Habib Sadeghirad

University of Queensland

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Arutha Kulasinghe

University of Queensland

Kenneth J. O’Byrne

Queensland University of Technology

James Monkman

University of Queensland

Brett Hughes

Royal Brisbane and Women's Hospital

Majid Ebrahimi Warkiani

University of Technology Sydney

Rahul Ladwa

Princess Alexandra Hospital

Chin Wee Tan

Walter and Eliza Hall Institute of Medical Research

Vahid Yaghoubi Naei

University of Technology Sydney

Ning Liu

China Medical University

Kirsty R. Short

University of Queensland

Cooperative Institutions

University of Queensland

Translational Research Institute

Queensland University of Technology

Princess Alexandra Hospital

Pontifícia Universidade Católica do Paraná

University of Melbourne

Universidade Federal do Paraná

Tehran University of Medical Sciences

Nanostring Technologies (United States)

Walter and Eliza Hall Institute of Medical Research

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Spatial proteomic profiling of tumor and stromal compartments in non‐small‐cell lung cancer identifies signatures associated with overall survival

Clinical & Translational Immunology (2024)

Vahid Yaghoubi Naei James Monkman Habib Sadeghirad Ahmed M. Mehdi Tony Blick

Abstract Objectives Non‐small‐cell lung carcinoma (NSCLC) is the most prevalent and lethal form of lung cancer. The need for biomarker‐informed stratification of targeted therapies has underpinned the need to uncover the underlying properties of the tumor microenvironment (TME) through high‐plex quantitative assays. Methods In this study, we profiled resected NSCLC tissues from 102 patients by targeted spatial proteomics of 78 proteins across tumor, immune activation, immune cell typing, immune‐oncology, drug targets, cell death and PI3K/AKT modules to identify the tumor and stromal signatures associated with overall survival (OS). Results Survival analysis revealed that stromal CD56 (HR = 0.384, P = 0.06) and tumoral TIM3 (HR = 0.703, P = 0.05) were associated with better survival in univariate Cox models. In contrast, after adjusting for stage, BCLXL (HR = 2.093, P = 0.02) and cleaved caspase 9 (HR = 1.575, P = 0.1) negatively influenced survival. Delta testing indicated the protective effect of TIM‐3 (HR = 0.614, P = 0.04) on OS. In multivariate analysis, CD56 (HR = 0.172, P = 0.001) was associated with better survival in the stroma, while B7.H3 (HR = 1.72, P = 0.008) was linked to poorer survival in the tumor. Conclusions Deciphering the TME using high‐plex spatially resolved methods is giving us new insights into compartmentalised tumor and stromal protein signatures associated with clinical endpoints in NSCLC.

Univariate analysis

10.1002/cti2.1522

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Spatial dynamics of tertiary lymphoid aggregates in head and neck cancer: insights into immunotherapy response

Journal of Translational Medicine (2024)

Habib Sadeghirad James Monkman Chin Wee Tan Ning Liu Joseph Yunis

Abstract Background Recurrent/metastatic head and neck squamous cell carcinoma (R/M HNSCC) generally has a poor prognosis for patients with limited treatment options. While incorporating immune checkpoint inhibitors (ICIs) has now become the standard of care, the efficacy is variable, with only a subset of patients responding. The complexity of the tumor microenvironment (TME) and the role of tertiary lymphoid structures (TLS) have emerged as critical determinants for immunotherapeutic response. Methods In this study, we analyzed two independently collected R/M HNSCC patient tissue cohorts to better understand the role of TLS in response to ICIs. Utilizing a multi-omics approach, we first performed targeted proteomic profiling using the Nanostring GeoMx Digital Spatial Profiler to quantify immune-related protein expression with spatial resolution. This was further characterized by spatially resolved whole transcriptome profiling of TLSs and germinal centers (GCs). Deeper single-cell resolved proteomic profiling of the TLSs was performed using the Akoya Biosciences Phenocycler Fusion platform. Results Our proteomic analysis revealed the presence of T lymphocyte markers, including CD3, CD45, and CD8, expressing cells and upregulation of immune checkpoint marker PD-L1 within tumor compartments of patients responsive to ICIs, indicative of ‘hot tumor’ phenotypes. We also observed the presence of antigen-presenting cells marked by expression of CD40, CD68, CD11c, and CD163 with upregulation of antigen-presentation marker HLA-DR, in patients responding to ICIs. Transcriptome analysis of TLS and GCs uncovered a marked elevation in the expression of genes related to immune modulation, diverse immune cell recruitment, and a potent interferon response within the TLS structure. Notably, the distribution of TLS-tumor distance was found to be significantly different across response groups (H = 9.28, p = 0.026). The proximity of TLSs to tumor cells was found to be a critical indicator of ICI response, implying that patients with TLSs located further from tumor cells have worse outcomes. Conclusion The study underscores the multifaceted role of TLSs in modulating the immunogenic landscape of the TME in R/M HNSCC, likely influencing the efficacy of ICIs. Spatially resolved multi-omics approaches offer valuable insights into potential biomarkers for ICI response and highlight the importance of profiling the TME complexity when developing therapeutic strategies and patient stratification.

Immune checkpoint

Cancer Immunotherapy

10.1186/s12967-024-05409-y

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The development of a high-plex spatial proteomic methodology for the characterisation of the head and neck tumour microenvironment

Research Square (Research Square) (2024)

Chin Wee Tan Naomi Berrell Meg L Donovan James Monkman Habib Sadeghirad

Abstract Mucosal head and neck squamous cell carcinoma (HNSCC) is a debilitating disease that accounts for an estimated 890,000 new cases per year, making it the seventh most common cancer globally. HNSCC is a heterogenous group of cancers that affect various regions of the head and neck which stem from the epithelial cells in the mucosal lining. Despite advancements in chemotherapy, radiotherapy, surgery and immunotherapy, the prognosis of HNSCC has remained relatively unchanged for more than a decade. There is a need to better understand the tumour microenvironment (TME) using spatially resolved approaches, to gain insights into the TME associated with clinical endpoints such as Disease-Free Survival (DFS) and Overall Survival (OS). Here, we profiled 84 mucosal HNSCC tissue samples using next-generation ultra-high plex spatial protein profiling (580-proteins, Immuno-Oncology Proteome Atlas) and spatial transcriptome mapping (18,000 mRNA, Whole Transcriptome Atlas) from Nanostring Technologies (Bruker). Patient specimens were collected during tumour resection, where patients then went on to receive either chemotherapy and/or radiotherapy. Each patient tissue sample was subdivided into tumour and stromal regions prior to digital spatial profiling. We found that patient survival outcomes (both DFS and OS) were associated with anatomical locations and tumour stage. Notably, there were specific proteomic and transcriptomic features in both the tumour and stromal regions that associated with DFS and OS. Independent validation of key proteomic findings (including CD34 and CD44) was performed using single-cell protein profiling (PhenoCycler-Fusion, Akoya Biosciences). Finally, cell type deconvolution based on transcriptomic signatures revealed cell types associated with patient survival. Taken together, this study provides a systematic workflow for discovery and validation of high-plex protein and transcriptomic profiling in mucosal HNSCC.

10.21203/rs.3.rs-5272207/v1

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Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies placental dysfunction signatures

bioRxiv (Cold Spring Harbor Laboratory) (2023)

Nataly Stylianou Ismail Sebina Nicholas Matigian James Monkman Hadeel Doehler

ABSTRACT Objectives Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus infection in pregnancy is associated with higher incidence of placental dysfunction, referred to by a few studies as a “preeclampsia-like syndrome”. However, the mechanisms underpinning SARS-CoV-2-induced placental malfunction are still unclear. Here, we investigated whether the transcriptional architecture of the placenta is altered in response to SARS-CoV-2 infection. Methods We utilized whole-transcriptome, digital spatial profiling, to examine gene expression patterns in placental tissues from participants who contracted SARS-CoV-2 in the third trimester of their pregnancy (n=7) and those collected prior to the start of the coronavirus disease 2019 (COVID-19) pandemic (n=9). Results Through comprehensive spatial transcriptomic analyses of the trophoblast and villous core stromal cell subpopulations in the placenta, we identified signatures associated with hypoxia and placental dysfunction during SARS-CoV-2 infection in pregnancy. Notably, genes associated with vasodilation ( NOS3 ), oxidative stress ( GDF15 , CRH ), and preeclampsia ( FLT1, EGFR, KISS1, PAPPA2), were enriched with SARS-CoV-2. Pathways related to increased nutrient uptake, vascular tension, hypertension, and inflammation, were also enriched in SARS-CoV-2 samples compared to uninfected controls. Conclusions Our findings demonstrate the utility of spatially resolved transcriptomic analysis in defining the underlying pathogenic mechanisms of SARS-CoV-2 in pregnancy, particularly its role in placental dysfunction. Furthermore, this study highlights the significance of digital spatial profiling in mapping the intricate crosstalk between trophoblasts and villous core stromal cells, thus shedding light on pathways associated with placental dysfunction in pregnancies with SARS-CoV-2 infection. Graphical abstract In this study, using spatial digital profiling transcriptomic approaches, we demonstrate that SARS-CoV-2 infection in pregnancy disrupts optimal placental function by altering the genomic architecture of trophoblasts and villous core stromal cells.

Trophoblast

Endothelial Dysfunction

Placentation

10.1101/2023.01.20.524893

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In situ characterization of the tumor microenvironment

Current Opinion in Biotechnology (2024)

Habib Sadeghirad Vahid Yaghoubi Naei Kenneth J. O’Byrne Majid Ebrahimi Warkiani Arutha Kulasinghe

The development of new therapies for cancer is underpinned by an increasing need to comprehensively characterize the tumor microenvironment (TME). While traditional approaches have relied on bulk or single-cell approaches, these are limited in their ability to provide cellular context. Deconvolution of the complex TME is fundamental to understanding tumor dynamics and treatment resistance. Spatially resolved characterization of the TME is likely to provide greater insights into the cellular architecture, tumor-immune cell interactions, receptor-ligand interactions, and cell niches. In turn, these aid in dictating the optimal way in which to target each patient's individual cancer. In this review, we discuss a number of cutting-edge in situ spatial profiling methods giving us new insights into tumor biology.

Characterization

10.1016/j.copbio.2024.103083

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Abstract 1154: Spatial profiling of the tumor microenvironment in head and neck squamous cell carcinoma revealed immune cell type infiltration into the TME as a predictor of immunotherapy response

Cancer Research (2024)

Habib Sadeghirad Chin Wee Tan Ning Liu James Monkman Caroline Cooper

Abstract Background: Immunotherapy has shown promising results in advanced head and neck cancer patients, however, only a subset of patients are responsive to immune checkpoint blockade therapy. The molecular and cellular characterization of the tumor microenvironment (TME) may reveal clues as to why some head and neck tumors are responsive or resistant to the therapy. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples were collected from 34 patients at two major Queensland Hospitals with advanced head and neck squamous cell carcinoma (HNSCC), prior to immunotherapy. To investigate the cellular and molecular characteristics of the HNSCC TME, we used the Nanostring GeoMx Digital Spatial Profiler (DSP) spanning modules in an immune-oncology panel, which included immune cell typing and profiling, cell death, PI3K/AKT signaling, drug target, immune activation, and pan tumor protein biomarkers. A deeper structural analysis was performed using the Nanostring whole transcriptome atlas (WTA) panel of tertiary lymphoid structures (TLSs) and germinal centers (GCs). Results: Out of 34 patients, 3 had a complete response (CR), 7 had a partial response (PR), 5 had stable disease (SD), and 19 had progressive disease (PD), based on the Response Evaluation Criteria in Solid Tumors (RECIST). When we compared patient responders (patients with CR, PR, and SD) to patient non-responders (patients with PD), we found that the former had a higher infiltration of immune cell type markers representatives of CD8+ T cells, dendritic cells, and macrophages, into their tumor microenvironment than the latter. Then, to investigate differentially expressed genes between patients with complete response and patients with partial response to immunotherapy, we performed DE analyses and we found that patients with PR had higher Ki-67 expression than those with CR. Spatial transcriptomic mapping of TLS’s (peripheral, intra-tumoral) and normal germinal centers revealed interferon pathway enrichment in the TLS’s. In a subset, these appear to be linked with HPV viral infection. Conclusion: In this study, we found that immune cell type infiltration into the tumor microenvironment of head and neck cancers could be predictive of response to immunotherapy. Furthermore, it was revealed that patients with a high expression of Ki-67 might be less likely to respond completely to immunotherapy. Spatially resolved whole transcriptome analysis of HNSCC tissues revealed the presence of tertiary lymphoid structures with a higher enrichment of interferon pathway genes. Citation Format: Habib Sadeghirad, Chin Wee Tan, Ning Liu, James Monkman, Caroline Cooper, Ken O’Byrne, Melissa Davis, Brett Hughes, Arutha Kulasinghe. Spatial profiling of the tumor microenvironment in head and neck squamous cell carcinoma revealed immune cell type infiltration into the TME as a predictor of immunotherapy response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1154.

Infiltration (HVAC)

10.1158/1538-7445.am2024-1154

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Cardiovascular disease in SARS‐CoV‐2 infection

Clinical & Translational Immunology (2021)

Kei Sato Jane E. Sinclair Habib Sadeghirad John F. Fraser Kirsty R. Short

Abstract Pre‐existing cardiovascular disease (CVD) increases the morbidity and mortality of COVID‐19 and is strongly associated with poor disease outcomes. However, SARS‐CoV‐2 infection can also trigger de novo acute and chronic cardiovascular disease. Acute cardiac complications include arrhythmia, myocarditis and heart failure, which are significantly associated with higher in‐hospital mortality. The possible mechanisms by which SARS‐CoV‐2 causes this acute cardiac disease include direct damage caused by viral invasion of cardiomyocytes as well as indirect damage through systemic inflammation. The long‐term cardiac complications associated with COVID‐19 are incompletely characterised and thought to include hypertension, arrhythmia, coronary atherosclerosis and heart failure. Although some cardiac‐related symptoms can last over 6 months, the effect of these complications on long‐term patient health remains unclear. The risk factors associated with long‐term cardiovascular disease remain poorly defined. Determining which patients are most at‐risk of long‐term cardiovascular disease is vital so that targeted follow‐up and patient care can be provided. The aim of this review was to summarise the current evidence of the acute and long‐term cardiovascular consequences of SARS‐CoV‐2 infection and the mechanisms by which SARS‐CoV‐2 may cause cardiovascular disease.

10.1002/cti2.1343

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Whole transcriptome profiling of placental pathobiology in SARS‐CoV‐2 pregnancies identifies placental dysfunction signatures

Clinical & Translational Immunology (2024)

Nataly Stylianou Ismail Sebina Nicholas Matigian James Monkman Hadeel Doehler

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus infection in pregnancy is associated with higher incidence of placental dysfunction, referred to by a few studies as a 'preeclampsia-like syndrome'. However, the mechanisms underpinning SARS-CoV-2-induced placental malfunction are still unclear. Here, we investigated whether the transcriptional architecture of the placenta is altered in response to SARS-CoV-2 infection.

Coronavirus

Pandemic

2019-20 coronavirus outbreak

10.1002/cti2.1488

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Citations (5)

Immunotherapeutic targets in non‐small cell lung cancer

Immunology (2022)

Habib Sadeghirad Tayyeb Bahrami Sepideh Mehrpour Layeghi Hassan Yousefi Meysam Rezaei

Non-small cell lung cancer (NSCLC) is one of the most common types of cancer in the world and has a 5-year survival rate of ~20%. Immunotherapies have shown promising results leading to durable responses, however, they are only effective for a subset of patients. To determine the best therapeutic approach, a thorough and in-depth profiling of the tumour microenvironment (TME) is required. The TME is a complex network of cell types that form an interconnected network, promoting tumour cell initiation, growth and dissemination. The stroma, immune cells and endothelial cells that comprise the TME generate a plethora of cytotoxic or cytoprotective signalling pathways. In this review, we discuss immunotherapeutic targets in NSCLC tumours and how the TME may influence patients' response to immunotherapy.

10.1111/imm.13562

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Transcriptomic profiling of cardiac tissues from SARS-CoV-2 patients identifies DNA damage

medRxiv (Cold Spring Harbor Laboratory) (2022)

Arutha Kulasinghe Ning Liu Chin Wee Tan James Monkman Jane E. Sinclair

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is known to present with pulmonary and extra-pulmonary organ complications. In comparison with the 2009 pandemic (pH1N1), SARS-CoV-2 infection is likely to lead to more severe disease, with multi-organ effects, including cardiovascular disease. SARS-CoV-2 has been associated with acute and long-term cardiovascular disease, but the molecular changes govern this remain unknown. In this study, we investigated the landscape of cardiac tissues collected at rapid autopsy from SARS-CoV-2, pH1N1, and control patients using targeted spatial transcriptomics approaches. Although SARS-CoV-2 was not detected in cardiac tissue, host transcriptomics showed upregulation of genes associated with DNA damage and repair, heat shock, and M1-like macrophage infiltration in the cardiac tissues of COVID-19 patients. The DNA damage present in the SARS-CoV-2 patient samples, were further confirmed by γ−H2Ax immunohistochemistry. In comparison, pH1N1 showed upregulation of Interferon-stimulated genes (ISGs), in particular interferon and complement pathways, when compared with COVID-19 patients. These data demonstrate the emergence of distinct transcriptomic profiles in cardiac tissues of SARS-CoV-2 and pH1N1 influenza infection supporting the need for a greater understanding of the effects on extra-pulmonary organs, including the cardiovascular system of COVID-19 patients, to delineate the immunopathobiology of SARS-CoV-2 infection, and long term impact on health.

10.1101/2022.03.24.22272732

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Citations (4)