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Jain V, Sakhuja P, Agarwal AK, Sirdeshmukh R, Siraj F, Gautam P. Lymph Node Metastasis in Gastrointestinal Carcinomas: A View from a Proteomics Perspective. Curr Oncol 2024; 31:4455-4475. [PMID: 39195316 DOI: 10.3390/curroncol31080333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/14/2024] [Accepted: 05/23/2024] [Indexed: 08/29/2024] Open
Abstract
Lymph node metastasis (LNM) is one of the major prognostic factors in human gastrointestinal carcinomas (GICs). The lymph node-positive patients have poorer survival than node-negative patients. LNM is directly associated with the recurrence and poor survival of patients with GICs. The early detection of LNM in patients and designing effective therapies to suppress LNM may significantly impact the survival of these patients. The rapid progress made in proteomic technologies could be successfully applied to identify molecular targets for cancers at high-throughput levels. LC-MS/MS analysis enables the identification of proteins involved in LN metastasis, which can be utilized for diagnostic and therapeutic applications. This review summarizes the studies on LN metastasis in GICs using proteomic approaches to date.
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Affiliation(s)
- Vaishali Jain
- Indian Council of Medical Research, National Institute of Pathology, New Delhi 110029, India
- Faculty of Health Sciences, Manipal Academy of Higher Education (MAHE), Manipal 576104, India
| | - Puja Sakhuja
- Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi 110002, India
| | - Anil Kumar Agarwal
- Govind Ballabh Pant Institute of Postgraduate Medical Education and Research (GIPMER), New Delhi 110002, India
| | - Ravi Sirdeshmukh
- Faculty of Health Sciences, Manipal Academy of Higher Education (MAHE), Manipal 576104, India
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Fouzia Siraj
- Indian Council of Medical Research, National Institute of Pathology, New Delhi 110029, India
| | - Poonam Gautam
- Indian Council of Medical Research, National Institute of Pathology, New Delhi 110029, India
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Gould R, Brady S. Identifying mRNAs Residing in Myelinating Oligodendrocyte Processes as a Basis for Understanding Internode Autonomy. Life (Basel) 2023; 13:life13040945. [PMID: 37109474 PMCID: PMC10142070 DOI: 10.3390/life13040945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/07/2023] Open
Abstract
In elaborating and maintaining myelin sheaths on multiple axons/segments, oligodendrocytes distribute translation of some proteins, including myelin basic protein (MBP), to sites of myelin sheath assembly, or MSAS. As mRNAs located at these sites are selectively trapped in myelin vesicles during tissue homogenization, we performed a screen to identify some of these mRNAs. To confirm locations, we used real-time quantitative polymerase chain reaction (RT-qPCR), to measure mRNA levels in myelin (M) and ‘non-myelin’ pellet (P) fractions, and found that five (LPAR1, TRP53INP2, TRAK2, TPPP, and SH3GL3) of thirteen mRNAs were highly enriched in myelin (M/P), suggesting residences in MSAS. Because expression by other cell-types will increase p-values, some MSAS mRNAs might be missed. To identify non-oligodendrocyte expression, we turned to several on-line resources. Although neurons express TRP53INP2, TRAK2 and TPPP mRNAs, these expressions did not invalidate recognitions as MSAS mRNAs. However, neuronal expression likely prevented recognition of KIF1A and MAPK8IP1 mRNAs as MSAS residents and ependymal cell expression likely prevented APOD mRNA assignment to MSAS. Complementary in situ hybridization (ISH) is recommended to confirm residences of mRNAs in MSAS. As both proteins and lipids are synthesized in MSAS, understanding myelination should not only include efforts to identify proteins synthesized in MSAS, but also the lipids.
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Affiliation(s)
- Robert Gould
- Whitman Research Center, Marine Biology Laboratory, Woods Hole, MA 02543, USA
| | - Scott Brady
- Departments of Anatomy and Cell Biology, University of Illinois at Chicago, Chicago, IL 60612, USA
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Pisano A, Pera LL, Carletti R, Cerbelli B, Pignataro MG, Pernazza A, Ferre F, Lombardi M, Lazzeroni D, Olivotto I, Rimoldi OE, Foglieni C, Camici PG, d'Amati G. RNA-seq profiling reveals different pathways between remodeled vessels and myocardium in hypertrophic cardiomyopathy. Microcirculation 2022; 29:e12790. [PMID: 36198058 PMCID: PMC9787970 DOI: 10.1111/micc.12790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 09/01/2022] [Accepted: 09/30/2022] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Coronary microvascular dysfunction (CMD) is a key pathophysiological feature of hypertrophic cardiomyopathy (HCM), contributing to myocardial ischemia and representing a critical determinant of patients' adverse outcome. The molecular mechanisms underlying the morphological and functional changes of CMD are still unknown. Aim of this study was to obtain insights on the molecular pathways associated with microvessel remodeling in HCM. METHODS Interventricular septum myectomies from patients with obstructive HCM (n = 20) and donors' hearts (CTRL, discarded for technical reasons, n = 7) were collected. Remodeled intramyocardial arterioles and cardiomyocytes were microdissected by laser capture and next-generation sequencing was used to delineate the transcriptome profile. RESULTS We identified 720 exclusive differentially expressed genes (DEGs) in cardiomyocytes and 1315 exclusive DEGs in remodeled arterioles of HCM. Performing gene ontology and pathway enrichment analyses, we identified selectively altered pathways between remodeled arterioles and cardiomyocytes in HCM patients and controls. CONCLUSIONS We demonstrate the existence of distinctive pathways between remodeled arterioles and cardiomyocytes in HCM patients and controls at the transcriptome level.
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Affiliation(s)
- Annalinda Pisano
- Department of Radiological, Oncological and Pathological SciencesSapienza University of RomeRomeItaly
| | - Loredana Le Pera
- Italian National Institute of Health (ISS), Core FacilitiesRomeItaly
- National Research Council (IBIOM‐CNR)Institute of Biomembranes, Bioenergetics and Molecular BiotechnologiesBariItaly
| | - Raffaella Carletti
- Department of Translational and Precision MedicineSapienza University of RomeRomeItaly
| | - Bruna Cerbelli
- Department of Medico‐Surgical Sciences and BiotechnologiesSapienza University of RomeLatinaItaly
| | - Maria G. Pignataro
- Department of Chemistry and Drug TechnologiesSapienza University of RomeRomeItaly
| | - Angelina Pernazza
- Department of Medico‐Surgical Sciences and BiotechnologiesSapienza University of RomeLatinaItaly
| | - Fabrizio Ferre
- Department of Pharmacy and Biotechnology (FABIT)University of BolognaBolognaItaly
| | - Maria Lombardi
- Cardiovascular Research CenterIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Davide Lazzeroni
- Cardiovascular Research CenterIRCCS San Raffaele Scientific InstituteMilanItaly
| | | | - Ornella E. Rimoldi
- National Research Council (IBFM‐CNR)Institute of Molecular Bioimaging and PhysiologyMilanItaly
| | - Chiara Foglieni
- Cardiovascular Research CenterIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Paolo G. Camici
- Cardiovascular Research CenterIRCCS San Raffaele Scientific InstituteMilanItaly
- Faculty of Medicine and SurgeryVita‐Salute UniversityMilanItaly
| | - Giulia d'Amati
- Department of Radiological, Oncological and Pathological SciencesSapienza University of RomeRomeItaly
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Dong C, Donnarumma F, Murray KK. Infrared Laser Ablation Microsampling for Small Volume Proteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1003-1010. [PMID: 35536596 DOI: 10.1021/jasms.2c00063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Infrared (IR) laser ablation was used to remove localized tissue regions from which proteins were extracted and processed with a low volume sample preparation workflow for bottom-up proteomics by liquid chromatography tandem mass spectrometry (LC-MS/MS). A polytetrafluoroethylene (PTFE) coated glass slide with 2 mm diameter microwells was used to capture ablated rat brain tissue for in situ protein digestion with submicroliter solution volumes. The resulting peptides were analyzed with LC-MS/MS for protein identification and label-free quantification. The method was used to identify an average of 600, 1350, and 1900 proteins from ablation areas of 0.01, 0.04, and 0.1 mm2, respectively, from a 50 μm thick rat brain tissue section. Differential proteomics of 0.01 mm2 regions captured from cerebral cortex and corpus callosum was accomplished to demonstrate the capabilities of the approach.
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Affiliation(s)
- Chao Dong
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Fabrizio Donnarumma
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kermit K Murray
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Dong C, Richardson LT, Solouki T, Murray KK. Infrared Laser Ablation Microsampling with a Reflective Objective. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:463-470. [PMID: 35104132 PMCID: PMC8895455 DOI: 10.1021/jasms.1c00306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
A Schwarzschild reflective objective with a numerical aperture of 0.3 and working distance of 10 cm was used for laser ablation sampling of tissue for off-line mass spectrometry. The objective focused the laser to a diameter of 5 μm and produced 10 μm ablation spots on thin ink films and tissue sections. Rat brain tissue sections 50 μm thick were ablated in transmission geometry, and the ablated material was captured in a microcentrifuge tube containing solvent. Proteins from ablated tissue sections were quantified with a Bradford assay, which indicated that approximately 300 ng of protein was captured from a 1 mm2 area of ablated tissue. Areas of tissue ranging from 0.01 to 1 mm2 were ablated and captured for bottom-up proteomics. Proteins were extracted from the captured tissue and digested for liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for peptide and protein identification.
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Affiliation(s)
- Chao Dong
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Luke T. Richardson
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Touradj Solouki
- Department
of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Kermit K. Murray
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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Chen Y, Jiang H, Xiong J, Shang J, Chen Z, Wu A, Wang H. Insight into the Molecular Characteristics of Langhans Giant Cell by Combination of Laser Capture Microdissection and RNA Sequencing. J Inflamm Res 2022; 15:621-634. [PMID: 35140495 PMCID: PMC8818977 DOI: 10.2147/jir.s337241] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 01/16/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose The presence of Langhans giant cell (LGC) is a hallmark of mycobacterium-induced granuloma. The molecular characteristics and functions of LGC remain unclear to date. The study aimed to systematically characterize the molecular characteristics of LGC and reveal the potential functions. Methods Human LGCs were purified through laser capture microdissection (LCM) in vitro. RNA sequencing and in-depth transcriptome analysis were performed for purified LGCs and macrophages in the same system. Skin samples from mycobacterial infection patients were used to confirm some of the transcriptional expression. Results Human LGCs have different expression pattern from macrophages in the same in vitro system. A total of 967 differentially expressed genes were found. Bioinformatics analysis showed that LGCs are is characterized by active cell shape regulation, increased cytoskeletal components, weakened energy metabolism level, and reduced immune response. CCL7 may be a specific molecular for LGC to communicate with CCR1-expression cells in granuloma. Conclusion LGCs have unique molecular characteristics different from that of macrophages. They may play a role in maintaining the hemostasis in granuloma.
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Affiliation(s)
- Yanqing Chen
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, People’s Republic of China
| | - Haiqin Jiang
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, People’s Republic of China
| | - Jingshu Xiong
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, People’s Republic of China
| | - Jingzhe Shang
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, People’s Republic of China
- Center of Systems Medicine, Suzhou Institute of Systems Medicine, Suzhou, People’s Republic of China
| | - Zhiming Chen
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, People’s Republic of China
| | - Aiping Wu
- Center for Systems Medicine, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Suzhou, People’s Republic of China
- Center of Systems Medicine, Suzhou Institute of Systems Medicine, Suzhou, People’s Republic of China
| | - Hongsheng Wang
- Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, People’s Republic of China
- Correspondence: Hongsheng Wang; Haiqin Jiang, Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, No. 12, St Jiangwangmiao, Nanjing, 210042, Jiangsu, People’s Republic of China, Tel +86-25-85478953, Fax +86-25-85478944, Email ;
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Wu Y, Guo T, Li J, Niu C, Sun W, Zhu S, Zhao H, Qiao G, Han M, He X, Lu Z, Yuan C, Han J, Liu J, Yang B, Yue Y. The Transcriptional Cell Atlas of Testis Development in Sheep at Pre-Sexual Maturity. Curr Issues Mol Biol 2022; 44:483-497. [PMID: 35723319 PMCID: PMC8929108 DOI: 10.3390/cimb44020033] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 01/15/2022] [Accepted: 01/16/2022] [Indexed: 12/12/2022] Open
Abstract
Sheep testes undergo a dramatic rate of development with structural changes during pre-sexual maturity, including the proliferation and maturation of somatic niche cells and the initiation of spermatogenesis. To explore this complex process, 12,843 testicular cells from three males at pre-sexual maturity (three-month-old) were sequenced using the 10× Genomics ChromiumTM single-cell RNA-seq (scRNA-seq) technology. Nine testicular somatic cell types (Sertoli cells, myoid cells, monocytes, macrophages, Leydig cells, dendritic cells, endothelial cells, smooth muscle cells, and leukocytes) and an unknown cell cluster were observed. In particular, five male germ cell types (including two types of undifferentiated spermatogonia (Apale and Adark), primary spermatocytes, secondary spermatocytes, and sperm cells) were identified. Interestingly, Apale and Adark were found to be two distinct states of undifferentiated spermatogonia. Further analysis identified specific marker genes, including UCHL1, DDX4, SOHLH1, KITLG, and PCNA, in the germ cells at different states of differentiation. The study revealed significant changes in germline stem cells at pre-sexual maturation, paving the way to explore the candidate factors and pathways for the regulation of germ and somatic cells, and to provide us with opportunities for the establishment of livestock stem cell breeding programs.
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Affiliation(s)
- Yi Wu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Jianye Li
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Weibo Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Guoyan Qiao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Mei Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Xue He
- College of Biological Sciences, Northwest Minzu University, Lanzhou 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory of Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
- Livestock Genetics Program, International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou 730050, China
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Zhang L, Li F, Lei P, Guo M, Liu R, Wang L, Yu T, Lv Y, Zhang T, Zeng W, Lu H, Zheng Y. Single-cell RNA-sequencing reveals the dynamic process and novel markers in porcine spermatogenesis. J Anim Sci Biotechnol 2021; 12:122. [PMID: 34872612 PMCID: PMC8650533 DOI: 10.1186/s40104-021-00638-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022] Open
Abstract
Background Spermatogenesis is the process by which male gametes are formed from spermatogonial stem cells and it is essential for the reliable transmission of genetic information between generations. To date, the dynamic transcriptional changes of defined populations of male germ cells in pigs have not been reported. Results To characterize the atlas of porcine spermatogenesis, we profiled the transcriptomes of ~ 16,966 testicular cells from a 150-day-old pig testis through single-cell RNA-sequencing (scRNA-seq). The scRNA-seq analysis identified spermatogonia, spermatocytes, spermatids and three somatic cell types in porcine testes. The functional enrichment analysis demonstrated that these cell types played diverse roles in porcine spermatogenesis. The accuracy of the defined porcine germ cell types was further validated by comparing the data from scRNA-seq with those from bulk RNA-seq. Since we delineated four distinct spermatogonial subsets, we further identified CD99 and PODXL2 as novel cell surface markers for undifferentiated and differentiating spermatogonia, respectively. Conclusions The present study has for the first time analyzed the transcriptome of male germ cells and somatic cells in porcine testes through scRNA-seq. Four subsets of spermatogonia were identified and two novel cell surface markers were discovered, which would be helpful for studies on spermatogonial differentiation in pigs. The datasets offer valuable information on porcine spermatogenesis, and pave the way for identification of key molecular markers involved in development of male germ cells. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00638-3.
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Affiliation(s)
- Lingkai Zhang
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fuyuan Li
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Peipei Lei
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ming Guo
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ruifang Liu
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, Shaanxi, China
| | - Taiyong Yu
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yinghua Lv
- College of Chemistry and Pharmacy, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, Shaanxi, China
| | - Wenxian Zeng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, 723001, Shaanxi, China.
| | - Yi Zheng
- Key Laboratory for Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Yang H, Ma J, Wan Z, Wang Q, Wang Z, Zhao J, Wang F, Zhang Y. Characterization of sheep spermatogenesis through single-cell RNA sequencing. FASEB J 2020; 35:e21187. [PMID: 33197070 DOI: 10.1096/fj.202001035rrr] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 10/20/2020] [Accepted: 10/29/2020] [Indexed: 12/15/2022]
Abstract
Spermatogenesis is an important biological process in male reproduction. The interaction between male germ cells and somatic cells during spermatogenesis, is necessary for male reproductive activities. This cellular heterogeneity has made it difficult to profile distinct cell types at different stages of development. Here, we present the first comprehensive, unbiased single-cell transcriptomic study of sheep spermatogenesis using 10× genomics single cell sequencing (scRNA-seq). We collected scRNA-seq data from 11 772 cells from the adult sheep testis and identified all known germ cells (including early primary spermatocytes, late primary spermatocytes, round spermatids, elongated spermatids, and sperm), and somatic cells (Sertoli cells and Leydig cells), as well as one somatic cell that unexpectedly contained leukocytes. The functional enrichment analysis indicated that several pathways of cell cycle, gamete generation, protein processing, and mRNA surveillance pathways were significantly enriched in testicular germ cell types, and ribosome pathway was significantly enriched in testicular somatic cell types. Further analysis identified several stage-specific marker genes of sheep germ cells, such as EZH2, SOX18, SCP2, PCNA, and PRKCD. Our research explored for the first time of the changes in the transcription level of various cell types during the process of sheep spermatogenesis, providing new insights for sheep spermatogenesis and spermatogenic cell development.
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Affiliation(s)
- Hua Yang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China
| | - Jianyu Ma
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zhen Wan
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China
| | - Qi Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China
| | - Zhibo Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China
| | - Jie Zhao
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China
| | - Feng Wang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China
| | - Yanli Zhang
- Jiangsu Livestock Embryo Engineering Laboratory, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, P.R. China
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Forsthoefel DJ, Cejda NI, Khan UW, Newmark PA. Cell-type diversity and regionalized gene expression in the planarian intestine. eLife 2020; 9:e52613. [PMID: 32240093 PMCID: PMC7117911 DOI: 10.7554/elife.52613] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 03/06/2020] [Indexed: 12/17/2022] Open
Abstract
Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration.
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Affiliation(s)
- David J Forsthoefel
- Genes and Human Disease Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Nicholas I Cejda
- Genes and Human Disease Research Program, Oklahoma Medical Research FoundationOklahoma CityUnited States
| | - Umair W Khan
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Phillip A Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
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Hodgson AJ, Shang YM, Boulianne P, Downes MR, Hwang D, Slodkowska E. A Practical Approach to Investigating Cross-Contaminants in the Anatomical Pathology Laboratory. Int J Surg Pathol 2020; 28:700-710. [PMID: 32188330 DOI: 10.1177/1066896920913110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Tissue contaminants in anatomical pathology are not uncommon. While issues related to the presence of extraneous tissue on glass slides are often easily resolved, this is not always the case and several factors may contribute to diagnostic difficulty. Because of this, familiarity with the different steps involved in handling specimens in the anatomical pathology laboratory is essential when troubleshooting possible cross-contaminants. Most commonly, the specimen constituting the source of cross-contamination is handled before the actual contaminated case; however, this is not always so. In this article, we review the steps involved in processing pathology specimens as they pertain to cross-contamination; share an approach covering how to troubleshoot and prevent tissue contaminants in a systematic and practical manner; present some examples from our own experiences; and compare our experience to what is reported in the literature. The information included in this article will be of use to all members of the anatomical pathology team including medical laboratory technologists, laboratory managers and supervisors, pathologist assistants, trainees in pathology, and pathologists.
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Affiliation(s)
- Anjelica J Hodgson
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
| | - Yan Ming Shang
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | | | - Michelle R Downes
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
| | - David Hwang
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
| | - Elzbieta Slodkowska
- Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,University of Toronto, Toronto, Ontario, Canada
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Basudan AM, Yang Y. Optimizing Laser Capture Microdissection Protocol for Isolating Zone-Specific Cell Populations from Mandibular Condylar Cartilage. Int J Dent 2019; 2019:5427326. [PMID: 31885587 PMCID: PMC6914897 DOI: 10.1155/2019/5427326] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/24/2019] [Accepted: 11/02/2019] [Indexed: 01/06/2023] Open
Abstract
Mandibular condylar cartilage (MCC) is a multizonal heterogeneous fibrocartilage consisting of fibrous (FZ), proliferative (PZ), mature (MZ), and hypertrophic (HZ) zones. Gross sampling of the whole tissue may conceal some important information and compromise the validity of the molecular analysis. Laser capture microdissection (LCM) technology allows isolating zonal (homogenous) cell populations and consequently generating more accurate molecular and genetic data, but the challenges during tissue preparation and microdissection procedures are to obtain acceptable tissue section morphology that allows histological identification of the desirable cell type and to minimize RNA degradation. Therefore, our aim is to optimize an LCM protocol for isolating four homogenous zone-specific cell populations from their respective MCC zones while preserving the quality of RNA recovered. MCC and FCC (femoral condylar cartilage) specimens were harvested from 5-week-old Sprague-Dawley male rats. Formalin-fixed and frozen unfixed tissue sections were prepared and compared histologically. Additional specimens were microdissected to prepare LCM samples from FCC and each MCC zone individually. Then, to evaluate LCM-RNA integrity, 3'/m ratios of glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and beta-actin (β-Actin) using quantitative reverse transcription-polymerase chain reaction (qRT-PCR) were calculated. Both fixed and unfixed tissue sections allowed reliable identification of MCC zones. The improved morphology of the frozen sections of our protocol has extended the range of cell types to be isolated. Under the empirically set LCM parameters, four homogeneous cell populations were efficiently isolated from their respective zones. The 3'/m ratio means of GAPDH and β-Actin ranged between 1.11-1.56 and 1.41-2.12, respectively. These values are in line with the reported quality control requirements. The present study shows that the optimized LCM protocol could allow isolation of four homogenous zone-specific cell populations from MCC, meanwhile preserving RNA integrity to meet the high quality requirements for subsequent molecular analyses. Thereby, accurate molecular and genetic data could be generated.
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Affiliation(s)
- Aisha M. Basudan
- Division of Orthodontics, Dental Services Department, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
- College of Dentistry King Saud Bin Abdulaziz University for Health Sciences (KSAU-HS), Riyadh, Saudi Arabia
| | - Yanqi Yang
- Department of Orthodontics, Faculty of Dentistry, The University of Hong Kong, Pokfulam, Hong Kong
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