Ignite Creation Date:
2024-06-16 @ 11:48 AM
Last Modification Date:
2024-10-26 @ 3:31 PM
Study NCT ID:
NCT06438107
Status:
NOT_YET_RECRUITING
Last Update Posted:
2024-05-31
First Post:
2024-02-19
Brief Title:
Deep Phenotyping of the Renal Allograft to Prognosticate Clinical Outcomes
Sponsor:
University of Pittsburgh
Organization:
University of Pittsburgh
Study Overview
Official Title:
Deep Phenotyping of the Renal Allograft to Prognosticate Clinical Outcomes
Status:
NOT_YET_RECRUITING
Status Verified Date:
2024-05
Last Known Status:
None
Delayed Posting:
No
If Stopped, Why?:
Not Stopped
Has Expanded Access:
False
If Expanded Access, NCT#:
N/A
Has Expanded Access, NCT# Status:
N/A
Acronym:
None
Brief Summary:
The goal of this observational study is to determine phenotypic transcriptional and epigenetic underpinnings of renal allograft rejection in renal transplant rejection The main questions it aims to answer are
To determine the phenotype frequency location and the inter-cellular interactions between the cells that constitute intra-graft inflammatory infiltrate in acute ejection
To determine the phenotype frequency location and the inter-cellular interactions between the cells that constitute intra-graft inflammatory infiltrate in recurrentrecalcitrant rejection vs rejection that resolves with therapy
To generate a scRNA sequencing scRNAseq map of the intra-graft immune cells and the renal parenchymal cells and compare the transcriptional and epigenetic changes within these cells in recurrentrecalcitrant rejection vs rejection that resolves with therapy
To determine phenotypic changes associated with chronic rejection
Participants will be asked to provide the following research specimens
Renal biopsy specimens at the following timepoints day of transplantation pre-implantation and post-perfusion routine protocol biopsies at 3 months and 12 months and clinically indicated for-cause biopsies at any timepoint from time-0 to 1-yr post-transplantation The 1st research core will be used for routine histopathological examination and left over tissue from this core will be used for deep phenotyping using multiparameter immunophenotyping and digital spatial profiling The second research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq
Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses For each collection timepoint up to 75 mL about 5 tablespoons will be collected
Prospective clinical data and outcomes will be collected from participant medical records
Follow-Up Period For-cause biopsies from 1-yr to 5-yr post-transplantation by the transplant nephrologist no additional cores will be obtained for research from these biopsies The left-over tissue from the clinically indicated biopsy cores will be analyzed by deep phenotyping and digital spatial profiling Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses
To determine the phenotype frequency location and the inter-cellular interactions between the cells that constitute intra-graft inflammatory infiltrate in acute ejection
To determine the phenotype frequency location and the inter-cellular interactions between the cells that constitute intra-graft inflammatory infiltrate in recurrentrecalcitrant rejection vs rejection that resolves with therapy
To generate a scRNA sequencing scRNAseq map of the intra-graft immune cells and the renal parenchymal cells and compare the transcriptional and epigenetic changes within these cells in recurrentrecalcitrant rejection vs rejection that resolves with therapy
To determine phenotypic changes associated with chronic rejection
Participants will be asked to provide the following research specimens
Renal biopsy specimens at the following timepoints day of transplantation pre-implantation and post-perfusion routine protocol biopsies at 3 months and 12 months and clinically indicated for-cause biopsies at any timepoint from time-0 to 1-yr post-transplantation The 1st research core will be used for routine histopathological examination and left over tissue from this core will be used for deep phenotyping using multiparameter immunophenotyping and digital spatial profiling The second research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq
Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses For each collection timepoint up to 75 mL about 5 tablespoons will be collected
Prospective clinical data and outcomes will be collected from participant medical records
Follow-Up Period For-cause biopsies from 1-yr to 5-yr post-transplantation by the transplant nephrologist no additional cores will be obtained for research from these biopsies The left-over tissue from the clinically indicated biopsy cores will be analyzed by deep phenotyping and digital spatial profiling Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses
Detailed Description:
This study is exploratory in nature and aims to elucidate the phenotypic transcriptional and epigenetic underpinnings of renal transplant rejection The study is designed to provide improved understanding of the regulation of intra-graft alloimmune response in the renal transplant recipients
In this single center prospective longitudinal observational cohort study sequential assessment of renal biopsies will be performed at baseline pre-implantation 3 months and at one-year post-transplantation in addition to any for-cause biopsies within the first five years post-transplantation Blood samples will be also collected at the time of renal biopsies for comparison analyses
HYPOTHESIS It is proposed that unique phenotypic transcriptional and epigenetic changes within the parenchymal and the infiltrating nonparenchymal inflammatory cells dictate the evolution of renal allograft inflammation and rejection
The following research specimens will be obtained from each study participant
1 The day of transplantation by the UPMC operating surgeon Pre-implantation core renal biopsy and post-perfusion core renal biopsy Two research cores for each biopsy will be taken from the transplanted kidney The pre-implantation biopsy specimens are obtained on the back table and the post-perfusion cores are taken prior to closure of the surgical incision The 1st research core will be used for routine histopathological examination and left over tissue from this core will be used for deep phenotyping using multiparameter immunophenotyping and digital spatial profiling The second research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses For each collection timepoint up to 75 mL about 5 tablespoons will be collected
2 Protocol biopsies at 3 months and 12 months by the transplant nephrologist Renal transplant recipients at UPMC routinely undergo clinical post-transplant biopsies at 3 months and at 12 months An additional research core will be collected along with the clinically indicated biopsy cores at both these time points 3 total passes of the biopsy needle for each collection Left over tissue from the clinically indicated core will be used for deep phenotyping using multiparameter immunophenotyping and digital spatial profiling The research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses
3 For-cause biopsies from time-0 to 1-yr post-transplantation by the transplant nephrologist Along with the protocol biopsies UPMC renal transplant patients also undergo biopsies for clinical indication for-cause biopsies Again an additional research core will be collected along with the clinically indicated biopsy cores whenever a patient undergoes any for-cause biopsy between time-0 and 1-year post-transplantation 3 total passes of the biopsy needle for each collection Left over tissue from the clinically indicated core will be used for deep phenotyping using multiparameter immunophenotyping and digital spatial profiling The research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses
The investigators will review procedures associated with the consent with participants again at the time of each of these biopsies to confirm their continued interest in participation As these procedures are a part of the standard of care biopsies that the patients undergo no additional hospital visits are expected The research specimens will be delivered to and processed by laboratory research members
Prospective clinical data and outcomes will be collected from participant medical records
The following clinical data will be collected from each research participant
1 Demographic characteristics eg age gender ethnicity cause of renal disease
2 Pre-transplant clinical variables eg ho prior transplant HLA mismatches panel reactive antibodies prior use of immunosuppression cold ischemia time warm ischemia time
3 De-identified donor data eg donor age gender ethnicity donor type KDPI as available at time of transplant
4 Immunosuppression details eg induction and maintenance agents trough CNI levels through the 1st post-transplant year
5 Clinical outcomes eg DGF detection of DSA biopsy clinical reports Serum Creatinine and eGFR at 1 3 6 and 12 months and then at 2 3 4 and 5 years graft and patient survival at 5 years
Follow-Up Period For-cause biopsies from 1-yr to 5-yr post-transplantation by the transplant nephrologist These are the standard-of-care indication biopsies that are performed beyond the 1st post-transplant year up to 5 years post-transplantation While no additional cores will be obtained for research from these biopsies about 2 passes of the biopsy needle per standard practices we will analyze the left-over tissue from the clinically indicated biopsy cores by deep phenotyping Marcus Clark Lab University of Chicago MTA in place and digital spatial profiling Randhawa Lab University of Pittsburgh Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses
STUDY AIMS Aim 1 To determine phenotypic transcriptional and epigenetic underpinnings of renal allograft rejection
1 A To determine the phenotype frequency location and the inter-cellular interactions between the cells that constitute intra-graft inflammatory infiltrate in acute ejection 1B To generate a scRNA sequencing scRNAseq map of the intra-graft immune cells and the renal parenchymal cells and determine the transcriptional and epigenetic changes within these cells at baseline prior to the diagnosis and at the diagnosis of acute rejection Analysis of these changes longitudinally through the 1st post-transplant year will allow us to delineate the natural history of renal allograft rejection
Aim 2 To determine phenotypic transcriptional and epigenetic differences that underlie persistence vs resolution of acute rejection after renal transplantation
2 A To determine the phenotype frequency location and the inter-cellular interactions between the cells that constitute intra-graft inflammatory infiltrate in recurrentrecalcitrant rejection vs rejection that resolves with therapy 2B To generate a scRNA sequencing scRNAseq map of the intra-graft immune cells and the renal parenchymal cells and compare the transcriptional and epigenetic changes within these cells in recurrentrecalcitrant rejection vs rejection that resolves with therapy
Aim 3 To determine phenotypic changes associated with chronic rejection In a subset of patient in whom for-cause transplant biopsies are available past the 1st year and up to 5 years after transplantation we will perform multi-parameter immunophenotyping and spatial transcriptional analysis to explore cellular infiltrate and transcriptional changes associated with chronic rejection
Exploratory Endpoints
1 To correlate the frequency and phenotype of the intra-graft inflammatory infiltrate with histological diagnosis within the 1st post-transplant year acute rejection vs borderline rejection vs no acute rejection
2 To determine the transcriptional and epigenetic changes within intra-graft immune cells and graft parenchymal cells at baseline prior to and at the diagnosis of acute rejection or borderline rejection in comparison to no rejection
3 To determine phenotypic transcriptional and epigenetic differences that underlie persistence vs resolution of acute rejection in the 1st post-transplant year
4 To determine the phenotypic and transcriptional changes associated with chronic rejection
5 To correlate histological phenotypes with peripheral blood phenotypes
In this single center prospective longitudinal observational cohort study sequential assessment of renal biopsies will be performed at baseline pre-implantation 3 months and at one-year post-transplantation in addition to any for-cause biopsies within the first five years post-transplantation Blood samples will be also collected at the time of renal biopsies for comparison analyses
HYPOTHESIS It is proposed that unique phenotypic transcriptional and epigenetic changes within the parenchymal and the infiltrating nonparenchymal inflammatory cells dictate the evolution of renal allograft inflammation and rejection
The following research specimens will be obtained from each study participant
1 The day of transplantation by the UPMC operating surgeon Pre-implantation core renal biopsy and post-perfusion core renal biopsy Two research cores for each biopsy will be taken from the transplanted kidney The pre-implantation biopsy specimens are obtained on the back table and the post-perfusion cores are taken prior to closure of the surgical incision The 1st research core will be used for routine histopathological examination and left over tissue from this core will be used for deep phenotyping using multiparameter immunophenotyping and digital spatial profiling The second research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses For each collection timepoint up to 75 mL about 5 tablespoons will be collected
2 Protocol biopsies at 3 months and 12 months by the transplant nephrologist Renal transplant recipients at UPMC routinely undergo clinical post-transplant biopsies at 3 months and at 12 months An additional research core will be collected along with the clinically indicated biopsy cores at both these time points 3 total passes of the biopsy needle for each collection Left over tissue from the clinically indicated core will be used for deep phenotyping using multiparameter immunophenotyping and digital spatial profiling The research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses
3 For-cause biopsies from time-0 to 1-yr post-transplantation by the transplant nephrologist Along with the protocol biopsies UPMC renal transplant patients also undergo biopsies for clinical indication for-cause biopsies Again an additional research core will be collected along with the clinically indicated biopsy cores whenever a patient undergoes any for-cause biopsy between time-0 and 1-year post-transplantation 3 total passes of the biopsy needle for each collection Left over tissue from the clinically indicated core will be used for deep phenotyping using multiparameter immunophenotyping and digital spatial profiling The research core will be used for extraction of cells and nuclei for scRNAseq and snATACseq Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses
The investigators will review procedures associated with the consent with participants again at the time of each of these biopsies to confirm their continued interest in participation As these procedures are a part of the standard of care biopsies that the patients undergo no additional hospital visits are expected The research specimens will be delivered to and processed by laboratory research members
Prospective clinical data and outcomes will be collected from participant medical records
The following clinical data will be collected from each research participant
1 Demographic characteristics eg age gender ethnicity cause of renal disease
2 Pre-transplant clinical variables eg ho prior transplant HLA mismatches panel reactive antibodies prior use of immunosuppression cold ischemia time warm ischemia time
3 De-identified donor data eg donor age gender ethnicity donor type KDPI as available at time of transplant
4 Immunosuppression details eg induction and maintenance agents trough CNI levels through the 1st post-transplant year
5 Clinical outcomes eg DGF detection of DSA biopsy clinical reports Serum Creatinine and eGFR at 1 3 6 and 12 months and then at 2 3 4 and 5 years graft and patient survival at 5 years
Follow-Up Period For-cause biopsies from 1-yr to 5-yr post-transplantation by the transplant nephrologist These are the standard-of-care indication biopsies that are performed beyond the 1st post-transplant year up to 5 years post-transplantation While no additional cores will be obtained for research from these biopsies about 2 passes of the biopsy needle per standard practices we will analyze the left-over tissue from the clinically indicated biopsy cores by deep phenotyping Marcus Clark Lab University of Chicago MTA in place and digital spatial profiling Randhawa Lab University of Pittsburgh Blood samples will be processed to obtain plasma for cytokine chemokine and DSA measurements and PBMC for deep phenotyping and molecular analyses
STUDY AIMS Aim 1 To determine phenotypic transcriptional and epigenetic underpinnings of renal allograft rejection
1 A To determine the phenotype frequency location and the inter-cellular interactions between the cells that constitute intra-graft inflammatory infiltrate in acute ejection 1B To generate a scRNA sequencing scRNAseq map of the intra-graft immune cells and the renal parenchymal cells and determine the transcriptional and epigenetic changes within these cells at baseline prior to the diagnosis and at the diagnosis of acute rejection Analysis of these changes longitudinally through the 1st post-transplant year will allow us to delineate the natural history of renal allograft rejection
Aim 2 To determine phenotypic transcriptional and epigenetic differences that underlie persistence vs resolution of acute rejection after renal transplantation
2 A To determine the phenotype frequency location and the inter-cellular interactions between the cells that constitute intra-graft inflammatory infiltrate in recurrentrecalcitrant rejection vs rejection that resolves with therapy 2B To generate a scRNA sequencing scRNAseq map of the intra-graft immune cells and the renal parenchymal cells and compare the transcriptional and epigenetic changes within these cells in recurrentrecalcitrant rejection vs rejection that resolves with therapy
Aim 3 To determine phenotypic changes associated with chronic rejection In a subset of patient in whom for-cause transplant biopsies are available past the 1st year and up to 5 years after transplantation we will perform multi-parameter immunophenotyping and spatial transcriptional analysis to explore cellular infiltrate and transcriptional changes associated with chronic rejection
Exploratory Endpoints
1 To correlate the frequency and phenotype of the intra-graft inflammatory infiltrate with histological diagnosis within the 1st post-transplant year acute rejection vs borderline rejection vs no acute rejection
2 To determine the transcriptional and epigenetic changes within intra-graft immune cells and graft parenchymal cells at baseline prior to and at the diagnosis of acute rejection or borderline rejection in comparison to no rejection
3 To determine phenotypic transcriptional and epigenetic differences that underlie persistence vs resolution of acute rejection in the 1st post-transplant year
4 To determine the phenotypic and transcriptional changes associated with chronic rejection
5 To correlate histological phenotypes with peripheral blood phenotypes
Study Oversight
Has Oversight DMC:
None
Is a FDA Regulated Drug?:
False
Is a FDA Regulated Device?:
False
Is an Unapproved Device?:
None
Is a PPSD?:
None
Is a US Export?:
None
Is an FDA AA801 Violation?:
None