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Zilberleyb I, Kugel C, Patel P, Tam C, Hsu PL, Franke Y, Pahuja KB. End-to-End Semi-automated Mid-scale Protein Screening Platform for Drug Discovery Research. Curr Protoc 2023; 3:e872. [PMID: 37671955 DOI: 10.1002/cpz1.872] [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: 09/07/2023]
Abstract
The drug discovery landscape is ever-evolving and constantly demands revolutionary technology advancements in protein expression and production laboratories. We have built a higher-throughput mid-scale semi-automated protein expression and screening platform to accelerate drug discovery research. The workflow described here enables comprehensive expression and purification screening assessment of challenging or difficult-to-express recombinant proteins in a fast and efficient manner by delivering small but sufficient amounts of high-quality proteins. The platform has been implemented for a wide range of applications that include identification of optimal constructs and chaperones for poorly expressing proteins, assessment of co-expression partners for expressing stable multiprotein complexes, and suitable buffer/additive screening for insoluble or aggregation-prone proteins. The approach allows parallel expression, purification, and characterization of 24 different samples using co-infection or a polycistronic approach in insect cells and enables parallel testing of multiple parameters to improve protein yields. The strategy has been successfully adopted for screening intracellular and secreted proteins in Escherichia coli, mammalian transient expression, and baculovirus expression vector systems. Proteins purified from this platform are used for several structural and functional screens, such as negative staining, biochemical activity assays, mass spectrometry, surface plasmon resonance, and DNA-encoded chemical library screens. In this article, for simplicity, we have focused on detailed expression and purification screening of intracellular protein complexes from insect cells. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Baculovirus generation via homologous recombination Support Protocol 1: Anti-glycoprotein 64 antibody assay Basic Protocol 2: Generation of insect cell biomass expressing target protein(s) Basic Protocol 3: Mid-scale affinity purification Support Protocol 2: Automated method for affinity purification on Hamilton STAR Basic Protocol 4: Size exclusion chromatography Support Protocol 3: Chromeleon 7 operation on Vanquish Duo.
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Affiliation(s)
- Inna Zilberleyb
- Biomolecular Research, Genentech, South San Francisco, California
| | - Christine Kugel
- Biomolecular Research, Genentech, South San Francisco, California
| | - Purvit Patel
- Biomolecular Research, Genentech, South San Francisco, California
| | - Christine Tam
- Biomolecular Research, Genentech, South San Francisco, California
| | - Peter L Hsu
- Structural Biology, Genentech, South San Francisco, California
| | - Yvonne Franke
- Biochemical and Cellular Pharmacology, Genentech, South San Francisco, California
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2
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Hsiao YC, Chen YJJ, Goldstein LD, Wu J, Lin Z, Schneider K, Chaudhuri S, Antony A, Bajaj Pahuja K, Modrusan Z, Seshasayee D, Seshagiri S, Hötzel I. Restricted epitope specificity determined by variable region germline segment pairing in rodent antibody repertoires. MAbs 2021; 12:1722541. [PMID: 32041466 PMCID: PMC7039645 DOI: 10.1080/19420862.2020.1722541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Indexed: 12/21/2022] Open
Abstract
Antibodies from B-cell clonal lineages share sequence and structural properties as well as epitope specificity. Clonally unrelated antibodies can similarly share sequence and specificity properties and are said to be convergent. Convergent antibody responses against several antigens have been described in humans and mice and include different classes of shared sequence features. In particular, some antigens and epitopes can induce convergent responses of clonally unrelated antibodies with restricted heavy (VH) and light (VL) chain variable region germline segment usage without similarity in the heavy chain third complementarity-determining region (CDR H3), a critical specificity determinant. Whether these V germline segment-restricted responses reflect a general epitope specificity restriction of antibodies with shared VH/VL pairing is not known. Here, we investigated this question by determining patterns of antigen binding competition between clonally unrelated antigen-specific rat antibodies from paired-chain deep sequencing datasets selected based solely on VH/VL pairing. We found that antibodies with shared VH/VL germline segment pairings but divergent CDR H3 sequences almost invariably have restricted epitope specificity indicated by shared binding competition patterns. This epitope restriction included 82 of 85 clonally unrelated antibodies with 13 different VH/VL pairings binding in 8 epitope groups in 2 antigens. The corollary that antibodies with shared VH/VL pairing and epitope-restricted binding can accommodate widely divergent CDR H3 sequences was confirmed by in vitro selection of variants of anti-human epidermal growth factor receptor 2 antibodies known to mediate critical antigen interactions through CDR H3. Our results show that restricted epitope specificity determined by VH/VL germline segment pairing is a general property of rodent antigen-specific antibodies.
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Affiliation(s)
- Yi-Chun Hsiao
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Ying-Jiun J Chen
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Leonard D Goldstein
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA.,Department of Bioinformatics and Computational Biology, Genentech, South San Francisco, CA, USA
| | - Jia Wu
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Zhonghua Lin
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Kellen Schneider
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Cochin, India
| | | | - Zora Modrusan
- Department of Molecular Biology, Genentech, South San Francisco, CA, USA
| | - Dhaya Seshasayee
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
| | | | - Isidro Hötzel
- Department of Antibody Engineering, Genentech, South San Francisco, CA, USA
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3
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Goldstein LD, Chen YJJ, Wu J, Chaudhuri S, Hsiao YC, Schneider K, Hoi KH, Lin Z, Guerrero S, Jaiswal BS, Stinson J, Antony A, Pahuja KB, Seshasayee D, Modrusan Z, Hötzel I, Seshagiri S. Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies. Commun Biol 2019; 2:304. [PMID: 31428692 PMCID: PMC6689056 DOI: 10.1038/s42003-019-0551-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [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: 01/17/2019] [Accepted: 07/15/2019] [Indexed: 01/24/2023] Open
Abstract
Obtaining full-length antibody heavy- and light-chain variable regions from individual B cells at scale remains a challenging problem. Here we use high-throughput single-cell B-cell receptor sequencing (scBCR-seq) to obtain accurately paired full-length variable regions in a massively parallel fashion. We sequenced more than 250,000 B cells from rat, mouse and human repertoires to characterize their lineages and expansion. In addition, we immunized rats with chicken ovalbumin and profiled antigen-reactive B cells from lymph nodes of immunized animals. The scBCR-seq data recovered 81% (n = 56/69) of B-cell lineages identified from hybridomas generated from the same set of B cells subjected to scBCR-seq. Importantly, scBCR-seq identified an additional 710 candidate lineages not recovered as hybridomas. We synthesized, expressed and tested 93 clones from the identified lineages and found that 99% (n = 92/93) of the clones were antigen-reactive. Our results establish scBCR-seq as a powerful tool for antibody discovery.
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Affiliation(s)
- Leonard D. Goldstein
- Molecular Biology, Genentech, South San Francisco, CA 94080 USA
- Bioinformatics & Computational Biology, Genentech, South San Francisco, CA 94080 USA
| | | | - Jia Wu
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | | | - Yi-Chun Hsiao
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Kellen Schneider
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Kam Hon Hoi
- Bioinformatics & Computational Biology, Genentech, South San Francisco, CA 94080 USA
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Zhonghua Lin
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Steve Guerrero
- Bioinformatics & Computational Biology, Genentech, South San Francisco, CA 94080 USA
| | | | - Jeremy Stinson
- Molecular Biology, Genentech, South San Francisco, CA 94080 USA
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Cochin, Kerala 682037 India
| | | | - Dhaya Seshasayee
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Zora Modrusan
- Molecular Biology, Genentech, South San Francisco, CA 94080 USA
| | - Isidro Hötzel
- Antibody Engineering, Genentech, South San Francisco, CA 94080 USA
| | - Somasekar Seshagiri
- Molecular Biology, Genentech, South San Francisco, CA 94080 USA
- Present Address: SciGenom Research Foundation, Bangalore, 560099 India
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4
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Pahuja KB, Nguyen TT, Jaiswal BS, Prabhash K, Thaker TM, Senger K, Chaudhuri S, Kljavin NM, Antony A, Phalke S, Kumar P, Mravic M, Stawiski EW, Vargas D, Durinck S, Gupta R, Khanna-Gupta A, Trabucco SE, Sokol ES, Hartmaier RJ, Singh A, Chougule A, Trivedi V, Dutt A, Patil V, Joshi A, Noronha V, Ziai J, Banavali SD, Ramprasad V, DeGrado WF, Bueno R, Jura N, Seshagiri S. Actionable Activating Oncogenic ERBB2/HER2 Transmembrane and Juxtamembrane Domain Mutations. Cancer Cell 2018; 34:792-806.e5. [PMID: 30449325 PMCID: PMC6248889 DOI: 10.1016/j.ccell.2018.09.010] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/26/2018] [Accepted: 09/24/2018] [Indexed: 02/08/2023]
Abstract
Deregulated HER2 is a target of many approved cancer drugs. We analyzed 111,176 patient tumors and identified recurrent mutations in HER2 transmembrane domain (TMD) and juxtamembrane domain (JMD) that include G660D, R678Q, E693K, and Q709L. Using a saturation mutagenesis screen and testing of patient-derived mutations we found several activating TMD and JMD mutations. Structural modeling and analysis showed that the TMD/JMD mutations function by improving the active dimer interface or stabilizing an activating conformation. Further, we found that HER2 G660D employed asymmetric kinase dimerization for activation and signaling. Importantly, anti-HER2 antibodies and small-molecule kinase inhibitors blocked the activity of TMD/JMD mutants. Consistent with this, a G660D germline mutant lung cancer patient showed remarkable clinical response to HER2 blockade.
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Affiliation(s)
- Kanika Bajaj Pahuja
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Tarjani M Thaker
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA
| | - Kate Senger
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Noelyn M Kljavin
- Molecular Oncology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Aju Antony
- Department of Molecular Biology, SciGenom Labs, Cochin, Kerala 682037, India
| | - Sameer Phalke
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Prasanna Kumar
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA; Bioinformatics and Computational Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Derek Vargas
- Research and Development Department, MedGenome Inc., Foster City, CA 94404, USA
| | - Steffen Durinck
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA; Bioinformatics and Computational Biology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | - Ravi Gupta
- Bioinformatics Department, MeGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Arati Khanna-Gupta
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - Sally E Trabucco
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ethan S Sokol
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ryan J Hartmaier
- Foundation Medicine Inc., 150 Second Street, Cambridge, MA 02141, USA
| | - Ashish Singh
- Department of Medical Oncology, Christian Medical College and Hospital, Vellore 632004, India
| | | | | | - Amit Dutt
- ACTREC, Tata Memorial Centre, Navi Mumbai 410210, India; Homi Bhaba National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Vijay Patil
- Tata Memorial Hospital, Parel, Mumbai 400012, India
| | - Amit Joshi
- Tata Memorial Hospital, Parel, Mumbai 400012, India
| | | | - James Ziai
- Pathology Department, Genentech Inc., South San Francisco, CA 94080, USA
| | | | - Vedam Ramprasad
- Research Division, MedGenome Labs Pvt. Ltd., Bangalore, Karnataka 560099, India
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Raphael Bueno
- Division of Thoracic Surgery, The Lung Center and the International Mesothelioma Program, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Natalia Jura
- Cardiovascular Research Institute, University of California San Francisco, San Francisco, CA 94158, USA; Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech Inc., South San Francisco, CA 94080, USA.
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5
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Mohan V, Radha V, Nguyen TT, Stawiski EW, Pahuja KB, Goldstein LD, Tom J, Anjana RM, Kong-Beltran M, Bhangale T, Jahnavi S, Chandni R, Gayathri V, George P, Zhang N, Murugan S, Phalke S, Chaudhuri S, Gupta R, Zhang J, Santhosh S, Stinson J, Modrusan Z, Ramprasad VL, Seshagiri S, Peterson AS. Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India. BMC Med Genet 2018; 19:22. [PMID: 29439679 PMCID: PMC5811965 DOI: 10.1186/s12881-018-0528-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 01/19/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND Maturity-onset diabetes of the young (MODY) is an early-onset, autosomal dominant form of non-insulin dependent diabetes. Genetic diagnosis of MODY can transform patient management. Earlier data on the genetic predisposition to MODY have come primarily from familial studies in populations of European origin. METHODS In this study, we carried out a comprehensive genomic analysis of 289 individuals from India that included 152 clinically diagnosed MODY cases to identify variants in known MODY genes. Further, we have analyzed exome data to identify putative MODY relevant variants in genes previously not implicated in MODY. Functional validation of MODY relevant variants was also performed. RESULTS We found MODY 3 (HNF1A; 7.2%) to be most frequently mutated followed by MODY 12 (ABCC8; 3.3%). They together account for ~ 11% of the cases. In addition to known MODY genes, we report the identification of variants in RFX6, WFS1, AKT2, NKX6-1 that may contribute to development of MODY. Functional assessment of the NKX6-1 variants showed that they are functionally impaired. CONCLUSIONS Our findings showed HNF1A and ABCC8 to be the most frequently mutated MODY genes in south India. Further we provide evidence for additional MODY relevant genes, such as NKX6-1, and these require further validation.
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Affiliation(s)
- Viswanathan Mohan
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India.
| | - Venkatesan Radha
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India
| | - Thong T Nguyen
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Eric W Stawiski
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kanika Bajaj Pahuja
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Leonard D Goldstein
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jennifer Tom
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ranjit Mohan Anjana
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India
| | - Monica Kong-Beltran
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Tushar Bhangale
- Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.,Department of Human Genetics, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Suresh Jahnavi
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India
| | | | - Vijay Gayathri
- Madras Diabetes Research Foundation & Dr. Mohan's Diabetes Specialities Centre, No. 4, Conran Smith Road, Gopalapuram, Chennai, Tamil Nadu, 600 086, India
| | - Paul George
- MedGenome, Bangalore, Karnataka, 560 099, India
| | - Na Zhang
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | | | - Subhra Chaudhuri
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ravi Gupta
- MedGenome, Bangalore, Karnataka, 560 099, India
| | - Jingli Zhang
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Jeremy Stinson
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Zora Modrusan
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Somasekar Seshagiri
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Andrew S Peterson
- Department of Molecular Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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6
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Goldstein LD, Chen YJJ, Dunne J, Mir A, Hubschle H, Guillory J, Yuan W, Zhang J, Stinson J, Jaiswal B, Pahuja KB, Mann I, Schaal T, Chan L, Anandakrishnan S, Lin CW, Espinoza P, Husain S, Shapiro H, Swaminathan K, Wei S, Srinivasan M, Seshagiri S, Modrusan Z. Massively parallel nanowell-based single-cell gene expression profiling. BMC Genomics 2017; 18:519. [PMID: 28687070 PMCID: PMC5501953 DOI: 10.1186/s12864-017-3893-1] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [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: 01/02/2017] [Accepted: 06/21/2017] [Indexed: 11/23/2022] Open
Abstract
Background Technological advances have enabled transcriptome characterization of cell types at the single-cell level providing new biological insights. New methods that enable simple yet high-throughput single-cell expression profiling are highly desirable. Results Here we report a novel nanowell-based single-cell RNA sequencing system, ICELL8, which enables processing of thousands of cells per sample. The system employs a 5,184-nanowell-containing microchip to capture ~1,300 single cells and process them. Each nanowell contains preprinted oligonucleotides encoding poly-d(T), a unique well barcode, and a unique molecular identifier. The ICELL8 system uses imaging software to identify nanowells containing viable single cells and only wells with single cells are processed into sequencing libraries. Here, we report the performance and utility of ICELL8 using samples of increasing complexity from cultured cells to mouse solid tissue samples. Our assessment of the system to discriminate between mixed human and mouse cells showed that ICELL8 has a low cell multiplet rate (< 3%) and low cross-cell contamination. We characterized single-cell transcriptomes of more than a thousand cultured human and mouse cells as well as 468 mouse pancreatic islets cells. We were able to identify distinct cell types in pancreatic islets, including alpha, beta, delta and gamma cells. Conclusions Overall, ICELL8 provides efficient and cost-effective single-cell expression profiling of thousands of cells, allowing researchers to decipher single-cell transcriptomes within complex biological samples. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3893-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Leonard D Goldstein
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ying-Jiun Jasmine Chen
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jude Dunne
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | - Alain Mir
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | | | - Joseph Guillory
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Wenlin Yuan
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jingli Zhang
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jeremy Stinson
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Bijay Jaiswal
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Kanika Bajaj Pahuja
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Ishminder Mann
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | - Thomas Schaal
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | - Leo Chan
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | | | - Chun-Wah Lin
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | - Patricio Espinoza
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | - Syed Husain
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | - Harris Shapiro
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | | | - Sherry Wei
- Wafergen Biosystems Inc., 34700 Campus Drive, Fremont, CA, 94555, USA
| | | | - Somasekar Seshagiri
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Zora Modrusan
- Molecular Biology Department, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
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7
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Durinck S, Stawiski EW, Pavía-Jiménez A, Modrusan Z, Kapur P, Jaiswal BS, Zhang N, Toffessi-Tcheuyap V, Nguyen TT, Pahuja KB, Chen YJ, Saleem S, Chaudhuri S, Heldens S, Jackson M, Peña-Llopis S, Guillory J, Toy K, Ha C, Harris CJ, Holloman E, Hill HM, Stinson J, Rivers CS, Janakiraman V, Wang W, Kinch LN, Grishin NV, Haverty PM, Chow B, Gehring JS, Reeder J, Pau G, Wu TD, Margulis V, Lotan Y, Sagalowsky A, Pedrosa I, de Sauvage FJ, Brugarolas J, Seshagiri S. Spectrum of diverse genomic alterations define non-clear cell renal carcinoma subtypes. Nat Genet 2014; 47:13-21. [PMID: 25401301 DOI: 10.1038/ng.3146] [Citation(s) in RCA: 270] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/24/2014] [Indexed: 12/17/2022]
Abstract
To further understand the molecular distinctions between kidney cancer subtypes, we analyzed exome, transcriptome and copy number alteration data from 167 primary human tumors that included renal oncocytomas and non-clear cell renal cell carcinomas (nccRCCs), consisting of papillary (pRCC), chromophobe (chRCC) and translocation (tRCC) subtypes. We identified ten significantly mutated genes in pRCC, including MET, NF2, SLC5A3, PNKD and CPQ. MET mutations occurred in 15% (10/65) of pRCC samples and included previously unreported recurrent activating mutations. In chRCC, we found TP53, PTEN, FAAH2, PDHB, PDXDC1 and ZNF765 to be significantly mutated. Gene expression analysis identified a five-gene set that enabled the molecular classification of chRCC, renal oncocytoma and pRCC. Using RNA sequencing, we identified previously unreported gene fusions, including ACTG1-MITF fusion. Ectopic expression of the ACTG1-MITF fusion led to cellular transformation and induced the expression of downstream target genes. Finally, we observed upregulation of the anti-apoptotic factor BIRC7 in MiTF-high RCC tumors, suggesting a potential therapeutic role for BIRC7 inhibitors.
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Affiliation(s)
- Steffen Durinck
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA.,Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Eric W Stawiski
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA.,Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Andrea Pavía-Jiménez
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zora Modrusan
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Payal Kapur
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bijay S Jaiswal
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Na Zhang
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Vanina Toffessi-Tcheuyap
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Thong T Nguyen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Kanika Bajaj Pahuja
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Ying-Jiun Chen
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Sadia Saleem
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Subhra Chaudhuri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Sherry Heldens
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Marlena Jackson
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Samuel Peña-Llopis
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joseph Guillory
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Karen Toy
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Connie Ha
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Corissa J Harris
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Eboni Holloman
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Haley M Hill
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jeremy Stinson
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | | | | | - Weiru Wang
- Structural Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Lisa N Kinch
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Nick V Grishin
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Hughes Medical Institute, Chevy Chase, Maryland, USA
| | - Peter M Haverty
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Bernard Chow
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Julian S Gehring
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Jens Reeder
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Gregoire Pau
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Thomas D Wu
- Bioinformatics and Computational Biology Department, Genentech, Inc., South San Francisco, California, USA
| | - Vitaly Margulis
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Yair Lotan
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Arthur Sagalowsky
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Urology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ivan Pedrosa
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Frederic J de Sauvage
- Molecular Oncology Department, Genentech, Inc., South San Francisco, California, USA
| | - James Brugarolas
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Department of Developmental Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Somasekar Seshagiri
- Molecular Biology Department, Genentech, Inc., South San Francisco, California, USA
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8
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Kim SD, Bajaj Pahuja K, Ravazzola M, Yoon J, Boyadjiev SA, Hamamoto S, Schekman R, Orci L, Kim J. The SEC23-SEC31 interface plays critical role for export of procollagen from the endoplasmic reticulum. J Biol Chem 2012. [DOI: 10.1074/jbc.a111.283382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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9
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Kim SD, Pahuja KB, Ravazzola M, Yoon J, Boyadjiev SA, Hammamoto S, Schekman R, Orci L, Kim J. The [corrected] SEC23-SEC31 [corrected] interface plays critical role for export of procollagen from the endoplasmic reticulum. J Biol Chem 2012; 287:10134-10144. [PMID: 22298774 DOI: 10.1074/jbc.m111.283382] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
COPII proteins are essential for exporting most cargo molecules from the endoplasmic reticulum. The membrane-facing surface of the COPII proteins (especially SEC23-SEC24) interacts directly or indirectly with the cargo molecules destined for exit. As we characterized the SEC23A mutations at the SEC31 binding site identified from patients with cranio-lenticulo-sutural dysplasia, we discovered that the SEC23-SEC31 interface can also influence cargo selection. Remarkably, M702V SEC23A does not compromise COPII assembly, vesicle size, and packaging of cargo molecules into COPII vesicles that we have tested but induces accumulation of procollagen in the endoplasmic reticulum when expressed in normal fibroblasts. We observed that M702V SEC23A activates SAR1B GTPase more than wild-type SEC23A when SEC13-SEC31 is present, indicating that M702V SEC23A causes premature dissociation of COPII from the membrane. Our results indicate that a longer stay of COPII proteins on the membrane is required to cargo procollagen than other molecules and suggest that the SEC23-SEC31 interface plays a critical role in capturing various cargo molecules.
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Affiliation(s)
- Sun-Don Kim
- Section of Genetics, Department of Pediatrics, University of California Davis Medical Center, Sacramento, California 95817
| | - Kanika Bajaj Pahuja
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, and
| | - Mariella Ravazzola
- Department of Cell Physiology and Metabolism, University of Geneva Medical Center, 1211 Geneva 4, Switzerland
| | - Joonsik Yoon
- Section of Genetics, Department of Pediatrics, University of California Davis Medical Center, Sacramento, California 95817
| | - Simeon A Boyadjiev
- Section of Genetics, Department of Pediatrics, University of California Davis Medical Center, Sacramento, California 95817
| | - Susan Hammamoto
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, and
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California Berkeley, Berkeley, California 94720, and
| | - Lelio Orci
- Department of Cell Physiology and Metabolism, University of Geneva Medical Center, 1211 Geneva 4, Switzerland
| | - Jinoh Kim
- Section of Genetics, Department of Pediatrics, University of California Davis Medical Center, Sacramento, California 95817,.
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10
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Abstract
Secretory proteins are transported to the Golgi complex in vesicles that bud from the endoplasmic reticulum. The cytoplasmic coat protein complex II (COPII) is responsible for cargo sorting and vesicle morphogenesis. COPII was first described in Saccharomyces cerevisiae, but its basic function is conserved throughout all eukaryotes. Nevertheless, the COPII coat has adapted to the higher complexity of mammalian physiology, achieving more sophisticated levels of secretory regulation. In this review we cover aspects of mammalian COPII-mediated regulation of secretion, in particular related to the function of COPII paralogues, the spatial organization of cargo export and the role of accessory proteins.
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Affiliation(s)
- Giulia Zanetti
- Department of Molecular and Cell Biology and Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
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