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Article: copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling.

Kovaleva, Vasilisa A / Pattinson, David J / Barton, Carl / Chapin, Sarah R / Minervina, Anastasia A / Richards, Katherine A / Sant, Andrea J / Thomas, Paul G / Pogorelyy, Mikhail V / Meyer, Hannah V

bioRxiv : the preprint server for biology

2024

Abstract: T cell receptor (TCR) repertoire diversity enables the orchestration of antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR/antigen binding pairs from the large TCR repertoire and antigen space is crucial for ... ...

Abstract	T cell receptor (TCR) repertoire diversity enables the orchestration of antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR/antigen binding pairs from the large TCR repertoire and antigen space is crucial for biomedical research. Here, we introduce
Language	English
Publishing date	2024-02-08
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.11.28.569052
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Article ; Online: Newly synthesized polycystin-1 takes different trafficking pathways to the apical and ciliary membranes.

Gilder, Allison L / Chapin, Hannah C / Padovano, Valeria / Hueschen, Christina L / Rajendran, Vanathy / Caplan, Michael J

Traffic (Copenhagen, Denmark)

2018 Volume 19, Issue 12, Page(s) 933–945

Abstract: ... noncovalently attached to the transmembrane C-terminus. Exposing cells to alkaline solutions elutes the N ... terminal fragment while the C-terminal fragment is retained in the cell membrane. Utilizing ...

Abstract	Mutations in the genes encoding polycystin-1 (PC1) and polycystin 2 (PC2) cause autosomal dominant polycystic kidney disease. These transmembrane proteins colocalize in the primary cilia of renal epithelial cells, where they may participate in sensory processes. PC1 is also found in the apical membrane when expressed in cultured epithelial cells. PC1 undergoes autocatalytic cleavage, producing an extracellular N-terminal fragment that remains noncovalently attached to the transmembrane C-terminus. Exposing cells to alkaline solutions elutes the N-terminal fragment while the C-terminal fragment is retained in the cell membrane. Utilizing this observation, we developed a "strip-recovery" synchronization protocol to study PC1 trafficking in polarized LLC-PK1 renal epithelial cells. Following alkaline strip, a new cohort of PC1 repopulates the cilia within 30 minutes, while apical delivery of PC1 was not detectable until 3 hours. Brefeldin A (BFA) blocked apical PC1 delivery, while ciliary delivery of PC1 was BFA insensitive. Incubating cells at 20°C to block trafficking out of the trans-Golgi network also inhibits apical but not ciliary delivery. These results suggest that newly synthesized PC1 takes distinct pathways to the ciliary and apical membranes. Ciliary PC1 appears to by-pass BFA sensitive Golgi compartments, while apical delivery of PC1 traverses these compartments.
MeSH term(s)	Animals ; Cell Line ; Cell Membrane/metabolism ; Cell Polarity ; Endoplasmic Reticulum/metabolism ; Epithelial Cells/metabolism ; Kidney/cytology ; Protein Sorting Signals ; Protein Transport ; Swine ; TRPP Cation Channels/chemistry ; TRPP Cation Channels/metabolism
Chemical Substances	Protein Sorting Signals ; TRPP Cation Channels ; polycystic kidney disease 1 protein
Language	English
Publishing date	2018-09-24
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1483852-7
ISSN	1600-0854 ; 1398-9219
ISSN (online)	1600-0854
ISSN	1398-9219
DOI	10.1111/tra.12612
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Article ; Online: The cell biology of polycystic kidney disease.

Chapin, Hannah C / Caplan, Michael J

The Journal of cell biology

2010 Volume 191, Issue 4, Page(s) 701–710

Abstract: Polycystic kidney disease is a common genetic disorder in which fluid-filled cysts displace normal renal tubules. Here we focus on autosomal dominant polycystic kidney disease, which is attributable to mutations in the PKD1 and PKD2 genes and which is ... ...

Abstract	Polycystic kidney disease is a common genetic disorder in which fluid-filled cysts displace normal renal tubules. Here we focus on autosomal dominant polycystic kidney disease, which is attributable to mutations in the PKD1 and PKD2 genes and which is characterized by perturbations of renal epithelial cell growth control, fluid transport, and morphogenesis. The mechanisms that connect the underlying genetic defects to disease pathogenesis are poorly understood, but their exploration is shedding new light on interesting cell biological processes and suggesting novel therapeutic targets.
MeSH term(s)	Animals ; GTP-Binding Proteins/metabolism ; Humans ; Kidney/pathology ; Kidney/physiopathology ; Models, Molecular ; Polycystic Kidney, Autosomal Dominant/genetics ; Polycystic Kidney, Autosomal Dominant/pathology ; Polycystic Kidney, Autosomal Dominant/physiopathology ; Signal Transduction/physiology ; TRPP Cation Channels/chemistry ; TRPP Cation Channels/genetics ; TRPP Cation Channels/metabolism ; Wnt Proteins/metabolism
Chemical Substances	TRPP Cation Channels ; Wnt Proteins ; polycystic kidney disease 1 protein ; polycystic kidney disease 2 protein ; GTP-Binding Proteins (EC 3.6.1.-)
Language	English
Publishing date	2010-11-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
DOI	10.1083/jcb.201006173
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Article ; Online: Tissue-specific autophagy responses to aging and stress in C. elegans.

Chapin, Hannah C / Okada, Megan / Merz, Alexey J / Miller, Dana L

Aging

2015 Volume 7, Issue 6, Page(s) 419–434

Abstract: ... on autophagy under different conditions. To generate a tissue-specific map of autophagy in C. elegans we used ... consistent with an age-dependent shift in proteostasis. These novel measures of autophagic flux in C. elegans ...

Abstract	Cellular function relies on a balance between protein synthesis and breakdown. Macromolecular breakdown through autophagy is broadly required for cellular and tissue development, function, and recovery from stress. While Caenorhabditis elegans is frequently used to explore cellular responses to development and stress, the most common assays for autophagy in this system lack tissue-level resolution. Different tissues within an organism have unique functional characteristics and likely vary in their reliance on autophagy under different conditions. To generate a tissue-specific map of autophagy in C. elegans we used a dual fluorescent protein (dFP) tag that releases monomeric fluorescent protein (mFP) upon arrival at the lysosome. Tissue-specific expression of dFP::LGG-1 revealed autophagic flux in all tissues, but mFP accumulation was most dramatic in the intestine. We also observed variable responses to stress: starvation increased autophagic mFP release in all tissues, whereas anoxia primarily increased intestinal autophagic flux. We observed autophagic flux with tagged LGG-1, LGG-2, and two autophagic cargo reporters: a soluble cytoplasmic protein, and mitochondrial TOMM-7. Finally, an increase in mFP in older worms was consistent with an age-dependent shift in proteostasis. These novel measures of autophagic flux in C. elegans reveal heterogeneity in autophagic response across tissues during stress and aging.
MeSH term(s)	Aging/physiology ; Animals ; Autophagy/physiology ; Caenorhabditis elegans/physiology ; Gene Expression Regulation/physiology ; Stress, Physiological/physiology
Language	English
Publishing date	2015-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1945-4589
ISSN (online)	1945-4589
DOI	10.18632/aging.100765
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Article ; Online: Repertoires of SARS-CoV-2 epitopes targeted by antibodies vary according to severity of COVID-19.

Gregory, David J / Vannier, Augustin / Duey, Akiro H / Roady, Tyler J / Dzeng, Richard K / Pavlovic, Maia N / Chapin, Michael H / Mukherjee, Sonia / Wilmot, Hannah / Chronos, Nic / Charles, Richelle C / Ryan, Edward T / LaRocque, Regina C / Miller, Tyler E / Garcia-Beltran, Wilfredo F / Thierauf, Julia C / Iafrate, A John / Mullenbrock, Steven / Stump, Mark D /

Wetzel, Randall K / Polakiewicz, Roberto D / Naranbhai, Vivek / Poznansky, Mark C

Virulence

2022 Volume 13, Issue 1, Page(s) 890–902

Abstract: Antibodies to SARS-CoV-2 are central to recovery and immunity from COVID-19. However, the relationship between disease severity and the repertoire of antibodies against specific SARS-CoV-2 epitopes an individual develops following exposure remains ... ...

Abstract	Antibodies to SARS-CoV-2 are central to recovery and immunity from COVID-19. However, the relationship between disease severity and the repertoire of antibodies against specific SARS-CoV-2 epitopes an individual develops following exposure remains incompletely understood. Here, we studied seroprevalence of antibodies to specific SARS-CoV-2 and other betacoronavirus antigens in a well-annotated, community sample of convalescent and never-infected individuals obtained in August 2020. One hundred and twenty-four participants were classified into five groups: previously exposed but without evidence of infection, having no known exposure or evidence of infection, seroconverted without symptoms, previously diagnosed with symptomatic COVID-19, and recovered after hospitalization with COVID-19. Prevalence of IgGs specific to the following antigens was compared between the five groups: recombinant SARS-CoV-2 and betacoronavirus spike and nucleocapsid protein domains, peptides from a tiled array of 22-mers corresponding to the entire spike and nucleocapsid proteins, and peptides corresponding to predicted immunogenic regions from other proteins of SARS-CoV-2. Antibody abundance generally correlated positively with severity of prior illness. A number of specific immunogenic peptides and some that may be associated with milder illness or protection from symptomatic infection were identified. No convincing association was observed between antibodies to Receptor Binding Domain(s) (RBDs) of less pathogenic betacoronaviruses HKU1 or OC43 and COVID-19 severity. However, apparent cross-reaction with SARS-CoV RBD was evident and some predominantly asymptomatic individuals had antibodies to both MERS-CoV and SARS-CoV RBDs. Findings from this pilot study may inform development of diagnostics, vaccines, and therapeutic antibodies, and provide insight into viral pathogenic mechanisms.
MeSH term(s)	Antibodies, Neutralizing ; Antibodies, Viral ; COVID-19 ; Epitopes ; Humans ; Pilot Projects ; SARS-CoV-2 ; Seroepidemiologic Studies ; Spike Glycoprotein, Coronavirus
Chemical Substances	Antibodies, Neutralizing ; Antibodies, Viral ; Epitopes ; Spike Glycoprotein, Coronavirus ; spike protein, SARS-CoV-2
Language	English
Publishing date	2022-05-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2657572-3
ISSN	2150-5608 ; 2150-5594
ISSN (online)	2150-5608
ISSN	2150-5594
DOI	10.1080/21505594.2022.2073025
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Article: The cell biology of polycystic kidney disease

Chapin, Hannah C / Caplan, Michael J

Journal of cell biology. 2010, v. 191, no. 4

2010

Abstract	Polycystic kidney disease is a common genetic disorder in which fluid-filled cysts displace normal renal tubules. Here we focus on autosomal dominant polycystic kidney disease, which is attributable to mutations in the PKD1 and PKD2 genes and which is characterized by perturbations of renal epithelial cell growth control, fluid transport, and morphogenesis. The mechanisms that connect the underlying genetic defects to disease pathogenesis are poorly understood, but their exploration is shedding new light on interesting cell biological processes and suggesting novel therapeutic targets.
Language	English
Size	p. 701-710.
Publishing place	The Rockefeller University Press
Document type	Article
ZDB-ID	218154-x
ISSN	1540-8140 ; 0021-9525
ISSN (online)	1540-8140
ISSN	0021-9525
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Polycystin-1 surface localization is stimulated by polycystin-2 and cleavage at the G protein-coupled receptor proteolytic site.

Chapin, Hannah C / Rajendran, Vanathy / Caplan, Michael J

Molecular biology of the cell

2010 Volume 21, Issue 24, Page(s) 4338–4348

Abstract: ... channel-inhibiting PC2 mutations. PC1 and PC2 can interact through their C-terminal tails, but removing ... the C-terminal tail of either protein has no effect on PC1 surface localization in human embryonic ...

Abstract	Polycystin (PC)1 and PC2 are membrane proteins implicated in autosomal dominant polycystic kidney disease. A physiologically relevant cleavage at PC1's G protein-coupled receptor proteolytic site (GPS) occurs early in the secretory pathway. Our results suggest that PC2 increases both PC1 GPS cleavage and PC1's appearance at the plasma membrane. Mutations that prevent PC1's GPS cleavage prevent its plasma membrane localization. PC2 is a member of the trp family of cation channels and is an important PC1 binding partner. The effect of PC2 on PC1 localization is independent of PC2 channel activity, as tested using channel-inhibiting PC2 mutations. PC1 and PC2 can interact through their C-terminal tails, but removing the C-terminal tail of either protein has no effect on PC1 surface localization in human embryonic kidney 293 cells. Experiments in polarized LLC-PK cells show that apical and ciliary PC1 localization requires PC2 and that this delivery is sensitive to PC2 truncation. In sum, our work shows that PC2 expression is required for the movement of PC1 to the plasma and ciliary membranes. In fibroblast cells this localization effect is independent of PC2's channel activity or PC1 binding ability but involves a stimulation of PC1's GPS cleavage before the PC1 protein's surface delivery.
MeSH term(s)	Animals ; Blotting, Western ; Cell Membrane ; Cilia/metabolism ; Fluorescent Antibody Technique ; HEK293 Cells ; Humans ; Immunoprecipitation ; Kidney/metabolism ; Kidney/pathology ; LLC-PK1 Cells ; Mutation ; Polycystic Kidney, Autosomal Dominant/genetics ; Polycystic Kidney, Autosomal Dominant/metabolism ; Protein Binding ; Protein Isoforms ; Protein Processing, Post-Translational ; Protein Structure, Tertiary ; Protein Transport ; Swine ; TRPP Cation Channels/chemistry ; TRPP Cation Channels/genetics ; TRPP Cation Channels/metabolism
Chemical Substances	Protein Isoforms ; TRPP Cation Channels ; polycystic kidney disease 1 protein ; polycystic kidney disease 2 protein
Language	English
Publishing date	2010-10-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1098979-1
ISSN	1939-4586 ; 1059-1524
ISSN (online)	1939-4586
ISSN	1059-1524
DOI	10.1091/mbc.E10-05-0407
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Article ; Online: Polycystin-1 cleavage and the regulation of transcriptional pathways.

Merrick, David / Bertuccio, Claudia A / Chapin, Hannah C / Lal, Mark / Chauvet, Veronique / Caplan, Michael J

Pediatric nephrology (Berlin, Germany)

2013 Volume 29, Issue 4, Page(s) 505–511

Abstract: Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic cause of end-stage renal disease, affecting approximately 1 in 1,000 people. The disease is characterized by the development of numerous large fluid-filled renal cysts over ... ...

Abstract	Autosomal dominant polycystic kidney disease (ADPKD) is the most common genetic cause of end-stage renal disease, affecting approximately 1 in 1,000 people. The disease is characterized by the development of numerous large fluid-filled renal cysts over the course of decades. These cysts compress the surrounding renal parenchyma and impair its function. Mutations in two genes are responsible for ADPKD. The protein products of both of these genes, polycystin-1 and polycystin-2, localize to the primary cilium and participate in a wide variety of signaling pathways. Polycystin-1 undergoes several proteolytic cleavages that produce fragments which manifest biological activities. Recent results suggest that the production of polycystin-1 cleavage fragments is necessary and sufficient to account for at least some, although certainly not all, of the physiological functions of the parent protein.
MeSH term(s)	Animals ; Gene Expression Regulation/physiology ; Humans ; Mutation ; Polycystic Kidney, Autosomal Dominant/genetics ; Polycystic Kidney, Autosomal Dominant/metabolism ; TRPP Cation Channels/genetics ; TRPP Cation Channels/metabolism ; Transcription, Genetic
Chemical Substances	TRPP Cation Channels ; polycystic kidney disease 1 protein
Language	English
Publishing date	2013-07-04
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	631932-4
ISSN	1432-198X ; 0931-041X
ISSN (online)	1432-198X
ISSN	0931-041X
DOI	10.1007/s00467-013-2548-y
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Article ; Online: copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling

Kovaleva, Vasilisa A / Pattinson, David J / Barton, Carl / Chapin, Sarah R / Minerva, Anastasia A / Richards, Katherine A / Sant, Andrea J / Thomas, Paul G / Pogorelyy, Mikhail V / Meyer, Hannah V

bioRxiv

Abstract	T cell receptor (TCR) repertoire diversity enables the orchestration of antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR/antigen binding pairs from the large TCR repertoire and antigen space is crucial for biomedical research. Here, we introduce copepodTCR, an open-access tool for the design and interpretation of high-throughput experimental assays to determine TCR specificity. copepodTCR implements a combinatorial peptide pooling scheme for efficient experimental testing of T cell responses against large overlapping peptide libraries, useful for "deorphaning" TCRs of unknown specificity. The scheme detects experimental errors and, coupled with a hierarchical Bayesian model for unbiased results interpretation, identifies the response-eliciting peptide for a TCR of interest out of hundreds of peptides tested using a simple experimental set-up. We experimentally validated our approach on a library of 253 overlapping peptides covering the SARS-CoV-2 spike protein. We provide experimental guides for efficient design of larger screens covering thousands of peptides which will be crucial for the identification of antigen-specific T cells and their targets from limited clinical material.
Keywords	covid19
Language	English
Publishing date	2023-11-29
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.11.28.569052
Database	COVID19

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Article ; Online: copepodTCR: Identification of Antigen-Specific T Cell Receptors with combinatorial peptide pooling

Kovaleva, Vasilisa A. / Pattinson, David J. / Barton, Carl / Chapin, Sarah R. / Minervina, Anastasia A. / Richards, Katherine A. / Sant, Andrea J. / Thomas, Paul G. / Pogorelyy, Mikhail V. / Meyer, Hannah V.

bioRxiv

Abstract	T cell receptor (TCR) repertoire diversity enables the orchestration of antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR/antigen binding pairs from the large TCR repertoire and antigen space is crucial for biomedical research. Here, we introduce copepodTCR, an open-access tool for the design and interpretation of high-throughput experimental assays to determine TCR specificity. copepodTCR implements a combinatorial peptide pooling scheme for efficient experimental testing of T cell responses against large overlapping peptide libraries, useful for "deorphaning" TCRs of unknown specificity. The scheme detects experimental errors and, coupled with a hierarchical Bayesian model for unbiased results interpretation, identifies the response-eliciting peptide for a TCR of interest out of hundreds of peptides tested using a simple experimental set-up. We experimentally validated our approach on a library of 253 overlapping peptides covering the SARS-CoV-2 spike protein. We provide experimental guides for efficient design of larger screens covering thousands of peptides which will be crucial for the identification of antigen-specific T cells and their targets from limited clinical material.
Keywords	covid19
Language	English
Publishing date	2023-11-29
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.11.28.569052
Database	COVID19

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