.523668

M. J. McBride, C. J. Hunter, J. Rabinowitz

Affiliations

Princeton University

check out this new preprint from Rabinowitz lab! Did you know that the body makes net glycine into serine (rather than the reverse)?

2023-01-17

Excited to share my Rabinowitz lab postdoc work on glycine & serine! Metabolomics & tracing show SHMT is a net consumer (not producer!) of whole-body glycine. Homeostasis is by tuning this consumption to dietary levels without change in de novo synthesis

2023-01-13

Also on my to-read list, the preprint of yesterday’s nice story from ⁦@mcbride_matthew⁩ and Josh Rabinowitz #cmsw23

Glycine homeostasis requires reverse SHMT flux | bioRxiv

2023-05-09

cancer-and-disease

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Cell death & disease

Inhibition of autophagy and MEK promotes ferroptosis in Lkb1-deficient Kras-driven lung tumors.

2023-01-26

PubMed:36702816; DOI:10.1038/s41419-023-05592-8

Vrushank Bhatt¹, Taijin Lan¹, Wenping Wang¹, Jerry Kong¹, Eduardo Cararo Lopes¹, Jianming Wang¹, Khoosheh Khayati¹, Akash Raju¹, Michael Rangel¹, Enrique Lopez¹, Zhixian Sherrie Hu¹, Xuefei Luo¹, Xiaoyang Su¹, Jyoti Malhotra¹, Wenwei Hu¹, Sharon R Pine¹, Eileen White¹, Jessie Yanxiang Guo²

Affiliations

Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA
Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, 08901, USA.

Happy to share our recent publication @ https://nature.com/articles/s41419-023-05592-8… Thanks my lab members @vrushank_bhatt @KhooshehK and collaborators @EileenWhitePhD @CararoLopes et al.

2023-01-29

An amazing work by @YanxiangGuo and @vrushank_bhatt shows how the combination of MEK and autophagy inhibition promotes ferroptosis in Lung Cancer.

2023-01-26

Proteomics

A differential proteomics study of cerebrospinal fluid from individuals with Niemann-Pick disease, Type C1.

2023-01-13

PubMed:36638187; DOI:10.1002/pmic.202200378

Wenping Li¹, Melissa R Pergande¹, Christopher A Crutchfield², Brian C Searle³, Peter S Backlund², Jaqueline A Picache², Kathryn Burkert², Nicole M Yanjanin-Farhat², Paul S Blank², Cynthia L Toth², Christopher A Wassif², Forbes D Porter², Stephanie M Cologna¹

Affiliations

Department of Chemistry, University of Illinois Chicago, Chicago, Illinois, USA
Eunice Kennedy Shriver, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
Department of Biomedical Informatics, The Ohio State University Medical Center, Columbus, Ohio, USA

human-health

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Frontiers in veterinary science

Temporal metabolic profiling of bone healing in a caprine tibia segmental defect model.

2023-01-17

PubMed:36733424; DOI:10.3389/fvets.2022.1023650

Austin J Bow¹, Rebecca E Rifkin¹, Caitlin Priester², Courtney J Christopher³, Remigiusz M Grzeskowiak¹, Silke Hecht⁴, Steve H Adair¹, Pierre-Yves Mulon¹, Hector F Castro³, Shawn R Campagna³, David E Anderson⁵

Affiliations

Department of Large Animal Clinical Sciences, University of Tennessee College of Veterinary Medicine, Knoxville, TN, United States
Department of Animal Science, University of Tennessee, Knoxville, Knoxville, TN, United States
Department of Chemistry, University of Tennessee, Knoxville, Knoxville, TN, United States
Department of Small Animal Clinical Sciences, University of Tennessee College of Veterinary Medicine, Knoxville, TN, United States
University of Tennessee College of Veterinary Medicine, Knoxville, TN, United States

New Research: Temporal metabolic profiling of bone healing in a caprine tibia segmental defect model: Bone tissue engineering is an emerging field of regenerative medicine, with a wide array of biomaterial technologies and therapeutics… https://frontiersin.org/articles/10.3389/fvets.2022.1023650?utm_source=S-TWT&utm_medium=SNET&utm_campaign=ECO_FVETS_XXXXXXXX_auto-dlvrit… #VetScience

2023-01-17

Lab animal

Investigating trajectories of aging using high-dimensional phenotyping in mice.

2023-01-24

PubMed:36693909; DOI:10.1038/s41684-023-01122-3

Michael R MacArthur¹, Sarah J Mitchell²

Affiliations

Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

I like the concept of clinical threshold & “late-onset baseline” model (Fig. 1d). See: Investigating trajectories of #aging using high-dimensional #phenotyping in #mice. By @MikeMacArthur8 & @sarahmitchelphd https://doi.org/10.1038/s41684-023-01122-3…

2023-01-29

bioRxiv

Adaptations to water stress and pastoralism in the Turkana of northwest Kenya

2023-01-19

DOI:10.1101/2023.01.17.524066

A. J. Lea, I. V. Caldas, K. M. Garske, J. Echwa, M. Gurven, C. Handley, J. Kahumbu, J. Kamau, P. Kinyua, F. Lotukoi, A. Lopurudoi, S. Lowasa, R. Mallarino, D. Martins, P. W. Messer, C. Miano, B. Muhoya, J. Peng, T. Phung, J. D. Rabinowitz, A. Roichman, R. Siford, A. Stone, A. M. Taravella-Oill, S. Mathew, M. A. Wilson, J. F. Ayroles

Affiliations

Department of Ecology and Evolutionary Biology, Princeton University

metabolism

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JVS-vascular science

Cystathionine-γ-lyase overexpression modulates oxidized nicotinamide adenine dinucleotide biosynthesis and enhances neovascularization.

2023-01-13

PubMed:36852171; DOI:10.1016/j.jvssci.2022.11.003

Kevin Kiesworo¹, Michael R MacArthur², Peter Kip³, Thomas Agius¹, Diane Macabrey¹, Martine Lambelet¹, Lauriane Hamard⁴, C-Keith Ozaki³, James R Mitchell², Sébastien Déglise¹, Sarah J Mitchell², Florent Allagnat¹, Alban Longchamp¹

Affiliations

Department of Vascular Surgery, Lausanne University Hospital, Lausanne, Switzerland
Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
Department of Surgery and Heart and Vascular Center, Brigham & Women’s Hospital and Harvard Medical School, Boston, MA
Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland

Congrats to @kevinkiesworo and @AlbanLongchamp on a new paper showing beneficial effects of overexpression of the hydrogen sulfide producing enzyme CGL on revascularization. Potential mechanism may be an unexpected link between CGL OE and NAD metabolism.

2023-01-26

metabolic-engineering

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Metabolic engineering

Evaluation of 1,2-diacyl-3-acetyl triacylglycerol production in Yarrowia lipolytica.

2023-01-07

PubMed:36626963; DOI:10.1016/j.ymben.2023.01.003

Qiang Yan¹, Tyler B Jacobson², Zhou Ye³, Yoel R Cortés-Pena⁴, Sarang S Bhagwat⁴, Susan Hubbard¹, William T Cordell¹, Rebecca E Oleniczak¹, Francesca V Gambacorta⁵, Julio Rivera Vazquez⁶, Eric V Shusta⁷, Daniel Amador-Noguez⁸, Jeremy S Guest⁴, Brian F Pfleger⁹

Affiliations

Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; DOE Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA; Department of Civil and Environmental Engineering, University of Illinois Urbana-Champaign, 3221 Newmark Civil Engineering Laboratory, 205 N. Mathews Avenue, Urbana, IL, 61801, USA
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; DOE Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; Department of Neurological Surgery, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; DOE Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation (CABBI), University of Illinois Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA
Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA.

Congrats to Julio Rivera Vazquez and the @theDANlab for their recent collaboration published in Metabolic Engineering!

2023-01-16

Latest from my group – an inter-BRC collaboration led by former @CABBIbio and now DSM researcher Dr. Qiang Yan. Yarrowia lipolytica engineered to produce modified lipids that could be useful as low-grade diesel or lubricants.

2023-01-08

microbes

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FEMS microbiology ecology

Microbial survival mechanisms within serpentinizing Mariana forearc sediments.

2023-01-11

PubMed:36631299; DOI:10.1093/femsec/fiad003

Megan M Mullis¹, Jason D Selwyn¹, Richard Kevorkian², Eric D Tague², Hector F Castro², Shawn R Campagna², Karen G Lloyd², Brandi Kiel Reese³

Affiliations

Life Sciences Department, Texas A&M University – Corpus Christi, Corpus Christi, TX, United States
Microbiology Department, University of Tennessee, Knoxville, TN, United States
Dauphin Island Sea Lab, Mobile, AL, United States

Our latest publication with @archaearama Lab. @CHEMISTRYUTK @UTKMicrobiology @FEMSmicro

2023-01-14

bioRxiv

Listeria monocytogenes requires DHNA-dependent intracellular redox homeostasis facilitated by Ndh2 for survival and virulence

2023-01-14

DOI:10.1101/2023.01.13.524026

H. B. Smith, K. Lee, D. M. Stevenson, D. Amador-Noguez, J.-D. Sauer

Affiliations

University of Wisconsin-Madison

Listeria monocytogenes requires DHNA-dependent intracellular redox homeostasis facilitated by Ndh2 for survival and virulence https://biorxiv.org/cgi/content/short/2023.01.13.524026v1… #bioRxiv

2023-01-15

kedalionlabs.com

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