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Gabby LC, Jones CK, McIntyre BB, Manalo Z, Meads M, Pizzo DP, Diaz-Vigil J, Soncin F, Fisch KM, Ramos GA, Jacobs MB, Parast MM. Chronic villitis as a distinctive feature of placental injury in maternal SARS-CoV-2 infection. Am J Obstet Gynecol 2024:S0002-9378(24)00480-0. [PMID: 38580043 DOI: 10.1016/j.ajog.2024.04.002] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/19/2024] [Accepted: 04/01/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND SARS-CoV-2 infection during pregnancy is associated with an increased risk for stillbirth, preeclampsia, and preterm birth. However, this does not seem to be caused by intrauterine fetal infection because vertical transmission is rarely reported. There is a paucity of data regarding the associated placental SARS-CoV-2 histopathology and their relationship with the timing and severity of infection. OBJECTIVE This study aimed to determine if maternal SARS-CoV-2 infection was associated with specific patterns of placental injury and if these findings differed by gestational age at time of infection or disease severity. STUDY DESIGN A retrospective cohort study was performed at the University of California San Diego between March 2020 and February 2021. Placentas from pregnancies with a positive SARS-CoV-2 test were matched with 2 sets of controls; 1 set was time-matched by delivery date and sent to pathology for routine clinical indications, and the other was chosen from a cohort of placentas previously collected for research purposes without clinical indications for pathologic examination before the SARS-CoV-2 outbreak. Placental pathologic lesions were defined based on standard criteria and included maternal and fetal vascular malperfusion and acute and chronic inflammatory lesions. A bivariate analysis was performed using the independent Student t test and Pearson chi-square test. A logistic regression was used to control for relevant covariates. Regions of SARS-CoV-2-associated villitis were further investigated using protein-based digital spatial profiling assays on the GeoMx platform, validated by immunohistochemistry, and compared with cases of infectious villitis and villitis of unknown etiology. Differential expression analysis was performed to identify protein expression differences between these groups of villitis. RESULTS We included 272 SARS-CoV-2 positive cases, 272 time-matched controls, and 272 historic controls. The mean age of SARS-CoV-2 affected subjects was 30.1±5.5 years and the majority were Hispanic (53.7%) and parous (65.7%). SARS-CoV-2 placentas demonstrated a higher frequency of the 4 major patterns of placental injury (all P<.001) than the historic controls. SARS-CoV-2 placentas also showed a higher frequency of chronic villitis and severe chronic villitis (P=.03 for both) than the time-matched controls, which remained significant after controlling for gestational age at delivery (adjusted odds ratio, 1.52; 95% confidence interval, 1.01-2.28; adjusted odds ratio, 2.12; 95% confidence interval, 1.16-3.88, respectively). Digital spatial profiling revealed that programmed death-ligand 1 was increased in villitis-positive regions of the SARS-CoV-2 (logFC, 0.47; adjusted P value =.002) and villitis of unknown etiology (logFC, 0.58; adjusted P value =.003) cases, but it was conversely decreased in villitis-positive regions of the infectious villitis group (log FC, -1.40; adjusted P value <.001). CONCLUSION Chronic villitis seems to be the most specific histopathologic finding associated with SARS-CoV-2 maternal infection. Chronic villitis involves damage to the vasculosyncytial membrane of the chorionic villi, which are involved in gas and nutrient exchange, suggesting potential mechanisms of placental (and perhaps neonatal) injury, even in the absence of vertical transmission. Surprisingly, changes in protein expression in SARS-CoV-2-associated villitis seem to be more similar to villitis of unknown etiology than to infectious villitis.
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Affiliation(s)
- Lauryn C Gabby
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, CA
| | - Chelsea K Jones
- University of California San Diego School of Medicine, La Jolla, CA
| | | | - Zoe Manalo
- Department of Pathology, University of California San Diego, La Jolla, CA; Sanford Consortium for Regenerative Medicine, La Jolla, CA
| | - Morgan Meads
- Department of Pathology, University of California San Diego, La Jolla, CA
| | - Donald P Pizzo
- Department of Pathology, University of California San Diego, La Jolla, CA
| | - Jessica Diaz-Vigil
- Department of Pathology, University of California San Diego, La Jolla, CA
| | - Francesca Soncin
- Department of Pathology, University of California San Diego, La Jolla, CA; Sanford Consortium for Regenerative Medicine, La Jolla, CA
| | - Kathleen M Fisch
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, CA
| | - Gladys A Ramos
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, CA
| | - Marni B Jacobs
- Division of Maternal-Fetal Medicine, Department of Obstetrics, Gynecology & Reproductive Sciences, University of California San Diego, La Jolla, CA
| | - Mana M Parast
- Department of Pathology, University of California San Diego, La Jolla, CA; Sanford Consortium for Regenerative Medicine, La Jolla, CA.
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Duan S, Sawyer TW, Witten BL, Song H, Else T, Merchant JL. Spatial profiling reveals tissue-specific neuro-immune interactions in gastroenteropancreatic neuroendocrine tumors. J Pathol 2024; 262:362-376. [PMID: 38229586 PMCID: PMC10869639 DOI: 10.1002/path.6241] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 10/14/2023] [Accepted: 11/24/2023] [Indexed: 01/18/2024]
Abstract
Gastroenteropancreatic neuroendocrine tumors (GEP-NETs) are heterogeneous malignancies that arise from complex cellular interactions within the tissue microenvironment. Here, we sought to decipher tumor-derived signals from the surrounding microenvironment by applying digital spatial profiling (DSP) to hormone-secreting and non-functional GEP-NETs. By combining this approach with in vitro studies of human-derived organoids, we demonstrated the convergence of cell autonomous immune and pro-inflammatory proteins that suggests their role in neuroendocrine differentiation and tumorigenesis. DSP was used to evaluate the expression of 40 neural- and immune-related proteins in surgically resected duodenal and pancreatic NETs (n = 20) primarily consisting of gastrinomas (18/20). A total of 279 regions of interest were examined between tumors, adjacent normal and abnormal-appearing epithelium, and the surrounding stroma. The results were stratified by tissue type and multiple endocrine neoplasia I (MEN1) status, whereas protein expression was validated by immunohistochemistry (IHC). A tumor immune cell autonomous inflammatory signature was further evaluated by IHC and RNAscope, while functional pro-inflammatory signaling was confirmed using patient-derived duodenal organoids. Gastrin-secreting and non-functional pancreatic NETs showed a higher abundance of immune cell markers and immune infiltrate compared with duodenal gastrinomas. Compared with non-MEN1 tumors, MEN1 gastrinomas and preneoplastic lesions showed strong immune exclusion and upregulated expression of neuropathological proteins. Despite a paucity of immune cells, duodenal gastrinomas expressed the pro-inflammatory and pro-neural factor IL-17B. Treatment of human duodenal organoids with IL-17B activated NF-κB and STAT3 signaling and induced the expression of neuroendocrine markers. In conclusion, multiplexed spatial protein analysis identified tissue-specific neuro-immune signatures in GEP-NETs. Duodenal gastrinomas are characterized by an immunologically cold microenvironment that permits cellular reprogramming and neoplastic transformation of the preneoplastic epithelium. Moreover, duodenal gastrinomas cell autonomously express immune and pro-inflammatory factors, including tumor-derived IL-17B, that stimulate the neuroendocrine phenotype. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Suzann Duan
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Travis W. Sawyer
- Department of Optical Sciences, University of Arizona Wyant College of Optical Sciences, Tucson, AZ, USA
| | - Brandon L. Witten
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Heyu Song
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
| | - Tobias Else
- Department of Internal Medicine, Endocrinology, University of Michigan, Ann Harbor, Michigan, USA
| | - Juanita L. Merchant
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Arizona College of Medicine, Tucson, AZ, USA
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López J, Hogan M, Sutton B, Church S, Angulo J, Nunes-Xavier C. Distinct spatial landscapes in clear-cell renal cell carcinoma as revealed by whole transcriptome analysis. Immunooncol Technol 2024; 21:100690. [PMID: 38292905 PMCID: PMC10825646 DOI: 10.1016/j.iotech.2023.100690] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Clear-cell renal cell carcinoma (ccRCC) is the most common and aggressive form of renal cancer and a paradigm of inter- and intratumor heterogeneity. We carried out an exploratory digital spatial profiling of the tumor interior and periphery of two ccRCC tumor specimens and mapped spatially the molecular and cellular composition of their tumor microenvironment and ecosystem. Materials and methods Digital spatial profiling of the whole transcriptome of 19 regions of interest (ROIs) was carried out from two selected highly immunogenic stage pT3a/grade 3 (G3) and stage pT3a/grade 4 (G4) ccRCC. A total of 9-10 ROIs were selected from distinct areas from each tumor, including tumor interior and tumor periphery, and differences in gene expression were analyzed by RNA sequencing, pathway enrichment analysis, and cell deconvolution. Results The distinct areas from the two locally advanced tumors displayed unique gene expression spatial patterns defining distinct biological pathways. Dimensional reduction analysis showed that the G3 ccRCC, compared to the G4 ccRCC, correlated with more variability between regions from the tumor interior and tumor periphery. Cell deconvolution analysis illustrated higher abundance of immune cells, including macrophages, myeloid dendritic cells, and CD4 T cells, and lower abundance of regulatory T cells in the tumor periphery compared to the tumor interior. Conclusions Transcriptome spatial profiling revealed high inter- and intratumor heterogeneity in the analyzed tumors and provided information with potential clinical utility. This included the finding of less intratumor heterogeneity and more tumor-infiltrated T cells in the ccRCC tumor specimen with a higher grade.
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Affiliation(s)
- J.I. López
- Biobizkaia Health Research Institute, Barakaldo, Spain
| | | | - B. Sutton
- NanoString Technologies, Seattle, USA
| | | | - J.C. Angulo
- Service of Urology, University Hospital of Getafe, Getafe, Madrid
- Clinical Department, Faculty of Biomedical Sciences, European University of Madrid, Madrid, Spain
| | - C.E. Nunes-Xavier
- Biobizkaia Health Research Institute, Barakaldo, Spain
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
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Stylianou N, Sebina I, Matigian N, Monkman J, Doehler H, Röhl J, Allenby M, Nam A, Pan L, Rockstroh A, Sadeghirad H, Chung K, Sobanski T, O'Byrne K, Almeida ACSF, Rebutini PZ, Machado‐Souza C, Stonoga ETS, Warkiani ME, Salomon C, Short K, McClements L, de Noronha L, Huang R, Belz GT, Souza‐Fonseca‐Guimaraes F, Clifton V, Kulasinghe A. Whole transcriptome profiling of placental pathobiology in SARS-CoV-2 pregnancies identifies placental dysfunction signatures. Clin Transl Immunology 2024; 13:e1488. [PMID: 38322491 PMCID: PMC10846628 DOI: 10.1002/cti2.1488] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 02/08/2024]
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 utilised 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 SARS-CoV-2 to promote signatures associated with hypoxia and placental dysfunction. 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.
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Affiliation(s)
- Nataly Stylianou
- Australian Prostate Cancer Research Centre – Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQLDAustralia
| | - Ismail Sebina
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | | | - James Monkman
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Hadeel Doehler
- Australian Prostate Cancer Research Centre – Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQLDAustralia
| | - Joan Röhl
- Faculty of Health Sciences and MedicineBond UniversityRobinaQLDAustralia
| | - Mark Allenby
- BioMimetic Systems Engineering Lab, School of Chemical EngineeringUniversity of Queensland (UQ)St LuciaQLDAustralia
| | - Andy Nam
- Nanostring Technologies, Inc.SeattleWAUSA
| | - Liuliu Pan
- Nanostring Technologies, Inc.SeattleWAUSA
| | - Anja Rockstroh
- Australian Prostate Cancer Research Centre – Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQLDAustralia
| | - Habib Sadeghirad
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Kimberly Chung
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Thais Sobanski
- Australian Prostate Cancer Research Centre – Queensland, Centre for Genomics and Personalised Health, School of Biomedical Sciences, Faculty of HealthQueensland University of TechnologyBrisbaneQLDAustralia
| | - Ken O'Byrne
- Princess Alexandra HospitalWoolloongabbaQLDAustralia
| | | | - Patricia Zadorosnei Rebutini
- Postgraduate Program of Health Sciences, School of MedicinePontifícia Universidade Católica do Paraná ´ –PUCPRCuritibaBrazil
| | - Cleber Machado‐Souza
- Postgraduate Program in Biotechnology Applied in Health of Children and AdolescentInstituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno PríncipeCuritibaBrazil
| | | | - Majid E Warkiani
- School of Life Sciences & Institute for Biomedical Materials and Devices, Faculty of ScienceUniversity of Technology SydneySydneyNSWAustralia
| | - Carlos Salomon
- Exosome Biology Laboratory, Centre for Clinical Diagnostics, University of Queensland Centre for Clinical Research, Royal Brisbane and Women's Hospital, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | - Kirsty Short
- School of Chemistry and Molecular Biosciences, Faculty of ScienceThe University of QueenslandSt LuciaQLDAustralia
| | - Lana McClements
- School of Life Sciences & Institute for Biomedical Materials and Devices, Faculty of ScienceUniversity of Technology SydneySydneyNSWAustralia
| | - Lucia de Noronha
- Postgraduate Program of Health Sciences, School of MedicinePontifícia Universidade Católica do Paraná ´ –PUCPRCuritibaBrazil
| | - Ruby Huang
- School of Medicine, College of MedicineNational Taiwan UniversityTaipeiTaiwan
| | - Gabrielle T Belz
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
| | | | - Vicki Clifton
- Mater Medical Research InstituteUniversity of QueenslandBrisbaneQLDAustralia
| | - Arutha Kulasinghe
- Frazer Institute, Faculty of MedicineThe University of QueenslandBrisbaneQLDAustralia
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Duggan WP, Kisakol B, Woods I, Azimi M, Dussmann H, Fay J, O’Grady T, Maguire B, Reynolds IS, Salvucci M, Slade DJ, McNamara DA, Burke JP, Prehn JH. Spatial transcriptomic analysis reveals local effects of intratumoral fusobacterial infection on DNA damage and immune signaling in rectal cancer. Gut Microbes 2024; 16:2350149. [PMID: 38709233 PMCID: PMC11086019 DOI: 10.1080/19490976.2024.2350149] [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] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 04/26/2024] [Indexed: 05/07/2024]
Abstract
Mucinous colorectal cancer (CRC) is a common histological subtype of colorectal adenocarcinoma, associated with a poor response to chemoradiotherapy. The commensal facultative anaerobes fusobacteria, have been associated with poor prognosis specifically in mesenchymal CRC. Interestingly, fusobacterial infection is especially prevalent in mucinous CRC. The objective of this study was therefore to increase our understanding of beneficial and detrimental effects of fusobacterial infection, by contrasting host cell signaling and immune responses in areas of high vs. low infection, using mucinous rectal cancer as a clinically relevant example. We employed spatial transcriptomic profiling of 106 regions of interest from 8 mucinous rectal cancer samples to study gene expression in the epithelial and immune segments across regions of high versus low fusobacterial infection. Fusobacteria high regions were associated with increased oxidative stress, DNA damage, and P53 signaling. Meanwhile regions of low fusobacterial prevalence were characterized by elevated JAK-STAT, Il-17, Il-1, chemokine and TNF signaling. Immune masks within fusobacterial high regions were characterized by elevated proportions of cytotoxic (CD8+) T cells (p = 0.037), natural killer (NK) cells (p < 0.001), B-cells (p < 0.001), and gamma delta T cells (p = 0.003). Meanwhile, fusobacteria low regions were associated with significantly greater M2 macrophage (p < 0.001), fibroblast (p < 0.001), pericyte (p = 0.002), and endothelial (p < 0.001) counts.
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Affiliation(s)
- William P. Duggan
- Department of Colorectal Surgery, Beaumont Hospital, Dublin 9, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Batuhan Kisakol
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ina Woods
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Mohammedreza Azimi
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Heiko Dussmann
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Joanna Fay
- Department of Pathology, Beaumont Hospital, Dublin 9, Ireland
| | - Tony O’Grady
- Department of Pathology, Beaumont Hospital, Dublin 9, Ireland
| | - Barry Maguire
- Department of Colorectal Surgery, Beaumont Hospital, Dublin 9, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Ian S. Reynolds
- Department of Colorectal Surgery, Beaumont Hospital, Dublin 9, Ireland
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Daniel J. Slade
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | | | - John P. Burke
- Department of Colorectal Surgery, Beaumont Hospital, Dublin 9, Ireland
| | - Jochen H.M. Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, Ireland
- RCSI Centre for Systems Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
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Uddin MH, Al‐Hallak MN, Khan HY, Aboukameel A, Li Y, Bannoura SF, Dyson G, Kim S, Mzannar Y, Azar I, Odisho T, Mohamed A, Landesman Y, Kim S, Beydoun R, Mohammad RM, Philip PA, Shields AF, Azmi AS. Molecular analysis of XPO1 inhibitor and gemcitabine-nab-paclitaxel combination in KPC pancreatic cancer mouse model. Clin Transl Med 2023; 13:e1513. [PMID: 38131168 PMCID: PMC10739156 DOI: 10.1002/ctm2.1513] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023]
Abstract
BACKGROUND The majority of pancreatic ductal adenocarcinoma (PDAC) patients experience disease progression while on treatment with gemcitabine and nanoparticle albumin-bound (nab)-paclitaxel (GemPac) necessitating the need for a more effective treatment strategy for this refractory disease. Previously, we have demonstrated that nuclear exporter protein exportin 1 (XPO1) is a valid therapeutic target in PDAC, and the selective inhibitor of nuclear export selinexor (Sel) synergistically enhances the efficacy of GemPac in pancreatic cancer cells, spheroids and patient-derived tumours, and had promising activity in a phase I study. METHODS Here, we investigated the impact of selinexor-gemcitabine-nab-paclitaxel (Sel-GemPac) combination on LSL-KrasG12D/+ ; LSL-Trp53R172H/+ ; Pdx1-Cre (KPC) mouse model utilising digital spatial profiling (DSP) and single nuclear RNA sequencing (snRNAseq). RESULTS Sel-GemPac synergistically inhibited the growth of the KPC tumour-derived cell line. The Sel-GemPac combination reduced the 2D colony formation and 3D spheroid formation. In the KPC mouse model, at a sub-maximum tolerated dose (sub-MTD) , Sel-GemPac enhanced the survival of treated mice compared to controls (p < .05). Immunohistochemical analysis of residual KPC tumours showed re-organisation of tumour stromal architecture, suppression of proliferation and nuclear retention of tumour suppressors, such as Forkhead Box O3a (FOXO3a). DSP revealed the downregulation of tumour promoting genes such as chitinase-like protein 3 (CHIL3/CHI3L3/YM1) and multiple pathways including phosphatidylinositol 3'-kinase-Akt (PI3K-AKT) signalling. The snRNAseq demonstrated a significant loss of cellular clusters in the Sel-GemPac-treated mice tumours including the CD44+ stem cell population. CONCLUSION Taken together, these results demonstrate that the Sel-GemPac treatment caused broad perturbation of PDAC-supporting signalling networks in the KPC mouse model. HIGHLIGHTS The majority of pancreatic ductal adenocarcinoma (PDAC) patients experience disease progression while on treatment with gemcitabine and nanoparticle albumin-bound (nab)-paclitaxel (GemPac). Exporter protein exportin 1 (XPO1) inhibitor selinexor (Sel) with GemPac synergistically inhibited the growth of LSL-KrasG12D/+; LSL-Trp53R172H/+; Pdx1-Cre (KPC) mouse derived cell line and enhanced the survival of mice. Digital spatial profiling shows that Sel-GemPac causes broad perturbation of PDAC-supporting signalling in the KPC model.
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Affiliation(s)
- Md. Hafiz Uddin
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Mohammad Najeeb Al‐Hallak
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Husain Yar Khan
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Amro Aboukameel
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Yiwei Li
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Sahar F. Bannoura
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Gregory Dyson
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Seongho Kim
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Yosef Mzannar
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Ibrahim Azar
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | | | - Amr Mohamed
- UH Seidman Cancer CenterUniversity Hospitals, Case Western Reserve UniversityClevelandOhioUSA
| | | | - Steve Kim
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Rafic Beydoun
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
- Department of PathologyWayne State University School of MedicineDetroitMichiganUSA
| | - Ramzi M. Mohammad
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | | | - Anthony F. Shields
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
| | - Asfar S. Azmi
- Department of OncologyKarmanos Cancer InstituteWayne State University School of MedicineDetroitMichiganUSA
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Qiu C, Lin Q, Ji S, Han C, Yang Q. Expression of IDO1 in Tumor Microenvironment Significantly Predicts the Risk of Recurrence/Distant Metastasis for Patients With Esophageal Squamous Cell Carcinoma. Lab Invest 2023; 103:100263. [PMID: 37839637 DOI: 10.1016/j.labinv.2023.100263] [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] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/17/2023]
Abstract
In this study, we aimed to explore immune markers predicting locoregional recurrence/distant metastasis (R/M) for patients with esophageal squamous cell carcinoma (ESCC) post-surgical intervention by using a novel high-throughput spatial tool to quantify multiple immune proteins expressed in ESCC and lymphocytes in tumor microenvironment (TME-L). First, formalin-fixed paraffin-embedded tissues from surgical patients with ESCC (n = 94) were constructed on a microarray, which was then divided into discovery (n = 36) and validation cohorts (n = 58). Using a newly developed GeoMx digital spatial profiling tool, 31 immune proteins in paired ESCC and TME-L, morphologically segmented by PANCK and CD45, respectively, from the discovery cohort were quantified, releasing 2,232 variables. Next, the correlation matrix was analyzed using the Corrplot package in R Studio, resulting in 6 closely correlated clusters. The Least Absolute Shrinkage and Selection Operator regression scoring model predictive of R/M risk with superior specificity was successfully established based on the 3 following hierarchically clustered immune proteins: ARG1 in ESCC/PANCK+, STING, and IDO1 in TME-L/CD45+. Moreover, the expression of IDO1 in TME-L, rather than in ESCC, significantly predicted the R/M risk score with an area under curve of 0.9598. In addition, its correlation with R/M status was further validated by dual immunohistochemistry staining of IDO1 and CD45 in discovery and validation cohorts. Above all, our findings not only provide a more accurate scoring approach based on quantitative immune proteins for the prediction of R/M risk, but also propose that IDO1 in TME-L potentially plays a driving role in mediating R/M in ESCC.
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Affiliation(s)
- Cen Qiu
- Department of Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingyuan Lin
- Department of Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Saiyan Ji
- Department of Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenjie Han
- Department of Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingyuan Yang
- Department of Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Iwasa YI, Nakajima T, Hori K, Yokota Y, Kitoh R, Uehara T, Takumi Y. A Spatial Transcriptome Reveals Changes in Tumor and Tumor Microenvironment in Oral Cancer with Acquired Resistance to Immunotherapy. Biomolecules 2023; 13:1685. [PMID: 38136558 PMCID: PMC10742283 DOI: 10.3390/biom13121685] [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] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 10/26/2023] [Accepted: 11/13/2023] [Indexed: 12/24/2023]
Abstract
Although anti-programmed death-1 (PD-1) antibody therapy improves the prognosis in patients with head and neck squamous cell carcinoma (HNSCC), some patients exhibit disease progression even after showing a good response to the treatment initially because of acquired resistance. Here, we aimed to reveal the dynamic changes in the tumor and tumor microenvironment (TME) in a 77-year-old man diagnosed with oral squamous cell carcinoma who developed acquired resistance after the administration of nivolumab using spatial transcriptomics. The results showed that, before immunotherapy, the activated pathways in the tumor area were mainly related to the cancer immune system, including antigen processing cross-presentation, interferon-gamma signaling, and the innate immune system. After immunotherapy, the activated pathways were mainly related to epigenetic modification, including RMTs methylate histone arginine and HDAC deacetylates histones. Before immunotherapy, the activated pathways in the TME were mainly related to the metabolism of proteins, including SRP-dependent co-translational protein targeting the membrane. After immunotherapy, the activated pathways in the TME were related to sensory perception and signal transduction. Our study revealed that epigenetic-modification-related pathways were mainly activated after establishing acquired resistance, suggesting that epigenetic modification in the tumor may prevent cancer immune system activation via the anti-PD-1 antibody.
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Affiliation(s)
- Yoh-ichiro Iwasa
- Department of Otorhinolaryngology-Head and Neck Surgery, Shinshu University School of Medicine, Matsumoto 390-8621, Japan; (K.H.); (Y.Y.); (R.K.); (Y.T.)
| | - Tomoyuki Nakajima
- Department of Laboratory Medicine, Shinshu University School of Medicine, Matsumoto 390-8621, Japan; (T.N.); (T.U.)
| | - Kentaro Hori
- Department of Otorhinolaryngology-Head and Neck Surgery, Shinshu University School of Medicine, Matsumoto 390-8621, Japan; (K.H.); (Y.Y.); (R.K.); (Y.T.)
| | - Yoh Yokota
- Department of Otorhinolaryngology-Head and Neck Surgery, Shinshu University School of Medicine, Matsumoto 390-8621, Japan; (K.H.); (Y.Y.); (R.K.); (Y.T.)
| | - Ryosuke Kitoh
- Department of Otorhinolaryngology-Head and Neck Surgery, Shinshu University School of Medicine, Matsumoto 390-8621, Japan; (K.H.); (Y.Y.); (R.K.); (Y.T.)
| | - Takeshi Uehara
- Department of Laboratory Medicine, Shinshu University School of Medicine, Matsumoto 390-8621, Japan; (T.N.); (T.U.)
| | - Yutaka Takumi
- Department of Otorhinolaryngology-Head and Neck Surgery, Shinshu University School of Medicine, Matsumoto 390-8621, Japan; (K.H.); (Y.Y.); (R.K.); (Y.T.)
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9
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Huang H, Li N, Liang Y, Li R, Tong X, Xiao J, Tang H, Jiang D, Xie K, Fang C, Chen S, Li G, Wang B, Wang J, Luo H, Guo L, Ma H, Jiang W, Feng Y. Multi-omics analyses reveal spatial heterogeneity in primary and metastatic oesophageal squamous cell carcinoma. Clin Transl Med 2023; 13:e1493. [PMID: 38009315 PMCID: PMC10679972 DOI: 10.1002/ctm2.1493] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/07/2023] [Accepted: 11/14/2023] [Indexed: 11/28/2023]
Abstract
BACKGROUND Biopsies obtained from primary oesophageal squamous cell carcinoma (ESCC) guide diagnosis and treatment. However, spatial intra-tumoral heterogeneity (ITH) influences biopsy-derived information and patient responsiveness to therapy. Here, we aimed to elucidate the spatial ITH of ESCC and matched lymph node metastasis (LNmet ). METHODS Primary tumour superficial (PTsup ), deep (PTdeep ) and LNmet subregions of patients with locally advanced resectable ESCC were evaluated using whole-exome sequencing (WES), whole-transcriptome sequencing and spatially resolved digital spatial profiling (DSP). To validate the findings, immunohistochemistry was conducted and a single-cell transcriptomic dataset was analysed. RESULTS WES revealed 15.72%, 5.02% and 32.00% unique mutations in PTsup , PTdeep and LNmet , respectively. Copy number alterations and phylogenetic trees showed spatial ITH among subregions both within and among patients. Driver mutations had a mixed intra-tumoral clonal status among subregions. Transcriptome data showed distinct differentially expressed genes among subregions. LNmet exhibited elevated expression of immunomodulatory genes and enriched immune cells, particularly when compared with PTsup (all P < .05). DSP revealed orthogonal support of bulk transcriptome results, with differences in protein and immune cell abundance between subregions in a spatial context. The integrative analysis of multi-omics data revealed complex heterogeneity in mRNA/protein levels and immune cell abundance within each subregion. CONCLUSIONS This study comprehensively characterised spatial ITH in ESCC, and the findings highlight the clinical significance of unbiased molecular classification based on multi-omics data and their potential to improve the understanding and management of ESCC. The current practices for tissue sampling are insufficient for guiding precision medicine for ESCC, and routine profiling of PTdeep and/or LNmet should be systematically performed to obtain a more comprehensive understanding of ESCC and better inform treatment decisions.
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Affiliation(s)
- Haitao Huang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Na Li
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Yingkuan Liang
- Department of Thoracic SurgeryNanjing Medical University Affiliated Cancer HospitalNanjingChina
| | - Rutao Li
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Xing Tong
- Department of Pathologythe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Jinyuan Xiao
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Hongzhen Tang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Dong Jiang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Kai Xie
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Chen Fang
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Shaomu Chen
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Guangbin Li
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
| | - Bin Wang
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Jiaqian Wang
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Haitao Luo
- Shenzhen Engineering Center for Translational Medicine of Precision Cancer Immunodiagnosis and TherapyYuceBio Technology Co., LtdShenzhenChina
| | - Lingchuan Guo
- Department of Pathologythe First Affiliated Hospital of Soochow UniversitySuzhouJiangsuChina
| | - Haitao Ma
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Wei Jiang
- Department of Thoracic SurgeryDushu Lake Hospital Affiliated to Soochow UniversitySuzhouChina
| | - Yu Feng
- Department of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
- Institute of Thoracic Surgerythe First Affiliated Hospital of Soochow UniversitySuzhouChina
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10
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Chang SH, Mezzano-Robinson V, Zhou H, Moreira A, Pillai R, Ramaswami S, Loomis C, Heguy A, Tsirigos A, Pass HI. Digital Spatial Profiling to Predict Recurrence in Grade 3 Stage I Lung Adenocarcinoma. J Thorac Cardiovasc Surg 2023:S0022-5223(23)01004-8. [PMID: 37890657 DOI: 10.1016/j.jtcvs.2023.10.047] [Citation(s) in RCA: 1] [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] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/18/2023] [Accepted: 10/21/2023] [Indexed: 10/29/2023]
Abstract
OBJECTIVE Early-stage lung adenocarcinoma (LUAD) is treated with local therapy alone, though patients with grade 3 stage I LUAD a 50% 5-year recurrence rate. Our objective is to determine if analysis of the tumor microenvironment can create a predictive model for recurrence. METHODS Thirty-four grade 3 stage I LUAD patients underwent surgical resection. Digital spatial profiling was utilized to perform genomic (n=31) and proteomic (n=34) analysis of pancytokeratin positive (PanCK+) and negative (PanCK-) tumor cells. K-means clustering was performed on the top 50 differential genes and top 20 differential proteins, with Kaplan-Meier recurrence curves based on patient clustering. External validation of high expression genes was performed with Kaplan-Meier Plotter. RESULTS There were no significant clinicopathologic differences between patients who did (n=14) and did not (n=20) recur. Median time to recurrence was 806 days; median follow up with no recurrence was 2897 days. K-means clustering of PanCK+ genes resulted in a model with a Kaplan-Meier curve with C-index of 0.75. K-means clustering for PanCK- genes was less successful at differentiating recurrence (C-index 0.6). Genes upregulated or downregulated for recurrence were externally validated using available public databases. Proteomic data did not reach statistical significance but did internally validate the genomic data described above. CONCLUSIONS Genomic difference in LUAD may be able to predict risk of recurrence. After further validation, stratifying patients by this risk may help guide who will benefit from adjuvant therapy.
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Affiliation(s)
| | | | - Hua Zhou
- NYU Langone Health, Department of Pathology, Applied Bioinformatics Laboratory
| | - Andre Moreira
- NYU Langone Health, Department of Pathology, Center for Biomarker Research and Development
| | - Raymond Pillai
- NYU Langone Health, Department of Medicine, Division of Pulmonary Critical Care
| | | | - Cynthia Loomis
- NYU Langone Health, Experimental Pathology Research Laboratory
| | - Adriana Heguy
- NYU Langone Health, Department of Pathology, Genome Technology Center
| | | | - Harvey I Pass
- NYU Langone Health, Department of Cardiothoracic Surgery
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11
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Kremsky I, Ali S, Stanbouly S, Holley J, Justinen S, Pecaut M, Crapo J, Mao X. Spaceflight-Induced Gene Expression Profiles in the Mouse Brain Are Attenuated by Treatment with the Antioxidant BuOE. Int J Mol Sci 2023; 24:13569. [PMID: 37686374 PMCID: PMC10487739 DOI: 10.3390/ijms241713569] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023]
Abstract
The demands of deep space pose a health risk to the central nervous system that has long been a concern when sending humans to space. While little is known about how spaceflight affects transcription spatially in the brain, a greater understanding of this process has the potential to aid strategies that mitigate the effects of spaceflight on the brain. Therefore, we performed GeoMx Digital Spatial Profiling of mouse brains subjected to either spaceflight or grounded controls. Four brain regions were selected: Cortex, Frontal Cortex, Corunu Ammonis I, and Dentate Gyrus. Antioxidants have emerged as a potential means of attenuating the effects of spaceflight, so we treated a subset of the mice with a superoxide dismutase mimic, MnTnBuOE-2-PyP 5+ (BuOE). Our analysis revealed hundreds of differentially expressed genes due to spaceflight in each of the four brain regions. Both common and region-specific transcriptomic responses were observed. Metabolic pathways and pathways sensitive to oxidative stress were enriched in the four brain regions due to spaceflight. These findings enhance our understanding of brain regional variation in susceptibility to spaceflight conditions. BuOE reduced the transcriptomic effects of spaceflight at a large number of genes, suggesting that this compound may attenuate oxidative stress-induced brain damage caused by the spaceflight environment.
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Affiliation(s)
- Isaac Kremsky
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; (I.K.); (S.A.); (S.S.); (J.H.); (S.J.); (M.P.)
- Center for Genomics, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Samir Ali
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; (I.K.); (S.A.); (S.S.); (J.H.); (S.J.); (M.P.)
| | - Seta Stanbouly
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; (I.K.); (S.A.); (S.S.); (J.H.); (S.J.); (M.P.)
| | - Jacob Holley
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; (I.K.); (S.A.); (S.S.); (J.H.); (S.J.); (M.P.)
| | - Stephen Justinen
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; (I.K.); (S.A.); (S.S.); (J.H.); (S.J.); (M.P.)
| | - Michael Pecaut
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; (I.K.); (S.A.); (S.S.); (J.H.); (S.J.); (M.P.)
| | - James Crapo
- Department of Medicine, Division of Pulmonary, Critical Care & Sleep Medicine, National Jewish Health, University of Colorado Denver, Denver, CO 80206, USA;
| | - Xiaowen Mao
- Department of Basic Sciences, Division of Biomedical Engineering Sciences (BMES), Loma Linda University School of Medicine, Loma Linda, CA 92350, USA; (I.K.); (S.A.); (S.S.); (J.H.); (S.J.); (M.P.)
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12
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Tripodo C, Bertolazzi G, Cancila V, Morello G, Iannitto E. Pseudotemporal ordering of spatial lymphoid tissue microenvironment profiles trails Unclassified DLBCL at the periphery of the follicle. Front Immunol 2023; 14:1207959. [PMID: 37680642 PMCID: PMC10482233 DOI: 10.3389/fimmu.2023.1207959] [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] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 08/02/2023] [Indexed: 09/09/2023]
Abstract
We have established a pseudotemporal ordering for the transcriptional signatures of distinct microregions within reactive lymphoid tissues, namely germinal center dark zones (DZ), germinal center light zones (LZ), and peri-follicular areas (Peri). By utilizing this pseudotime trajectory derived from the functional microenvironments of DZ, LZ, and Peri, we have ordered the transcriptomes of Diffuse Large B-cell Lymphoma cases. The apex of the resulting pseudotemporal trajectory, which is characterized by enrichment of molecular programs fronted by TNFR signaling and inhibitory immune checkpoint overexpression, intercepts a discrete peri-follicular biology. This observation is associated with DLBCL cases that are enriched in the Unclassified/type-3 COO category, raising questions about the potential extra-GC microenvironment imprint of this peculiar group of cases. This report offers a thought-provoking perspective on the relationship between transcriptional profiling of functional lymphoid tissue microenvironments and the evolving concept of the cell of origin in Diffuse Large B-cell Lymphomas.
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Affiliation(s)
- Claudio Tripodo
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
- Histopathology Unit, Institute of Molecular Oncology Foundation (IFOM) ETS - The AIRC Institute of Molecular Oncology, Milan, Italy
| | - Giorgio Bertolazzi
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
- Department of Economics, Business, and Statistics, University of Palermo, Palermo, Italy
| | - Valeria Cancila
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Gaia Morello
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Emilio Iannitto
- Tumor Immunology Unit, Department of Sciences for Health Promotion and Mother-Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
- Department of Oncology, Hematology and Bone Marrow Transplants Unit La Maddalena, Palermo, Italy
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13
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Szeitz B, Glasz T, Herold Z, Tóth G, Balbisi M, Fillinger J, Horváth S, Mohácsi R, Kwon HJ, Moldvay J, Turiák L, Szász AM. Spatially Resolved Proteomic and Transcriptomic Profiling of Anaplastic Lymphoma Kinase-Rearranged Pulmonary Adenocarcinomas Reveals Key Players in Inter- and Intratumoral Heterogeneity. Int J Mol Sci 2023; 24:11369. [PMID: 37511126 PMCID: PMC10380216 DOI: 10.3390/ijms241411369] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 06/28/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023]
Abstract
Pulmonary adenocarcinomas (pADCs) with an ALK rearrangement are a rare cancer subtype, necessitating comprehensive molecular investigations to unravel their heterogeneity and improve therapeutic strategies. In this pilot study, we employed spatial transcriptomic (NanoString GeoMx) and proteomic profiling to investigate seven treatment-naïve pADCs with an ALK rearrangement. On each FFPE tumor slide, 12 smaller and 2-6 larger histopathologically annotated regions were selected for transcriptomic and proteomic analysis, respectively. The correlation between proteomics and transcriptomics was modest (average Pearson's r = 0.43 at the gene level). Intertumoral heterogeneity was more pronounced than intratumoral heterogeneity, and normal adjacent tissue exhibited distinct molecular characteristics. We identified potential markers and dysregulated pathways associated with tumors, with a varying extent of immune infiltration, as well as with mucin and stroma content. Notably, some markers appeared to be specific to the ALK-driven subset of pADCs. Our data showed that within tumors, elements of the extracellular matrix, including FN1, exhibited substantial variability. Additionally, we mapped the co-localization patterns of tumor microenvironment elements. This study represents the first spatially resolved profiling of ALK-driven pADCs at both the gene and protein expression levels. Our findings may contribute to a better understanding of this cancer type prior to treatment with ALK inhibitors.
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Affiliation(s)
- Beáta Szeitz
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary
| | - Tibor Glasz
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, 1091 Budapest, Hungary
| | - Zoltán Herold
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary
| | - Gábor Tóth
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Mirjam Balbisi
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, 1085 Budapest, Hungary
| | - János Fillinger
- Department of Pathology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Szabolcs Horváth
- Department of Pathology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Réka Mohácsi
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary
| | - Ho Jeong Kwon
- Department of Biotechnology, Division of Life Sciences, Yonsei University, Seoul 03722, Republic of Korea
| | - Judit Moldvay
- 1st Department of Pulmonology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Institute of Organic Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary
- Doctoral School of Pharmaceutical Sciences, Semmelweis University, 1085 Budapest, Hungary
| | - Attila Marcell Szász
- Division of Oncology, Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary
- Department of Tumor Biology, National Korányi Institute of Pulmonology, 1121 Budapest, Hungary
- Department of Bioinformatics, Semmelweis University, 1094 Budapest, Hungary
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14
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Jiang J, Liu Y. The Technical Feasibility of Digital Spatial Profiling in Immune/Inflammation Study of Thrombosis. J Inflamm Res 2023; 16:2431-2436. [PMID: 37313309 PMCID: PMC10259595 DOI: 10.2147/jir.s405903] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 06/02/2023] [Indexed: 06/15/2023]
Abstract
Background A comprehensive study of the distribution and role of immune/inflammatory cells in thrombosis is still lacking because traditional pathology techniques cannot accomplish the analysis of numerous protein and genetic data simultaneously. We aimed to evaluate the feasibility of digital spatial profiling (DSP) to study immune/inflammation reaction in thrombosis progression. Methods and Results An 82-year-old male patient underwent iliofemoral thrombectomy at our institution. The white, mixed and red thrombi were fixed in formalin, dehydrated in ethanol and embedded in paraffin, which were incubated with morphology-labeled fluorescent antibodies (CD45, SYTO13) and the entire target mixture in GeoMx Whole Transcriptome Atlas panel. DSP system was applied to investigate the regions of interest from fluorescence imaging. Fluorescence imaging showed infiltration of immune/inflammation cells in white, mixed and red thrombosis. Whole genome sequencing revealed 16 genes differentially expressed. Pathway enrichment analysis revealed that these genes were significantly enriched in ligand binding and uptake related signaling pathways of the scavenger receptor. The distribution of immune/inflammation cell subsets was different in white, mixed and red thrombosis. The abundance of endothelial cells, CD8 naive T cells, and macrophages in red thrombosis was significantly higher than in mixed and white thrombosis. Conclusion The results showed that DSP can facilitate efficient analysis using very few thrombosis samples and provide valuable new leads, suggesting that DSP may be a viable and important new tool to study thrombosis and inflammation.
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Affiliation(s)
- Jianjun Jiang
- Department of General Surgery, Vascular Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, People’s Republic of China
| | - Yang Liu
- Department of General Surgery, Vascular Surgery, Qilu Hospital of Shandong University, Jinan, Shandong, People’s Republic of China
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15
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Wiley MB, Bauer J, Mehrotra K, Zessner-Spitzenberg J, Kolics Z, Cheng W, Castellanos K, Nash MG, Gui X, Kone L, Maker AV, Qiao G, Reddi D, Church DN, Kerr RS, Kerr DJ, Grippo PJ, Jung B. Non-Canonical Activin A Signaling Stimulates Context-Dependent and Cellular-Specific Outcomes in CRC to Promote Tumor Cell Migration and Immune Tolerance. Cancers (Basel) 2023; 15:3003. [PMID: 37296966 PMCID: PMC10252122 DOI: 10.3390/cancers15113003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/27/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
We have shown that activin A (activin), a TGF-β superfamily member, has pro-metastatic effects in colorectal cancer (CRC). In lung cancer, activin activates pro-metastatic pathways to enhance tumor cell survival and migration while augmenting CD4+ to CD8+ communications to promote cytotoxicity. Here, we hypothesized that activin exerts cell-specific effects in the tumor microenvironment (TME) of CRC to promote anti-tumoral activity of immune cells and the pro-metastatic behavior of tumor cells in a cell-specific and context-dependent manner. We generated an Smad4 epithelial cell specific knockout (Smad4-/-) which was crossed with TS4-Cre mice to identify SMAD-specific changes in CRC. We also performed IHC and digital spatial profiling (DSP) of tissue microarrays (TMAs) obtained from 1055 stage II and III CRC patients in the QUASAR 2 clinical trial. We transfected the CRC cells to reduce their activin production and injected them into mice with intermittent tumor measurements to determine how cancer-derived activin alters tumor growth in vivo. In vivo, Smad4-/- mice displayed elevated colonic activin and pAKT expression and increased mortality. IHC analysis of the TMA samples revealed increased activin was required for TGF-β-associated improved outcomes in CRC. DSP analysis identified that activin co-localization in the stroma was coupled with increases in T-cell exhaustion markers, activation markers of antigen presenting cells (APCs), and effectors of the PI3K/AKT pathway. Activin-stimulated PI3K-dependent CRC transwell migration, and the in vivo loss of activin lead to smaller CRC tumors. Taken together, activin is a targetable, highly context-dependent molecule with effects on CRC growth, migration, and TME immune plasticity.
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Affiliation(s)
- Mark B. Wiley
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Jessica Bauer
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Kunaal Mehrotra
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Jasmin Zessner-Spitzenberg
- Clinical Department for Gastroenterology and Hepatology, Medical University of Vienna, 1090 Vienna, Austria
| | - Zoe Kolics
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Wenxuan Cheng
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
| | - Karla Castellanos
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Michael G. Nash
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Xianyong Gui
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Lyonell Kone
- Department of Surgery, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Ajay V. Maker
- Department of Surgery, University of California-San Francisco, San Francisco, CA 94115, USA
| | - Guilin Qiao
- Department of Surgery, University of California-San Francisco, San Francisco, CA 94115, USA
| | - Deepti Reddi
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - David N. Church
- Nuffield Department of Medicine, University of Oxford, Oxford OX1 4BH, UK
- NIHR Oxford Comprehensive Biomedical Research Center, Oxford University Hospitals NHS Foundation Trust, University of Oxford, Oxford OX1 4BH, UK
| | - Rachel S. Kerr
- Department of Oncology, University of Oxford, Oxford OX1 4BH, UK
| | - David J. Kerr
- Radcliffe Department of Medicine, University of Oxford, Oxford OX1 4BH, UK
| | - Paul J. Grippo
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Barbara Jung
- Department of Medicine, University of Washington, Seattle, WA 98195, USA; (M.B.W.); (K.M.)
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16
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Sobti A, Sakellariou C, Nilsson JS, Askmyr D, Greiff L, Lindstedt M. Exploring Spatial Heterogeneity of Immune Cells in Nasopharyngeal Cancer. Cancers (Basel) 2023; 15:cancers15072165. [PMID: 37046826 PMCID: PMC10093565 DOI: 10.3390/cancers15072165] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023]
Abstract
Nasopharyngeal cancer (NPC) is a malignant tumor. In a recent publication, we described the presence and distribution of CD8+ T cells in NPC and used the information to identify 'inflamed', 'immune-excluded', and 'desert' immune phenotypes, where 'inflamed' and 'immune-excluded' NPCs were correlated with CD8 T cell infiltration and survival. Arguably, more detailed and, in particular, spatially resolved data are required for patient stratification and for the identification of new treatment targets. In this study, we investigate the phenotype of CD45+ leukocytes in the previously analyzed NPC samples by applying multiplexed tissue analysis to assess the spatial distribution of cell types and to quantify selected biomarkers. A total of 47 specified regions-of-interest (ROIs) were generated based on CD45, CD8, and PanCK morphological staining. Using the GeoMx® Digital Spatial Profiler (DSP), 49 target proteins were digitally quantified from the selected ROIs of a tissue microarray consisting of 30 unique NPC biopsies. Protein targets associated with B cells (CD20), NK cells (CD56), macrophages (CD68), and regulatory T cells (PD-1, FOXP3) were most differentially expressed in CD45+ segments within 'immune-rich cancer cell islet' regions of the tumor (cf. 'surrounding stromal leukocyte' regions). In contrast, markers associated with suppressive populations of myeloid cells (CD163, B7-H3, VISTA) and T cells (CD4, LAG3, Tim-3) were expressed at a higher level in CD45+ segments in the 'surrounding stromal leukocyte' regions (cf. 'immune-rich cancer cell islet' regions). When comparing the three phenotypes, the 'inflamed' profile (cf. 'immune-excluded' and 'desert') exhibited higher expression of markers associated with B cells, NK cells, macrophages, and myeloid cells. Myeloid markers were highly expressed in the 'immune-excluded' phenotype. Granulocyte markers and immune-regulatory markers were higher in the 'desert' profile (cf. 'inflamed' and 'immune-excluded'). In conclusion, this study describes the spatial heterogeneity of the immune microenvironment in NPC and highlights immune-related biomarkers in immune phenotypes, which may aid in the stratification of patients for therapeutic purposes.
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Affiliation(s)
- Aastha Sobti
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
| | | | - Johan S Nilsson
- Department of ORL, Head & Neck Surgery, Skåne University Hospital, 221 85 Lund, Sweden
- Department Clinical Sciences, Lund University, 221 00 Lund, Sweden
| | - David Askmyr
- Department of ORL, Head & Neck Surgery, Skåne University Hospital, 221 85 Lund, Sweden
- Department Clinical Sciences, Lund University, 221 00 Lund, Sweden
| | - Lennart Greiff
- Department of ORL, Head & Neck Surgery, Skåne University Hospital, 221 85 Lund, Sweden
- Department Clinical Sciences, Lund University, 221 00 Lund, Sweden
| | - Malin Lindstedt
- Department of Immunotechnology, Lund University, 223 81 Lund, Sweden
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17
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Hernandez S, Das P, Holliday EB, Shen L, Lu W, Johnson B, Messick CA, Taniguchi CM, Skibber J, Ludmir EB, You YN, Smith GL, Bednarski B, Kostousov L, Koay EJ, Minsky BD, Tillman M, Portier S, Eng C, Koong AC, Chang GJ, Foo WC, Wang J, Soto LS, Morris VK. Differential Spatial Gene and Protein Expression Associated with Recurrence Following Chemoradiation for Localized Anal Squamous Cell Cancer. Cancers (Basel) 2023; 15:1701. [PMID: 36980587 PMCID: PMC10046657 DOI: 10.3390/cancers15061701] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/02/2023] [Accepted: 03/04/2023] [Indexed: 03/12/2023]
Abstract
The identification of transcriptomic and protein biomarkers prognosticating recurrence risk after chemoradiation of localized squamous cell carcinoma of the anus (SCCA) has been limited by a lack of available fresh tissue at initial presentation. We analyzed archival FFPE SCCA specimens from pretreatment biopsies prior to chemoradiation for protein and RNA biomarkers from patients with localized SCCA who recurred (N = 23) and who did not recur (N = 25). Tumor cells and the tumor microenvironment (TME) were analyzed separately to identify biomarkers with significantly different expression between the recurrent and non-recurrent groups. Recurrent patients had higher mean protein expression of FoxP3, MAPK-activation markers (BRAF, p38-MAPK) and PI3K/Akt activation (phospho-Akt) within the tumor regions. The TME was characterized by the higher protein expression of immune checkpoint biomarkers such as PD-1, OX40L and LAG3. For patients with recurrent SCCA, the higher mean protein expression of fibronectin was observed in the tumor and TME compartments. No significant differences in RNA expression were observed. The higher baseline expression of immune checkpoint biomarkers, together with markers of MAPK and PI3K/Akt signaling, are associated with recurrence following chemoradiation for patients with localized SCCA. These data provide a rationale towards the application of immune-based therapeutic strategies to improve curative-intent outcomes beyond conventional therapies for patients with SCCA.
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Affiliation(s)
- Sharia Hernandez
- Translational Molecular Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA; (S.H.)
| | - Prajnan Das
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Emma B. Holliday
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Shen
- Bioinformatics, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wei Lu
- Translational Molecular Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA; (S.H.)
| | - Benny Johnson
- Gastrointestinal Medical Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Craig A. Messick
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cullen M. Taniguchi
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John Skibber
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ethan B. Ludmir
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Y. Nancy You
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Grace Li Smith
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brian Bednarski
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Larisa Kostousov
- Translational Molecular Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA; (S.H.)
| | - Eugene J. Koay
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Bruce D. Minsky
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Tillman
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shaelynn Portier
- Gastrointestinal Medical Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Cathy Eng
- Vanderbilt-Ingram Cancer Center, Nashville, TN 37232, USA
| | - Albert C. Koong
- Gastrointestinal Radiation Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George J. Chang
- Colon and Rectal Surgery, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Wai Chin Foo
- Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Bioinformatics, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Luisa Solis Soto
- Translational Molecular Pathology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA; (S.H.)
| | - Van K. Morris
- Gastrointestinal Medical Oncology, The University of Texas—MD Anderson Cancer Center, Houston, TX 77030, USA
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18
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Jain S, Ma K, Morris LGT. CD66b as a prognostic and predictive biomarker in patients with non-small cell lung cancer treated with checkpoint blockade immunotherapy. Transl Cancer Res 2023; 12:447-451. [PMID: 36915573 PMCID: PMC10007870 DOI: 10.21037/tcr-22-2880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 01/09/2023] [Indexed: 02/24/2023]
Affiliation(s)
- Swati Jain
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kevin Ma
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Luc G T Morris
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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19
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Ling Y, Zhong J, Weng Z, Lin G, Liu C, Pan C, Yang H, Wei X, Xie X, Wei X, Zhang H, Wang G, Fu J, Wen J. The prognostic value and molecular properties of tertiary lymphoid structures in oesophageal squamous cell carcinoma. Clin Transl Med 2022; 12:e1074. [PMID: 36245289 PMCID: PMC9574489 DOI: 10.1002/ctm2.1074] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 08/26/2022] [Accepted: 09/23/2022] [Indexed: 02/05/2023]
Abstract
BACKGROUND Tertiary lymphoid structures (TLSs) play key roles in tumour adaptive immunity. However, the prognostic value and molecular properties of TLSs in oesophageal squamous cell carcinoma (ESCC) patients have not been studied. METHODS The prognostic values of the presence and maturation status of tumour-associated TLSs were determined in 394 and 256 ESCC patients from Sun Yat-sen University Cancer Center (Centre A) and the Cancer Hospital of Shantou University Medical College (Centre B), respectively. A deep-learning (DL) TLS classifier was established with haematoxylin and eosin (H&E)-stained slides using an inception-resnet-v2 neural network. Digital spatial profiling was performed to determine the cellular and molecular properties of TLSs in ESCC tissues. RESULTS TLSs were observed in 73.1% of ESCCs from Centre A via pathological examination of H&E-stained primary tumour slides, among which 42.9% were TLS-mature and 30.2% were TLS-immature tumours. The established DL TLS classifier yielded favourable sensitivities and specificities for patient TLS identification and maturation evaluation, with which 55.1%, 39.5% and 5.5% of ESCCs from Centre B were identified as TLS-mature, TLS-immature and TLS-negative tumours. Multivariate analyses proved that the presence of mature TLSs was an independent prognostic factor in both the Centre A and Centre B cohorts (p < .05). Increased proportions of proliferative B, plasma and CD4+ T helper (Th) cells and increased B memory and Th17 signatures were observed in mature TLSs compared to immature ones. Intratumoural CD8+ T infiltration was increased in TLS-mature ESCC tissues compared to mature TLS-absent tissues. The combination of mature TLS presence and high CD8+ T infiltration was associated with the best survival in ESCC patients. CONCLUSIONS Mature TLSs improve the prognosis of ESCC patients who underwent complete resection. The use of the DL TLS classifier would facilitate precise and efficient evaluation of TLS maturation status and offer a novel probability of ESCC treatment individualization.
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Affiliation(s)
- Yihong Ling
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jian Zhong
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Thoracic OncologySun Yat‐sen University Cancer CenterGuangzhouChina
- Guangdong Esophageal Cancer InstituteGuangzhouChina
| | - Zelin Weng
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Guangrong Lin
- Yinhe Hangtian Internet Technology Company LimitedBeijingChina
| | - Caixia Liu
- Department of Preventive MedicineShantou University Medical CollegeShantouChina
| | - Chuqing Pan
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Hong Yang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Thoracic OncologySun Yat‐sen University Cancer CenterGuangzhouChina
- Guangdong Esophageal Cancer InstituteGuangzhouChina
| | - Xiaolong Wei
- Department of PathologyCancer Hospital of Shantou University Medical CollegeShantouChina
| | - Xiuying Xie
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
- Guangdong Esophageal Cancer InstituteGuangzhouChina
| | - Xiaoli Wei
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Huizhong Zhang
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of PathologySun Yat‐sen University Cancer CenterGuangzhouChina
| | - Geng Wang
- Department of Thoracic Surgery Cancer Hospital of Shantou University Medical College Shantou China
| | - Jianhua Fu
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
- Department of Thoracic OncologySun Yat‐sen University Cancer Center,GuangzhouChina
- Guangdong Esophageal Cancer Institute, GuangzhouChina
| | - Jing Wen
- State Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
- Guangdong Esophageal Cancer Institute, Guangzhou China
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20
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Petterson SA, Sørensen MD, Burton M, Thomassen M, Kruse TA, Michaelsen SR, Kristensen BW. Differential expression of checkpoint markers in the normoxic and hypoxic microenvironment of glioblastomas. Brain Pathol 2022; 33:e13111. [PMID: 36093941 PMCID: PMC9836374 DOI: 10.1111/bpa.13111] [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] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/29/2022] [Indexed: 01/21/2023]
Abstract
Glioblastoma is the most common primary malignant brain tumor in adults with an overall survival of only 14.6 months. Hypoxia is known to play a role in tumor aggressiveness but the influence of hypoxia on the immune microenvironment is not fully understood. The aim of this study was to investigate the expression of immune-related proteins in normoxic and hypoxic tumor areas by digital spatial profiling. Tissue samples from 10 glioblastomas were stained with a panel of 40 antibodies conjugated to photo-cleavable oligonucleotides. The free oligo-tags from normoxic and hypoxic areas were hybridized to barcodes for digital counting. Differential expression patterns were validated by Ivy Glioblastoma Atlas Project (GAP) data and an independent patient cohort. We found that CD44, Beta-catenin and B7-H3 were upregulated in hypoxia, whereas VISTA, CD56, KI-67, CD68 and CD11c were downregulated. PD-L1 and PD-1 were not affected by hypoxia. Focusing on the checkpoint-related markers CD44, B7-H3 and VISTA, our findings for CD44 and VISTA could be confirmed with Ivy GAP RNA sequencing data. Immunohistochemical staining and digital quantification of CD44, B7-H3 and VISTA in an independent cohort confirmed our findings for all three markers. Additional stainings revealed fewer T cells and high but equal amounts of tumor-associated microglia and macrophages in both hypoxic and normoxic regions. In conclusion, we found that CD44 and B7-H3 were upregulated in areas with hypoxia whereas VISTA was downregulated together with the presence of fewer T cells. This heterogeneous expression should be taken into consideration when developing novel therapeutic strategies.
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Affiliation(s)
- Stine Asferg Petterson
- Department of PathologyOdense University HospitalOdenseDenmark,Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Mia Dahl Sørensen
- Department of PathologyOdense University HospitalOdenseDenmark,Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark
| | - Mark Burton
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark,Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Mads Thomassen
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark,Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Torben A. Kruse
- Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark,Department of Clinical GeneticsOdense University HospitalOdense CDenmark
| | - Signe Regner Michaelsen
- Department of Pathology, The Bartholin Institute, RigshospitaletCopenhagen University HospitalCopenhagenDenmark,Department of Clinical Medicine and Biotech Research & Innovation Centre (BRIC)University of CopenhagenCopenhagenDenmark
| | - Bjarne Winther Kristensen
- Department of PathologyOdense University HospitalOdenseDenmark,Department of Clinical ResearchUniversity of Southern DenmarkOdenseDenmark,Department of Pathology, The Bartholin Institute, RigshospitaletCopenhagen University HospitalCopenhagenDenmark,Department of Clinical Medicine and Biotech Research & Innovation Centre (BRIC)University of CopenhagenCopenhagenDenmark
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21
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Therien AD, Beasley GM, Rhodin KE, Farrow NE, Tyler DS, Boczkowski D, Al-Rohil RN, Holl EK, Nair SK. Spatial biology analysis reveals B cell follicles in secondary lymphoid structures may regulate anti-tumor responses at initial melanoma diagnosis. Front Immunol 2022; 13:952220. [PMID: 36052068 PMCID: PMC9425113 DOI: 10.3389/fimmu.2022.952220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 05/24/2022] [Accepted: 07/18/2022] [Indexed: 01/09/2023]
Abstract
Introduction B cells are key regulators of immune responses in melanoma. We aimed to explore differences in the histologic location and activation status of B cell follicles in sentinel lymph nodes (SLN) of melanoma patients. Methods Flow cytometry was performed on fresh tumor draining lymph nodes (LN). Paraffin slides from a separate cohort underwent NanoString Digital Spatial Profiling (DSP)®. After staining with fluorescent markers for CD20 (B cells), CD3 (T cells), CD11c (antigen presenting cells) and a nuclear marker (tumor) was performed, regions of interest (ROI) were selected based on the location of B cell regions (B cell follicles). A panel of 68 proteins was then analyzed from the ROIs. Results B cell percentage trended higher in patients with tumor in LN (n=3) compared to patients with nSLN (n=10) by flow cytometry. B cell regions from a separate cohort of patients with tumor in the (pSLN) (n=8) vs. no tumor (nSLN) (n=16) were examined with DSP. Within B cell regions of the SLN, patients with pSLN had significantly higher expression of multiple activation markers including Ki-67 compared to nSLN patients. Among 4 patients with pSLN, we noted variability in arrangement of B cell follicles which were either surrounding the tumor deposit or appeared to be infiltrating the tumor. The B cell follicle infiltrative pattern was associated with prolonged recurrence free survival. Conclusion These data suggest a role for B cell follicles in coordinating effective adaptive immune responses in melanoma when low volume metastatic disease is present in tumor draining LN.
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Affiliation(s)
- Aaron D. Therien
- Department of Surgery, Duke University, Durham, NC, United States
| | - Georgia M. Beasley
- Department of Surgery, Duke University, Durham, NC, United States,Department of Medicine, Duke University, Durham, NC, United States
| | | | - Norma E. Farrow
- Department of Surgery, Duke University, Durham, NC, United States
| | - Douglas S. Tyler
- Department of Surgery, University Texas Medical Branch, Galveston, TX, United States
| | - David Boczkowski
- Department of Surgery, Duke University, Durham, NC, United States
| | - Rami N. Al-Rohil
- Department of Pathology, Duke University, Durham, NC, United States
| | - Eda K. Holl
- Department of Surgery, Duke University, Durham, NC, United States,*Correspondence: Eda K. Holl, ; Smita K. Nair,
| | - Smita K. Nair
- Department of Surgery, Duke University, Durham, NC, United States,Department of Pathology, Duke University, Durham, NC, United States,Department of Neurosurgery, Duke University, Durham, NC, United States,*Correspondence: Eda K. Holl, ; Smita K. Nair,
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22
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Hernandez S, Lazcano R, Serrano A, Powell S, Kostousov L, Mehta J, Khan K, Lu W, Solis LM. Challenges and Opportunities for Immunoprofiling Using a Spatial High-Plex Technology: The NanoString GeoMx ® Digital Spatial Profiler. Front Oncol 2022; 12:890410. [PMID: 35847846 PMCID: PMC9277770 DOI: 10.3389/fonc.2022.890410] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [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: 03/05/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022]
Abstract
Characterization of the tumor microenvironment through immunoprofiling has become an essential resource for the understanding of the complex immune cell interactions and the assessment of biomarkers for prognosis and prediction of immunotherapy response; however, these studies are often limited by tissue heterogeneity and sample size. The nanoString GeoMx® Digital Spatial Profiler (DSP) is a platform that allows high-plex profiling at the protein and RNA level, providing spatial and temporal assessment of tumors in frozen or formalin-fixed paraffin-embedded limited tissue sample. Recently, high-impact studies have shown the feasibility of using this technology to identify biomarkers in different settings, including predictive biomarkers for immunotherapy in different tumor types. These studies showed that compared to other multiplex and high-plex platforms, the DSP can interrogate a higher number of biomarkers with higher throughput; however, it does not provide single-cell resolution, including co-expression of biomarker or spatial information at the single-cell level. In this review, we will describe the technical overview of the platform, present current evidence of the advantages and limitations of the applications of this technology, and provide important considerations for the experimental design for translational immune-oncology research using this tissue-based high-plex profiling approach.
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Affiliation(s)
- Sharia Hernandez
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rossana Lazcano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Alejandra Serrano
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Steven Powell
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Larissa Kostousov
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jay Mehta
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Khaja Khan
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Wei Lu
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Luisa M Solis
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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23
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Han S, Fu D, Tushoski GW, Meng L, Herremans KM, Riner AN, Geoge TJ, Huo Z, Hughes SJ. Single-cell profiling of microenvironment components by spatial localization in pancreatic ductal adenocarcinoma. Theranostics 2022; 12:4980-4992. [PMID: 35836806 PMCID: PMC9274743 DOI: 10.7150/thno.73222] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/04/2022] [Indexed: 02/01/2023]
Abstract
Rationale: The biology of the pancreatic ductal adenocarcinoma (PDAC) is heterogenous, but how heterogenity of the tumor microenvironment contributes to disparate patient outcomes remains essentially unstudied. Methods: A strategy employing multiplex digital spatial profiling (mplxDSP) technology was employed to evaluate the nature and dynamics of microenvironment components including cancer associated fibroblasts (CAFs) and infiltrating immune cells at the single-cell level based upon their spatial relationship within the tumor. Results: We report that myofibroblasts directly adjacent to PDAC tumors comparatively overexpress genes (BATF3, IL12B, ITGB8, CD4 and IFNAR1), constructing pathways prone to stimulating an adaptive immune response. Markers of innate immune cells (Natural Killer cells, Dendritic Cells and macrophages) are predominant in CD45+ cells immediately adjacent to PDAC tumor, however, the checkpoint protein CTLA4 is also overwhelmingly expressed, fostering tolerance. Finaly, mRNA profiling of adjacent CAFs identified clusters of genes that correlate with survival. Conclusion: CAFs and leukocytes in close proximity to PDAC significantly differ from those remote from the tumor, providing insight into microenvironment influence on immune tolerance mediated through relative populations of leukocytes and subsets of CAFs and monocytes. mRNA expression profiling of CAFs adjacent to PDAC cells may hold promise for prognostication.
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Affiliation(s)
- Song Han
- Department of Surgery, College of Medicine; University of Florida, Gainesville, FL 32610
| | - Dongtao Fu
- Department of Pathology, College of Medicine; University of Florida, Gainesville, FL 32610
| | - Gerik W Tushoski
- Department of Surgery, College of Medicine; University of Florida, Gainesville, FL 32610
| | - Lingsong Meng
- Department of Biostatistics, College of Medicine; University of Florida, Gainesville, FL 32610
| | - Kelly M. Herremans
- Department of Surgery, College of Medicine; University of Florida, Gainesville, FL 32610
| | - Andrea N. Riner
- Department of Surgery, College of Medicine; University of Florida, Gainesville, FL 32610
| | - Thomas J. Geoge
- Department of Medicine, College of Medicine; University of Florida, Gainesville, FL 32610
| | - Zhiguang Huo
- Department of Biostatistics, College of Medicine; University of Florida, Gainesville, FL 32610
| | - Steven J. Hughes
- Department of Surgery, College of Medicine; University of Florida, Gainesville, FL 32610
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24
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Sadeghirad H, Monkman J, Mehdi AM, Ladwa R, O’Byrne K, Hughes BGM, Kulasinghe A. Dissecting Tissue Compartment-Specific Protein Signatures in Primary and Metastatic Oropharyngeal Squamous Cell Carcinomas. Front Immunol 2022; 13:895513. [PMID: 35651606 PMCID: PMC9149425 DOI: 10.3389/fimmu.2022.895513] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) often presents with locoregional or distant disease, despite multimodal therapeutic approaches, which include surgical resection, chemoradiotherapy, and more recently, immunotherapy for metastatic or recurrent HNSCC. Therapies often target the primary and nodal regional HNSCC sites, and their efficacy at controlling occult distant sites remains poor. While our understanding of the tumor microenvironment conducive to effective therapies is increasing, the biology underpinning locoregional sites remains unclear. Here, we applied targeted spatial proteomic approaches to primary and lymph node metastasis from an oropharyngeal SCC (OPSCC) cohort to understand the expression of proteins within tumors, and stromal compartments of the respective sites in samples of both matched and unmatched patients. In unmatched analyses of n = 43 primary and 11 nodal metastases, our data indicated that tumor cells in nodal metastases had higher levels of Ki-67, PARP, BAD, and cleaved caspase 9, suggesting a role for increased proliferation, DNA repair, and apoptosis within these metastatic cells. Conversely, in matched analyses (n = 7), pro-apoptotic markers BIM and BAD were enriched in the stroma of primary tumors. Univariate, overall survival (OS) analysis indicated CD25 in tumor regions of primary tumors to be associated with reduced survival (HR = 3.3, p = 0.003), while progesterone receptor (PR) was associated with an improved OS (HR = 0.33, p = 0.015). This study highlights the utility of spatial proteomics for delineating the tumor and stromal compartment composition, and utility toward understanding these properties in locoregional metastasis. These findings indicate unique biological properties of lymph node metastases that may elucidate further understanding of distant metastatic in OPSCC.
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Affiliation(s)
- Habib Sadeghirad
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - James Monkman
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
| | - Ahmed M. Mehdi
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
- Queensland Cyber Infrastructure Foundation Ltd., QCIF Facility for Advanced Bioinformatics, Brisbane, QLD, Australia
| | - Rahul Ladwa
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia
| | - Ken O’Byrne
- Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Brett G. M. Hughes
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia
- Cancer Care Services, Royal Brisbane and Women’s Hospital, Herston, QLD, Australia
| | - Arutha Kulasinghe
- The University of Queensland Diamantina Institute, The University of Queensland, Woolloongabba, QLD, Australia
- Faculty of Medicine, University of Queensland, Herston, QLD, Australia
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25
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Wang N, Wang R, Li X, Song Z, Xia L, Wang J, Zhang L, Wu A, Ding Z. Tumor Microenvironment Profiles Reveal Distinct Therapy-Oriented Proteogenomic Characteristics in Colorectal Cancer. Front Bioeng Biotechnol 2021; 9:757378. [PMID: 34778231 PMCID: PMC8581216 DOI: 10.3389/fbioe.2021.757378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/12/2021] [Accepted: 09/16/2021] [Indexed: 12/17/2022]
Abstract
Advances in immunotherapy have made an unprecedented leap in treating colorectal cancer (CRC). However, more effective therapeutic regimes need a deeper understanding of molecular architectures for precise patient stratification and therapeutic improvement. We profiled patients receiving neoadjuvant chemotherapy alone or in combination with immunotherapy (PD-1 checkpoint inhibitor) using Digital Spatial Profiler (DSP), a high-plex spatial proteogenomic technology. Compartmentalization-based high-plex profiling of both proteins and mRNAs revealed pronounced immune infiltration at tumor regions associated with immunotherapy treatment. The protein and the corresponding mRNA levels within the same selected regions of those patient samples correlate, indicating an overall concordance between the transcriptional and translational levels. An elevated expression of PD-L1 at both protein and the mRNA levels was discovered in the tumor compartment of immunotherapy-treated patients compared with chemo-treated patients, indicating potential prognostic biomarkers are explorable in a spatial manner at the local tumor microenvironment (TME). An elevated expression of PD-L1 was verified by immunohistochemistry. Other compartment-specific biomarkers were also differentially expressed between the tumor and stromal regions, indicating a dynamic interplay that can potentiate novel biomarker discovery from the TME perspectives. Simultaneously, a high-plex spatial profiling of protein and mRNA in the tumor microenvironment of colorectal cancer was performed.
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Affiliation(s)
- Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Rongshui Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Xia Li
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Zhentao Song
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Lingbo Xia
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
| | - Jue Wang
- Department of Oncology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Li Zhang
- Department of Pathology, Beijing Cancer Hospital, Beijing, China
| | - Aiwen Wu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Gastrointestinal Surgery, Peking University, Beijing, China
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, China
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26
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Grosser B, Glückstein MI, Dhillon C, Schiele S, Dintner S, VanSchoiack A, Kroeppler D, Martin B, Probst A, Vlasenko D, Schenkirsch G, Märkl B. Stroma AReactive Invasion Front Areas (SARIFA) - a new prognostic biomarker in gastric cancer related to tumor-promoting adipocytes. J Pathol 2021; 256:71-82. [PMID: 34580877 DOI: 10.1002/path.5810] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/14/2021] [Accepted: 09/24/2021] [Indexed: 12/24/2022]
Abstract
Compared to other malignancies, there is a lack of easy-to-evaluate biomarkers for gastric cancer, which is associated with an adverse clinical outcome in many cases. Here, we present Stroma AReactive Invasion Front Areas (SARIFA) as a new histological prognostic marker. We defined SARIFA as the direct contact between a cluster of tumor glands/cells comprising at least five tumor cells and inconspicuous surrounding adipose tissue at the invasion front. A total of 480 adenocarcinomas of the stomach and the gastroesophageal junction from two different collections were classified according to SARIFA. To understand the potential underlying mechanisms, a transcriptome analysis was conducted using digital spatial profiling (DSP). It was found that 20% of the tumors were SARIFA-positive. Kappa values between the three pathologists were good in both collections: 0.74 and 0.78. Patients who presented SARIFA-positive tumors had a significantly lower overall survival in Collections A (median: 20.0 versus 44.0 months; p = 0.014, n = 160) and B (median: 15.0 versus 41.0 months; p < 0.0001, n = 320). SARIFA positivity emerged as a negative independent prognostic factor for overall survival (HR 1.638, 95% CI 1.153-2.326, p = 0.006). Using DSP, the most upregulated genes in SARIFA-positive cases were those associated with triglyceride catabolism and endogenous sterols. COL15A1, FABP2, and FABP4 were differentially expressed in positive cases. At the protein level, the expression of proteins related to lipid metabolism was confirmed. SARIFA combines low inter-observer variability, minimal effort, and high prognostic relevance, and is therefore an extremely promising biomarker related to tumor-promoting adipocytes in gastric cancer. © 2021 The Authors. The Journal of Pathology published by John Wiley & Sons, Ltd. on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Bianca Grosser
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Marie-Isabelle Glückstein
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Christine Dhillon
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Stefan Schiele
- Institute of Mathematics and Computational Statistics, University of Augsburg, Augsburg, Germany
| | - Sebastian Dintner
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | | | | | - Benedikt Martin
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
| | - Andreas Probst
- Department of Gastroenterology, University Hospital Augsburg, Augsburg, Germany
| | - Dmytro Vlasenko
- General, Visceral and Transplantation Surgery, University Hospital of Augsburg, Augsburg, Germany
| | | | - Bruno Märkl
- General Pathology and Molecular Diagnostics, Medical Faculty, University of Augsburg, Augsburg, Germany
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27
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Omilian AR, Sheng H, Hong CC, Bandera EV, Khoury T, Ambrosone CB, Yao S. Multiplexed digital spatial profiling of invasive breast tumors from Black and White women. Mol Oncol 2021; 16:54-68. [PMID: 34018684 PMCID: PMC8732343 DOI: 10.1002/1878-0261.13017] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 11/02/2020] [Revised: 04/19/2021] [Accepted: 05/18/2021] [Indexed: 12/17/2022]
Abstract
The NanoString GeoMx digital spatial profiling is a new multiplexed platform that quantifies the abundance of tumor‐ and immune‐related proteins in a spatially resolved manner. We performed DSP for the simultaneous assessment of 52 analytes within spatially resolved tissue compartments defined by pan‐cytokeratin expression. We compared protein targets between 94 African American/Black and 65 European American/White cases, tumor and stromal tissue compartments, estrogen receptor alpha (ER)‐positive and ER‐negative cases, and explored potential biomarkers of survival. Of 33 analytes with robust signal for analysis, results were highly replicable. For a subset of markers, correlative analyses between DSP analytes and traditional immunohistochemistry scores revealed moderate to very strong associations between the two platforms. Similarly, DSP analytes and gene expression scores were concordant for 21 of 25 markers with overlap between the two datasets. Several analytes varied by ER status, and across the 25 immune markers surveyed, 14 had a significant inverse association with ER expression. B7 homolog 3 (B7‐H3; encoded by CD276) was the only analyte to show a significant difference by race, being lower in both the tumor and stromal compartments in Black women. DSP markers that were associated with survival included CD8, CD25, CD56, CD127, EpCAM, ER, Ki‐67, and STING. We conclude that DSP is an efficient tool for screening tumor‐ and immune‐related markers in a simultaneous fashion and yields results that are concordant with established immune profiling assays. DSP immune analytes were inversely associated with ER expression, in agreement with a substantial body of previous work that documents higher immune infiltration in ER‐negative breast cancers. This technology revealed that scores of the B7‐H3 protein were significantly lower in breast cancers from Black women compared with White women, an intriguing finding that requires replication in independent and racially diverse female populations.
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Affiliation(s)
- Angela R Omilian
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Haiyang Sheng
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA.,Department of Biostatistics, The State University of New York at Buffalo, NY, USA
| | - Chi-Chen Hong
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Elisa V Bandera
- Department of Biostatistics and Epidemiology, Rutgers School of Public Health, Piscataway, NJ, USA.,Cancer Epidemiology and Health Outcomes, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Thaer Khoury
- Department of Pathology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
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28
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Shimizu S, Sakai K, Chikugo T, Satou T, Shiraishi N, Mitsudomi T, Nishio K. Integrin-linked kinase pathway in heterogeneous pulmonary sarcomatoid carcinoma. Oncol Lett 2021; 21:320. [PMID: 33692852 DOI: 10.3892/ol.2021.12582] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022]
Abstract
Pulmonary sarcomatoid carcinoma (PSC) is classified as poorly differentiated, and non-small cell lung carcinomas that contained a component of sarcoma or sarcoma-like differentiation are rare. The underlying carcinogenetic mechanism governing PSC remains unclear. The current study investigated the underlying carcinogenetic mechanism of PSC based on the hypothesis that it involves the epithelial-mesenchymal transition (EMT) process. Mutation analysis of PSCs, including carcinosarcoma, pleomorphic carcinoma and epithelial carcinoma specimens, was performed using targeted deep sequencing, whole transcriptome analysis and digital spatial profiling (DSP). PSCs exhibit a distinct mutation profile, with TP53, SYNE1 and APC mutations. Therefore, clustering of the gene expression profiles allowed the PSCs to be distinguished from the epithelial carcinomas. Increased gene expression of fibronectin in PSC was an important contributor to differential profiles. Pathway analysis revealed enhanced activity of the integrin-linked kinase (ILK) signaling pathway in the PSCs. DSP analysis using 56 antibodies of marker proteins confirmed significantly higher expression of fibronectin in PSCs. Intratumor heterogeneity of fibronectin expression was observed in sarcoma components. In conclusion, epithelial-mesenchymal transition process mediated by ILK signaling may be associated with carcinogenetic mechanisms of PSC. Overexpression of fibronectin mediated by ILK signaling appears to serve a role in the EMT involved in the PSC transformation process.
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Affiliation(s)
- Shigeki Shimizu
- Department of Diagnostic Pathology, Kindai University Hospital, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuko Sakai
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Takaaki Chikugo
- Department of Diagnostic Pathology, Kindai University Hospital, Osaka-Sayama, Osaka 589-8511, Japan
| | - Takao Satou
- Department of Diagnostic Pathology, Kindai University Hospital, Osaka-Sayama, Osaka 589-8511, Japan
| | - Naoki Shiraishi
- Department of Diagnostic Pathology, Kindai University Hospital, Osaka-Sayama, Osaka 589-8511, Japan
| | - Tetsuya Mitsudomi
- Department of Thoracic Surgery, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
| | - Kazuto Nishio
- Department of Genome Biology, Kindai University Faculty of Medicine, Osaka-Sayama, Osaka 589-8511, Japan
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29
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Barriuso J, Nagaraju RT, Belgamwar S, Chakrabarty B, Burghel GJ, Schlecht H, Foster L, Kilgour E, Wallace AJ, Braun M, Dive C, Evans DG, Bristow RG, Saunders MP, O'Dwyer ST, Aziz O. Early Adaptation of Colorectal Cancer Cells to the Peritoneal Cavity Is Associated with Activation of "Stemness" Programs and Local Inflammation. Clin Cancer Res 2021; 27:1119-1130. [PMID: 33257424 PMCID: PMC7611320 DOI: 10.1158/1078-0432.ccr-20-3320] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/20/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022]
Abstract
PURPOSE At diagnosis, colorectal cancer presents with synchronous peritoneal metastasis in up to 10% of patients. The peritoneum is poorly characterized with respect to its superspecialized microenvironment. Our aim was to describe the differences between peritoneal metastases and their matched primary tumors excised simultaneously at the time of surgery. Also, we tested the hypothesis of these differences being present in primary colorectal tumors and having prognostic capacity. EXPERIMENTAL DESIGN We report a comprehensive analysis of 30 samples from peritoneal metastasis with their matched colorectal cancer primaries obtained during cytoreductive surgery. We tested and validated the prognostic value of our findings in a pooled series of 660 colorectal cancer primary samples with overall survival (OS) information and 743 samples with disease-free survival (DFS) information from publicly available databases. RESULTS We identified 20 genes dysregulated in peritoneal metastasis that promote an early increasing role of "stemness" in conjunction with tumor-favorable inflammatory changes. When adjusted for age, gender, and stage, the 20-gene peritoneal signature proved to have prognostic value for both OS [adjusted HR for the high-risk group (vs. low-risk) 2.32 (95% confidence interval, CI, 1.69-3.19; P < 0.0001)] and for DFS [adjusted HR 2.08 (95% CI, 1.50-2.91; P < 0.0001)]. CONCLUSIONS Our findings indicated that the activation of "stemness" pathways and adaptation to the peritoneal-specific environment are key to early stages of peritoneal carcinomatosis. The in silico analysis suggested that this 20-gene peritoneal signature may hold prognostic information with potential for development of new precision medicine strategies in this setting.
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Affiliation(s)
- Jorge Barriuso
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom.
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Raghavendar T Nagaraju
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
| | - Shreya Belgamwar
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Bipasha Chakrabarty
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Department of Pathology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - George J Burghel
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Helene Schlecht
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Lucy Foster
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Elaine Kilgour
- Cancer Research UK Manchester Institute, Cancer Biomarker Centre, University of Manchester, Manchester, England, United Kingdom
| | - Andrew J Wallace
- NW GLH (Manchester), Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, England, United Kingdom
| | - Michael Braun
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
- Department of Medical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Caroline Dive
- Cancer Research UK Manchester Institute, Cancer Biomarker Centre, University of Manchester, Manchester, England, United Kingdom
| | - D Gareth Evans
- Department of Genomic Medicine, Division of Evolution and Genomic Science, University of Manchester, England, United Kingdom
| | - Robert G Bristow
- Manchester Cancer Research Centre, CRUK Manchester Institute, University of Manchester, Manchester, England, United Kingdom
| | - Mark P Saunders
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Department of Clinical Oncology, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
| | - Sarah T O'Dwyer
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
| | - Omer Aziz
- Colorectal and Peritoneal Oncology Centre, The Christie NHS Foundation Trust, Manchester, England, United Kingdom.
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, England, United Kingdom
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30
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Kulasinghe A, Taheri T, O'Byrne K, Hughes BGM, Kenny L, Punyadeera C. Highly Multiplexed Digital Spatial Profiling of the Tumor Microenvironment of Head and Neck Squamous Cell Carcinoma Patients. Front Oncol 2021; 10:607349. [PMID: 33542903 PMCID: PMC7851078 DOI: 10.3389/fonc.2020.607349] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [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: 09/17/2020] [Accepted: 12/03/2020] [Indexed: 01/10/2023]
Abstract
Background Immune checkpoint inhibitors (ICI) have shown durable and long-term benefits in a subset of head and neck squamous cell carcinoma (HNSCC) patients. To identify patient-responders from non-responders, biomarkers are needed which are predictive of outcome to ICI therapy. Cues in the tumor microenvironment (TME) have been informative in understanding the tumor-immune contexture. Methods In this preliminary study, the NanoString GeoMx™ Digital Spatial Profiling (DSP) technology was used to determine the immune marker and compartment specific measurements in a cohort of HNSCC tumors from patients receiving ICI therapy. Results Our data revealed that markers involved with immune cell infiltration (CD8 T-cells) were not predictive of outcome to ICI therapy. Rather, a number of immune cell types and protein markers (CD4, CD68, CD45, CD44, CD66b) were found to correlate with progressive disease. Cross platform comparison with the Opal Vectra (Perkin Elmer) for a number of markers across similar regions of interest demonstrated concordance for pan-cytokeratin, CD8, and PD-L1. Conclusion This study, to our knowledge, represents the first digital spatial analysis of HNSCC tumors. A larger cohort of HNSCC will be required to orthogonally validate the findings.
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Affiliation(s)
- Arutha Kulasinghe
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia
| | - Touraj Taheri
- Department of Pathology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia.,Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Ken O'Byrne
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia.,Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Brett G M Hughes
- Royal Brisbane and Women's Hospital, Herston, QLD, Australia.,School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Liz Kenny
- Royal Brisbane and Women's Hospital, Herston, QLD, Australia.,School of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Chamindie Punyadeera
- The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia.,Translational Research Institute, Brisbane, QLD, Australia
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31
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Sadeghi Rad H, Bazaz SR, Monkman J, Ebrahimi Warkiani M, Rezaei N, O'Byrne K, Kulasinghe A. The evolving landscape of predictive biomarkers in immuno-oncology with a focus on spatial technologies. Clin Transl Immunology 2020; 9:e1215. [PMID: 33251010 PMCID: PMC7680923 DOI: 10.1002/cti2.1215] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 08/09/2020] [Revised: 09/16/2020] [Accepted: 10/25/2020] [Indexed: 02/06/2023]
Abstract
Immunotherapies have shown long-lasting and unparalleled responses for cancer patients compared to conventional therapy. However, they seem to only be effective in a subset of patients. Therefore, it has become evident that a greater understanding of the tumor microenvironment (TME) is required to understand the nuances which may be at play for a favorable outcome to therapy. The immune contexture of the TME is an important factor in dictating how well a tumor may respond to immune checkpoint inhibitors. While traditional immunohistochemistry techniques allow for the profiling of cells in the tumor, this is often lost when tumors are analysed using bulk tissue genomic approaches. Moreover, the actual cellular proportions, cellular heterogeneity and deeper spatial distribution are lacking in characterisation. Advances in tissue interrogation technologies have given rise to spatially resolved characterisation of the TME. This review aims to provide an overview of the current methodologies that are used to profile the TME, which may provide insights into the immunopathology associated with a favorable outcome to immunotherapy.
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Affiliation(s)
| | - Sajad Razavi Bazaz
- School of Biomedical EngineeringUniversity of Technology SydneySydneyNSWAustralia
| | - James Monkman
- The School of Biomedical Science, Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQLDAustralia
- Translational Research InstituteWoolloongabbaQLDAustralia
| | - Majid Ebrahimi Warkiani
- School of Biomedical EngineeringUniversity of Technology SydneySydneyNSWAustralia
- Institute of Molecular MedicineSechenov UniversityMoscowRussia
| | - Nima Rezaei
- School of MedicineTehran University of Medical SciencesTehranIran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA)Universal Scientific Education and Research Network (USERN)TehranIran
- Research Center for ImmunodeficienciesChildren's Medical CenterTehran University of Medical SciencesTehranIran
| | - Ken O'Byrne
- The School of Biomedical Science, Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQLDAustralia
- Translational Research InstituteWoolloongabbaQLDAustralia
- Princess Alexandra HospitalWoolloongabbaQLDAustralia
| | - Arutha Kulasinghe
- The School of Biomedical Science, Institute of Health and Biomedical InnovationQueensland University of TechnologyBrisbaneQLDAustralia
- Translational Research InstituteWoolloongabbaQLDAustralia
- Institute for Molecular BiosciencesUniversity of QueenslandBrisbaneQLDAustralia
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32
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Nerurkar SN, Goh D, Cheung CCL, Nga PQY, Lim JCT, Yeong JPS. Transcriptional Spatial Profiling of Cancer Tissues in the Era of Immunotherapy: The Potential and Promise. Cancers (Basel) 2020; 12:E2572. [PMID: 32917035 PMCID: PMC7563386 DOI: 10.3390/cancers12092572] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [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: 08/21/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 12/18/2022]
Abstract
Intratumoral heterogeneity poses a major challenge to making an accurate diagnosis and establishing personalized treatment strategies for cancer patients. Moreover, this heterogeneity might underlie treatment resistance, disease progression, and cancer relapse. For example, while immunotherapies can confer a high success rate, selective pressures coupled with dynamic evolution within a tumour can drive the emergence of drug-resistant clones that allow tumours to persist in certain patients. To improve immunotherapy efficacy, researchers have used transcriptional spatial profiling techniques to identify and subsequently block the source of tumour heterogeneity. In this review, we describe and assess the different technologies available for such profiling within a cancer tissue. We first outline two well-known approaches, in situ hybridization and digital spatial profiling. Then, we highlight the features of an emerging technology known as Visium Spatial Gene Expression Solution. Visium generates quantitative gene expression data and maps them to the tissue architecture. By retaining spatial information, we are well positioned to identify novel biomarkers and perform computational analyses that might inform on novel combinatorial immunotherapies.
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Affiliation(s)
- Sanjna Nilesh Nerurkar
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore;
| | - Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | | | - Pei Qi Yvonne Nga
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore 138648, Singapore
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Zugazagoitia J, Gupta S, Liu Y, Fuhrman K, Gettinger S, Herbst RS, Schalper KA, Rimm DL. Biomarkers Associated with Beneficial PD-1 Checkpoint Blockade in Non-Small Cell Lung Cancer (NSCLC) Identified Using High-Plex Digital Spatial Profiling. Clin Cancer Res 2020; 26:4360-4368. [PMID: 32253229 PMCID: PMC7442721 DOI: 10.1158/1078-0432.ccr-20-0175] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/05/2020] [Accepted: 04/02/2020] [Indexed: 12/11/2022]
Abstract
PURPOSE Only a minority of patients with advanced non-small cell lung cancer (NSCLC) truly benefits from single-agent PD-1 checkpoint blockade, and more robust predictive biomarkers are needed. EXPERIMENTAL DESIGN We assessed tumor samples from 67 immunotherapy-treated NSCLC cases represented in a tissue microarray, 53 of whom had pretreatment samples and received monotherapy. Using GeoMx Digital Spatial Profiling System (NanoString Technologies), we quantified 39 immune parameters simultaneously in four tissue compartments defined by fluorescence colocalization [tumor (panCK+), leucocytes (CD45+), macrophages (CD68+), and nonimmune stroma]. RESULTS A total of 156 protein variables were generated per case. In the univariate unadjusted analysis, we found 18 markers associated with outcome in spatial context, five of which remained significant after multiplicity adjustment. In the multivariate analysis, high levels of CD56 and CD4 measured in the CD45 compartment were the only markers that were predictive for all clinical outcomes, including progression-free survival (PFS, HR: 0.24, P = 0.006; and HR: 0.31, P = 0.011, respectively), and overall survival (OS, HR: 0.26, P = 0.014; and HR: 0.23, P = 0.007, respectively). Then, using an orthogonal method based on multiplex immunofluorescence and cell counting (inForm), we validated that high CD56+ immune cell counts in the stroma were associated with PFS and OS in the same cohort. CONCLUSIONS This pilot scale discovery study shows the potential of the digital spatial profiling technology in the identification of spatially informed biomarkers of response to PD-1 checkpoint blockade in NSCLC. We identified a number of relevant candidate immune predictors in spatial context that deserve validation in larger independent cohorts.
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Affiliation(s)
- Jon Zugazagoitia
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut.
| | - Swati Gupta
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Yuting Liu
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Kit Fuhrman
- NanoString Technologies, Seattle, Washington
| | - Scott Gettinger
- Department of Medicine (Oncology), Yale University School of Medicine and Yale Cancer Center, New Haven, Connecticut
| | - Roy S Herbst
- Department of Medicine (Oncology), Yale University School of Medicine and Yale Cancer Center, New Haven, Connecticut
| | - Kurt A Schalper
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
- Department of Medicine (Oncology), Yale University School of Medicine and Yale Cancer Center, New Haven, Connecticut
| | - David L Rimm
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
- Department of Medicine (Oncology), Yale University School of Medicine and Yale Cancer Center, New Haven, Connecticut
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Figueiredo CR, Kalirai H, Sacco JJ, Azevedo RA, Duckworth A, Slupsky JR, Coulson JM, Coupland SE. Loss of BAP1 expression is associated with an immunosuppressive microenvironment in uveal melanoma, with implications for immunotherapy development. J Pathol 2020; 250:420-439. [PMID: 31960425 PMCID: PMC7216965 DOI: 10.1002/path.5384] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [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: 09/08/2019] [Revised: 12/28/2019] [Accepted: 01/14/2020] [Indexed: 12/22/2022]
Abstract
Immunotherapy using immune checkpoint inhibitors (ICIs) induces durable responses in many metastatic cancers. Metastatic uveal melanoma (mUM), typically occurring in the liver, is one of the most refractory tumours to ICIs and has dismal outcomes. Monosomy 3 (M3), polysomy 8q, and BAP1 loss in primary uveal melanoma (pUM) are associated with poor prognoses. The presence of tumour‐infiltrating lymphocytes (TILs) within pUM and surrounding mUM – and some evidence of clinical responses to adoptive TIL transfer – strongly suggests that UMs are indeed immunogenic despite their low mutational burden. The mechanisms that suppress TILs in pUM and mUM are unknown. We show that BAP1 loss is correlated with upregulation of several genes associated with suppressive immune responses, some of which build an immune suppressive axis, including HLA‐DR, CD38, and CD74. Further, single‐cell analysis of pUM by mass cytometry confirmed the expression of these and other markers revealing important functions of infiltrating immune cells in UM, most being regulatory CD8+ T lymphocytes and tumour‐associated macrophages (TAMs). Transcriptomic analysis of hepatic mUM revealed similar immune profiles to pUM with BAP1 loss, including the expression of IDO1. At the protein level, we observed TAMs and TILs entrapped within peritumoural fibrotic areas surrounding mUM, with increased expression of IDO1, PD‐L1, and β‐catenin (CTNNB1), suggesting tumour‐driven immune exclusion and hence the immunotherapy resistance. These findings aid the understanding of how the immune response is organised in BAP1− mUM, which will further enable functional validation of detected biomarkers and the development of focused immunotherapeutic approaches. © 2020 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Carlos R Figueiredo
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK.,Department of the Faculty of Medicine, MediCity Research Laboratory and Institute of Biomedicine, University of Turku, Turku, Finland
| | - Helen Kalirai
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK
| | - Joseph J Sacco
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK.,Department of Medical Oncology, The Clatterbridge Cancer Centre, Wirral, UK
| | - Ricardo A Azevedo
- Department of Cancer Biology, The University of Texas-MD Anderson Cancer Center, Houston, TX, USA
| | - Andrew Duckworth
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK
| | - Joseph R Slupsky
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK
| | - Judy M Coulson
- Department of Cellular and Molecular Physiology, University of Liverpool, Liverpool, UK
| | - Sarah E Coupland
- Department of Molecular and Clinical Cancer Medicine, ITM, University of Liverpool, Liverpool, UK.,Liverpool Clinical Laboratories, Royal Liverpool University Hospital, Liverpool, UK
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Wang Y, Mashock M, Tong Z, Mu X, Chen H, Zhou X, Zhang H, Zhao G, Liu B, Li X. Changing Technologies of RNA Sequencing and Their Applications in Clinical Oncology. Front Oncol 2020; 10:447. [PMID: 32328458 PMCID: PMC7160325 DOI: 10.3389/fonc.2020.00447] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [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: 11/12/2019] [Accepted: 03/13/2020] [Indexed: 12/20/2022]
Abstract
RNA sequencing (RNAseq) is one of the most commonly used techniques in life sciences, and has been widely used in cancer research, drug development, and cancer diagnosis and prognosis. Driven by various biological and technical questions, the techniques of RNAseq have progressed rapidly from bulk RNAseq, laser-captured micro-dissected RNAseq, and single-cell RNAseq to digital spatial RNA profiling, spatial transcriptomics, and direct in situ sequencing. These different technologies have their unique strengths, weaknesses, and suitable applications in the field of clinical oncology. To guide cancer researchers to select the most appropriate RNAseq technique for their biological questions, we will discuss each of these technologies, technical features, and clinical applications in cancer. We will help cancer researchers to understand the key differences of these RNAseq technologies and their optimal applications.
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Affiliation(s)
- Ye Wang
- Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, China
| | - Michael Mashock
- Department of Pathology & Laboratory Medicine, UCLA Technology Center for Genomics & Bioinformatics, Los Angeles, CA, United States
| | - Zhuang Tong
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Xiaofeng Mu
- Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, China.,Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, China
| | - Hong Chen
- Qiqihaer First Hospital, Qiqihar, China
| | - Xin Zhou
- Qiqihaer First Hospital, Qiqihar, China
| | - Hong Zhang
- Department of Pathology & Laboratory Medicine, UCLA Technology Center for Genomics & Bioinformatics, Los Angeles, CA, United States
| | - Gexin Zhao
- Department of Pathology & Laboratory Medicine, UCLA Technology Center for Genomics & Bioinformatics, Los Angeles, CA, United States
| | - Bin Liu
- Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
| | - Xinmin Li
- Department of Pathology & Laboratory Medicine, UCLA Technology Center for Genomics & Bioinformatics, Los Angeles, CA, United States
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