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Fu J, McKinley B, James B, Chrisler W, Markillie LM, Gaffrey MJ, Mitchell HD, Riaz MR, Marcial B, Orr G, Swaminathan K, Mullet J, Marshall-Colon A. Cell-type-specific transcriptomics uncovers spatial regulatory networks in bioenergy sorghum stems. Plant J 2024. [PMID: 38407828 DOI: 10.1111/tpj.16690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/17/2023] [Accepted: 02/07/2024] [Indexed: 02/27/2024]
Abstract
Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell-type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type-specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type-specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data (https://mc-lab.shinyapps.io/lcm-dataset/).
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Affiliation(s)
- Jie Fu
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA
- DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA
| | - Brandon James
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - William Chrisler
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | | | - Matthew J Gaffrey
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Hugh D Mitchell
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Muhammad Rizwan Riaz
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
| | - Brenda Marcial
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - Galya Orr
- Pacific Northwest National Laboratory, Richland, Washington, 99354, USA
| | - Kankshita Swaminathan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, 35806, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, 77843, USA
- DOE Great Lakes Bioenergy Resource Center, Madison, Wisconsin, 53726, USA
| | - Amy Marshall-Colon
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois, 61801, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, Illinois, 61801, USA
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Zemaitis KJ, Fulcher JM, Kumar R, Degnan DJ, Lewis LA, Liao YC, Veličković M, Williams SM, Moore RJ, Bramer LM, Veličković D, Zhu Y, Zhou M, Paša-Tolić L. Spatial top-down proteomics for the functional characterization of human kidney. bioRxiv 2024:2024.02.13.580062. [PMID: 38405958 PMCID: PMC10888776 DOI: 10.1101/2024.02.13.580062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Background The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.
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Affiliation(s)
- Kevin J Zemaitis
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - James M Fulcher
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Rashmi Kumar
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - David J Degnan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Logan A Lewis
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Yen-Chen Liao
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Marija Veličković
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Sarah M Williams
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ronald J Moore
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Lisa M Bramer
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Dušan Veličković
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ying Zhu
- Department of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, 1 DNA Way, San Francisco, CA 94080, United States
| | - Mowei Zhou
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental and Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, United States
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Navrazhina K, Garcet S, Williams SC, Gulati N, Kiecker F, Frew JW, Mitsui H, Krueger JG. Laser capture microdissection provides a novel molecular profile of human primary cutaneous melanoma. Pigment Cell Melanoma Res 2024; 37:81-89. [PMID: 37776566 PMCID: PMC10841058 DOI: 10.1111/pcmr.13121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 10/02/2023]
Abstract
Melanoma accounts for the majority of skin cancer-related mortality, highlighting the need to better understand melanoma initiation and progression. In-depth molecular analysis of neoplastic melanocytes in whole tissue biopsies may be diluted by inflammatory infiltration, which may obscure gene signatures specific to neoplastic cells. Thus, a method is needed to precisely uncover molecular changes specific to tumor cells from a limited sample of primary melanomas. Here, we performed laser capture microdissection (LCM) and gene expression profiling of patient-derived frozen sections of pigmented lesions and primary cutaneous melanoma. Compared to bulk tissue analysis, analysis of LCM-derived samples identified 9528 additional differentially expressed genes (DEGs) including melanocyte-specific genes like PMEL and TYR, with enriched of pathways related to cell proliferation. LCM methodology also identified potentially targetable kinases specific to melanoma cells that were not detected by bulk tissue analysis. Taken together, our data demonstrate that there are marked differences in gene expression profiles depending on the method of sample isolation. We found that LCM captured higher expression of melanoma-related genes while whole tissue biopsy identified a wider range of inflammatory markers. Taken together, our data demonstrate that LCM is a valid approach to identify melanoma-specific changes using a relatively small amount of primary patient-derived melanoma sample.
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Affiliation(s)
- Kristina Navrazhina
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY
| | - Sandra Garcet
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Samuel C. Williams
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD program, New York, NY
| | - Nicholas Gulati
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Department of Dermatology, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Felix Kiecker
- Department of Dermatology and Allergy, Skin Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - John W. Frew
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
| | - Hiroshi Mitsui
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
- Department of Dermatology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - James G. Krueger
- Laboratory of Investigative Dermatology, The Rockefeller University, New York, NY, USA
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Das S, Li Z, Wachter A, Alla S, Noori A, Abdourahman A, Tamm JA, Woodbury ME, Talanian RV, Biber K, Karran EH, Hyman BT, Serrano‐Pozo A. Distinct transcriptomic responses to Aβ plaques, neurofibrillary tangles, and APOE in Alzheimer's disease. Alzheimers Dement 2024; 20:74-90. [PMID: 37461318 PMCID: PMC10792109 DOI: 10.1002/alz.13387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/07/2023] [Accepted: 06/11/2023] [Indexed: 07/28/2023]
Abstract
INTRODUCTION Omics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimer's disease (AD) but the spatial relationships with plaques and tangles and APOE-linked differences remain unclear. METHODS We performed laser capture microdissection of amyloid beta (Aβ) plaques, the 50 μm halo around them, tangles with the 50 μm halo around them, and areas distant (> 50 μm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing. RESULTS Aβ plaques exhibited upregulated microglial (neuroinflammation/phagocytosis) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. Aβ plaques had more differentially expressed genes than tangles. We identified a gradient Aβ plaque > peri-plaque > tangle > distant for these changes. AD APOE ε4 homozygotes had greater changes than APOE ε3 across locations, especially within Aβ plaques. DISCUSSION Transcriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with Aβ plaques, and are exacerbated by the APOE ε4 allele.
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Affiliation(s)
- Sudeshna Das
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Massachusetts Alzheimer's Disease Research CenterCharlestownMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Zhaozhi Li
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Massachusetts Alzheimer's Disease Research CenterCharlestownMassachusettsUSA
| | - Astrid Wachter
- AbbVie Deutschland GmbH & Co. KGGenomics Research CenterLudwigshafenGermany
| | - Srinija Alla
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
| | - Ayush Noori
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
| | | | - Joseph A. Tamm
- AbbVie, Cambridge Research CenterCambridgeMassachusettsUSA
| | | | | | - Knut Biber
- AbbVie Deutschland GmbH & Co. KGNeuroscience Research CenterLudwigshafenGermany
| | - Eric H. Karran
- AbbVie, Cambridge Research CenterCambridgeMassachusettsUSA
| | - Bradley T. Hyman
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Massachusetts Alzheimer's Disease Research CenterCharlestownMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
| | - Alberto Serrano‐Pozo
- Neurology DepartmentMassachusetts General HospitalBostonMassachusettsUSA
- Massachusetts Alzheimer's Disease Research CenterCharlestownMassachusettsUSA
- Harvard Medical SchoolBostonMassachusettsUSA
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5
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Lu C, Luo ZF, Tang D, Zheng F, Li S, Liu S, Qiu J, Liu F, Dai Y, Sui WG, Yan Q. Proteomic analysis of glomeruli, tubules and renal interstitium in idiopathic membranous nephropathy (IMN): A statistically observational study. Medicine (Baltimore) 2023; 102:e36476. [PMID: 38115247 PMCID: PMC10727647 DOI: 10.1097/md.0000000000036476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 10/03/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
Idiopathic membranous nephropathy (IMN) is a common type of primary glomerulonephritis, which pathogenesis are highly involved protein and immune regulation. Therefore, we investigated protein expression in different microregions of the IMN kidney tissue. We used laser capture microdissection and mass spectrometry to identify the proteins in the kidney tissue. Using MSstats software to identify the differently expressed protein (DEP). Gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used to predict and enrich the potential functions of the DEPs, and DEPs were compared to the Public data in the gene expression omnibus (GEO) database for screening biomarkers of IMN. Immune infiltration analysis was used to analyze the immune proportion in IMN. Three significantly up-regulated proteins were identified in the glomeruli of patients with IMN; 9 significantly up-regulated and 6 significantly down-regulated proteins were identified in the interstitium of patients with IMN. Gene ontology analysis showed that the DEPs in the glomerulus and interstitium were mostly enriched in "biological regulation, the immune system, and metabolic processes." Kyoto Encyclopedia of Genes and Genomes analysis showed that the DEPs in the glomerulus and interstitium were mostly enriched in the "immune system" and the "complement and coagulation cascades. " According to the public information of the GEO database, DEPs in our study, Coatomer subunit delta Archain 1, Laminin subunit alpha-5, and Galectin-1 were highly expressed in the IMN samples from the GEO database; in the immune infiltration analysis, the proportion of resting memory CD4 T cells and activated NK cells in IMN were significantly higher than in the normal group. This study confirmed that there were significant differences in protein expression in different micro-regions of patients with IMN, The protein Coatomer subunit delta Archain 1, Laminin subunit alpha 5, Galectin-1 are potential biomarkers of IMN, the memory T cells CD4 and NK cells, maybe involved in the immunologic mechanism in the development of IMN.
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Affiliation(s)
- Chang Lu
- The Organ Transplantation Department of No.924 Hospital of PLA Joint Logistic Support Force, Medical quality specialty of the Joint Logistic Support Force, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi, P.R. China
| | - Zhi-Feng Luo
- The Organ Transplantation Department of No.924 Hospital of PLA Joint Logistic Support Force, Medical quality specialty of the Joint Logistic Support Force, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi, P.R. China
- The Second Department of Urology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, P.R. China
| | - Donge Tang
- The Organ Transplantation Department of No.924 Hospital of PLA Joint Logistic Support Force, Medical quality specialty of the Joint Logistic Support Force, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi, P.R. China
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, P.R. China
| | - Fengping Zheng
- The Organ Transplantation Department of No.924 Hospital of PLA Joint Logistic Support Force, Medical quality specialty of the Joint Logistic Support Force, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi, P.R. China
| | - Shanshan Li
- The Organ Transplantation Department of No.924 Hospital of PLA Joint Logistic Support Force, Medical quality specialty of the Joint Logistic Support Force, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi, P.R. China
| | - Shizhen Liu
- Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, P.R. China
| | - Jing Qiu
- The Organ Transplantation Department of No.924 Hospital of PLA Joint Logistic Support Force, Medical quality specialty of the Joint Logistic Support Force, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi, P.R. China
| | - Fanna Liu
- Institute of Nephrology and Blood Purification, the First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, P.R. China
| | - Yong Dai
- The Organ Transplantation Department of No.924 Hospital of PLA Joint Logistic Support Force, Medical quality specialty of the Joint Logistic Support Force, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, Guangxi, P.R. China
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, P.R. China
| | - Wei-Guo Sui
- The Second Department of Urology, Affiliated Hospital of Guilin Medical University, Guilin, Guangxi, P.R. China
| | - Qiang Yan
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, P.R. China
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Paul ED, Huraiová B, Valková N, Birknerova N, Gábrišová D, Gubova S, Ignačáková H, Ondris T, Bendíková S, Bíla J, Buranovská K, Drobná D, Krchnakova Z, Kryvokhyzha M, Lovíšek D, Mamoilyk V, Mančíková V, Vojtaššáková N, Ristová M, Comino-Méndez I, Andrašina I, Morozov P, Tuschl T, Pareja F, Čekan P. Multiplexed RNA-FISH-guided Laser Capture Microdissection RNA Sequencing Improves Breast Cancer Molecular Subtyping, Prognostic Classification, and Predicts Response to Antibody Drug Conjugates. medRxiv 2023:2023.12.05.23299341. [PMID: 38105959 PMCID: PMC10723508 DOI: 10.1101/2023.12.05.23299341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
On a retrospective cohort of 1,082 FFPE breast tumors, we demonstrated the analytical validity of a test using multiplexed RNA-FISH-guided laser capture microdissection (LCM) coupled with RNA-sequencing (mFISHseq), which showed 93% accuracy compared to immunohistochemistry. The combination of these technologies makes strides in i) precisely assessing tumor heterogeneity, ii) obtaining pure tumor samples using LCM to ensure accurate biomarker expression and multigene testing, and iii) providing thorough and granular data from whole transcriptome profiling. We also constructed a 293-gene intrinsic subtype classifier that performed equivalent to the research based PAM50 and AIMS classifiers. By combining three molecular classifiers for consensus subtyping, mFISHseq alleviated single sample discordance, provided near perfect concordance with other classifiers (κ > 0.85), and reclassified 30% of samples into different subtypes with prognostic implications. We also use a consensus approach to combine information from 4 multigene prognostic classifiers and clinical risk to characterize high, low, and ultra-low risk patients that relapse early (< 5 years), late (> 10 years), and rarely, respectively. Lastly, to identify potential patient subpopulations that may be responsive to treatments like antibody drug-conjugates (ADC), we curated a list of 92 genes and 110 gene signatures to interrogate their association with molecular subtype and overall survival. Many genes and gene signatures related to ADC processing (e.g., antigen/payload targets, endocytosis, and lysosome activity) were independent predictors of overall survival in multivariate Cox regression models, thus highlighting potential ADC treatment-responsive subgroups. To test this hypothesis, we constructed a unique 19-feature classifier using multivariate logistic regression with elastic net that predicted response to trastuzumab emtansine (T-DM1; AUC = 0.96) better than either ERBB2 mRNA or Her2 IHC alone in the T-DM1 arm of the I-SPY2 trial. This test was deployed in a research-use only format on 26 patients and revealed clinical insights into patient selection for novel therapies like ADCs and immunotherapies and de-escalation of adjuvant chemotherapy.
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Affiliation(s)
- Evan D. Paul
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Barbora Huraiová
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Natália Valková
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
- Institute of Clinical Biochemistry and Diagnostics, University Hospital, Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czech Republic
| | - Natalia Birknerova
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Daniela Gábrišová
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Sona Gubova
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Helena Ignačáková
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Tomáš Ondris
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Silvia Bendíková
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Jarmila Bíla
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Katarína Buranovská
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Diana Drobná
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Zuzana Krchnakova
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Maryna Kryvokhyzha
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Daniel Lovíšek
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Viktoriia Mamoilyk
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Veronika Mančíková
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Nina Vojtaššáková
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
| | - Michaela Ristová
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, Scotland, UK
| | - Iñaki Comino-Méndez
- Unidad de Gestión Clínica Intercentros de Oncología Medica, Hospitales Universitarios Regional y Virgen de la Victoria. The Biomedical Research Institute of Málaga (IBIMA-CIMES-UMA), Málaga, Spain
| | - Igor Andrašina
- Department of Radiotherapy and Oncology, East Slovakia Institute of Oncology, Košice, Slovakia
| | - Pavel Morozov
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York NY, USA
| | - Thomas Tuschl
- Laboratory for RNA Molecular Biology, The Rockefeller University, New York NY, USA
| | - Fresia Pareja
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pavol Čekan
- MultiplexDX, s.r.o., Comenius University Science Park, Bratislava, Slovakia
- MultiplexDX, Inc., Rockville, MD, USA
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7
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Schnabel E, Thomas J, El-Hawaz R, Gao Y, Poehlman WL, Chavan S, Pasha A, Esteban E, Provart N, Feltus FA, Frugoli J. Laser Capture Microdissection Transcriptome Reveals Spatiotemporal Tissue Gene Expression Patterns of Medicago truncatula Roots Responding to Rhizobia. Mol Plant Microbe Interact 2023; 36:805-820. [PMID: 37717250 DOI: 10.1094/mpmi-03-23-0029-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
We report a public resource for examining the spatiotemporal RNA expression of 54,893 Medicago truncatula genes during the first 72 h of response to rhizobial inoculation. Using a methodology that allows synchronous inoculation and growth of more than 100 plants in a single media container, we harvested the same segment of each root responding to rhizobia in the initial inoculation over a time course, collected individual tissues from these segments with laser capture microdissection, and created and sequenced RNA libraries generated from these tissues. We demonstrate the utility of the resource by examining the expression patterns of a set of genes induced very early in nodule signaling, as well as two gene families (CLE peptides and nodule specific PLAT-domain proteins) and show that despite similar whole-root expression patterns, there are tissue differences in expression between the genes. Using a rhizobial response dataset generated from transcriptomics on intact root segments, we also examined differential temporal expression patterns and determined that, after nodule tissue, the epidermis and cortical cells contained the most temporally patterned genes. We circumscribed gene lists for each time and tissue examined and developed an expression pattern visualization tool. Finally, we explored transcriptomic differences between the inner cortical cells that become nodules and those that do not, confirming that the expression of 1-aminocyclopropane-1-carboxylate synthases distinguishes inner cortical cells that become nodules and provide and describe potential downstream genes involved in early nodule cell division. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Elise Schnabel
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Jacklyn Thomas
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Rabia El-Hawaz
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - Yueyao Gao
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
| | - William L Poehlman
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Sage Bionetworks, Seattle, WA 98121, U.S.A
| | - Suchitra Chavan
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Leidos, Inc., Atlanta, GA 30345, U.S.A
| | - Asher Pasha
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Eddi Esteban
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - Nicholas Provart
- Department of Cell and Systems Biology, University of Toronto, ON M5S 3B2, Canada
| | - F Alex Feltus
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
- Biomedical Data Science and Informatics Program, Clemson University, Clemson, SC 29634, U.S.A
- Clemson Center for Human Genetics, Clemson University, Greenwood, SC 29636, U.S.A
| | - Julia Frugoli
- Department of Genetics & Biochemistry, Clemson University, Clemson, SC 29634, U.S.A
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8
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Carraro C, Bonaguro L, Srinivasa R, van Uelft M, Isakzai V, Schulte-Schrepping J, Gambhir P, Elmzzahi T, Montgomery JV, Hayer H, Li Y, Theis H, Kraut M, Mahbubani KT, Aschenbrenner AC, König I, Fava E, Fried HU, De Domenico E, Beyer M, Saglam A, Schultze JL. Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq. Cell Rep Methods 2023; 3:100598. [PMID: 37776856 PMCID: PMC10626193 DOI: 10.1016/j.crmeth.2023.100598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/04/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
Spatially resolved omics technologies reveal context-dependent cellular regulatory networks in tissues of interest. Beyond transcriptome analysis, information on epigenetic traits and chromatin accessibility can provide further insights on gene regulation in health and disease. Nevertheless, compared to the enormous advancements in spatial transcriptomics technologies, the field of spatial epigenomics is much younger and still underexplored. In this study, we report laser capture microdissection coupled to ATAC-seq (LCM-ATAC-seq) applied to fresh frozen samples for the spatial characterization of chromatin accessibility. We first demonstrate the efficient use of LCM coupled to in situ tagmentation and evaluate its performance as a function of cell number, microdissected areas, and tissue type. Further, we demonstrate its use for the targeted chromatin accessibility analysis of discrete contiguous or scattered cell populations in tissues via single-nuclei capture based on immunostaining for specific cellular markers.
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Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Rachana Srinivasa
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Victoria Isakzai
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Prerna Gambhir
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tarek Elmzzahi
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Jessica V Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hannah Hayer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Yuanfang Li
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Ireen König
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Eugenio Fava
- Core Research Facilities and Services, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hans-Ulrich Fried
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Marc Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany.
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
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Delaleu N, Marti HP, Strauss P, Sekulic M, Osman T, Tøndel C, Skrunes R, Leh S, Svarstad E, Nowak A, Gaspert A, Rusu E, Kwee I, Rinaldi A, Flatberg A, Eikrem O. Systems analyses of the Fabry kidney transcriptome and its response to enzyme replacement therapy identified and cross-validated enzyme replacement therapy-resistant targets amenable to drug repurposing. Kidney Int 2023; 104:803-819. [PMID: 37419447 DOI: 10.1016/j.kint.2023.06.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 05/19/2023] [Accepted: 06/22/2023] [Indexed: 07/09/2023]
Abstract
Fabry disease is a rare disorder caused by variations in the alpha-galactosidase gene. To a degree, Fabry disease is manageable via enzyme replacement therapy (ERT). By understanding the molecular basis of Fabry nephropathy (FN) and ERT's long-term impact, here we aimed to provide a framework for selection of potential disease biomarkers and drug targets. We obtained biopsies from eight control individuals and two independent FN cohorts comprising 16 individuals taken prior to and after up to ten years of ERT, and performed RNAseq analysis. Combining pathway-centered analyses with network-science allowed computation of transcriptional landscapes from four nephron compartments and their integration with existing proteome and drug-target interactome data. Comparing these transcriptional landscapes revealed high inter-cohort heterogeneity. Kidney compartment transcriptional landscapes comprehensively reflected differences in FN cohort characteristics. With exception of a few aspects, in particular arteries, early ERT in patients with classical Fabry could lastingly revert FN gene expression patterns to closely match that of control individuals. Pathways nonetheless consistently altered in both FN cohorts pre-ERT were mostly in glomeruli and arteries and related to the same biological themes. While keratinization-related processes in glomeruli were sensitive to ERT, a majority of alterations, such as transporter activity and responses to stimuli, remained dysregulated or reemerged despite ERT. Inferring an ERT-resistant genetic module of expressed genes identified 69 drugs for potential repurposing matching the proteins encoded by 12 genes. Thus, we identified and cross-validated ERT-resistant gene product modules that, when leveraged with external data, allowed estimating their suitability as biomarkers to potentially track disease course or treatment efficacy and potential targets for adjunct pharmaceutical treatment.
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Affiliation(s)
- Nicolas Delaleu
- 2cSysBioMed, Contra, Switzerland; Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Hans-Peter Marti
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Philipp Strauss
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Miroslav Sekulic
- Department of Pathology and Cell Biology, Columbia University, New York, New York, USA
| | - Tarig Osman
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Camilla Tøndel
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Pediatrics, Haukeland University Hospital, Bergen, Norway
| | - Rannveig Skrunes
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Einar Svarstad
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Albina Nowak
- Department of Endocrinology and Clinical Nutrition, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Ariana Gaspert
- Department of Pathology and Molecular Pathology, University Hospital Zurich, Zurich, Switzerland
| | - Elena Rusu
- Department of Nephrology, Fundeni Clinical Institute, Bucharest, Romania; Department of Nephrology, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Ivo Kwee
- BigOmics Analytics, Lugano, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Arnar Flatberg
- Central Administration, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway; Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Oystein Eikrem
- Department of Clinical Medicine, University of Bergen, Bergen, Norway; Department of Medicine, Haukeland University Hospital, Bergen, Norway.
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Zhou J, Lin L, Liu L, Wang J, Xia G, Wang C. The transcriptome reveals the molecular regulatory network of primordial follicle depletion in obese mice. Fertil Steril 2023; 120:899-910. [PMID: 37247688 DOI: 10.1016/j.fertnstert.2023.05.165] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To explore the dynamic transcriptional regulatory network of primordial follicle fate in obese mice to elucidate the potential mechanism of primordial follicle depletion. DESIGN Experimental study and transcriptomic analysis. ANIMALS Healthy (n=15) and obese (n=15) female mice. INTERVENTIONS Six-week-old CD-1 mice were divided into healthy and high-fat diet groups and fed continuously for 12 weeks. The diet of healthy mice contained 10% fat. The diet of high-fat mice contained 60% fat. MAIN OUTCOME MEASURES Primordial to primary follicle transition rate, gene expression changes, enriched Kyoto Encyclopedia of Genes and Genomes pathways, and ferroptosis. RESULTS Primordial follicle depletion was increased in the ovaries of obese mice. We found that deposited fat around primordial and primary follicles of obese mice was higher than that for healthy mice. The proliferation of granulosa cells around primary follicles was increased in obese mice. In addition, we uncovered specific gene signatures associated with the primordial to primary follicle transition (PPT) in obese mice using laser capture microdissection RNA sequencing analysis. Gene set enrichment analysis indicated that ferroptosis, cell oxidation, vascular endothelial growth factor, and mammalian target of rapamycin signaling were increased significantly in the primordial follicles of obese mice. Notably, the ferritin, acyl CoA synthetase long-chain family member 4, and solid carrier family 7 member 11 associated proteins of the ferroptosis signaling pathway were significantly increased in the PPT phase of obese mice. CONCLUSION Our work suggests that ferroptosis is a key pathway activated within immature ovarian follicles in the context of obesity and that the process may be involved in the physiological regulation of the PPT as well.
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Affiliation(s)
- Jiaqi Zhou
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Lin Lin
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China
| | - Longping Liu
- School of Life Sciences and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Jianbin Wang
- School of Life Sciences and Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Guoliang Xia
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China; Key Laboratory of Ministry of Education for Conservation and Utilization of Special Biological Resources in Western China, College of Life Science, Ningxia University, People's Republic of China
| | - Chao Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, People's Republic of China.
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11
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Lu L, Yang H, Xu Y, Zhang L, Wu J, Yi H. Laser capture microdissection-based spatiotemporal transcriptomes uncover regulatory networks during seed abortion in seedless Ponkan (Citrus reticulata). Plant J 2023; 115:642-661. [PMID: 37077034 DOI: 10.1111/tpj.16251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 05/03/2023]
Abstract
Seed abortion is an important process in the formation of seedless characteristics in citrus fruits. However, the molecular regulatory mechanism underlying citrus seed abortion is poorly understood. Laser capture microdissection-based RNA-seq combined with Pacbio-seq was used to profile seed development in the Ponkan cultivars 'Huagan No. 4' (seedless Ponkan) (Citrus reticulata) and 'E'gan No. 1' (seeded Ponkan) (C. reticulata) in two types of seed tissue across three developmental stages. Through comparative transcriptome and dynamic phytohormone analyses, plant hormone signal, cell division and nutrient metabolism-related processes were revealed to play critical roles in the seed abortion of 'Huagan No. 4'. Moreover, several genes may play indispensable roles in seed abortion of 'Huagan No. 4', such as CrWRKY74, CrWRKY48 and CrMYB3R4. Overexpression of CrWRKY74 in Arabidopsis resulted in severe seed abortion. By analyzing the downstream regulatory network, we further determined that CrWRKY74 participated in seed abortion regulation by inducing abnormal programmed cell death. Of particular importance is that a preliminary model was proposed to depict the regulatory networks underlying seed abortion in citrus. The results of this study provide novel insights into the molecular mechanism across citrus seed development, and reveal the master role of CrWRKY74 in seed abortion of 'Huagan No. 4'.
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Affiliation(s)
- Liqing Lu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Haijian Yang
- Fruit Tree Research Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, P.R. China
| | - Yanhui Xu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Li Zhang
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Juxun Wu
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
| | - Hualin Yi
- National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, P.R. China
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12
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Leitner DF, Kanshin E, Faustin A, Thierry M, Friedman D, Devore S, Ueberheide B, Devinsky O, Wisniewski T. Localized proteomic differences in the choroid plexus of Alzheimer's disease and epilepsy patients. Front Neurol 2023; 14:1221775. [PMID: 37521285 PMCID: PMC10379643 DOI: 10.3389/fneur.2023.1221775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Alzheimer's disease (AD) and epilepsy are reciprocally related. Among sporadic AD patients, clinical seizures occur in 10-22% and subclinical epileptiform abnormalities occur in 22-54%. Cognitive deficits, especially short-term memory impairments, occur in most epilepsy patients. Common neurophysiological and molecular mechanisms occur in AD and epilepsy. The choroid plexus undergoes pathological changes in aging, AD, and epilepsy, including decreased CSF turnover, amyloid beta (Aβ), and tau accumulation due to impaired clearance and disrupted CSF amino acid homeostasis. This pathology may contribute to synaptic dysfunction in AD and epilepsy. Methods We evaluated control (n = 8), severe AD (n = 8; A3, B3, C3 neuropathology), and epilepsy autopsy cases (n = 12) using laser capture microdissection (LCM) followed by label-free quantitative mass spectrometry on the choroid plexus adjacent to the hippocampus at the lateral geniculate nucleus level. Results Proteomics identified 2,459 proteins in the choroid plexus. At a 5% false discovery rate (FDR), 616 proteins were differentially expressed in AD vs. control, 1 protein in epilepsy vs. control, and 438 proteins in AD vs. epilepsy. There was more variability in the epilepsy group across syndromes. The top 20 signaling pathways associated with differentially expressed proteins in AD vs. control included cell metabolism pathways; activated fatty acid beta-oxidation (p = 2.00 x 10-7, z = 3.00), and inhibited glycolysis (p = 1.00 x 10-12, z = -3.46). For AD vs. epilepsy, the altered pathways included cell metabolism pathways, activated complement system (p = 5.62 x 10-5, z = 2.00), and pathogen-induced cytokine storm (p = 2.19 x 10-2, z = 3.61). Of the 617 altered proteins in AD and epilepsy vs. controls, 497 (81%) were positively correlated (p < 0.0001, R2 = 0.27). Discussion We found altered signaling pathways in the choroid plexus of severe AD cases and many correlated changes in the protein expression of cell metabolism pathways in AD and epilepsy cases. The shared molecular mechanisms should be investigated further to distinguish primary pathogenic changes from the secondary ones. These mechanisms could inform novel therapeutic strategies to prevent disease progression or restore normal function. A focus on dual-diagnosed AD/epilepsy cases, specific epilepsy syndromes, such as temporal lobe epilepsy, and changes across different severity levels in AD and epilepsy would add to our understanding.
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Affiliation(s)
- Dominique F. Leitner
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, United States
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Evgeny Kanshin
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, United States
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, United States
| | - Arline Faustin
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
| | - Manon Thierry
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Daniel Friedman
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Sasha Devore
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Beatrix Ueberheide
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University Grossman School of Medicine, New York, NY, United States
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, United States
| | - Orrin Devinsky
- Comprehensive Epilepsy Center, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
| | - Thomas Wisniewski
- Center for Cognitive Neurology, Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Neurology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Pathology, New York University Grossman School of Medicine, New York, NY, United States
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, United States
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13
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Chavan S, Schnabel E, Saski C, Frugoli J. Fixation and Laser Capture Microdissection of Plant Tissue for RNA Extraction and RNASeq Library Preparation. Curr Protoc 2023; 3:e844. [PMID: 37486164 DOI: 10.1002/cpz1.844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
To study the transcriptome of individual plant cells at specific points in time, we developed protocols for fixation, embedding, and sectioning of plant tissue followed by laser capture microdissection (LCM) and processing for RNA recovery. LCM allows the isolation of individual cell types from heterogeneous tissue sections and is particularly suited to plant processing because it does not require the breakdown of cell walls. This approach allows accurate separation of a small volume of cells that can be used to study gene expression profiles in different tissues or cell layers. The technique requires neither separation of cells by enzymatic digestion of any kind nor cell-specific reporter genes, and it allows storage of fixed and embedded tissue for months before capture. The methods for fixation, embedding, sectioning, and capturing of plant cells that we describe yield high-quality RNA suitable for making libraries for RNASeq. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Tissue Preparation for Laser Capture Microdissection Basic Protocol 2: Tissue Sectioning Basic Protocol 3: Laser Capture Microdissection of Embedded Tissue Basic Protocol 4: RNA Extraction from Laser Capture Microdissection Samples.
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Affiliation(s)
- Suchitra Chavan
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Elise Schnabel
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
| | - Christopher Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina
| | - Julia Frugoli
- Department of Genetics and Biochemistry, Clemson University, Clemson, South Carolina
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14
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Guise AJ, Misal SA, Carson R, Boekweg H, Watt DVD, Truong T, Liang Y, Chu JH, Welsh NC, Gagnon J, Payne SH, Plowey ED, Kelly RT. TDP-43-stratified single-cell proteomic profiling of postmortem human spinal motor neurons reveals protein dynamics in amyotrophic lateral sclerosis. bioRxiv 2023:2023.06.08.544233. [PMID: 37333094 PMCID: PMC10274884 DOI: 10.1101/2023.06.08.544233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Unbiased proteomics has been employed to interrogate central nervous system (CNS) tissues (brain, spinal cord) and fluid matrices (CSF, plasma) from amyotrophic lateral sclerosis (ALS) patients; yet, a limitation of conventional bulk tissue studies is that motor neuron (MN) proteome signals may be confounded by admixed non-MN proteins. Recent advances in trace sample proteomics have enabled quantitative protein abundance datasets from single human MNs (Cong et al., 2020b). In this study, we leveraged laser capture microdissection (LCM) and nanoPOTS (Zhu et al., 2018c) single-cell mass spectrometry (MS)-based proteomics to query changes in protein expression in single MNs from postmortem ALS and control donor spinal cord tissues, leading to the identification of 2515 proteins across MNs samples (>900 per single MN) and quantitative comparison of 1870 proteins between disease groups. Furthermore, we studied the impact of enriching/stratifying MN proteome samples based on the presence and extent of immunoreactive, cytoplasmic TDP-43 inclusions, allowing identification of 3368 proteins across MNs samples and profiling of 2238 proteins across TDP-43 strata. We found extensive overlap in differential protein abundance profiles between MNs with or without obvious TDP-43 cytoplasmic inclusions that together point to early and sustained dysregulation of oxidative phosphorylation, mRNA splicing and translation, and retromer-mediated vesicular transport in ALS. Our data are the first unbiased quantification of single MN protein abundance changes associated with TDP-43 proteinopathy and begin to demonstrate the utility of pathology-stratified trace sample proteomics for understanding single-cell protein abundance changes in human neurologic diseases.
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Affiliation(s)
| | - Santosh A. Misal
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Richard Carson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Hannah Boekweg
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | - Thy Truong
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | | | | | | | - Samuel H. Payne
- Biology Department, Brigham Young University, Provo, UT 84602, USA
| | | | - Ryan T. Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
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15
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Alldred MJ, Pidikiti H, Heguy A, Roussos P, Ginsberg SD. Basal forebrain cholinergic neurons are vulnerable in a mouse model of Down syndrome and their molecular fingerprint is rescued by maternal choline supplementation. FASEB J 2023; 37:e22944. [PMID: 37191946 PMCID: PMC10292934 DOI: 10.1096/fj.202202111rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023]
Abstract
Basal forebrain cholinergic neuron (BFCN) degeneration is a hallmark of Down syndrome (DS) and Alzheimer's disease (AD). Current therapeutics in these disorders have been unsuccessful in slowing disease progression, likely due to poorly understood complex pathological interactions and dysregulated pathways. The Ts65Dn trisomic mouse model recapitulates both cognitive and morphological deficits of DS and AD, including BFCN degeneration and has shown lifelong behavioral changes due to maternal choline supplementation (MCS). To test the impact of MCS on trisomic BFCNs, we performed laser capture microdissection to individually isolate choline acetyltransferase-immunopositive neurons in Ts65Dn and disomic littermates, in conjunction with MCS at the onset of BFCN degeneration. We utilized single population RNA sequencing (RNA-seq) to interrogate transcriptomic changes within medial septal nucleus (MSN) BFCNs. Leveraging multiple bioinformatic analysis programs on differentially expressed genes (DEGs) by genotype and diet, we identified key canonical pathways and altered physiological functions within Ts65Dn MSN BFCNs, which were attenuated by MCS in trisomic offspring, including the cholinergic, glutamatergic and GABAergic pathways. We linked differential gene expression bioinformatically to multiple neurological functions, including motor dysfunction/movement disorder, early onset neurological disease, ataxia and cognitive impairment via Ingenuity Pathway Analysis. DEGs within these identified pathways may underlie aberrant behavior in the DS mice, with MCS attenuating the underlying gene expression changes. We propose MCS ameliorates aberrant BFCN gene expression within the septohippocampal circuit of trisomic mice through normalization of principally the cholinergic, glutamatergic, and GABAergic signaling pathways, resulting in attenuation of underlying neurological disease functions.
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Affiliation(s)
- Melissa J. Alldred
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
| | - Harshitha Pidikiti
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, USA
| | - Adriana Heguy
- Genome Technology Center, New York University Grossman School of Medicine, New York, NY, USA
| | - Panos Roussos
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, USA
- Departments of Genetics and Genomic Sciences and Psychiatry and the Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Stephen D. Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY, USA
- Departments of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY, USA
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16
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Alldred MJ, Ginsberg SD. Microisolation of Spatially Characterized Single Populations of Neurons for RNA Sequencing from Mouse and Postmortem Human Brain Tissues. J Clin Med 2023; 12:3304. [PMID: 37176744 PMCID: PMC10179294 DOI: 10.3390/jcm12093304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/28/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
Single-cell and single-population RNA sequencing (RNA-seq) is a rapidly evolving new field of intense investigation. Recent studies indicate unique transcriptomic profiles are derived based on the spatial localization of neurons within circuits and regions. Individual neuronal subtypes can have vastly different transcriptomic fingerprints, well beyond the basic excitatory neuron and inhibitory neuron designations. To study single-population gene expression profiles of spatially characterized neurons, we have developed a methodology combining laser capture microdissection (LCM), RNA purification of single populations of neurons, and subsequent library preparation for downstream applications, including RNA-seq. LCM provides the benefit of isolating single neurons characterized by morphology or via transmitter-identified and/or receptor immunoreactivity and enables spatial localization within the sample. We utilize unfixed human postmortem and mouse brain tissue that is frozen to preserve RNA quality in order to isolate the desired neurons of interest. Microisolated neurons are then pooled for RNA purification utilizing as few as 250 individual neurons from a tissue section, precluding extraneous nonspecific tissue contaminants. Library preparation is performed from picogram RNA quantities extracted from LCM-captured neurons. Single-population RNA-seq analysis demonstrates that microisolated neurons from both postmortem human and mouse brain tissues are viable for transcriptomic profiling, including differential gene expression assessment and bioinformatic pathway inquiry.
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Affiliation(s)
- Melissa J. Alldred
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Stephen D. Ginsberg
- Center for Dementia Research, Nathan Kline Institute, Orangeburg, NY 10962, USA
- Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA
- Department of Neuroscience & Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
- NYU Neuroscience Institute, New York University Grossman School of Medicine, New York, NY 10016, USA
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17
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Hertig C, Rutten T, Melzer M, Schippers JHM, Thiel J. Dissection of Developmental Programs and Regulatory Modules Directing Endosperm Transfer Cell and Aleurone Identity in the Syncytial Endosperm of Barley. Plants (Basel) 2023; 12:1594. [PMID: 37111818 PMCID: PMC10142620 DOI: 10.3390/plants12081594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Endosperm development in barley starts with the formation of a multinucleate syncytium, followed by cellularization in the ventral part of the syncytium generating endosperm transfer cells (ETCs) as first differentiating subdomain, whereas aleurone (AL) cells will originate from the periphery of the enclosing syncytium. Positional signaling in the syncytial stage determines cell identity in the cereal endosperm. Here, we performed a morphological analysis and employed laser capture microdissection (LCM)-based RNA-seq of the ETC region and the peripheral syncytium at the onset of cellularization to dissect developmental and regulatory programs directing cell specification in the early endosperm. Transcriptome data revealed domain-specific characteristics and identified two-component signaling (TCS) and hormone activities (auxin, ABA, ethylene) with associated transcription factors (TFs) as the main regulatory links for ETC specification. On the contrary, differential hormone signaling (canonical auxin, gibberellins, cytokinin) and interacting TFs control the duration of the syncytial phase and timing of cellularization of AL initials. Domain-specific expression of candidate genes was validated by in situ hybridization and putative protein-protein interactions were confirmed by split-YFP assays. This is the first transcriptome analysis dissecting syncytial subdomains of cereal seeds and provides an essential framework for initial endosperm differentiation in barley, which is likely also valuable for comparative studies with other cereal crops.
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Affiliation(s)
- Christian Hertig
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Twan Rutten
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Michael Melzer
- Department of Physiology and Cell Biology, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Jos H. M. Schippers
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
| | - Johannes Thiel
- Department of Molecular Genetics, Leibniz Institute for Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland, Germany
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18
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Das S, Li Z, Wachter A, Alla S, Noori A, Abdourahman A, Tamm JA, Woodbury ME, Talanian RV, Biber K, Karran EH, Hyman BT, Serrano-Pozo A. Distinct Transcriptomic Responses to Aβ plaques, Neurofibrillary Tangles, and APOE in Alzheimer's Disease. bioRxiv 2023:2023.03.20.533303. [PMID: 36993332 PMCID: PMC10055287 DOI: 10.1101/2023.03.20.533303] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
INTRODUCTION Omics studies have revealed that various brain cell types undergo profound molecular changes in Alzheimer's disease (AD) but the spatial relationships with plaques and tangles and APOE -linked differences remain unclear. METHODS We performed laser capture microdissection of Aβ plaques, the 50μm halo around them, tangles with the 50μm halo around them, and areas distant (>50μm) from plaques and tangles in the temporal cortex of AD and control donors, followed by RNA-sequencing. RESULTS Aβ plaques exhibited upregulated microglial (neuroinflammation/phagocytosis) and downregulated neuronal (neurotransmission/energy metabolism) genes, whereas tangles had mostly downregulated neuronal genes. Aβ plaques had more differentially expressed genes than tangles. We identified a gradient Aβ plaque>peri-plaque>tangle>distant for these changes. AD APOE ε4 homozygotes had greater changes than APOE ε3 across locations, especially within Aβ plaques. DISCUSSION Transcriptomic changes in AD consist primarily of neuroinflammation and neuronal dysfunction, are spatially associated mainly with Aβ plaques, and are exacerbated by the APOE ε4 allele.
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Affiliation(s)
- Sudeshna Das
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA 02129
- Harvard Medical School, Boston, MA 02115
| | - Zhaozhi Li
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA 02129
| | - Astrid Wachter
- AbbVie Deutschland GmbH & Co. KG, Genomics Research Center, Knollstrasse, 67061 Ludwigshafen
| | - Srinija Alla
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
| | - Ayush Noori
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
| | - Aicha Abdourahman
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Joseph A. Tamm
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Maya E. Woodbury
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Robert V. Talanian
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Knut Biber
- AbbVie Deutschland GmbH & Co. KG, Neuroscience Research Center, Knollstrasse, 67061 Ludwigshafen
| | - Eric H. Karran
- AbbVie, Cambridge Research Center, 200 Sidney Street, Cambridge, MA 02139
| | - Bradley T. Hyman
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA 02129
- Harvard Medical School, Boston, MA 02115
| | - Alberto Serrano-Pozo
- Massachusetts General Hospital, Neurology Dept. Boston, MA 02114
- Massachusetts Alzheimer’s Disease Research Center, Charlestown, MA 02129
- Harvard Medical School, Boston, MA 02115
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19
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Häyrinen MJ, Kiiskilä J, Ranki A, Väkevä L, Barton HJ, Kuusisto MEL, Porvari K, Kuitunen H, Haapasaari KM, Teppo HR, Kuittinen O. The Transcription Factor Twist1 Has a Significant Role in Mycosis Fungoides (MF) Cell Biology: An RNA Sequencing Study of 40 MF Cases. Cancers (Basel) 2023; 15. [PMID: 36900319 DOI: 10.3390/cancers15051527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/05/2023] Open
Abstract
The purpose of this RNA sequencing study was to investigate the biological mechanism underlying how the transcription factors (TFs) Twist1 and Zeb1 influence the prognosis of mycosis fungoides (MF). We used laser-captured microdissection to dissect malignant T-cells obtained from 40 skin biopsies from 40 MF patients with stage I-IV disease. Immunohistochemistry (IHC) was used to determinate the protein expression levels of Twist1 and Zeb1. Based on RNA sequencing, principal component analysis (PCA), differential expression (DE) analysis, ingenuity pathway analysis (IPA), and hub gene analysis were performed between the high and low Twist1 IHC expression cases. The DNA from 28 samples was used to analyze the TWIST1 promoter methylation level. In the PCA, Twist1 IHC expression seemed to classify cases into different groups. The DE analysis yielded 321 significant genes. In the IPA, 228 significant upstream regulators and 177 significant master regulators/causal networks were identified. In the hub gene analysis, 28 hub genes were found. The methylation level of TWIST1 promoter regions did not correlate with Twist1 protein expression. Zeb1 protein expression did not show any major correlation with global RNA expression in the PCA. Many of the observed genes and pathways associated with high Twist1 expression are known to be involved in immunoregulation, lymphocyte differentiation, and aggressive tumor biology. In conclusion, Twist1 might be an important regulator in the disease progression of MF.
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20
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Tantillo E, Scalera M, De Santis E, Meneghetti N, Cerri C, Menicagli M, Mazzoni A, Costa M, Mazzanti CM, Vannini E, Caleo M. Molecular changes underlying decay of sensory responses and enhanced seizure propensity in peritumoral neurons. Neuro Oncol 2023:7048460. [PMID: 36805257 PMCID: PMC10398807 DOI: 10.1093/neuonc/noad035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Glioblastoma growth impacts on the structure and physiology of peritumoral neuronal networks, altering the activity of pyramidal neurons which drives further tumor progression. It is therefore of paramount importance to identify glioma-induced changes in pyramidal neurons, since they represent a key therapeutic target. METHODS We longitudinal monitored visual evoked potentials after the orthotopic implant of murine glioma cells into the mouse occipital cortex. With laser microdissection we analysed layer II-III pyramidal neurons molecular profile and with Local Field Potentials (LFP) recordings we evaluated the propensity to seizures in glioma-bearing animals with respect to control mice. RESULTS We determine the time course of neuronal dysfunction of glioma-bearing mice and we identify a symptomatic stage, based on the decay of visual response. At that time point, we microdissect layer II-III pyramidal neurons and evaluate the expression of a panel of genes involved in synaptic transmission and neuronal excitability. Compared to the control group, peritumoral neurons show a decrease in the expression of the SNARE complex gene SNAP-25 and the alpha1 subunit of the GABA-A receptor. No significant changes are detected in glutamatergic (i.e., AMPA or NMDA receptor subunit) markers. Further reduction of GABA-A signalling by delivery of a benzodiazepine inverse agonist, DMCM (methyl-6,7-dimethoxy-4-ethyl-beta-carboline-3-carboxylate) precipitates seizures in two mouse models of tumor-bearing mice. CONCLUSIONS These studies reveal novel molecular changes that occur in the principal cells of the tumor-adjacent zone. These modifications may be therapeutically targeted to ameliorate patients' quality of life.
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Affiliation(s)
- Elena Tantillo
- CNR Neuroscience Institute, via G Moruzzi 1, 56124 Pisa.,Fondazione Pisana per la Scienza Onlus (FPS) via F. Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Marta Scalera
- CNR Neuroscience Institute, via G Moruzzi 1, 56124 Pisa
| | | | - Nicolò Meneghetti
- Department of Excellence for Robotics and AI, Scuola Superiore Sant'Anna, 56025 Pisa, Italy.,The Biorobotics Institute, Scuola Superiore Sant'Anna, 56025 Pisa, Italy
| | - Chiara Cerri
- Fondazione Umberto Veronesi, 20122 Milan, Italy.,Department of Pharmacy, University of Pisa, Pisa 56126, Italy
| | - Michele Menicagli
- Fondazione Pisana per la Scienza Onlus (FPS) via F. Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Alberto Mazzoni
- Department of Excellence for Robotics and AI, Scuola Superiore Sant'Anna, 56025 Pisa, Italy.,The Biorobotics Institute, Scuola Superiore Sant'Anna, 56025 Pisa, Italy
| | - Mario Costa
- CNR Neuroscience Institute, via G Moruzzi 1, 56124 Pisa.,Centro Pisano ricerca e implementazione clinica Flash Radiotherapy "CPFR@CISUP", "S. Chiara" Hospital, Pisa, Italy.,Laboratory of Biology BIO@SNS, Scuola Normale Superiore, Piazza di Cavalieri 7, Pisa, 56124, Italy
| | - Chiara Maria Mazzanti
- Fondazione Pisana per la Scienza Onlus (FPS) via F. Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Eleonora Vannini
- CNR Neuroscience Institute, via G Moruzzi 1, 56124 Pisa.,Fondazione Umberto Veronesi, 20122 Milan, Italy.,Centro Pisano ricerca e implementazione clinica Flash Radiotherapy "CPFR@CISUP", "S. Chiara" Hospital, Pisa, Italy
| | - Matteo Caleo
- CNR Neuroscience Institute, via G Moruzzi 1, 56124 Pisa.,Department of Biomedical Sciences, University of Padua, via G. Colombo 3, 35121 Padua
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21
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Wei Y, Xu Z, Hu M, Wu Z, Liu A, Czajkowsky DM, Guo Y, Shao Z. Time-resolved transcriptomics of mouse gastric pit cells during postnatal development reveals features distinct from whole stomach development. FEBS Lett 2023; 597:418-426. [PMID: 36285639 DOI: 10.1002/1873-3468.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/27/2022] [Accepted: 10/10/2022] [Indexed: 11/05/2022]
Abstract
Whole-organ transcriptomic analyses have emerged as a common method for characterizing developmental transitions in mammalian organs. However, it is unclear if all cell types in an organ follow the whole-organ defined developmental trajectory. Recently, a postnatal two-stage developmental process was described for the mouse stomach. Here, using laser capture microdissection to obtain in situ transcriptomic data, we show that mouse gastric pit cells exhibit four postnatal developmental stages. Interestingly, early stages are characterized by the up-regulation of genes associated with metabolism, a functionality not typically associated with pit cells. Hence, beyond revealing that not all constituent cells develop according to the whole-organ determined pathway, these results broaden our understanding of the pit cell phenotypic landscape during stomach development.
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Affiliation(s)
- Ying Wei
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Zeqian Xu
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Miaomiao Hu
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Zhongqin Wu
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Axian Liu
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Daniel M Czajkowsky
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Yan Guo
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
| | - Zhifeng Shao
- School of Biomedical Engineering, State Key Laboratory for Oncogenes and Bio-ID Center, Shanghai Jiao Tong University, China
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22
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Liao YC, Fulcher JM, Degnan DJ, Williams SM, Bramer LM, Veličković D, Zemaitis KJ, Veličković M, Sontag RL, Moore RJ, Paša-Tolić L, Zhu Y, Zhou M. Spatially Resolved Top-Down Proteomics of Tissue Sections Based on a Microfluidic Nanodroplet Sample Preparation Platform. Mol Cell Proteomics 2023; 22:100491. [PMID: 36603806 DOI: 10.1016/j.mcpro.2022.100491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 12/10/2022] [Accepted: 12/20/2022] [Indexed: 01/04/2023] Open
Abstract
Conventional proteomic approaches measure the averaged signal from mixed cell populations or bulk tissues, leading to the dilution of signals arising from subpopulations of cells that might serve as important biomarkers. Recent developments in bottom-up proteomics have enabled spatial mapping of cellular heterogeneity in tissue microenvironments. However, bottom-up proteomics cannot unambiguously define and quantify proteoforms, which are intact (i.e., functional) forms of proteins capturing genetic variations, alternatively spliced transcripts and posttranslational modifications. Herein, we described a spatially resolved top-down proteomics (TDP) platform for proteoform identification and quantitation directly from tissue sections. The spatial TDP platform consisted of a nanodroplet processing in one pot for trace samples-based sample preparation system and an laser capture microdissection-based cell isolation system. We improved the nanodroplet processing in one pot for trace samples sample preparation by adding benzonase in the extraction buffer to enhance the coverage of nucleus proteins. Using ∼200 cultured cells as test samples, this approach increased total proteoform identifications from 493 to 700; with newly identified proteoforms primarily corresponding to nuclear proteins. To demonstrate the spatial TDP platform in tissue samples, we analyzed laser capture microdissection-isolated tissue voxels from rat brain cortex and hypothalamus regions. We quantified 509 proteoforms within the union of top-down mass spectrometry-based proteoform identification and characterization and TDPortal identifications to match with features from protein mass extractor. Several proteoforms corresponding to the same gene exhibited mixed abundance profiles between two tissue regions, suggesting potential posttranslational modification-specific spatial distributions. The spatial TDP workflow has prospects for biomarker discovery at proteoform level from small tissue sections.
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23
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Dong J, Zheng F, Liu F, He J, Li S, Pu W, Xu H, Luo Z, Liu S, Yin L, Tang D, Dai Y. Global-feature of autoimmune glomerulonephritis using proteomic analysis of laser capture microdissected glomeruli. Front Immunol 2023; 14:1131164. [PMID: 37033921 PMCID: PMC10077062 DOI: 10.3389/fimmu.2023.1131164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/13/2023] [Indexed: 04/11/2023] Open
Abstract
Background IgA nephropathy (IgAN), (LN), membranous nephropathy (MN), and minimal change nephropathy (MCN) are all belonged to autoimmune glomerulonephritis. This study aimed to identify the specific proteomic characteristics of the four GNs diseases in order to provide frameworks for developing the appropriate drug for patients diagnosed with GNs disease. Methods Liquid chromatography-tandem mass spectrometry (LC-MS/MS) was utilized to investigate proteomic features of glomerular tissues obtained by laser capture microdissection (LCM). 8 normal control cases, 11 IgAN cases, 19 LN cases, 5 MN cases, and 3 MCN cases in this study were selected for bioinformatics analyses. Results The shared overlapping proteins among the top 100 DEPs of each GNs type were mostly downregulated, in which only FLII was significantly downregulated in the four GNs diseases. A2M was significantly upregulated in MN, IgAN, and LN subgroups. The pathway of complement and coagulation cascades was notably activated with NES value ranging 2.77 to 3.39 among MCN, MN, IgAN, and LN diseases, but the pattern of protein expression level were significantly different. In LN patients, the increased activity of complement and coagulation cascades was contributed by the high expression of multiple complements (C1QB, C3, C4A, C4B, C6, C8B, C8G, C9). Meanwhile, both C1QC and C4B were remarkably upregulated in MN patients. On the contrary, complement-regulating proteins (CD59) was substantially decreased in MCN and IgAN subgroup. Conclusions The integrative proteomics analysis of the four GNs diseases provide insights into unique characteristics of GNs diseases and further serve as frameworks for precision medicine diagnosis and provide novel targets for drug development.
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Affiliation(s)
- Jingjing Dong
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Fengping Zheng
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
- Department of Nephrology, Peking University Shenzhen Hospital, Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center, Shenzhen, Guangdong, China
| | - Fanna Liu
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Jingquan He
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Shanshan Li
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Wenjun Pu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Huixuan Xu
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
| | - Zhifeng Luo
- Guangxi Key Laboratory of Metabolic Disease Research, The 924th Hospital of the Chinese People’s Liberation Army Joint Logistic Support Force, Guilin, Guangxi, China
| | - Shizhen Liu
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Lianghong Yin
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
- *Correspondence: Lianghong Yin, ; Donge Tang, ; Yong Dai,
| | - Donge Tang
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
- *Correspondence: Lianghong Yin, ; Donge Tang, ; Yong Dai,
| | - Yong Dai
- Clinical Medical Research Center, The Second Clinical Medical College of Jinan University, Shenzhen People’s Hospital, Shenzhen, Guangdong, China
- Guangxi Key Laboratory of Metabolic Disease Research, The 924th Hospital of the Chinese People’s Liberation Army Joint Logistic Support Force, Guilin, Guangxi, China
- *Correspondence: Lianghong Yin, ; Donge Tang, ; Yong Dai,
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Pandey S, Jarkovska D, Tuma Z, Smrhova T, Chottova Dvorakova M. Regulation of Prepro-NeuropeptideW/B and Its Receptor in the Heart of ZDF Rats: An Animal Model of Type II DM. Int J Mol Sci 2022; 23. [PMID: 36499546 DOI: 10.3390/ijms232315219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
Neuropeptide B (NPB) and neuropeptide W (NPW) are neuropeptides, which constitute NPB/W signaling systems together with G-protein coupled receptors NPBWR1. The location and function of NPB/W signaling systems have been predominantly detected and mapped within the CNS, including their role in the modulation of inflammatory pain, neuroendocrine functions, and autonomic nervous systems. The aim of the study is to investigate the impact of diabetes on the neuropeptide B/W signaling system in different heart compartments and neurons which innervates it. In the RT-qPCR analysis, we observed the upregulation of mRNA for preproNPB in RV, for preproNPW in LA, and for NPBWR1 in DRG in diabetic rats. On the contrary, the expression of mRNA for NPBWR1 was downregulated in LV in diabetic rats. In the WB analysis, significant downregulation of NPBWR1 in LV (0.54-fold, p = 0.046) in diabetic rats was observed at the proteomic level. The presence of NPBWR1 was also confirmed in a dissected LCM section of cardiomyocytes and coronary arteries. The positive inotropic effect of NPW described on the diabetic cardiomyocytes in vitro could point to a possible therapeutic target for compensation of the contractile dysfunction in the diabetic heart. In conclusion, the NPB/W signaling system is involved in the regulation of heart functions and long-term diabetes leads to changes in the expression of individual members of this signaling system differently in each cardiac compartment, which is related to the different morphology and function of these cardiac chambers.
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Swensen AC, Veličković D, Williams SM, Moore RJ, Day LZ, Niessen S, Hennessy S, Posso C, Monetti M, Qian WJ, Jacobs J, Whiteley L, Zhu Y, Piehowski PD. Proteomic Profiling of Intra-Islet Features Reveals Substructure-Specific Protein Signatures. Mol Cell Proteomics 2022; 21:100426. [PMID: 36244662 DOI: 10.1016/j.mcpro.2022.100426] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 08/30/2022] [Accepted: 09/04/2022] [Indexed: 11/11/2022] Open
Abstract
Despite their diminutive size, islets of Langerhans play a large role in maintaining systemic energy balance in the body. New technologies have enabled us to go from studying the whole pancreas to isolated whole islets, to partial islet sections, and now to islet substructures isolated from within the islet. Using a microfluidic nanodroplet-based proteomics platform coupled with laser capture microdissection and field asymmetric waveform ion mobility spectrometry, we present an in-depth investigation of protein profiles specific to features within the islet. These features include the islet-acinar interface vascular tissue, inner islet vasculature, isolated endocrine cells, whole islet with vasculature, and acinar tissue from around the islet. Compared to interface vasculature, unique protein signatures observed in the inner vasculature indicate increased innervation and intra-islet neuron-like crosstalk. We also demonstrate the utility of these data for identifying localized structure-specific drug-target interactions using existing protein/drug binding databases.
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Woo J, Schoenfeld M, Sun X, Iraguha T, Zhou Z, Zhang Q. Mouse Paneth Cell-Enriched Proteome Enabled by Laser Capture Microdissection. J Proteome Res 2022; 21:2435-2442. [PMID: 36153828 PMCID: PMC9671084 DOI: 10.1021/acs.jproteome.2c00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Paneth cells are antimicrobial peptide-secreting cells located at the base of the crypts of the small intestine. The proteome of Paneth cells is not well defined because of their coexistence with stem cells, making it difficult to culture Paneth cells alone in vitro. Using a simplified toluidine blue O method for staining mouse intestinal tissue, laser capture microdissection (LCM) to isolate cells from the crypt region, and surfactant-assisted one-pot protein digestion, we identified more than 1300 proteins from crypts equivalent to 18,000 cells. Compared with the proteomes of villi and smooth muscle regions, the crypt proteome is highly enriched in defensins, lysozymes, and other antimicrobial peptides that are characteristic of Paneth cells. The sensitivity of the LCM-based proteomics approach was also assessed using a smaller number of cell equivalent tissues: a comparable proteomic coverage can be achieved with 3600 cells. This work is the first proteomics study of intestinal tissue enriched with Paneth cells. The simplified workflow enables profiling of Paneth cell-associated pathological changes at the proteome level directly from frozen intestinal tissue. It may also be useful for proteomics studies of other spatially resolved cell types from other tissues.
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Affiliation(s)
- Jongmin Woo
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC 28081
| | - Madeline Schoenfeld
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC 28081
| | - Xinguo Sun
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC 28081
| | - Thierry Iraguha
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC 28081
| | - Zhanxiang Zhou
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC 28081
- Department of Nutrition, University of North Carolina at Greensboro, Greensboro, NC 27402
| | - Qibin Zhang
- Center for Translational Biomedical Research, University of North Carolina at Greensboro, North Carolina Research Campus, Kannapolis, NC 28081
- Department of Chemistry & Biochemistry, University of North Carolina at Greensboro, Greensboro, NC 27402
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Abstract
Changes in the spatial organization, or biogeography, of colonic microbes have been observed in human inflammatory bowel disease (IBD) and mouse models of IBD. We have developed a mouse model of IBD that occurs spontaneously and consistently in the absence of adaptive immunity. Mice expressing tumor necrosis factor-induced protein 3 (TNFAIP3) in intestinal epithelial cells (villin-TNFAIP3) develop colitis when interbred with Recombination Activating 1-deficient mice (RAG1<sup>-/-</sup>). The colitis in villin-TNFAIP3 × RAG1<sup>-/-</sup> (TRAG) mice is prevented by antibiotics, indicating a role for microbes in this innate colitis. We therefore explored the biogeography of microbes and responses to antibiotics in TRAG colitis. Laser capture microdissection and 16S rRNA sequencing revealed altered microbial populations across the transverse axis of the colon as the inner mucus layer of TRAG, but not RAG1<sup>-/-</sup>, mice was infiltrated by microbes, which included increased abundance of the classes Gammaproteobacteria and Actinobacteria. Along the longitudinal axis differences in the efficacy of antibiotics to prevent colitis were evident. Neomycin was most effective for prevention of inflammation in the cecum, while ampicillin was most effective in the proximal and distal colon. RAG1<sup>-/-</sup>, but not TRAG, mice exhibited a structured pattern of bacterial abundance with decreased Firmicutes and Proteobacteria but increased Bacteroidetes along the proximal to distal axis of the gut. TRAG mice exhibited increased relative abundance of potential pathobionts including <i>Bifidobacterium animalis</i> along the longitudinal axis of the gut whereas others, like <i>Helicobacter hepaticus</i> were increased only in the cecum. Potential beneficial organisms including <i>Roseburia</i> were decreased in the proximal regions of the TRAG colon, while <i>Bifidobacterium pseudolongulum</i> was decreased in the TRAG distal colon. Thus, the innate immune system maintains a structured, spatially organized, gut microbiome along the transverse and longitudinal axis of the gut, and disruption of this biogeography is a feature of innate immune colitis.
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Affiliation(s)
- Antonia Boger-May
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA
| | - Theodore Reed
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | - Diana LaTorre
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | - Katelyn Ruley-Haase
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA
| | - Hunter Hoffman
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA
| | - Lauren English
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | - Connor Roncagli
- Department of Biology, University of Notre Dame, South Bend, IN, USA
| | - Anne-Marie Overstreet
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA
| | - David Boone
- Department of Microbiology and Immunology, Indiana University School of Medicine, South Bend, IN, USA,Department of Biology, University of Notre Dame, South Bend, IN, USA,CONTACT David Boone IUSM-SB, 1234 N. Notre Dame Ave., RCH122, South BendIN, USA46617
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Almeida D, Turecki G. Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection. Methods 2022; 207:3-10. [PMID: 36064002 DOI: 10.1016/j.ymeth.2022.08.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
The transcriptome of a cell constitutes an essential piece of cellular identity and contributes to the multifaceted complexity and heterogeneity of cell-types within the mammalian brain. Thus, while a wealth of studies have investigated transcriptomic alterations underlying the pathophysiology of diseases of the brain, their use of bulk-tissue homogenates makes it difficult to tease apart whether observed differences are explained by disease state or cellular composition. Cell-type-specific enrichment strategies are, therefore, crucial in the context of gene expression profiling. Laser capture microdissection (LCM) is one such strategy that allows for the capture of specific cell-types, or regions of interest, under microscopic visualization. In this review, we focus on using LCM for cell-type specific gene expression profiling in post-mortem human brain samples. We begin with a discussion of various LCM systems, followed by a walk-through of each step in the LCM to gene expression profiling workflow and a description of some of the limitations associated with LCM. Throughout the review, we highlight important considerations when using LCM with post-mortem human brain samples. Whenever applicable, commercially available kits that have proven successful in the context of LCM with post-mortem human brain samples are described.
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Affiliation(s)
- Daniel Almeida
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3
| | - Gustavo Turecki
- McGill Group for Suicide Studies, Douglas Hospital Research Center, Montreal, QC, Canada, H4H 1R3; Department of Psychiatry, McGill University, Montreal, QC, Canada, H3A 1A1.
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Liu WY, Yu CP, Chang CK, Chen HJ, Li MY, Chen YH, Shiu SH, Ku MSB, Tu SL, Lu MJ, Li WH. Regulators of early maize leaf development inferred from transcriptomes of laser capture microdissection (LCM)-isolated embryonic leaf cells. Proc Natl Acad Sci U S A 2022; 119:e2208795119. [PMID: 36001691 DOI: 10.1073/pnas.2208795119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The superior photosynthetic efficiency of C4 leaves over C3 leaves is owing to their unique Kranz anatomy, in which the vein is surrounded by one layer of bundle sheath (BS) cells and one layer of mesophyll (M) cells. Kranz anatomy development starts from three contiguous ground meristem (GM) cells, but its regulators and underlying molecular mechanism are largely unknown. To identify the regulators, we obtained the transcriptomes of 11 maize embryonic leaf cell types from five stages of pre-Kranz cells starting from median GM cells and six stages of pre-M cells starting from undifferentiated cells. Principal component and clustering analyses of transcriptomic data revealed rapid pre-Kranz cell differentiation in the first two stages but slow differentiation in the last three stages, suggesting early Kranz cell fate determination. In contrast, pre-M cells exhibit a more prolonged transcriptional differentiation process. Differential gene expression and coexpression analyses identified gene coexpression modules, one of which included 3 auxin transporter and 18 transcription factor (TF) genes, including known regulators of Kranz anatomy and/or vascular development. In situ hybridization of 11 TF genes validated their expression in early Kranz development. We determined the binding motifs of 15 TFs, predicted TF target gene relationships among the 18 TF and 3 auxin transporter genes, and validated 67 predictions by electrophoresis mobility shift assay. From these data, we constructed a gene regulatory network for Kranz development. Our study sheds light on the regulation of early maize leaf development and provides candidate leaf development regulators for future study.
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Qin W, Li Y, Peng B, Liu H, Chen T, Yan X, Zhang Y, Wang C, Yao X, Fu X, Li L, Tang K. A high-efficiency trichome collection system by laser capture microdissection. Front Plant Sci 2022; 13:985969. [PMID: 36072328 PMCID: PMC9441851 DOI: 10.3389/fpls.2022.985969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
Trichomes, which are classified as glandular or non-glandular, are hair-like epidermal structures that are present on aerial parts of most plant species. Glandular secretory trichomes (GSTs) have the capacity to secrete and store specialized metabolites, which are widely used as natural pesticides, food additives, fragrance ingredients or pharmaceuticals. Isolating individual trichomes is an essential way for identifying trichome-specific gene functions and discovering novel metabolites. However, the isolation of trichomes is difficult and time-consuming. Here, we report a method to isolate the GSTs from leaf epidermis dispense with fixation using laser capture microdissection (LCM). In this study, 150 GSTs were captured efficiently from Artemisia annua leaves and enriched for artemisinin measurement. UPLC analysis of microdissected samples indicated specific accumulation of secondary metabolites could be detected from a small number of GSTs. In addition, qRT-PCR revealed that the GST-specific structural genes involved in artemisinin biosynthesis pathway were highly expressed in GSTs. Taken together, we developed an efficient method to collect comparatively pure GSTs from unfixed leaved, so that the metabolites were relatively obtained intact. This method can be implemented in metabolomics research of purely specific plant cell populations and has the potential to discover novel secondary metabolites.
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Acland M, Mittal P, Arentz G, Whitehead F, Hoffmann P, Klingler-Hoffmann M, Oehler MK. A Protocol for the Acquisition of Comprehensive Proteomics Data from Single Cases Using Formalin-Fixed Paraffin Embedded Sections. Methods Protoc 2022; 5:57. [PMID: 35893583 DOI: 10.3390/mps5040057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/26/2022] [Accepted: 07/06/2022] [Indexed: 11/16/2022] Open
Abstract
The molecular analysis of small or rare patient tissue samples is challenging and often limited by available technologies and resources, such as reliable antibodies against a protein of interest. Although targeted approaches provide some insight, here, we describe the workflow of two complementary mass spectrometry approaches, which provide a more comprehensive and non-biased analysis of the molecular features of the tissue of interest. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) generates spatial intensity maps of molecular features, which can be easily correlated with histology. Additionally, liquid chromatography tandem mass spectrometry (LC-MS/MS) can identify and quantify proteins of interest from a consecutive section of the same tissue. Here, we present data from concurrent precancerous lesions from the endometrium and fallopian tube of a single patient. Using this complementary approach, we monitored the abundance of hundreds of proteins within the precancerous and neighboring healthy regions. The method described here represents a useful tool to maximize the number of molecular data acquired from small sample sizes or even from a single case. Our initial data are indicative of a migratory phenotype in these lesions and warrant further research into their malignant capabilities.
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Nogueira M, Golbert DCF, Landeira B, Leão RN. Laser Capture Microdissection Optimization for High-Quality RNA in Mouse Brain Tissue. Curr Protoc 2022; 2:e457. [PMID: 35822833 DOI: 10.1002/cpz1.457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Laser Capture Microdissection (LCM) is a method that allows one to select and dissect well-defined structures, specific cell subpopulations, or even single cells from different types of tissue for subsequent extraction of DNA, RNA, or proteins. Its precision allows the dissection of specific groups of cells, avoiding unwanted cells. However, despite its efficiency, several steps can affect the sample RNA integrity. RNA instability represents a challenge in the LCM method, and low RNA integrity can introduce biases, as different transcripts often have different degradation rates. Here we describe an optimized protocol to provide good-concentration and high-quality RNA from specific structures: dentate gyrus and CA1 in the hippocampus, basolateral amygdala, and anterior cingulate cortex of mouse brain tissue. However, the protocol is applicable to other areas of interest. © 2022 Wiley Periodicals LLC. Basic Protocol: Laser capture microdissection of mouse brain tissue.
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Affiliation(s)
- Margareth Nogueira
- Neurodynamics Lab, Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Daiane C F Golbert
- Neurodynamics Lab, Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Bruna Landeira
- Neurodynamics Lab, Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
| | - Richardson N Leão
- Neurodynamics Lab, Brain Institute, Federal University of Rio Grande do Norte, Natal, Brazil
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Zhou X, Huang K, Teng C, Abdelgawad A, Batish M, Meyers BC, Walbot V. 24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers. New Phytol 2022; 235:488-501. [PMID: 35451503 DOI: 10.1111/nph.18167] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
In maize, 24-nt phased, secondary small interfering RNAs (phasiRNAs) are abundant in meiotic stage anthers, but their distribution and functions are not precisely known. Using laser capture microdissection, we analyzed tapetal cells, meiocytes and other somatic cells at several stages of anther development to establish the timing of 24-PHAS precursor transcripts and the 24-nt phasiRNA products. By integrating RNA and small RNA profiling plus single-molecule and small RNA FISH (smFISH or sRNA-FISH) spatial detection, we demonstrate that the tapetum is the primary site of 24-PHAS precursor and Dcl5 transcripts and the resulting 24-nt phasiRNAs. Interestingly, 24-nt phasiRNAs accumulate in all cell types, with the highest levels in meiocytes, followed by tapetum. Our data support the conclusion that 24-nt phasiRNAs are mobile from tapetum to meiocytes and to other somatic cells. We discuss possible roles for 24-nt phasiRNAs in anther cell types.
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Affiliation(s)
- Xue Zhou
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Kun Huang
- Department of Plant and Soil Sciences, University of Delaware, Newark, DE, 19716, USA
- Delaware Biotechnology Institute, University of Delaware, Newark, DE, 19716, USA
- Dana-Farber Cancer Institute Molecular Imaging Core, 360 Longwood Ave, Boston, MA, 02215, USA
| | - Chong Teng
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
| | - Ahmed Abdelgawad
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE, 19716, USA
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE, 19716, USA
| | - Blake C Meyers
- Donald Danforth Plant Science Center, St Louis, MO, 63132, USA
- Division of Plant Sciences, University of Missouri - Columbia, Columbia, MO, 65211, USA
| | - Virginia Walbot
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
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Torp AM, Kamguyan K, Christfort JF, Kristensen KA, Guerra P, Daniel N, Nielsen LH, Zòr K, Chassaing B, Boisen A, Bahl MI, Licht TR. Local Delivery of Streptomycin in Microcontainers Facilitates Colonization of Streptomycin-Resistant Escherichia coli in the Rat Colon. Appl Environ Microbiol 2022;:e0073422. [PMID: 35758759 DOI: 10.1128/aem.00734-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Oral antibiotic treatment is often applied in animal studies in order to allow establishment of an introduced antibiotic-resistant bacterium in the gut. Here, we compared the application of streptomycin dosed orally in microcontainers to dosage through drinking water. The selective effect on a resistant bacterial strain, as well as the effects on fecal, luminal, and mucosal microbiota composition, were investigated. Three groups of rats (n = 10 per group) were orally dosed with microcontainers daily for 3 days. One of these groups (STR-M) received streptomycin-loaded microcontainers designed for release in the distal ileum, while the other two groups (controls [CTR] and STR-W) received empty microcontainers. The STR-W group was additionally dosed with streptomycin through the drinking water. A streptomycin-resistant Escherichia coli strain was orally inoculated into all animals. Three days after inoculation, the resistant E. coli was found only in the cecum and colon of animals receiving streptomycin in microcontainers but in all intestinal compartments of animals receiving streptomycin in the drinking water. 16S rRNA amplicon sequencing revealed significant changes in the fecal microbiota of both groups of streptomycin-treated animals. Investigation of the inner colonic mucus layer by confocal laser scanning microscopy and laser capture microdissection revealed no significant effect of streptomycin treatment on the mucus-inhabiting microbiota or on E. coli encroachment into the inner mucus. Streptomycin-loaded microcontainers thus enhanced proliferation of an introduced streptomycin-resistant E. coli in the cecum and colon without affecting the small intestine environment. While improvements of the drug delivery system are needed to facilitate optimal local concentration and release of streptomycin, the application of microcontainers provides new prospects for antibiotic treatment. IMPORTANCE Delivery of antibiotics in microcontainer devices designed for release at specific sites of the gut represents a novel approach which might reduce the amount of antibiotic needed to obtain a local selective effect. We propose that the application of microcontainers may have the potential to open novel opportunities for antibiotic treatment of humans and animals with fewer side effects on nontarget bacterial populations. In the current study, we therefore elucidated the effects of streptomycin, delivered in microcontainers coated with pH-sensitive lids, on the selective effect on a resistant bacterium, as well as on the surrounding intestinal microbiota in rats.
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Boualem A, Berthet S, Devani RS, Camps C, Fleurier S, Morin H, Troadec C, Giovinazzo N, Sari N, Dogimont C, Bendahmane A. Ethylene plays a dual role in sex determination and fruit shape in cucurbits. Curr Biol 2022; 32:2390-2401.e4. [PMID: 35525245 DOI: 10.1016/j.cub.2022.04.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/21/2022] [Accepted: 04/08/2022] [Indexed: 10/18/2022]
Abstract
Shapes of vegetables and fruits are the result of adaptive evolution and human selection. Modules controlling organ shape have been identified. However, little is known about signals coordinating organ development and shape. Here, we describe the characterization of a melon mutation rf1, leading to round fruit. Histological analysis of rf1 flower and fruits revealed fruit shape is determined at flower stage 8, after sex determination and before flower fertilization. Using positional cloning, we identified the causal gene as the monoecy sex determination gene CmACS7, and survey of melon germplasms showed strong association between fruit shape and sexual types. We show that CmACS7-mediated ethylene production in carpel primordia enhances cell expansion and represses cell division, leading to elongated fruit. Cell size is known to rise as a result of endoreduplication. At stage 8 and anthesis, we found no variation in ploidy levels between female and hermaphrodite flowers, ruling out endoreduplication as a factor in fruit shape determination. To pinpoint the gene networks controlling elongated versus round fruit phenotype, we analyzed the transcriptomes of laser capture microdissected carpels of wild-type and rf1 mutant. These high-resolution spatiotemporal gene expression dynamics revealed the implication of two regulatory modules. The first module implicates E2F-DP transcription factors, controlling cell elongation versus cell division. The second module implicates OVATE- and TRM5-related proteins, controlling cell division patterns. Our finding highlights the dual role of ethylene in the inhibition of the stamina development and the elongation of ovary and fruit in cucurbits.
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Affiliation(s)
- Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Serge Berthet
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Ravi Sureshbhai Devani
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Celine Camps
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Sebastien Fleurier
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Halima Morin
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Christelle Troadec
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France
| | - Nathalie Giovinazzo
- INRAE GAFL, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Nebahat Sari
- INRAE GAFL, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Catherine Dogimont
- INRAE GAFL, Génétique et Amélioration des Fruits et Légumes, 84143 Montfavet, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif sur Yvette, France.
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Ortigosa F, Lobato-Fernández C, Shikano H, Ávila C, Taira S, Cánovas FM, Cañas RA. Ammonium regulates the development of pine roots through hormonal crosstalk and differential expression of transcription factors in the apex. Plant Cell Environ 2022; 45:915-935. [PMID: 34724238 DOI: 10.1111/pce.14214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/25/2021] [Indexed: 06/13/2023]
Abstract
Ammonium is a prominent source of inorganic nitrogen for plant nutrition, but excessive amounts can be toxic for many species. However, most conifers are tolerant to ammonium, a relevant physiological feature of this ancient evolutionary lineage. For a better understanding of the molecular basis of this trait, ammonium-induced changes in the transcriptome of maritime pine (Pinus pinaster Ait.) root apex have been determined by laser capture microdissection and RNA sequencing. Ammonium promoted changes in the transcriptional profiles of multiple transcription factors, such as SHORT-ROOT, and phytohormone-related transcripts, such as ACO, involved in the development of the root meristem. Nano-PALDI-MSI and transcriptomic analyses showed that the distributions of IAA and CKs were altered in the root apex in response to ammonium nutrition. Taken together, the data suggest that this early response is involved in the increased lateral root branching and principal root growth, which characterize the long-term response to ammonium supply in pine. All these results suggest that ammonium induces changes in the root system architecture through the IAA-CK-ET phytohormone crosstalk and transcriptional regulation.
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Affiliation(s)
- Francisco Ortigosa
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - César Lobato-Fernández
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Hitomi Shikano
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Concepción Ávila
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Shu Taira
- Faculty of Food and Agricultural Sciences, Fukushima University, Kanayagawa, Fukushima, Japan
| | - Francisco M Cánovas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
| | - Rafael A Cañas
- Grupo de Biología Molecular y Biotecnología, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
- Integrative Molecular Biology Lab, Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Campus Universitario de Teatinos, Málaga, Spain
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Ohni S, Yamaguchi H, Hirotani Y, Nakanishi Y, Midorikawa Y, Sugitani M, Naruse H, Nakayama T, Makishima M, Esumi M. Direct molecular evidence for both multicentric and monoclonal carcinogenesis followed by transdifferentiation from hepatocellular carcinoma to cholangiocarcinoma in a case of metachronous liver cancer. Oncol Lett 2021; 23:22. [PMID: 34868359 PMCID: PMC8630812 DOI: 10.3892/ol.2021.13140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/18/2021] [Indexed: 01/21/2023] Open
Abstract
Frequent recurrence is a major issue in liver cancer and histological heterogeneity frequently occurs in this cancer type. However, it has remained elusive whether such cancers are multicentric or monoclonal. To elucidate the clonal evolution of hepatocellular carcinoma (HCC) recurrence and combined hepatocellular-cholangiocarcinoma (cHCC-CCA) development, the somatic mutation frequency and signatures in a patient with triple occurrence of liver cancer every three years were examined, with samples designated as #1HCC, #2HCC and #3cHCC-CCA, respectively. A total of four tumor regions, including HCC (#3HCC) and intrahepatic CCA (#3iCCA) components of #3cHCC-CCA, and three nontumor regions (#1N, #2N and #3N) were precisely dissected from formalin-fixed paraffin-embedded tissues of each surgical specimen. DNA was extracted and subjected to tumor-specific somatic mutation determination. Of note, five nonsynonymous single-nucleotide variants (SNVs), namely those of KMT2D, TP53, DNMT3A, PKHD1 and TLR4, were identified in #3cHCC-CCA. All five SNVs were detected in both #3HCC and #3iCCA and #2HCC but not in #1HCC. The telomerase reverse transcriptase (TERT) promoter mutation C228T, but not C250T, was observed in all tumors. Digital PCR of C228T also indicated the presence of the TERT promoter mutation C228T in nontumorous liver tissues (#1N, #2N and #3N) at a frequency of 0.11–0.83% compared with normal liver and blood samples. These results suggest the following phylogenetic evolution of three metachronous liver cancers: #1HCC was not related to #2HCC, #3HCC and #3iCCA; both #3HCC and #3iCCA arose from #2HCC. From the above, three novel findings were deduced: i) Both multicentric occurrence and intrahepatic metastasis may be involved in liver cancer in a three-year interval; ii) transdifferentiation from HCC to iCCA is a possible pathogenic mechanism of cHCC-CCA; and iii) a nontumorous, noncirrhotic liver may contain a preneoplastic region with a cancer driver mutation in the TERT promoter.
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Affiliation(s)
- Sumie Ohni
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Hiromi Yamaguchi
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yukari Hirotani
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yoko Nakanishi
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Yutaka Midorikawa
- Department of Surgery, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Masahiko Sugitani
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Hiromu Naruse
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Tomohiro Nakayama
- Department of Pathology and Microbiology, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Makoto Makishima
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Mariko Esumi
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
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Yang X, Song Y, Liang T, Wang Q, Li R, Liu W. Application of laser capture microdissection and PCR sequencing in the diagnosis of Coccidioides spp. infection: A case report and literature review in China. Emerg Microbes Infect 2021; 10:331-341. [PMID: 33576325 PMCID: PMC7919914 DOI: 10.1080/22221751.2021.1889931] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 01/19/2021] [Accepted: 02/09/2021] [Indexed: 02/08/2023]
Abstract
Coccidioidomycosis is endemic to California, Arizona, and Mexico. In recent years, the reported cases of coccidioidomycosis have increased in nonendemic regions. Here, we reported a case of imported pulmonary coccidioidomycosis in a Chinese patient. A 63-year-old man presented with dry cough and fatigue for 6 months, and a computed tomography scan revealed a solitary nodule in the right lower lung and small nodules in both lungs. The diagnosis of coccidioidomycosis was initially confirmed by histopathologic examination. The pathogen Coccidioides spp. was identified by laser capture microdissection (LCM) combined with subsequent molecular techniques based on the positive histopathologic features. Additionally, we reviewed 47 reported cases of coccidioidomycosis in China. The number of reported cases is increasing, and the incidence of disseminated infection has exhibited a trend of shifting towards healthy young adults in China. Since clinical presentations and imaging findings lack specificity, a majority of domestic cases of coccidioidomycosis were initially misdiagnosed as tumours or tuberculosis. Moreover, the diagnosis of endemic mycoses may be challenging because of their rarity and the limited availability of diagnostic tests. The diagnosis was mainly confirmed by histopathological examination. The species involved were identified based on positive cultures in only 4 cases. To our knowledge, this is the first study to use LCM and molecular techniques to identify Coccidioides spp. in the histopathologically positive but uncultivable specimen. Comparing with previous reported studies, LCM combined with nucleic acid amplification techniques improve the ability of species identification for the timely diagnosis of coccidioidomycosis.
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Affiliation(s)
- Xinyu Yang
- Department of Dermatology and Venereology, National Clinical Research Center for Skin and Immune Diseases, Research Center for Medical Mycology, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing, People’s Republic of China
| | - Yinggai Song
- Department of Dermatology and Venereology, National Clinical Research Center for Skin and Immune Diseases, Research Center for Medical Mycology, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing, People’s Republic of China
| | - TianYu Liang
- Department of Dermatology and Venereology, National Clinical Research Center for Skin and Immune Diseases, Research Center for Medical Mycology, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing, People’s Republic of China
| | - Qiqi Wang
- Department of Dermatology and Venereology, National Clinical Research Center for Skin and Immune Diseases, Research Center for Medical Mycology, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing, People’s Republic of China
| | - Ruoyu Li
- Department of Dermatology and Venereology, National Clinical Research Center for Skin and Immune Diseases, Research Center for Medical Mycology, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing, People’s Republic of China
| | - Wei Liu
- Department of Dermatology and Venereology, National Clinical Research Center for Skin and Immune Diseases, Research Center for Medical Mycology, Beijing Key Laboratory of Molecular Diagnosis on Dermatoses, Peking University First Hospital, Beijing, People’s Republic of China
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Filipecki M, Żurczak M, Matuszkiewicz M, Święcicka M, Kurek W, Olszewski J, Koter MD, Lamont D, Sobczak M. Profiling the Proteome of Cyst Nematode-Induced Syncytia on Tomato Roots. Int J Mol Sci 2021; 22:ijms222212147. [PMID: 34830029 PMCID: PMC8625192 DOI: 10.3390/ijms222212147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 11/05/2021] [Accepted: 11/07/2021] [Indexed: 02/06/2023] Open
Abstract
Cyst nematodes are important herbivorous pests in agriculture that obtain nutrients through specialized root structures termed syncytia. Syncytium initiation, development, and functioning are a research focus because syncytia are the primary interface for molecular interactions between the host plant and parasite. The small size and complex development (over approximately two weeks) of syncytia hinder precise analyses, therefore most studies have analyzed the transcriptome of infested whole-root systems or syncytia-containing root segments. Here, we describe an effective procedure to microdissect syncytia induced by Globodera rostochiensis from tomato roots and to analyze the syncytial proteome using mass spectrometry. As little as 15 mm2 of 10-µm-thick sections dissected from 30 syncytia enabled the identification of 100–200 proteins in each sample, indicating that mass-spectrometric methods currently in use achieved acceptable sensitivity for proteome profiling of microscopic samples of plant tissues (approximately 100 µg). Among the identified proteins, 48 were specifically detected in syncytia and 7 in uninfected roots. The occurrence of approximately 50% of these proteins in syncytia was not correlated with transcript abundance estimated by quantitative reverse-transcription PCR analysis. The functional categories of these proteins confirmed that protein turnover, stress responses, and intracellular trafficking are important components of the proteome dynamics of developing syncytia.
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Affiliation(s)
- Marcin Filipecki
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Faculty of Biology and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (M.Ż.); (M.M.); (M.D.K.)
- Correspondence: ; Tel.: +48-22-5932171
| | - Marek Żurczak
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Faculty of Biology and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (M.Ż.); (M.M.); (M.D.K.)
| | - Mateusz Matuszkiewicz
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Faculty of Biology and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (M.Ż.); (M.M.); (M.D.K.)
| | - Magdalena Święcicka
- Department of Botany, Institute of Biology, Faculty of Biology and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (M.Ś.); (W.K.); (M.S.)
| | - Wojciech Kurek
- Department of Botany, Institute of Biology, Faculty of Biology and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (M.Ś.); (W.K.); (M.S.)
| | - Jarosław Olszewski
- Veterinary Research Centre, Centre for Biomedicine Research, Centre for Regenerative Medicine, Department of Large Animal Diseases and Clinic, Institute for Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 100, 02-797 Warsaw, Poland;
| | - Marek Daniel Koter
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Faculty of Biology and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (M.Ż.); (M.M.); (M.D.K.)
| | - Douglas Lamont
- ‘FingerPrints’ Proteomics Facility, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK;
| | - Mirosław Sobczak
- Department of Botany, Institute of Biology, Faculty of Biology and Biotechnology, Warsaw University of Life Sciences, Nowoursynowska 159, 02-776 Warsaw, Poland; (M.Ś.); (W.K.); (M.S.)
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Trailin A, Mrazova P, Hruba P, Voska L, Sticova E, Slavcev A, Novotny M, Kocik M, Viklicky O. Chronic Active Antibody-Mediated Rejection Is Associated With the Upregulation of Interstitial But Not Glomerular Transcripts. Front Immunol 2021; 12:729558. [PMID: 34616398 PMCID: PMC8488163 DOI: 10.3389/fimmu.2021.729558] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/25/2021] [Indexed: 01/02/2023] Open
Abstract
Molecular assessment of renal allografts has already been suggested in antibody-mediated rejection (ABMR), but little is known about the gene transcript patterns in particular renal compartments. We used laser capture microdissection coupled with quantitative RT-PCR to distinguish the transcript patterns in the glomeruli and tubulointerstitium of kidney allografts in sensitized retransplant recipients at high risk of ABMR. The expressions of 13 genes were quantified in biopsies with acute active ABMR, chronic active ABMR, acute tubular necrosis (ATN), and normal findings. The transcripts were either compartment specific (TGFB1 in the glomeruli and HAVCR1 and IGHG1 in the tubulointerstitium), ABMR specific (GNLY), or follow-up specific (CXCL10 and CX3CR1). The transcriptional profiles of early acute ABMR shared similarities with ATN. The transcripts of CXCL10 and TGFB1 increased in the glomeruli in both acute ABMR and chronic active ABMR. Chronic active ABMR was associated with the upregulation of most genes (SH2D1B, CX3CR1, IGHG1, MS4A1, C5, CD46, and TGFB1) in the tubulointerstitium. In this study, we show distinct gene expression patterns in specific renal compartments reflecting cellular infiltration observed by conventional histology. In comparison with active ABMR, chronic active ABMR is associated with increased transcripts of tubulointerstitial origin.
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Affiliation(s)
- Andriy Trailin
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Petra Mrazova
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Petra Hruba
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Ludek Voska
- Department of Clinical and Transplant Pathology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Eva Sticova
- Department of Clinical and Transplant Pathology, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Antonij Slavcev
- Department of Immunogenetics, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Marek Novotny
- Department of Nephrology, Transplant Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia.,Institute of Physiology, 1st Faculty of Medicine, Charles University, Prague, Czechia
| | - Matej Kocik
- Transplantation Surgery Department, Institute for Clinical and Experimental Medicine, Prague, Czechia
| | - Ondrej Viklicky
- Transplant Laboratory, Institute for Clinical and Experimental Medicine, Prague, Czechia.,Department of Nephrology, Transplant Centre, Institute for Clinical and Experimental Medicine, Prague, Czechia
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Shetty R, Jensen B, Shelton D, Jørgensen K, Pedas P, Jørgensen HJL. Site-specific, silicon-induced structural and molecular defence responses against powdery mildew infection in roses. Pest Manag Sci 2021; 77:4545-4554. [PMID: 34075680 DOI: 10.1002/ps.6493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/18/2021] [Accepted: 06/02/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Silicon (Si) application to miniature potted roses can decrease severity of powdery mildew (Podosphaera pannosa) and this is associated with increased accumulation of callose and hydrogen peroxide (H2 O2 ) as well as hypersensitive (HR) cells. We used microscopy, gene expression and specific inhibitors of callose and H2 O2 to determine how effective these plant responses are in stopping infection. RESULTS Pathogen arrest in Si-treated (Si+) plants was accompanied by increased accumulation of callose and H2 O2 in papillae and HR cells, respectively. These responses were reduced by application of specific inhibitors (2-deoxy-d-glucose for callose and catalase for H2 O2 ), which increased disease severity in Si+, but not in Si- plants. As markers for HR and callose, expression of the HR-specific gene hsr203J and the wound-related callose synthase GSL5, respectively, was studied. An up-regulation of expression was only seen after isolation of HR cells with laser capture microdissection. The up-regulation was higher in Si+ than in Si- plants and occurred concomitantly with more efficient photosynthesis in Si+ plants at high disease severity as compared to Si- plants. CONCLUSION Silicon-mediated activation of callose and H2 O2 are decisive factors in the defence of rose against P. pannosa and these responses were accompanied with more efficient photosynthesis to strengthen the plant. Only by isolation of HR cells using laser capture microdissection as compared to analysis of whole leaf tissues allowed detection of elevated transcript levels of hsr203J and GSL5 at infection sites as markers for HR. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Radhakrishna Shetty
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Faculty of Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Birgit Jensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Faculty of Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Dale Shelton
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Faculty of Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kirsten Jørgensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Faculty of Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Pai Pedas
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Faculty of Sciences, University of Copenhagen, Frederiksberg C, Denmark
- Carlsberg Research Laboratory, Carlsberg Group, J.C. Jacobsens Gade 1, Copenhagen V, Denmark
| | - Hans Jørgen Lyngs Jørgensen
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Centre, Faculty of Sciences, University of Copenhagen, Frederiksberg C, Denmark
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Wang Z, Cantrell LS, Schey KL. Spatially Resolved Proteomic Analysis of the Lens Extracellular Diffusion Barrier. Invest Ophthalmol Vis Sci 2021; 62:25. [PMID: 34554179 PMCID: PMC8475287 DOI: 10.1167/iovs.62.12.25] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/05/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose The presence of a physical barrier to molecular diffusion through lenticular extracellular space has been repeatedly detected. This extracellular diffusion barrier has been proposed to restrict the movement of solutes into the lens and to direct nutrients into the lens core via the sutures at both poles. The purpose of this study is to characterize the molecular components that could contribute to the formation of this barrier. Methods Three distinct regions in the bovine lens cortex were captured by laser capture microdissection guided by dye penetration. Proteins were digested by Lys C and trypsin. Mass spectrometry-based proteomic analysis followed by gene ontology and protein interaction network analysis was performed. Results Dye penetration showed that fiber cells first shrink the extracellular spaces of the broad sides followed by closure of the extracellular space between narrow sides at a normalized lens distance (r/a) of 0.9. Accompanying the closure of extracellular space of the broad sides, dramatic proteomic changes were detected, including upregulation of several cell junctional proteins. AQP0 and its interacting partners, Ezrin and Radixin, were among a few proteins that were upregulated, accompanying the closure of extracellular space of the narrow sides, suggesting a particularly important role for AQP0 in controlling the narrowing of the extracellular spaces between fiber cells. The results also provided important information related to biological processes that occur during fiber cell differentiation such as organelle degradation, cytoskeletal remodeling, and glutathione synthesis. Conclusions The formation of a lens extracellular diffusion barrier is accompanied by significant membrane and cytoskeletal protein remodeling.
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Affiliation(s)
- Zhen Wang
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States
| | - Lee S. Cantrell
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States
| | - Kevin L. Schey
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee, United States
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Berkowitz O, Xu Y, Liew LC, Wang Y, Zhu Y, Hurgobin B, Lewsey MG, Whelan J. RNA-seq analysis of laser microdissected Arabidopsis thaliana leaf epidermis, mesophyll and vasculature defines tissue-specific transcriptional responses to multiple stress treatments. Plant J 2021; 107:938-955. [PMID: 33974297 DOI: 10.1111/tpj.15314] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/28/2021] [Accepted: 05/05/2021] [Indexed: 06/12/2023]
Abstract
Acclimation of plants to adverse conditions requires the coordination of gene expression and signalling pathways between tissues and cell types. As the energy and carbon capturing organs, leaves are significantly affected by abiotic and biotic stresses. However, tissue- or cell type-specific analyses of stress responses have focussed on the Arabidopsis root. Here, we comparatively explore the transcriptomes of three leaf tissues (epidermis, mesophyll, vasculature) after induction of diverse stress pathways by chemical stimuli (antimycin A, 3-amino-1,2,4-triazole, methyl viologen, salicylic acid) and ultraviolet light in Arabidopsis using laser capture microdissection followed by RNA sequencing. Stimulation of stress pathways caused an overall reduction in the number of genes expressed in a tissue-specific manner, though a small subset gained or changed their tissue specificity. We find no evidence of a common stress response, with only a few genes consistently responsive to two or more treatments in the analysed tissues. However, differentially expressed genes overlap between tissues for individual treatments. A focussed analysis provided evidence for an interaction of auxin and ethylene that mediates retrograde signalling during mitochondrial dysfunction specifically in the epidermis, and a gene regulatory network defined the hierarchy of interactions. Taken together, we have generated an extensive reference dataset that will be valuable for future experiments analysing transcriptional responses on a tissue or single-cell level. Our results will enable the tailoring of the tissue-specific engineering of stress-tolerant plants.
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Affiliation(s)
- Oliver Berkowitz
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yue Xu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Lim Chee Liew
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yan Wang
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Yanqiao Zhu
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Bhavna Hurgobin
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - Mathew G Lewsey
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, AgriBio Building La Trobe University, Bundoora, Victoria, 3086, Australia
- Australian Research Council Research Hub for Medicinal Agriculture, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
- Department of Animal, Plant and Soil Science, La Trobe University, AgriBio Building, Bundoora, Victoria, 3086, Australia
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Hua L, Stevenson SR, Reyna-Llorens I, Xiong H, Kopriva S, Hibberd JM. The bundle sheath of rice is conditioned to play an active role in water transport as well as sulfur assimilation and jasmonic acid synthesis. Plant J 2021; 107:268-286. [PMID: 33901336 DOI: 10.1111/tpj.15292] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 06/12/2023]
Abstract
Leaves comprise multiple cell types but our knowledge of the patterns of gene expression that underpin their functional specialization is fragmentary. Our understanding and ability to undertake the rational redesign of these cells is therefore limited. We aimed to identify genes associated with the incompletely understood bundle sheath of C3 plants, which represents a key target associated with engineering traits such as C4 photosynthesis into Oryza sativa (rice). To better understand the veins, bundle sheath and mesophyll cells of rice, we used laser capture microdissection followed by deep sequencing. Gene expression of the mesophyll is conditioned to allow coenzyme metabolism and redox homeostasis, as well as photosynthesis. In contrast, the bundle sheath is specialized in water transport, sulphur assimilation and jasmonic acid biosynthesis. Despite the small chloroplast compartment of bundle sheath cells, substantial photosynthesis gene expression was detected. These patterns of gene expression were not associated with the presence or absence of specific transcription factors in each cell type, but were instead associated with gradients in expression across the leaf. Comparative analysis with C3 Arabidopsis identified a small gene set preferentially expressed in the bundle sheath cells of both species. This gene set included genes encoding transcription factors from 14 orthogroups and proteins allowing water transport, sulphate assimilation and jasmonic acid synthesis. The most parsimonious explanation for our findings is that bundle sheath cells from the last common ancestor of rice and Arabidopsis were specialized in this manner, and as the species diverged these patterns of gene expression have been maintained.
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Affiliation(s)
- Lei Hua
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Sean R Stevenson
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Ivan Reyna-Llorens
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Haiyan Xiong
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Stanislav Kopriva
- Institute for Plant Sciences, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Zülpicher Str. 47b, Cologne, 50674, Germany
| | - Julian M Hibberd
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
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Balasubramanian VK, Purvine SO, Liang Y, Kelly RT, Pasa-Tolic L, Chrisler WB, Blumwald E, Stewart CN, Zhu Y, Ahkami AH. Cell-Type-Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform. Curr Protoc 2021; 1:e153. [PMID: 34043287 DOI: 10.1002/cpz1.153] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plant organs and tissues contain multiple cell types, which are well organized in 3-dimensional structure to efficiently perform physiological functions such as homeostasis and response to environmental perturbation and pathogen infection. It is critically important to perform molecular measurements at the cell-type-specific level to discover mechanisms and unique features of cell populations that govern differentiation and respond to external perturbations. Although mass spectrometry-based proteomics has been demonstrated as an enabling discovery tool for studying plant physiology, conventional approaches require millions of cells to generate robust biological conclusions. Such requirements mask the cell-to-cell heterogeneities and limit the comprehensive profiling of plant proteins at spatially resolved and cell-type-specific resolutions. This article describes a recently developed proteomics workflow for studying a small number of plant cells by integrating laser capture microdissection, microfluidic nanodroplet-based sample preparation, and ultrasensitive liquid chromatography-mass spectrometry. Using poplar as a model tree species, we provide detailed protocols, including plant leaf and root tissue harvest, sample preparation, cryosectioning, laser microdissection, protein digestion, mass spectrometry measurement, and data analysis. We show that the workflow enables the precise identification and quantification of thousands of proteins from hundreds of isolated plant root and leaf cells. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Plant tissue fixation and embedding Support Protocol 1: Preparation of 2.5% CMC solution Support Protocol 2: Slow freezing of CMC blocks to avoid crack development in the block Basic Protocol 2: Preparation of cryosections Alternate Protocol: Using a vacuum manifold to dehydrate the cryosection slides (primarily for root tissues) Basic Protocol 3: Laser capture microdissection of specific types of plant cells Basic Protocol 4: Nanodroplet-based sample preparation for ultrasensitive proteomic analysis Support Protocol 3: Fabrication of nanowell chips Basic Protocol 5: Liquid chromatography and mass spectrometry.
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Affiliation(s)
- Vimal K Balasubramanian
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, California
| | - C Neal Stewart
- Department of Plant Sciences, Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, Tennessee
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
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Pandey S, Tuma Z, Smrhova T, Cedikova M, Macanova T, Chottova Dvorakova M. Laser Capture Microdissection Coupled Capillary Immunoassay to Study the Expression of PCK-2 on Spatially-Resolved Islets of Rat Langerhans. Pharmaceutics 2021; 13:pharmaceutics13060883. [PMID: 34203686 PMCID: PMC8232303 DOI: 10.3390/pharmaceutics13060883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 11/25/2022] Open
Abstract
The platform for precise proteomic profiling of targeted cell populations from heterogeneous tissue sections is developed. We demonstrate a seamless and systematic integration of LCM with an automated cap-IA for the handling of a very small-sized dissected tissues section from the kidney, liver and pancreatic Langerhans islet of rats. Our analysis reveals that the lowest LCM section area ≥ 0.125 mm2 with 10 µm thickness can be optimized for the detection of proteins through LCM-cap-IA integration. We detect signals ranging from a highly-abundant protein, β-actin, to a low-abundance protein, LC-3AB, using 0.125 mm2 LCM section from rat kidney, but, so far, a relatively large section is required for good quality of results. This integration is applicable for a highly-sensitive and accurate assessment of microdissected tissue sections to decipher hidden proteomic information of pure targeted cells. To validate this integration, PCK2 protein expression is studied within Langerhans islets of normal and diabetic rats. Our results show significant overexpression of PCK2 in Langerhans islets of rats with long-term diabetes.
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Affiliation(s)
- Shashank Pandey
- Department of Pharmacology and Toxicology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic; (Z.T.); (M.C.); (M.C.D.)
- Correspondence:
| | - Zdenek Tuma
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic; (Z.T.); (M.C.); (M.C.D.)
| | - Tereza Smrhova
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic;
| | - Miroslava Cedikova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic; (Z.T.); (M.C.); (M.C.D.)
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic;
| | - Tereza Macanova
- Department of Biology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic;
| | - Magdalena Chottova Dvorakova
- Biomedical Center, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic; (Z.T.); (M.C.); (M.C.D.)
- Department of Physiology, Faculty of Medicine in Pilsen, Charles University, Alej Svobody 1655/76, 32300 Pilsen, Czech Republic;
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Cefalo CMA, Mezza T, Giaccari A, Kulkarni RN. A Systematic Comparison of Protocols for Recovery of High-Quality RNA from Human Islets Extracted by Laser Capture Microdissection. Biomolecules 2021; 11:625. [PMID: 33922227 DOI: 10.3390/biom11050625] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 12/21/2022] Open
Abstract
The isolation of high-quality RNA from endocrine pancreas sections represents a considerable challenge largely due to the high ribonuclease levels. Laser capture microdissection (LCM) of mammalian islets, in association with RNA extraction protocols, has emerged as a feasible approach to characterizing their genetic and proteomic profiles. However, a validated protocol to obtain high-quality RNA from LCM-derived human pancreas specimens that is appropriate for next-generation sequencing analysis is still lacking. In this study, we applied four methods (Picopure extraction kit, Qiazol protocol, Qiazol + Clean-up kit, and RNeasy Microkit + Carrier) to extract RNA from human islets obtained from both non-diabetic individuals and patients with type 2 diabetes who had undergone partial pancreatectomy, as well as handpicked islets from both non-diabetic and diabetic organ donors. The yield and purity of total RNA were determined by 260/280 absorbance using Nanodrop 100 and the RNA integrity number with a bioanalyzer. The results indicated that among the four methods, the RNeasy MicroKit + Carrier (Qiagen) provides the highest yield and purity.
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Marcu A, Nitusca D, Vaduva A, Baderca F, Cireap N, Coricovac D, Dehelean CA, Seclaman E, Ilina R, Marian C. Long Non-Coding RNA Expression in Laser Micro-Dissected Luminal A and Triple Negative Breast Cancer Tissue Samples-A Pilot Study. ACTA ACUST UNITED AC 2021; 57:medicina57040371. [PMID: 33921283 PMCID: PMC8069050 DOI: 10.3390/medicina57040371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/05/2021] [Accepted: 04/08/2021] [Indexed: 01/04/2023]
Abstract
Background and Objectives: Breast cancer (BC) remains one of the major causes of cancer death in women worldwide. The difficulties in assessing the deep molecular mechanisms involved in this pathology arise from its high complexity and diverse tissue subtypes. Long non-coding RNAs (lncRNAs) were shown to have great tissue specificity, being differentially expressed within the BC tissue subtypes. Materials and Methods: Herein, we performed lncRNA profiling by PCR array in triple negative breast cancer (TNBC) and luminal A tissue samples from 18 BC patients (nine TNBC and nine luminal A), followed by individual validation in BC tissue and cell lines. Tissue samples were previously archived in formalin-fixed paraffin-embedded (FFPE) samples, and the areas of interest were dissected using laser capture microdissection (LCM) technology. Results: Two lncRNAs (OTX2-AS1 and SOX2OT) were differentially expressed in the profiling analysis (fold change of 205.22 and 0.02, respectively, p < 0.05 in both cases); however, they did not reach statistical significance in the individual validation measurement (p > 0.05) when analyzed with specific individual assays. In addition, GAS5 and NEAT1 lncRNAs were individually assessed as they were previously described in the literature as being associated with BC. GAS5 was significantly downregulated in both TNBC tissues and cell lines compared to luminal A samples, while NEAT1 was significantly downregulated only in TNBC cells vs. luminal A. Conclusions: Therefore, we identified GAS5 lncRNA as having a differential expression in TNBC tissues and cells compared to luminal A, with possible implications in the molecular mechanisms of the TNBC subtype. This proof of principle study also suggests that LCM could be a useful technique for limiting the sample heterogeneity for lncRNA gene expression analysis in BC FFPE tissues. Future studies of larger cohort sizes are needed in order to assess the biomarker potential of lncRNA GAS5 in BC.
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Affiliation(s)
- Anca Marcu
- Department of Biochemistry and Pharmacology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr.2, 300041 Timişoara, Romania; (A.M.); (D.N.); (E.S.); (C.M.)
| | - Diana Nitusca
- Department of Biochemistry and Pharmacology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr.2, 300041 Timişoara, Romania; (A.M.); (D.N.); (E.S.); (C.M.)
| | - Adrian Vaduva
- Department of Microscopic Morphology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr.2, 300041 Timişoara, Romania; (A.V.); (F.B.)
| | - Flavia Baderca
- Department of Microscopic Morphology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr.2, 300041 Timişoara, Romania; (A.V.); (F.B.)
- Department of Pathology, Emergency City Hospital, 300041 Timişoara, Romania
| | - Natalia Cireap
- Department of Surgical Oncology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr.2, 300041 Timişoara, Romania;
- Department of Surgical Oncology, Municipal Hospital, Str. Gheorghe Dima Nr.5, 300254 Timişoara, Romania
| | - Dorina Coricovac
- Faculty of Pharmacy, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (D.C.); (C.A.D.)
| | - Cristina Adriana Dehelean
- Faculty of Pharmacy, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (D.C.); (C.A.D.)
| | - Edward Seclaman
- Department of Biochemistry and Pharmacology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr.2, 300041 Timişoara, Romania; (A.M.); (D.N.); (E.S.); (C.M.)
| | - Razvan Ilina
- Department of Surgical Oncology, Municipal Hospital, Str. Gheorghe Dima Nr.5, 300254 Timişoara, Romania
- Correspondence:
| | - Catalin Marian
- Department of Biochemistry and Pharmacology, Victor Babeş University of Medicine and Pharmacy, Pta Eftimie Murgu Nr.2, 300041 Timişoara, Romania; (A.M.); (D.N.); (E.S.); (C.M.)
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49
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Nitusca D, Marcu A, Dema A, Balacescu L, Balacescu O, Bardan R, Cumpanas AA, Sirbu IO, Petrut B, Seclaman E, Marian C. Long Noncoding RNA NEAT1 as a Potential Candidate Biomarker for Prostate Cancer. Life (Basel) 2021; 11:life11040320. [PMID: 33917553 PMCID: PMC8067529 DOI: 10.3390/life11040320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 11/18/2022] Open
Abstract
Background: Prostate cancer (PCa) remains one of the leading causes of cancer-related mortality in men worldwide, mainly due to unsatisfactory diagnostic methods used at present, which lead to overdiagnosis, unnecessary biopsies and treatment, or misdiagnosis in early asymptomatic stages. New diagnostic biomarkers are needed for a correct and early diagnosis. Long noncoding RNAs (lncRNAs) have been broadly studied for their involvement in PCa biology, as well as for their potential role as diagnostic biomarkers. Methods: We conducted lncRNA profiling in plasma and microdissected formalin-fixed paraffin-embedded (FFPE) tissues of PCa patients and attempted validation for commonly dysregulated individual lncRNAs. Results: Plasma profiling revealed eight dysregulated lncRNAs, while microarray analysis revealed 717 significantly dysregulated lncRNAs, out of which only nuclear-enriched abundant transcript 1 (NEAT1) was commonly upregulated in plasma samples and FFPE tissues. NEAT1’s individual validation revealed statistically significant upregulation (FC = 2.101, p = 0.009). Receiver operating characteristic (ROC) analysis showed an area under the curve (AUC) value of 0.7298 for NEAT1 (95% CI = 0.5812–0.8785), suggesting a relatively high diagnostic value, thus having a potential biomarker role for this malignancy. Conclusions: We present herein data suggesting that NEAT1 could serve as a diagnostic biomarker for PCa. Additional studies of larger cohorts are needed to confirm our findings, as well as the oncogenic mechanism of NEAT1 in the development of PCa.
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Affiliation(s)
- Diana Nitusca
- Department of Biochemistry and Pharmacology, “Victor Babeş” University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (D.N.); (A.M.); (I.O.S.); (E.S.)
| | - Anca Marcu
- Department of Biochemistry and Pharmacology, “Victor Babeş” University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (D.N.); (A.M.); (I.O.S.); (E.S.)
| | - Alis Dema
- Department of Pathology, “Victor Babeş” University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania;
| | - Loredana Balacescu
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 400015 Cluj-Napoca, Romania; (L.B.); (O.B.)
| | - Ovidiu Balacescu
- Department of Genetics, Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 400015 Cluj-Napoca, Romania; (L.B.); (O.B.)
| | - Razvan Bardan
- Department of Urology, “Victor Babeş” University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (R.B.); (A.A.C.)
- Urology Clinic, Timisoara Emergency County Hospital, 300723 Timisoara, Romania
| | - Alin Adrian Cumpanas
- Department of Urology, “Victor Babeş” University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (R.B.); (A.A.C.)
- Urology Clinic, Timisoara Emergency County Hospital, 300723 Timisoara, Romania
| | - Ioan Ovidiu Sirbu
- Department of Biochemistry and Pharmacology, “Victor Babeş” University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (D.N.); (A.M.); (I.O.S.); (E.S.)
| | - Bogdan Petrut
- Department of Urology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 400015 Cluj-Napoca, Romania;
| | - Edward Seclaman
- Department of Biochemistry and Pharmacology, “Victor Babeş” University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (D.N.); (A.M.); (I.O.S.); (E.S.)
| | - Catalin Marian
- Department of Biochemistry and Pharmacology, “Victor Babeş” University of Medicine and Pharmacy, Pta Eftimie Murgu Nr. 2, 300041 Timişoara, Romania; (D.N.); (A.M.); (I.O.S.); (E.S.)
- Correspondence:
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50
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Chen M, Lin JY, Wu X, Apuya NR, Henry KF, Le BH, Bui AQ, Pelletier JM, Cokus S, Pellegrini M, Harada JJ, Goldberg RB. Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies. Proc Natl Acad Sci U S A 2021; 118:e2024704118. [PMID: 33536344 PMCID: PMC8017943 DOI: 10.1073/pnas.2024704118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
An important question is what genes govern the differentiation of plant embryos into suspensor and embryo proper regions following fertilization and division of the zygote. We compared embryo proper and suspensor transcriptomes of four plants that vary in embryo morphology within the suspensor region. We determined that genes encoding enzymes in several metabolic pathways leading to the formation of hormones, such as gibberellic acid, and other metabolites are up-regulated in giant scarlet runner bean and common bean suspensors. Genes involved in transport and Golgi body organization are up-regulated within the suspensors of these plants as well, strengthening the view that giant specialized suspensors serve as a hormone factory and a conduit for transferring substances to the developing embryo proper. By contrast, genes controlling transcriptional regulation, development, and cell division are up-regulated primarily within the embryo proper. Transcriptomes from less specialized soybean and Arabidopsis suspensors demonstrated that fewer genes encoding metabolic enzymes and hormones are up-regulated. Genes active in the embryo proper, however, are functionally similar to those active in scarlet runner bean and common bean embryo proper regions. We uncovered a set of suspensor- and embryo proper-specific transcription factors (TFs) that are shared by all embryos irrespective of morphology, suggesting that they are involved in early differentiation processes common to all plants. Chromatin immunoprecipitation sequencing (ChIP-Seq) experiments with scarlet runner bean and soybean WOX9, an up-regulated suspensor TF, gained entry into a regulatory network important for suspensor development irrespective of morphology.
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Affiliation(s)
- Min Chen
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Jer-Young Lin
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Xiaomeng Wu
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Nestor R Apuya
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Kelli F Henry
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Brandon H Le
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Anhthu Q Bui
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Julie M Pelletier
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Shawn Cokus
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - Matteo Pellegrini
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095
| | - John J Harada
- Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA 95616
| | - Robert B Goldberg
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095;
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