The immune microenvironment in mantle cell lymphoma : Targeted liquid and spatial proteomic analyses
(2023)- Abstract
- The complex interplay of the tumour and immune cells affects tumour growth, progression, and response to treatment. Restoration
of effective immune response forms the basis of onco-immunology, which further enabled the development of immunotherapy. In
the era of precision medicine, pin-pointing patient biological heterogeneity especially in relation to patient-specific immune
microenvironment is a necessity for the discovery of novel biomarkers and for development of patient stratification tools for targeted
therapeutics. Mantle cell lymphoma (MCL) is a rare and aggressive subtype of B-cell lymphoma with poor survival and high relapse
rates. Previous investigations of MCL have largely focused on the tumour itself and... (More) - The complex interplay of the tumour and immune cells affects tumour growth, progression, and response to treatment. Restoration
of effective immune response forms the basis of onco-immunology, which further enabled the development of immunotherapy. In
the era of precision medicine, pin-pointing patient biological heterogeneity especially in relation to patient-specific immune
microenvironment is a necessity for the discovery of novel biomarkers and for development of patient stratification tools for targeted
therapeutics. Mantle cell lymphoma (MCL) is a rare and aggressive subtype of B-cell lymphoma with poor survival and high relapse
rates. Previous investigations of MCL have largely focused on the tumour itself and explorations of the immune microenvironment
have been limited. This thesis and the included five papers, investigates multiple aspects of the immune microenvironment with
respect to proteomic analysis performed on tissue and liquid biopsies of diagnostic and relapsed/refractory (R/R) MCL cohorts.
Analyses based on liquid biopsies (serum) in particular are relevant for aggressive cases such as in relapse, where invasive
procedures for extracting tissues is not recommended. Thus, paper I-II probes the possibility of using serum for treatment and
outcome-associated biomarker discovery in R/R MCL, using a targeted affinity-based protein microarray platform quantifying
immune-regulatory and tumor-secretory proteins in sera. Analysis performed in paper I using pre-treatment samples, identifies 11-
plex biomarker signature (RIS – relapsed immune signature) associated with overall survival. Further integration of RIS with mantle
cell lymphoma international prognostic index (MIPI) led to the development of MIPIris index for the stratification of R/R MCL into
three risk groups. Moreover, longitudinal analysis can be important in understanding how patient respond to treatment and this
can further guide therapeutic interventions. Thus, paper II is a follow-up study wherein longitudinal analyses was performed on
paired samples collected at pre-treatment (baseline) and after three months of chemo-immunotherapy (on-treatment). We show
how genetic aberrations can influence systemic profiles and thus integrating genetic information can be crucial for treatment
selection. Furthermore, we observe that the inter-patient heterogeneity associated with absolute values can be circumvented by
using velocity of change to capture general changes over time in groups of patients. Thus, using velocity of change in serum
proteins between pre- and on-treatment samples identified response biomarkers associated with minimal residual disease and
progression. While exploratory analysis using high dimensional omics-based data can be important for accelerating discovery,
translating such information for clinical utility is a necessity. Thus, in paper III, we show how serum quantification can be used
complementary tissue-identified prognostic biomarkers and this can enable faster clinical implementation. Presence of CD163+
M2-like macrophages has shown to be associated with poor outcome in MCL tissues. We show that higher expression of sCD163
levels in sera quantified using ELISA, is also associated with poor outcome in diagnostic and relapsed MCL. Furthermore, we
suggest a cut-off for sCD163 levels that can be used for clinical utility. Further exploration of the dynamic interplay of tumourimmune
microenvironment is now possible using spatial resolved omics for tissue-based analysis. Thus, in paper IV and V, we
analyse cell-type specific proteomic data collected from tumour and immune cells using GeoMx™ digital spatial profiler. In paper
IV, we show that presence as well as spatial localization of CD163+ macrophage with respect to tumour regions impacts
macrophage phenotypic profiles. Further modulation in the profile of surrounding tumour and T-cells is observed when
macrophages are present in the vicinity. Based on this analysis, we suggest MAPK pathway as a potential therapeutic target in
tumours with CD163+ macrophages. Immune composition can be defined not just by the type of cells, but also with respect to
frequency and spatial localization and this is explored in paper V with respect to T-cell subtypes. Thus, in paper V, we optimized
a workflow of multiplexed immunofluorescence image segmentation that allowed us to extract cell metrics for four subtypes of
CD3+ T-cells. Using this data, we show that higher infiltration of T-cells is associated with a positive outcome in MCL. Moreover,
by combining image derived metrics to cell specific spatial omics data, we were able to identify immunosuppressive
microenvironment associated with highly infiltrated tumours and suggests new potential targets of immunotherapy with respect to
IDO1, GITR and STING. In conclusion, this thesis explores systemic and tumor-associated immune microenvironment in MCL, for
defining patient heterogeneity, developing methods of patient stratification and for identifying novel and actionable biomarkers. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/89a92059-7c18-4377-a414-fe8480261998
- author
- Lokhande, Lavanya LU
- supervisor
-
- Sara Ek LU
- Mats Jerkeman LU
- Anna Sandström Gerdtsson LU
- opponent
-
- Prof. Dybkӕr, Karen, Aalborg University Hospital, Denmark.
- organization
- publishing date
- 2023-01-18
- type
- Thesis
- publication status
- published
- subject
- keywords
- Mantle cell lymphoma (MCL), proteomic analyses, spatial analysis, Biomarker discovery, immune microenviroment, serum proteomics
- pages
- 94 pages
- publisher
- Department of Immunotechnology, Lund University
- defense location
- Lecture Hall Hörsalen, Medicon Village, Scheelevägen 2, Faculty of Engineering LTH, Lund University, Lund. The dissertation will be live streamed, but part of the premises is to be excluded from the live stream.
- defense date
- 2023-03-02 09:00:00
- ISBN
- 978-91-8039-546-5
- 978-91-8039-547-2
- language
- English
- LU publication?
- yes
- id
- 89a92059-7c18-4377-a414-fe8480261998
- date added to LUP
- 2023-02-05 21:52:35
- date last changed
- 2024-02-13 10:53:50
@phdthesis{89a92059-7c18-4377-a414-fe8480261998,
abstract = {{The complex interplay of the tumour and immune cells affects tumour growth, progression, and response to treatment. Restoration<br/>of effective immune response forms the basis of onco-immunology, which further enabled the development of immunotherapy. In<br/>the era of precision medicine, pin-pointing patient biological heterogeneity especially in relation to patient-specific immune<br/>microenvironment is a necessity for the discovery of novel biomarkers and for development of patient stratification tools for targeted<br/>therapeutics. Mantle cell lymphoma (MCL) is a rare and aggressive subtype of B-cell lymphoma with poor survival and high relapse<br/>rates. Previous investigations of MCL have largely focused on the tumour itself and explorations of the immune microenvironment<br/>have been limited. This thesis and the included five papers, investigates multiple aspects of the immune microenvironment with<br/>respect to proteomic analysis performed on tissue and liquid biopsies of diagnostic and relapsed/refractory (R/R) MCL cohorts.<br/>Analyses based on liquid biopsies (serum) in particular are relevant for aggressive cases such as in relapse, where invasive<br/>procedures for extracting tissues is not recommended. Thus, paper I-II probes the possibility of using serum for treatment and<br/>outcome-associated biomarker discovery in R/R MCL, using a targeted affinity-based protein microarray platform quantifying<br/>immune-regulatory and tumor-secretory proteins in sera. Analysis performed in paper I using pre-treatment samples, identifies 11-<br/>plex biomarker signature (RIS – relapsed immune signature) associated with overall survival. Further integration of RIS with mantle<br/>cell lymphoma international prognostic index (MIPI) led to the development of MIPIris index for the stratification of R/R MCL into<br/>three risk groups. Moreover, longitudinal analysis can be important in understanding how patient respond to treatment and this<br/>can further guide therapeutic interventions. Thus, paper II is a follow-up study wherein longitudinal analyses was performed on<br/>paired samples collected at pre-treatment (baseline) and after three months of chemo-immunotherapy (on-treatment). We show<br/>how genetic aberrations can influence systemic profiles and thus integrating genetic information can be crucial for treatment<br/>selection. Furthermore, we observe that the inter-patient heterogeneity associated with absolute values can be circumvented by<br/>using velocity of change to capture general changes over time in groups of patients. Thus, using velocity of change in serum<br/>proteins between pre- and on-treatment samples identified response biomarkers associated with minimal residual disease and<br/>progression. While exploratory analysis using high dimensional omics-based data can be important for accelerating discovery,<br/>translating such information for clinical utility is a necessity. Thus, in paper III, we show how serum quantification can be used<br/>complementary tissue-identified prognostic biomarkers and this can enable faster clinical implementation. Presence of CD163+<br/>M2-like macrophages has shown to be associated with poor outcome in MCL tissues. We show that higher expression of sCD163<br/>levels in sera quantified using ELISA, is also associated with poor outcome in diagnostic and relapsed MCL. Furthermore, we<br/>suggest a cut-off for sCD163 levels that can be used for clinical utility. Further exploration of the dynamic interplay of tumourimmune<br/>microenvironment is now possible using spatial resolved omics for tissue-based analysis. Thus, in paper IV and V, we<br/>analyse cell-type specific proteomic data collected from tumour and immune cells using GeoMx™ digital spatial profiler. In paper<br/>IV, we show that presence as well as spatial localization of CD163+ macrophage with respect to tumour regions impacts<br/>macrophage phenotypic profiles. Further modulation in the profile of surrounding tumour and T-cells is observed when<br/>macrophages are present in the vicinity. Based on this analysis, we suggest MAPK pathway as a potential therapeutic target in<br/>tumours with CD163+ macrophages. Immune composition can be defined not just by the type of cells, but also with respect to<br/>frequency and spatial localization and this is explored in paper V with respect to T-cell subtypes. Thus, in paper V, we optimized<br/>a workflow of multiplexed immunofluorescence image segmentation that allowed us to extract cell metrics for four subtypes of<br/>CD3+ T-cells. Using this data, we show that higher infiltration of T-cells is associated with a positive outcome in MCL. Moreover,<br/>by combining image derived metrics to cell specific spatial omics data, we were able to identify immunosuppressive<br/>microenvironment associated with highly infiltrated tumours and suggests new potential targets of immunotherapy with respect to<br/>IDO1, GITR and STING. In conclusion, this thesis explores systemic and tumor-associated immune microenvironment in MCL, for<br/>defining patient heterogeneity, developing methods of patient stratification and for identifying novel and actionable biomarkers.}},
author = {{Lokhande, Lavanya}},
isbn = {{978-91-8039-546-5}},
keywords = {{Mantle cell lymphoma (MCL); proteomic analyses; spatial analysis; Biomarker discovery; immune microenviroment; serum proteomics}},
language = {{eng}},
month = {{01}},
publisher = {{Department of Immunotechnology, Lund University}},
school = {{Lund University}},
title = {{The immune microenvironment in mantle cell lymphoma : Targeted liquid and spatial proteomic analyses}},
url = {{https://lup.lub.lu.se/search/files/136776532/Lavanya_Lokhande_WEBB.pdf}},
year = {{2023}},
}